* using log directory ‘/data/gannet/ripley/R/packages/tests-Suggests/inDAGO.Rcheck’ * using R Under development (unstable) (2026-03-03 r89531) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (GCC) 15.2.1 20260123 (Red Hat 15.2.1-7) GNU Fortran (GCC) 15.2.1 20260123 (Red Hat 15.2.1-7) * running under: Fedora Linux 42 (Workstation Edition) * using session charset: UTF-8 * current time: 2026-03-04 16:19:28 UTC * using option ‘--no-stop-on-test-error’ * checking for file ‘inDAGO/DESCRIPTION’ ... OK * this is package ‘inDAGO’ version ‘1.0.3’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for executable files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘inDAGO’ can be installed ... [45s/45s] OK * checking package directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... [31s/32s] OK * checking whether the package can be loaded with stated dependencies ... [31s/31s] OK * checking whether the package can be unloaded cleanly ... [31s/31s] OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking whether startup messages can be suppressed ... [31s/32s] OK * checking use of S3 registration ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... [73s/74s] OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd line widths ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking examples ... NONE * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ [28m/18m] [28m/18m] ERROR Running the tests in ‘tests/testthat.R’ failed. Complete output: > # This file is part of the standard setup for testthat. > # It is recommended that you do not modify it. > # > # Where should you do additional test configuration? > # Learn more about the roles of various files in: > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview > # * https://testthat.r-lib.org/articles/special-files.html > > # library("testthat") > # library("inDAGO") > > testthat::test_check("inDAGO") Loading required package: inDAGO The following packages are not installed: BiocManager, XVector, ShortRead, S4Vectors, rtracklayer, Rsubread, Rsamtools, limma, HTSFilter, edgeR, Biostrings, BiocGenerics. To enable all the features of inDAGO, install with: if (!requireNamespace('BiocManager', quietly=TRUE)) install.packages('BiocManager') BiocManager::install(c("BiocManager", "XVector", "ShortRead", "S4Vectors", "rtracklayer", "Rsubread", "Rsamtools", "limma", "HTSFilter", "edgeR", "Biostrings", "BiocGenerics")) Installing package into '/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874' (as 'lib' is unspecified) * installing *source* package ‘BiocManager’ ... ** this is package ‘BiocManager’ version ‘1.30.27’ ** package ‘BiocManager’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (BiocManager) 'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package = "BiocManager")' for details. Replacement repositories: CRAN: file:///data/gannet/ripley/R Bioconductor version 3.23 (BiocManager 1.30.27), R Under development (unstable) (2026-03-03 r89531) Installing package(s) 'BiocVersion', 'XVector' also installing the dependencies 'BiocGenerics', 'S4Vectors', 'IRanges' trying URL 'https://bioconductor.org/packages/3.23/bioc/src/contrib/BiocGenerics_0.57.0.tar.gz' trying URL 'https://bioconductor.org/packages/3.23/bioc/src/contrib/S4Vectors_0.49.0.tar.gz' trying URL 'https://bioconductor.org/packages/3.23/bioc/src/contrib/IRanges_2.45.0.tar.gz' trying URL 'https://bioconductor.org/packages/3.23/bioc/src/contrib/BiocVersion_3.23.1.tar.gz' trying URL 'https://bioconductor.org/packages/3.23/bioc/src/contrib/XVector_0.51.0.tar.gz' * installing *source* package ‘BiocGenerics’ ... ** this is package ‘BiocGenerics’ version ‘0.57.0’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading Creating a new generic function for ‘aperm’ in package ‘BiocGenerics’ Creating a new generic function for ‘append’ in package ‘BiocGenerics’ Creating a new generic function for ‘as.data.frame’ in package ‘BiocGenerics’ Creating a new generic function for ‘cbind’ in package ‘BiocGenerics’ Creating a new generic function for ‘rbind’ in package ‘BiocGenerics’ Creating a new generic function for ‘do.call’ in package ‘BiocGenerics’ Creating a new generic function for ‘duplicated’ in package ‘BiocGenerics’ Creating a new generic function for ‘anyDuplicated’ in package ‘BiocGenerics’ Creating a new generic function for ‘eval’ in package ‘BiocGenerics’ Creating a new generic function for ‘pmax’ in package ‘BiocGenerics’ Creating a new generic function for ‘pmin’ in package ‘BiocGenerics’ Creating a new generic function for ‘pmax.int’ in package ‘BiocGenerics’ Creating a new generic function for ‘pmin.int’ in package ‘BiocGenerics’ Creating a new generic function for ‘Reduce’ in package ‘BiocGenerics’ Creating a new generic function for ‘Filter’ in package ‘BiocGenerics’ Creating a new generic function for ‘Find’ in package ‘BiocGenerics’ Creating a new generic function for ‘Map’ in package ‘BiocGenerics’ Creating a new generic function for ‘Position’ in package ‘BiocGenerics’ Creating a new generic function for ‘get’ in package ‘BiocGenerics’ Creating a new generic function for ‘mget’ in package ‘BiocGenerics’ Creating a new generic function for ‘grep’ in package ‘BiocGenerics’ Creating a new generic function for ‘grepl’ in package ‘BiocGenerics’ Creating a new generic function for ‘is.unsorted’ in package ‘BiocGenerics’ Creating a new generic function for ‘lapply’ in package ‘BiocGenerics’ Creating a new generic function for ‘sapply’ in package ‘BiocGenerics’ Creating a new generic function for ‘mapply’ in package ‘BiocGenerics’ Creating a new generic function for ‘match’ in package ‘BiocGenerics’ Creating a new generic function for ‘order’ in package ‘BiocGenerics’ Creating a new generic function for ‘paste’ in package ‘BiocGenerics’ Creating a new generic function for ‘rank’ in package ‘BiocGenerics’ Creating a new generic function for ‘rownames’ in package ‘BiocGenerics’ Creating a new generic function for ‘colnames’ in package ‘BiocGenerics’ Creating a new generic function for ‘saveRDS’ in package ‘BiocGenerics’ Creating a new generic function for ‘table’ in package ‘BiocGenerics’ Creating a new generic function for ‘tapply’ in package ‘BiocGenerics’ Creating a new generic function for ‘unique’ in package ‘BiocGenerics’ Creating a new generic function for ‘unsplit’ in package ‘BiocGenerics’ Creating a new generic function for ‘which.min’ in package ‘BiocGenerics’ Creating a new generic function for ‘which.max’ in package ‘BiocGenerics’ Creating a new generic function for ‘IQR’ in package ‘BiocGenerics’ Creating a new generic function for ‘mad’ in package ‘BiocGenerics’ Creating a new generic function for ‘var’ in package ‘BiocGenerics’ Creating a new generic function for ‘sd’ in package ‘BiocGenerics’ Creating a new generic function for ‘xtabs’ in package ‘BiocGenerics’ Creating a new generic function for ‘basename’ in package ‘BiocGenerics’ Creating a new generic function for ‘dirname’ in package ‘BiocGenerics’ ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (BiocGenerics) * installing *source* package ‘BiocVersion’ ... ** this is package ‘BiocVersion’ version ‘3.23.1’ ** using staged installation ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (BiocVersion) * installing *source* package ‘S4Vectors’ ... ** this is package ‘S4Vectors’ version ‘0.49.0’ ** using staged installation ** libs using C compiler: ‘gcc (GCC) 15.2.1 20260123 (Red Hat 15.2.1-7)’ make[2]: Entering directory '/tmp/Rtmp7CAajn/working_dir/RtmpV3YgHv/R.INSTALL350c384f7d8f44/S4Vectors/src' gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c AEbufs.c -o AEbufs.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c DFrame_class.c -o DFrame_class.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c Hits_class.c -o Hits_class.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c LLint_class.c -o LLint_class.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c List_class.c -o List_class.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c R_init_S4Vectors.c -o R_init_S4Vectors.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c Rle_class.c -o Rle_class.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c Rle_utils.c -o Rle_utils.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c SEXP_utils.c -o SEXP_utils.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c SimpleList_class.c -o SimpleList_class.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c character_utils.c -o character_utils.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c eval_utils.c -o eval_utils.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c hash_utils.c -o hash_utils.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c integer_utils.c -o integer_utils.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c logical_utils.c -o logical_utils.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c map_ranges_to_runs.c -o map_ranges_to_runs.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c raw_utils.c -o raw_utils.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c safe_arithm.c -o safe_arithm.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c sort_utils.c -o sort_utils.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c subsetting_utils.c -o subsetting_utils.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c vector_utils.c -o vector_utils.o sort_utils.c:267:13: warning: ‘sort_uchar_array’ defined but not used [-Wunused-function] 267 | static void sort_uchar_array(unsigned char *x, int nelt, int desc) | ^~~~~~~~~~~~~~~~ In file included from /usr/include/string.h:548, from /data/gannet/ripley/R/R-devel/include/R_ext/RS.h:34, from /data/gannet/ripley/R/R-devel/include/Rdefines.h:38, from ../inst/include/S4Vectors_defines.h:18, from S4Vectors.h:1, from Hits_class.c:4: In function ‘memcpy’, inlined from ‘tsort_hits’ at Hits_class.c:113:3: /usr/include/bits/string_fortified.h:29:10: warning: ‘__builtin_memcpy’ specified bound between 18446744065119617024 and 18446744073709551612 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] 29 | return __builtin___memcpy_chk (__dest, __src, __len, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 30 | __glibc_objsize0 (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘memcpy’, inlined from ‘qsort_hits’ at Hits_class.c:74:4: /usr/include/bits/string_fortified.h:29:10: warning: ‘__builtin_memcpy’ specified bound between 18446744065119617024 and 18446744073709551612 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] 29 | return __builtin___memcpy_chk (__dest, __src, __len, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 30 | __glibc_objsize0 (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/bits/string_fortified.h:29:10: warning: ‘__builtin_memcpy’ specified bound between 18446744065119617024 and 18446744073709551612 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] In file included from /data/gannet/ripley/R/R-devel/include/Rdefines.h:41: Hits_class.c: In function ‘Hits_new’: /data/gannet/ripley/R/R-devel/include/Rinternals.h:890:33: warning: ‘revmap’ may be used uninitialized [-Wmaybe-uninitialized] 890 | #define defineVar Rf_defineVar Hits_class.c:291:9: note: in expansion of macro ‘defineVar’ 291 | defineVar(install(translateChar(symbol)), revmap, revmap_envir); | ^~~~~~~~~ Hits_class.c:266:19: note: ‘revmap’ was declared here 266 | SEXP ans, revmap, symbol; | ^~~~~~ Hits_class.c: In function ‘select_hits’: Hits_class.c:395:48: warning: ‘is_used’ may be used uninitialized [-Wmaybe-uninitialized] 395 | is_used->elts[ans_elt - 1] = 1; | ~~~~~~~^~~~~~ Hits_class.c:360:17: note: ‘is_used’ was declared here 360 | CharAE *is_used; | ^~~~~~~ gcc -shared -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -L/usr/local/lib64 -o S4Vectors.so AEbufs.o DFrame_class.o Hits_class.o LLint_class.o List_class.o R_init_S4Vectors.o Rle_class.o Rle_utils.o SEXP_utils.o SimpleList_class.o character_utils.o eval_utils.o hash_utils.o integer_utils.o logical_utils.o map_ranges_to_runs.o raw_utils.o safe_arithm.o sort_utils.o subsetting_utils.o vector_utils.o make[2]: Leaving directory '/tmp/Rtmp7CAajn/working_dir/RtmpV3YgHv/R.INSTALL350c384f7d8f44/S4Vectors/src' make[2]: Entering directory '/tmp/Rtmp7CAajn/working_dir/RtmpV3YgHv/R.INSTALL350c384f7d8f44/S4Vectors/src' make[2]: Leaving directory '/tmp/Rtmp7CAajn/working_dir/RtmpV3YgHv/R.INSTALL350c384f7d8f44/S4Vectors/src' installing to /tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/00LOCK-S4Vectors/00new/S4Vectors/libs ** R ** inst ** byte-compile and prepare package for lazy loading in method for ‘normalizeSingleBracketReplacementValue’ with signature ‘"List"’: no definition for class “List” Creating a new generic function for ‘unname’ in package ‘S4Vectors’ Creating a new generic function for ‘expand.grid’ in package ‘S4Vectors’ Creating a new generic function for ‘findMatches’ in package ‘S4Vectors’ in method for ‘coerce’ with signature ‘"Hits","DFrame"’: no definition for class “DFrame” Creating a generic function for ‘as.factor’ from package ‘base’ in package ‘S4Vectors’ Creating a generic function for ‘tabulate’ from package ‘base’ in package ‘S4Vectors’ Creating a generic function for ‘cov’ from package ‘stats’ in package ‘S4Vectors’ Creating a generic function for ‘cor’ from package ‘stats’ in package ‘S4Vectors’ Creating a generic function for ‘smoothEnds’ from package ‘stats’ in package ‘S4Vectors’ Creating a generic function for ‘runmed’ from package ‘stats’ in package ‘S4Vectors’ Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’ Creating a generic function for ‘substr’ from package ‘base’ in package ‘S4Vectors’ Creating a generic function for ‘substring’ from package ‘base’ in package ‘S4Vectors’ Creating a generic function for ‘chartr’ from package ‘base’ in package ‘S4Vectors’ Creating a generic function for ‘tolower’ from package ‘base’ in package ‘S4Vectors’ Creating a generic function for ‘toupper’ from package ‘base’ in package ‘S4Vectors’ Creating a generic function for ‘sub’ from package ‘base’ in package ‘S4Vectors’ Creating a generic function for ‘gsub’ from package ‘base’ in package ‘S4Vectors’ Creating a generic function for ‘nlevels’ from package ‘base’ in package ‘S4Vectors’ in method for ‘coerce’ with signature ‘"data.table","DFrame"’: no definition for class “data.table” Creating a generic function for ‘complete.cases’ from package ‘stats’ in package ‘S4Vectors’ ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (S4Vectors) * installing *source* package ‘IRanges’ ... ** this is package ‘IRanges’ version ‘2.45.0’ ** using staged installation ** libs using C compiler: ‘gcc (GCC) 15.2.1 20260123 (Red Hat 15.2.1-7)’ make[2]: Entering directory '/tmp/Rtmp7CAajn/working_dir/Rtmp8AsZ16/R.INSTALL3534205bcad20d/IRanges/src' gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c CompressedAtomicList_utils.c -o CompressedAtomicList_utils.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c CompressedIRangesList_class.c -o CompressedIRangesList_class.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c CompressedList_class.c -o CompressedList_class.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c Grouping_class.c -o Grouping_class.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c IPosRanges_comparison.c -o IPosRanges_comparison.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c IRanges_class.c -o IRanges_class.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c IRanges_constructor.c -o IRanges_constructor.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c NCList.c -o NCList.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c R_init_IRanges.c -o R_init_IRanges.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c Ranges_class.c -o Ranges_class.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c RleViews_summarization.c -o RleViews_summarization.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c S4Vectors_stubs.c -o S4Vectors_stubs.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c SimpleIRangesList_class.c -o SimpleIRangesList_class.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c coverage_methods.c -o coverage_methods.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c extractListFragments.c -o extractListFragments.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c inter_range_methods.c -o inter_range_methods.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c thread_control.c -o thread_control.o extractListFragments.c: In function ‘C_find_partition_overlaps’: extractListFragments.c:85:25: warning: ‘split_partitions_buf’ may be used uninitialized [-Wmaybe-uninitialized] 85 | IntAE_insert_at(split_partitions_buf, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 86 | IntAE_get_nelt(split_partitions_buf), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 87 | q_prev_end); | ~~~~~~~~~~~ extractListFragments.c:35:16: note: ‘split_partitions_buf’ was declared here 35 | IntAE *split_partitions_buf; | ^~~~~~~~~~~~~~~~~~~~ NCList.c:1303:13: warning: ‘NCList_get_y_overlaps_rec’ defined but not used [-Wunused-function] 1303 | static void NCList_get_y_overlaps_rec(const NCList *x_nclist, | ^~~~~~~~~~~~~~~~~~~~~~~~~ NCList.c:203:22: warning: ‘next_top_down’ defined but not used [-Wunused-function] 203 | static const NCList *next_top_down(NCListWalkingStack *stack, | ^~~~~~~~~~~~~ inter_range_methods.c: In function ‘reduce_ranges.isra’: inter_range_methods.c:154:39: warning: ‘gapwidth’ may be used uninitialized [-Wmaybe-uninitialized] 154 | delta += gapwidth; | ~~~~~~^~~~~~~~~~~ inter_range_methods.c:102:38: note: ‘gapwidth’ was declared here 102 | append_or_drop, max_end, gapwidth, delta, width_inc; | ^~~~~~~~ In function ‘shift_and_clip_ranges’, inlined from ‘compute_coverage_from_IRanges_holder’ at coverage_methods.c:609:12: coverage_methods.c:579:35: warning: ‘x_end’ may be used uninitialized [-Wmaybe-uninitialized] 579 | if (*out_ranges_are_tiles && x_end != cvg_len) | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ coverage_methods.c: In function ‘compute_coverage_from_IRanges_holder’: coverage_methods.c:495:28: note: ‘x_end’ was declared here 495 | i, j, x_start, x_end, shift_elt, tmp; | ^~~~~ In function ‘viewWhichMaxs_int_RleViews’, inlined from ‘viewWhichMaxs_RleViews’ at RleViews_summarization.c:579:3, inlined from ‘C_summarize_RleViews’ at RleViews_summarization.c:694:9: RleViews_summarization.c:325:54: warning: ‘max’ may be used uninitialized [-Wmaybe-uninitialized] 325 | if (!max_is_initialized || v > max) { | ~~^~~~~ RleViews_summarization.c: In function ‘C_summarize_RleViews’: RleViews_summarization.c:316:21: note: ‘max’ was declared here 316 | int max; /* uninitialized */ | ^~~ In function ‘viewWhichMins_int_RleViews’, inlined from ‘viewWhichMins_RleViews’ at RleViews_summarization.c:546:3, inlined from ‘C_summarize_RleViews’ at RleViews_summarization.c:686:9: RleViews_summarization.c:293:54: warning: ‘min’ may be used uninitialized [-Wmaybe-uninitialized] 293 | if (!min_is_initialized || v < min) { | ~~^~~~~ RleViews_summarization.c: In function ‘C_summarize_RleViews’: RleViews_summarization.c:284:21: note: ‘min’ was declared here 284 | int min; /* uninitialized */ | ^~~ In function ‘viewMaxs_int_RleViews’, inlined from ‘viewMaxs_RleViews’ at RleViews_summarization.c:443:3, inlined from ‘C_summarize_RleViews’ at RleViews_summarization.c:665:9: RleViews_summarization.c:67:54: warning: ‘max’ may be used uninitialized [-Wmaybe-uninitialized] 67 | if (!max_is_initialized || v > max) { | ~~^~~~~ RleViews_summarization.c: In function ‘C_summarize_RleViews’: RleViews_summarization.c:54:21: note: ‘max’ was declared here 54 | int max; /* uninitialized */ | ^~~ In function ‘viewMins_int_RleViews’, inlined from ‘viewMins_RleViews’ at RleViews_summarization.c:413:3, inlined from ‘C_summarize_RleViews’ at RleViews_summarization.c:660:9: RleViews_summarization.c:36:54: warning: ‘min’ may be used uninitialized [-Wmaybe-uninitialized] 36 | if (!min_is_initialized || v < min) { | ~~^~~~~ RleViews_summarization.c: In function ‘C_summarize_RleViews’: RleViews_summarization.c:23:21: note: ‘min’ was declared here 23 | int min; /* uninitialized */ | ^~~ NCList.c: In function ‘C_find_overlaps_in_groups_NCList’: NCList.c:1782:24: warning: ‘ans’ may be used uninitialized [-Wmaybe-uninitialized] 1782 | return ans; | ^~~ NCList.c:1751:14: note: ‘ans’ was declared here 1751 | SEXP ans; | ^~~ gcc -shared -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -L/usr/local/lib64 -o IRanges.so CompressedAtomicList_utils.o CompressedIRangesList_class.o CompressedList_class.o Grouping_class.o IPosRanges_comparison.o IRanges_class.o IRanges_constructor.o NCList.o R_init_IRanges.o Ranges_class.o RleViews_summarization.o S4Vectors_stubs.o SimpleIRangesList_class.o coverage_methods.o extractListFragments.o inter_range_methods.o thread_control.o -fopenmp make[2]: Leaving directory '/tmp/Rtmp7CAajn/working_dir/Rtmp8AsZ16/R.INSTALL3534205bcad20d/IRanges/src' make[2]: Entering directory '/tmp/Rtmp7CAajn/working_dir/Rtmp8AsZ16/R.INSTALL3534205bcad20d/IRanges/src' make[2]: Leaving directory '/tmp/Rtmp7CAajn/working_dir/Rtmp8AsZ16/R.INSTALL3534205bcad20d/IRanges/src' installing to /tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/00LOCK-IRanges/00new/IRanges/libs ** R ** inst ** byte-compile and prepare package for lazy loading Creating a generic function for ‘drop’ from package ‘base’ in package ‘IRanges’ Creating a generic function for ‘runmed’ from package ‘stats’ in package ‘IRanges’ Creating a generic function for ‘chartr’ from package ‘base’ in package ‘IRanges’ Creating a generic function for ‘toupper’ from package ‘base’ in package ‘IRanges’ Creating a generic function for ‘tolower’ from package ‘base’ in package ‘IRanges’ Creating a generic function for ‘sub’ from package ‘base’ in package ‘IRanges’ Creating a generic function for ‘gsub’ from package ‘base’ in package ‘IRanges’ Creating a generic function for ‘startsWith’ from package ‘base’ in package ‘IRanges’ Creating a generic function for ‘endsWith’ from package ‘base’ in package ‘IRanges’ Creating a generic function for ‘smoothEnds’ from package ‘stats’ in package ‘IRanges’ ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (IRanges) * installing *source* package ‘XVector’ ... ** this is package ‘XVector’ version ‘0.51.0’ ** using staged installation ** libs using C compiler: ‘gcc (GCC) 15.2.1 20260123 (Red Hat 15.2.1-7)’ make[2]: Entering directory '/tmp/Rtmp7CAajn/working_dir/Rtmp5tLqX8/R.INSTALL358dfb1954a405/XVector/src' gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c IRanges_stubs.c -o IRanges_stubs.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c Ocopy_byteblocks.c -o Ocopy_byteblocks.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c RDS_random_access.c -o RDS_random_access.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c R_init_XVector.c -o R_init_XVector.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c S4Vectors_stubs.c -o S4Vectors_stubs.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c SharedDouble_class.c -o SharedDouble_class.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c SharedInteger_class.c -o SharedInteger_class.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c SharedRaw_class.c -o SharedRaw_class.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c SharedVector_class.c -o SharedVector_class.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c XDouble_class.c -o XDouble_class.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c XInteger_class.c -o XInteger_class.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c XRawList_comparison.c -o XRawList_comparison.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c XRaw_class.c -o XRaw_class.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c XVectorList_class.c -o XVectorList_class.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c XVector_class.c -o XVector_class.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c io_utils.c -o io_utils.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c slice_methods.c -o slice_methods.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c vector_copy.c -o vector_copy.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c view_summarization_methods.c -o view_summarization_methods.o SharedInteger_class.c: In function ‘SharedInteger_get_show_string’: SharedInteger_class.c:41:84: warning: format ‘%p’ expects argument of type ‘void *’, but argument 5 has type ‘int *’ [-Wformat=] 41 | "%d-integer SharedInteger object (data starting at memory address %p)", | ~^ | | | void * | %ls 42 | tag_length, INTEGER(tag)); | ~~~~~~~~~~~~ | | | int * SharedDouble_class.c: In function ‘SharedDouble_get_show_string’: SharedDouble_class.c:42:82: warning: format ‘%p’ expects argument of type ‘void *’, but argument 5 has type ‘double *’ [-Wformat=] 42 | "%d-number SharedDouble object (data starting at memory address %p)", | ~^ | | | void * 43 | tag_length, REAL(tag)); | ~~~~~~~~~ | | | double * RDS_random_access.c: In function ‘RDS_extract_subarray’: RDS_random_access.c:796:25: warning: unused variable ‘ans’ [-Wunused-variable] 796 | SEXP subscript, ans; | ^~~ RDS_random_access.c:793:18: warning: variable ‘x_type’ set but not used [-Wunused-but-set-variable] 793 | SEXPTYPE x_type; | ^~~~~~ SharedRaw_class.c: In function ‘SharedRaw_read_complexes_from_subscript’: SharedRaw_class.c:396:20: warning: variable ‘src_tag’ set but not used [-Wunused-but-set-variable] 396 | SEXP dest, src_tag; | ^~~~~~~ SharedVector_class.c: In function ‘address_as_CHARSXP’: SharedVector_class.c:22:38: warning: format ‘%p’ expects argument of type ‘void *’, but argument 4 has type ‘SEXP’ {aka ‘struct SEXPREC *’} [-Wformat=] 22 | snprintf(buf, sizeof(buf), "%p", x); | ~^ ~ | | | | | SEXP {aka struct SEXPREC *} | void * SharedVector_class.c: In function ‘externalptr_show’: SharedVector_class.c:110:32: warning: format ‘%p’ expects argument of type ‘void *’, but argument 2 has type ‘SEXP’ {aka ‘struct SEXPREC *’} [-Wformat=] 110 | Rprintf(" x address: %p\n", x); | ~^ ~ | | | | | SEXP {aka struct SEXPREC *} | void * SharedVector_class.c:114:42: warning: format ‘%p’ expects argument of type ‘void *’, but argument 2 has type ‘SEXP’ {aka ‘struct SEXPREC *’} [-Wformat=] 114 | Rprintf(" R_ExternalPtrTag(x): %p\n", s); | ~^ ~ | | | | | SEXP {aka struct SEXPREC *} | void * SharedVector_class.c:118:48: warning: format ‘%p’ expects argument of type ‘void *’, but argument 2 has type ‘SEXP’ {aka ‘struct SEXPREC *’} [-Wformat=] 118 | Rprintf(" R_ExternalPtrProtected(x): %p\n", s); | ~^ ~ | | | | | SEXP {aka struct SEXPREC *} | void * view_summarization_methods.c: In function ‘get_which_min_from_Ints_holder’: view_summarization_methods.c:219:45: warning: ‘cur_min’ may be used uninitialized [-Wmaybe-uninitialized] 219 | if (which_min == NA_INTEGER || x < cur_min) { | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ view_summarization_methods.c:208:19: note: ‘cur_min’ was declared here 208 | int xlen, cur_min, which_min, i, x; | ^~~~~~~ view_summarization_methods.c: In function ‘get_which_min_from_Doubles_holder’: view_summarization_methods.c:246:45: warning: ‘cur_min’ may be used uninitialized [-Wmaybe-uninitialized] 246 | if (which_min == NA_INTEGER || x < cur_min) { | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ view_summarization_methods.c:235:16: note: ‘cur_min’ was declared here 235 | double cur_min, x; | ^~~~~~~ view_summarization_methods.c: In function ‘get_which_max_from_Ints_holder’: view_summarization_methods.c:269:45: warning: ‘cur_max’ may be used uninitialized [-Wmaybe-uninitialized] 269 | if (which_max == NA_INTEGER || x > cur_max) { | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ view_summarization_methods.c:258:19: note: ‘cur_max’ was declared here 258 | int xlen, cur_max, which_max, i, x; | ^~~~~~~ view_summarization_methods.c: In function ‘get_which_max_from_Doubles_holder’: view_summarization_methods.c:296:45: warning: ‘cur_max’ may be used uninitialized [-Wmaybe-uninitialized] 296 | if (which_max == NA_INTEGER || x > cur_max) { | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ view_summarization_methods.c:285:16: note: ‘cur_max’ was declared here 285 | double cur_max, x; | ^~~~~~~ XVectorList_class.c: In function ‘_new_XRawList_from_CharAEAE’: XVectorList_class.c:459:17: warning: ‘lkup_length’ may be used uninitialized [-Wmaybe-uninitialized] 459 | _Ocopy_bytes_to_i1i2_with_lkup(0, dest.length - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 460 | (char *) dest.ptr, dest.length, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 461 | src->elts, CharAE_get_nelt(src), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 462 | lkup0, lkup_length); | ~~~~~~~~~~~~~~~~~~~ XVectorList_class.c:434:13: note: ‘lkup_length’ was declared here 434 | int lkup_length, nelt, i; | ^~~~~~~~~~~ gcc -shared -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -L/usr/local/lib64 -o XVector.so IRanges_stubs.o Ocopy_byteblocks.o RDS_random_access.o R_init_XVector.o S4Vectors_stubs.o SharedDouble_class.o SharedInteger_class.o SharedRaw_class.o SharedVector_class.o XDouble_class.o XInteger_class.o XRawList_comparison.o XRaw_class.o XVectorList_class.o XVector_class.o io_utils.o slice_methods.o vector_copy.o view_summarization_methods.o -lz make[2]: Leaving directory '/tmp/Rtmp7CAajn/working_dir/Rtmp5tLqX8/R.INSTALL358dfb1954a405/XVector/src' make[2]: Entering directory '/tmp/Rtmp7CAajn/working_dir/Rtmp5tLqX8/R.INSTALL358dfb1954a405/XVector/src' make[2]: Leaving directory '/tmp/Rtmp7CAajn/working_dir/Rtmp5tLqX8/R.INSTALL358dfb1954a405/XVector/src' installing to /tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/00LOCK-XVector/00new/XVector/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (XVector) The downloaded source packages are in '/tmp/Rtmp7CAajn/working_dir/RtmpjyO0Wr/downloaded_packages' 'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package = "BiocManager")' for details. Replacement repositories: CRAN: file:///data/gannet/ripley/R Bioconductor version 3.23 (BiocManager 1.30.27), R Under development (unstable) (2026-03-03 r89531) Installing package(s) 'ShortRead' also installing the dependencies 'formatR', 'abind', 'SparseArray', 'lambda.r', 'futile.options', 'MatrixGenerics', 'S4Arrays', 'DelayedArray', 'deldir', 'RcppEigen', 'futile.logger', 'snow', 'bitops', 'SummarizedExperiment', 'cigarillo', 'png', 'jpeg', 'interp', 'BiocParallel', 'Biostrings', 'Rsamtools', 'GenomicAlignments', 'Biobase', 'Seqinfo', 'GenomicRanges', 'pwalign', 'hwriter', 'latticeExtra', 'Rhtslib' trying URL 'https://bioconductor.org/packages/3.23/bioc/src/contrib/SparseArray_1.11.10.tar.gz' trying URL 'https://bioconductor.org/packages/3.23/bioc/src/contrib/MatrixGenerics_1.23.0.tar.gz' trying URL 'https://bioconductor.org/packages/3.23/bioc/src/contrib/S4Arrays_1.11.1.tar.gz' trying URL 'https://bioconductor.org/packages/3.23/bioc/src/contrib/DelayedArray_0.37.0.tar.gz' trying URL 'https://bioconductor.org/packages/3.23/bioc/src/contrib/SummarizedExperiment_1.41.1.tar.gz' trying URL 'https://bioconductor.org/packages/3.23/bioc/src/contrib/cigarillo_1.1.0.tar.gz' trying URL 'https://bioconductor.org/packages/3.23/bioc/src/contrib/BiocParallel_1.45.0.tar.gz' trying URL 'https://bioconductor.org/packages/3.23/bioc/src/contrib/Biostrings_2.79.4.tar.gz' trying URL 'https://bioconductor.org/packages/3.23/bioc/src/contrib/Rsamtools_2.27.0.tar.gz' trying URL 'https://bioconductor.org/packages/3.23/bioc/src/contrib/GenomicAlignments_1.47.0.tar.gz' trying URL 'https://bioconductor.org/packages/3.23/bioc/src/contrib/Biobase_2.71.0.tar.gz' trying URL 'https://bioconductor.org/packages/3.23/bioc/src/contrib/Seqinfo_1.1.0.tar.gz' trying URL 'https://bioconductor.org/packages/3.23/bioc/src/contrib/GenomicRanges_1.63.1.tar.gz' trying URL 'https://bioconductor.org/packages/3.23/bioc/src/contrib/pwalign_1.7.0.tar.gz' trying URL 'https://bioconductor.org/packages/3.23/bioc/src/contrib/Rhtslib_3.7.0.tar.gz' trying URL 'https://bioconductor.org/packages/3.23/bioc/src/contrib/ShortRead_1.69.2.tar.gz' * installing *source* package ‘formatR’ ... ** this is package ‘formatR’ version ‘1.14’ ** package ‘formatR’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (formatR) * installing *source* package ‘abind’ ... ** this is package ‘abind’ version ‘1.4-8’ ** package ‘abind’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (abind) * installing *source* package ‘futile.options’ ... ** this is package ‘futile.options’ version ‘1.0.1’ ** package ‘futile.options’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (futile.options) * installing *source* package ‘MatrixGenerics’ ... ** this is package ‘MatrixGenerics’ version ‘1.23.0’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading Creating a new generic function for ‘rowAlls’ in package ‘MatrixGenerics’ Creating a new generic function for ‘colAlls’ in package ‘MatrixGenerics’ Creating a new generic function for ‘rowAnyNAs’ in package ‘MatrixGenerics’ Creating a new generic function for ‘colAnyNAs’ in package ‘MatrixGenerics’ Creating a new generic function for ‘rowAnys’ in package ‘MatrixGenerics’ Creating a new generic function for ‘colAnys’ in package ‘MatrixGenerics’ Creating a new generic function for ‘rowAvgsPerColSet’ in package ‘MatrixGenerics’ Creating a new generic function for ‘colAvgsPerRowSet’ in package ‘MatrixGenerics’ Creating a new generic function for ‘rowCollapse’ in package ‘MatrixGenerics’ Creating a new generic function for ‘colCollapse’ in package ‘MatrixGenerics’ Creating a new generic function for ‘rowCounts’ in package ‘MatrixGenerics’ Creating a new generic function for ‘colCounts’ in package ‘MatrixGenerics’ Creating a new generic function for ‘rowCummaxs’ in package ‘MatrixGenerics’ Creating a new generic function for ‘colCummaxs’ in package ‘MatrixGenerics’ Creating a new generic function for ‘rowCummins’ in package ‘MatrixGenerics’ Creating a new generic function for ‘colCummins’ in package ‘MatrixGenerics’ Creating a new generic function for ‘rowCumprods’ in package ‘MatrixGenerics’ Creating a new generic function for ‘colCumprods’ in package ‘MatrixGenerics’ Creating a new generic function for ‘rowCumsums’ in package ‘MatrixGenerics’ Creating a new generic function for ‘colCumsums’ in package ‘MatrixGenerics’ Creating a new generic function for ‘rowDiffs’ in package ‘MatrixGenerics’ Creating a new generic function for ‘colDiffs’ in package ‘MatrixGenerics’ Creating a new generic function for ‘rowIQRDiffs’ in package ‘MatrixGenerics’ Creating a new generic function for ‘colIQRDiffs’ in package ‘MatrixGenerics’ Creating a new generic function for ‘rowIQRs’ in package ‘MatrixGenerics’ Creating a new generic function for ‘colIQRs’ in package ‘MatrixGenerics’ Creating a new generic function for ‘rowLogSumExps’ in package ‘MatrixGenerics’ Creating a new generic function for ‘colLogSumExps’ in package ‘MatrixGenerics’ Creating a new generic function for ‘rowMadDiffs’ in package ‘MatrixGenerics’ Creating a new generic function for ‘colMadDiffs’ in package ‘MatrixGenerics’ Creating a new generic function for ‘rowMads’ in package ‘MatrixGenerics’ Creating a new generic function for ‘colMads’ in package ‘MatrixGenerics’ Creating a new generic function for ‘rowMaxs’ in package ‘MatrixGenerics’ Creating a new generic function for ‘colMaxs’ in package ‘MatrixGenerics’ Creating a new generic function for ‘rowMeans2’ in package ‘MatrixGenerics’ Creating a new generic function for ‘colMeans2’ in package ‘MatrixGenerics’ Creating a new generic function for ‘rowMedians’ in package ‘MatrixGenerics’ Creating a new generic function for ‘colMedians’ in package ‘MatrixGenerics’ Creating a new generic function for ‘rowMins’ in package ‘MatrixGenerics’ Creating a new generic function for ‘colMins’ in package ‘MatrixGenerics’ Creating a new generic function for ‘rowOrderStats’ in package ‘MatrixGenerics’ Creating a new generic function for ‘colOrderStats’ in package ‘MatrixGenerics’ Creating a new generic function for ‘rowProds’ in package ‘MatrixGenerics’ Creating a new generic function for ‘colProds’ in package ‘MatrixGenerics’ Creating a new generic function for ‘rowQuantiles’ in package ‘MatrixGenerics’ Creating a new generic function for ‘colQuantiles’ in package ‘MatrixGenerics’ Creating a new generic function for ‘rowRanges’ in package ‘MatrixGenerics’ Creating a new generic function for ‘colRanges’ in package ‘MatrixGenerics’ Creating a new generic function for ‘rowRanks’ in package ‘MatrixGenerics’ Creating a new generic function for ‘colRanks’ in package ‘MatrixGenerics’ Creating a new generic function for ‘rowSdDiffs’ in package ‘MatrixGenerics’ Creating a new generic function for ‘colSdDiffs’ in package ‘MatrixGenerics’ Creating a new generic function for ‘rowSds’ in package ‘MatrixGenerics’ Creating a new generic function for ‘colSds’ in package ‘MatrixGenerics’ Creating a new generic function for ‘rowSums2’ in package ‘MatrixGenerics’ Creating a new generic function for ‘colSums2’ in package ‘MatrixGenerics’ Creating a new generic function for ‘rowTabulates’ in package ‘MatrixGenerics’ Creating a new generic function for ‘colTabulates’ in package ‘MatrixGenerics’ Creating a new generic function for ‘rowVarDiffs’ in package ‘MatrixGenerics’ Creating a new generic function for ‘colVarDiffs’ in package ‘MatrixGenerics’ Creating a new generic function for ‘rowVars’ in package ‘MatrixGenerics’ Creating a new generic function for ‘colVars’ in package ‘MatrixGenerics’ Creating a new generic function for ‘rowWeightedMads’ in package ‘MatrixGenerics’ Creating a new generic function for ‘colWeightedMads’ in package ‘MatrixGenerics’ Creating a new generic function for ‘rowWeightedMeans’ in package ‘MatrixGenerics’ Creating a new generic function for ‘colWeightedMeans’ in package ‘MatrixGenerics’ Creating a new generic function for ‘rowWeightedMedians’ in package ‘MatrixGenerics’ Creating a new generic function for ‘colWeightedMedians’ in package ‘MatrixGenerics’ Creating a new generic function for ‘rowWeightedSds’ in package ‘MatrixGenerics’ Creating a new generic function for ‘colWeightedSds’ in package ‘MatrixGenerics’ Creating a new generic function for ‘rowWeightedVars’ in package ‘MatrixGenerics’ Creating a new generic function for ‘colWeightedVars’ in package ‘MatrixGenerics’ ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (MatrixGenerics) * installing *source* package ‘deldir’ ... ** this is package ‘deldir’ version ‘2.0-4’ ** package ‘deldir’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc (GCC) 15.2.1 20260123 (Red Hat 15.2.1-7)’ using Fortran compiler: ‘GNU Fortran (GCC) 15.2.1 20260123 (Red Hat 15.2.1-7)’ make[2]: Entering directory '/tmp/Rtmp7CAajn/working_dir/RtmpIfD1yT/R.INSTALL35b7287f7308e1/deldir/src' gfortran -fpic -g -O2 -mtune=native -Wall -pedantic -c acchk.f90 -o acchk.o gfortran -fpic -g -O2 -mtune=native -Wall -pedantic -c addpt.f90 -o addpt.o gfortran -fpic -g -O2 -mtune=native -Wall -pedantic -c adjchk.f90 -o adjchk.o gfortran -fpic -g -O2 -mtune=native -Wall -pedantic -c binsrt.f90 -o binsrt.o gfortran -fpic -g -O2 -mtune=native -Wall -pedantic -c circen.f90 -o circen.o gfortran -fpic -g -O2 -mtune=native -Wall -pedantic -c cross.f90 -o cross.o gfortran -fpic -g -O2 -mtune=native -Wall -pedantic -c delet.f90 -o delet.o gfortran -fpic -g -O2 -mtune=native -Wall -pedantic -c delet1.f90 -o delet1.o gfortran -fpic -g -O2 -mtune=native -Wall -pedantic -c delout.f90 -o delout.o gfortran -fpic -g -O2 -mtune=native -Wall -pedantic -c delseg.f90 -o delseg.o gfortran -fpic -g -O2 -mtune=native -Wall -pedantic -c dirout.f90 -o dirout.o gfortran -fpic -g -O2 -mtune=native -Wall -pedantic -c dirseg.f90 -o dirseg.o gfortran -fpic -g -O2 -mtune=native -Wall -pedantic -c dldins.f90 -o dldins.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c init.c -o init.o gfortran -fpic -g -O2 -mtune=native -Wall -pedantic -c initad.f90 -o initad.o gfortran -fpic -g -O2 -mtune=native -Wall -pedantic -c insrt.f90 -o insrt.o gfortran -fpic -g -O2 -mtune=native -Wall -pedantic -c insrt1.f90 -o insrt1.o gfortran -fpic -g -O2 -mtune=native -Wall -pedantic -c intri.f90 -o intri.o gfortran -fpic -g -O2 -mtune=native -Wall -pedantic -c locn.f90 -o locn.o gfortran -fpic -g -O2 -mtune=native -Wall -pedantic -c master.f90 -o master.o gfortran -fpic -g -O2 -mtune=native -Wall -pedantic -c mnnd.f90 -o mnnd.o gfortran -fpic -g -O2 -mtune=native -Wall -pedantic -c pred.f90 -o pred.o gfortran -fpic -g -O2 -mtune=native -Wall -pedantic -c qtest.f90 -o qtest.o gfortran -fpic -g -O2 -mtune=native -Wall -pedantic -c qtest1.f90 -o qtest1.o gfortran -fpic -g -O2 -mtune=native -Wall -pedantic -c stoke.f90 -o stoke.o gfortran -fpic -g -O2 -mtune=native -Wall -pedantic -c succ.f90 -o succ.o gfortran -fpic -g -O2 -mtune=native -Wall -pedantic -c swap.f90 -o swap.o gfortran -fpic -g -O2 -mtune=native -Wall -pedantic -c testeq.f90 -o testeq.o gfortran -fpic -g -O2 -mtune=native -Wall -pedantic -c triar.f90 -o triar.o gfortran -fpic -g -O2 -mtune=native -Wall -pedantic -c trifnd.f90 -o trifnd.o cross.f90:101:23: 101 | cprd = (a*d - b*c)/smin | ^ Warning: ‘smin’ may be used uninitialized [-Wmaybe-uninitialized] cross.f90:23:5: 23 | smin = -one | ^~~~ note: ‘smin’ was declared here gcc -shared -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -L/usr/local/lib64 -o deldir.so acchk.o addpt.o adjchk.o binsrt.o circen.o cross.o delet.o delet1.o delout.o delseg.o dirout.o dirseg.o dldins.o init.o initad.o insrt.o insrt1.o intri.o locn.o master.o mnnd.o pred.o qtest.o qtest1.o stoke.o succ.o swap.o testeq.o triar.o trifnd.o -lgfortran -lm -lquadmath make[2]: Leaving directory '/tmp/Rtmp7CAajn/working_dir/RtmpIfD1yT/R.INSTALL35b7287f7308e1/deldir/src' make[2]: Entering directory '/tmp/Rtmp7CAajn/working_dir/RtmpIfD1yT/R.INSTALL35b7287f7308e1/deldir/src' make[2]: Leaving directory '/tmp/Rtmp7CAajn/working_dir/RtmpIfD1yT/R.INSTALL35b7287f7308e1/deldir/src' installing to /tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/00LOCK-deldir/00new/deldir/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (deldir) * installing *source* package ‘RcppEigen’ ... ** this is package ‘RcppEigen’ version ‘0.3.4.0.2’ ** package ‘RcppEigen’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++ (GCC) 15.2.1 20260123 (Red Hat 15.2.1-7)’ make[2]: Entering directory '/tmp/Rtmp7CAajn/working_dir/RtmprYLAEY/R.INSTALL35bd3c2b5087e1/RcppEigen/src' g++ -std=gnu++20 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/Rcpp/include' -I/usr/local/include -I../inst/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c RcppEigen.cpp -o RcppEigen.o g++ -std=gnu++20 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/Rcpp/include' -I/usr/local/include -I../inst/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++20 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/Rcpp/include' -I/usr/local/include -I../inst/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c fastLm.cpp -o fastLm.o In file included from ../inst/include/Eigen/Core:337, from ../inst/include/Eigen/Dense:1, from ../inst/include/RcppEigenForward.h:28, from ../inst/include/RcppEigen.h:25, from fastLm.h:25, from fastLm.cpp:23: ../inst/include/Eigen/src/Core/products/SelfadjointMatrixVector.h: In function ‘static void Eigen::internal::selfadjoint_product_impl::run(Dest&, const Lhs&, const Rhs&, const Scalar&) [with Dest = Eigen::Block, -1, 1, false>; Lhs = Eigen::Block, -1, -1, false>; int LhsMode = 17; Rhs = Eigen::CwiseBinaryOp, const Eigen::CwiseNullaryOp, const Eigen::Matrix >, const Eigen::Block, -1, 1, true>, -1, 1, false> >]’: ../inst/include/Eigen/src/Core/products/SelfadjointMatrixVector.h:229:7: warning: ‘result’ may be used uninitialized [-Wmaybe-uninitialized] 227 | internal::selfadjoint_matrix_vector_product::Flags&RowMajorBit) ? RowMajor : ColMajor, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 228 | int(LhsUpLo), bool(LhsBlasTraits::NeedToConjugate), bool(RhsBlasTraits::NeedToConjugate)>::run | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 229 | ( | ^ 230 | lhs.rows(), // size | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 231 | &lhs.coeffRef(0,0), lhs.outerStride(), // lhs info | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 232 | actualRhsPtr, // rhs info | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 233 | actualDestPtr, // result info | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 234 | actualAlpha // scale factor | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 235 | ); | ~ ../inst/include/Eigen/src/Core/products/SelfadjointMatrixVector.h:41:6: note: by argument 4 of type ‘const double*’ to ‘static void Eigen::internal::selfadjoint_matrix_vector_product::run(Index, const Scalar*, Index, const Scalar*, Scalar*, Scalar) [with Scalar = double; Index = long int; int StorageOrder = 0; int UpLo = 1; bool ConjugateLhs = false; bool ConjugateRhs = false; int Version = 0]’ declared here 41 | void selfadjoint_matrix_vector_product::run( | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ../inst/include/Eigen/Core:341: ../inst/include/Eigen/src/Core/products/TriangularMatrixVector.h: In function ‘static void Eigen::internal::trmv_selector::run(const Lhs&, const Rhs&, Dest&, const typename Dest::Scalar&) [with Lhs = Eigen::Transpose, -1, -1, false>, -1, -1, false> >; Rhs = Eigen::Transpose, const Eigen::CwiseNullaryOp, const Eigen::Matrix >, const Eigen::Transpose, -1, -1, false>, -1, 1, true>, -1, 1, false> > > >; Dest = Eigen::Transpose, 1, -1, true>, 1, -1, false> >; int Mode = 6]’: ../inst/include/Eigen/src/Core/products/TriangularMatrixVector.h:332:12: warning: ‘result’ may be used uninitialized [-Wmaybe-uninitialized] 327 | internal::triangular_matrix_vector_product | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 328 | | ~~~~~~~~~ 332 | ::run(actualLhs.rows(),actualLhs.cols(), | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 333 | actualLhs.data(),actualLhs.outerStride(), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 334 | actualRhsPtr,1, | ~~~~~~~~~~~~~~~ 335 | dest.data(),dest.innerStride(), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 336 | actualAlpha); | ~~~~~~~~~~~~ ../inst/include/Eigen/src/Core/products/TriangularMatrixVector.h:105:24: note: by argument 5 of type ‘const double*’ to ‘static void Eigen::internal::triangular_matrix_vector_product::run(Index, Index, const LhsScalar*, Index, const RhsScalar*, Index, ResScalar*, Index, const ResScalar&) [with Index = long int; int Mode = 6; LhsScalar = double; bool ConjLhs = false; RhsScalar = double; bool ConjRhs = false; int Version = 0]’ declared here 105 | EIGEN_DONT_INLINE void triangular_matrix_vector_product | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -std=gnu++20 -shared -L/usr/local/lib64 -o RcppEigen.so RcppEigen.o RcppExports.o fastLm.o -llapack -L/data/gannet/ripley/R/R-devel/lib -lRblas -lgfortran -lm -lquadmath make[2]: Leaving directory '/tmp/Rtmp7CAajn/working_dir/RtmprYLAEY/R.INSTALL35bd3c2b5087e1/RcppEigen/src' make[2]: Entering directory '/tmp/Rtmp7CAajn/working_dir/RtmprYLAEY/R.INSTALL35bd3c2b5087e1/RcppEigen/src' make[2]: Leaving directory '/tmp/Rtmp7CAajn/working_dir/RtmprYLAEY/R.INSTALL35bd3c2b5087e1/RcppEigen/src' installing to /tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/00LOCK-RcppEigen/00new/RcppEigen/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (RcppEigen) * installing *source* package ‘snow’ ... ** this is package ‘snow’ version ‘0.4-4’ ** package ‘snow’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (snow) * installing *source* package ‘bitops’ ... ** this is package ‘bitops’ version ‘1.0-9’ ** package ‘bitops’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc (GCC) 15.2.1 20260123 (Red Hat 15.2.1-7)’ make[2]: Entering directory '/tmp/Rtmp7CAajn/working_dir/RtmpxYZGKU/R.INSTALL3607d617e87c71/bitops/src' gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c bit-ops.c -o bit-ops.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c cksum.c -o cksum.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c init.c -o init.o gcc -shared -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -L/usr/local/lib64 -o bitops.so bit-ops.o cksum.o init.o make[2]: Leaving directory '/tmp/Rtmp7CAajn/working_dir/RtmpxYZGKU/R.INSTALL3607d617e87c71/bitops/src' make[2]: Entering directory '/tmp/Rtmp7CAajn/working_dir/RtmpxYZGKU/R.INSTALL3607d617e87c71/bitops/src' make[2]: Leaving directory '/tmp/Rtmp7CAajn/working_dir/RtmpxYZGKU/R.INSTALL3607d617e87c71/bitops/src' installing to /tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/00LOCK-bitops/00new/bitops/libs ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (bitops) * installing *source* package ‘png’ ... ** this is package ‘png’ version ‘0.1-8’ ** package ‘png’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc (GCC) 15.2.1 20260123 (Red Hat 15.2.1-7)’ make[2]: Entering directory '/tmp/Rtmp7CAajn/working_dir/Rtmp9nhzF2/R.INSTALL360a7a55eae0b6/png/src' gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include `libpng-config --cflags` -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c dummy.c -o dummy.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include `libpng-config --cflags` -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c read.c -o read.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include `libpng-config --cflags` -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c write.c -o write.o gcc -shared -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -L/usr/local/lib64 -o png.so dummy.o read.o write.o -L/usr/lib64 -lpng16 -lm -lz -lm make[2]: Leaving directory '/tmp/Rtmp7CAajn/working_dir/Rtmp9nhzF2/R.INSTALL360a7a55eae0b6/png/src' make[2]: Entering directory '/tmp/Rtmp7CAajn/working_dir/Rtmp9nhzF2/R.INSTALL360a7a55eae0b6/png/src' make[2]: Leaving directory '/tmp/Rtmp7CAajn/working_dir/Rtmp9nhzF2/R.INSTALL360a7a55eae0b6/png/src' installing to /tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/00LOCK-png/00new/png/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (png) * installing *source* package ‘jpeg’ ... ** this is package ‘jpeg’ version ‘0.1-11’ ** package ‘jpeg’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc (GCC) 15.2.1 20260123 (Red Hat 15.2.1-7)’ make[2]: Entering directory '/tmp/Rtmp7CAajn/working_dir/RtmpZIZSZb/R.INSTALL360db2351f36c5/jpeg/src' gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c read.c -o read.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c reg.c -o reg.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c write.c -o write.o gcc -shared -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -L/usr/local/lib64 -o jpeg.so read.o reg.o write.o -ljpeg make[2]: Leaving directory '/tmp/Rtmp7CAajn/working_dir/RtmpZIZSZb/R.INSTALL360db2351f36c5/jpeg/src' make[2]: Entering directory '/tmp/Rtmp7CAajn/working_dir/RtmpZIZSZb/R.INSTALL360db2351f36c5/jpeg/src' make[2]: Leaving directory '/tmp/Rtmp7CAajn/working_dir/RtmpZIZSZb/R.INSTALL360db2351f36c5/jpeg/src' installing to /tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/00LOCK-jpeg/00new/jpeg/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (jpeg) * installing *source* package ‘Biobase’ ... ** this is package ‘Biobase’ version ‘2.71.0’ ** using staged installation ** libs using C compiler: ‘gcc (GCC) 15.2.1 20260123 (Red Hat 15.2.1-7)’ make[2]: Entering directory '/tmp/Rtmp7CAajn/working_dir/RtmpkE9xri/R.INSTALL3610d52475aa17/Biobase/src' gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c Rinit.c -o Rinit.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c envir.c -o envir.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c matchpt.c -o matchpt.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c rowMedians.c -o rowMedians.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c sublist_extract.c -o sublist_extract.o gcc -shared -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -L/usr/local/lib64 -o Biobase.so Rinit.o envir.o matchpt.o rowMedians.o sublist_extract.o make[2]: Leaving directory '/tmp/Rtmp7CAajn/working_dir/RtmpkE9xri/R.INSTALL3610d52475aa17/Biobase/src' make[2]: Entering directory '/tmp/Rtmp7CAajn/working_dir/RtmpkE9xri/R.INSTALL3610d52475aa17/Biobase/src' make[2]: Leaving directory '/tmp/Rtmp7CAajn/working_dir/RtmpkE9xri/R.INSTALL3610d52475aa17/Biobase/src' installing to /tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/00LOCK-Biobase/00new/Biobase/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (Biobase) * installing *source* package ‘Seqinfo’ ... ** this is package ‘Seqinfo’ version ‘1.1.0’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (Seqinfo) * installing *source* package ‘hwriter’ ... ** this is package ‘hwriter’ version ‘1.3.2.1’ ** package ‘hwriter’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (hwriter) * installing *source* package ‘Rhtslib’ ... ** this is package ‘Rhtslib’ version ‘3.7.0’ ** using non-staged installation via StagedInstall field ** libs using C compiler: ‘gcc (GCC) 15.2.1 20260123 (Red Hat 15.2.1-7)’ make[2]: Entering directory '/tmp/Rtmp7CAajn/working_dir/Rtmp2lPyq0/R.INSTALL362eff693c499d/Rhtslib/src' cd "htslib-1.18" && make -f "Makefile.Rhtslib" mkdir -p "/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/Rhtslib/include/htslib" mkdir -p "/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/Rhtslib/usrlib" mkdir -p "/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/Rhtslib/testdata/tabix" make[3]: Entering directory '/tmp/Rtmp7CAajn/working_dir/Rtmp2lPyq0/R.INSTALL362eff693c499d/Rhtslib/src/htslib-1.18' cd "htslib-1.18/test" && (cp *.sam *.bam *.vcf *.bcf *.cram *.fa *.fa.fai *.gff *.bed "/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/Rhtslib/testdata" 2>/dev/null || true) && cd tabix && (cp *.sam *.bam *.vcf *.bcf *.cram *.fa *.fa.fai *.gff *.bed "/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/Rhtslib/testdata/tabix" 2>/dev/null || true) gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o kfunc.o kfunc.c gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o kstring.o kstring.c gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o bcf_sr_sort.o bcf_sr_sort.c gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o bgzf.o bgzf.c gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o errmod.o errmod.c gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o faidx.o faidx.c gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o header.o header.c gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o hfile.o hfile.c echo '#define HTS_VERSION_TEXT "1.18"' > version.h printf '#define HTS_CC "%s"\n#define HTS_CPPFLAGS "%s"\n#define HTS_CFLAGS "%s"\n#define HTS_LDFLAGS "%s"\n#define HTS_LIBS "%s"\n' \ 'gcc' \ '-I/usr/local/include -D_FILE_OFFSET_BITS=64' \ '-g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -fvisibility=hidden' \ '-L/usr/local/lib64 -fvisibility=hidden' \ '-lz -lm -lbz2 -llzma -lcurl' > config_vars.h gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o hts_expr.o hts_expr.c gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o hts_os.o hts_os.c gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o md5.o md5.c gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o multipart.o multipart.c gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o probaln.o probaln.c gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o realn.o realn.c gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o regidx.o regidx.c gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o region.o region.c gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o sam.o sam.c gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o sam_mods.o sam_mods.c gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o synced_bcf_reader.o synced_bcf_reader.c gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o vcf_sweep.o vcf_sweep.c gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o tbx.o tbx.c gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o textutils.o textutils.c gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o thread_pool.o thread_pool.c gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o vcf.o vcf.c gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o vcfutils.o vcfutils.c gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_codecs.o cram/cram_codecs.c gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_decode.o cram/cram_decode.c gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_encode.o cram/cram_encode.c gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_external.o cram/cram_external.c gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_index.o cram/cram_index.c gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_io.o cram/cram_io.c gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_stats.o cram/cram_stats.c gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/mFILE.o cram/mFILE.c gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/open_trace_file.o cram/open_trace_file.c gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/pooled_alloc.o cram/pooled_alloc.c gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/string_alloc.o cram/string_alloc.c gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/arith_dynamic.c gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/fqzcomp_qual.c gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/htscodecs.c gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/pack.o htscodecs/htscodecs/pack.c gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static4x16pr.c gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/rANS_static32x16pr_avx2.o htscodecs/htscodecs/rANS_static32x16pr_avx2.c gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/rANS_static32x16pr_avx512.o htscodecs/htscodecs/rANS_static32x16pr_avx512.c gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/rANS_static32x16pr_sse4.o htscodecs/htscodecs/rANS_static32x16pr_sse4.c gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/rANS_static32x16pr_neon.o htscodecs/htscodecs/rANS_static32x16pr_neon.c gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/rANS_static32x16pr.o htscodecs/htscodecs/rANS_static32x16pr.c gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rANS_static.c gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/rle.o htscodecs/htscodecs/rle.c gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/tokenise_name3.c gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/utils.o htscodecs/htscodecs/utils.c gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o hfile_libcurl.o hfile_libcurl.c gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o kfunc.pico kfunc.c gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o kstring.pico kstring.c gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o bcf_sr_sort.pico bcf_sr_sort.c gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o bgzf.pico bgzf.c gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o errmod.pico errmod.c gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o faidx.pico faidx.c gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o header.pico header.c gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o hfile.pico hfile.c gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o hts.pico hts.c gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o hts_expr.pico hts_expr.c gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o hts_os.pico hts_os.c gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o md5.pico md5.c gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o multipart.pico multipart.c gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o probaln.pico probaln.c gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o realn.pico realn.c gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o regidx.pico regidx.c gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o region.pico region.c gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o sam.pico sam.c gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o sam_mods.pico sam_mods.c gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o synced_bcf_reader.pico synced_bcf_reader.c gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o vcf_sweep.pico vcf_sweep.c gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o tbx.pico tbx.c gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o textutils.pico textutils.c gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o thread_pool.pico thread_pool.c gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o vcf.pico vcf.c gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o vcfutils.pico vcfutils.c gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_codecs.pico cram/cram_codecs.c gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_decode.pico cram/cram_decode.c gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_encode.pico cram/cram_encode.c gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_external.pico cram/cram_external.c gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_index.pico cram/cram_index.c gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_io.pico cram/cram_io.c gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_stats.pico cram/cram_stats.c gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/mFILE.pico cram/mFILE.c gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/open_trace_file.pico cram/open_trace_file.c gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/pooled_alloc.pico cram/pooled_alloc.c gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/string_alloc.pico cram/string_alloc.c gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/arith_dynamic.pico htscodecs/htscodecs/arith_dynamic.c gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/fqzcomp_qual.pico htscodecs/htscodecs/fqzcomp_qual.c gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/htscodecs.pico htscodecs/htscodecs/htscodecs.c gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/pack.pico htscodecs/htscodecs/pack.c gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/rANS_static4x16pr.pico htscodecs/htscodecs/rANS_static4x16pr.c gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/rANS_static32x16pr_avx2.pico htscodecs/htscodecs/rANS_static32x16pr_avx2.c gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/rANS_static32x16pr_avx512.pico htscodecs/htscodecs/rANS_static32x16pr_avx512.c gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/rANS_static32x16pr_sse4.pico htscodecs/htscodecs/rANS_static32x16pr_sse4.c gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/rANS_static32x16pr_neon.pico htscodecs/htscodecs/rANS_static32x16pr_neon.c gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/rANS_static32x16pr.pico htscodecs/htscodecs/rANS_static32x16pr.c gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/rANS_static.pico htscodecs/htscodecs/rANS_static.c gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/rle.pico htscodecs/htscodecs/rle.c gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/tokenise_name3.pico htscodecs/htscodecs/tokenise_name3.c gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/utils.pico htscodecs/htscodecs/utils.c gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o hfile_libcurl.pico hfile_libcurl.c gcc -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o hts.o hts.c gcc-ar -rc libhts.a kfunc.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o header.o hfile.o hts.o hts_expr.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o region.o sam.o sam_mods.o synced_bcf_reader.o vcf_sweep.o tbx.o textutils.o thread_pool.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_stats.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/string_alloc.o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/pack.o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static32x16pr_avx2.o htscodecs/htscodecs/rANS_static32x16pr_avx512.o htscodecs/htscodecs/rANS_static32x16pr_sse4.o htscodecs/htscodecs/rANS_static32x16pr_neon.o htscodecs/htscodecs/rANS_static32x16pr.o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rle.o htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/utils.o hfile_libcurl.o gcc-ranlib libhts.a gcc -shared -Wl,-soname,libhts.so.3 -Wl,-version-script,htslib.map -L/usr/local/lib64 -fvisibility=hidden -o libhts.so kfunc.pico kstring.pico bcf_sr_sort.pico bgzf.pico errmod.pico faidx.pico header.pico hfile.pico hts.pico hts_expr.pico hts_os.pico md5.pico multipart.pico probaln.pico realn.pico regidx.pico region.pico sam.pico sam_mods.pico synced_bcf_reader.pico vcf_sweep.pico tbx.pico textutils.pico thread_pool.pico vcf.pico vcfutils.pico cram/cram_codecs.pico cram/cram_decode.pico cram/cram_encode.pico cram/cram_external.pico cram/cram_index.pico cram/cram_io.pico cram/cram_stats.pico cram/mFILE.pico cram/open_trace_file.pico cram/pooled_alloc.pico cram/string_alloc.pico htscodecs/htscodecs/arith_dynamic.pico htscodecs/htscodecs/fqzcomp_qual.pico htscodecs/htscodecs/htscodecs.pico htscodecs/htscodecs/pack.pico htscodecs/htscodecs/rANS_static4x16pr.pico htscodecs/htscodecs/rANS_static32x16pr_avx2.pico htscodecs/htscodecs/rANS_static32x16pr_avx512.pico htscodecs/htscodecs/rANS_static32x16pr_sse4.pico htscodecs/htscodecs/rANS_static32x16pr_neon.pico htscodecs/htscodecs/rANS_static32x16pr.pico htscodecs/htscodecs/rANS_static.pico htscodecs/htscodecs/rle.pico htscodecs/htscodecs/tokenise_name3.pico htscodecs/htscodecs/utils.pico hfile_libcurl.pico -lz -lm -lbz2 -llzma -lcurl -lpthread ln -sf libhts.so libhts.so.3 make[3]: Leaving directory '/tmp/Rtmp7CAajn/working_dir/Rtmp2lPyq0/R.INSTALL362eff693c499d/Rhtslib/src/htslib-1.18' cd "htslib-1.18/htslib" && cp * "/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/Rhtslib/include/htslib" cd "htslib-1.18" && cp libhts.so libhts.a "/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/Rhtslib/usrlib" gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/Rhtslib/include" -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c R_init_Rhtslib.c -o R_init_Rhtslib.o cd "/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/Rhtslib/usrlib" && ln -s libhts.so libhts.so.2 gcc -shared -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -L/usr/local/lib64 -o Rhtslib.so R_init_Rhtslib.o /tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/Rhtslib/usrlib/libhts.a -lcurl -lbz2 -llzma -lz make[2]: Leaving directory '/tmp/Rtmp7CAajn/working_dir/Rtmp2lPyq0/R.INSTALL362eff693c499d/Rhtslib/src' make[2]: Entering directory '/tmp/Rtmp7CAajn/working_dir/Rtmp2lPyq0/R.INSTALL362eff693c499d/Rhtslib/src' cd "htslib-1.18" && make -f "Makefile.Rhtslib" mkdir -p "/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/Rhtslib/include/htslib" make[3]: Entering directory '/tmp/Rtmp7CAajn/working_dir/Rtmp2lPyq0/R.INSTALL362eff693c499d/Rhtslib/src/htslib-1.18' make[3]: Leaving directory '/tmp/Rtmp7CAajn/working_dir/Rtmp2lPyq0/R.INSTALL362eff693c499d/Rhtslib/src/htslib-1.18' cd "htslib-1.18/htslib" && cp * "/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/Rhtslib/include/htslib" gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/Rhtslib/include" -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c R_init_Rhtslib.c -o R_init_Rhtslib.o make[2]: Leaving directory '/tmp/Rtmp7CAajn/working_dir/Rtmp2lPyq0/R.INSTALL362eff693c499d/Rhtslib/src' installing to /tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/Rhtslib/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (Rhtslib) * installing *source* package ‘lambda.r’ ... ** this is package ‘lambda.r’ version ‘1.2.4’ ** package ‘lambda.r’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (lambda.r) * installing *source* package ‘S4Arrays’ ... ** this is package ‘S4Arrays’ version ‘1.11.1’ ** using staged installation ** libs using C compiler: ‘gcc (GCC) 15.2.1 20260123 (Red Hat 15.2.1-7)’ make[2]: Entering directory '/tmp/Rtmp7CAajn/working_dir/RtmpB43AOO/R.INSTALL363e174da6efc1/S4Arrays/src' gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c R_init_S4Arrays.c -o R_init_S4Arrays.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c S4Vectors_stubs.c -o S4Vectors_stubs.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c abind.c -o abind.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c array_selection.c -o array_selection.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c dim_tuning_utils.c -o dim_tuning_utils.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c rowsum.c -o rowsum.o gcc -shared -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -L/usr/local/lib64 -o S4Arrays.so R_init_S4Arrays.o S4Vectors_stubs.o abind.o array_selection.o dim_tuning_utils.o rowsum.o make[2]: Leaving directory '/tmp/Rtmp7CAajn/working_dir/RtmpB43AOO/R.INSTALL363e174da6efc1/S4Arrays/src' make[2]: Entering directory '/tmp/Rtmp7CAajn/working_dir/RtmpB43AOO/R.INSTALL363e174da6efc1/S4Arrays/src' make[2]: Leaving directory '/tmp/Rtmp7CAajn/working_dir/RtmpB43AOO/R.INSTALL363e174da6efc1/S4Arrays/src' installing to /tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/00LOCK-S4Arrays/00new/S4Arrays/libs ** R ** inst ** byte-compile and prepare package for lazy loading Creating a new generic function for ‘rowsum’ in package ‘S4Arrays’ Creating a new generic function for ‘abind’ in package ‘S4Arrays’ ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (S4Arrays) * installing *source* package ‘interp’ ... ** this is package ‘interp’ version ‘1.1-6’ ** package ‘interp’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc (GCC) 15.2.1 20260123 (Red Hat 15.2.1-7)’ using Fortran compiler: ‘GNU Fortran (GCC) 15.2.1 20260123 (Red Hat 15.2.1-7)’ using C++ compiler: ‘g++ (GCC) 15.2.1 20260123 (Red Hat 15.2.1-7)’ make[2]: Entering directory '/tmp/Rtmp7CAajn/working_dir/RtmphvGBlL/R.INSTALL3655021a3bb10a/interp/src' g++ -std=gnu++20 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/Rcpp/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/RcppEigen/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c BiLin.cpp -o BiLin.o g++ -std=gnu++20 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/Rcpp/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/RcppEigen/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++20 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/Rcpp/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/RcppEigen/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c aSpline.cpp -o aSpline.o gfortran -fpic -g -O2 -mtune=native -Wall -pedantic -c bilinear.f -o bilinear.o g++ -std=gnu++20 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/Rcpp/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/RcppEigen/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c circum.cpp -o circum.o g++ -std=gnu++20 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/Rcpp/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/RcppEigen/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c common.cpp -o common.o g++ -std=gnu++20 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/Rcpp/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/RcppEigen/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c convexHull.cpp -o convexHull.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/Rcpp/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/RcppEigen/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c init.c -o init.o g++ -std=gnu++20 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/Rcpp/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/RcppEigen/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c interp.cpp -o interp.o g++ -std=gnu++20 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/Rcpp/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/RcppEigen/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c partDeriv.cpp -o partDeriv.o g++ -std=gnu++20 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/Rcpp/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/RcppEigen/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c s_hull_pro.cpp -o s_hull_pro.o g++ -std=gnu++20 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/Rcpp/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/RcppEigen/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c shullDeltri.cpp -o shullDeltri.o s_hull_pro.cpp: In function ‘int s_hull_pro(std::vector&, std::vector&, int)’: s_hull_pro.cpp:638:25: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘long unsigned int’} and ‘__gnu_cxx::__alloc_traits, int>::value_type’ {aka ‘int’} [-Wsign-compare] 638 | if(triads.size()>=tridx[p]+1){ | ~~~~~~~~~~~~~^~~~~~~~~~~~ s_hull_pro.cpp:712:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 712 | if(nits>2*(2*pts.size()-ch_size-2)){ | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ convexHull.cpp: In function ‘Rcpp::List ConvexHull(Rcpp::NumericVector, Rcpp::NumericVector)’: convexHull.cpp:122:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 122 | for(int i=0; i, std::vector, double, double, int)’: shullDeltri.cpp:308:11: warning: ‘pt.Shx::tr’ may be used uninitialized [-Wmaybe-uninitialized] 308 | Shx pt; | ^~ shullDeltri.cpp:308:11: warning: ‘pt.Shx::tc’ may be used uninitialized [-Wmaybe-uninitialized] In file included from /tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/RcppEigen/include/Eigen/Core:337, from /tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/RcppEigen/include/Eigen/Dense:1, from /tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/RcppEigen/include/RcppEigenForward.h:28, from /tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/RcppEigen/include/RcppEigen.h:25, from interp.h:7, from partDeriv.cpp:2: /tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/RcppEigen/include/Eigen/src/Core/products/SelfadjointMatrixVector.h: In function ‘static void Eigen::internal::selfadjoint_product_impl::run(Dest&, const Lhs&, const Rhs&, const Scalar&) [with Dest = Eigen::Block, -1, 1, false>; Lhs = Eigen::Block, -1, -1, false>; int LhsMode = 17; Rhs = Eigen::CwiseBinaryOp, const Eigen::CwiseNullaryOp, const Eigen::Matrix >, const Eigen::Block, -1, 1, true>, -1, 1, false> >]’: /tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/RcppEigen/include/Eigen/src/Core/products/SelfadjointMatrixVector.h:229:7: warning: ‘result’ may be used uninitialized [-Wmaybe-uninitialized] 227 | internal::selfadjoint_matrix_vector_product::Flags&RowMajorBit) ? RowMajor : ColMajor, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 228 | int(LhsUpLo), bool(LhsBlasTraits::NeedToConjugate), bool(RhsBlasTraits::NeedToConjugate)>::run | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 229 | ( | ^ 230 | lhs.rows(), // size | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 231 | &lhs.coeffRef(0,0), lhs.outerStride(), // lhs info | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 232 | actualRhsPtr, // rhs info | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 233 | actualDestPtr, // result info | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 234 | actualAlpha // scale factor | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 235 | ); | ~ /tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/RcppEigen/include/Eigen/src/Core/products/SelfadjointMatrixVector.h:41:6: note: by argument 4 of type ‘const double*’ to ‘static void Eigen::internal::selfadjoint_matrix_vector_product::run(Index, const Scalar*, Index, const Scalar*, Scalar*, Scalar) [with Scalar = double; Index = long int; int StorageOrder = 0; int UpLo = 1; bool ConjugateLhs = false; bool ConjugateRhs = false; int Version = 0]’ declared here 41 | void selfadjoint_matrix_vector_product::run( | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/RcppEigen/include/Eigen/Core:341: /tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/RcppEigen/include/Eigen/src/Core/products/TriangularMatrixVector.h: In function ‘static void Eigen::internal::trmv_selector::run(const Lhs&, const Rhs&, Dest&, const typename Dest::Scalar&) [with Lhs = Eigen::Transpose, -1, -1, false>, -1, -1, false> >; Rhs = Eigen::Transpose, const Eigen::CwiseNullaryOp, const Eigen::Matrix >, const Eigen::Transpose, -1, -1, false>, -1, 1, true>, -1, 1, false> > > >; Dest = Eigen::Transpose, 1, -1, true>, 1, -1, false> >; int Mode = 6]’: /tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/RcppEigen/include/Eigen/src/Core/products/TriangularMatrixVector.h:332:12: warning: ‘result’ may be used uninitialized [-Wmaybe-uninitialized] 327 | internal::triangular_matrix_vector_product | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 328 | | ~~~~~~~~~ 332 | ::run(actualLhs.rows(),actualLhs.cols(), | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 333 | actualLhs.data(),actualLhs.outerStride(), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 334 | actualRhsPtr,1, | ~~~~~~~~~~~~~~~ 335 | dest.data(),dest.innerStride(), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 336 | actualAlpha); | ~~~~~~~~~~~~ /tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/RcppEigen/include/Eigen/src/Core/products/TriangularMatrixVector.h:105:24: note: by argument 5 of type ‘const double*’ to ‘static void Eigen::internal::triangular_matrix_vector_product::run(Index, Index, const LhsScalar*, Index, const RhsScalar*, Index, ResScalar*, Index, const ResScalar&) [with Index = long int; int Mode = 6; LhsScalar = double; bool ConjLhs = false; RhsScalar = double; bool ConjRhs = false; int Version = 0]’ declared here 105 | EIGEN_DONT_INLINE void triangular_matrix_vector_product | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/RcppEigen/include/Eigen/Core:295: In constructor ‘Eigen::Matrix<_Scalar, _Rows, _Cols, _Options, _MaxRows, _MaxCols>::Matrix(const T0&, const T1&) [with T0 = int; T1 = int; _Scalar = double; int _Rows = -1; int _Cols = -1; int _Options = 0; int _MaxRows = -1; int _MaxCols = -1]’, inlined from ‘PDEst pD(Rcpp::NumericVector, Rcpp::NumericVector, Rcpp::NumericVector, NN, double, double, Rcpp::CharacterVector, Rcpp::NumericVector, std::string, int)’ at partDeriv.cpp:299:18: /tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/RcppEigen/include/Eigen/src/Core/Matrix.h:340:35: warning: ‘p’ may be used uninitialized [-Wmaybe-uninitialized] 340 | Base::template _init2(x, y); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ partDeriv.cpp: In function ‘PDEst pD(Rcpp::NumericVector, Rcpp::NumericVector, Rcpp::NumericVector, NN, double, double, Rcpp::CharacterVector, Rcpp::NumericVector, std::string, int)’: partDeriv.cpp:289:7: note: ‘p’ declared here 289 | int p; | ^ g++ -std=gnu++20 -shared -L/usr/local/lib64 -o interp.so BiLin.o RcppExports.o aSpline.o bilinear.o circum.o common.o convexHull.o init.o interp.o partDeriv.o s_hull_pro.o shullDeltri.o -lgfortran -lm -lquadmath make[2]: Leaving directory '/tmp/Rtmp7CAajn/working_dir/RtmphvGBlL/R.INSTALL3655021a3bb10a/interp/src' make[2]: Entering directory '/tmp/Rtmp7CAajn/working_dir/RtmphvGBlL/R.INSTALL3655021a3bb10a/interp/src' make[2]: Leaving directory '/tmp/Rtmp7CAajn/working_dir/RtmphvGBlL/R.INSTALL3655021a3bb10a/interp/src' installing to /tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/00LOCK-interp/00new/interp/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (interp) * installing *source* package ‘Biostrings’ ... ** this is package ‘Biostrings’ version ‘2.79.4’ ** using staged installation ** libs using C compiler: ‘gcc (GCC) 15.2.1 20260123 (Red Hat 15.2.1-7)’ make[2]: Entering directory '/tmp/Rtmp7CAajn/working_dir/RtmpH2Nelh/R.INSTALL3684681d75633a/Biostrings/src' gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c BAB_class.c -o BAB_class.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c BitMatrix.c -o BitMatrix.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c IRanges_stubs.c -o IRanges_stubs.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c MIndex_class.c -o MIndex_class.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c PreprocessedTB_class.c -o PreprocessedTB_class.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c R_init_Biostrings.c -o R_init_Biostrings.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c RoSeqs_utils.c -o RoSeqs_utils.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c S4Vectors_stubs.c -o S4Vectors_stubs.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c SparseList_utils.c -o SparseList_utils.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c XStringSetList_class.c -o XStringSetList_class.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c XStringSet_class.c -o XStringSet_class.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c XString_class.c -o XString_class.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c XVector_stubs.c -o XVector_stubs.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c find_palindromes.c -o find_palindromes.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c gtestsim.c -o gtestsim.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c inject_code.c -o inject_code.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c lcsuffix.c -o lcsuffix.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c letter_frequency.c -o letter_frequency.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c lowlevel_matching.c -o lowlevel_matching.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c match_PWM.c -o match_PWM.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c match_pattern.c -o match_pattern.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c match_pattern_boyermoore.c -o match_pattern_boyermoore.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c match_pattern_indels.c -o match_pattern_indels.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c match_pattern_shiftor.c -o match_pattern_shiftor.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c match_pdict.c -o match_pdict.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c match_pdict_ACtree2.c -o match_pdict_ACtree2.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c match_pdict_Twobit.c -o match_pdict_Twobit.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c match_pdict_utils.c -o match_pdict_utils.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c match_reporting.c -o match_reporting.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c read_fasta_files.c -o read_fasta_files.o In file included from /data/gannet/ripley/R/R-devel/include/Rdefines.h:41, from /tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include/S4Vectors_defines.h:18, from /tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include/IRanges_defines.h:18, from ../inst/include/Biostrings_defines.h:18, from Biostrings.h:1, from match_pdict_Twobit.c:10: In function ‘Twobit_asLIST’, inlined from ‘build_Twobit’ at match_pdict_Twobit.c:145:2: match_pdict_Twobit.c:75:27: warning: ‘twobit_sign2pos’ may be used uninitialized [-Wmaybe-uninitialized] 75 | PROTECT(ans_elt = new_XInteger_from_tag("XInteger", twobit_sign2pos)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /data/gannet/ripley/R/R-devel/include/Rinternals.h:366:36: note: in definition of macro ‘PROTECT’ 366 | #define PROTECT(s) Rf_protect(s) | ^ match_pdict_Twobit.c: In function ‘build_Twobit’: match_pdict_Twobit.c:110:19: note: ‘twobit_sign2pos’ was declared here 110 | SEXP ans, twobit_sign2pos; | ^~~~~~~~~~~~~~~ match_pdict_utils.c: In function ‘match_ppheadtail0’: match_pdict_utils.c:653:56: warning: unused variable ‘ncol’ [-Wunused-variable] 653 | int nelt, min_safe_tb_end, max_safe_tb_end, j, ncol; | ^~~~ match_pdict_utils.c: In function ‘match_ppheadtail’: match_pdict_utils.c:713:13: warning: unused variable ‘nelt’ [-Wunused-variable] 713 | int nelt, nkey0, nkey1, nkey2, i, key; | ^~~~ match_pdict_utils.c: In function ‘_match_pdict_all_flanks’: match_pdict_utils.c:820:51: warning: unused variable ‘subtotal_NFC’ [-Wunused-variable] 820 | static unsigned long int total_NFC = 0UL, subtotal_NFC = 0UL; | ^~~~~~~~~~~~ match_pdict_utils.c:820:34: warning: unused variable ‘total_NFC’ [-Wunused-variable] 820 | static unsigned long int total_NFC = 0UL, subtotal_NFC = 0UL; | ^~~~~~~~~ match_pdict_utils.c:819:40: warning: unused variable ‘NFC’ [-Wunused-variable] 819 | unsigned long int ndup, nloci, NFC; // NFC = Number of Flank Comparisons | ^~~ match_pdict_utils.c:819:33: warning: unused variable ‘nloci’ [-Wunused-variable] 819 | unsigned long int ndup, nloci, NFC; // NFC = Number of Flank Comparisons | ^~~~~ match_pdict_utils.c:819:27: warning: unused variable ‘ndup’ [-Wunused-variable] 819 | unsigned long int ndup, nloci, NFC; // NFC = Number of Flank Comparisons | ^~~~ match_pdict_utils.c: At top level: match_pdict_utils.c:261:13: warning: ‘match_headtail_by_loc’ defined but not used [-Wunused-function] 261 | static void match_headtail_by_loc(const HeadTail *headtail, | ^~~~~~~~~~~~~~~~~~~~~ MIndex_class.c: In function ‘SparseMIndex_endIndex’: MIndex_class.c:184:27: warning: unused variable ‘poffsets_order’ [-Wunused-variable] 184 | IntAE *poffsets, *poffsets_order; | ^~~~~~~~~~~~~~ gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c read_fastq_files.c -o read_fastq_files.o match_pattern_indels.c:7:13: warning: ‘test_match_pattern_indels’ defined but not used [-Wunused-function] 7 | static void test_match_pattern_indels(const char *p, const char *s, | ^~~~~~~~~~~~~~~~~~~~~~~~~ SparseList_utils.c: In function ‘_get_val_from_env’: SparseList_utils.c:42:34: error: implicit declaration of function ‘NAMED’ [-Wimplicit-function-declaration] 42 | if (ans != R_NilValue && NAMED(ans) == 0) | ^~~~~ SparseList_utils.c:43:17: error: implicit declaration of function ‘SET_NAMED’; did you mean ‘SET_NAMES’? [-Wimplicit-function-declaration] 43 | SET_NAMED(ans, 1); | ^~~~~~~~~ | SET_NAMES gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c replaceAt.c -o replaceAt.o letter_frequency.c: In function ‘XStringSet_two_way_letter_frequency’: letter_frequency.c:957:48: warning: unused variable ‘x_pos’ [-Wunused-variable] 957 | int x_width, y_width, x_length, *ans_mat, i, x_pos; | ^~~~~ match_pdict_ACtree2.c: In function ‘split_and_move_pointers’: match_pdict_ACtree2.c:1031:17: warning: variable ‘node0’ set but not used [-Wunused-but-set-variable] 1031 | ACnode *node0, *node1, *node2; | ^~~~~ match_pdict_ACtree2.c: In function ‘merge_pointers’: match_pdict_ACtree2.c:1076:17: warning: variable ‘node0’ set but not used [-Wunused-but-set-variable] 1076 | ACnode *node0, *node1, *node2; | ^~~~~ make[2]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: SparseList_utils.o] Error 1 gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c replace_letter_at.c -o replace_letter_at.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c strutils.c -o strutils.o match_pdict_ACtree2.c: At top level: match_pdict_ACtree2.c:602:21: warning: ‘a_nice_max_nodeextbuf_nelt’ defined but not used [-Wunused-function] 602 | static unsigned int a_nice_max_nodeextbuf_nelt(int nnodes) | ^~~~~~~~~~~~~~~~~~~~~~~~~~ match_pdict_ACtree2.c:139:13: warning: ‘debug_node_counting_functions’ defined but not used [-Wunused-function] 139 | static void debug_node_counting_functions(int maxdepth) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BitMatrix.c:299:13: warning: ‘BitMatrix_print’ defined but not used [-Wunused-function] 299 | static void BitMatrix_print(BitMatrix *bitmat) | ^~~~~~~~~~~~~~~ gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c translate.c -o translate.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c unstrsplit_methods.c -o unstrsplit_methods.o XStringSet_class.c: In function ‘new_XStringSet_from_CHARACTER’: XStringSet_class.c:124:17: warning: ‘lkup_len’ may be used uninitialized [-Wmaybe-uninitialized] 124 | _copy_CHARSXP_to_Chars_holder(&ans_elt_holder, x_elt, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 125 | INTEGER(start)[i], lkup0, lkup_len); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ XStringSet_class.c:103:22: note: ‘lkup_len’ was declared here 103 | int ans_len, lkup_len, i; | ^~~~~~~~ gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c utils.c -o utils.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c xscat.c -o xscat.o In function ‘vcount_PDict3Parts_XStringSet’, inlined from ‘vmatch_PDict3Parts_XStringSet’ at match_pdict.c:508:10: match_pdict.c:419:33: warning: ‘ans_col’ may be used uninitialized [-Wmaybe-uninitialized] 419 | ans_col += tb_length; | ~~~~~~~~^~~~~~~~~~~~ match_pdict.c: In function ‘vmatch_PDict3Parts_XStringSet’: match_pdict.c:392:65: note: ‘ans_col’ was declared here 392 | int tb_length, S_length, collapse0, i, j, match_count, *ans_col; | ^~~~~~~ utils.c: In function ‘_get_twobit_signature’: utils.c:157:16: warning: ‘twobit_sign’ may be used uninitialized [-Wmaybe-uninitialized] 157 | return twobit_sign; | ^~~~~~~~~~~ utils.c:150:16: note: ‘twobit_sign’ was declared here 150 | int i, twobit_sign; | ^~~~~~~~~~~ utils.c: In function ‘_get_twobit_signature_at’: utils.c:174:16: warning: ‘twobit_sign’ may be used uninitialized [-Wmaybe-uninitialized] 174 | return twobit_sign; | ^~~~~~~~~~~ utils.c:164:19: note: ‘twobit_sign’ was declared here 164 | int i, j, twobit_sign; | ^~~~~~~~~~~ In file included from /data/gannet/ripley/R/R-devel/include/Rdefines.h:41, from /tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include/S4Vectors_defines.h:18, from /tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include/IRanges_defines.h:18, from ../inst/include/Biostrings_defines.h:18, from Biostrings.h:1, from xscat.c:1: xscat.c: In function ‘XString_xscat’: /data/gannet/ripley/R/R-devel/include/Rdefines.h:91:33: warning: ‘ans_length’ may be used uninitialized [-Wmaybe-uninitialized] 91 | #define NEW_RAW(n) Rf_allocVector(RAWSXP,n) | ^~~~~~~~~~~~~~~~~~~~~~~~ /data/gannet/ripley/R/R-devel/include/Rinternals.h:366:36: note: in definition of macro ‘PROTECT’ 366 | #define PROTECT(s) Rf_protect(s) | ^ xscat.c:38:27: note: in expansion of macro ‘NEW_RAW’ 38 | PROTECT(ans_tag = NEW_RAW(ans_length)); | ^~~~~~~ xscat.c:18:20: note: ‘ans_length’ was declared here 18 | int nargs, ans_length, tag_offset, j; | ^~~~~~~~~~ xscat.c:52:23: warning: ‘ans_classname’ may be used uninitialized [-Wmaybe-uninitialized] 52 | PROTECT(ans = new_XRaw_from_tag(ans_classname, ans_tag)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /data/gannet/ripley/R/R-devel/include/Rinternals.h:366:36: note: in definition of macro ‘PROTECT’ 366 | #define PROTECT(s) Rf_protect(s) | ^ xscat.c:20:21: note: ‘ans_classname’ was declared here 20 | const char *ans_classname; | ^~~~~~~~~~~~~ In function ‘vcount_XStringSet_XStringSet’, inlined from ‘vmatch_XStringSet_XStringSet’ at match_pdict.c:542:10: match_pdict.c:470:41: warning: ‘ans_elt’ may be used uninitialized [-Wmaybe-uninitialized] 470 | ans_elt += P_length; | ~~~~~~~~^~~~~~~~~~~ match_pdict.c: In function ‘vmatch_XStringSet_XStringSet’: match_pdict.c:441:64: note: ‘ans_elt’ was declared here 441 | int P_length, S_length, collapse0, i, j, match_count, *ans_elt; | ^~~~~~~ read_fastq_files.c: In function ‘parse_FASTQ_file’: read_fastq_files.c:408:28: warning: ‘dont_load’ may be used uninitialized [-Wmaybe-uninitialized] 408 | if (dont_load || loader->new_qualid_hook == NULL) | ^ read_fastq_files.c:311:26: note: ‘dont_load’ was declared here 311 | lineinrecno, dont_load; | ^~~~~~~~~ xscat.c: In function ‘XStringSet_xscat’: /data/gannet/ripley/R/R-devel/include/Rdefines.h:85:33: warning: ‘ans_length’ may be used uninitialized [-Wmaybe-uninitialized] 85 | #define NEW_INTEGER(n) Rf_allocVector(INTSXP,n) | ^~~~~~~~~~~~~~~~~~~~~~~~ /data/gannet/ripley/R/R-devel/include/Rinternals.h:366:36: note: in definition of macro ‘PROTECT’ 366 | #define PROTECT(s) Rf_protect(s) | ^ xscat.c:91:29: note: in expansion of macro ‘NEW_INTEGER’ 91 | PROTECT(ans_width = NEW_INTEGER(ans_length)); | ^~~~~~~~~~~ xscat.c:66:39: note: ‘ans_length’ was declared here 66 | int nargs, *arg_lengths, *ii, ans_length, i, j, *width; | ^~~~~~~~~~ xscat.c:108:23: warning: ‘ans_element_type’ may be used uninitialized [-Wmaybe-uninitialized] 108 | PROTECT(ans = _alloc_XStringSet(ans_element_type, ans_width)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /data/gannet/ripley/R/R-devel/include/Rinternals.h:366:36: note: in definition of macro ‘PROTECT’ 366 | #define PROTECT(s) Rf_protect(s) | ^ xscat.c:68:21: note: ‘ans_element_type’ was declared here 68 | const char *ans_element_type; | ^~~~~~~~~~~~~~~~ make[2]: Target 'all' not remade because of errors. make[2]: Leaving directory '/tmp/Rtmp7CAajn/working_dir/RtmpH2Nelh/R.INSTALL3684681d75633a/Biostrings/src' ERROR: compilation failed for package ‘Biostrings’ * removing ‘/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/Biostrings’ * installing *source* package ‘GenomicRanges’ ... ** this is package ‘GenomicRanges’ version ‘1.63.1’ ** using staged installation ** libs using C compiler: ‘gcc (GCC) 15.2.1 20260123 (Red Hat 15.2.1-7)’ make[2]: Entering directory '/tmp/Rtmp7CAajn/working_dir/Rtmp3B6jKF/R.INSTALL3687da317455d3/GenomicRanges/src' gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c IRanges_stubs.c -o IRanges_stubs.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c R_init_GenomicRanges.c -o R_init_GenomicRanges.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c S4Vectors_stubs.c -o S4Vectors_stubs.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c transcript_utils.c -o transcript_utils.o In function ‘tloc2rloc’, inlined from ‘tlocs2rlocs’ at transcript_utils.c:208:26: transcript_utils.c:143:45: warning: ‘start’ may be used uninitialized [-Wmaybe-uninitialized] 143 | return on_minus_strand ? end - tloc : start + tloc; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ transcript_utils.c: In function ‘tlocs2rlocs’: transcript_utils.c:120:24: note: ‘start’ was declared here 120 | int nexons, j, start, end, width; | ^~~~~ In function ‘tloc2rloc’, inlined from ‘tlocs2rlocs’ at transcript_utils.c:208:26: transcript_utils.c:143:45: warning: ‘end’ may be used uninitialized [-Wmaybe-uninitialized] 143 | return on_minus_strand ? end - tloc : start + tloc; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ transcript_utils.c: In function ‘tlocs2rlocs’: transcript_utils.c:120:31: note: ‘end’ was declared here 120 | int nexons, j, start, end, width; | ^~~ gcc -shared -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -L/usr/local/lib64 -o GenomicRanges.so IRanges_stubs.o R_init_GenomicRanges.o S4Vectors_stubs.o transcript_utils.o make[2]: Leaving directory '/tmp/Rtmp7CAajn/working_dir/Rtmp3B6jKF/R.INSTALL3687da317455d3/GenomicRanges/src' make[2]: Entering directory '/tmp/Rtmp7CAajn/working_dir/Rtmp3B6jKF/R.INSTALL3687da317455d3/GenomicRanges/src' make[2]: Leaving directory '/tmp/Rtmp7CAajn/working_dir/Rtmp3B6jKF/R.INSTALL3687da317455d3/GenomicRanges/src' installing to /tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/00LOCK-GenomicRanges/00new/GenomicRanges/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (GenomicRanges) * installing *source* package ‘SparseArray’ ... ** this is package ‘SparseArray’ version ‘1.11.10’ ** using staged installation ** libs using C compiler: ‘gcc (GCC) 15.2.1 20260123 (Red Hat 15.2.1-7)’ make[2]: Entering directory '/tmp/Rtmp7CAajn/working_dir/RtmphKjpcb/R.INSTALL369f2733b7907d/SparseArray/src' gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c ExtendableJaggedArray.c -o ExtendableJaggedArray.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c IRanges_stubs.c -o IRanges_stubs.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c OPBufTree.c -o OPBufTree.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c R_init_SparseArray.c -o R_init_SparseArray.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c Rvector_summarization.c -o Rvector_summarization.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c Rvector_utils.c -o Rvector_utils.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c S4Vectors_stubs.c -o S4Vectors_stubs.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c SBT_utils.c -o SBT_utils.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c SVT_SparseArray_class.c -o SVT_SparseArray_class.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c SparseArray_Arith_methods.c -o SparseArray_Arith_methods.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c SparseArray_Compare_methods.c -o SparseArray_Compare_methods.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c SparseArray_Complex_methods.c -o SparseArray_Complex_methods.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c SparseArray_Logic_methods.c -o SparseArray_Logic_methods.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c SparseArray_Math_methods.c -o SparseArray_Math_methods.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c SparseArray_abind.c -o SparseArray_abind.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c SparseArray_aperm.c -o SparseArray_aperm.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c SparseArray_dim_tuning.c -o SparseArray_dim_tuning.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c SparseArray_matrixStats.c -o SparseArray_matrixStats.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c SparseArray_misc_methods.c -o SparseArray_misc_methods.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c SparseArray_subassignment.c -o SparseArray_subassignment.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c SparseArray_subsetting.c -o SparseArray_subsetting.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c SparseArray_summarization.c -o SparseArray_summarization.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c SparseMatrix_mult.c -o SparseMatrix_mult.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c SparseVec.c -o SparseVec.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c SparseVec_Arith.c -o SparseVec_Arith.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c SparseVec_Compare.c -o SparseVec_Compare.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c SparseVec_Logic.c -o SparseVec_Logic.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c SparseVec_Math.c -o SparseVec_Math.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c SparseVec_dotprod.c -o SparseVec_dotprod.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c SparseVec_subassignment.c -o SparseVec_subassignment.o In file included from SparseArray_Compare_methods.c:7: SparseVec.h: In function ‘toSparseVec’: SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration] 125 | sv.nzvals = DATAPTR(nzvals); | ^~~~~~~ | DATAPTR_RO SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion] 125 | sv.nzvals = DATAPTR(nzvals); | ^ In file included from leaf_utils.h:6, from SparseArray_dim_tuning.c:7: SparseVec.h: In function ‘toSparseVec’: SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration] 125 | sv.nzvals = DATAPTR(nzvals); | ^~~~~~~ | DATAPTR_RO SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion] 125 | sv.nzvals = DATAPTR(nzvals); | ^ make[2]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: SparseArray_Compare_methods.o] Error 1 gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c SparseVec_subsetting.c -o SparseVec_subsetting.o make[2]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: SparseArray_dim_tuning.o] Error 1 gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c XVector_stubs.c -o XVector_stubs.o In file included from SparseVec_Compare.h:6, from SparseVec_Compare.c:4: SparseVec.h: In function ‘toSparseVec’: SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration] 125 | sv.nzvals = DATAPTR(nzvals); | ^~~~~~~ | DATAPTR_RO SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion] 125 | sv.nzvals = DATAPTR(nzvals); | ^ In file included from leaf_utils.h:6, from SparseArray_abind.c:11: SparseVec.h: In function ‘toSparseVec’: SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration] 125 | sv.nzvals = DATAPTR(nzvals); | ^~~~~~~ | DATAPTR_RO SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion] 125 | sv.nzvals = DATAPTR(nzvals); | ^ make[2]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: SparseVec_Compare.o] Error 1 gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c argcheck_utils.c -o argcheck_utils.o In file included from leaf_utils.h:6, from ExtendableJaggedArray.c:8: SparseVec.h: In function ‘toSparseVec’: SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration] 125 | sv.nzvals = DATAPTR(nzvals); | ^~~~~~~ | DATAPTR_RO SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion] 125 | sv.nzvals = DATAPTR(nzvals); | ^ In file included from SparseVec.c:4: SparseVec.h: In function ‘toSparseVec’: SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration] 125 | sv.nzvals = DATAPTR(nzvals); | ^~~~~~~ | DATAPTR_RO SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion] 125 | sv.nzvals = DATAPTR(nzvals); | ^ make[2]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: SparseArray_abind.o] Error 1 gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c coerceVector2.c -o coerceVector2.o In file included from SparseVec_subsetting.h:6, from SparseVec_subsetting.c:4: SparseVec.h: In function ‘toSparseVec’: SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration] 125 | sv.nzvals = DATAPTR(nzvals); | ^~~~~~~ | DATAPTR_RO SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion] 125 | sv.nzvals = DATAPTR(nzvals); | ^ make[2]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: SparseVec.o] Error 1 gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c leaf_utils.c -o leaf_utils.o In file included from SparseVec_Math.h:6, from SparseVec_Math.c:4: SparseVec.h: In function ‘toSparseVec’: SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration] 125 | sv.nzvals = DATAPTR(nzvals); | ^~~~~~~ | DATAPTR_RO SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion] 125 | sv.nzvals = DATAPTR(nzvals); | ^ In file included from leaf_utils.h:6, from R_init_SparseArray.c:6: SparseVec.h: In function ‘toSparseVec’: SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration] 125 | sv.nzvals = DATAPTR(nzvals); | ^~~~~~~ | DATAPTR_RO SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion] 125 | sv.nzvals = DATAPTR(nzvals); | ^ Rvector_utils.c: In function ‘_fill_Rvector_block_with_val’: Rvector_utils.c:245:43: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration] 245 | _set_elts_to_val(TYPEOF(Rvector), DATAPTR(Rvector), | ^~~~~~~ | DATAPTR_RO Rvector_utils.c:245:43: error: passing argument 2 of ‘_set_elts_to_val’ makes pointer from integer without a cast [-Wint-conversion] 245 | _set_elts_to_val(TYPEOF(Rvector), DATAPTR(Rvector), | ^~~~~~~~~~~~~~~~ | | | int Rvector_utils.c:99:45: note: expected ‘void *’ but argument is of type ‘int’ 99 | void _set_elts_to_val(SEXPTYPE Rtype, void *x, R_xlen_t offset, R_xlen_t n, | ~~~~~~^ Rvector_utils.c: In function ‘_fill_Rvector_block_with_zeros’: Rvector_utils.c:263:34: error: passing argument 2 of ‘_set_elts_to_zero’ makes pointer from integer without a cast [-Wint-conversion] 263 | _set_elts_to_zero(Rtype, DATAPTR(Rvector), block_offset, block_len); | ^~~~~~~~~~~~~~~~ | | | int Rvector_utils.c:122:46: note: expected ‘void *’ but argument is of type ‘int’ 122 | void _set_elts_to_zero(SEXPTYPE Rtype, void *x, R_xlen_t offset, R_xlen_t n) | ~~~~~~^ Rvector_utils.c: In function ‘_fill_Rvector_block_with_ones’: Rvector_utils.c:271:43: error: passing argument 2 of ‘_set_elts_to_one’ makes pointer from integer without a cast [-Wint-conversion] 271 | _set_elts_to_one(TYPEOF(Rvector), DATAPTR(Rvector), | ^~~~~~~~~~~~~~~~ | | | int Rvector_utils.c:137:45: note: expected ‘void *’ but argument is of type ‘int’ 137 | void _set_elts_to_one(SEXPTYPE Rtype, void *x, R_xlen_t offset, R_xlen_t n) | ~~~~~~^ In file included from SparseArray_Arith_methods.c:7: SparseVec.h: In function ‘toSparseVec’: SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration] 125 | sv.nzvals = DATAPTR(nzvals); | ^~~~~~~ | DATAPTR_RO SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion] 125 | sv.nzvals = DATAPTR(nzvals); | ^ Rvector_utils.c: In function ‘_fill_Rvector_block_with_minus_one’: Rvector_utils.c:280:49: error: passing argument 2 of ‘_set_elts_to_minus_one’ makes pointer from integer without a cast [-Wint-conversion] 280 | _set_elts_to_minus_one(TYPEOF(Rvector), DATAPTR(Rvector), | ^~~~~~~~~~~~~~~~ | | | int Rvector_utils.c:159:51: note: expected ‘void *’ but argument is of type ‘int’ 159 | void _set_elts_to_minus_one(SEXPTYPE Rtype, void *x, | ~~~~~~^ Rvector_utils.c: In function ‘_fill_Rvector_block_with_NA’: Rvector_utils.c:296:32: error: passing argument 2 of ‘_set_elts_to_NA’ makes pointer from integer without a cast [-Wint-conversion] 296 | _set_elts_to_NA(Rtype, DATAPTR(Rvector), block_offset, block_len); | ^~~~~~~~~~~~~~~~ | | | int Rvector_utils.c:184:44: note: expected ‘void *’ but argument is of type ‘int’ 184 | void _set_elts_to_NA(SEXPTYPE Rtype, void *x, R_xlen_t offset, R_xlen_t n) | ~~~~~~^ make[2]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: SparseVec_subsetting.o] Error 1 gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c misc_utils.c -o misc_utils.o Rvector_utils.c: In function ‘_fill_Rvector_subset_with_zeros’: Rvector_utils.c:463:43: error: passing argument 2 of ‘_set_selected_elts_to_zero’ makes pointer from integer without a cast [-Wint-conversion] 463 | _set_selected_elts_to_zero(Rtype, DATAPTR(Rvector), | ^~~~~~~~~~~~~~~~ | | | int Rvector_utils.c:365:55: note: expected ‘void *’ but argument is of type ‘int’ 365 | void _set_selected_elts_to_zero(SEXPTYPE Rtype, void *x, | ~~~~~~^ Rvector_utils.c: In function ‘_fill_Rvector_subset_with_ones’: Rvector_utils.c:473:52: error: passing argument 2 of ‘_set_selected_elts_to_one’ makes pointer from integer without a cast [-Wint-conversion] 473 | _set_selected_elts_to_one(TYPEOF(Rvector), DATAPTR(Rvector), | ^~~~~~~~~~~~~~~~ | | | int Rvector_utils.c:397:54: note: expected ‘void *’ but argument is of type ‘int’ 397 | void _set_selected_elts_to_one(SEXPTYPE Rtype, void *x, | ~~~~~~^ make[2]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: SparseVec_Math.o] Error 1 gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c randomSparseArray.c -o randomSparseArray.o In file included from leaf_utils.h:6, from SBT_utils.c:7: SparseVec.h: In function ‘toSparseVec’: SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration] 125 | sv.nzvals = DATAPTR(nzvals); | ^~~~~~~ | DATAPTR_RO SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion] 125 | sv.nzvals = DATAPTR(nzvals); | ^ make[2]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: ExtendableJaggedArray.o] Error 1 gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c readSparseCSV.c -o readSparseCSV.o make[2]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: R_init_SparseArray.o] Error 1 gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c rowsum_methods.c -o rowsum_methods.o In file included from leaf_utils.h:6, from SparseArray_misc_methods.c:8: SparseVec.h: In function ‘toSparseVec’: SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration] 125 | sv.nzvals = DATAPTR(nzvals); | ^~~~~~~ | DATAPTR_RO SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion] 125 | sv.nzvals = DATAPTR(nzvals); | ^ In file included from leaf_utils.h:6, from SparseArray_Complex_methods.c:6: SparseVec.h: In function ‘toSparseVec’: SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration] 125 | sv.nzvals = DATAPTR(nzvals); | ^~~~~~~ | DATAPTR_RO SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion] 125 | sv.nzvals = DATAPTR(nzvals); | ^ In file included from leaf_utils.h:6, from SparseArray_aperm.c:16: SparseVec.h: In function ‘toSparseVec’: SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration] 125 | sv.nzvals = DATAPTR(nzvals); | ^~~~~~~ | DATAPTR_RO SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion] 125 | sv.nzvals = DATAPTR(nzvals); | ^ In file included from leaf_utils.h:6, from SVT_SparseArray_class.c:9: SparseVec.h: In function ‘toSparseVec’: SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration] 125 | sv.nzvals = DATAPTR(nzvals); | ^~~~~~~ | DATAPTR_RO SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion] 125 | sv.nzvals = DATAPTR(nzvals); | ^ In file included from SparseArray_Logic_methods.c:7: SparseVec.h: In function ‘toSparseVec’: SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration] 125 | sv.nzvals = DATAPTR(nzvals); | ^~~~~~~ | DATAPTR_RO SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion] 125 | sv.nzvals = DATAPTR(nzvals); | ^ In file included from SparseArray_matrixStats.c:15: SparseVec.h: In function ‘toSparseVec’: SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration] 125 | sv.nzvals = DATAPTR(nzvals); | ^~~~~~~ | DATAPTR_RO SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion] 125 | sv.nzvals = DATAPTR(nzvals); | ^ In file included from leaf_utils.h:6, from SparseArray_subassignment.c:13: SparseVec.h: In function ‘toSparseVec’: SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration] 125 | sv.nzvals = DATAPTR(nzvals); | ^~~~~~~ | DATAPTR_RO SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion] 125 | sv.nzvals = DATAPTR(nzvals); | ^ In file included from leaf_utils.h:6, from SparseArray_subsetting.c:14: SparseVec.h: In function ‘toSparseVec’: SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration] 125 | sv.nzvals = DATAPTR(nzvals); | ^~~~~~~ | DATAPTR_RO SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion] 125 | sv.nzvals = DATAPTR(nzvals); | ^ In file included from SparseVec_Arith.h:6, from SparseVec_Arith.c:4: SparseVec.h: In function ‘toSparseVec’: SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration] 125 | sv.nzvals = DATAPTR(nzvals); | ^~~~~~~ | DATAPTR_RO SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion] 125 | sv.nzvals = DATAPTR(nzvals); | ^ make[2]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: Rvector_utils.o] Error 1 gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c sparseMatrix_utils.c -o sparseMatrix_utils.o Rvector_summarization.c:1370:12: warning: ‘count_NA_list_elts’ defined but not used [-Wunused-function] 1370 | static int count_NA_list_elts(SEXP x) | ^~~~~~~~~~~~~~~~~~ Rvector_summarization.c:1360:12: warning: ‘any_NA_list_elt’ defined but not used [-Wunused-function] 1360 | static int any_NA_list_elt(SEXP x) | ^~~~~~~~~~~~~~~ make[2]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: SparseArray_Arith_methods.o] Error 1 make[2]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: SparseArray_Complex_methods.o] Error 1 make[2]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: SparseArray_misc_methods.o] Error 1 gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c test.c -o test.o In file included from SparseArray_Math_methods.c:7: SparseVec.h: In function ‘toSparseVec’: SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration] 125 | sv.nzvals = DATAPTR(nzvals); | ^~~~~~~ | DATAPTR_RO SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion] 125 | sv.nzvals = DATAPTR(nzvals); | ^ gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c thread_control.c -o thread_control.o In file included from SparseMatrix_mult.c:14: SparseVec.h: In function ‘toSparseVec’: SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration] 125 | sv.nzvals = DATAPTR(nzvals); | ^~~~~~~ | DATAPTR_RO SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion] 125 | sv.nzvals = DATAPTR(nzvals); | ^ SparseArray_aperm.c: In function ‘spray_integer_leaf’: SparseArray_aperm.c:724:28: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 724 | nzvals_p = (const type *) DATAPTR(nzvals); \ | ^ SparseArray_aperm.c:746:39: note: in expansion of macro ‘FUNDEF_spray_leaf’ 746 | static inline void spray_integer_leaf FUNDEF_spray_leaf(int) | ^~~~~~~~~~~~~~~~~ SparseArray_aperm.c: In function ‘spray_double_leaf’: SparseArray_aperm.c:724:28: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 724 | nzvals_p = (const type *) DATAPTR(nzvals); \ | ^ SparseArray_aperm.c:747:38: note: in expansion of macro ‘FUNDEF_spray_leaf’ 747 | static inline void spray_double_leaf FUNDEF_spray_leaf(double) | ^~~~~~~~~~~~~~~~~ SparseArray_aperm.c: In function ‘spray_complex_leaf’: SparseArray_aperm.c:724:28: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 724 | nzvals_p = (const type *) DATAPTR(nzvals); \ | ^ SparseArray_aperm.c:748:39: note: in expansion of macro ‘FUNDEF_spray_leaf’ 748 | static inline void spray_complex_leaf FUNDEF_spray_leaf(Rcomplex) | ^~~~~~~~~~~~~~~~~ SparseArray_aperm.c: In function ‘spray_raw_leaf’: SparseArray_aperm.c:724:28: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 724 | nzvals_p = (const type *) DATAPTR(nzvals); \ | ^ SparseArray_aperm.c:749:35: note: in expansion of macro ‘FUNDEF_spray_leaf’ 749 | static inline void spray_raw_leaf FUNDEF_spray_leaf(Rbyte) | ^~~~~~~~~~~~~~~~~ SparseArray_matrixStats.c: In function ‘C_colStats_SVT’: SparseArray_matrixStats.c:275:26: error: passing argument 6 of ‘REC_colStats_SVT’ makes pointer from integer without a cast [-Wint-conversion] 275 | DATAPTR(ans), ans_Rtype, | ^~~~~~~~~~~~ | | | int SparseArray_matrixStats.c:203:23: note: expected ‘void *’ but argument is of type ‘int’ 203 | void *out, SEXPTYPE out_Rtype, | ~~~~~~^~~ In file included from SparseVec_subassignment.h:6, from SparseVec_subassignment.c:4: SparseVec.h: In function ‘toSparseVec’: SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration] 125 | sv.nzvals = DATAPTR(nzvals); | ^~~~~~~ | DATAPTR_RO SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion] 125 | sv.nzvals = DATAPTR(nzvals); | ^ In file included from leaf_utils.h:6, from SparseArray_summarization.c:12: SparseVec.h: In function ‘toSparseVec’: SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration] 125 | sv.nzvals = DATAPTR(nzvals); | ^~~~~~~ | DATAPTR_RO SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion] 125 | sv.nzvals = DATAPTR(nzvals); | ^ In file included from leaf_utils.h:6, from randomSparseArray.c:6: SparseVec.h: In function ‘toSparseVec’: SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration] 125 | sv.nzvals = DATAPTR(nzvals); | ^~~~~~~ | DATAPTR_RO SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion] 125 | sv.nzvals = DATAPTR(nzvals); | ^ SparseArray_subsetting.c: In function ‘REC_subset_SVT_as_SVT’: SparseArray_subsetting.c:843:26: warning: comparison between pointer and integer 843 | if (offs != i2 || ans_elt != subSVT) | ^~ In file included from SparseVec_dotprod.h:4, from SparseVec_dotprod.c:4: SparseVec.h: In function ‘toSparseVec’: SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration] 125 | sv.nzvals = DATAPTR(nzvals); | ^~~~~~~ | DATAPTR_RO SparseArray_matrixStats.c: In function ‘C_rowStats_SVT’: SparseArray_matrixStats.c:1178:25: error: passing argument 8 of ‘SVT_rowMinsMaxs’ makes pointer from integer without a cast [-Wint-conversion] 1178 | DATAPTR(ans), LENGTH(ans), ans_Rtype, | ^~~~~~~~~~~~ | | | int SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion] 125 | sv.nzvals = DATAPTR(nzvals); | ^ make[2]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: SparseArray_Logic_methods.o] Error 1 SparseArray_matrixStats.c:966:23: note: expected ‘void *’ but argument is of type ‘int’ 966 | void *out, R_xlen_t out_len, SEXPTYPE out_Rtype, | ~~~~~~^~~ make[2]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: SparseArray_Math_methods.o] Error 1 make[2]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: SparseArray_aperm.o] Error 1 make[2]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: SparseArray_subassignment.o] Error 1 In file included from SparseVec_Logic.h:6, from SparseVec_Logic.c:4: SparseVec.h: In function ‘toSparseVec’: SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration] 125 | sv.nzvals = DATAPTR(nzvals); | ^~~~~~~ | DATAPTR_RO SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion] 125 | sv.nzvals = DATAPTR(nzvals); | ^ make[2]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: SparseArray_summarization.o] Error 1 make[2]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: randomSparseArray.o] Error 1 make[2]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: SparseVec_Logic.o] Error 1 make[2]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: SVT_SparseArray_class.o] Error 1 make[2]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: SparseVec_Arith.o] Error 1 make[2]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: SparseVec_dotprod.o] Error 1 make[2]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: SparseArray_subsetting.o] Error 1 make[2]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: SBT_utils.o] Error 1 In file included from leaf_utils.h:6, from leaf_utils.c:4: SparseVec.h: In function ‘toSparseVec’: SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration] 125 | sv.nzvals = DATAPTR(nzvals); | ^~~~~~~ | DATAPTR_RO SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion] 125 | sv.nzvals = DATAPTR(nzvals); | ^ SparseMatrix_mult.c: At top level: SparseMatrix_mult.c:346:13: warning: ‘crossprod2_doublemat_doubleSV’ defined but not used [-Wunused-function] 346 | static void crossprod2_doublemat_doubleSV( | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SparseMatrix_mult.c:306:13: warning: ‘crossprod2_doubleSV_doublemat’ defined but not used [-Wunused-function] 306 | static void crossprod2_doubleSV_doublemat( | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ make[2]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: SparseMatrix_mult.o] Error 1 leaf_utils.c: In function ‘_make_leaf_from_two_arrays’: leaf_utils.c:132:24: error: passing argument 1 of ‘memcpy’ makes pointer from integer without a cast [-Wint-conversion] 132 | memcpy(DATAPTR(ans_nzvals), nzvals_p, Rtype_size * nzcount); | ^~~~~~~~~~~~~~~~~~~ | | | int In file included from /usr/include/features.h:524, from /usr/include/bits/libc-header-start.h:33, from /usr/include/string.h:26, from /data/gannet/ripley/R/R-devel/include/R_ext/RS.h:34, from /data/gannet/ripley/R/R-devel/include/Rdefines.h:38, from leaf_utils.h:4: /usr/include/bits/string_fortified.h:26:1: note: expected ‘void *’ but argument is of type ‘int’ 26 | __NTH (memcpy (void *__restrict __dest, const void *__restrict __src, | ^~~~~ make[2]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: SparseArray_matrixStats.o] Error 1 make[2]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: SparseVec_subassignment.o] Error 1 make[2]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: leaf_utils.o] Error 1 In file included from leaf_utils.h:6, from readSparseCSV.c:10: SparseVec.h: In function ‘toSparseVec’: SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration] 125 | sv.nzvals = DATAPTR(nzvals); | ^~~~~~~ | DATAPTR_RO SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion] 125 | sv.nzvals = DATAPTR(nzvals); | ^ make[2]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: readSparseCSV.o] Error 1 In file included from leaf_utils.h:6, from rowsum_methods.c:9: SparseVec.h: In function ‘toSparseVec’: SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration] 125 | sv.nzvals = DATAPTR(nzvals); | ^~~~~~~ | DATAPTR_RO SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion] 125 | sv.nzvals = DATAPTR(nzvals); | ^ make[2]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: rowsum_methods.o] Error 1 make[2]: Target 'all' not remade because of errors. make[2]: Leaving directory '/tmp/Rtmp7CAajn/working_dir/RtmphKjpcb/R.INSTALL369f2733b7907d/SparseArray/src' ERROR: compilation failed for package ‘SparseArray’ * removing ‘/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/SparseArray’ * installing *source* package ‘futile.logger’ ... ** this is package ‘futile.logger’ version ‘1.4.9’ ** package ‘futile.logger’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (futile.logger) ERROR: dependency ‘Biostrings’ is not available for package ‘cigarillo’ Perhaps try a variation of: install.packages('Biostrings') * removing ‘/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/cigarillo’ ERROR: dependency ‘Biostrings’ is not available for package ‘pwalign’ Perhaps try a variation of: install.packages('Biostrings') * removing ‘/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/pwalign’ * installing *source* package ‘latticeExtra’ ... ** this is package ‘latticeExtra’ version ‘0.6-31’ ** package ‘latticeExtra’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (latticeExtra) ERROR: dependency ‘SparseArray’ is not available for package ‘DelayedArray’ Perhaps try a variation of: install.packages('SparseArray') * removing ‘/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/DelayedArray’ Warning: SystemRequirements specified C++11: support has been removed * installing *source* package ‘BiocParallel’ ... ** this is package ‘BiocParallel’ version ‘1.45.0’ ** using staged installation checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C++... yes checking whether g++ -std=gnu++20 accepts -g... yes checking for g++ -std=gnu++20 option to enable C++11 features... none needed checking for library containing shm_open... none required checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for sys/mman.h... yes configure: creating ./config.status config.status: creating src/Makevars ** libs specified C++11 using C++ compiler: ‘g++ (GCC) 15.2.1 20260123 (Red Hat 15.2.1-7)’ make[2]: Entering directory '/tmp/Rtmp7CAajn/working_dir/RtmptEou0G/R.INSTALL36add91eb083cf/BiocParallel/src' g++ -std=gnu++20 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I"./" -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/BH/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/cpp11/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c cpp11.cpp -o cpp11.o g++ -std=gnu++20 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I"./" -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/BH/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/cpp11/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c ipcmutex.cpp -o ipcmutex.o g++ -std=gnu++20 -shared -L/usr/local/lib64 -o BiocParallel.so cpp11.o ipcmutex.o make[2]: Leaving directory '/tmp/Rtmp7CAajn/working_dir/RtmptEou0G/R.INSTALL36add91eb083cf/BiocParallel/src' make[2]: Entering directory '/tmp/Rtmp7CAajn/working_dir/RtmptEou0G/R.INSTALL36add91eb083cf/BiocParallel/src' make[2]: Leaving directory '/tmp/Rtmp7CAajn/working_dir/RtmptEou0G/R.INSTALL36add91eb083cf/BiocParallel/src' installing to /tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/00LOCK-BiocParallel/00new/BiocParallel/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (BiocParallel) ERROR: dependency ‘DelayedArray’ is not available for package ‘SummarizedExperiment’ Perhaps try a variation of: install.packages('DelayedArray') * removing ‘/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/SummarizedExperiment’ ERROR: dependency ‘Biostrings’ is not available for package ‘Rsamtools’ Perhaps try a variation of: install.packages('Biostrings') * removing ‘/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/Rsamtools’ ERROR: dependencies ‘SummarizedExperiment’, ‘Biostrings’, ‘Rsamtools’, ‘cigarillo’ are not available for package ‘GenomicAlignments’ Perhaps try a variation of: install.packages(c('SummarizedExperiment', 'Biostrings', 'Rsamtools', 'cigarillo')) * removing ‘/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/GenomicAlignments’ ERROR: dependencies ‘Biostrings’, ‘Rsamtools’, ‘GenomicAlignments’, ‘pwalign’ are not available for package ‘ShortRead’ Perhaps try a variation of: install.packages(c('Biostrings', 'Rsamtools', 'GenomicAlignments', 'pwalign')) * removing ‘/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/ShortRead’ The downloaded source packages are in '/tmp/Rtmp7CAajn/working_dir/RtmpjyO0Wr/downloaded_packages' 'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package = "BiocManager")' for details. Replacement repositories: CRAN: file:///data/gannet/ripley/R Bioconductor version 3.23 (BiocManager 1.30.27), R Under development (unstable) (2026-03-03 r89531) Installing package(s) 'rtracklayer' also installing the dependencies 'SparseArray', 'DelayedArray', 'SummarizedExperiment', 'cigarillo', 'RCurl', 'rjson', 'XML', 'Biostrings', 'Rsamtools', 'GenomicAlignments', 'BiocIO', 'restfulr' trying URL 'https://bioconductor.org/packages/3.23/bioc/src/contrib/SparseArray_1.11.10.tar.gz' trying URL 'https://bioconductor.org/packages/3.23/bioc/src/contrib/DelayedArray_0.37.0.tar.gz' trying URL 'https://bioconductor.org/packages/3.23/bioc/src/contrib/SummarizedExperiment_1.41.1.tar.gz' trying URL 'https://bioconductor.org/packages/3.23/bioc/src/contrib/cigarillo_1.1.0.tar.gz' trying URL 'https://bioconductor.org/packages/3.23/bioc/src/contrib/Biostrings_2.79.4.tar.gz' trying URL 'https://bioconductor.org/packages/3.23/bioc/src/contrib/Rsamtools_2.27.0.tar.gz' trying URL 'https://bioconductor.org/packages/3.23/bioc/src/contrib/GenomicAlignments_1.47.0.tar.gz' trying URL 'https://bioconductor.org/packages/3.23/bioc/src/contrib/BiocIO_1.21.0.tar.gz' trying URL 'https://bioconductor.org/packages/3.23/bioc/src/contrib/rtracklayer_1.71.3.tar.gz' * installing *source* package ‘SparseArray’ ... ** this is package ‘SparseArray’ version ‘1.11.10’ ** using staged installation ** libs using C compiler: ‘gcc (GCC) 15.2.1 20260123 (Red Hat 15.2.1-7)’ make[2]: Entering directory '/tmp/Rtmp7CAajn/working_dir/RtmpD9xVCM/R.INSTALL36d36a5e6dad2c/SparseArray/src' gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c ExtendableJaggedArray.c -o ExtendableJaggedArray.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c IRanges_stubs.c -o IRanges_stubs.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c OPBufTree.c -o OPBufTree.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c R_init_SparseArray.c -o R_init_SparseArray.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c Rvector_summarization.c -o Rvector_summarization.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c Rvector_utils.c -o Rvector_utils.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c S4Vectors_stubs.c -o S4Vectors_stubs.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c SBT_utils.c -o SBT_utils.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c SVT_SparseArray_class.c -o SVT_SparseArray_class.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c SparseArray_Arith_methods.c -o SparseArray_Arith_methods.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c SparseArray_Compare_methods.c -o SparseArray_Compare_methods.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c SparseArray_Complex_methods.c -o SparseArray_Complex_methods.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c SparseArray_Logic_methods.c -o SparseArray_Logic_methods.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c SparseArray_Math_methods.c -o SparseArray_Math_methods.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c SparseArray_abind.c -o SparseArray_abind.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c SparseArray_aperm.c -o SparseArray_aperm.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c SparseArray_dim_tuning.c -o SparseArray_dim_tuning.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c SparseArray_matrixStats.c -o SparseArray_matrixStats.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c SparseArray_misc_methods.c -o SparseArray_misc_methods.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c SparseArray_subassignment.c -o SparseArray_subassignment.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c SparseArray_subsetting.c -o SparseArray_subsetting.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c SparseArray_summarization.c -o SparseArray_summarization.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c SparseMatrix_mult.c -o SparseMatrix_mult.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c SparseVec.c -o SparseVec.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c SparseVec_Arith.c -o SparseVec_Arith.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c SparseVec_Compare.c -o SparseVec_Compare.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c SparseVec_Logic.c -o SparseVec_Logic.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c SparseVec_Math.c -o SparseVec_Math.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c SparseVec_dotprod.c -o SparseVec_dotprod.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c SparseVec_subassignment.c -o SparseVec_subassignment.o In file included from leaf_utils.h:6, from SparseArray_abind.c:11: SparseVec.h: In function ‘toSparseVec’: SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration] 125 | sv.nzvals = DATAPTR(nzvals); | ^~~~~~~ | DATAPTR_RO SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion] 125 | sv.nzvals = DATAPTR(nzvals); | ^ In file included from SparseVec_subassignment.h:6, from SparseVec_subassignment.c:4: SparseVec.h: In function ‘toSparseVec’: SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration] 125 | sv.nzvals = DATAPTR(nzvals); | ^~~~~~~ | DATAPTR_RO SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion] 125 | sv.nzvals = DATAPTR(nzvals); | ^ make[2]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: SparseArray_abind.o] Error 1 gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c SparseVec_subsetting.c -o SparseVec_subsetting.o In file included from leaf_utils.h:6, from R_init_SparseArray.c:6: SparseVec.h: In function ‘toSparseVec’: SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration] 125 | sv.nzvals = DATAPTR(nzvals); | ^~~~~~~ | DATAPTR_RO SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion] 125 | sv.nzvals = DATAPTR(nzvals); | ^ make[2]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: SparseVec_subassignment.o] Error 1 gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c XVector_stubs.c -o XVector_stubs.o In file included from leaf_utils.h:6, from SparseArray_Complex_methods.c:6: SparseVec.h: In function ‘toSparseVec’: SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration] 125 | sv.nzvals = DATAPTR(nzvals); | ^~~~~~~ | DATAPTR_RO SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion] 125 | sv.nzvals = DATAPTR(nzvals); | ^ In file included from leaf_utils.h:6, from SBT_utils.c:7: SparseVec.h: In function ‘toSparseVec’: SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration] 125 | sv.nzvals = DATAPTR(nzvals); | ^~~~~~~ | DATAPTR_RO SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion] 125 | sv.nzvals = DATAPTR(nzvals); | ^ In file included from leaf_utils.h:6, from SparseArray_subsetting.c:14: SparseVec.h: In function ‘toSparseVec’: SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration] 125 | sv.nzvals = DATAPTR(nzvals); | ^~~~~~~ | DATAPTR_RO SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion] 125 | sv.nzvals = DATAPTR(nzvals); | ^ In file included from leaf_utils.h:6, from SparseArray_aperm.c:16: SparseVec.h: In function ‘toSparseVec’: SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration] 125 | sv.nzvals = DATAPTR(nzvals); | ^~~~~~~ | DATAPTR_RO SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion] 125 | sv.nzvals = DATAPTR(nzvals); | ^ make[2]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: R_init_SparseArray.o] Error 1 gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c argcheck_utils.c -o argcheck_utils.o make[2]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: SparseArray_Complex_methods.o] Error 1 gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c coerceVector2.c -o coerceVector2.o In file included from leaf_utils.h:6, from SparseArray_summarization.c:12: SparseVec.h: In function ‘toSparseVec’: SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration] 125 | sv.nzvals = DATAPTR(nzvals); | ^~~~~~~ | DATAPTR_RO SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion] 125 | sv.nzvals = DATAPTR(nzvals); | ^ In file included from SparseVec_Logic.h:6, from SparseVec_Logic.c:4: SparseVec.h: In function ‘toSparseVec’: SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration] 125 | sv.nzvals = DATAPTR(nzvals); | ^~~~~~~ | DATAPTR_RO SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion] 125 | sv.nzvals = DATAPTR(nzvals); | ^ SparseArray_subsetting.c: In function ‘REC_subset_SVT_as_SVT’: SparseArray_subsetting.c:843:26: warning: comparison between pointer and integer 843 | if (offs != i2 || ans_elt != subSVT) | ^~ In file included from leaf_utils.h:6, from SparseArray_subassignment.c:13: SparseVec.h: In function ‘toSparseVec’: SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration] 125 | sv.nzvals = DATAPTR(nzvals); | ^~~~~~~ | DATAPTR_RO SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion] 125 | sv.nzvals = DATAPTR(nzvals); | ^ make[2]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: SparseArray_summarization.o] Error 1 gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c leaf_utils.c -o leaf_utils.o In file included from SparseArray_Logic_methods.c:7: SparseVec.h: In function ‘toSparseVec’: SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration] 125 | sv.nzvals = DATAPTR(nzvals); | ^~~~~~~ | DATAPTR_RO SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion] 125 | sv.nzvals = DATAPTR(nzvals); | ^ In file included from SparseArray_Arith_methods.c:7: SparseVec.h: In function ‘toSparseVec’: SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration] 125 | sv.nzvals = DATAPTR(nzvals); | ^~~~~~~ | DATAPTR_RO SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion] 125 | sv.nzvals = DATAPTR(nzvals); | ^ In file included from SparseVec_dotprod.h:4, from SparseVec_dotprod.c:4: SparseVec.h: In function ‘toSparseVec’: SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration] 125 | sv.nzvals = DATAPTR(nzvals); | ^~~~~~~ | DATAPTR_RO SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion] 125 | sv.nzvals = DATAPTR(nzvals); | ^ In file included from SparseVec_Arith.h:6, from SparseVec_Arith.c:4: SparseVec.h: In function ‘toSparseVec’: SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration] 125 | sv.nzvals = DATAPTR(nzvals); | ^~~~~~~ | DATAPTR_RO SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion] 125 | sv.nzvals = DATAPTR(nzvals); | ^ In file included from SparseArray_Compare_methods.c:7: SparseVec.h: In function ‘toSparseVec’: SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration] 125 | sv.nzvals = DATAPTR(nzvals); | ^~~~~~~ | DATAPTR_RO SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion] 125 | sv.nzvals = DATAPTR(nzvals); | ^ make[2]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: SparseVec_Logic.o] Error 1 gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c misc_utils.c -o misc_utils.o Rvector_utils.c: In function ‘_fill_Rvector_block_with_val’: Rvector_utils.c:245:43: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration] 245 | _set_elts_to_val(TYPEOF(Rvector), DATAPTR(Rvector), | ^~~~~~~ | DATAPTR_RO Rvector_utils.c:245:43: error: passing argument 2 of ‘_set_elts_to_val’ makes pointer from integer without a cast [-Wint-conversion] 245 | _set_elts_to_val(TYPEOF(Rvector), DATAPTR(Rvector), | ^~~~~~~~~~~~~~~~ | | | int Rvector_utils.c:99:45: note: expected ‘void *’ but argument is of type ‘int’ 99 | void _set_elts_to_val(SEXPTYPE Rtype, void *x, R_xlen_t offset, R_xlen_t n, | ~~~~~~^ In file included from leaf_utils.h:6, from SparseArray_dim_tuning.c:7: SparseVec.h: In function ‘toSparseVec’: Rvector_utils.c: In function ‘_fill_Rvector_block_with_zeros’: Rvector_utils.c:263:34: error: passing argument 2 of ‘_set_elts_to_zero’ makes pointer from integer without a cast [-Wint-conversion] 263 | _set_elts_to_zero(Rtype, DATAPTR(Rvector), block_offset, block_len); | ^~~~~~~~~~~~~~~~ | | | int Rvector_utils.c:122:46: note: expected ‘void *’ but argument is of type ‘int’ 122 | void _set_elts_to_zero(SEXPTYPE Rtype, void *x, R_xlen_t offset, R_xlen_t n) | ~~~~~~^ Rvector_utils.c: In function ‘_fill_Rvector_block_with_ones’: Rvector_utils.c:271:43: error: passing argument 2 of ‘_set_elts_to_one’ makes pointer from integer without a cast [-Wint-conversion] 271 | _set_elts_to_one(TYPEOF(Rvector), DATAPTR(Rvector), | ^~~~~~~~~~~~~~~~ | | | int Rvector_utils.c:137:45: note: expected ‘void *’ but argument is of type ‘int’ 137 | void _set_elts_to_one(SEXPTYPE Rtype, void *x, R_xlen_t offset, R_xlen_t n) | ~~~~~~^ Rvector_utils.c: In function ‘_fill_Rvector_block_with_minus_one’: Rvector_utils.c:280:49: error: passing argument 2 of ‘_set_elts_to_minus_one’ makes pointer from integer without a cast [-Wint-conversion] 280 | _set_elts_to_minus_one(TYPEOF(Rvector), DATAPTR(Rvector), | ^~~~~~~~~~~~~~~~ | | | int Rvector_utils.c:159:51: note: expected ‘void *’ but argument is of type ‘int’ 159 | void _set_elts_to_minus_one(SEXPTYPE Rtype, void *x, | ~~~~~~^ Rvector_utils.c: In function ‘_fill_Rvector_block_with_NA’: Rvector_utils.c:296:32: error: passing argument 2 of ‘_set_elts_to_NA’ makes pointer from integer without a cast [-Wint-conversion] 296 | _set_elts_to_NA(Rtype, DATAPTR(Rvector), block_offset, block_len); | ^~~~~~~~~~~~~~~~ | | | int Rvector_utils.c:184:44: note: expected ‘void *’ but argument is of type ‘int’ 184 | void _set_elts_to_NA(SEXPTYPE Rtype, void *x, R_xlen_t offset, R_xlen_t n) | ~~~~~~^ SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration] 125 | sv.nzvals = DATAPTR(nzvals); | ^~~~~~~ | DATAPTR_RO SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion] 125 | sv.nzvals = DATAPTR(nzvals); | ^ In file included from leaf_utils.h:6, from ExtendableJaggedArray.c:8: SparseVec.h: In function ‘toSparseVec’: SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration] 125 | sv.nzvals = DATAPTR(nzvals); | ^~~~~~~ | DATAPTR_RO SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion] 125 | sv.nzvals = DATAPTR(nzvals); | ^ make[2]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: SparseVec_dotprod.o] Error 1 gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c randomSparseArray.c -o randomSparseArray.o In file included from SparseArray_matrixStats.c:15: SparseVec.h: In function ‘toSparseVec’: SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration] 125 | sv.nzvals = DATAPTR(nzvals); | ^~~~~~~ | DATAPTR_RO SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion] 125 | sv.nzvals = DATAPTR(nzvals); | ^ make[2]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: SparseArray_subsetting.o] Error 1 gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c readSparseCSV.c -o readSparseCSV.o SparseArray_aperm.c: In function ‘spray_integer_leaf’: SparseArray_aperm.c:724:28: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 724 | nzvals_p = (const type *) DATAPTR(nzvals); \ | ^ SparseArray_aperm.c:746:39: note: in expansion of macro ‘FUNDEF_spray_leaf’ 746 | static inline void spray_integer_leaf FUNDEF_spray_leaf(int) | ^~~~~~~~~~~~~~~~~ SparseArray_aperm.c: In function ‘spray_double_leaf’: SparseArray_aperm.c:724:28: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 724 | nzvals_p = (const type *) DATAPTR(nzvals); \ | ^ SparseArray_aperm.c:747:38: note: in expansion of macro ‘FUNDEF_spray_leaf’ 747 | static inline void spray_double_leaf FUNDEF_spray_leaf(double) | ^~~~~~~~~~~~~~~~~ Rvector_utils.c: In function ‘_fill_Rvector_subset_with_zeros’: Rvector_utils.c:463:43: error: passing argument 2 of ‘_set_selected_elts_to_zero’ makes pointer from integer without a cast [-Wint-conversion] 463 | _set_selected_elts_to_zero(Rtype, DATAPTR(Rvector), | ^~~~~~~~~~~~~~~~ | | | int Rvector_utils.c:365:55: note: expected ‘void *’ but argument is of type ‘int’ 365 | void _set_selected_elts_to_zero(SEXPTYPE Rtype, void *x, | ~~~~~~^ Rvector_utils.c: In function ‘_fill_Rvector_subset_with_ones’: Rvector_utils.c:473:52: error: passing argument 2 of ‘_set_selected_elts_to_one’ makes pointer from integer without a cast [-Wint-conversion] 473 | _set_selected_elts_to_one(TYPEOF(Rvector), DATAPTR(Rvector), | ^~~~~~~~~~~~~~~~ | | | int Rvector_utils.c:397:54: note: expected ‘void *’ but argument is of type ‘int’ 397 | void _set_selected_elts_to_one(SEXPTYPE Rtype, void *x, | ~~~~~~^ SparseArray_aperm.c: In function ‘spray_complex_leaf’: SparseArray_aperm.c:724:28: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 724 | nzvals_p = (const type *) DATAPTR(nzvals); \ | ^ SparseArray_aperm.c:748:39: note: in expansion of macro ‘FUNDEF_spray_leaf’ 748 | static inline void spray_complex_leaf FUNDEF_spray_leaf(Rcomplex) | ^~~~~~~~~~~~~~~~~ In file included from SparseMatrix_mult.c:14: SparseVec.h: In function ‘toSparseVec’: SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration] 125 | sv.nzvals = DATAPTR(nzvals); | ^~~~~~~ | DATAPTR_RO SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion] 125 | sv.nzvals = DATAPTR(nzvals); | ^ SparseArray_aperm.c: In function ‘spray_raw_leaf’: SparseArray_aperm.c:724:28: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 724 | nzvals_p = (const type *) DATAPTR(nzvals); \ | ^ SparseArray_aperm.c:749:35: note: in expansion of macro ‘FUNDEF_spray_leaf’ 749 | static inline void spray_raw_leaf FUNDEF_spray_leaf(Rbyte) | ^~~~~~~~~~~~~~~~~ make[2]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: SparseArray_Logic_methods.o] Error 1 gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c rowsum_methods.c -o rowsum_methods.o In file included from leaf_utils.h:6, from SVT_SparseArray_class.c:9: SparseVec.h: In function ‘toSparseVec’: SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration] 125 | sv.nzvals = DATAPTR(nzvals); | ^~~~~~~ | DATAPTR_RO SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion] 125 | sv.nzvals = DATAPTR(nzvals); | ^ make[2]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: SBT_utils.o] Error 1 gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c sparseMatrix_utils.c -o sparseMatrix_utils.o SparseArray_matrixStats.c: In function ‘C_colStats_SVT’: SparseArray_matrixStats.c:275:26: error: passing argument 6 of ‘REC_colStats_SVT’ makes pointer from integer without a cast [-Wint-conversion] 275 | DATAPTR(ans), ans_Rtype, | ^~~~~~~~~~~~ | | | int SparseArray_matrixStats.c:203:23: note: expected ‘void *’ but argument is of type ‘int’ 203 | void *out, SEXPTYPE out_Rtype, | ~~~~~~^~~ make[2]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: SparseArray_Compare_methods.o] Error 1 gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c test.c -o test.o In file included from SparseArray_Math_methods.c:7: SparseVec.h: In function ‘toSparseVec’: SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration] 125 | sv.nzvals = DATAPTR(nzvals); | ^~~~~~~ | DATAPTR_RO SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion] 125 | sv.nzvals = DATAPTR(nzvals); | ^ In file included from leaf_utils.h:6, from SparseArray_misc_methods.c:8: SparseVec.h: In function ‘toSparseVec’: SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration] 125 | sv.nzvals = DATAPTR(nzvals); | ^~~~~~~ | DATAPTR_RO SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion] 125 | sv.nzvals = DATAPTR(nzvals); | ^ make[2]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: SparseArray_subassignment.o] Error 1 gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c thread_control.c -o thread_control.o SparseArray_matrixStats.c: In function ‘C_rowStats_SVT’: SparseArray_matrixStats.c:1178:25: error: passing argument 8 of ‘SVT_rowMinsMaxs’ makes pointer from integer without a cast [-Wint-conversion] 1178 | DATAPTR(ans), LENGTH(ans), ans_Rtype, | ^~~~~~~~~~~~ | | | int SparseArray_matrixStats.c:966:23: note: expected ‘void *’ but argument is of type ‘int’ 966 | void *out, R_xlen_t out_len, SEXPTYPE out_Rtype, | ~~~~~~^~~ Rvector_summarization.c:1370:12: warning: ‘count_NA_list_elts’ defined but not used [-Wunused-function] 1370 | static int count_NA_list_elts(SEXP x) | ^~~~~~~~~~~~~~~~~~ Rvector_summarization.c:1360:12: warning: ‘any_NA_list_elt’ defined but not used [-Wunused-function] 1360 | static int any_NA_list_elt(SEXP x) | ^~~~~~~~~~~~~~~ make[2]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: SparseArray_Arith_methods.o] Error 1 make[2]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: SparseArray_dim_tuning.o] Error 1 In file included from SparseVec.c:4: SparseVec.h: In function ‘toSparseVec’: SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration] 125 | sv.nzvals = DATAPTR(nzvals); | ^~~~~~~ | DATAPTR_RO SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion] 125 | sv.nzvals = DATAPTR(nzvals); | ^ In file included from SparseVec_Math.h:6, from SparseVec_Math.c:4: SparseVec.h: In function ‘toSparseVec’: SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration] 125 | sv.nzvals = DATAPTR(nzvals); | ^~~~~~~ | DATAPTR_RO SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion] 125 | sv.nzvals = DATAPTR(nzvals); | ^ make[2]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: SparseVec_Arith.o] Error 1 make[2]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: SparseArray_Math_methods.o] Error 1 SparseMatrix_mult.c: At top level: SparseMatrix_mult.c:346:13: warning: ‘crossprod2_doublemat_doubleSV’ defined but not used [-Wunused-function] 346 | static void crossprod2_doublemat_doubleSV( | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SparseMatrix_mult.c:306:13: warning: ‘crossprod2_doubleSV_doublemat’ defined but not used [-Wunused-function] 306 | static void crossprod2_doubleSV_doublemat( | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ make[2]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: ExtendableJaggedArray.o] Error 1 make[2]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: SparseArray_misc_methods.o] Error 1 make[2]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: SparseArray_matrixStats.o] Error 1 make[2]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: Rvector_utils.o] Error 1 make[2]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: SparseMatrix_mult.o] Error 1 make[2]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: SparseArray_aperm.o] Error 1 make[2]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: SVT_SparseArray_class.o] Error 1 make[2]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: SparseVec.o] Error 1 make[2]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: SparseVec_Math.o] Error 1 In file included from SparseVec_subsetting.h:6, from SparseVec_subsetting.c:4: SparseVec.h: In function ‘toSparseVec’: SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration] 125 | sv.nzvals = DATAPTR(nzvals); | ^~~~~~~ | DATAPTR_RO SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion] 125 | sv.nzvals = DATAPTR(nzvals); | ^ In file included from leaf_utils.h:6, from rowsum_methods.c:9: SparseVec.h: In function ‘toSparseVec’: SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration] 125 | sv.nzvals = DATAPTR(nzvals); | ^~~~~~~ | DATAPTR_RO SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion] 125 | sv.nzvals = DATAPTR(nzvals); | ^ make[2]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: rowsum_methods.o] Error 1 In file included from SparseVec_Compare.h:6, from SparseVec_Compare.c:4: SparseVec.h: In function ‘toSparseVec’: SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration] 125 | sv.nzvals = DATAPTR(nzvals); | ^~~~~~~ | DATAPTR_RO SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion] 125 | sv.nzvals = DATAPTR(nzvals); | ^ In file included from leaf_utils.h:6, from leaf_utils.c:4: SparseVec.h: In function ‘toSparseVec’: SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration] 125 | sv.nzvals = DATAPTR(nzvals); | ^~~~~~~ | DATAPTR_RO SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion] 125 | sv.nzvals = DATAPTR(nzvals); | ^ In file included from leaf_utils.h:6, from randomSparseArray.c:6: SparseVec.h: In function ‘toSparseVec’: SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration] 125 | sv.nzvals = DATAPTR(nzvals); | ^~~~~~~ | DATAPTR_RO SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion] 125 | sv.nzvals = DATAPTR(nzvals); | ^ In file included from leaf_utils.h:6, from readSparseCSV.c:10: SparseVec.h: In function ‘toSparseVec’: SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration] 125 | sv.nzvals = DATAPTR(nzvals); | ^~~~~~~ | DATAPTR_RO SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion] 125 | sv.nzvals = DATAPTR(nzvals); | ^ leaf_utils.c: In function ‘_make_leaf_from_two_arrays’: leaf_utils.c:132:24: error: passing argument 1 of ‘memcpy’ makes pointer from integer without a cast [-Wint-conversion] 132 | memcpy(DATAPTR(ans_nzvals), nzvals_p, Rtype_size * nzcount); | ^~~~~~~~~~~~~~~~~~~ | | | int In file included from /usr/include/features.h:524, from /usr/include/bits/libc-header-start.h:33, from /usr/include/string.h:26, from /data/gannet/ripley/R/R-devel/include/R_ext/RS.h:34, from /data/gannet/ripley/R/R-devel/include/Rdefines.h:38, from leaf_utils.h:4: /usr/include/bits/string_fortified.h:26:1: note: expected ‘void *’ but argument is of type ‘int’ 26 | __NTH (memcpy (void *__restrict __dest, const void *__restrict __src, | ^~~~~ make[2]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: randomSparseArray.o] Error 1 make[2]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: leaf_utils.o] Error 1 make[2]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: readSparseCSV.o] Error 1 make[2]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: SparseVec_Compare.o] Error 1 make[2]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: SparseVec_subsetting.o] Error 1 make[2]: Target 'all' not remade because of errors. make[2]: Leaving directory '/tmp/Rtmp7CAajn/working_dir/RtmpD9xVCM/R.INSTALL36d36a5e6dad2c/SparseArray/src' ERROR: compilation failed for package ‘SparseArray’ * removing ‘/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/SparseArray’ * installing *source* package ‘RCurl’ ... ** this is package ‘RCurl’ version ‘1.98-1.17’ ** package ‘RCurl’ successfully unpacked and MD5 sums checked ** using staged installation checking for curl-config... /usr/bin/curl-config checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking how to run the C preprocessor... gcc -E Version has a libidn field Version has CURLOPT_URL Version has CURLINFO_EFFECTIVE_URL Version has CURLINFO_RESPONSE_CODE Version has CURLINFO_TOTAL_TIME Version has CURLINFO_NAMELOOKUP_TIME Version has CURLINFO_CONNECT_TIME Version has CURLINFO_PRETRANSFER_TIME Version has CURLINFO_SIZE_UPLOAD Version has CURLINFO_SIZE_DOWNLOAD Version has CURLINFO_SPEED_DOWNLOAD Version has CURLINFO_SPEED_UPLOAD Version has CURLINFO_HEADER_SIZE Version has CURLINFO_REQUEST_SIZE Version has CURLINFO_SSL_VERIFYRESULT Version has CURLINFO_FILETIME Version has CURLINFO_CONTENT_LENGTH_DOWNLOAD Version has CURLINFO_CONTENT_LENGTH_UPLOAD Version has CURLINFO_STARTTRANSFER_TIME Version has CURLINFO_CONTENT_TYPE Version has CURLINFO_REDIRECT_TIME Version has CURLINFO_REDIRECT_COUNT Version has CURLINFO_PRIVATE Version has CURLINFO_HTTP_CONNECTCODE Version has CURLINFO_HTTPAUTH_AVAIL Version has CURLINFO_PROXYAUTH_AVAIL Version has CURLINFO_OS_ERRNO Version has CURLINFO_NUM_CONNECTS Version has CURLINFO_SSL_ENGINES Version has CURLINFO_COOKIELIST Version has CURLINFO_LASTSOCKET Version has CURLINFO_FTP_ENTRY_PATH Version has CURLINFO_REDIRECT_URL Version has CURLINFO_PRIMARY_IP Version has CURLINFO_APPCONNECT_TIME Version has CURLINFO_CERTINFO Version has CURLINFO_CONDITION_UNMET Version has CURLOPT_WRITEDATA Version has CURLOPT_KEYPASSWD Version has CURLOPT_DIRLISTONLY Version has CURLOPT_APPEND Version has CURLOPT_KRBLEVEL Version has CURLOPT_USE_SSL Version has CURLOPT_TIMEOUT_MS Version has CURLOPT_CONNECTTIMEOUT_MS Version has CURLOPT_HTTP_TRANSFER_DECODING Version has CURLOPT_HTTP_CONTENT_DECODING Version has CURLOPT_NEW_FILE_PERMS Version has CURLOPT_NEW_DIRECTORY_PERMS Version has CURLOPT_POSTREDIR Version has CURLOPT_OPENSOCKETFUNCTION Version has CURLOPT_OPENSOCKETDATA Version has CURLOPT_COPYPOSTFIELDS Version has CURLOPT_PROXY_TRANSFER_MODE Version has CURLOPT_SEEKFUNCTION Version has CURLOPT_SEEKDATA Version has CURLOPT_CRLFILE Version has CURLOPT_ISSUERCERT Version has CURLOPT_ADDRESS_SCOPE Version has CURLOPT_CERTINFO Version has CURLOPT_USERNAME Version has CURLOPT_PASSWORD Version has CURLOPT_PROXYUSERNAME Version has CURLOPT_PROXYPASSWORD Version has CURLOPT_SSH_HOST_PUBLIC_KEY_MD5 Version has CURLOPT_NOPROXY Version has CURLOPT_TFTP_BLKSIZE Version has CURLOPT_SOCKS5_GSSAPI_SERVICE Version has CURLOPT_SOCKS5_GSSAPI_NEC Version has CURLOPT_PROTOCOLS Version has CURLOPT_REDIR_PROTOCOLS Version has CURLOPT_SSH_AUTH_TYPES Version has CURLOPT_SSH_PUBLIC_KEYFILE Version has CURLOPT_SSH_PRIVATE_KEYFILE Version has CURLOPT_FTP_SSL_CCC Version has CURLOPT_COOKIELIST Version has CURLOPT_IGNORE_CONTENT_LENGTH Version has CURLOPT_FTP_SKIP_PASV_IP Version has CURLOPT_FTP_FILEMETHOD Version has CURLOPT_LOCALPORT Version has CURLOPT_LOCALPORTRANGE Version has CURLOPT_CONNECT_ONLY Version has CURLOPT_CONV_FROM_NETWORK_FUNCTION Version has CURLOPT_CONV_TO_NETWORK_FUNCTION Version has CURLOPT_CONV_FROM_UTF8_FUNCTION Version has CURLOPT_MAX_SEND_SPEED_LARGE Version has CURLOPT_MAX_RECV_SPEED_LARGE Version has CURLOPT_FTP_ALTERNATIVE_TO_USER Version has CURLOPT_SOCKOPTFUNCTION Version has CURLOPT_SOCKOPTDATA Version has CURLOPT_SSL_SESSIONID_CACHE libcurl version: libcurl 8.11.1 configure: creating ./config.status config.status: creating src/Makevars ** libs using C compiler: ‘gcc (GCC) 15.2.1 20260123 (Red Hat 15.2.1-7)’ make[2]: Entering directory '/tmp/Rtmp7CAajn/working_dir/Rtmpri85JE/R.INSTALL36d5261e844dc6/RCurl/src' gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DCURL_DISABLE_DEPRECATION -DHAVE_LIBIDN_FIELD=1 -DHAVE_CURLOPT_URL=1 -DHAVE_CURLINFO_EFFECTIVE_URL=1 -DHAVE_CURLINFO_RESPONSE_CODE=1 -DHAVE_CURLINFO_TOTAL_TIME=1 -DHAVE_CURLINFO_NAMELOOKUP_TIME=1 -DHAVE_CURLINFO_CONNECT_TIME=1 -DHAVE_CURLINFO_PRETRANSFER_TIME=1 -DHAVE_CURLINFO_SIZE_UPLOAD=1 -DHAVE_CURLINFO_SIZE_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_UPLOAD=1 -DHAVE_CURLINFO_HEADER_SIZE=1 -DHAVE_CURLINFO_REQUEST_SIZE=1 -DHAVE_CURLINFO_SSL_VERIFYRESULT=1 -DHAVE_CURLINFO_FILETIME=1 -DHAVE_CURLINFO_CONTENT_LENGTH_DOWNLOAD=1 -DHAVE_CURLINFO_CONTENT_LENGTH_UPLOAD=1 -DHAVE_CURLINFO_STARTTRANSFER_TIME=1 -DHAVE_CURLINFO_CONTENT_TYPE=1 -DHAVE_CURLINFO_REDIRECT_TIME=1 -DHAVE_CURLINFO_REDIRECT_COUNT=1 -DHAVE_CURLINFO_PRIVATE=1 -DHAVE_CURLINFO_HTTP_CONNECTCODE=1 -DHAVE_CURLINFO_HTTPAUTH_AVAIL=1 -DHAVE_CURLINFO_PROXYAUTH_AVAIL=1 -DHAVE_CURLINFO_OS_ERRNO=1 -DHAVE_CURLINFO_NUM_CONNECTS=1 -DHAVE_CURLINFO_SSL_ENGINES=1 -DHAVE_CURLINFO_COOKIELIST=1 -DHAVE_CURLINFO_LASTSOCKET=1 -DHAVE_CURLINFO_FTP_ENTRY_PATH=1 -DHAVE_CURLINFO_REDIRECT_URL=1 -DHAVE_CURLINFO_PRIMARY_IP=1 -DHAVE_CURLINFO_APPCONNECT_TIME=1 -DHAVE_CURLINFO_CERTINFO=1 -DHAVE_CURLINFO_CONDITION_UNMET=1 -DHAVE_CURLOPT_WRITEDATA=1 -DHAVE_CURLOPT_KEYPASSWD=1 -DHAVE_CURLOPT_DIRLISTONLY=1 -DHAVE_CURLOPT_APPEND=1 -DHAVE_CURLOPT_KRBLEVEL=1 -DHAVE_CURLOPT_USE_SSL=1 -DHAVE_CURLOPT_TIMEOUT_MS=1 -DHAVE_CURLOPT_CONNECTTIMEOUT_MS=1 -DHAVE_CURLOPT_HTTP_TRANSFER_DECODING=1 -DHAVE_CURLOPT_HTTP_CONTENT_DECODING=1 -DHAVE_CURLOPT_NEW_FILE_PERMS=1 -DHAVE_CURLOPT_NEW_DIRECTORY_PERMS=1 -DHAVE_CURLOPT_POSTREDIR=1 -DHAVE_CURLOPT_OPENSOCKETFUNCTION=1 -DHAVE_CURLOPT_OPENSOCKETDATA=1 -DHAVE_CURLOPT_COPYPOSTFIELDS=1 -DHAVE_CURLOPT_PROXY_TRANSFER_MODE=1 -DHAVE_CURLOPT_SEEKFUNCTION=1 -DHAVE_CURLOPT_SEEKDATA=1 -DHAVE_CURLOPT_CRLFILE=1 -DHAVE_CURLOPT_ISSUERCERT=1 -DHAVE_CURLOPT_ADDRESS_SCOPE=1 -DHAVE_CURLOPT_CERTINFO=1 -DHAVE_CURLOPT_USERNAME=1 -DHAVE_CURLOPT_PASSWORD=1 -DHAVE_CURLOPT_PROXYUSERNAME=1 -DHAVE_CURLOPT_PROXYPASSWORD=1 -DHAVE_CURLOPT_SSH_HOST_PUBLIC_KEY_MD5=1 -DHAVE_CURLOPT_NOPROXY=1 -DHAVE_CURLOPT_TFTP_BLKSIZE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_SERVICE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_NEC=1 -DHAVE_CURLOPT_PROTOCOLS=1 -DHAVE_CURLOPT_REDIR_PROTOCOLS=1 -DHAVE_CURLOPT_SSH_AUTH_TYPES=1 -DHAVE_CURLOPT_SSH_PUBLIC_KEYFILE=1 -DHAVE_CURLOPT_SSH_PRIVATE_KEYFILE=1 -DHAVE_CURLOPT_FTP_SSL_CCC=1 -DHAVE_CURLOPT_COOKIELIST=1 -DHAVE_CURLOPT_IGNORE_CONTENT_LENGTH=1 -DHAVE_CURLOPT_FTP_SKIP_PASV_IP=1 -DHAVE_CURLOPT_FTP_FILEMETHOD=1 -DHAVE_CURLOPT_LOCALPORT=1 -DHAVE_CURLOPT_LOCALPORTRANGE=1 -DHAVE_CURLOPT_CONNECT_ONLY=1 -DHAVE_CURLOPT_CONV_FROM_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_TO_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_FROM_UTF8_FUNCTION=1 -DHAVE_CURLOPT_MAX_SEND_SPEED_LARGE=1 -DHAVE_CURLOPT_MAX_RECV_SPEED_LARGE=1 -DHAVE_CURLOPT_FTP_ALTERNATIVE_TO_USER=1 -DHAVE_CURLOPT_SOCKOPTFUNCTION=1 -DHAVE_CURLOPT_SOCKOPTDATA=1 -DHAVE_CURLOPT_SSL_SESSIONID_CACHE=1 -I/usr/include/libxml2 -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c base64.c -o base64.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DCURL_DISABLE_DEPRECATION -DHAVE_LIBIDN_FIELD=1 -DHAVE_CURLOPT_URL=1 -DHAVE_CURLINFO_EFFECTIVE_URL=1 -DHAVE_CURLINFO_RESPONSE_CODE=1 -DHAVE_CURLINFO_TOTAL_TIME=1 -DHAVE_CURLINFO_NAMELOOKUP_TIME=1 -DHAVE_CURLINFO_CONNECT_TIME=1 -DHAVE_CURLINFO_PRETRANSFER_TIME=1 -DHAVE_CURLINFO_SIZE_UPLOAD=1 -DHAVE_CURLINFO_SIZE_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_UPLOAD=1 -DHAVE_CURLINFO_HEADER_SIZE=1 -DHAVE_CURLINFO_REQUEST_SIZE=1 -DHAVE_CURLINFO_SSL_VERIFYRESULT=1 -DHAVE_CURLINFO_FILETIME=1 -DHAVE_CURLINFO_CONTENT_LENGTH_DOWNLOAD=1 -DHAVE_CURLINFO_CONTENT_LENGTH_UPLOAD=1 -DHAVE_CURLINFO_STARTTRANSFER_TIME=1 -DHAVE_CURLINFO_CONTENT_TYPE=1 -DHAVE_CURLINFO_REDIRECT_TIME=1 -DHAVE_CURLINFO_REDIRECT_COUNT=1 -DHAVE_CURLINFO_PRIVATE=1 -DHAVE_CURLINFO_HTTP_CONNECTCODE=1 -DHAVE_CURLINFO_HTTPAUTH_AVAIL=1 -DHAVE_CURLINFO_PROXYAUTH_AVAIL=1 -DHAVE_CURLINFO_OS_ERRNO=1 -DHAVE_CURLINFO_NUM_CONNECTS=1 -DHAVE_CURLINFO_SSL_ENGINES=1 -DHAVE_CURLINFO_COOKIELIST=1 -DHAVE_CURLINFO_LASTSOCKET=1 -DHAVE_CURLINFO_FTP_ENTRY_PATH=1 -DHAVE_CURLINFO_REDIRECT_URL=1 -DHAVE_CURLINFO_PRIMARY_IP=1 -DHAVE_CURLINFO_APPCONNECT_TIME=1 -DHAVE_CURLINFO_CERTINFO=1 -DHAVE_CURLINFO_CONDITION_UNMET=1 -DHAVE_CURLOPT_WRITEDATA=1 -DHAVE_CURLOPT_KEYPASSWD=1 -DHAVE_CURLOPT_DIRLISTONLY=1 -DHAVE_CURLOPT_APPEND=1 -DHAVE_CURLOPT_KRBLEVEL=1 -DHAVE_CURLOPT_USE_SSL=1 -DHAVE_CURLOPT_TIMEOUT_MS=1 -DHAVE_CURLOPT_CONNECTTIMEOUT_MS=1 -DHAVE_CURLOPT_HTTP_TRANSFER_DECODING=1 -DHAVE_CURLOPT_HTTP_CONTENT_DECODING=1 -DHAVE_CURLOPT_NEW_FILE_PERMS=1 -DHAVE_CURLOPT_NEW_DIRECTORY_PERMS=1 -DHAVE_CURLOPT_POSTREDIR=1 -DHAVE_CURLOPT_OPENSOCKETFUNCTION=1 -DHAVE_CURLOPT_OPENSOCKETDATA=1 -DHAVE_CURLOPT_COPYPOSTFIELDS=1 -DHAVE_CURLOPT_PROXY_TRANSFER_MODE=1 -DHAVE_CURLOPT_SEEKFUNCTION=1 -DHAVE_CURLOPT_SEEKDATA=1 -DHAVE_CURLOPT_CRLFILE=1 -DHAVE_CURLOPT_ISSUERCERT=1 -DHAVE_CURLOPT_ADDRESS_SCOPE=1 -DHAVE_CURLOPT_CERTINFO=1 -DHAVE_CURLOPT_USERNAME=1 -DHAVE_CURLOPT_PASSWORD=1 -DHAVE_CURLOPT_PROXYUSERNAME=1 -DHAVE_CURLOPT_PROXYPASSWORD=1 -DHAVE_CURLOPT_SSH_HOST_PUBLIC_KEY_MD5=1 -DHAVE_CURLOPT_NOPROXY=1 -DHAVE_CURLOPT_TFTP_BLKSIZE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_SERVICE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_NEC=1 -DHAVE_CURLOPT_PROTOCOLS=1 -DHAVE_CURLOPT_REDIR_PROTOCOLS=1 -DHAVE_CURLOPT_SSH_AUTH_TYPES=1 -DHAVE_CURLOPT_SSH_PUBLIC_KEYFILE=1 -DHAVE_CURLOPT_SSH_PRIVATE_KEYFILE=1 -DHAVE_CURLOPT_FTP_SSL_CCC=1 -DHAVE_CURLOPT_COOKIELIST=1 -DHAVE_CURLOPT_IGNORE_CONTENT_LENGTH=1 -DHAVE_CURLOPT_FTP_SKIP_PASV_IP=1 -DHAVE_CURLOPT_FTP_FILEMETHOD=1 -DHAVE_CURLOPT_LOCALPORT=1 -DHAVE_CURLOPT_LOCALPORTRANGE=1 -DHAVE_CURLOPT_CONNECT_ONLY=1 -DHAVE_CURLOPT_CONV_FROM_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_TO_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_FROM_UTF8_FUNCTION=1 -DHAVE_CURLOPT_MAX_SEND_SPEED_LARGE=1 -DHAVE_CURLOPT_MAX_RECV_SPEED_LARGE=1 -DHAVE_CURLOPT_FTP_ALTERNATIVE_TO_USER=1 -DHAVE_CURLOPT_SOCKOPTFUNCTION=1 -DHAVE_CURLOPT_SOCKOPTDATA=1 -DHAVE_CURLOPT_SSL_SESSIONID_CACHE=1 -I/usr/include/libxml2 -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c curl.c -o curl.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DCURL_DISABLE_DEPRECATION -DHAVE_LIBIDN_FIELD=1 -DHAVE_CURLOPT_URL=1 -DHAVE_CURLINFO_EFFECTIVE_URL=1 -DHAVE_CURLINFO_RESPONSE_CODE=1 -DHAVE_CURLINFO_TOTAL_TIME=1 -DHAVE_CURLINFO_NAMELOOKUP_TIME=1 -DHAVE_CURLINFO_CONNECT_TIME=1 -DHAVE_CURLINFO_PRETRANSFER_TIME=1 -DHAVE_CURLINFO_SIZE_UPLOAD=1 -DHAVE_CURLINFO_SIZE_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_UPLOAD=1 -DHAVE_CURLINFO_HEADER_SIZE=1 -DHAVE_CURLINFO_REQUEST_SIZE=1 -DHAVE_CURLINFO_SSL_VERIFYRESULT=1 -DHAVE_CURLINFO_FILETIME=1 -DHAVE_CURLINFO_CONTENT_LENGTH_DOWNLOAD=1 -DHAVE_CURLINFO_CONTENT_LENGTH_UPLOAD=1 -DHAVE_CURLINFO_STARTTRANSFER_TIME=1 -DHAVE_CURLINFO_CONTENT_TYPE=1 -DHAVE_CURLINFO_REDIRECT_TIME=1 -DHAVE_CURLINFO_REDIRECT_COUNT=1 -DHAVE_CURLINFO_PRIVATE=1 -DHAVE_CURLINFO_HTTP_CONNECTCODE=1 -DHAVE_CURLINFO_HTTPAUTH_AVAIL=1 -DHAVE_CURLINFO_PROXYAUTH_AVAIL=1 -DHAVE_CURLINFO_OS_ERRNO=1 -DHAVE_CURLINFO_NUM_CONNECTS=1 -DHAVE_CURLINFO_SSL_ENGINES=1 -DHAVE_CURLINFO_COOKIELIST=1 -DHAVE_CURLINFO_LASTSOCKET=1 -DHAVE_CURLINFO_FTP_ENTRY_PATH=1 -DHAVE_CURLINFO_REDIRECT_URL=1 -DHAVE_CURLINFO_PRIMARY_IP=1 -DHAVE_CURLINFO_APPCONNECT_TIME=1 -DHAVE_CURLINFO_CERTINFO=1 -DHAVE_CURLINFO_CONDITION_UNMET=1 -DHAVE_CURLOPT_WRITEDATA=1 -DHAVE_CURLOPT_KEYPASSWD=1 -DHAVE_CURLOPT_DIRLISTONLY=1 -DHAVE_CURLOPT_APPEND=1 -DHAVE_CURLOPT_KRBLEVEL=1 -DHAVE_CURLOPT_USE_SSL=1 -DHAVE_CURLOPT_TIMEOUT_MS=1 -DHAVE_CURLOPT_CONNECTTIMEOUT_MS=1 -DHAVE_CURLOPT_HTTP_TRANSFER_DECODING=1 -DHAVE_CURLOPT_HTTP_CONTENT_DECODING=1 -DHAVE_CURLOPT_NEW_FILE_PERMS=1 -DHAVE_CURLOPT_NEW_DIRECTORY_PERMS=1 -DHAVE_CURLOPT_POSTREDIR=1 -DHAVE_CURLOPT_OPENSOCKETFUNCTION=1 -DHAVE_CURLOPT_OPENSOCKETDATA=1 -DHAVE_CURLOPT_COPYPOSTFIELDS=1 -DHAVE_CURLOPT_PROXY_TRANSFER_MODE=1 -DHAVE_CURLOPT_SEEKFUNCTION=1 -DHAVE_CURLOPT_SEEKDATA=1 -DHAVE_CURLOPT_CRLFILE=1 -DHAVE_CURLOPT_ISSUERCERT=1 -DHAVE_CURLOPT_ADDRESS_SCOPE=1 -DHAVE_CURLOPT_CERTINFO=1 -DHAVE_CURLOPT_USERNAME=1 -DHAVE_CURLOPT_PASSWORD=1 -DHAVE_CURLOPT_PROXYUSERNAME=1 -DHAVE_CURLOPT_PROXYPASSWORD=1 -DHAVE_CURLOPT_SSH_HOST_PUBLIC_KEY_MD5=1 -DHAVE_CURLOPT_NOPROXY=1 -DHAVE_CURLOPT_TFTP_BLKSIZE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_SERVICE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_NEC=1 -DHAVE_CURLOPT_PROTOCOLS=1 -DHAVE_CURLOPT_REDIR_PROTOCOLS=1 -DHAVE_CURLOPT_SSH_AUTH_TYPES=1 -DHAVE_CURLOPT_SSH_PUBLIC_KEYFILE=1 -DHAVE_CURLOPT_SSH_PRIVATE_KEYFILE=1 -DHAVE_CURLOPT_FTP_SSL_CCC=1 -DHAVE_CURLOPT_COOKIELIST=1 -DHAVE_CURLOPT_IGNORE_CONTENT_LENGTH=1 -DHAVE_CURLOPT_FTP_SKIP_PASV_IP=1 -DHAVE_CURLOPT_FTP_FILEMETHOD=1 -DHAVE_CURLOPT_LOCALPORT=1 -DHAVE_CURLOPT_LOCALPORTRANGE=1 -DHAVE_CURLOPT_CONNECT_ONLY=1 -DHAVE_CURLOPT_CONV_FROM_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_TO_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_FROM_UTF8_FUNCTION=1 -DHAVE_CURLOPT_MAX_SEND_SPEED_LARGE=1 -DHAVE_CURLOPT_MAX_RECV_SPEED_LARGE=1 -DHAVE_CURLOPT_FTP_ALTERNATIVE_TO_USER=1 -DHAVE_CURLOPT_SOCKOPTFUNCTION=1 -DHAVE_CURLOPT_SOCKOPTDATA=1 -DHAVE_CURLOPT_SSL_SESSIONID_CACHE=1 -I/usr/include/libxml2 -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c curlInit.c -o curlInit.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DCURL_DISABLE_DEPRECATION -DHAVE_LIBIDN_FIELD=1 -DHAVE_CURLOPT_URL=1 -DHAVE_CURLINFO_EFFECTIVE_URL=1 -DHAVE_CURLINFO_RESPONSE_CODE=1 -DHAVE_CURLINFO_TOTAL_TIME=1 -DHAVE_CURLINFO_NAMELOOKUP_TIME=1 -DHAVE_CURLINFO_CONNECT_TIME=1 -DHAVE_CURLINFO_PRETRANSFER_TIME=1 -DHAVE_CURLINFO_SIZE_UPLOAD=1 -DHAVE_CURLINFO_SIZE_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_UPLOAD=1 -DHAVE_CURLINFO_HEADER_SIZE=1 -DHAVE_CURLINFO_REQUEST_SIZE=1 -DHAVE_CURLINFO_SSL_VERIFYRESULT=1 -DHAVE_CURLINFO_FILETIME=1 -DHAVE_CURLINFO_CONTENT_LENGTH_DOWNLOAD=1 -DHAVE_CURLINFO_CONTENT_LENGTH_UPLOAD=1 -DHAVE_CURLINFO_STARTTRANSFER_TIME=1 -DHAVE_CURLINFO_CONTENT_TYPE=1 -DHAVE_CURLINFO_REDIRECT_TIME=1 -DHAVE_CURLINFO_REDIRECT_COUNT=1 -DHAVE_CURLINFO_PRIVATE=1 -DHAVE_CURLINFO_HTTP_CONNECTCODE=1 -DHAVE_CURLINFO_HTTPAUTH_AVAIL=1 -DHAVE_CURLINFO_PROXYAUTH_AVAIL=1 -DHAVE_CURLINFO_OS_ERRNO=1 -DHAVE_CURLINFO_NUM_CONNECTS=1 -DHAVE_CURLINFO_SSL_ENGINES=1 -DHAVE_CURLINFO_COOKIELIST=1 -DHAVE_CURLINFO_LASTSOCKET=1 -DHAVE_CURLINFO_FTP_ENTRY_PATH=1 -DHAVE_CURLINFO_REDIRECT_URL=1 -DHAVE_CURLINFO_PRIMARY_IP=1 -DHAVE_CURLINFO_APPCONNECT_TIME=1 -DHAVE_CURLINFO_CERTINFO=1 -DHAVE_CURLINFO_CONDITION_UNMET=1 -DHAVE_CURLOPT_WRITEDATA=1 -DHAVE_CURLOPT_KEYPASSWD=1 -DHAVE_CURLOPT_DIRLISTONLY=1 -DHAVE_CURLOPT_APPEND=1 -DHAVE_CURLOPT_KRBLEVEL=1 -DHAVE_CURLOPT_USE_SSL=1 -DHAVE_CURLOPT_TIMEOUT_MS=1 -DHAVE_CURLOPT_CONNECTTIMEOUT_MS=1 -DHAVE_CURLOPT_HTTP_TRANSFER_DECODING=1 -DHAVE_CURLOPT_HTTP_CONTENT_DECODING=1 -DHAVE_CURLOPT_NEW_FILE_PERMS=1 -DHAVE_CURLOPT_NEW_DIRECTORY_PERMS=1 -DHAVE_CURLOPT_POSTREDIR=1 -DHAVE_CURLOPT_OPENSOCKETFUNCTION=1 -DHAVE_CURLOPT_OPENSOCKETDATA=1 -DHAVE_CURLOPT_COPYPOSTFIELDS=1 -DHAVE_CURLOPT_PROXY_TRANSFER_MODE=1 -DHAVE_CURLOPT_SEEKFUNCTION=1 -DHAVE_CURLOPT_SEEKDATA=1 -DHAVE_CURLOPT_CRLFILE=1 -DHAVE_CURLOPT_ISSUERCERT=1 -DHAVE_CURLOPT_ADDRESS_SCOPE=1 -DHAVE_CURLOPT_CERTINFO=1 -DHAVE_CURLOPT_USERNAME=1 -DHAVE_CURLOPT_PASSWORD=1 -DHAVE_CURLOPT_PROXYUSERNAME=1 -DHAVE_CURLOPT_PROXYPASSWORD=1 -DHAVE_CURLOPT_SSH_HOST_PUBLIC_KEY_MD5=1 -DHAVE_CURLOPT_NOPROXY=1 -DHAVE_CURLOPT_TFTP_BLKSIZE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_SERVICE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_NEC=1 -DHAVE_CURLOPT_PROTOCOLS=1 -DHAVE_CURLOPT_REDIR_PROTOCOLS=1 -DHAVE_CURLOPT_SSH_AUTH_TYPES=1 -DHAVE_CURLOPT_SSH_PUBLIC_KEYFILE=1 -DHAVE_CURLOPT_SSH_PRIVATE_KEYFILE=1 -DHAVE_CURLOPT_FTP_SSL_CCC=1 -DHAVE_CURLOPT_COOKIELIST=1 -DHAVE_CURLOPT_IGNORE_CONTENT_LENGTH=1 -DHAVE_CURLOPT_FTP_SKIP_PASV_IP=1 -DHAVE_CURLOPT_FTP_FILEMETHOD=1 -DHAVE_CURLOPT_LOCALPORT=1 -DHAVE_CURLOPT_LOCALPORTRANGE=1 -DHAVE_CURLOPT_CONNECT_ONLY=1 -DHAVE_CURLOPT_CONV_FROM_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_TO_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_FROM_UTF8_FUNCTION=1 -DHAVE_CURLOPT_MAX_SEND_SPEED_LARGE=1 -DHAVE_CURLOPT_MAX_RECV_SPEED_LARGE=1 -DHAVE_CURLOPT_FTP_ALTERNATIVE_TO_USER=1 -DHAVE_CURLOPT_SOCKOPTFUNCTION=1 -DHAVE_CURLOPT_SOCKOPTDATA=1 -DHAVE_CURLOPT_SSL_SESSIONID_CACHE=1 -I/usr/include/libxml2 -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c curl_base64.c -o curl_base64.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DCURL_DISABLE_DEPRECATION -DHAVE_LIBIDN_FIELD=1 -DHAVE_CURLOPT_URL=1 -DHAVE_CURLINFO_EFFECTIVE_URL=1 -DHAVE_CURLINFO_RESPONSE_CODE=1 -DHAVE_CURLINFO_TOTAL_TIME=1 -DHAVE_CURLINFO_NAMELOOKUP_TIME=1 -DHAVE_CURLINFO_CONNECT_TIME=1 -DHAVE_CURLINFO_PRETRANSFER_TIME=1 -DHAVE_CURLINFO_SIZE_UPLOAD=1 -DHAVE_CURLINFO_SIZE_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_UPLOAD=1 -DHAVE_CURLINFO_HEADER_SIZE=1 -DHAVE_CURLINFO_REQUEST_SIZE=1 -DHAVE_CURLINFO_SSL_VERIFYRESULT=1 -DHAVE_CURLINFO_FILETIME=1 -DHAVE_CURLINFO_CONTENT_LENGTH_DOWNLOAD=1 -DHAVE_CURLINFO_CONTENT_LENGTH_UPLOAD=1 -DHAVE_CURLINFO_STARTTRANSFER_TIME=1 -DHAVE_CURLINFO_CONTENT_TYPE=1 -DHAVE_CURLINFO_REDIRECT_TIME=1 -DHAVE_CURLINFO_REDIRECT_COUNT=1 -DHAVE_CURLINFO_PRIVATE=1 -DHAVE_CURLINFO_HTTP_CONNECTCODE=1 -DHAVE_CURLINFO_HTTPAUTH_AVAIL=1 -DHAVE_CURLINFO_PROXYAUTH_AVAIL=1 -DHAVE_CURLINFO_OS_ERRNO=1 -DHAVE_CURLINFO_NUM_CONNECTS=1 -DHAVE_CURLINFO_SSL_ENGINES=1 -DHAVE_CURLINFO_COOKIELIST=1 -DHAVE_CURLINFO_LASTSOCKET=1 -DHAVE_CURLINFO_FTP_ENTRY_PATH=1 -DHAVE_CURLINFO_REDIRECT_URL=1 -DHAVE_CURLINFO_PRIMARY_IP=1 -DHAVE_CURLINFO_APPCONNECT_TIME=1 -DHAVE_CURLINFO_CERTINFO=1 -DHAVE_CURLINFO_CONDITION_UNMET=1 -DHAVE_CURLOPT_WRITEDATA=1 -DHAVE_CURLOPT_KEYPASSWD=1 -DHAVE_CURLOPT_DIRLISTONLY=1 -DHAVE_CURLOPT_APPEND=1 -DHAVE_CURLOPT_KRBLEVEL=1 -DHAVE_CURLOPT_USE_SSL=1 -DHAVE_CURLOPT_TIMEOUT_MS=1 -DHAVE_CURLOPT_CONNECTTIMEOUT_MS=1 -DHAVE_CURLOPT_HTTP_TRANSFER_DECODING=1 -DHAVE_CURLOPT_HTTP_CONTENT_DECODING=1 -DHAVE_CURLOPT_NEW_FILE_PERMS=1 -DHAVE_CURLOPT_NEW_DIRECTORY_PERMS=1 -DHAVE_CURLOPT_POSTREDIR=1 -DHAVE_CURLOPT_OPENSOCKETFUNCTION=1 -DHAVE_CURLOPT_OPENSOCKETDATA=1 -DHAVE_CURLOPT_COPYPOSTFIELDS=1 -DHAVE_CURLOPT_PROXY_TRANSFER_MODE=1 -DHAVE_CURLOPT_SEEKFUNCTION=1 -DHAVE_CURLOPT_SEEKDATA=1 -DHAVE_CURLOPT_CRLFILE=1 -DHAVE_CURLOPT_ISSUERCERT=1 -DHAVE_CURLOPT_ADDRESS_SCOPE=1 -DHAVE_CURLOPT_CERTINFO=1 -DHAVE_CURLOPT_USERNAME=1 -DHAVE_CURLOPT_PASSWORD=1 -DHAVE_CURLOPT_PROXYUSERNAME=1 -DHAVE_CURLOPT_PROXYPASSWORD=1 -DHAVE_CURLOPT_SSH_HOST_PUBLIC_KEY_MD5=1 -DHAVE_CURLOPT_NOPROXY=1 -DHAVE_CURLOPT_TFTP_BLKSIZE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_SERVICE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_NEC=1 -DHAVE_CURLOPT_PROTOCOLS=1 -DHAVE_CURLOPT_REDIR_PROTOCOLS=1 -DHAVE_CURLOPT_SSH_AUTH_TYPES=1 -DHAVE_CURLOPT_SSH_PUBLIC_KEYFILE=1 -DHAVE_CURLOPT_SSH_PRIVATE_KEYFILE=1 -DHAVE_CURLOPT_FTP_SSL_CCC=1 -DHAVE_CURLOPT_COOKIELIST=1 -DHAVE_CURLOPT_IGNORE_CONTENT_LENGTH=1 -DHAVE_CURLOPT_FTP_SKIP_PASV_IP=1 -DHAVE_CURLOPT_FTP_FILEMETHOD=1 -DHAVE_CURLOPT_LOCALPORT=1 -DHAVE_CURLOPT_LOCALPORTRANGE=1 -DHAVE_CURLOPT_CONNECT_ONLY=1 -DHAVE_CURLOPT_CONV_FROM_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_TO_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_FROM_UTF8_FUNCTION=1 -DHAVE_CURLOPT_MAX_SEND_SPEED_LARGE=1 -DHAVE_CURLOPT_MAX_RECV_SPEED_LARGE=1 -DHAVE_CURLOPT_FTP_ALTERNATIVE_TO_USER=1 -DHAVE_CURLOPT_SOCKOPTFUNCTION=1 -DHAVE_CURLOPT_SOCKOPTDATA=1 -DHAVE_CURLOPT_SSL_SESSIONID_CACHE=1 -I/usr/include/libxml2 -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c enums.c -o enums.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DCURL_DISABLE_DEPRECATION -DHAVE_LIBIDN_FIELD=1 -DHAVE_CURLOPT_URL=1 -DHAVE_CURLINFO_EFFECTIVE_URL=1 -DHAVE_CURLINFO_RESPONSE_CODE=1 -DHAVE_CURLINFO_TOTAL_TIME=1 -DHAVE_CURLINFO_NAMELOOKUP_TIME=1 -DHAVE_CURLINFO_CONNECT_TIME=1 -DHAVE_CURLINFO_PRETRANSFER_TIME=1 -DHAVE_CURLINFO_SIZE_UPLOAD=1 -DHAVE_CURLINFO_SIZE_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_UPLOAD=1 -DHAVE_CURLINFO_HEADER_SIZE=1 -DHAVE_CURLINFO_REQUEST_SIZE=1 -DHAVE_CURLINFO_SSL_VERIFYRESULT=1 -DHAVE_CURLINFO_FILETIME=1 -DHAVE_CURLINFO_CONTENT_LENGTH_DOWNLOAD=1 -DHAVE_CURLINFO_CONTENT_LENGTH_UPLOAD=1 -DHAVE_CURLINFO_STARTTRANSFER_TIME=1 -DHAVE_CURLINFO_CONTENT_TYPE=1 -DHAVE_CURLINFO_REDIRECT_TIME=1 -DHAVE_CURLINFO_REDIRECT_COUNT=1 -DHAVE_CURLINFO_PRIVATE=1 -DHAVE_CURLINFO_HTTP_CONNECTCODE=1 -DHAVE_CURLINFO_HTTPAUTH_AVAIL=1 -DHAVE_CURLINFO_PROXYAUTH_AVAIL=1 -DHAVE_CURLINFO_OS_ERRNO=1 -DHAVE_CURLINFO_NUM_CONNECTS=1 -DHAVE_CURLINFO_SSL_ENGINES=1 -DHAVE_CURLINFO_COOKIELIST=1 -DHAVE_CURLINFO_LASTSOCKET=1 -DHAVE_CURLINFO_FTP_ENTRY_PATH=1 -DHAVE_CURLINFO_REDIRECT_URL=1 -DHAVE_CURLINFO_PRIMARY_IP=1 -DHAVE_CURLINFO_APPCONNECT_TIME=1 -DHAVE_CURLINFO_CERTINFO=1 -DHAVE_CURLINFO_CONDITION_UNMET=1 -DHAVE_CURLOPT_WRITEDATA=1 -DHAVE_CURLOPT_KEYPASSWD=1 -DHAVE_CURLOPT_DIRLISTONLY=1 -DHAVE_CURLOPT_APPEND=1 -DHAVE_CURLOPT_KRBLEVEL=1 -DHAVE_CURLOPT_USE_SSL=1 -DHAVE_CURLOPT_TIMEOUT_MS=1 -DHAVE_CURLOPT_CONNECTTIMEOUT_MS=1 -DHAVE_CURLOPT_HTTP_TRANSFER_DECODING=1 -DHAVE_CURLOPT_HTTP_CONTENT_DECODING=1 -DHAVE_CURLOPT_NEW_FILE_PERMS=1 -DHAVE_CURLOPT_NEW_DIRECTORY_PERMS=1 -DHAVE_CURLOPT_POSTREDIR=1 -DHAVE_CURLOPT_OPENSOCKETFUNCTION=1 -DHAVE_CURLOPT_OPENSOCKETDATA=1 -DHAVE_CURLOPT_COPYPOSTFIELDS=1 -DHAVE_CURLOPT_PROXY_TRANSFER_MODE=1 -DHAVE_CURLOPT_SEEKFUNCTION=1 -DHAVE_CURLOPT_SEEKDATA=1 -DHAVE_CURLOPT_CRLFILE=1 -DHAVE_CURLOPT_ISSUERCERT=1 -DHAVE_CURLOPT_ADDRESS_SCOPE=1 -DHAVE_CURLOPT_CERTINFO=1 -DHAVE_CURLOPT_USERNAME=1 -DHAVE_CURLOPT_PASSWORD=1 -DHAVE_CURLOPT_PROXYUSERNAME=1 -DHAVE_CURLOPT_PROXYPASSWORD=1 -DHAVE_CURLOPT_SSH_HOST_PUBLIC_KEY_MD5=1 -DHAVE_CURLOPT_NOPROXY=1 -DHAVE_CURLOPT_TFTP_BLKSIZE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_SERVICE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_NEC=1 -DHAVE_CURLOPT_PROTOCOLS=1 -DHAVE_CURLOPT_REDIR_PROTOCOLS=1 -DHAVE_CURLOPT_SSH_AUTH_TYPES=1 -DHAVE_CURLOPT_SSH_PUBLIC_KEYFILE=1 -DHAVE_CURLOPT_SSH_PRIVATE_KEYFILE=1 -DHAVE_CURLOPT_FTP_SSL_CCC=1 -DHAVE_CURLOPT_COOKIELIST=1 -DHAVE_CURLOPT_IGNORE_CONTENT_LENGTH=1 -DHAVE_CURLOPT_FTP_SKIP_PASV_IP=1 -DHAVE_CURLOPT_FTP_FILEMETHOD=1 -DHAVE_CURLOPT_LOCALPORT=1 -DHAVE_CURLOPT_LOCALPORTRANGE=1 -DHAVE_CURLOPT_CONNECT_ONLY=1 -DHAVE_CURLOPT_CONV_FROM_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_TO_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_FROM_UTF8_FUNCTION=1 -DHAVE_CURLOPT_MAX_SEND_SPEED_LARGE=1 -DHAVE_CURLOPT_MAX_RECV_SPEED_LARGE=1 -DHAVE_CURLOPT_FTP_ALTERNATIVE_TO_USER=1 -DHAVE_CURLOPT_SOCKOPTFUNCTION=1 -DHAVE_CURLOPT_SOCKOPTDATA=1 -DHAVE_CURLOPT_SSL_SESSIONID_CACHE=1 -I/usr/include/libxml2 -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c json.c -o json.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DCURL_DISABLE_DEPRECATION -DHAVE_LIBIDN_FIELD=1 -DHAVE_CURLOPT_URL=1 -DHAVE_CURLINFO_EFFECTIVE_URL=1 -DHAVE_CURLINFO_RESPONSE_CODE=1 -DHAVE_CURLINFO_TOTAL_TIME=1 -DHAVE_CURLINFO_NAMELOOKUP_TIME=1 -DHAVE_CURLINFO_CONNECT_TIME=1 -DHAVE_CURLINFO_PRETRANSFER_TIME=1 -DHAVE_CURLINFO_SIZE_UPLOAD=1 -DHAVE_CURLINFO_SIZE_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_UPLOAD=1 -DHAVE_CURLINFO_HEADER_SIZE=1 -DHAVE_CURLINFO_REQUEST_SIZE=1 -DHAVE_CURLINFO_SSL_VERIFYRESULT=1 -DHAVE_CURLINFO_FILETIME=1 -DHAVE_CURLINFO_CONTENT_LENGTH_DOWNLOAD=1 -DHAVE_CURLINFO_CONTENT_LENGTH_UPLOAD=1 -DHAVE_CURLINFO_STARTTRANSFER_TIME=1 -DHAVE_CURLINFO_CONTENT_TYPE=1 -DHAVE_CURLINFO_REDIRECT_TIME=1 -DHAVE_CURLINFO_REDIRECT_COUNT=1 -DHAVE_CURLINFO_PRIVATE=1 -DHAVE_CURLINFO_HTTP_CONNECTCODE=1 -DHAVE_CURLINFO_HTTPAUTH_AVAIL=1 -DHAVE_CURLINFO_PROXYAUTH_AVAIL=1 -DHAVE_CURLINFO_OS_ERRNO=1 -DHAVE_CURLINFO_NUM_CONNECTS=1 -DHAVE_CURLINFO_SSL_ENGINES=1 -DHAVE_CURLINFO_COOKIELIST=1 -DHAVE_CURLINFO_LASTSOCKET=1 -DHAVE_CURLINFO_FTP_ENTRY_PATH=1 -DHAVE_CURLINFO_REDIRECT_URL=1 -DHAVE_CURLINFO_PRIMARY_IP=1 -DHAVE_CURLINFO_APPCONNECT_TIME=1 -DHAVE_CURLINFO_CERTINFO=1 -DHAVE_CURLINFO_CONDITION_UNMET=1 -DHAVE_CURLOPT_WRITEDATA=1 -DHAVE_CURLOPT_KEYPASSWD=1 -DHAVE_CURLOPT_DIRLISTONLY=1 -DHAVE_CURLOPT_APPEND=1 -DHAVE_CURLOPT_KRBLEVEL=1 -DHAVE_CURLOPT_USE_SSL=1 -DHAVE_CURLOPT_TIMEOUT_MS=1 -DHAVE_CURLOPT_CONNECTTIMEOUT_MS=1 -DHAVE_CURLOPT_HTTP_TRANSFER_DECODING=1 -DHAVE_CURLOPT_HTTP_CONTENT_DECODING=1 -DHAVE_CURLOPT_NEW_FILE_PERMS=1 -DHAVE_CURLOPT_NEW_DIRECTORY_PERMS=1 -DHAVE_CURLOPT_POSTREDIR=1 -DHAVE_CURLOPT_OPENSOCKETFUNCTION=1 -DHAVE_CURLOPT_OPENSOCKETDATA=1 -DHAVE_CURLOPT_COPYPOSTFIELDS=1 -DHAVE_CURLOPT_PROXY_TRANSFER_MODE=1 -DHAVE_CURLOPT_SEEKFUNCTION=1 -DHAVE_CURLOPT_SEEKDATA=1 -DHAVE_CURLOPT_CRLFILE=1 -DHAVE_CURLOPT_ISSUERCERT=1 -DHAVE_CURLOPT_ADDRESS_SCOPE=1 -DHAVE_CURLOPT_CERTINFO=1 -DHAVE_CURLOPT_USERNAME=1 -DHAVE_CURLOPT_PASSWORD=1 -DHAVE_CURLOPT_PROXYUSERNAME=1 -DHAVE_CURLOPT_PROXYPASSWORD=1 -DHAVE_CURLOPT_SSH_HOST_PUBLIC_KEY_MD5=1 -DHAVE_CURLOPT_NOPROXY=1 -DHAVE_CURLOPT_TFTP_BLKSIZE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_SERVICE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_NEC=1 -DHAVE_CURLOPT_PROTOCOLS=1 -DHAVE_CURLOPT_REDIR_PROTOCOLS=1 -DHAVE_CURLOPT_SSH_AUTH_TYPES=1 -DHAVE_CURLOPT_SSH_PUBLIC_KEYFILE=1 -DHAVE_CURLOPT_SSH_PRIVATE_KEYFILE=1 -DHAVE_CURLOPT_FTP_SSL_CCC=1 -DHAVE_CURLOPT_COOKIELIST=1 -DHAVE_CURLOPT_IGNORE_CONTENT_LENGTH=1 -DHAVE_CURLOPT_FTP_SKIP_PASV_IP=1 -DHAVE_CURLOPT_FTP_FILEMETHOD=1 -DHAVE_CURLOPT_LOCALPORT=1 -DHAVE_CURLOPT_LOCALPORTRANGE=1 -DHAVE_CURLOPT_CONNECT_ONLY=1 -DHAVE_CURLOPT_CONV_FROM_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_TO_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_FROM_UTF8_FUNCTION=1 -DHAVE_CURLOPT_MAX_SEND_SPEED_LARGE=1 -DHAVE_CURLOPT_MAX_RECV_SPEED_LARGE=1 -DHAVE_CURLOPT_FTP_ALTERNATIVE_TO_USER=1 -DHAVE_CURLOPT_SOCKOPTFUNCTION=1 -DHAVE_CURLOPT_SOCKOPTDATA=1 -DHAVE_CURLOPT_SSL_SESSIONID_CACHE=1 -I/usr/include/libxml2 -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c memoryManagement.c -o memoryManagement.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DCURL_DISABLE_DEPRECATION -DHAVE_LIBIDN_FIELD=1 -DHAVE_CURLOPT_URL=1 -DHAVE_CURLINFO_EFFECTIVE_URL=1 -DHAVE_CURLINFO_RESPONSE_CODE=1 -DHAVE_CURLINFO_TOTAL_TIME=1 -DHAVE_CURLINFO_NAMELOOKUP_TIME=1 -DHAVE_CURLINFO_CONNECT_TIME=1 -DHAVE_CURLINFO_PRETRANSFER_TIME=1 -DHAVE_CURLINFO_SIZE_UPLOAD=1 -DHAVE_CURLINFO_SIZE_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_UPLOAD=1 -DHAVE_CURLINFO_HEADER_SIZE=1 -DHAVE_CURLINFO_REQUEST_SIZE=1 -DHAVE_CURLINFO_SSL_VERIFYRESULT=1 -DHAVE_CURLINFO_FILETIME=1 -DHAVE_CURLINFO_CONTENT_LENGTH_DOWNLOAD=1 -DHAVE_CURLINFO_CONTENT_LENGTH_UPLOAD=1 -DHAVE_CURLINFO_STARTTRANSFER_TIME=1 -DHAVE_CURLINFO_CONTENT_TYPE=1 -DHAVE_CURLINFO_REDIRECT_TIME=1 -DHAVE_CURLINFO_REDIRECT_COUNT=1 -DHAVE_CURLINFO_PRIVATE=1 -DHAVE_CURLINFO_HTTP_CONNECTCODE=1 -DHAVE_CURLINFO_HTTPAUTH_AVAIL=1 -DHAVE_CURLINFO_PROXYAUTH_AVAIL=1 -DHAVE_CURLINFO_OS_ERRNO=1 -DHAVE_CURLINFO_NUM_CONNECTS=1 -DHAVE_CURLINFO_SSL_ENGINES=1 -DHAVE_CURLINFO_COOKIELIST=1 -DHAVE_CURLINFO_LASTSOCKET=1 -DHAVE_CURLINFO_FTP_ENTRY_PATH=1 -DHAVE_CURLINFO_REDIRECT_URL=1 -DHAVE_CURLINFO_PRIMARY_IP=1 -DHAVE_CURLINFO_APPCONNECT_TIME=1 -DHAVE_CURLINFO_CERTINFO=1 -DHAVE_CURLINFO_CONDITION_UNMET=1 -DHAVE_CURLOPT_WRITEDATA=1 -DHAVE_CURLOPT_KEYPASSWD=1 -DHAVE_CURLOPT_DIRLISTONLY=1 -DHAVE_CURLOPT_APPEND=1 -DHAVE_CURLOPT_KRBLEVEL=1 -DHAVE_CURLOPT_USE_SSL=1 -DHAVE_CURLOPT_TIMEOUT_MS=1 -DHAVE_CURLOPT_CONNECTTIMEOUT_MS=1 -DHAVE_CURLOPT_HTTP_TRANSFER_DECODING=1 -DHAVE_CURLOPT_HTTP_CONTENT_DECODING=1 -DHAVE_CURLOPT_NEW_FILE_PERMS=1 -DHAVE_CURLOPT_NEW_DIRECTORY_PERMS=1 -DHAVE_CURLOPT_POSTREDIR=1 -DHAVE_CURLOPT_OPENSOCKETFUNCTION=1 -DHAVE_CURLOPT_OPENSOCKETDATA=1 -DHAVE_CURLOPT_COPYPOSTFIELDS=1 -DHAVE_CURLOPT_PROXY_TRANSFER_MODE=1 -DHAVE_CURLOPT_SEEKFUNCTION=1 -DHAVE_CURLOPT_SEEKDATA=1 -DHAVE_CURLOPT_CRLFILE=1 -DHAVE_CURLOPT_ISSUERCERT=1 -DHAVE_CURLOPT_ADDRESS_SCOPE=1 -DHAVE_CURLOPT_CERTINFO=1 -DHAVE_CURLOPT_USERNAME=1 -DHAVE_CURLOPT_PASSWORD=1 -DHAVE_CURLOPT_PROXYUSERNAME=1 -DHAVE_CURLOPT_PROXYPASSWORD=1 -DHAVE_CURLOPT_SSH_HOST_PUBLIC_KEY_MD5=1 -DHAVE_CURLOPT_NOPROXY=1 -DHAVE_CURLOPT_TFTP_BLKSIZE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_SERVICE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_NEC=1 -DHAVE_CURLOPT_PROTOCOLS=1 -DHAVE_CURLOPT_REDIR_PROTOCOLS=1 -DHAVE_CURLOPT_SSH_AUTH_TYPES=1 -DHAVE_CURLOPT_SSH_PUBLIC_KEYFILE=1 -DHAVE_CURLOPT_SSH_PRIVATE_KEYFILE=1 -DHAVE_CURLOPT_FTP_SSL_CCC=1 -DHAVE_CURLOPT_COOKIELIST=1 -DHAVE_CURLOPT_IGNORE_CONTENT_LENGTH=1 -DHAVE_CURLOPT_FTP_SKIP_PASV_IP=1 -DHAVE_CURLOPT_FTP_FILEMETHOD=1 -DHAVE_CURLOPT_LOCALPORT=1 -DHAVE_CURLOPT_LOCALPORTRANGE=1 -DHAVE_CURLOPT_CONNECT_ONLY=1 -DHAVE_CURLOPT_CONV_FROM_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_TO_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_FROM_UTF8_FUNCTION=1 -DHAVE_CURLOPT_MAX_SEND_SPEED_LARGE=1 -DHAVE_CURLOPT_MAX_RECV_SPEED_LARGE=1 -DHAVE_CURLOPT_FTP_ALTERNATIVE_TO_USER=1 -DHAVE_CURLOPT_SOCKOPTFUNCTION=1 -DHAVE_CURLOPT_SOCKOPTDATA=1 -DHAVE_CURLOPT_SSL_SESSIONID_CACHE=1 -I/usr/include/libxml2 -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c myUTF8.c -o myUTF8.o curl.c: In function ‘R_curl_easy_setopt’: curl.c:176:29: warning: ISO C forbids conversion of object pointer to function pointer type [-Wpedantic] 176 | f = (curl_write_callback) val; | ^ gcc -shared -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -L/usr/local/lib64 -o RCurl.so base64.o curl.o curlInit.o curl_base64.o enums.o json.o memoryManagement.o myUTF8.o -lcurl -lxml2 -lz -llzma -lm make[2]: Leaving directory '/tmp/Rtmp7CAajn/working_dir/Rtmpri85JE/R.INSTALL36d5261e844dc6/RCurl/src' make[2]: Entering directory '/tmp/Rtmp7CAajn/working_dir/Rtmpri85JE/R.INSTALL36d5261e844dc6/RCurl/src' make[2]: Leaving directory '/tmp/Rtmp7CAajn/working_dir/Rtmpri85JE/R.INSTALL36d5261e844dc6/RCurl/src' installing to /tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/00LOCK-RCurl/00new/RCurl/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (RCurl) * installing *source* package ‘rjson’ ... ** this is package ‘rjson’ version ‘0.2.23’ ** package ‘rjson’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc (GCC) 15.2.1 20260123 (Red Hat 15.2.1-7)’ using C++ compiler: ‘g++ (GCC) 15.2.1 20260123 (Red Hat 15.2.1-7)’ make[2]: Entering directory '/tmp/Rtmp7CAajn/working_dir/RtmpgQ4VGs/R.INSTALL36e6a371d845f5/rjson/src' g++ -std=gnu++20 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c dump.cpp -o dump.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c parser.c -o parser.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c register.c -o register.o g++ -std=gnu++20 -shared -L/usr/local/lib64 -o rjson.so dump.o parser.o register.o make[2]: Leaving directory '/tmp/Rtmp7CAajn/working_dir/RtmpgQ4VGs/R.INSTALL36e6a371d845f5/rjson/src' make[2]: Entering directory '/tmp/Rtmp7CAajn/working_dir/RtmpgQ4VGs/R.INSTALL36e6a371d845f5/rjson/src' make[2]: Leaving directory '/tmp/Rtmp7CAajn/working_dir/RtmpgQ4VGs/R.INSTALL36e6a371d845f5/rjson/src' installing to /tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/00LOCK-rjson/00new/rjson/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (rjson) * installing *source* package ‘XML’ ... ** this is package ‘XML’ version ‘3.99-0.22’ ** package ‘XML’ successfully unpacked and MD5 sums checked ** using staged installation checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking how to run the C preprocessor... gcc -E checking for sed... /usr/bin/sed checking for pkg-config... /usr/bin/pkg-config checking for xml2-config... /usr/bin/xml2-config USE_XML2 = yes SED_EXTENDED_ARG: -E Minor 12, Patch 10 for 2.12.10 Located parser file -I/usr/include/libxml2/parser.h Checking for 1.8: -I/usr/include/libxml2 Using libxml2.* checking for gzopen in -lz... yes checking for xmlParseFile in -lxml2... yes checking for xmlHashSize in -lxml2... yes Using built-in xmlHashSize Checking DTD parsing (presence of externalSubset)... checking for xmlHashSize in -lxml2... (cached) yes Found xmlHashSize checking for xmlOutputBufferCreateBuffer in -lxml2... yes have xmlOutputBufferCreateBuffer() checking for xmlDocDumpFormatMemoryEnc in -lxml2... yes checking for libxml/xmlversion.h... yes Expat: FALSE Checking for return type of xmlHashScan element routine. No return value for xmlHashScan xmlNs has a context field Checking for cetype_t enumeration Using recent version of R with cetype_t enumeration type for encoding checking for xmlsec1-config... no nodegc default xml-debug default Version has XML_WITH_ZLIB Version has xmlHasFeature() **************************************** Configuration information: Libxml settings libxml include directory: -I/usr/include/libxml2 libxml library directory: -lxml2 -lz -llzma -lm -lz -lxml2 libxml 2: -DLIBXML2=1 Compilation flags: -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DNO_CHECKED_ENTITY_FIELD=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 -DHAVE_R_CETYPE_T=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 -DUSE_R=1 -D_R_=1 -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1 Link flags: -lxml2 -lz -llzma -lm -lz -lxml2 **************************************** configure: creating ./config.status config.status: creating src/Makevars config.status: creating R/supports.R config.status: creating inst/scripts/RSXML.csh config.status: creating inst/scripts/RSXML.bsh ** libs using C compiler: ‘gcc (GCC) 15.2.1 20260123 (Red Hat 15.2.1-7)’ make[2]: Entering directory '/tmp/Rtmp7CAajn/working_dir/RtmprVvTqA/R.INSTALL36eb7d509dc2a3/XML/src' gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DNO_CHECKED_ENTITY_FIELD=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 -DHAVE_R_CETYPE_T=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 -DNO_XML_MEMORY_SHOW_ROUTINE=1 -DUSE_R=1 -D_R_=1 -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1 -I. -DLIBXML2=1 -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c DocParse.c -o DocParse.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DNO_CHECKED_ENTITY_FIELD=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 -DHAVE_R_CETYPE_T=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 -DNO_XML_MEMORY_SHOW_ROUTINE=1 -DUSE_R=1 -D_R_=1 -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1 -I. -DLIBXML2=1 -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c EventParse.c -o EventParse.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DNO_CHECKED_ENTITY_FIELD=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 -DHAVE_R_CETYPE_T=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 -DNO_XML_MEMORY_SHOW_ROUTINE=1 -DUSE_R=1 -D_R_=1 -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1 -I. -DLIBXML2=1 -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c ExpatParse.c -o ExpatParse.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DNO_CHECKED_ENTITY_FIELD=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 -DHAVE_R_CETYPE_T=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 -DNO_XML_MEMORY_SHOW_ROUTINE=1 -DUSE_R=1 -D_R_=1 -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1 -I. -DLIBXML2=1 -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c HTMLParse.c -o HTMLParse.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DNO_CHECKED_ENTITY_FIELD=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 -DHAVE_R_CETYPE_T=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 -DNO_XML_MEMORY_SHOW_ROUTINE=1 -DUSE_R=1 -D_R_=1 -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1 -I. -DLIBXML2=1 -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c NodeGC.c -o NodeGC.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DNO_CHECKED_ENTITY_FIELD=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 -DHAVE_R_CETYPE_T=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 -DNO_XML_MEMORY_SHOW_ROUTINE=1 -DUSE_R=1 -D_R_=1 -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1 -I. -DLIBXML2=1 -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c RUtils.c -o RUtils.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DNO_CHECKED_ENTITY_FIELD=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 -DHAVE_R_CETYPE_T=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 -DNO_XML_MEMORY_SHOW_ROUTINE=1 -DUSE_R=1 -D_R_=1 -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1 -I. -DLIBXML2=1 -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c Rcatalog.c -o Rcatalog.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DNO_CHECKED_ENTITY_FIELD=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 -DHAVE_R_CETYPE_T=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 -DNO_XML_MEMORY_SHOW_ROUTINE=1 -DUSE_R=1 -D_R_=1 -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1 -I. -DLIBXML2=1 -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c Utils.c -o Utils.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DNO_CHECKED_ENTITY_FIELD=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 -DHAVE_R_CETYPE_T=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 -DNO_XML_MEMORY_SHOW_ROUTINE=1 -DUSE_R=1 -D_R_=1 -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1 -I. -DLIBXML2=1 -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c XMLEventParse.c -o XMLEventParse.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DNO_CHECKED_ENTITY_FIELD=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 -DHAVE_R_CETYPE_T=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 -DNO_XML_MEMORY_SHOW_ROUTINE=1 -DUSE_R=1 -D_R_=1 -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1 -I. -DLIBXML2=1 -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c XMLHashTree.c -o XMLHashTree.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DNO_CHECKED_ENTITY_FIELD=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 -DHAVE_R_CETYPE_T=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 -DNO_XML_MEMORY_SHOW_ROUTINE=1 -DUSE_R=1 -D_R_=1 -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1 -I. -DLIBXML2=1 -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c XMLTree.c -o XMLTree.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DNO_CHECKED_ENTITY_FIELD=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 -DHAVE_R_CETYPE_T=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 -DNO_XML_MEMORY_SHOW_ROUTINE=1 -DUSE_R=1 -D_R_=1 -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1 -I. -DLIBXML2=1 -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c fixNS.c -o fixNS.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DNO_CHECKED_ENTITY_FIELD=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 -DHAVE_R_CETYPE_T=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 -DNO_XML_MEMORY_SHOW_ROUTINE=1 -DUSE_R=1 -D_R_=1 -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1 -I. -DLIBXML2=1 -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c libxmlFeatures.c -o libxmlFeatures.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DNO_CHECKED_ENTITY_FIELD=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 -DHAVE_R_CETYPE_T=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 -DNO_XML_MEMORY_SHOW_ROUTINE=1 -DUSE_R=1 -D_R_=1 -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1 -I. -DLIBXML2=1 -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c schema.c -o schema.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DNO_CHECKED_ENTITY_FIELD=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 -DHAVE_R_CETYPE_T=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 -DNO_XML_MEMORY_SHOW_ROUTINE=1 -DUSE_R=1 -D_R_=1 -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1 -I. -DLIBXML2=1 -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c xmlsecurity.c -o xmlsecurity.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DNO_CHECKED_ENTITY_FIELD=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 -DHAVE_R_CETYPE_T=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 -DNO_XML_MEMORY_SHOW_ROUTINE=1 -DUSE_R=1 -D_R_=1 -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1 -I. -DLIBXML2=1 -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c xpath.c -o xpath.o xpath.c: In function ‘R_addXMLInternalDocument_finalizer’: xpath.c:182:18: warning: ISO C forbids conversion of object pointer to function pointer type [-Wpedantic] 182 | action = (R_CFinalizer_t) R_ExternalPtrAddr(fun); | ^ xpath.c: In function ‘RS_XML_xpathEval’: xpath.c:255:22: warning: ISO C forbids assignment between function pointer and ‘void *’ [-Wpedantic] 255 | routine = R_ExternalPtrAddr(el); | ^ XMLTree.c: In function ‘RS_XML_printXMLNode’: XMLTree.c:1415:9: warning: unused variable ‘oldIndent’ [-Wunused-variable] 1415 | int oldIndent; | ^~~~~~~~~ RUtils.c: In function ‘RS_XML_getStructuredErrorHandler’: RUtils.c:279:46: warning: ISO C forbids conversion of function pointer to object pointer type [-Wpedantic] 279 | SET_VECTOR_ELT(ans, 1, R_MakeExternalPtr((void *)xmlStructuredError, Rf_install("xmlStructuredErrorFunc"), R_NilValue)); | ^ RUtils.c: In function ‘RS_XML_setStructuredErrorHandler’: RUtils.c:311:44: warning: ISO C forbids conversion of object pointer to function pointer type [-Wpedantic] 311 | handler = (sym == R_NilValue) ? NULL : (xmlStructuredErrorFunc) R_ExternalPtrAddr(sym); | ^ gcc -shared -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -L/usr/local/lib64 -o XML.so DocParse.o EventParse.o ExpatParse.o HTMLParse.o NodeGC.o RUtils.o Rcatalog.o Utils.o XMLEventParse.o XMLHashTree.o XMLTree.o fixNS.o libxmlFeatures.o schema.o xmlsecurity.o xpath.o -lxml2 -lz -llzma -lm -lz -lxml2 make[2]: Leaving directory '/tmp/Rtmp7CAajn/working_dir/RtmprVvTqA/R.INSTALL36eb7d509dc2a3/XML/src' make[2]: Entering directory '/tmp/Rtmp7CAajn/working_dir/RtmprVvTqA/R.INSTALL36eb7d509dc2a3/XML/src' make[2]: Leaving directory '/tmp/Rtmp7CAajn/working_dir/RtmprVvTqA/R.INSTALL36eb7d509dc2a3/XML/src' installing to /tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/00LOCK-XML/00new/XML/libs ** R ** inst ** byte-compile and prepare package for lazy loading Creating a generic function for ‘source’ from package ‘base’ in package ‘XML’ in method for ‘xmlAttrsToDataFrame’ with signature ‘"AsIs"’: no definition for class “AsIs” in method for ‘readKeyValueDB’ with signature ‘"AsIs"’: no definition for class “AsIs” in method for ‘readSolrDoc’ with signature ‘"AsIs"’: no definition for class “AsIs” ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (XML) * installing *source* package ‘Biostrings’ ... ** this is package ‘Biostrings’ version ‘2.79.4’ ** using staged installation ** libs using C compiler: ‘gcc (GCC) 15.2.1 20260123 (Red Hat 15.2.1-7)’ make[2]: Entering directory '/tmp/Rtmp7CAajn/working_dir/RtmpG7N5jl/R.INSTALL36ffe17875fbf2/Biostrings/src' gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c BAB_class.c -o BAB_class.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c BitMatrix.c -o BitMatrix.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c IRanges_stubs.c -o IRanges_stubs.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c MIndex_class.c -o MIndex_class.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c PreprocessedTB_class.c -o PreprocessedTB_class.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c R_init_Biostrings.c -o R_init_Biostrings.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c RoSeqs_utils.c -o RoSeqs_utils.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c S4Vectors_stubs.c -o S4Vectors_stubs.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c SparseList_utils.c -o SparseList_utils.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c XStringSetList_class.c -o XStringSetList_class.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c XStringSet_class.c -o XStringSet_class.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c XString_class.c -o XString_class.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c XVector_stubs.c -o XVector_stubs.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c find_palindromes.c -o find_palindromes.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c gtestsim.c -o gtestsim.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c inject_code.c -o inject_code.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c lcsuffix.c -o lcsuffix.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c letter_frequency.c -o letter_frequency.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c lowlevel_matching.c -o lowlevel_matching.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c match_PWM.c -o match_PWM.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c match_pattern.c -o match_pattern.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c match_pattern_boyermoore.c -o match_pattern_boyermoore.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c match_pattern_indels.c -o match_pattern_indels.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c match_pattern_shiftor.c -o match_pattern_shiftor.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c match_pdict.c -o match_pdict.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c match_pdict_ACtree2.c -o match_pdict_ACtree2.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c match_pdict_Twobit.c -o match_pdict_Twobit.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c match_pdict_utils.c -o match_pdict_utils.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c match_reporting.c -o match_reporting.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c read_fasta_files.c -o read_fasta_files.o match_pdict_utils.c: In function ‘match_ppheadtail0’: match_pdict_utils.c:653:56: warning: unused variable ‘ncol’ [-Wunused-variable] 653 | int nelt, min_safe_tb_end, max_safe_tb_end, j, ncol; | ^~~~ match_pdict_utils.c: In function ‘match_ppheadtail’: match_pdict_utils.c:713:13: warning: unused variable ‘nelt’ [-Wunused-variable] 713 | int nelt, nkey0, nkey1, nkey2, i, key; | ^~~~ match_pdict_utils.c: In function ‘_match_pdict_all_flanks’: match_pdict_utils.c:820:51: warning: unused variable ‘subtotal_NFC’ [-Wunused-variable] 820 | static unsigned long int total_NFC = 0UL, subtotal_NFC = 0UL; | ^~~~~~~~~~~~ match_pdict_utils.c:820:34: warning: unused variable ‘total_NFC’ [-Wunused-variable] 820 | static unsigned long int total_NFC = 0UL, subtotal_NFC = 0UL; | ^~~~~~~~~ match_pdict_utils.c:819:40: warning: unused variable ‘NFC’ [-Wunused-variable] 819 | unsigned long int ndup, nloci, NFC; // NFC = Number of Flank Comparisons | ^~~ match_pdict_utils.c:819:33: warning: unused variable ‘nloci’ [-Wunused-variable] 819 | unsigned long int ndup, nloci, NFC; // NFC = Number of Flank Comparisons | ^~~~~ match_pdict_utils.c:819:27: warning: unused variable ‘ndup’ [-Wunused-variable] 819 | unsigned long int ndup, nloci, NFC; // NFC = Number of Flank Comparisons | ^~~~ match_pdict_utils.c: At top level: match_pdict_utils.c:261:13: warning: ‘match_headtail_by_loc’ defined but not used [-Wunused-function] 261 | static void match_headtail_by_loc(const HeadTail *headtail, | ^~~~~~~~~~~~~~~~~~~~~ gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c read_fastq_files.c -o read_fastq_files.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c replaceAt.c -o replaceAt.o MIndex_class.c: In function ‘SparseMIndex_endIndex’: MIndex_class.c:184:27: warning: unused variable ‘poffsets_order’ [-Wunused-variable] 184 | IntAE *poffsets, *poffsets_order; | ^~~~~~~~~~~~~~ SparseList_utils.c: In function ‘_get_val_from_env’: SparseList_utils.c:42:34: error: implicit declaration of function ‘NAMED’ [-Wimplicit-function-declaration] 42 | if (ans != R_NilValue && NAMED(ans) == 0) | ^~~~~ SparseList_utils.c:43:17: error: implicit declaration of function ‘SET_NAMED’; did you mean ‘SET_NAMES’? [-Wimplicit-function-declaration] 43 | SET_NAMED(ans, 1); | ^~~~~~~~~ | SET_NAMES BitMatrix.c:299:13: warning: ‘BitMatrix_print’ defined but not used [-Wunused-function] 299 | static void BitMatrix_print(BitMatrix *bitmat) | ^~~~~~~~~~~~~~~ letter_frequency.c: In function ‘XStringSet_two_way_letter_frequency’: letter_frequency.c:957:48: warning: unused variable ‘x_pos’ [-Wunused-variable] 957 | int x_width, y_width, x_length, *ans_mat, i, x_pos; | ^~~~~ match_pattern_indels.c:7:13: warning: ‘test_match_pattern_indels’ defined but not used [-Wunused-function] 7 | static void test_match_pattern_indels(const char *p, const char *s, | ^~~~~~~~~~~~~~~~~~~~~~~~~ gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c replace_letter_at.c -o replace_letter_at.o match_pdict_ACtree2.c: In function ‘split_and_move_pointers’: match_pdict_ACtree2.c:1031:17: warning: variable ‘node0’ set but not used [-Wunused-but-set-variable] 1031 | ACnode *node0, *node1, *node2; | ^~~~~ match_pdict_ACtree2.c: In function ‘merge_pointers’: match_pdict_ACtree2.c:1076:17: warning: variable ‘node0’ set but not used [-Wunused-but-set-variable] 1076 | ACnode *node0, *node1, *node2; | ^~~~~ match_pdict_ACtree2.c: At top level: match_pdict_ACtree2.c:602:21: warning: ‘a_nice_max_nodeextbuf_nelt’ defined but not used [-Wunused-function] 602 | static unsigned int a_nice_max_nodeextbuf_nelt(int nnodes) | ^~~~~~~~~~~~~~~~~~~~~~~~~~ match_pdict_ACtree2.c:139:13: warning: ‘debug_node_counting_functions’ defined but not used [-Wunused-function] 139 | static void debug_node_counting_functions(int maxdepth) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c strutils.c -o strutils.o make[2]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: SparseList_utils.o] Error 1 gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c translate.c -o translate.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c unstrsplit_methods.c -o unstrsplit_methods.o XStringSet_class.c: In function ‘new_XStringSet_from_CHARACTER’: XStringSet_class.c:124:17: warning: ‘lkup_len’ may be used uninitialized [-Wmaybe-uninitialized] 124 | _copy_CHARSXP_to_Chars_holder(&ans_elt_holder, x_elt, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 125 | INTEGER(start)[i], lkup0, lkup_len); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ XStringSet_class.c:103:22: note: ‘lkup_len’ was declared here 103 | int ans_len, lkup_len, i; | ^~~~~~~~ gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c utils.c -o utils.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c xscat.c -o xscat.o In file included from /data/gannet/ripley/R/R-devel/include/Rdefines.h:41, from /tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include/S4Vectors_defines.h:18, from /tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include/IRanges_defines.h:18, from ../inst/include/Biostrings_defines.h:18, from Biostrings.h:1, from match_pdict_Twobit.c:10: In function ‘Twobit_asLIST’, inlined from ‘build_Twobit’ at match_pdict_Twobit.c:145:2: match_pdict_Twobit.c:75:27: warning: ‘twobit_sign2pos’ may be used uninitialized [-Wmaybe-uninitialized] 75 | PROTECT(ans_elt = new_XInteger_from_tag("XInteger", twobit_sign2pos)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /data/gannet/ripley/R/R-devel/include/Rinternals.h:366:36: note: in definition of macro ‘PROTECT’ 366 | #define PROTECT(s) Rf_protect(s) | ^ match_pdict_Twobit.c: In function ‘build_Twobit’: match_pdict_Twobit.c:110:19: note: ‘twobit_sign2pos’ was declared here 110 | SEXP ans, twobit_sign2pos; | ^~~~~~~~~~~~~~~ In function ‘vcount_PDict3Parts_XStringSet’, inlined from ‘vmatch_PDict3Parts_XStringSet’ at match_pdict.c:508:10: match_pdict.c:419:33: warning: ‘ans_col’ may be used uninitialized [-Wmaybe-uninitialized] 419 | ans_col += tb_length; | ~~~~~~~~^~~~~~~~~~~~ match_pdict.c: In function ‘vmatch_PDict3Parts_XStringSet’: match_pdict.c:392:65: note: ‘ans_col’ was declared here 392 | int tb_length, S_length, collapse0, i, j, match_count, *ans_col; | ^~~~~~~ In function ‘vcount_XStringSet_XStringSet’, inlined from ‘vmatch_XStringSet_XStringSet’ at match_pdict.c:542:10: match_pdict.c:470:41: warning: ‘ans_elt’ may be used uninitialized [-Wmaybe-uninitialized] 470 | ans_elt += P_length; | ~~~~~~~~^~~~~~~~~~~ match_pdict.c: In function ‘vmatch_XStringSet_XStringSet’: match_pdict.c:441:64: note: ‘ans_elt’ was declared here 441 | int P_length, S_length, collapse0, i, j, match_count, *ans_elt; | ^~~~~~~ read_fastq_files.c: In function ‘parse_FASTQ_file’: read_fastq_files.c:408:28: warning: ‘dont_load’ may be used uninitialized [-Wmaybe-uninitialized] 408 | if (dont_load || loader->new_qualid_hook == NULL) | ^ read_fastq_files.c:311:26: note: ‘dont_load’ was declared here 311 | lineinrecno, dont_load; | ^~~~~~~~~ In file included from /data/gannet/ripley/R/R-devel/include/Rdefines.h:41, from /tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include/S4Vectors_defines.h:18, from /tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include/IRanges_defines.h:18, from ../inst/include/Biostrings_defines.h:18, from Biostrings.h:1, from xscat.c:1: xscat.c: In function ‘XString_xscat’: /data/gannet/ripley/R/R-devel/include/Rdefines.h:91:33: warning: ‘ans_length’ may be used uninitialized [-Wmaybe-uninitialized] 91 | #define NEW_RAW(n) Rf_allocVector(RAWSXP,n) | ^~~~~~~~~~~~~~~~~~~~~~~~ /data/gannet/ripley/R/R-devel/include/Rinternals.h:366:36: note: in definition of macro ‘PROTECT’ 366 | #define PROTECT(s) Rf_protect(s) | ^ xscat.c:38:27: note: in expansion of macro ‘NEW_RAW’ 38 | PROTECT(ans_tag = NEW_RAW(ans_length)); | ^~~~~~~ xscat.c:18:20: note: ‘ans_length’ was declared here 18 | int nargs, ans_length, tag_offset, j; | ^~~~~~~~~~ xscat.c:52:23: warning: ‘ans_classname’ may be used uninitialized [-Wmaybe-uninitialized] 52 | PROTECT(ans = new_XRaw_from_tag(ans_classname, ans_tag)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /data/gannet/ripley/R/R-devel/include/Rinternals.h:366:36: note: in definition of macro ‘PROTECT’ 366 | #define PROTECT(s) Rf_protect(s) | ^ xscat.c:20:21: note: ‘ans_classname’ was declared here 20 | const char *ans_classname; | ^~~~~~~~~~~~~ xscat.c: In function ‘XStringSet_xscat’: /data/gannet/ripley/R/R-devel/include/Rdefines.h:85:33: warning: ‘ans_length’ may be used uninitialized [-Wmaybe-uninitialized] 85 | #define NEW_INTEGER(n) Rf_allocVector(INTSXP,n) | ^~~~~~~~~~~~~~~~~~~~~~~~ /data/gannet/ripley/R/R-devel/include/Rinternals.h:366:36: note: in definition of macro ‘PROTECT’ 366 | #define PROTECT(s) Rf_protect(s) | ^ xscat.c:91:29: note: in expansion of macro ‘NEW_INTEGER’ 91 | PROTECT(ans_width = NEW_INTEGER(ans_length)); | ^~~~~~~~~~~ xscat.c:66:39: note: ‘ans_length’ was declared here 66 | int nargs, *arg_lengths, *ii, ans_length, i, j, *width; | ^~~~~~~~~~ xscat.c:108:23: warning: ‘ans_element_type’ may be used uninitialized [-Wmaybe-uninitialized] 108 | PROTECT(ans = _alloc_XStringSet(ans_element_type, ans_width)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /data/gannet/ripley/R/R-devel/include/Rinternals.h:366:36: note: in definition of macro ‘PROTECT’ 366 | #define PROTECT(s) Rf_protect(s) | ^ xscat.c:68:21: note: ‘ans_element_type’ was declared here 68 | const char *ans_element_type; | ^~~~~~~~~~~~~~~~ utils.c: In function ‘_get_twobit_signature’: utils.c:157:16: warning: ‘twobit_sign’ may be used uninitialized [-Wmaybe-uninitialized] 157 | return twobit_sign; | ^~~~~~~~~~~ utils.c:150:16: note: ‘twobit_sign’ was declared here 150 | int i, twobit_sign; | ^~~~~~~~~~~ utils.c: In function ‘_get_twobit_signature_at’: utils.c:174:16: warning: ‘twobit_sign’ may be used uninitialized [-Wmaybe-uninitialized] 174 | return twobit_sign; | ^~~~~~~~~~~ utils.c:164:19: note: ‘twobit_sign’ was declared here 164 | int i, j, twobit_sign; | ^~~~~~~~~~~ make[2]: Target 'all' not remade because of errors. make[2]: Leaving directory '/tmp/Rtmp7CAajn/working_dir/RtmpG7N5jl/R.INSTALL36ffe17875fbf2/Biostrings/src' ERROR: compilation failed for package ‘Biostrings’ * removing ‘/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/Biostrings’ * installing *source* package ‘BiocIO’ ... ** this is package ‘BiocIO’ version ‘1.21.0’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (BiocIO) ERROR: dependency ‘SparseArray’ is not available for package ‘DelayedArray’ Perhaps try a variation of: install.packages('SparseArray') * removing ‘/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/DelayedArray’ ERROR: dependency ‘Biostrings’ is not available for package ‘cigarillo’ Perhaps try a variation of: install.packages('Biostrings') * removing ‘/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/cigarillo’ ERROR: dependency ‘Biostrings’ is not available for package ‘Rsamtools’ Perhaps try a variation of: install.packages('Biostrings') * removing ‘/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/Rsamtools’ * installing *source* package ‘restfulr’ ... ** this is package ‘restfulr’ version ‘0.0.16’ ** package ‘restfulr’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc (GCC) 15.2.1 20260123 (Red Hat 15.2.1-7)’ make[2]: Entering directory '/tmp/Rtmp7CAajn/working_dir/RtmpG0ygDc/R.INSTALL370a5a1120b9f5/restfulr/src' gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c init.c -o init.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c raggedListToDF.c -o raggedListToDF.o gcc -shared -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -L/usr/local/lib64 -o restfulr.so init.o raggedListToDF.o make[2]: Leaving directory '/tmp/Rtmp7CAajn/working_dir/RtmpG0ygDc/R.INSTALL370a5a1120b9f5/restfulr/src' make[2]: Entering directory '/tmp/Rtmp7CAajn/working_dir/RtmpG0ygDc/R.INSTALL370a5a1120b9f5/restfulr/src' make[2]: Leaving directory '/tmp/Rtmp7CAajn/working_dir/RtmpG0ygDc/R.INSTALL370a5a1120b9f5/restfulr/src' installing to /tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/00LOCK-restfulr/00new/restfulr/libs ** R ** inst ** byte-compile and prepare package for lazy loading Creating a new generic function for ‘assign’ in package ‘restfulr’ ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (restfulr) ERROR: dependency ‘DelayedArray’ is not available for package ‘SummarizedExperiment’ Perhaps try a variation of: install.packages('DelayedArray') * removing ‘/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/SummarizedExperiment’ ERROR: dependencies ‘SummarizedExperiment’, ‘Biostrings’, ‘Rsamtools’, ‘cigarillo’ are not available for package ‘GenomicAlignments’ Perhaps try a variation of: install.packages(c('SummarizedExperiment', 'Biostrings', 'Rsamtools', 'cigarillo')) * removing ‘/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/GenomicAlignments’ ERROR: dependencies ‘Biostrings’, ‘Rsamtools’, ‘GenomicAlignments’ are not available for package ‘rtracklayer’ Perhaps try a variation of: install.packages(c('Biostrings', 'Rsamtools', 'GenomicAlignments')) * removing ‘/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/rtracklayer’ The downloaded source packages are in '/tmp/Rtmp7CAajn/working_dir/RtmpjyO0Wr/downloaded_packages' 'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package = "BiocManager")' for details. Replacement repositories: CRAN: file:///data/gannet/ripley/R Bioconductor version 3.23 (BiocManager 1.30.27), R Under development (unstable) (2026-03-03 r89531) Installing package(s) 'Rsubread' trying URL 'https://bioconductor.org/packages/3.23/bioc/src/contrib/Rsubread_2.25.1.tar.gz' Content type 'application/x-gzip' length 13600088 bytes (13.0 MB) ================================================== downloaded 13.0 MB * installing *source* package ‘Rsubread’ ... ** this is package ‘Rsubread’ version ‘2.25.1’ ** using staged installation @@@@@ The operating system is Linux. ** libs using C compiler: ‘gcc (GCC) 15.2.1 20260123 (Red Hat 15.2.1-7)’ make[2]: Entering directory '/tmp/Rtmp7CAajn/working_dir/RtmpMVIi7w/R.INSTALL3712d43eaab2d5/Rsubread/src' gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.1\"" -g3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c HelperFunctions.c -o HelperFunctions.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.1\"" -g3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c LRMbase-index.c -o LRMbase-index.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.1\"" -g3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c LRMchro-event.c -o LRMchro-event.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.1\"" -g3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c LRMfile-io.c -o LRMfile-io.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.1\"" -g3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c LRMhashtable.c -o LRMhashtable.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.1\"" -g3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c LRMhelper.c -o LRMhelper.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.1\"" -g3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c LRMseek-zlib.c -o LRMseek-zlib.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.1\"" -g3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c LRMsorted-hashtable.c -o LRMsorted-hashtable.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.1\"" -g3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c R_wrapper.c -o R_wrapper.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.1\"" -g3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c RsimReads.c -o RsimReads.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.1\"" -g3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c SNPCalling.c -o SNPCalling.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.1\"" -g3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c aligner.c -o aligner.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.1\"" -g3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c atgcContent.c -o atgcContent.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.1\"" -g3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c build-sam-index.c -o build-sam-index.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.1\"" -g3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c cell-counts.c -o cell-counts.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.1\"" -g3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c core-bigtable.c -o core-bigtable.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.1\"" -g3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c core-indel.c -o core-indel.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.1\"" -g3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c core-interface-aligner.c -o core-interface-aligner.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.1\"" -g3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c core-interface-subjunc.c -o core-interface-subjunc.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.1\"" -g3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c core-junction.c -o core-junction.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.1\"" -g3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c core.c -o core.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.1\"" -g3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c detection-calls.c -o detection-calls.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.1\"" -g3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c detectionCall.c -o detectionCall.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.1\"" -g3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c detectionCallAnnotation.c -o detectionCallAnnotation.o aligner.c:2: warning: ISO C forbids an empty translation unit [-Wpedantic] gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.1\"" -g3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c exon-algorithms.c -o exon-algorithms.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.1\"" -g3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c exon-align-indel.c -o exon-align-indel.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.1\"" -g3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c exon-align.c -o exon-align.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.1\"" -g3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c flattenAnnotations.c -o flattenAnnotations.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.1\"" -g3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c fullscan.c -o fullscan.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.1\"" -g3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c fusion-align.c -o fusion-align.o exon-algorithms.c:2: warning: ISO C forbids an empty translation unit [-Wpedantic] gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.1\"" -g3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c gen_rand_reads.c -o gen_rand_reads.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.1\"" -g3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c gene-algorithms.c -o gene-algorithms.o build-sam-index.c:2: warning: ISO C forbids an empty translation unit [-Wpedantic] exon-align-indel.c:2: warning: ISO C forbids an empty translation unit [-Wpedantic] fusion-align.c:2: warning: ISO C forbids an empty translation unit [-Wpedantic] exon-align.c:2: warning: ISO C forbids an empty translation unit [-Wpedantic] gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.1\"" -g3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c gene-value-index.c -o gene-value-index.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.1\"" -g3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c hashtable.c -o hashtable.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.1\"" -g3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c index-builder.c -o index-builder.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.1\"" -g3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c input-blc.c -o input-blc.o SNPCalling.c: In function ‘put_hash_to_pile’: SNPCalling.c:229:57: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 229 | int base_N_qual = cursor->value - NULL; | ^ SNPCalling.c:230:51: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 230 | int POI_pos = cursor->key - NULL - 100; | ^ SNPCalling.c: In function ‘read_tmp_block’: SNPCalling.c:383:100: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 383 | unsigned int original_value = HashTableGet(merge_table,NULL+POI_pos)-NULL; | ^ SNPCalling.c:383:109: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 383 | unsigned int original_value = HashTableGet(merge_table,NULL+POI_pos)-NULL; | ^ SNPCalling.c:388:79: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 388 | HashTablePut(merge_table, NULL+POI_pos, NULL+base_N_qual); | ^ SNPCalling.c:388:93: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 388 | HashTablePut(merge_table, NULL+POI_pos, NULL+base_N_qual); | ^ SNPCalling.c:403:87: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 403 | HashTablePut(merge_table, NULL+POI_pos, NULL+base_N_qual); | ^ SNPCalling.c:403:101: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 403 | HashTablePut(merge_table, NULL+POI_pos, NULL+base_N_qual); | ^ SNPCalling.c: In function ‘process_snp_votes’: SNPCalling.c:939:109: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 939 | long long int indel_no = HashTableGet(parameters -> cigar_event_table, event_token) - NULL; | ^ SNPCalling.c:943:114: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 943 | long long int tmpv = HashTableGet(parameters -> cigar_event_table, event_token2) - NULL; | ^ RsimReads.c: In function ‘Rgen_one_read_here’: RsimReads.c:71:66: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 71 | int trans_len = HashTableGet(grc->transcript_lengths, seq_name)-NULL-1; | ^ RsimReads.c: In function ‘Rgrc_put_new_trans’: RsimReads.c:114:65: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 114 | HashTablePut( grc->transcript_lengths, strdup(seq_name) , NULL+lbuf_len +1); | ^ RsimReads.c:114:75: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 114 | HashTablePut( grc->transcript_lengths, strdup(seq_name) , NULL+lbuf_len +1); | ^ RsimReads.c: In function ‘init_grc_by_file’: RsimReads.c:144:92: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 144 | HashTablePut(grc -> expression_levels, strdup(input_order_transcript_names[xk1]), NULL +1); | ^ RsimReads.c:155:125: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 155 | int ov = HashTableGet( grc -> expression_levels, input_order_transcript_names[input_order_transcript_per_read[xk1]-1] ) -NULL; | ^ RsimReads.c:158:125: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 158 | HashTablePutReplace(grc -> expression_levels, input_order_transcript_names[input_order_transcript_per_read[xk1]-1], NULL+ov, 0); | ^ detection-calls.c: In function ‘DTCload_fasta’: detection-calls.c:95:97: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 95 | HashTablePut(context -> chro_length_table, curr_chro_mem , NULL + base_current_chro_len); | ^ RsimReads.c:183:70: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 183 | long seq_exp = HashTableGet(grc->expression_levels, seq_name)-NULL; | ^ RsimReads.c:185:63: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 185 | if(seq_exp>1)HashTablePut(seq_duplicate_tab, md5mem, 1+NULL); | ^ detection-calls.c:136:81: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 136 | HashTablePut(context -> chro_length_table, curr_chro_mem , NULL + base_current_chro_len); | ^ RsimReads.c:241:66: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 241 | long seq_exp = HashTableGet(grc->expression_levels, seq_name)-NULL; | ^ detection-calls.c: In function ‘DTCprint_lentab_items’: detection-calls.c:160:68: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 160 | SUBREADprintf("%s => %ld\n", (char*)key, (long)(hashed_obj - NULL)); | ^ detection-calls.c: In function ‘DTCtotal_GC_bases’: detection-calls.c:168:82: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 168 | unsigned int chro_len = HashTableGet(context -> chro_length_table, chro) - NULL; | ^ detection-calls.c:175:76: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 175 | chro_len = HashTableGet(context -> chro_length_table, tna) - NULL; | ^ detection-calls.c:182:76: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 182 | chro_len = HashTableGet(context -> chro_length_table, tna) - NULL; | ^ detection-calls.c: In function ‘DTCparse_GTF_and_Genome’: detection-calls.c:413:148: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 413 | DTCanno_fill_gap(context, current_chro_name_in_anno, top_end + 1, HashTableGet(context -> chro_length_table, current_chro) - NULL - 1); | ^ LRMhashtable.c: In function ‘LRMpointerHashFunction’: LRMhashtable.c:737:34: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 737 | return ((srUInt_64)( pointer - NULL )) ; | ^ LRMchro-event.c: In function ‘LRMevents_build_entries’: detection-calls.c: In function ‘DTCwrite_annotations’: LRMchro-event.c:87:97: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 87 | int * entries_list = LRMHashTableGet(context -> events_realignment, NULL+sidepos); | ^ detection-calls.c:155:9: warning: dangling pointer ‘gc_2int’ to an unnamed temporary may be used [-Wdangling-pointer=] 155 | DTCadd_annotation(context, gene_name, chro_name, start, end, is_negative_strand, gc_2int[0], gc_2int[1], 0); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ LRMchro-event.c:97:85: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 97 | LRMHashTablePut(context -> events_realignment , NULL+sidepos, entries_list); | ^ detection-calls.c:154:48: note: unnamed temporary defined here 154 | if(!gc_2int) gc_2int = (unsigned int[]){0,0,0}; | ^ LRMchro-event.c:120:84: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 120 | LRMHashTablePut(context -> events_realignment, NULL+sidepos, entries_list); | ^ detection-calls.c:155:109: warning: dangling pointer ‘gc_2int’ to an unnamed temporary may be used [-Wdangling-pointer=] 155 | DTCadd_annotation(context, gene_name, chro_name, start, end, is_negative_strand, gc_2int[0], gc_2int[1], 0); | ^ detection-calls.c:154:48: note: unnamed temporary defined here 154 | if(!gc_2int) gc_2int = (unsigned int[]){0,0,0}; | ^ In file included from core-indel.c:34: core-junction.h:111:9: warning: struct has no members [-Wpedantic] 111 | typedef struct{ | ^~~~~~ LRMchro-event.c: In function ‘LRMevents_search’: LRMchro-event.c:213:80: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 213 | int * event_here = LRMHashTableGet(context -> events_realignment, NULL + testing_pos); | ^ R_wrapper.c: In function ‘R_try_cell_barcode_wrapper’: R_wrapper.c:119:34: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 119 | int rv = (void*)c_argv[7]-NULL; | ^ R_wrapper.c:120:44: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 120 | int tested_reads = (void*)c_argv[8]-NULL; | ^ R_wrapper.c:121:49: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 121 | int sample_good_reads = (void*)c_argv[9]-NULL; | ^ R_wrapper.c:122:48: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 122 | int cell_good_reads = (void*)c_argv[10]-NULL; | ^ core-indel.c: In function ‘anti_support_thread_run’: core-indel.c:223:103: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 223 | long long cur_count = HashTableGet(atcont -> result_tab , NULL+small_side_ordered_event_ids[x1]+1 ) - NULL; | ^ core-indel.c:223:136: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 223 | long long cur_count = HashTableGet(atcont -> result_tab , NULL+small_side_ordered_event_ids[x1]+1 ) - NULL; | ^ core-indel.c:223:141: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 223 | long long cur_count = HashTableGet(atcont -> result_tab , NULL+small_side_ordered_event_ids[x1]+1 ) - NULL; | ^ core-indel.c:225:82: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 225 | HashTablePut( atcont -> result_tab , NULL+small_side_ordered_event_ids[x1]+1 , NULL+cur_count ); | ^ core-indel.c:225:115: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 225 | HashTablePut( atcont -> result_tab , NULL+small_side_ordered_event_ids[x1]+1 , NULL+cur_count ); | ^ core-indel.c:225:125: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 225 | HashTablePut( atcont -> result_tab , NULL+small_side_ordered_event_ids[x1]+1 , NULL+cur_count ); | ^ core-indel.c:247:111: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 247 | long long cur_count = HashTableGet(atcont -> result_tab , NULL+large_side_ordered_event_ids[x1]+1 ) - NULL; | ^ core-indel.c:247:144: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 247 | long long cur_count = HashTableGet(atcont -> result_tab , NULL+large_side_ordered_event_ids[x1]+1 ) - NULL; | ^ core-indel.c:247:149: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 247 | long long cur_count = HashTableGet(atcont -> result_tab , NULL+large_side_ordered_event_ids[x1]+1 ) - NULL; | ^ core-indel.c:249:90: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 249 | HashTablePut( atcont -> result_tab , NULL+large_side_ordered_event_ids[x1]+1 , NULL+cur_count ); | ^ core-indel.c:249:123: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 249 | HashTablePut( atcont -> result_tab , NULL+large_side_ordered_event_ids[x1]+1 , NULL+cur_count ); | ^ core-indel.c:249:133: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 249 | HashTablePut( atcont -> result_tab , NULL+large_side_ordered_event_ids[x1]+1 , NULL+cur_count ); | ^ core-indel.c: In function ‘anti_support_add_count’: core-indel.c:263:21: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 263 | int eno = ky-NULL-1; | ^ core-indel.c:265:51: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 265 | event_body -> anti_supporting_reads+= (va - NULL); | ^ In file included from core.c:55: core-junction.h:111:9: warning: struct has no members [-Wpedantic] 111 | typedef struct{ | ^~~~~~ gene-value-index.c: In function ‘is_offset_in_chro’: gene-value-index.c:85:33: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 85 | if( pos < chros -> padding || pos >= ( chros->read_offsets[n] - chros->read_offsets[n-1] - chros -> padding )) | ^~ In file included from gene-value-index.h:24, from gene-value-index.c:25: subread.h:153:24: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 153 | #define SUBREADprintf msgqu_printf | ^~~~~~~~~~~~ gene-value-index.c:87:41: note: in expansion of macro ‘SUBREADprintf’ 87 | SUBREADprintf("INCHRO:%d ; POS:%d\n", ret, pos); | ^~~~~~~~~~~~~ hashtable.c: In function ‘ArrayListToLookupTable_Int’: hashtable.c:43:91: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 43 | for(x1 = 0; x1 < arr->numOfElements; x1++) HashTablePut(ret, ArrayListGet(arr, x1)+1, NULL+x1+1); | ^ hashtable.c:43:99: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 43 | for(x1 = 0; x1 < arr->numOfElements; x1++) HashTablePut(ret, ArrayListGet(arr, x1)+1, NULL+x1+1); | ^ hashtable.c:43:102: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 43 | for(x1 = 0; x1 < arr->numOfElements; x1++) HashTablePut(ret, ArrayListGet(arr, x1)+1, NULL+x1+1); | ^ core-indel.c: In function ‘remove_neighbour’: core-indel.c:579:76: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 579 | unsigned int * res = HashTableGet(event_table, NULL+pos); | ^ core-indel.c:590:74: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 590 | HashTableRemove(event_table, NULL+pos); | ^ core-indel.c: In function ‘localPointerCmp_forEventEntry’: core-indel.c:609:50: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 609 | unsigned int v1 = (unsigned int)(pointer1-NULL); | ^ core-indel.c:610:50: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 610 | unsigned int v2 = (unsigned int)(pointer2-NULL); | ^ core-indel.c: In function ‘localPointerHashFunction_forEventEntry’: core-indel.c:616:34: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 616 | unsigned int v = (pointer-NULL); | ^ core-indel.c: In function ‘init_indel_tables’: core-indel.c:672:84: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 672 | indel_context -> local_reassembly_pileup_files -> appendix1 = NULL + max_open_file * 2/ 3; | ^ hashtable.c: In function ‘ArrayListSort_compare’: hashtable.c:169:75: warning: ISO C forbids initialization between function pointer and ‘void *’ [-Wpedantic] 169 | int (*comp_elems)(void * L_elem, void * R_elem, ArrayList * me) = sortdata[1]; | ^~~~~~~~ hashtable.c: In function ‘ArrayListSort_merge’: hashtable.c:188:75: warning: ISO C forbids initialization between function pointer and ‘void *’ [-Wpedantic] 188 | int (*comp_elems)(void * L_elem, void * R_elem, ArrayList * me) = sortdata[1]; | ^~~~~~~~ hashtable.c: In function ‘ArrayListSort’: hashtable.c:214:21: warning: ISO C forbids assignment between function pointer and ‘void *’ [-Wpedantic] 214 | sortdata[1] = compare_L_minus_R?compare_L_minus_R:ArrayListSort_comp_pntr; | ^ hashtable.c: In function ‘ArrayListLLUComparison’: hashtable.c:227:32: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 227 | srUInt_64 lint = L_elem-NULL; | ^ hashtable.c:228:32: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 228 | srUInt_64 rint = R_elem-NULL; | ^ hashtable.c: In function ‘ArrayListFindNextDent’: hashtable.c:236:35: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 236 | if( list -> elementList[h]- NULL <= value_less_than_dent )return -1l; | ^ hashtable.c:239:55: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 239 | srUInt_64 mv = list -> elementList[m] - NULL; | ^ hashtable.c:247:46: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 247 | for(; m>=0 && list -> elementList[m] - NULL >= value_less_than_dent; m--); | ^ hashtable.c:250:44: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 250 | if( list -> elementList[m] - NULL > value_less_than_dent )return m; | ^ hashtable.c: In function ‘HashTableInc’: hashtable.c:321:36: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 321 | HashTablePut(tab, key, oldv+1); | ^ hashtable.c:322:21: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 322 | return oldv - NULL+1; | ^ core-indel.c: In function ‘sort_junction_entry_table’: core-indel.c:920:87: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 920 | HashTablePut(indel_context -> event_entry_table, NULL + last_scannping_pos, id_list); | ^ HelperFunctions.c: In function ‘get_contig_fasta’: HelperFunctions.c:236:74: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 236 | unsigned int this_size = HashTableGet( tab -> size_table, chro ) - NULL; | ^ HelperFunctions.c: In function ‘read_contig_fasta’: HelperFunctions.c:310:89: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 310 | HashTablePut(tab -> size_table , mem_chro, NULL + inner_cursor); | ^ hashtable.c: In function ‘pointerHashFunction’: hashtable.c:987:36: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 987 | return (srUInt_64)(pointer - NULL); | ^ hashtable.c: In function ‘HashTableSortedIndexes’: hashtable.c:1089:21: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1089 | appx[1]=NULL+larger_value_first; | ^ In file included from core-junction.c:32: core-junction.h:111:9: warning: struct has no members [-Wpedantic] 111 | typedef struct{ | ^~~~~~ core.c: In function ‘write_single_fragment’: core.c:1909:111: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1909 | bktable_append(&global_context -> funky_table_BC, rec1 -> chro, rec1 -> offset , NULL + (2*pair_number)); | ^ core.c:1910:111: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1910 | bktable_append(&global_context -> funky_table_BC, rec2 -> chro, rec2 -> offset , NULL + (2*pair_number+1)); | ^ core.c:1914:111: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1914 | bktable_append(&global_context -> funky_table_DE, rec1 -> chro, rec1 -> offset , NULL + (2*pair_number + (rec1 -> offset > rec2 -> offset ? 1:0))); | ^ core.c:1915:111: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1915 | bktable_append(&global_context -> funky_table_DE, rec2 -> chro, rec2 -> offset , NULL + (2*pair_number + (rec1 -> offset < rec2 -> offset ? 1:0))); | ^ core-indel.c: In function ‘do_juncs_add_feature’: core-indel.c:1240:105: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 1240 | int access_n = HashTableGet( global_context -> chromosome_table.read_name_to_index, chro_name ) - NULL; | ^ core-indel.c: In function ‘put_new_event’: core-indel.c:1397:72: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1397 | unsigned int * id_list = HashTableGet(event_table, NULL+sides[xk1]); | ^ core-indel.c:1403:56: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1403 | HashTablePut(event_table , NULL+sides[xk1] , id_list); | ^ core-indel.c: In function ‘search_event’: core-indel.c:1439:60: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1439 | unsigned int * res = HashTableGet(event_table, NULL+pos); | ^ In file included from cell-counts.c:20: core-junction.h:111:9: warning: struct has no members [-Wpedantic] 111 | typedef struct{ | ^~~~~~ input-blc.c: In function ‘iBLC_guess_scan’: input-blc.c:128:93: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 128 | ArrayListPush(tilelist, NULL+tmpi); | ^ input-blc.c:149:102: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 149 | scancon -> cbcl_tile_numbers[ii] = ArrayListGet(tilelist,ii) - NULL; | ^ cell-counts.c: In function ‘cellCounts_cell_barcode_tabel_destroy’: cell-counts.c:482:15: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 482 | if(((a-NULL) & 0xfffffffff0000000llu ) ==IMPOSSIBLE_MEMORY_SPACE )return; | ^ cell-counts.c: In function ‘cellCounts_make_barcode_HT_table’: cell-counts.c:504:91: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 504 | HashTablePut(cct_context -> cell_barcode_head_tail_table, strdup(bc), NULL+xx1+IMPOSSIBLE_MEMORY_SPACE); | ^ cell-counts.c:504:95: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 504 | HashTablePut(cct_context -> cell_barcode_head_tail_table, strdup(bc), NULL+xx1+IMPOSSIBLE_MEMORY_SPACE); | ^ cell-counts.c:518:59: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 518 | ArrayListPush(array_of_codes, NULL+xx1); | ^ LRMfile-io.c: In function ‘LRMgenerate_bam_record’: LRMfile-io.c:275:89: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 275 | int chro_number = LRMHashTableGet(context->sam_bam_chromosome_table, chro_name) - NULL; | ^ LRMfile-io.c: In function ‘LRMwrite_chunk_compress_bam_block’: LRMfile-io.c:349:22: warning: overflow in conversion from ‘int’ to ‘char’ changes value from ‘255’ to ‘-1’ [-Woverflow] 349 | bam_buf[9] = 0xff; // OS | ^~~~ index-builder.c: In function ‘save_none_informative’: index-builder.c:78:40: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 78 | unsigned int subread_int = key - NULL; | ^ index-builder.c:79:34: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 79 | int repeats = hashed_obj - NULL; | ^ input-blc.c: In function ‘iCache_continuous_read_lanes’: input-blc.c:508:102: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 508 | ArrayListPush(tfp -> list_mapped_qscore, NULL+tov); | ^ input-blc.c:520:117: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 520 | HashTablePut(tfp -> digit4_to_compressed_start_of_next, NULL+tile_4digit, NULL+seek_start); | ^ input-blc.c:520:135: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 520 | HashTablePut(tfp -> digit4_to_compressed_start_of_next, NULL+tile_4digit, NULL+seek_start); | ^ input-blc.c:521:109: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 521 | HashTablePut(tfp -> digit4_to_total_read_no_P1, NULL+tile_4digit, NULL+1+reads_in_tile); | ^ input-blc.c:521:127: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 521 | HashTablePut(tfp -> digit4_to_total_read_no_P1, NULL+tile_4digit, NULL+1+reads_in_tile); | ^ input-blc.c:521:129: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 521 | HashTablePut(tfp -> digit4_to_total_read_no_P1, NULL+tile_4digit, NULL+1+reads_in_tile); | ^ input-blc.c:537:115: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 537 | int this_tile_reads = HashTableGet(tfp -> digit4_to_total_read_no_P1, NULL+tile_4digit) - NULL -1; | ^ input-blc.c:537:129: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 537 | int this_tile_reads = HashTableGet(tfp -> digit4_to_total_read_no_P1, NULL+tile_4digit) - NULL -1; | ^ input-blc.c:538:132: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 538 | srInt_64 next_tile_start_off = HashTableGet(tfp -> digit4_to_compressed_start_of_next, NULL+tile_4digit) - NULL; | ^ input-blc.c:538:146: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 538 | srInt_64 next_tile_start_off = HashTableGet(tfp -> digit4_to_compressed_start_of_next, NULL+tile_4digit) - NULL; | ^ LRMfile-io.c: In function ‘LRMload_offsets’: LRMfile-io.c:437:84: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 437 | LRMHashTablePut(context->sam_bam_chromosome_table, chro_name, NULL + chromosome_no + 1); | ^ LRMfile-io.c:437:100: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 437 | LRMHashTablePut(context->sam_bam_chromosome_table, chro_name, NULL + chromosome_no + 1); | ^ input-blc.c:558:130: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 558 | nch = (nch & 3) | (4*(tfp -> list_mapped_qscore -> elementList[ nch >>2 ]-NULL)); | ^ input-blc.c:577:115: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 577 | np1 = HashTableGet(tfp -> digit4_to_compressed_start_of_next, NULL+new_4digit); | ^ input-blc.c:580:59: warning: unused variable ‘npos’ [-Wunused-variable] 580 | long long npos = lseek(tfp -> cbcl_bin_fd, next_tile_start_off , SEEK_SET); | ^~~~ LRMfile-io.c:440:81: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 440 | LRMHashTablePut(context->chromosome_size_table, chro_name, NULL + (this_offset - last_end + 16 - context->current_index_padding * 2)); | ^ LRMfile-io.c:441:70: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 441 | LRMArrayListPush(context->chromosome_size_list, NULL + this_offset); | ^ index-builder.c: In function ‘build_gene_index’: index-builder.c:349:79: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 349 | int is_no_info = HashTableGet(huge_table, NULL+1+int_key)-NULL; | ^ index-builder.c:349:81: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 349 | int is_no_info = HashTableGet(huge_table, NULL+1+int_key)-NULL; | ^ index-builder.c:349:90: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 349 | int is_no_info = HashTableGet(huge_table, NULL+1+int_key)-NULL; | ^ LRMfile-io.c: In function ‘LRMsambam_write_header’: LRMfile-io.c:477:104: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 477 | int chro_length = LRMHashTableGet(context -> chromosome_size_table, chro_name) - NULL; | ^ core-indel.c: In function ‘insert_pileup_read’: core-junction.c: In function ‘find_donor_receptor’: core-junction.c:2099:25: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2099 | if(0&& FIXLENstrcmp("V0112_0155:7:1101:12618:2466#ACTTGA", rname) == 0) | ^~ core-indel.c:2550:88: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2550 | unsigned int next_jump_array = HashTableGet(current_table ,NULL+next_key_prefix) - NULL; | ^ core-junction.c:2103:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2103 | if( (end_site_mismatches + start_site_mismatches) * 500 + insertion_in_between_i < best_testing_score ){ | ^~ core-indel.c:2550:106: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 2550 | unsigned int next_jump_array = HashTableGet(current_table ,NULL+next_key_prefix) - NULL; | ^ core-indel.c:2558:58: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2558 | HashTablePut(current_table, NULL + next_key_prefix , NULL + next_jump_array); | ^ core-indel.c:2558:83: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2558 | HashTablePut(current_table, NULL + next_key_prefix , NULL + next_jump_array); | ^ LRMfile-io.c:513:96: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 513 | int chro_length = LRMHashTableGet(context -> chromosome_size_table, chro_name) - NULL; | ^ core-indel.c: In function ‘finalise_db_graph’: core-indel.c:2587:66: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2587 | next_moves = HashTableGet(de_brujin_graph , NULL + current_key) - NULL; | ^ core-indel.c:2587:81: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 2587 | next_moves = HashTableGet(de_brujin_graph , NULL + current_key) - NULL; | ^ cell-counts.c: In function ‘sheet_convert_ss_to_arr’: cell-counts.c:919:39: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 919 | hashed_arr -> appendix1 = NULL+ cct_context -> sample_id_to_name -> numOfElements; // One-based | ^ cell-counts.c:928:36: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 928 | push_arr[0] = NULL + lane_sample_int; | ^ cell-counts.c:929:36: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 929 | push_arr[1] = NULL + cct_context -> sample_id_to_name -> numOfElements; | ^ cell-counts.c:931:36: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 931 | push_arr[3] = NULL + (sbc_lane_sample[1]!=NULL && strlen(sbc_lane_sample[1])>12); | ^ cell-counts.c:933:78: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 933 | HashTablePut(cct_context -> lineno1B_to_sampleno1B_tab , NULL+line_no_in_sheet, NULL + cct_context -> sample_id_to_name -> numOfElements); | ^ cell-counts.c:933:102: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 933 | HashTablePut(cct_context -> lineno1B_to_sampleno1B_tab , NULL+line_no_in_sheet, NULL + cct_context -> sample_id_to_name -> numOfElements); | ^ gen_rand_reads.c: In function ‘gen_a_read_from_one_transcript’: gen_rand_reads.c:206:87: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 206 | int actual_transcript_len = HashTableGet(grc->transcript_lengths, trans_name) - NULL; | ^ cell-counts.c: In function ‘cellCounts_sample_SamBam_writers_new_files’: cell-counts.c:1048:50: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1048 | HashTablePut(fp_tab, NULL+x1+1 , wtrptr); | ^ cell-counts.c:1048:53: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1048 | HashTablePut(fp_tab, NULL+x1+1 , wtrptr); | ^ cell-counts.c: In function ‘cellCounts_write_one_chroEvent’: cell-counts.c:1157:86: warning: ordered comparison of pointer with integer zero [-Wpedantic] 1157 | if(ce->event_type == chroEvent_t_TYPE_JUNCTION && ce -> step2_supported_reads>0){ | ^ input-blc.c: In function ‘input_BLC_parse_SampleSheet’: input-blc.c:1002:41: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1002 | entry[0] = NULL + lane_no; | ^ cell-counts.c:1165:56: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 1165 | int pos2 = pos1 + ( (void*) ce->length - NULL ) +1; | ^ input-blc.c:1004:41: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1004 | entry[2] = NULL + stat1_line; // the N-th line in the file , 1 based | ^ cell-counts.c: In function ‘cellCounts_write_junction_sumtable’: cell-counts.c:1174:16: warning: unused variable ‘params’ [-Wunused-variable] 1174 | void * params [5]; | ^~~~~~ cell-counts.c: In function ‘cellCounts_set_chroEvent_details’: cell-counts.c:1186:107: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1186 | chroEvent_t * old_or_new_env = HashTableGet( cct_context -> chroEvent_detail_table[sample_i], NULL+envkey); | ^ core-indel.c: In function ‘rectify_read_text’: core-indel.c:2814:106: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2814 | char * neighbour_read_text = HashTableGet(block_context->read_sequence_table,NULL+neighbour_read_key); | ^ cell-counts.c:1192:117: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 1192 | if( old_or_new_env -> n_events == 1 ) oldlen = (void *)( old_or_new_env -> length ) - NULL; | ^ cell-counts.c:1201:95: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 1201 | int old_length = (void *)( old_or_new_env -> length ) - NULL; | ^ LRMfile-io.c: In function ‘LRMlocate_gene_position’: LRMfile-io.c:611:112: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 611 | while(n+jump_ns < total_offsets && LRMArrayListGet(context->chromosome_size_list, n + jump_ns) - NULL <= linear) | ^ LRMfile-io.c:619:73: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 619 | if ( (LRMArrayListGet(context->chromosome_size_list, n) - NULL) > linear) | ^ LRMfile-io.c:622:94: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 622 | if(n>0)(*pos) -= (LRMArrayListGet(context->chromosome_size_list, n-1)-NULL); | ^ LRMfile-io.c: In function ‘LRMlocate_chro_length’: LRMfile-io.c:640:112: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 640 | while(n+jump_ns < total_offsets && LRMArrayListGet(context->chromosome_size_list, n + jump_ns) - NULL <= linear) | ^ LRMfile-io.c:648:73: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 648 | if ( (LRMArrayListGet(context->chromosome_size_list, n) - NULL) > linear) { | ^ gen_rand_reads.c: In function ‘calc_N_from_M’: gen_rand_reads.c:299:132: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 299 | unsigned long long space_end = ArrayListGet(grc->transcript_hitting_space, grc->transcript_hitting_space->numOfElements -1)-NULL; | ^ gen_rand_reads.c:303:92: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 303 | unsigned long long thisv = ArrayListGet(grc->transcript_hitting_space, ti) - NULL; | ^ input-blc.c: In function ‘iCache_write_supIdx_result’: gen_rand_reads.c: In function ‘convert_hitting_space_to_num_of_reads’: input-blc.c:1126:53: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 1126 | fprintf(ofp, "%s\t%d\n", (char*)ky, (int)(va-NULL)); | ^ gen_rand_reads.c:339:132: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 339 | unsigned long long space_end = ArrayListGet(grc->transcript_hitting_space, grc->transcript_hitting_space->numOfElements -1)-NULL; | ^ gen_rand_reads.c:349:87: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 349 | int seq_len = HashTableGet(grc-> transcript_lengths, seq_name)-NULL; | ^ gen_rand_reads.c:350:104: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 350 | unsigned long long thisv = ArrayListGet(grc->transcript_hitting_space, read_i) - NULL; | ^ input-blc.c: In function ‘iCache_copy_sample_table_2_list’: input-blc.c:1139:36: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1139 | push_arr[0] = NULL + lane_sample_int; | ^ input-blc.c:1140:36: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1140 | push_arr[1] = NULL + cbclist -> numOfElements+1; | ^ input-blc.c:1140:62: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1140 | push_arr[1] = NULL + cbclist -> numOfElements+1; | ^ gen_rand_reads.c:366:66: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 366 | ArrayListPush(rescure_hitting_space, NULL+to_rescure_read_top); | ^ gen_rand_reads.c:367:72: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 367 | ArrayListPush(num_of_frags_per_transcript, NULL+expected_reads); | ^ input-blc.c: In function ‘iCache_get_cell_no’: index-builder.c: In function ‘scan_gene_index’: input-blc.c:1171:49: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 1171 | srInt_64 xint = xrawarr - NULL; | ^ index-builder.c:678:69: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 678 | HashTablePut(huge_table,NULL+1+ current_bucket -> item_keys[j], NULL+current_bucket -> item_values [j]); | ^ index-builder.c:678:71: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 678 | HashTablePut(huge_table,NULL+1+ current_bucket -> item_keys[j], NULL+current_bucket -> item_values [j]); | ^ gen_rand_reads.c:382:122: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 382 | unsigned long long expected_reads = ArrayListGet(num_of_frags_per_transcript, this_transcript_no)-NULL; | ^ cell-counts.c:1226:55: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1226 | old_or_new_env -> length = (void*)NULL+(tlen); // "tlen" is the number before "N" in cigar. | ^ index-builder.c:678:109: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 678 | HashTablePut(huge_table,NULL+1+ current_bucket -> item_keys[j], NULL+current_bucket -> item_values [j]); | ^ input-blc.c:1182:77: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 1182 | int bcno = ArrayListGet(rawarr, xx2)-NULL; | ^ gen_rand_reads.c:384:92: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 384 | num_of_frags_per_transcript->elementList[this_transcript_no] = NULL+expected_reads; | ^ cell-counts.c:1229:83: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1229 | HashTablePut(cct_context -> chroEvent_detail_table[sample_i], NULL+envkey, old_or_new_env); | ^ input-blc.c:1185:80: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1185 | if(ArrayListGet(ret, xx3)==NULL+bcno){ | ^ input-blc.c:1191:74: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1191 | if(!found)ArrayListPush(ret, NULL+bcno); | ^ LRMfile-io.c:650:88: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 650 | (* end_pos) = LRMArrayListGet(context->chromosome_size_list, n)-NULL; | ^ cell-counts.c: In function ‘cellCounts_add_or_update_chroEvent_in_table’: cell-counts.c:1251:63: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1251 | LR_roots[0]=IVT_insert(LR_roots[0], l, l, NULL+r); | ^ cell-counts.c:1252:63: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1252 | LR_roots[1]=IVT_insert(LR_roots[1], r, r, NULL+l); | ^ cell-counts.c:1257:23: warning: variable ‘new_details’ set but not used [-Wunused-but-set-variable] 1257 | chroEvent_t * new_details = NULL; | ^~~~~~~~~~~ cell-counts.c: In function ‘cellCounts_junction_in_table’: cell-counts.c:1285:71: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1285 | for(x2=0; x2attr == NULL+r ){known=1;break; } | ^ core-indel.c: In function ‘search_window_once’: core-indel.c:2903:85: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2903 | char * start_read_txt = HashTableGet(block_context->read_sequence_table,NULL+starter_read_key); | ^ core-indel.c:2907:83: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2907 | int start_read_pos = HashTableGet(block_context->read_position_table, NULL+starter_read_key) - NULL ; | ^ core-indel.c:2907:102: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 2907 | int start_read_pos = HashTableGet(block_context->read_position_table, NULL+starter_read_key) - NULL ; | ^ core-indel.c:2976:106: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2976 | int next_read_pos = HashTableGet(block_context->read_position_table, NULL+test_next_read_key) - NULL; | ^ input-blc.c:1200:49: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 1200 | int tbcn = ArrayListGet(ret,xx1)-NULL; | ^ core-indel.c:2976:127: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 2976 | int next_read_pos = HashTableGet(block_context->read_position_table, NULL+test_next_read_key) - NULL; | ^ core-indel.c:2991:108: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2991 | char * next_read_txt = HashTableGet(block_context->read_sequence_table,NULL+test_next_read_key); | ^ input-blc.c: In function ‘iCache_delete_bcb_key’: input-blc.c:1218:15: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 1218 | if(((k-NULL) & 0xFFFFFFFFF0000000llu)!= IMPOSSIBLE_MEMORY_ADDRESS) ArrayListDestroy(k); | ^ core-indel.c:3034:127: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 3034 | +(unsigned int)(HashTableGet(block_context -> read_quality_table, NULL+test_next_read_key)-NULL)/10 - wrong_bases * 20000; | ^ core-indel.c:3034:147: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 3034 | +(unsigned int)(HashTableGet(block_context -> read_quality_table, NULL+test_next_read_key)-NULL)/10 - wrong_bases * 20000; | ^ input-blc.c: In function ‘do_R_try_cell_barcode_files’: input-blc.c:1248:21: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1248 | argv[7]=NULL+rv; | ^ input-blc.c:1249:21: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1249 | argv[8]=NULL+tested_reads; | ^ input-blc.c:1250:21: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1250 | argv[9]=NULL+valid_sample_index; | ^ input-blc.c:1251:22: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1251 | argv[10]=NULL+valid_cell_barcode; | ^ gen_rand_reads.c: In function ‘grc_gen’: gen_rand_reads.c:412:79: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 412 | int seq_len = HashTableGet(grc-> transcript_lengths, seq_name)-NULL; | ^ gen_rand_reads.c:413:102: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 413 | unsigned long long expected_reads = ArrayListGet(num_of_frags_per_transcript, read_i)-NULL; | ^ gen_rand_reads.c:423:71: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 423 | ArrayListPush(per_transcript_reads_hitting_space, NULL+total_read_top); | ^ gen_rand_reads.c: In function ‘grc_summary_fasta’: gen_rand_reads.c:531:85: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 531 | long dupval = HashTableGet(seq_duplicate_tab,md5mem)-NULL; | ^ gen_rand_reads.c:533:85: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 533 | HashTablePutReplace( seq_duplicate_tab, md5mem, NULL+dupval , 0); | ^ gen_rand_reads.c:540:77: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 540 | HashTablePut( seq_length_tab, seq_name, NULL+seq_len); | ^ cell-counts.c: In function ‘cellCounts_copy_txn_to_juncs’: cell-counts.c:1326:57: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 1326 | srInt_64 ve = ArrayListGet(my_exons, x1)-NULL; | ^ gen_rand_reads.c:562:72: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 562 | HashTablePut(name_duplicate_tab, seq_name, NULL+1); | ^ cell-counts.c:1311:28: warning: variable ‘last_start’ set but not used [-Wunused-but-set-variable] 1311 | int last_end = -1, last_start = -1; | ^~~~~~~~~~ cell-counts.c: In function ‘features_load_one_line’: cell-counts.c:1431:37: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1431 | ArrayListPush(txn_exons,NULL+((start-1)*1LLU<<32)+end-1); | ^ core-indel.c:3056:128: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 3056 | + (unsigned int)(HashTableGet(block_context -> read_quality_table, NULL+test_next_read_key)-NULL)/10 - wrong_bases * 20000; | ^ cell-counts.c:1431:58: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1431 | ArrayListPush(txn_exons,NULL+((start-1)*1LLU<<32)+end-1); | ^ cell-counts.c:1431:62: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1431 | ArrayListPush(txn_exons,NULL+((start-1)*1LLU<<32)+end-1); | ^ core-indel.c:3056:148: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 3056 | + (unsigned int)(HashTableGet(block_context -> read_quality_table, NULL+test_next_read_key)-NULL)/10 - wrong_bases * 20000; | ^ cell-counts.c:1434:101: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 1434 | int access_n = HashTableGet(cct_context -> chromosome_table.read_name_to_index, chro_name ) - NULL; | ^ core-indel.c:3089:140: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 3089 | char *prev_read_txt = HashTableGet(block_context->read_sequence_table,NULL+test_prev_read_key); | ^ core.c: In function ‘do_anno_bitmap_add_feature’: core.c:3927:99: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 3927 | HashTablePut(global_context -> annotation_chro_table, memstrcpy( chro_name ), NULL+1); | ^ core.c:3930:105: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 3930 | int access_n = HashTableGet( global_context -> chromosome_table.read_name_to_index, chro_name ) - NULL; | ^ core-indel.c:3179:92: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 3179 | char * next_read_txt = HashTableGet(block_context->read_sequence_table,NULL+test_next_read_key); | ^ input-blc.c: In function ‘cacheBCL_quality_test’: input-blc.c:1425:70: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1425 | HashTablePut(cell_barcode_table, strdup(bcbstr), NULL+IMPOSSIBLE_MEMORY_ADDRESS+xx1); | ^ input-blc.c:1425:96: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1425 | HashTablePut(cell_barcode_table, strdup(bcbstr), NULL+IMPOSSIBLE_MEMORY_ADDRESS+xx1); | ^ input-blc.c:1440:59: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1440 | ArrayListPush(array_of_codes, NULL+xx1); | ^ gen_rand_reads.c:581:69: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 581 | long dupval = HashTableGet(seq_duplicate_tab,md5mem)-NULL; | ^ gen_rand_reads.c:583:69: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 583 | HashTablePutReplace( seq_duplicate_tab, md5mem, NULL+dupval ,0); | ^ gen_rand_reads.c:592:61: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 592 | HashTablePut( seq_length_tab, seq_name, NULL+seq_len); | ^ gen_rand_reads.c:601:76: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 601 | long md5repeated = HashTableGet(seq_duplicate_tab, md5str) - NULL; | ^ gen_rand_reads.c:603:66: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 603 | long seqlen = HashTableGet(seq_length_tab,seqnam)-NULL; | ^ index-builder.c: In function ‘check_and_convert_FastA’: index-builder.c:905:90: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 905 | int is_exist = HashTableGet(rep_name_table , line_buf+1) - NULL; | ^ gen_rand_reads.c:605:51: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 605 | HashTablePut(reprs_tab,md5str,NULL+1); | ^ index-builder.c:915:74: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 915 | HashTablePut(rep_name_table, keymem, NULL+1); | ^ gen_rand_reads.c: In function ‘grc_put_new_trans’: gen_rand_reads.c:627:62: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 627 | HashTablePut(grc-> transcript_lengths, seq_name, NULL+ seq_len); | ^ gen_rand_reads.c:628:95: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 628 | unsigned long long this_seq_exp_10000 = HashTableGet(grc->expression_levels, seq_name)-NULL; | ^ gen_rand_reads.c:636:58: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 636 | ArrayListPush(grc->transcript_hitting_space, NULL+*linear_space_top); | ^ cell-counts.c: In function ‘cellCounts_register_junc_feature’: cell-counts.c:1517:30: warning: unused variable ‘sample_i’ [-Wunused-variable] 1517 | int xk1, edge_tab_i, sample_i; | ^~~~~~~~ cell-counts.c: In function ‘cellCounts_find_or_insert_gene_name’: cell-counts.c:1600:70: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 1600 | srInt_64 gene_number = HashTableGet(genetable, feature_name) - NULL; | ^ cell-counts.c:1605:59: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1605 | HashTablePut(genetable, feature_name, NULL+gene_number+1); | ^ cell-counts.c:1605:71: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1605 | HashTablePut(genetable, feature_name, NULL+gene_number+1); | ^ gen_rand_reads.c: In function ‘grc_load_env’: gen_rand_reads.c:696:71: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 696 | HashTablePut(grc->expression_levels, seqname_buf, NULL+seqexp_int+1); | ^ gen_rand_reads.c:696:82: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 696 | HashTablePut(grc->expression_levels, seqname_buf, NULL+seqexp_int+1); | ^ gen_rand_reads.c:771:94: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 771 | long seq_exp = HashTableGet(grc->expression_levels, seq_name)-NULL; | ^ gen_rand_reads.c:773:87: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 773 | if(seq_exp>1)HashTablePut(seq_duplicate_tab, md5mem, 1+NULL); | ^ gen_rand_reads.c:829:78: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 829 | long seq_exp = HashTableGet(grc->expression_levels, seq_name)-NULL; | ^ HelperFunctions.c: In function ‘IVT_createNode’: HelperFunctions.c:3398:35: warning: format ‘%p’ expects argument of type ‘void *’, but argument 3 has type ‘IVT_IntervalTreeNode *’ [-Wformat=] 3398 | if(0) fprintf(stderr,"MEMTEST %p ALLOC\n", node); | ~^ ~~~~ | | | | void * IVT_IntervalTreeNode * cell-counts.c: In function ‘cellCounts_load_annotations’: cell-counts.c:1908:128: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 1908 | chro_stub -> chro_number = HashTableGet(cct_context -> chromosome_table.read_name_to_index, seq_name ) - NULL -1; | ^ core.c: In function ‘test_PE_and_same_chro_align’: core.c:4816:16: warning: ISO C forbids ‘return’ with expression, in function returning void [-Wpedantic] 4816 | return test_PE_and_same_chro_cigars(global_context, res1 -> first_base_position, res2 -> first_base_position, is_exonic_regions, is_PE_distance, is_same_chromosome , read_len_1 , read_len_2, res1 -> cigar_string, res2 -> cigar_string, read_name, res_tlen); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ core.c:4815:6: note: declared here 4815 | void test_PE_and_same_chro_align(global_context_t * global_context , realignment_result_t * res1, realignment_result_t * res2, int * is_exonic_regions, int * is_PE_distance, int * is_same_chromosome, int read_len_1, int read_len_2, char * read_name, int *res_tlen){ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ HelperFunctions.c: In function ‘IVT_freeTree’: HelperFunctions.c:3532:35: warning: format ‘%p’ expects argument of type ‘void *’, but argument 3 has type ‘IVT_IntervalTreeNode *’ [-Wformat=] 3532 | if(0) fprintf(stderr,"MEMTEST %p FREE\n", root); | ~^ ~~~~ | | | | void * IVT_IntervalTreeNode * core-indel.c: In function ‘finalise_pileup_file’: core-indel.c:3981:72: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 3981 | HashTablePut(read_position_table, NULL + read_hashed_key, NULL+first_base_pos+1); | ^ core-indel.c:3981:95: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 3981 | HashTablePut(read_position_table, NULL + read_hashed_key, NULL+first_base_pos+1); | ^ core-indel.c:3981:110: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 3981 | HashTablePut(read_position_table, NULL + read_hashed_key, NULL+first_base_pos+1); | ^ cell-counts.c: In function ‘cellCounts_chroEvent_freebuff’: cell-counts.c:2021:90: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 2021 | int inslen = (de -> n_events>1)? de -> length[0] :((void*)(de -> length) - NULL); | ^ core-indel.c:3982:64: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 3982 | HashTablePut(read_sequence_table, NULL + read_hashed_key, sequence_for_hash); | ^ core-indel.c:3983:63: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 3983 | HashTablePut(read_quality_table, NULL + read_hashed_key, NULL + qual_of_this_read); | ^ core-indel.c:3983:87: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 3983 | HashTablePut(read_quality_table, NULL + read_hashed_key, NULL + qual_of_this_read); | ^ core-indel.c:4052:108: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 4052 | char * start_read_txt = HashTableGet(block_context.read_sequence_table,NULL+starter_read_key); | ^ cell-counts.c: In function ‘cellCounts_load_cluster_related_junctions_n_cells’: cell-counts.c:2089:101: warning: ISO C forbids conversion of function pointer to object pointer type [-Wpedantic] 2089 | HashTableSetDeallocationFunctions(cct_context -> cluster_spec_junction_table, NULL, (void *)(void *)HashTableDestroy); | ^ cell-counts.c:2089:93: warning: ISO C forbids passing argument 3 of ‘HashTableSetDeallocationFunctions’ between function pointer and ‘void *’ [-Wpedantic] 2089 | HashTableSetDeallocationFunctions(cct_context -> cluster_spec_junction_table, NULL, (void *)(void *)HashTableDestroy); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from subread.h:35, from cell-counts.c:13: hashtable.h:491:47: note: expected ‘void (*)(void *)’ but argument is of type ‘void *’ 491 | void (*valueDeallocator)(void *value)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cell-counts.c:2140:123: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2140 | HashTable * this_cluster_table = (HashTable*)HashTableGet(cct_context -> cluster_spec_junction_table, NULL+(sample_i*1LLU<<56)+ cluster_no); | ^ cell-counts.c:2140:143: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2140 | HashTable * this_cluster_table = (HashTable*)HashTableGet(cct_context -> cluster_spec_junction_table, NULL+(sample_i*1LLU<<56)+ cluster_no); | ^ cell-counts.c:2143:86: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2143 | HashTablePut(cct_context -> cluster_spec_junction_table, NULL+(sample_i*1LLU<<56)+ cluster_no , this_cluster_table); | ^ cell-counts.c:2143:106: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2143 | HashTablePut(cct_context -> cluster_spec_junction_table, NULL+(sample_i*1LLU<<56)+ cluster_no , this_cluster_table); | ^ cell-counts.c:2145:54: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2145 | HashTablePut(this_cluster_table, NULL+( absstart_pos*1LLU<<32 ) + absend_pos , NULL+1); | ^ cell-counts.c:2145:81: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2145 | HashTablePut(this_cluster_table, NULL+( absstart_pos*1LLU<<32 ) + absend_pos , NULL+1); | ^ cell-counts.c:2145:100: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2145 | HashTablePut(this_cluster_table, NULL+( absstart_pos*1LLU<<32 ) + absend_pos , NULL+1); | ^ core-indel.c: In function ‘destroy_pileup_table’: core-indel.c:4316:38: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 4316 | if(fp != NULL+1) | ^ cell-counts.c:2161:99: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 2161 | int cellbc_no = HashTableGet(cct_context -> cell_barcode_head_tail_table, cellbc) -NULL - IMPOSSIBLE_MEMORY_SPACE; | ^ cell-counts.c:2163:73: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2163 | HashTablePut(cct_context -> cluster_cell_map_table, NULL+(sample_i*1LLU<<56)+cellbc_no, NULL+cluster_no); | ^ cell-counts.c:2163:93: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2163 | HashTablePut(cct_context -> cluster_cell_map_table, NULL+(sample_i*1LLU<<56)+cellbc_no, NULL+cluster_no); | ^ cell-counts.c:2163:109: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2163 | HashTablePut(cct_context -> cluster_cell_map_table, NULL+(sample_i*1LLU<<56)+cellbc_no, NULL+cluster_no); | ^ flattenAnnotations.c: In function ‘flatAnno_do_anno_chop_one_array’: flattenAnnotations.c:167:75: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 167 | if(ArrayListGet(edge_before_me_List,findi)-NULL == search_tag){ | ^ flattenAnnotations.c:172:77: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 172 | if(0==found) ArrayListPush(edge_before_me_List, NULL+search_tag); | ^ gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.1\"" -g3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c input-files.c -o input-files.o flattenAnnotations.c:180:77: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 180 | int an_edge_before_me = edge_before_me_List-> elementList[i]-NULL; | ^ flattenAnnotations.c:215:68: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 215 | curr_2i[0] = edge_before_me_List -> elementList[i] -NULL; | ^ flattenAnnotations.c:216:70: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 216 | curr_2i[1] = edge_before_me_List -> elementList[i+1] -NULL-1; | ^ cell-counts.c: In function ‘cellCounts_get_cellbarcode_no’: cell-counts.c:2487:80: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 2487 | int tbcn = ArrayListGet( xrawarr, xx3 )-NULL; | ^ cell-counts.c:2514:80: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 2514 | int tbcn = ArrayListGet( xrawarr, xx3 )-NULL; | ^ cell-counts.c:2546:57: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 2546 | srInt_64 xint = xrawarr - NULL; | ^ cell-counts.c:2557:85: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 2557 | int bcno = ArrayListGet(rawarr, xx2)-NULL; | ^ gene-algorithms.c: In function ‘linear_gene_position’: gene-algorithms.c:425:67: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 425 | n = HashTableGet(offsets -> read_name_to_index, chro_name)-NULL; | ^ cell-counts.c:2560:88: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2560 | if(ArrayListGet(ret, xx3)==NULL+bcno){ | ^ cell-counts.c:2566:82: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2566 | if(!found)ArrayListPush(ret, NULL+bcno); | ^ cell-counts.c:2573:57: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 2573 | int tbcn = ArrayListGet(ret,xx1)-NULL; | ^ cell-counts.c: In function ‘cellCounts_build_read_bin’: cell-counts.c:2611:107: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 2611 | if(chro_name) refID = HashTableGet(cct_context -> chromosome_table.read_name_to_index, chro_name) - NULL - 1; | ^ gene-algorithms.c: In function ‘find_and_explain_indel’: gene-algorithms.c:768:93: warning: overflow in conversion from ‘int’ to ‘char’ changes value from ‘255’ to ‘-1’ [-Woverflow] 768 | *(allvote -> max_indel_recorder + qid * allvote -> indel_recorder_length) = 0xff ; | ^~~~ cell-counts.c: In function ‘cellCounts_vote_and_add_count’: cell-counts.c:2837:85: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2837 | }else sample_bam_2fps = HashTableGet(cct_context -> sample_BAM_writers, NULL+(sample_no-1) + 1); // sample_id-1: 0,1,2,... | ^ cell-counts.c:2837:100: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2837 | }else sample_bam_2fps = HashTableGet(cct_context -> sample_BAM_writers, NULL+(sample_no-1) + 1); // sample_id-1: 0,1,2,... | ^ cell-counts.c:2797:139: warning: unused variable ‘testi’ [-Wunused-variable] 2797 | char * sample_seq=NULL, *sample_qual=NULL, *BC_qual=NULL, *BC_seq=NULL, *UMI_seq=NULL, *UMI_qual=NULL, *lane_str=NULL, *RG=NULL, *testi; | ^~~~~ cell-counts.c: In function ‘cellCounts_run_in_thread’: cell-counts.c:2925:38: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 2925 | int thread_no = parameters[1]-NULL; | ^ cell-counts.c:2926:33: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 2926 | int task = parameters[2]-NULL; | ^ cell-counts.c: In function ‘cellCounts_run_maybe_threads’: cell-counts.c:2975:41: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2975 | thr_parameters[1] = NULL+current_thread_no; | ^ cell-counts.c:2976:41: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2976 | thr_parameters[2] = NULL+task; | ^ gene-algorithms.c: In function ‘explain_indel_in_middle’: gene-algorithms.c:918:93: warning: overflow in conversion from ‘int’ to ‘char’ changes value from ‘253’ to ‘-3’ [-Woverflow] 918 | *(allvote -> max_indel_recorder + qid * allvote -> indel_recorder_length) = 0xfd; | ^~~~ gene-algorithms.c:945:93: warning: overflow in conversion from ‘int’ to ‘char’ changes value from ‘254’ to ‘-2’ [-Woverflow] 945 | *(allvote -> max_indel_recorder + qid * allvote -> indel_recorder_length) = 0xfe ; | ^~~~ cell-counts.c: In function ‘cellCounts_chroEvent_locks_opt’: cell-counts.c:3350:29: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 3350 | srInt_64 vn = entity-NULL; | ^ cell-counts.c: In function ‘cellCounts_convert_stack_to_cigar_str’: cell-counts.c:3363:60: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 3363 | if(stack[stack_depth].event_details == NULL+IMPOSSIBLE_MEMORY_SPACE)break; | ^ cell-counts.c:3386:99: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 3386 | if(event_details -> n_events == 1) Nlen = (void*) event_details -> length -NULL; | ^ cell-counts.c:3360:37: warning: unused variable ‘thread_context’ [-Wunused-variable] 3360 | cellcounts_align_thread_t * thread_context = cct_context -> all_thread_contexts + thread_no; | ^~~~~~~~~~~~~~ cell-counts.c: In function ‘cellCounts_end_build_candidature_from_stacks’: cell-counts.c:3449:90: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 3449 | if( HashTableGet(thread_context -> alignment_repating_table, NULL+hkey) )continue; | ^ cell-counts.c:3450:86: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 3450 | HashTablePut(thread_context -> alignment_repating_table, NULL+hkey, NULL+1); | ^ cell-counts.c:3450:97: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 3450 | HashTablePut(thread_context -> alignment_repating_table, NULL+hkey, NULL+1); | ^ cell-counts.c:3441:29: warning: unused variable ‘cigar_rlen’ [-Wunused-variable] 3441 | int cigar_rlen = cellCounts_reduce_Cigar(cigar_end5,final_cigar); | ^~~~~~~~~~ cell-counts.c:3408:29: warning: unused variable ‘x_candidate’ [-Wunused-variable] 3408 | int x_3end, x_5end, x_candidate; | ^~~~~~~~~~~ cell-counts.c: In function ‘cellCounts_build_junction_read_finalise_current_stack’: cell-counts.c:3545:204: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 3545 | if( thread_context -> realignment_event_stack_current_depth < JUNCTION_REALIGNMENT_MAX_DEPTH ) stack_copy_ptr[thread_context -> realignment_event_stack_current_depth].event_details = NULL+IMPOSSIBLE_MEMORY_SPACE; | ^ cell-counts.c: In function ‘cellCounts_tree_iterative_search’: cell-counts.c:3642:63: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 3642 | int evbposright = evb -> attr - NULL; | ^ cell-counts.c:3649:114: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 3649 | int my_cluster = HashTableGet(cct_context -> cluster_cell_map_table, NULL+(sample_i *1LLU<<56)+cellbc_no)-NULL; | ^ cell-counts.c:3649:135: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 3649 | int my_cluster = HashTableGet(cct_context -> cluster_cell_map_table, NULL+(sample_i *1LLU<<56)+cellbc_no)-NULL; | ^ cell-counts.c:3649:146: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 3649 | int my_cluster = HashTableGet(cct_context -> cluster_cell_map_table, NULL+(sample_i *1LLU<<56)+cellbc_no)-NULL; | ^ cell-counts.c:3652:137: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 3652 | HashTable * my_known_tab = HashTableGet(cct_context -> cluster_spec_junction_table, NULL+(sample_i *1LLU<<56)+my_cluster); | ^ cell-counts.c:3652:158: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 3652 | HashTable * my_known_tab = HashTableGet(cct_context -> cluster_spec_junction_table, NULL+(sample_i *1LLU<<56)+my_cluster); | ^ cell-counts.c:3654:102: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 3654 | event_known = HashTableGet(my_known_tab, NULL+(linear_env_L*1LLU<<32)+linear_env_R); | ^ cell-counts.c:3654:126: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 3654 | event_known = HashTableGet(my_known_tab, NULL+(linear_env_L*1LLU<<32)+linear_env_R); | ^ cell-counts.c:3662:123: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 3662 | chroEvent_t * envdtl = HashTableGet( cct_context -> chroEvent_detail_table[sample_i], NULL+ envkey); | ^ cell-counts.c:3666:83: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 3666 | int remote_first_matching_base_chro = evb -> attr - NULL, x2; | ^ cell-counts.c:3671:87: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 3671 | else inslen = (void*)envdtl -> length - NULL; | ^ cell-counts.c:3620:21: warning: unused variable ‘read_for_testing_len’ [-Wunused-variable] 3620 | int read_for_testing_len = edge_region_end - edge_region_start +1; | ^~~~~~~~~~~~~~~~~~~~ gene-algorithms.c: In function ‘load_offsets’: gene-algorithms.c:1355:80: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1355 | HashTablePut(offsets->read_name_to_index, read_name_mem , NULL + 1 + n); | ^ gene-algorithms.c:1355:84: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1355 | HashTablePut(offsets->read_name_to_index, read_name_mem , NULL + 1 + n); | ^ cell-counts.c: In function ‘cellCounts_explain_one_alignment’: cell-counts.c:3726:139: warning: unused variable ‘testi’ [-Wunused-variable] 3726 | char * sample_seq=NULL, *sample_qual=NULL, *BC_qual=NULL, *BC_seq=NULL, *UMI_seq=NULL, *UMI_qual=NULL, *lane_str=NULL, *RG=NULL, *testi; | ^~~~~ core-junction.c: In function ‘find_translocation_brk_PQR’: core-junction.c:5725:59: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 5725 | int event_no = event_ptr_list_A1[candA1i] - NULL; | ^ core-junction.c:5738:72: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 5738 | unsigned int event_no_P = event_ptr_list_A1[candBrkPi] - NULL; | ^ core-junction.c:5761:76: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 5761 | unsigned int event_no_Q = event_ptr_list_Q[candQi] - NULL; | ^ core-junction.c:5779:84: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 5779 | unsigned int event_no_R = event_ptr_list_R[candRi] - NULL; | ^ cell-counts.c: In function ‘cellCounts_add_covered_indels_in_table’: cell-counts.c:4005:1: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 4005 | if(1) cellCounts_add_or_update_chroEvent_in_table(cct_context, sample_i, chroEvent_t_TYPE_INDEL , chro_name, chro_pos -1, rposv, inslen_negative, 0); // thread safe | ^~ cell-counts.c:4006:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 4006 | if(nch=='D') chro_cursor += tmpi; | ^~ cell-counts.c:3987:13: warning: unused variable ‘retlen’ [-Wunused-variable] 3987 | int retlen = general_dynamic_align_moves_to_cigar(result_buffer, moved_len, result_cigar); | ^~~~~~ cell-counts.c: In function ‘cellCounts_call_juncs_put_in_tab’: cell-counts.c:4037:69: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 4037 | HashTablePut(iijj_to_chro_ptr , NULL+1+iijj, tstchro); | ^ cell-counts.c:4037:71: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 4037 | HashTablePut(iijj_to_chro_ptr , NULL+1+iijj, tstchro); | ^ cell-counts.c:4040:90: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 4040 | ArrayListPush( jstub_potential_mainhalf_list,NULL+iijj ); | ^ cell-counts.c:4056:102: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 4056 | srInt_64 maiijj = ArrayListGet( jstub_potential_mainhalf_list , mainhalf_i ) - NULL; | ^ cell-counts.c:4075:93: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 4075 | char * tstchro = HashTableGet(iijj_to_chro_ptr, NULL+1+iijj); | ^ cell-counts.c:4075:95: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 4075 | char * tstchro = HashTableGet(iijj_to_chro_ptr, NULL+1+iijj); | ^ core-junction.c: In function ‘finalise_translocations’: core-junction.c:6025:83: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 6025 | subread_read_number_t frag_S_no = (s_ptrs[cand_i] - NULL)/ 2; | ^ core-junction.c:6026:72: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 6026 | int frag_S_is_read_B = (s_ptrs[cand_i] - NULL) % 2; | ^ cell-counts.c:4102:45: warning: variable ‘rgap’ set but not used [-Wunused-but-set-variable] 4102 | int rgap = -1; | ^~~~ cell-counts.c:4135:110: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 4135 | srInt_64 maiijj= ArrayListGet(jstub_potential_mainhalf_list, best_major_half)-NULL; | ^ cell-counts.c:4176:74: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 4176 | if(NULL==HashTableGet(indel_dp_exed, NULL+1+(tstiijj & 0xffffffffffffllu))){ | ^ cell-counts.c:4176:76: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 4176 | if(NULL==HashTableGet(indel_dp_exed, NULL+1+(tstiijj & 0xffffffffffffllu))){ | ^ cell-counts.c:4177:73: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 4177 | HashTablePut(indel_dp_exed, NULL+1+(tstiijj & 0xffffffffffffllu), NULL+1); | ^ cell-counts.c:4177:75: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 4177 | HashTablePut(indel_dp_exed, NULL+1+(tstiijj & 0xffffffffffffllu), NULL+1); | ^ cell-counts.c:4177:111: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 4177 | HashTablePut(indel_dp_exed, NULL+1+(tstiijj & 0xffffffffffffllu), NULL+1); | ^ cell-counts.c:4167:37: warning: unused variable ‘is_update’ [-Wunused-variable] 4167 | int is_update = cellCounts_add_or_update_chroEvent_in_table(cct_context, sample_i, chroEvent_t_TYPE_JUNCTION, machro, mapos, tstpos, 0, 0);//mapos and tstpos are just borrowed variables. | ^~~~~~~~~ cell-counts.c:4155:37: warning: variable ‘rgap’ set but not used [-Wunused-but-set-variable] 4155 | int rgap = -1; | ^~~~ cell-counts.c:4142:37: warning: unused variable ‘manegative’ [-Wunused-variable] 4142 | int manegative = votetab -> masks[mai][maj]; | ^~~~~~~~~~ cell-counts.c:4181:66: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 4181 | if(NULL==HashTableGet(indel_dp_exed, NULL+1+(maiijj & 0xffffffffffffllu))){ | ^ cell-counts.c:4181:68: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 4181 | if(NULL==HashTableGet(indel_dp_exed, NULL+1+(maiijj & 0xffffffffffffllu))){ | ^ cell-counts.c:4182:65: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 4182 | HashTablePut(indel_dp_exed, NULL+1+(maiijj & 0xffffffffffffllu), NULL+1); | ^ cell-counts.c:4182:67: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 4182 | HashTablePut(indel_dp_exed, NULL+1+(maiijj & 0xffffffffffffllu), NULL+1); | ^ cell-counts.c:4182:102: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 4182 | HashTablePut(indel_dp_exed, NULL+1+(maiijj & 0xffffffffffffllu), NULL+1); | ^ cell-counts.c:4054:29: warning: variable ‘best_GTAG_negative’ set but not used [-Wunused-but-set-variable] 4054 | int best_GTAG_negative = -1; | ^~~~~~~~~~~~~~~~~~ cell-counts.c:4051:29: warning: variable ‘best_misma_no’ set but not used [-Wunused-but-set-variable] 4051 | int best_misma_no = -1; | ^~~~~~~~~~~~~ cell-counts.c:4022:38: warning: unused variable ‘distinct_vote_number_i’ [-Wunused-variable] 4022 | int i,j,reverse_text_offset, distinct_vote_number_i; | ^~~~~~~~~~~~~~~~~~~~~~ cell-counts.c:4022:17: warning: unused variable ‘reverse_text_offset’ [-Wunused-variable] 4022 | int i,j,reverse_text_offset, distinct_vote_number_i; | ^~~~~~~~~~~~~~~~~~~ core-junction.c: In function ‘finalise_inversions’: core-junction.c:6210:91: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 6210 | subread_read_number_t frag_S_no = (s_ptrs[cand_i] - NULL)/2; | ^ core-junction.c:6211:82: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 6211 | int frag_S_larger_read = (s_ptrs[cand_i] - NULL)%2; | ^ cell-counts.c: In function ‘cellCounts_add_supported_unsupported_reads_from_cigar’: cell-counts.c:4252:110: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 4252 | oneitem = HashTableGet( cct_context -> chroEvent_detail_table[sample_i], NULL+ envkey); | ^ cell-counts.c:4262:114: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 4262 | }else oneitem -> step2_supported_reads = (void*) oneitem -> step2_supported_reads+1; | ^ cell-counts.c:4265:37: warning: variable ‘on_chro_len’ set but not used [-Wunused-but-set-variable] 4265 | int on_chro_len = tmpi +1; | ^~~~~~~~~~~ cell-counts.c:4291:137: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 4291 | chroEvent_t * exed = HashTableGet(cct_context -> chroEvent_detail_table [sample_i], NULL+envkey); | ^ cell-counts.c:4303:118: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 4303 | exed -> step2_supported_reads = (void*) exed -> step2_supported_reads+1; | ^ cell-counts.c:4296:66: warning: variable ‘x2_not_matter’ set but not used [-Wunused-but-set-variable] 4296 | int is_the_last, x2_not_matter; | ^~~~~~~~~~~~~ cell-counts.c:4330:81: warning: array subscript has type ‘char’ [-Wchar-subscripts] 4330 | IVT_IntervalTreeNode * myroot = LR_roots[LRi]; | ^ cell-counts.c:4338:79: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 4338 | int evbposright = evb -> attr - NULL; | ^ cell-counts.c:4345:137: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 4345 | chroEvent_t * uned = HashTableGet(cct_context -> chroEvent_detail_table[sample_i] , NULL+envkey); | ^ cell-counts.c:4348:146: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 4348 | if(nch == 'N' && !(uned -> left_edge >= linear_cur && uned -> left_edge + ((void*) uned -> length-NULL) <= linear_env_R )) continue; // fly-over exons must be entirely in the "N" part. | ^ cell-counts.c:4354:153: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 4354 | if(!is_the_last) uned -> step2_non_supported_reads = (void *) uned -> step2_non_supported_reads +1 ; | ^ cell-counts.c:4222:41: warning: unused variable ‘x3’ [-Wunused-variable] 4222 | int nch, tmpi=0, x1=0, b1off=0, x3; | ^~ core-junction.c:6295:66: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 6295 | int event_no_Y = s1_ptrs[cand_Y] - NULL; | ^ core-junction.c:6305:82: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 6305 | int event_no_Z = s1_ptrs[cand_Z] - NULL; | ^ core-junction.c: In function ‘build_breakpoint_tables’: core-junction.c:6479:97: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 6479 | if(index_table) bktable_append(index_table, chro_name_left, chro_pos_left, NULL + xk1); | ^ core-junction.c:6480:99: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 6480 | if(index_table) bktable_append(index_table, chro_name_right, chro_pos_right, NULL + xk1); | ^ cell-counts.c: In function ‘cellCounts_get_sample_no_from_rname’: cell-counts.c:4862:89: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 4862 | sample_no = HashTableGet(cct_context -> lineno1B_to_sampleno1B_tab, NULL+lineno)-NULL; | ^ cell-counts.c:4862:97: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 4862 | sample_no = HashTableGet(cct_context -> lineno1B_to_sampleno1B_tab, NULL+lineno)-NULL; | ^ gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.1\"" -g3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c interval_merge.c -o interval_merge.o detection-calls.c:155:9: warning: dangling pointer ‘gc_2int’ to an unnamed temporary may be used [-Wdangling-pointer=] 155 | DTCadd_annotation(context, gene_name, chro_name, start, end, is_negative_strand, gc_2int[0], gc_2int[1], 0); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ detection-calls.c:154:48: note: unnamed temporary defined here 154 | if(!gc_2int) gc_2int = (unsigned int[]){0,0,0}; | ^ gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.1\"" -g3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c long-hashtable.c -o long-hashtable.o cell-counts.c: In function ‘cellCounts_do_one_batch_UMI_merge_one_cell’: cell-counts.c:5388:32: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 5388 | int sample_id = app1[3]-NULL; | ^ cell-counts.c:5376:83: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 5376 | #define ADD_count_hash(bc,gn,no) { HashTablePut(cellBCp0_genep0_P1_to_UMIs, NULL +1+(((1LLU*(bc))<<32)| (gn) ), HashTableGet( cellBCp0_genep0_P1_to_UMIs, NULL +1+(((1LLU*(bc))<<32)| (gn))) +(no) );\ | ^ cell-counts.c:5397:41: note: in expansion of macro ‘ADD_count_hash’ 5397 | ADD_count_hash(str1->cellbc, str1->gene_no,1); | ^~~~~~~~~~~~~~ cell-counts.c:5376:85: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 5376 | #define ADD_count_hash(bc,gn,no) { HashTablePut(cellBCp0_genep0_P1_to_UMIs, NULL +1+(((1LLU*(bc))<<32)| (gn) ), HashTableGet( cellBCp0_genep0_P1_to_UMIs, NULL +1+(((1LLU*(bc))<<32)| (gn))) +(no) );\ | ^ cell-counts.c:5397:41: note: in expansion of macro ‘ADD_count_hash’ 5397 | ADD_count_hash(str1->cellbc, str1->gene_no,1); | ^~~~~~~~~~~~~~ cell-counts.c:5376:164: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 5376 | #define ADD_count_hash(bc,gn,no) { HashTablePut(cellBCp0_genep0_P1_to_UMIs, NULL +1+(((1LLU*(bc))<<32)| (gn) ), HashTableGet( cellBCp0_genep0_P1_to_UMIs, NULL +1+(((1LLU*(bc))<<32)| (gn))) +(no) );\ | ^ cell-counts.c:5397:41: note: in expansion of macro ‘ADD_count_hash’ 5397 | ADD_count_hash(str1->cellbc, str1->gene_no,1); | ^~~~~~~~~~~~~~ cell-counts.c:5376:166: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 5376 | #define ADD_count_hash(bc,gn,no) { HashTablePut(cellBCp0_genep0_P1_to_UMIs, NULL +1+(((1LLU*(bc))<<32)| (gn) ), HashTableGet( cellBCp0_genep0_P1_to_UMIs, NULL +1+(((1LLU*(bc))<<32)| (gn))) +(no) );\ | ^ cell-counts.c:5397:41: note: in expansion of macro ‘ADD_count_hash’ 5397 | ADD_count_hash(str1->cellbc, str1->gene_no,1); | ^~~~~~~~~~~~~~ cell-counts.c:5376:194: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 5376 | #define ADD_count_hash(bc,gn,no) { HashTablePut(cellBCp0_genep0_P1_to_UMIs, NULL +1+(((1LLU*(bc))<<32)| (gn) ), HashTableGet( cellBCp0_genep0_P1_to_UMIs, NULL +1+(((1LLU*(bc))<<32)| (gn))) +(no) );\ | ^ cell-counts.c:5397:41: note: in expansion of macro ‘ADD_count_hash’ 5397 | ADD_count_hash(str1->cellbc, str1->gene_no,1); | ^~~~~~~~~~~~~~ cell-counts.c:5412:84: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 5412 | HashTablePut(filtered_CGU_table, strdup(replaced_key), NULL-1); | ^ cell-counts.c: In function ‘cellCounts_do_one_batch_UMI_merge_one_step’: cell-counts.c:5376:83: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 5376 | #define ADD_count_hash(bc,gn,no) { HashTablePut(cellBCp0_genep0_P1_to_UMIs, NULL +1+(((1LLU*(bc))<<32)| (gn) ), HashTableGet( cellBCp0_genep0_P1_to_UMIs, NULL +1+(((1LLU*(bc))<<32)| (gn))) +(no) );\ | ^ cell-counts.c:5544:66: note: in expansion of macro ‘ADD_count_hash’ 5544 | else if(is_UMI_step2 && str1->cellbc>=0) ADD_count_hash(str1->cellbc,str1->gene_no,1); | ^~~~~~~~~~~~~~ cell-counts.c:5376:85: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 5376 | #define ADD_count_hash(bc,gn,no) { HashTablePut(cellBCp0_genep0_P1_to_UMIs, NULL +1+(((1LLU*(bc))<<32)| (gn) ), HashTableGet( cellBCp0_genep0_P1_to_UMIs, NULL +1+(((1LLU*(bc))<<32)| (gn))) +(no) );\ | ^ cell-counts.c:5544:66: note: in expansion of macro ‘ADD_count_hash’ 5544 | else if(is_UMI_step2 && str1->cellbc>=0) ADD_count_hash(str1->cellbc,str1->gene_no,1); | ^~~~~~~~~~~~~~ cell-counts.c:5376:164: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 5376 | #define ADD_count_hash(bc,gn,no) { HashTablePut(cellBCp0_genep0_P1_to_UMIs, NULL +1+(((1LLU*(bc))<<32)| (gn) ), HashTableGet( cellBCp0_genep0_P1_to_UMIs, NULL +1+(((1LLU*(bc))<<32)| (gn))) +(no) );\ | ^ cell-counts.c:5544:66: note: in expansion of macro ‘ADD_count_hash’ 5544 | else if(is_UMI_step2 && str1->cellbc>=0) ADD_count_hash(str1->cellbc,str1->gene_no,1); | ^~~~~~~~~~~~~~ cell-counts.c:5376:166: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 5376 | #define ADD_count_hash(bc,gn,no) { HashTablePut(cellBCp0_genep0_P1_to_UMIs, NULL +1+(((1LLU*(bc))<<32)| (gn) ), HashTableGet( cellBCp0_genep0_P1_to_UMIs, NULL +1+(((1LLU*(bc))<<32)| (gn))) +(no) );\ | ^ cell-counts.c:5544:66: note: in expansion of macro ‘ADD_count_hash’ 5544 | else if(is_UMI_step2 && str1->cellbc>=0) ADD_count_hash(str1->cellbc,str1->gene_no,1); | ^~~~~~~~~~~~~~ cell-counts.c:5376:194: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 5376 | #define ADD_count_hash(bc,gn,no) { HashTablePut(cellBCp0_genep0_P1_to_UMIs, NULL +1+(((1LLU*(bc))<<32)| (gn) ), HashTableGet( cellBCp0_genep0_P1_to_UMIs, NULL +1+(((1LLU*(bc))<<32)| (gn))) +(no) );\ | ^ cell-counts.c:5544:66: note: in expansion of macro ‘ADD_count_hash’ 5544 | else if(is_UMI_step2 && str1->cellbc>=0) ADD_count_hash(str1->cellbc,str1->gene_no,1); | ^~~~~~~~~~~~~~ cell-counts.c: In function ‘cellCounts_do_one_batch_tab_to_struct_list_compare’: cell-counts.c:5601:47: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 5601 | int sort_by_geneid_then_umi = app1[1] - NULL; | ^ cell-counts.c: In function ‘cellCounts_do_one_batch_tab_to_struct_list’: cell-counts.c:5629:29: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 5629 | int supp_reads = val-NULL; | ^ cell-counts.c: In function ‘cellCounts_do_one_batch_write_UMIs’: cell-counts.c:5651:20: warning: wrong type argument to decrement [-Wpointer-arith] 5651 | vcell_gene --; | ^~ cell-counts.c: In function ‘cellCounts_merge_batches_worker’: cell-counts.c:5661:35: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 5661 | int my_worker_id = vpp[2] - NULL; | ^ cell-counts.c: In function ‘cellCounts_do_one_batch’: cell-counts.c:5879:143: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 5879 | srInt_64 this_batch_size_and_no = ArrayListGet(file_size_list, file_size_list->numOfElements-1 -this_batch_sorted_idx)-NULL; | ^ cell-counts.c:5857:68: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 5857 | srInt_64 supp_reads = HashTableGet(supp_reads_SCGU, my_key)-NULL; \ | ^ cell-counts.c:5930:41: note: in expansion of macro ‘ADD_key_struct’ 5930 | ADD_key_struct; | ^~~~~~~~~~~~~~ cell-counts.c:5858:76: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 5858 | if(1>supp_reads) HashTablePut(supp_reads_SCGU, strdup(my_key), NULL+1); \ | ^ cell-counts.c:5930:41: note: in expansion of macro ‘ADD_key_struct’ 5930 | ADD_key_struct; | ^~~~~~~~~~~~~~ cell-counts.c:5859:65: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 5859 | else HashTablePutReplaceEx(supp_reads_SCGU, my_key, NULL+supp_reads+1, 0,0,0); } | ^ cell-counts.c:5930:41: note: in expansion of macro ‘ADD_key_struct’ 5930 | ADD_key_struct; | ^~~~~~~~~~~~~~ cell-counts.c:5859:76: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 5859 | else HashTablePutReplaceEx(supp_reads_SCGU, my_key, NULL+supp_reads+1, 0,0,0); } | ^ cell-counts.c:5930:41: note: in expansion of macro ‘ADD_key_struct’ 5930 | ADD_key_struct; | ^~~~~~~~~~~~~~ cell-counts.c:5857:68: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 5857 | srInt_64 supp_reads = HashTableGet(supp_reads_SCGU, my_key)-NULL; \ | ^ cell-counts.c:5935:33: note: in expansion of macro ‘ADD_key_struct’ 5935 | ADD_key_struct; | ^~~~~~~~~~~~~~ cell-counts.c:5858:76: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 5858 | if(1>supp_reads) HashTablePut(supp_reads_SCGU, strdup(my_key), NULL+1); \ | ^ cell-counts.c:5935:33: note: in expansion of macro ‘ADD_key_struct’ 5935 | ADD_key_struct; | ^~~~~~~~~~~~~~ cell-counts.c:5859:65: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 5859 | else HashTablePutReplaceEx(supp_reads_SCGU, my_key, NULL+supp_reads+1, 0,0,0); } | ^ cell-counts.c:5935:33: note: in expansion of macro ‘ADD_key_struct’ 5935 | ADD_key_struct; | ^~~~~~~~~~~~~~ cell-counts.c:5859:76: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 5859 | else HashTablePutReplaceEx(supp_reads_SCGU, my_key, NULL+supp_reads+1, 0,0,0); } | ^ cell-counts.c:5935:33: note: in expansion of macro ‘ADD_key_struct’ 5935 | ADD_key_struct; | ^~~~~~~~~~~~~~ cell-counts.c:5963:39: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 5963 | app1[1] = NULL+1; | ^ cell-counts.c:5970:39: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 5970 | app1[1] = NULL+0; | ^ cell-counts.c:6014:39: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 6014 | if(umi == NULL-1) umi="-----------------------------------------"; | ^ cell-counts.c:6044:21: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 6044 | return NULL + removed_UMIs; | ^ cell-counts.c: In function ‘cellCounts_save_BAM_result’: cell-counts.c:6057:83: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 6057 | void ** fps = HashTableGet(cct_context -> sample_BAM_writers, NULL+sample_id); | ^ cell-counts.c: In function ‘cellCounts_merged_write_sparse_unique_genes’: cell-counts.c:6090:26: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 6090 | int cellbcP1 = ky-NULL; | ^ cell-counts.c:6091:70: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 6091 | if(used_cellnoP1_tab && !HashTableGet(used_cellnoP1_tab, NULL+cellbcP1))return; | ^ cell-counts.c:6097:131: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 6097 | if(!HashTableGet(unique_geneno1B_tab, ArrayListGet(g2ul,x1))) HashTablePut(unique_geneno1B_tab, geneno1B_ptr, NULL+1); | ^ cell-counts.c: In function ‘cellCounts_merged_write_sparse_matrix’: cell-counts.c:6137:80: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 6137 | int gene_index_0B = ArrayListGet(unique_NZ_genenosP1_list, x2) - NULL-1; | ^ cell-counts.c:6143:71: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 6143 | srInt_64 cellno = ArrayListGet(used_cell_barcodes, x1)-NULL; | ^ cell-counts.c:6149:71: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 6149 | srInt_64 cellno = ArrayListGet(used_cell_barcodes, x1)-NULL; | ^ cell-counts.c:6150:95: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 6150 | HashTable * geneno1B_to_UMIs = HashTableGet(cellP1_to_geneP1_to_umis_tab, NULL+1+cellno); | ^ cell-counts.c:6150:97: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 6150 | HashTable * geneno1B_to_UMIs = HashTableGet(cellP1_to_geneP1_to_umis_tab, NULL+1+cellno); | ^ cell-counts.c:6153:82: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 6153 | int geneno1B = ArrayListGet(unique_NZ_genenosP1_list, x2)-NULL; | ^ cell-counts.c:6154:76: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 6154 | int this_umis = HashTableGet(geneno1B_to_UMIs, NULL+geneno1B) -NULL; | ^ cell-counts.c:6154:87: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 6154 | int this_umis = HashTableGet(geneno1B_to_UMIs, NULL+geneno1B) -NULL; | ^ cell-counts.c: In function ‘cellCounts_merged_45K_to_90K_sum_SUM_Level2’: cell-counts.c:6168:105: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 6168 | HashTablePut(summed_gene_to_umis, GeneNo1B, vUMIs + (HashTableGet(summed_gene_to_umis, GeneNo1B)-NULL)); | ^ cell-counts.c:6168:59: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 6168 | HashTablePut(summed_gene_to_umis, GeneNo1B, vUMIs + (HashTableGet(summed_gene_to_umis, GeneNo1B)-NULL)); | ^ cell-counts.c: In function ‘cellCounts_merged_45K_to_90K_sum_WRT’: cell-counts.c:6185:78: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 6185 | unsigned char * gene_name = cct_context -> gene_name_array[ kyGeneID - NULL-1 ]; | ^ cell-counts.c:6186:68: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 6186 | fprintf(ofp, "%s\t%u\n", gene_name, (unsigned int) (valUMIs-NULL)); | ^ cell-counts.c: In function ‘cellCounts_merged_write_nozero_geneids_WRT’: cell-counts.c:6217:71: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 6217 | unsigned char* gene_symbol = cct_context -> gene_name_array [k-NULL-1]; | ^ cell-counts.c: In function ‘cellCounts_merged_to_tables_write_build_UMIcount_in’: cell-counts.c:6236:32: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 6236 | tab -> counter1 += (val-NULL); | ^ cell-counts.c: In function ‘cellCounts_merged_to_tables_write_build_UMIcounts’: cell-counts.c:6241:25: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 6241 | int cell_no = ky-NULL-1; | ^ cell-counts.c:6246:48: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 6246 | HashTablePut(cellbcP1_to_umis_tab, NULL+1+cell_no, NULL+geneP1_to_counts_tab -> counter1); | ^ cell-counts.c:6246:50: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 6246 | HashTablePut(cellbcP1_to_umis_tab, NULL+1+cell_no, NULL+geneP1_to_counts_tab -> counter1); | ^ cell-counts.c:6246:64: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 6246 | HashTablePut(cellbcP1_to_umis_tab, NULL+1+cell_no, NULL+geneP1_to_counts_tab -> counter1); | ^ cell-counts.c: In function ‘cellCounts_merged_ambient_rescure’: cell-counts.c:6262:129: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 6262 | srInt_64 median_umis = HashTableGet(cellnoP1_to_umis_tab, ArrayListGet(sorted_bcno_p1 , (high_conf_cells-1)/2))-NULL; | ^ cell-counts.c:6269:100: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 6269 | srInt_64 this_bc_umis = HashTableGet(cellnoP1_to_umis_tab, this_bc_pnt_p1) - NULL; | ^ cell-counts.c:6276:96: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 6276 | ArrayListPush(this_sample_ambient_rescure_candi, this_bc_pnt_p1-1); | ^ cell-counts.c:6281:100: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 6281 | ArrayListPush(this_sample_45k_90k_barcode_no_P0, ArrayListGet(sorted_bcno_p1 , x1)-1 ); | ^ cell-counts.c: In function ‘cellCounts_merged_bootstrap_a_sample’: cell-counts.c:6304:96: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 6304 | srInt_64 this_umis = HashTableGet(cellnoP1_to_umis_tab, cellbc_p1_ptr )-NULL; | ^ cell-counts.c:6306:100: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 6306 | ArrayListPush(highconf_cellbc_list, ArrayListGet( sorted_idx, x1 ) - 1 ); | ^ cell-counts.c:6317:105: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 6317 | srInt_64 this_umis = HashTableGet( cellnoP1_to_umis_tab, cellbc_p1_ptr )-NULL; | ^ cell-counts.c:6318:74: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 6318 | ArrayListPush(resampled_list_of_umis,NULL+this_umis); | ^ cell-counts.c:6321:159: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 6321 | srInt_64 UMIs_30th_div10 = ArrayListGet(resampled_list_of_umis, resampled_list_of_umis -> numOfElements - SCRNA_BOOTSTRAP_HIGH_INDEX) -NULL; | ^ cell-counts.c:6326:95: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 6326 | srInt_64 this_umis = ArrayListGet(resampled_list_of_umis, lli)-NULL; | ^ cell-counts.c:6338:70: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 6338 | ArrayListPush(highconf_cellbc_list, last_ptr - 1 ); | ^ cell-counts.c:6340:75: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 6340 | last_umi_no = HashTableGet(cellnoP1_to_umis_tab ,last_ptr)-NULL; | ^ cell-counts.c: In function ‘cellCounts_merged_to_tables_write’: cell-counts.c:6378:71: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 6378 | HashTablePut(sorted_order_p1_to_i_p1_tab, NULL+ feature1->sorted_order+1 , NULL+xk1+1 ); | ^ cell-counts.c:6378:95: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 6378 | HashTablePut(sorted_order_p1_to_i_p1_tab, NULL+ feature1->sorted_order+1 , NULL+xk1+1 ); | ^ cell-counts.c:6378:104: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 6378 | HashTablePut(sorted_order_p1_to_i_p1_tab, NULL+ feature1->sorted_order+1 , NULL+xk1+1 ); | ^ cell-counts.c:6378:108: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 6378 | HashTablePut(sorted_order_p1_to_i_p1_tab, NULL+ feature1->sorted_order+1 , NULL+xk1+1 ); | ^ cell-counts.c:6383:126: warning: wrong type argument to decrement [-Wpointer-arith] 6383 | for(xk1=0; xk1numOfElements; xk1++) all_barcode_index_list->elementList[xk1]--; | ^~ cell-counts.c: In function ‘cellCounts_do_cellbc_batches’: cell-counts.c:6449:59: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 6449 | ArrayListPush(file_size_list, NULL+( batchsize<<20 | xk1)); | ^ cell-counts.c:6471:31: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 6471 | vpp[1] = NULL + xk1; | ^ cell-counts.c:6480:39: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 6480 | removed_umis += (pret - NULL); | ^ cell-counts.c:6521:31: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 6521 | vpp[2] = NULL + xk1; | ^ cell-counts.c:6546:112: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 6546 | HashTable *gene_tab = HashTableGet(cellnoP1_to_genenoP1_to_UMIs[sample_i], NULL+cellbc_no+1); | ^ cell-counts.c:6546:122: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 6546 | HashTable *gene_tab = HashTableGet(cellnoP1_to_genenoP1_to_UMIs[sample_i], NULL+cellbc_no+1); | ^ cell-counts.c:6549:98: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 6549 | HashTablePut(cellnoP1_to_genenoP1_to_UMIs[sample_i], NULL+cellbc_no+1, gene_tab); | ^ cell-counts.c:6549:108: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 6549 | HashTablePut(cellnoP1_to_genenoP1_to_UMIs[sample_i], NULL+cellbc_no+1, gene_tab); | ^ cell-counts.c:6551:60: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 6551 | HashTablePut(gene_tab, NULL+gene_no0B+1 , NULL+umis); | ^ cell-counts.c:6551:70: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 6551 | HashTablePut(gene_tab, NULL+gene_no0B+1 , NULL+umis); | ^ cell-counts.c:6551:79: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 6551 | HashTablePut(gene_tab, NULL+gene_no0B+1 , NULL+umis); | ^ gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.1\"" -g3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c longread-mapping.c -o longread-mapping.o cell-counts.c: In function ‘cellCounts_determine_jcount_gene_transcript_report’: cell-counts.c:6891:91: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 6891 | HashTablePut(edge1P1_table, txp_ptr -> transcript_id, NULL+1+edge1_dist); | ^ cell-counts.c:6891:93: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 6891 | HashTablePut(edge1P1_table, txp_ptr -> transcript_id, NULL+1+edge1_dist); | ^ cell-counts.c:6894:103: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 6894 | HashTablePut(edge1exonNo_table, txp_ptr -> transcript_id, NULL+1+exactly_matched_exon_no); | ^ cell-counts.c:6894:105: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 6894 | HashTablePut(edge1exonNo_table, txp_ptr -> transcript_id, NULL+1+exactly_matched_exon_no); | ^ cell-counts.c:6919:91: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 6919 | HashTablePut(edge2P1_table, txp_ptr -> transcript_id, NULL+1+edge2_dist); | ^ cell-counts.c:6919:93: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 6919 | HashTablePut(edge2P1_table, txp_ptr -> transcript_id, NULL+1+edge2_dist); | ^ cell-counts.c:6922:103: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 6922 | HashTablePut(edge2exonNo_table, txp_ptr -> transcript_id, NULL+1+exactly_matched_exon_no); | ^ cell-counts.c:6922:105: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 6922 | HashTablePut(edge2exonNo_table, txp_ptr -> transcript_id, NULL+1+exactly_matched_exon_no); | ^ cell-counts.c:6932:81: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 6932 | int edge1_ptr = HashTableGet(edge1P1_table, edge1_txnid)-NULL; | ^ cell-counts.c:6934:81: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 6934 | int edge2_ptr = HashTableGet(edge2P1_table, edge1_txnid)-NULL; | ^ cell-counts.c:6936:92: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 6936 | int exonno_1 = HashTableGet(edge1exonNo_table, edge1_txnid)-NULL-1; | ^ cell-counts.c:6937:92: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 6937 | int exonno_2 = HashTableGet(edge2exonNo_table, edge1_txnid)-NULL-1; | ^ cell-counts.c:6949:77: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 6949 | HashTablePut(out_gene_tab, txnptr -> gene_name, NULL+1); | ^ cell-counts.c:6950:80: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 6950 | HashTablePut(out_txn_tab, txnptr -> transcript_id, NULL+1); | ^ cell-counts.c:6981:104: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 6981 | srInt_64 edge_dist = HashTableGet(this_side_olay_tab, this_side_txn_id)-NULL; | ^ cell-counts.c:6984:106: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 6984 | HashTablePut(this_side_reported_genes, txn_ptr -> gene_name, NULL+1); | ^ cell-counts.c: In function ‘cellCounts_find_nearest_gene_dist’: cell-counts.c:7074:69: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 7074 | if((void*)gene_name != NULL+IMPOSSIBLE_MEMORY_SPACE) HashTablePut(gene_name_tab, gene_name, NULL+1); | ^ cell-counts.c:7074:138: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 7074 | if((void*)gene_name != NULL+IMPOSSIBLE_MEMORY_SPACE) HashTablePut(gene_name_tab, gene_name, NULL+1); | ^ cell-counts.c: In function ‘cellCounts_copy_junc_table_to_output_table’: cell-counts.c:7113:68: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 7113 | locate_gene_position(ed -> left_edge + ((void*)ed -> length-NULL) +1, &cct_context -> chromosome_table, &chro, &pos_large); | ^ cell-counts.c:7122:59: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 7122 | srInt_64 cck = (void*)ed -> step2_supported_reads - NULL + report_0_junc; | ^ cell-counts.c:7123:66: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 7123 | cck = cck << 32 |((void*)ed -> step2_non_supported_reads - NULL); | ^ cell-counts.c: In function ‘cellCounts_write_final_other_events’: cell-counts.c:7150:62: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 7150 | envlen = (void*)ed -> length - NULL; | ^ cell-counts.c:7151:76: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 7151 | nsupp = (void*)ed -> step2_supported_reads - NULL; | ^ cell-counts.c:7152:82: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 7152 | nonsupp = (void*)ed -> step2_non_supported_reads - NULL; | ^ gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.1\"" -g3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c mergeVCF.c -o mergeVCF.o cell-counts.c: In function ‘cellCounts_write_final_junctions’: cell-counts.c:7220:21: warning: unused variable ‘unique_junctions’ [-Wunused-variable] 7220 | int unique_junctions = 0; | ^~~~~~~~~~~~~~~~ cell-counts.c:7199:20: warning: unused variable ‘ky_i2’ [-Wunused-variable] 7199 | int ky_i1, ky_i2; | ^~~~~ cell-counts.c:7199:13: warning: unused variable ‘ky_i1’ [-Wunused-variable] 7199 | int ky_i1, ky_i2; | ^~~~~ cell-counts.c:7197:81: warning: unused variable ‘gene_name_tail’ [-Wunused-variable] 7197 | char * gene_names = malloc(max_junction_genes * FEATURE_NAME_LENGTH), * gene_name_tail; | ^~~~~~~~~~~~~~ cell-counts.c:7163:13: warning: unused variable ‘infile_i’ [-Wunused-variable] 7163 | int infile_i, disk_is_full = 0, sample_i; | ^~~~~~~~ gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.1\"" -g3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c processExons.c -o processExons.o input-files.c: In function ‘get_temp_file_pointer’: input-files.c:1536:67: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1536 | if(temp_file_pointer == NULL || temp_file_pointer == NULL + 1) { | ^ input-files.c:1550:64: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 1550 | int maximum_open_file = fp_table -> appendix1 - NULL; | ^ input-files.c:1555:72: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1555 | HashTablePut(fp_table, key_name , NULL + 1); | ^ input-files.c: In function ‘my_fclose’: input-files.c:1565:28: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1565 | if(fp && fp != NULL+1) | ^ input-files.c: In function ‘add_cigar_indel_event’: input-files.c:1681:76: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 1681 | int exist_indel_count = HashTableGet(event_table_ptr, event_token) - NULL; | ^ input-files.c:1688:85: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 1688 | srInt_64 t64v = (HashTableGet(event_table_ptr, event_token)-NULL); | ^ input-files.c:1708:59: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1708 | memset(event_table_ptr->appendix2 + event_space_max_size * sizeof(short), 0, sizeof(short) * event_space_max_size); | ^ input-files.c:1718:68: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1718 | HashTablePut(event_table_ptr, token_1, NULL+1); | ^ input-files.c:1722:79: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1722 | HashTablePutReplace(event_table_ptr, event_token, NULL+exist_indel_count+1, 0); | ^ input-files.c:1722:97: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1722 | HashTablePutReplace(event_table_ptr, event_token, NULL+exist_indel_count+1, 0); | ^ input-files.c:1731:61: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1731 | HashTablePut(event_table_ptr, token_2, NULL + ((0xff & (0x80 + indels)) | ((indel_event_id_long&0xffffff) << 8))); | ^ input-files.c: In function ‘destroy_cigar_event_table’: input-files.c:1758:57: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 1758 | srInt_64 tmpv = cursor -> value - NULL; | ^ input-files.c: In function ‘break_SAM_file’: input-files.c:1885:38: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1885 | fp_table -> appendix1 = NULL + max_open_file * 2/ 3; | ^ input-files.c: In function ‘SAM_pairer_create’: input-files.c:2609:22: warning: ISO C forbids assignment between function pointer and ‘void *’ [-Wpedantic] 2609 | old_sig_TERM = signal (SIGTERM, REPAIR_SIGINT_hook); | ^ input-files.c:2610:21: warning: ISO C forbids assignment between function pointer and ‘void *’ [-Wpedantic] 2610 | old_sig_INT = signal (SIGINT, REPAIR_SIGINT_hook); | ^ input-files.c: In function ‘SAM_pairer_destroy’: input-files.c:2699:26: warning: ISO C forbids passing argument 2 of ‘signal’ between function pointer and ‘void *’ [-Wpedantic] 2699 | signal (SIGTERM, old_sig_TERM); | ^~~~~~~~~~~~ In file included from input-files.c:21: /usr/include/signal.h:88:57: note: expected ‘__sighandler_t’ {aka ‘void (*)(int)’} but argument is of type ‘void *’ 88 | extern __sighandler_t signal (int __sig, __sighandler_t __handler) | ~~~~~~~~~~~~~~~^~~~~~~~~ input-files.c:2700:25: warning: ISO C forbids passing argument 2 of ‘signal’ between function pointer and ‘void *’ [-Wpedantic] 2700 | signal (SIGINT, old_sig_INT); | ^~~~~~~~~~~ /usr/include/signal.h:88:57: note: expected ‘__sighandler_t’ {aka ‘void (*)(int)’} but argument is of type ‘void *’ 88 | extern __sighandler_t signal (int __sig, __sighandler_t __handler) | ~~~~~~~~~~~~~~~^~~~~~~~~ input-files.c: In function ‘SAM_pairer_get_next_read_BIN’: input-files.c:3126:112: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 3126 | HashTablePut(pairer -> sam_contig_number_table , mem_contig_name, NULL + 1 + header_contigs); | ^ input-files.c:3126:116: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 3126 | HashTablePut(pairer -> sam_contig_number_table , mem_contig_name, NULL + 1 + header_contigs); | ^ input-files.c: In function ‘online_register_contig’: input-files.c:3169:79: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 3169 | signed int refId = HashTableGet(pairer->sam_contig_number_table, ref) - NULL - 1; | ^ input-files.c:3176:77: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 3176 | HashTablePut(pairer->sam_contig_number_table, mem_ref, NULL + refId + 1); | ^ input-files.c:3176:85: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 3176 | HashTablePut(pairer->sam_contig_number_table, mem_ref, NULL + refId + 1); | ^ gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.1\"" -g3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c propmapped.c -o propmapped.o input-files.c: In function ‘reduce_SAM_to_BAM’: input-files.c:3228:79: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 3228 | signed int refID = HashTableGet(pairer->sam_contig_number_table, ref) - NULL - 1; | ^ input-files.c:3252:86: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 3252 | mate_refID = HashTableGet(pairer->sam_contig_number_table, mate_ref) - NULL - 1; | ^ input-files.c:3277:39: warning: overflow in conversion from ‘int’ to ‘char’ changes value from ‘255’ to ‘-1’ [-Woverflow] 3277 | bin_tmp[bin_ptr ++] = 0xff; | ^~~~ input-files.c:3278:39: warning: overflow in conversion from ‘int’ to ‘char’ changes value from ‘255’ to ‘-1’ [-Woverflow] 3278 | bin_tmp[bin_ptr ++] = 0xff; | ^~~~ input-files.c:3244:13: warning: unused variable ‘seq_len’ [-Wunused-variable] 3244 | int seq_len = qual - seq - 1; | ^~~~~~~ gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.1\"" -g3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c qualityScores.c -o qualityScores.o input-files.c: In function ‘SAM_pairer_make_dummy’: input-files.c:3683:37: warning: overflow in conversion from ‘int’ to ‘char’ changes value from ‘255’ to ‘-1’ [-Woverflow] 3683 | out_bin2[36 + len_name+1] = 0xff; | ^~~~ longread-mapping.c: In function ‘LRM_thread_runner’: longread-mapping.c:350:27: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 350 | int thid = argv[1]-NULL; | ^ longread-mapping.c:351:27: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 351 | int task = argv[2]-NULL; | ^ longread-mapping.c: In function ‘LRMstart_thread’: longread-mapping.c:391:43: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 391 | th_args[1] = NULL + th_id; | ^ longread-mapping.c:392:43: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 392 | th_args[2] = NULL + task; | ^ longread-mapping.c: In function ‘LRMis_gap_in_used_gap’: longread-mapping.c:636:102: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 636 | unsigned int used_start = LRMArrayListGet(iteration_context -> chain_used_gaps, xxi) - NULL; | ^ longread-mapping.c:637:102: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 637 | unsigned int used_end = LRMArrayListGet(iteration_context -> chain_used_gaps, xxi+1) - NULL; | ^ longread-mapping.c: In function ‘LRMbuild_chains’: longread-mapping.c:968:76: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 968 | LRMArrayListPush(iteration_context -> chain_used_gaps, NULL+this_gap_start_corr); | ^ longread-mapping.c:969:76: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 969 | LRMArrayListPush(iteration_context -> chain_used_gaps, NULL+this_gap_end_corr); | ^ input-files.c: In function ‘SAM_pairer_rescure_orphants_max_FP’: input-files.c:4236:43: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 4236 | int thread_no = (int)(param_ptr[1]-NULL); | ^ mergeVCF.c: In function ‘do_find_common’: mergeVCF.c:219:96: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 219 | int repeat_times = HashTableGet(extra_count_table, ky) - NULL; | ^ mergeVCF.c:222:89: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 222 | HashTablePut(extra_count_table, ky, NULL+1); | ^ mergeVCF.c:225:89: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 225 | HashTablePut(extra_qual_table, ky, NULL + qual + 1); | ^ mergeVCF.c:225:96: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 225 | HashTablePut(extra_qual_table, ky, NULL + qual + 1); | ^ mergeVCF.c:235:96: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 235 | int repeat_times = HashTableGet(extra_count_table, ky) - NULL; | ^ mergeVCF.c:238:99: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 238 | int old_qual = HashTableGet(extra_qual_table, ky) - NULL - 1; | ^ mergeVCF.c:240:97: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 240 | HashTablePutReplace(extra_count_table, ky, NULL + repeat_times, 0); | ^ mergeVCF.c:251:104: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 251 | HashTablePutReplace(extra_qual_table, ky, NULL + 1 + qual, 0); | ^ mergeVCF.c:251:108: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 251 | HashTablePutReplace(extra_qual_table, ky, NULL + 1 + qual, 0); | ^ mergeVCF.c:277:54: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 277 | int counts = cursor -> value - NULL; | ^ input-files.c: In function ‘SAM_pairer_thread_run’: input-files.c:4523:43: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 4523 | int thread_no = (int)(param_ptr[1]-NULL), is_disk_full = 0; | ^ input-files.c: In function ‘SAM_pairer_finish_margins’: input-files.c:4597:34: warning: wrong type argument to increment [-Wpointer-arith] 4597 | tab -> appendix2 ++; | ^~ input-files.c:4616:32: warning: wrong type argument to decrement [-Wpointer-arith] 4616 | }else tab -> appendix2 --; | ^~ input-files.c: In function ‘SAM_pairer_run_once’: input-files.c:4647:47: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 4647 | init_params[1] = (void *)(NULL+x1); | ^ input-files.c:4668:63: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 4668 | init_params[1] = (void *)(NULL+x1); | ^ gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.1\"" -g3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c read-repair.c -o read-repair.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.1\"" -g3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c readSummary.c -o readSummary.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.1\"" -g3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c removeDupReads.c -o removeDupReads.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.1\"" -g3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c sam2bed.c -o sam2bed.o input-files.c: In function ‘SAM_pairer_fix_format’: input-files.c:4863:50: warning: variable ‘readname’ set but not used [-Wunused-but-set-variable] 4863 | char tmpfname [MAX_FILE_NAME_LENGTH+14], readname[256]; | ^~~~~~~~ input-files.c: In function ‘SAM_nosort_thread_run’: input-files.c:5159:43: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 5159 | int thread_no = (int)(param_ptr[1]-NULL); | ^ input-files.c: In function ‘SAM_nosort_run_once’: input-files.c:5271:47: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 5271 | init_params[1] = (void *)(NULL+x1); | ^ input-files.c:5437:104: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 5437 | HashTablePut(pairer -> sam_contig_number_table , mem_contig_name, NULL + 1 + header_contigs); | ^ input-files.c:5437:108: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 5437 | HashTablePut(pairer -> sam_contig_number_table , mem_contig_name, NULL + 1 + header_contigs); | ^ input-files.c: In function ‘sort_SAM_create’: input-files.c:5678:22: warning: ISO C forbids assignment between function pointer and ‘void *’ [-Wpedantic] 5678 | old_sig_TERM = signal (SIGTERM, SAM_SORT_SIGINT_hook); | ^ input-files.c:5679:21: warning: ISO C forbids assignment between function pointer and ‘void *’ [-Wpedantic] 5679 | old_sig_INT = signal (SIGINT, SAM_SORT_SIGINT_hook); | ^ input-files.c: In function ‘sort_SAM_finalise’: input-files.c:5817:65: warning: overflow in conversion from ‘int’ to ‘char’ changes value from ‘255’ to ‘-1’ [-Woverflow] 5817 | old_line_mem[0]=0xff; | ^~~~ input-files.c:6048:26: warning: ISO C forbids passing argument 2 of ‘signal’ between function pointer and ‘void *’ [-Wpedantic] 6048 | signal (SIGTERM, old_sig_TERM); | ^~~~~~~~~~~~ /usr/include/signal.h:88:57: note: expected ‘__sighandler_t’ {aka ‘void (*)(int)’} but argument is of type ‘void *’ 88 | extern __sighandler_t signal (int __sig, __sighandler_t __handler) | ~~~~~~~~~~~~~~~^~~~~~~~~ input-files.c:6049:25: warning: ISO C forbids passing argument 2 of ‘signal’ between function pointer and ‘void *’ [-Wpedantic] 6049 | signal (SIGINT, old_sig_INT); | ^~~~~~~~~~~ /usr/include/signal.h:88:57: note: expected ‘__sighandler_t’ {aka ‘void (*)(int)’} but argument is of type ‘void *’ 88 | extern __sighandler_t signal (int __sig, __sighandler_t __handler) | ~~~~~~~~~~~~~~~^~~~~~~~~ gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.1\"" -g3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c sambam-file.c -o sambam-file.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.1\"" -g3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c seek-zlib.c -o seek-zlib.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.1\"" -g3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c sorted-hashtable.c -o sorted-hashtable.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.1\"" -g3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c sublog.c -o sublog.o propmapped.c: In function ‘get_FP_by_read_name’: propmapped.c:248:66: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 248 | FILE * ret = HashTableGet(context -> split_fp_table, NULL+1+(int)(hash_key)); | ^ propmapped.c:248:68: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 248 | FILE * ret = HashTableGet(context -> split_fp_table, NULL+1+(int)(hash_key)); | ^ propmapped.c:258:61: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 258 | HashTablePut(context -> split_fp_table, NULL+1+(int)(hash_key), ret); | ^ propmapped.c:258:63: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 258 | HashTablePut(context -> split_fp_table, NULL+1+(int)(hash_key), ret); | ^ propmapped.c: In function ‘prop_PE’: propmapped.c:409:91: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 409 | int old_OK = HashTableGet(rname_table, read_name) - NULL; | ^ propmapped.c:416:98: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 416 | HashTablePut(rname_table, read_name, NULL+2); | ^ propmapped.c:419:91: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 419 | HashTablePut(rname_table, read_name, NULL + new_OK + 1); | ^ propmapped.c:419:100: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 419 | HashTablePut(rname_table, read_name, NULL + new_OK + 1); | ^ propmapped.c:435:75: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 435 | if(cursor -> value == NULL+2) context -> mapped_reads++; | ^ gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.25.1\"" -g3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c tx-unique.c -o tx-unique.o readSummary.c: In function ‘load_feature_info’: readSummary.c:1260:134: warning: non-ISO-standard escape sequence, ‘\E’ [-Wpedantic] 1260 | SUBREADprintf("\Error: the feature on the %d-th line has zero coordinate or zero lengths\n\n", lineno); | ^ readSummary.c: In function ‘find_or_insert_gene_name’: readSummary.c:1409:70: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 1409 | srInt_64 gene_number = HashTableGet(genetable, feature_name) - NULL; | ^ readSummary.c:1415:59: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1415 | HashTablePut(genetable, feature_name, NULL+gene_number+1); | ^ readSummary.c:1415:71: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1415 | HashTablePut(genetable, feature_name, NULL+gene_number+1); | ^ sambam-file.c: In function ‘SamBam_writer_write_header’: sambam-file.c:1282:85: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1282 | char * chro_name = HashTableGet(writer -> chromosome_id_table, NULL + 1 + header_ptr); | ^ sambam-file.c:1282:89: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1282 | char * chro_name = HashTableGet(writer -> chromosome_id_table, NULL + 1 + header_ptr); | ^ sambam-file.c:1283:91: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1283 | unsigned int chro_len = HashTableGet(writer -> chromosome_len_table, NULL + 1 + header_ptr) - NULL - 1; | ^ sambam-file.c:1283:95: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1283 | unsigned int chro_len = HashTableGet(writer -> chromosome_len_table, NULL + 1 + header_ptr) - NULL - 1; | ^ sambam-file.c:1283:109: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 1283 | unsigned int chro_len = HashTableGet(writer -> chromosome_len_table, NULL + 1 + header_ptr) - NULL - 1; | ^ sambam-file.c: In function ‘SamBam_writer_add_chromosome’: sambam-file.c:1408:76: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1408 | HashTablePut(writer -> chromosome_name_table, chro_name_space, NULL+1+chro_id); | ^ sambam-file.c:1408:78: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1408 | HashTablePut(writer -> chromosome_name_table, chro_name_space, NULL+1+chro_id); | ^ sambam-file.c:1409:57: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1409 | HashTablePut(writer -> chromosome_id_table, NULL+1+chro_id, chro_name_space); | ^ sambam-file.c:1409:59: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1409 | HashTablePut(writer -> chromosome_id_table, NULL+1+chro_id, chro_name_space); | ^ sambam-file.c:1410:58: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1410 | HashTablePut(writer -> chromosome_len_table, NULL+1+chro_id, NULL + 1 + chro_length); | ^ sambam-file.c:1410:60: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1410 | HashTablePut(writer -> chromosome_len_table, NULL+1+chro_id, NULL + 1 + chro_length); | ^ sambam-file.c:1410:75: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1410 | HashTablePut(writer -> chromosome_len_table, NULL+1+chro_id, NULL + 1 + chro_length); | ^ sambam-file.c:1410:79: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1410 | HashTablePut(writer -> chromosome_len_table, NULL+1+chro_id, NULL + 1 + chro_length); | ^ sambam-file.c: In function ‘SamBam_writer_add_read’: sambam-file.c:1746:78: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 1746 | int refID = HashTableGet(writer -> chromosome_name_table, chro_name) - NULL - 1; | ^ sambam-file.c:1752:91: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 1752 | nextRefID = HashTableGet(writer -> chromosome_name_table, next_chro_name) - NULL - 1; | ^ sambam-file.c: In function ‘SamBam_writer_sort_bins_to_BAM_test_bins’: sambam-file.c:1946:56: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1946 | ArrayListPush(win16k_list, NULL+ this_Vpos); | ^ sambam-file.c:1950:65: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1950 | ArrayList * this_bin_chunks = HashTableGet(bin_tab, NULL+binno+1); | ^ sambam-file.c:1950:71: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1950 | ArrayList * this_bin_chunks = HashTableGet(bin_tab, NULL+binno+1); | ^ readSummary.c: In function ‘add_bin_new_tags’: readSummary.c:2644:47: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 2644 | int intv = vals[tagi] - NULL; | ^ sambam-file.c:1953:43: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1953 | HashTablePut(bin_tab, NULL+binno+1, this_bin_chunks); | ^ sambam-file.c:1953:49: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1953 | HashTablePut(bin_tab, NULL+binno+1, this_bin_chunks); | ^ sambam-file.c:1954:45: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1954 | ArrayListPush(bin_list, NULL+binno); | ^ sambam-file.c:1962:96: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 1962 | diff -=(this_bin_chunks -> elementList [ this_bin_chunks -> numOfElements - 1] - NULL)>>16; | ^ sambam-file.c:1964:101: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1964 | this_bin_chunks -> elementList [ this_bin_chunks -> numOfElements -1] = NULL+this_Vpos + block_len+4; | ^ sambam-file.c:1964:112: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1964 | this_bin_chunks -> elementList [ this_bin_chunks -> numOfElements -1] = NULL+this_Vpos + block_len+4; | ^ sambam-file.c:1964:123: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1964 | this_bin_chunks -> elementList [ this_bin_chunks -> numOfElements -1] = NULL+this_Vpos + block_len+4; | ^ sambam-file.c:1972:53: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1972 | ArrayListPush(this_bin_chunks, NULL + this_Vpos); | ^ sambam-file.c:1973:53: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1973 | ArrayListPush(this_bin_chunks, NULL + this_Vpos + block_len+4); | ^ sambam-file.c:1973:65: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1973 | ArrayListPush(this_bin_chunks, NULL + this_Vpos + block_len+4); | ^ sambam-file.c:1973:76: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1973 | ArrayListPush(this_bin_chunks, NULL + this_Vpos + block_len+4); | ^ sambam-file.c: In function ‘SamBam_writer_sorted_compress’: sambam-file.c:1981:37: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 1981 | int this_thread_no = vptr[1]-NULL; | ^ sambam-file.c: In function ‘SamBam_thread_wait_merge_write’: readSummary.c: In function ‘compress_read_detail_BAM’: readSummary.c:2706:38: warning: overflow in conversion from ‘int’ to ‘char’ changes value from ‘255’ to ‘-1’ [-Woverflow] 2706 | bam_buf[9] = 0xff; // OS | ^~~~ sambam-file.c:2015:69: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2015 | HashTablePut(writer -> block_no_p1_to_vpos_tab, NULL+1+writer -> writer_threads[thread_no].bam_block_no, NULL+fpos); | ^ sambam-file.c:2015:71: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2015 | HashTablePut(writer -> block_no_p1_to_vpos_tab, NULL+1+writer -> writer_threads[thread_no].bam_block_no, NULL+fpos); | ^ readSummary.c: In function ‘write_read_details_FP’: readSummary.c:2799:29: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2799 | vals[1]=NULL+feature_count; | ^ sambam-file.c:2015:126: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2015 | HashTablePut(writer -> block_no_p1_to_vpos_tab, NULL+1+writer -> writer_threads[thread_no].bam_block_no, NULL+fpos); | ^ readSummary.c: In function ‘warning_anno_BAM_chromosomes’: readSummary.c:2830:58: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2830 | HashTablePut(BAM_chro_tab, BAM_chro, NULL+1); | ^ readSummary.c:2838:86: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2838 | HashTablePut(ANNO_chro_tab, global_context -> exontable_chr[x1], NULL+1); | ^ sambam-file.c: In function ‘SamBam_writer_merge_chunks’: sambam-file.c:2173:45: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 2173 | ll[0] = ArrayListGet(chs, i)-NULL; | ^ sambam-file.c:2174:47: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 2174 | ll[1] = ArrayListGet(chs, i+1)-NULL; | ^ sambam-file.c:2181:32: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2181 | ArrayListPush(chs, NULL+ll0[0]); | ^ sambam-file.c:2182:32: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2182 | ArrayListPush(chs, NULL+ll0[1]); | ^ sambam-file.c:2185:80: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 2185 | long long last_end = ArrayListGet(chs, chs -> numOfElements-1) -NULL; | ^ sambam-file.c:2192:73: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2192 | chs-> elementList[chs -> numOfElements-1] = NULL+max(ll_this[1],last_end); | ^ sambam-file.c:2194:48: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2194 | ArrayListPush(chs, NULL+ll_this[0]); | ^ sambam-file.c:2195:48: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2195 | ArrayListPush(chs, NULL+ll_this[1]); | ^ sambam-file.c: In function ‘SamBam_writer_optimize_bins_level’: sambam-file.c:2211:53: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 2211 | int binno = ArrayListGet(bin_arr, i)-NULL; | ^ sambam-file.c:2213:77: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2213 | ArrayList * old_bin_arr = HashTableGet(bin_tab, NULL+1+binno); | ^ sambam-file.c:2213:79: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2213 | ArrayList * old_bin_arr = HashTableGet(bin_tab, NULL+1+binno); | ^ sambam-file.c:2215:59: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2215 | HashTablePut(new_tab, NULL+1+binno, ArrayListDuplicate(old_bin_arr)); | ^ sambam-file.c:2215:61: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2215 | HashTablePut(new_tab, NULL+1+binno, ArrayListDuplicate(old_bin_arr)); | ^ sambam-file.c:2216:61: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2216 | ArrayListPush(new_arrs, NULL+binno); | ^ sambam-file.c:2224:53: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 2224 | int binno = ArrayListGet(bin_arr, i)-NULL; | ^ sambam-file.c:2226:71: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2226 | ArrayList * small_bin_arr = HashTableGet(bin_tab, NULL+1+binno); | ^ sambam-file.c:2226:73: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2226 | ArrayList * small_bin_arr = HashTableGet(bin_tab, NULL+1+binno); | ^ sambam-file.c:2233:78: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 2233 | long long this_start = ArrayListGet(small_bin_arr, j)-NULL; | ^ sambam-file.c:2234:78: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 2234 | long long this_end = ArrayListGet(small_bin_arr, j+1)-NULL; | ^ sambam-file.c:2243:80: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2243 | ArrayList * parent_bin_arr = HashTableGet(new_tab, NULL+1+parent_binno); | ^ sambam-file.c:2243:82: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2243 | ArrayList * parent_bin_arr = HashTableGet(new_tab, NULL+1+parent_binno); | ^ sambam-file.c:2246:59: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2246 | HashTablePut(new_tab, NULL+1+parent_binno, parent_bin_arr); | ^ sambam-file.c:2246:61: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2246 | HashTablePut(new_tab, NULL+1+parent_binno, parent_bin_arr); | ^ sambam-file.c:2247:61: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2247 | ArrayListPush(new_arrs, NULL+parent_binno); | ^ sambam-file.c:2253:51: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2253 | HashTablePut(new_tab, NULL+1+binno, ArrayListDuplicate(small_bin_arr)); | ^ sambam-file.c:2253:53: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2253 | HashTablePut(new_tab, NULL+1+binno, ArrayListDuplicate(small_bin_arr)); | ^ sambam-file.c:2254:54: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2254 | ArrayListPush(new_arrs, NULL + binno); | ^ readSummary.c: In function ‘add_fragment_supported_junction’: readSummary.c:3463:49: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 3463 | srInt_64 count_junc = count_ptr - NULL; | ^ readSummary.c:3464:69: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 3464 | HashTablePut(junction_counting_table, this_key, NULL+count_junc + 1); | ^ readSummary.c:3464:81: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 3464 | HashTablePut(junction_counting_table, this_key, NULL+count_junc + 1); | ^ readSummary.c:3475:48: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 3475 | count_junc = count_ptr - NULL; | ^ readSummary.c:3476:73: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 3476 | HashTablePut(splicing_point_table, lr_key, NULL + count_junc + 1); | ^ readSummary.c:3476:86: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 3476 | HashTablePut(splicing_point_table, lr_key, NULL + count_junc + 1); | ^ sambam-file.c:2260:54: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 2260 | int binno = ArrayListGet(new_arrs, i)-NULL; | ^ sambam-file.c:2262:71: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2262 | ArrayList * large_bin_arr = HashTableGet(new_tab, NULL+1+binno); | ^ sambam-file.c:2262:73: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2262 | ArrayList * large_bin_arr = HashTableGet(new_tab, NULL+1+binno); | ^ sambam-file.c: In function ‘SamBam_write_BAI_for_1chr’: sambam-file.c:2317:60: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 2317 | int bin_no = ArrayListGet(*bins_list, bini)-NULL; | ^ sambam-file.c:2318:79: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2318 | ArrayList * chunks_list = HashTableGet(*bin_chunks_table, NULL+ bin_no+1); | ^ sambam-file.c:2318:87: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2318 | ArrayList * chunks_list = HashTableGet(*bin_chunks_table, NULL+ bin_no+1); | ^ sambam-file.c:2325:84: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 2325 | long long int Voff_st = ArrayListGet(chunks_list, chunk_i) - NULL; | ^ sambam-file.c:2326:86: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 2326 | long long int Voff_en = ArrayListGet(chunks_list, chunk_i+1) - NULL; | ^ sambam-file.c:2298:88: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2298 | #define SAMBAM_Block2Vpos(v) (v)=((HashTableGet(writer -> block_no_p1_to_vpos_tab, NULL+(v>>16)+1)-NULL )<<16 )|(v & 0xffff); | ^ sambam-file.c:2327:25: note: in expansion of macro ‘SAMBAM_Block2Vpos’ 2327 | SAMBAM_Block2Vpos(Voff_st); | ^~~~~~~~~~~~~~~~~ sambam-file.c:2298:96: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2298 | #define SAMBAM_Block2Vpos(v) (v)=((HashTableGet(writer -> block_no_p1_to_vpos_tab, NULL+(v>>16)+1)-NULL )<<16 )|(v & 0xffff); | ^ sambam-file.c:2327:25: note: in expansion of macro ‘SAMBAM_Block2Vpos’ 2327 | SAMBAM_Block2Vpos(Voff_st); | ^~~~~~~~~~~~~~~~~ sambam-file.c:2298:99: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 2298 | #define SAMBAM_Block2Vpos(v) (v)=((HashTableGet(writer -> block_no_p1_to_vpos_tab, NULL+(v>>16)+1)-NULL )<<16 )|(v & 0xffff); | ^ sambam-file.c:2327:25: note: in expansion of macro ‘SAMBAM_Block2Vpos’ 2327 | SAMBAM_Block2Vpos(Voff_st); | ^~~~~~~~~~~~~~~~~ sambam-file.c:2298:88: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2298 | #define SAMBAM_Block2Vpos(v) (v)=((HashTableGet(writer -> block_no_p1_to_vpos_tab, NULL+(v>>16)+1)-NULL )<<16 )|(v & 0xffff); | ^ sambam-file.c:2328:25: note: in expansion of macro ‘SAMBAM_Block2Vpos’ 2328 | SAMBAM_Block2Vpos(Voff_en); | ^~~~~~~~~~~~~~~~~ sambam-file.c:2298:96: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2298 | #define SAMBAM_Block2Vpos(v) (v)=((HashTableGet(writer -> block_no_p1_to_vpos_tab, NULL+(v>>16)+1)-NULL )<<16 )|(v & 0xffff); | ^ sambam-file.c:2328:25: note: in expansion of macro ‘SAMBAM_Block2Vpos’ 2328 | SAMBAM_Block2Vpos(Voff_en); | ^~~~~~~~~~~~~~~~~ sambam-file.c:2298:99: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 2298 | #define SAMBAM_Block2Vpos(v) (v)=((HashTableGet(writer -> block_no_p1_to_vpos_tab, NULL+(v>>16)+1)-NULL )<<16 )|(v & 0xffff); | ^ sambam-file.c:2328:25: note: in expansion of macro ‘SAMBAM_Block2Vpos’ 2328 | SAMBAM_Block2Vpos(Voff_en); | ^~~~~~~~~~~~~~~~~ sambam-file.c:2336:72: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 2336 | long long int Voff = ArrayListGet(*win16k_list , bini) - NULL; | ^ sambam-file.c:2298:88: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2298 | #define SAMBAM_Block2Vpos(v) (v)=((HashTableGet(writer -> block_no_p1_to_vpos_tab, NULL+(v>>16)+1)-NULL )<<16 )|(v & 0xffff); | ^ sambam-file.c:2337:17: note: in expansion of macro ‘SAMBAM_Block2Vpos’ 2337 | SAMBAM_Block2Vpos(Voff); | ^~~~~~~~~~~~~~~~~ sambam-file.c:2298:96: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2298 | #define SAMBAM_Block2Vpos(v) (v)=((HashTableGet(writer -> block_no_p1_to_vpos_tab, NULL+(v>>16)+1)-NULL )<<16 )|(v & 0xffff); | ^ sambam-file.c:2337:17: note: in expansion of macro ‘SAMBAM_Block2Vpos’ 2337 | SAMBAM_Block2Vpos(Voff); | ^~~~~~~~~~~~~~~~~ sambam-file.c:2298:99: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 2298 | #define SAMBAM_Block2Vpos(v) (v)=((HashTableGet(writer -> block_no_p1_to_vpos_tab, NULL+(v>>16)+1)-NULL )<<16 )|(v & 0xffff); | ^ sambam-file.c:2337:17: note: in expansion of macro ‘SAMBAM_Block2Vpos’ 2337 | SAMBAM_Block2Vpos(Voff); | ^~~~~~~~~~~~~~~~~ seek-zlib.c: In function ‘seekgz_open’: seek-zlib.c:136:45: warning: overflow in conversion from ‘int’ to ‘char’ changes value from ‘139’ to ‘-117’ [-Woverflow] 136 | fp -> in_zipped_buffer[1] = 0x8b; | ^~~~ sambam-file.c: In function ‘SamBam_writer_sort_bins_to_BAM’: sambam-file.c:2397:35: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2397 | thparam[1] = NULL + thread_i; | ^ readSummary.c: In function ‘vote_and_add_count’: readSummary.c:3900:58: warning: variable ‘assignment_target_number’ set but not used [-Wunused-but-set-variable] 3900 | srInt_64 assignment_target_number = tmp_voter_id; | ^~~~~~~~~~~~~~~~~~~~~~~~ readSummary.c: In function ‘fc_thread_merge_results’: readSummary.c:4046:93: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 4046 | globval += (cursor -> value - NULL); | ^ readSummary.c:4046:73: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 4046 | globval += (cursor -> value - NULL); | ^~ seek-zlib.c: In function ‘seekgz_load_1_block’: seek-zlib.c:327:75: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 327 | int zipped_data_used = (void *)fp -> stem.next_in - old_next_in; | ^ readSummary.c:4064:93: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 4064 | globval += (cursor -> value - NULL); | ^ readSummary.c:4064:73: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 4064 | globval += (cursor -> value - NULL); | ^~ readSummary.c:4123:69: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 4123 | globval += (cursor -> value - NULL); | ^ readSummary.c:4123:49: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 4123 | globval += (cursor -> value - NULL); | ^~ readSummary.c:4143:69: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 4143 | globval += (cursor -> value - NULL); | ^ sambam-file.c: In function ‘simple_bam_writer_update_index’: readSummary.c:4143:49: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 4143 | globval += (cursor -> value - NULL); | ^~ sambam-file.c:2531:107: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2531 | struct simple_bam_writer_index_per_chro * index_chro = HashTableGet(writer -> index_per_chro, NULL+chro_no+1); | ^ sambam-file.c:2531:115: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2531 | struct simple_bam_writer_index_per_chro * index_chro = HashTableGet(writer -> index_per_chro, NULL+chro_no+1); | ^ sambam-file.c:2534:60: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2534 | HashTablePut(writer -> index_per_chro, NULL+chro_no+1, index_chro); | ^ sambam-file.c:2534:68: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2534 | HashTablePut(writer -> index_per_chro, NULL+chro_no+1, index_chro); | ^ sambam-file.c:2546:56: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2546 | ArrayListPush(win16k_list, NULL+ this_Vpos); | ^ sambam-file.c:2549:89: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2549 | ArrayList * this_bin_chunks = HashTableGet(index_chro -> index_binP1_table, NULL+binno+1); | ^ sambam-file.c:2549:95: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2549 | ArrayList * this_bin_chunks = HashTableGet(index_chro -> index_binP1_table, NULL+binno+1); | ^ readSummary.c:3970:32: warning: unused variable ‘sample_i’ [-Wunused-variable] 3970 | int xk1, xk2, ret = 0, sample_i; | ^~~~~~~~ sambam-file.c:2552:67: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2552 | HashTablePut(index_chro -> index_binP1_table, NULL+binno+1, this_bin_chunks); | ^ sambam-file.c:2552:73: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2552 | HashTablePut(index_chro -> index_binP1_table, NULL+binno+1, this_bin_chunks); | ^ sambam-file.c:2553:67: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2553 | ArrayListPush(index_chro -> index_binP0_list, NULL+binno); | ^ sambam-file.c:2560:96: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 2560 | diff -=(this_bin_chunks -> elementList [ this_bin_chunks -> numOfElements - 1] - NULL)>>16; | ^ sambam-file.c:2562:102: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2562 | this_bin_chunks -> elementList [ this_bin_chunks -> numOfElements - 1] = NULL+this_Vpos + binlen + 4; | ^ sambam-file.c:2562:113: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2562 | this_bin_chunks -> elementList [ this_bin_chunks -> numOfElements - 1] = NULL+this_Vpos + binlen + 4; | ^ sambam-file.c:2562:122: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2562 | this_bin_chunks -> elementList [ this_bin_chunks -> numOfElements - 1] = NULL+this_Vpos + binlen + 4; | ^ sambam-file.c:2568:53: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2568 | ArrayListPush(this_bin_chunks, NULL + this_Vpos); | ^ sambam-file.c:2569:53: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2569 | ArrayListPush(this_bin_chunks, NULL + this_Vpos + binlen+4); | ^ sambam-file.c:2569:65: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2569 | ArrayListPush(this_bin_chunks, NULL + this_Vpos + binlen+4); | ^ sambam-file.c:2569:73: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2569 | ArrayListPush(this_bin_chunks, NULL + this_Vpos + binlen+4); | ^ sambam-file.c: In function ‘simple_bam_write_compressed_block’: sambam-file.c:2574:88: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2574 | if(block_number >= 0)HashTablePut(writer -> bam_blockP1_to_offset0B_table, NULL+1+block_number, NULL+ftello(writer -> bam_FP)); | ^ sambam-file.c:2574:90: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2574 | if(block_number >= 0)HashTablePut(writer -> bam_blockP1_to_offset0B_table, NULL+1+block_number, NULL+ftello(writer -> bam_FP)); | ^ sambam-file.c:2574:109: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2574 | if(block_number >= 0)HashTablePut(writer -> bam_blockP1_to_offset0B_table, NULL+1+block_number, NULL+ftello(writer -> bam_FP)); | ^ sambam-file.c: In function ‘simple_bam_write’: sambam-file.c:2591:21: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2591 | bin += concatinate_binlen; | ^~ sambam-file.c: In function ‘simple_bam_close’: sambam-file.c:2635:113: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2635 | struct simple_bam_writer_index_per_chro *this_idx = HashTableGet(writer -> index_per_chro , NULL+1+chri); | ^ sambam-file.c:2635:115: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2635 | struct simple_bam_writer_index_per_chro *this_idx = HashTableGet(writer -> index_per_chro , NULL+1+chri); | ^ sambam-file.c:2647:93: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 2647 | int binno = ArrayListGet(this_idx -> index_binP0_list, bini)-NULL; | ^ sambam-file.c:2648:103: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2648 | ArrayList * bingaps = HashTableGet(this_idx -> index_binP1_table, NULL+1+binno); | ^ sambam-file.c:2648:105: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2648 | ArrayList * bingaps = HashTableGet(this_idx -> index_binP1_table, NULL+1+binno); | ^ sambam-file.c:2653:97: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 2653 | srInt_64 rposone, vposone = ArrayListGet(bingaps , gapi)-NULL; | ^ sambam-file.c:2625:115: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2625 | #define vpos_to_rpos rposone = (vposone & 0xffff ) + ( (HashTableGet(writer -> bam_blockP1_to_offset0B_table, NULL+1+(vposone >>16)) - NULL) << 16 ) | ^ sambam-file.c:2654:41: note: in expansion of macro ‘vpos_to_rpos’ 2654 | vpos_to_rpos; | ^~~~~~~~~~~~ sambam-file.c:2625:117: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2625 | #define vpos_to_rpos rposone = (vposone & 0xffff ) + ( (HashTableGet(writer -> bam_blockP1_to_offset0B_table, NULL+1+(vposone >>16)) - NULL) << 16 ) | ^ sambam-file.c:2654:41: note: in expansion of macro ‘vpos_to_rpos’ 2654 | vpos_to_rpos; | ^~~~~~~~~~~~ sambam-file.c:2625:134: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 2625 | #define vpos_to_rpos rposone = (vposone & 0xffff ) + ( (HashTableGet(writer -> bam_blockP1_to_offset0B_table, NULL+1+(vposone >>16)) - NULL) << 16 ) | ^ sambam-file.c:2654:41: note: in expansion of macro ‘vpos_to_rpos’ 2654 | vpos_to_rpos; | ^~~~~~~~~~~~ sambam-file.c:2661:106: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 2661 | srInt_64 rposone, vposone = ArrayListGet(this_idx -> win16k_list , bini )-NULL; | ^ sambam-file.c:2625:115: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2625 | #define vpos_to_rpos rposone = (vposone & 0xffff ) + ( (HashTableGet(writer -> bam_blockP1_to_offset0B_table, NULL+1+(vposone >>16)) - NULL) << 16 ) | ^ sambam-file.c:2662:33: note: in expansion of macro ‘vpos_to_rpos’ 2662 | vpos_to_rpos; | ^~~~~~~~~~~~ sambam-file.c:2625:117: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2625 | #define vpos_to_rpos rposone = (vposone & 0xffff ) + ( (HashTableGet(writer -> bam_blockP1_to_offset0B_table, NULL+1+(vposone >>16)) - NULL) << 16 ) | ^ sambam-file.c:2662:33: note: in expansion of macro ‘vpos_to_rpos’ 2662 | vpos_to_rpos; | ^~~~~~~~~~~~ sambam-file.c:2625:134: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 2625 | #define vpos_to_rpos rposone = (vposone & 0xffff ) + ( (HashTableGet(writer -> bam_blockP1_to_offset0B_table, NULL+1+(vposone >>16)) - NULL) << 16 ) | ^ sambam-file.c:2662:33: note: in expansion of macro ‘vpos_to_rpos’ 2662 | vpos_to_rpos; | ^~~~~~~~~~~~ tx-unique.c: In function ‘txunique_process_gene_chro’: tx-unique.c:292:101: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 292 | int old_all_bases = HashTableGet(context -> result_table, hash_key) - NULL; | ^ tx-unique.c:294:86: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 294 | HashTablePut(context -> result_table, hash_key, NULL + old_all_bases + total_bases); | ^ tx-unique.c:294:102: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 294 | HashTablePut(context -> result_table, hash_key, NULL + old_all_bases + total_bases); | ^ tx-unique.c:298:97: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 298 | old_all_bases = HashTableGet(context -> result_table, hash_key) - NULL; | ^ tx-unique.c:300:86: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 300 | HashTablePut(context -> result_table, hash_key, NULL + old_all_bases + unique_bases); | ^ tx-unique.c:300:102: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 300 | HashTablePut(context -> result_table, hash_key, NULL + old_all_bases + unique_bases); | ^ tx-unique.c: In function ‘txunique_process_write_gene’: tx-unique.c:320:80: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 320 | int all_bases = HashTableGet(context -> result_table, hash_key)-NULL-1; | ^ tx-unique.c:322:83: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 322 | int unique_bases = HashTableGet(context -> result_table, hash_key)-NULL-1; | ^ readSummary.c: In function ‘determine_jcount_gene_transcript_report’: readSummary.c:5420:91: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 5420 | HashTablePut(edge1P1_table, txp_ptr -> transcript_id, NULL+1+edge1_dist); | ^ readSummary.c:5420:93: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 5420 | HashTablePut(edge1P1_table, txp_ptr -> transcript_id, NULL+1+edge1_dist); | ^ readSummary.c:5423:103: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 5423 | HashTablePut(edge1exonNo_table, txp_ptr -> transcript_id, NULL+1+exactly_matched_exon_no); | ^ readSummary.c:5423:105: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 5423 | HashTablePut(edge1exonNo_table, txp_ptr -> transcript_id, NULL+1+exactly_matched_exon_no); | ^ readSummary.c:5448:91: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 5448 | HashTablePut(edge2P1_table, txp_ptr -> transcript_id, NULL+1+edge2_dist); | ^ readSummary.c:5448:93: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 5448 | HashTablePut(edge2P1_table, txp_ptr -> transcript_id, NULL+1+edge2_dist); | ^ readSummary.c:5451:103: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 5451 | HashTablePut(edge2exonNo_table, txp_ptr -> transcript_id, NULL+1+exactly_matched_exon_no); | ^ readSummary.c:5451:105: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 5451 | HashTablePut(edge2exonNo_table, txp_ptr -> transcript_id, NULL+1+exactly_matched_exon_no); | ^ readSummary.c:5461:81: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 5461 | int edge1_ptr = HashTableGet(edge1P1_table, edge1_txnid)-NULL; | ^ readSummary.c:5463:81: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 5463 | int edge2_ptr = HashTableGet(edge2P1_table, edge1_txnid)-NULL; | ^ readSummary.c:5465:92: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 5465 | int exonno_1 = HashTableGet(edge1exonNo_table, edge1_txnid)-NULL-1; | ^ readSummary.c:5466:92: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 5466 | int exonno_2 = HashTableGet(edge2exonNo_table, edge1_txnid)-NULL-1; | ^ readSummary.c:5478:77: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 5478 | HashTablePut(out_gene_tab, txnptr -> gene_name, NULL+1); | ^ readSummary.c:5479:80: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 5479 | HashTablePut(out_txn_tab, txnptr -> transcript_id, NULL+1); | ^ readSummary.c:5510:104: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 5510 | srInt_64 edge_dist = HashTableGet(this_side_olay_tab, this_side_txn_id)-NULL; | ^ readSummary.c:5513:106: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 5513 | HashTablePut(this_side_reported_genes, txn_ptr -> gene_name, NULL+1); | ^ readSummary.c: In function ‘find_nearest_gene_dist’: readSummary.c:5603:84: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 5603 | HashTablePut(gene_name_tab, gene_name, NULL+1); | ^ readSummary.c: In function ‘fc_write_final_junctions’: readSummary.c:5651:97: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 5651 | unsigned int old_supp = HashTableGet(merged_splicing_table, ky) - NULL; | ^ readSummary.c:5652:62: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 5652 | old_supp += (cursor -> value - NULL); | ^ readSummary.c:5653:77: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 5653 | HashTablePut(merged_splicing_table, ky, NULL+old_supp); | ^ readSummary.c:5671:85: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 5671 | HashTablePut(merged_junction_table, ky, NULL+1); | ^ readSummary.c:5831:83: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 5831 | srInt_64 count = HashTableGet(junc_table, key_list[ky_i]) - NULL; | ^ readSummary.c:5724:21: warning: unused variable ‘unique_junctions’ [-Wunused-variable] 5724 | int unique_junctions = 0; | ^~~~~~~~~~~~~~~~ readSummary.c:5700:20: warning: unused variable ‘ky_i2’ [-Wunused-variable] 5700 | int ky_i1, ky_i2; | ^~~~~ readSummary.c:5700:13: warning: unused variable ‘ky_i1’ [-Wunused-variable] 5700 | int ky_i1, ky_i2; | ^~~~~ readSummary.c:5698:81: warning: unused variable ‘gene_name_tail’ [-Wunused-variable] 5698 | char * gene_names = malloc(max_junction_genes * FEATURE_NAME_LENGTH), * gene_name_tail; | ^~~~~~~~~~~~~~ readSummary.c: In function ‘readSummary’: readSummary.c:5971:52: warning: variable ‘scrna_total_BAM_no’ set but not used [-Wunused-but-set-variable] 5971 | int isGTF, n_input_files=0,is_dual_index, scrna_total_BAM_no; | ^~~~~~~~~~~~~~~~~~ cell-counts.c: In function ‘cellCounts_find_hits_for_mapped_section’: cell-counts.c:2375:19: warning: ‘search_start’ may be used uninitialized [-Wmaybe-uninitialized] 2375 | if(search_start>0xffffff00) return; | ^ cell-counts.c:2364:30: note: ‘search_start’ was declared here 2364 | unsigned int search_start, search_end, search_block_id; | ^~~~~~~~~~~~ readSummary.c: In function ‘vote_and_add_count’: readSummary.c:3833:66: warning: ‘longest_overlap_score’ may be used uninitialized [-Wmaybe-uninitialized] 3833 | if(longest_overlap_score > scoring_numbers[score_x1]) scoring_numbers[score_x1] = 0; | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ readSummary.c:3602:51: note: ‘longest_overlap_score’ was declared here 3602 | int scoring_count = 0, score_x1, longest_overlap_score; | ^~~~~~~~~~~~~~~~~~~~~ cell-counts.c: In function ‘cellCounts_write_final_other_events’: cell-counts.c:7130:40: warning: array subscript -999 is below array bounds of ‘HashTable *[65]’ [-Warray-bounds=] 7130 | ArrayList * small_large_keys = HashTableKeys(cct_context -> chroEvent_detail_table[sample_i]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cell-counts.c:324:27: note: while referencing ‘chroEvent_detail_table’ 324 | HashTable * chroEvent_detail_table[MAX_SCRNA_SAMPLE_NUMBER+1]; | ^~~~~~~~~~~~~~~~~~~~~~ cell-counts.c:7135:86: warning: array subscript -999 is below array bounds of ‘HashTable *[65]’ [-Warray-bounds=] 7135 | chroEvent_t * ed = HashTableGet(cct_context -> chroEvent_detail_table[sample_i] , ArrayListGet(small_large_keys,x1)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ cell-counts.c:324:27: note: while referencing ‘chroEvent_detail_table’ 324 | HashTable * chroEvent_detail_table[MAX_SCRNA_SAMPLE_NUMBER+1]; | ^~~~~~~~~~~~~~~~~~~~~~ gcc -shared -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -L/usr/local/lib64 -o Rsubread.so HelperFunctions.o LRMbase-index.o LRMchro-event.o LRMfile-io.o LRMhashtable.o LRMhelper.o LRMseek-zlib.o LRMsorted-hashtable.o R_wrapper.o RsimReads.o SNPCalling.o aligner.o atgcContent.o build-sam-index.o cell-counts.o core-bigtable.o core-indel.o core-interface-aligner.o core-interface-subjunc.o core-junction.o core.o detection-calls.o detectionCall.o detectionCallAnnotation.o exon-algorithms.o exon-align-indel.o exon-align.o flattenAnnotations.o fullscan.o fusion-align.o gen_rand_reads.o gene-algorithms.o gene-value-index.o hashtable.o index-builder.o input-blc.o input-files.o interval_merge.o long-hashtable.o longread-mapping.o mergeVCF.o processExons.o propmapped.o qualityScores.o read-repair.o readSummary.o removeDupReads.o sam2bed.o sambam-file.o seek-zlib.o sorted-hashtable.o sublog.o tx-unique.o -lz -lpthread -DMAKE_FOR_EXON make[2]: Leaving directory '/tmp/Rtmp7CAajn/working_dir/RtmpMVIi7w/R.INSTALL3712d43eaab2d5/Rsubread/src' make[2]: Entering directory '/tmp/Rtmp7CAajn/working_dir/RtmpMVIi7w/R.INSTALL3712d43eaab2d5/Rsubread/src' make[2]: Leaving directory '/tmp/Rtmp7CAajn/working_dir/RtmpMVIi7w/R.INSTALL3712d43eaab2d5/Rsubread/src' installing to /tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/00LOCK-Rsubread/00new/Rsubread/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (Rsubread) The downloaded source packages are in '/tmp/Rtmp7CAajn/working_dir/RtmpjyO0Wr/downloaded_packages' 'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package = "BiocManager")' for details. Replacement repositories: CRAN: file:///data/gannet/ripley/R Bioconductor version 3.23 (BiocManager 1.30.27), R Under development (unstable) (2026-03-03 r89531) Installing package(s) 'Rsamtools' also installing the dependency 'Biostrings' trying URL 'https://bioconductor.org/packages/3.23/bioc/src/contrib/Biostrings_2.79.4.tar.gz' trying URL 'https://bioconductor.org/packages/3.23/bioc/src/contrib/Rsamtools_2.27.0.tar.gz' * installing *source* package ‘Biostrings’ ... ** this is package ‘Biostrings’ version ‘2.79.4’ ** using staged installation ** libs using C compiler: ‘gcc (GCC) 15.2.1 20260123 (Red Hat 15.2.1-7)’ make[2]: Entering directory '/tmp/Rtmp7CAajn/working_dir/RtmpyUIR7f/R.INSTALL371fe514215431/Biostrings/src' gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c BAB_class.c -o BAB_class.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c BitMatrix.c -o BitMatrix.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c IRanges_stubs.c -o IRanges_stubs.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c MIndex_class.c -o MIndex_class.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c PreprocessedTB_class.c -o PreprocessedTB_class.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c R_init_Biostrings.c -o R_init_Biostrings.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c RoSeqs_utils.c -o RoSeqs_utils.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c S4Vectors_stubs.c -o S4Vectors_stubs.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c SparseList_utils.c -o SparseList_utils.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c XStringSetList_class.c -o XStringSetList_class.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c XStringSet_class.c -o XStringSet_class.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c XString_class.c -o XString_class.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c XVector_stubs.c -o XVector_stubs.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c find_palindromes.c -o find_palindromes.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c gtestsim.c -o gtestsim.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c inject_code.c -o inject_code.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c lcsuffix.c -o lcsuffix.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c letter_frequency.c -o letter_frequency.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c lowlevel_matching.c -o lowlevel_matching.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c match_PWM.c -o match_PWM.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c match_pattern.c -o match_pattern.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c match_pattern_boyermoore.c -o match_pattern_boyermoore.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c match_pattern_indels.c -o match_pattern_indels.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c match_pattern_shiftor.c -o match_pattern_shiftor.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c match_pdict.c -o match_pdict.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c match_pdict_ACtree2.c -o match_pdict_ACtree2.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c match_pdict_Twobit.c -o match_pdict_Twobit.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c match_pdict_utils.c -o match_pdict_utils.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c match_reporting.c -o match_reporting.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c read_fasta_files.c -o read_fasta_files.o BitMatrix.c:299:13: warning: ‘BitMatrix_print’ defined but not used [-Wunused-function] 299 | static void BitMatrix_print(BitMatrix *bitmat) | ^~~~~~~~~~~~~~~ SparseList_utils.c: In function ‘_get_val_from_env’: SparseList_utils.c:42:34: error: implicit declaration of function ‘NAMED’ [-Wimplicit-function-declaration] 42 | if (ans != R_NilValue && NAMED(ans) == 0) | ^~~~~ SparseList_utils.c:43:17: error: implicit declaration of function ‘SET_NAMED’; did you mean ‘SET_NAMES’? [-Wimplicit-function-declaration] 43 | SET_NAMED(ans, 1); | ^~~~~~~~~ | SET_NAMES make[2]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: SparseList_utils.o] Error 1 gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c read_fastq_files.c -o read_fastq_files.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c replaceAt.c -o replaceAt.o MIndex_class.c: In function ‘SparseMIndex_endIndex’: MIndex_class.c:184:27: warning: unused variable ‘poffsets_order’ [-Wunused-variable] 184 | IntAE *poffsets, *poffsets_order; | ^~~~~~~~~~~~~~ match_pdict_utils.c: In function ‘match_ppheadtail0’: match_pdict_utils.c:653:56: warning: unused variable ‘ncol’ [-Wunused-variable] 653 | int nelt, min_safe_tb_end, max_safe_tb_end, j, ncol; | ^~~~ match_pdict_utils.c: In function ‘match_ppheadtail’: match_pdict_utils.c:713:13: warning: unused variable ‘nelt’ [-Wunused-variable] 713 | int nelt, nkey0, nkey1, nkey2, i, key; | ^~~~ match_pdict_utils.c: In function ‘_match_pdict_all_flanks’: match_pdict_utils.c:820:51: warning: unused variable ‘subtotal_NFC’ [-Wunused-variable] 820 | static unsigned long int total_NFC = 0UL, subtotal_NFC = 0UL; | ^~~~~~~~~~~~ match_pdict_utils.c:820:34: warning: unused variable ‘total_NFC’ [-Wunused-variable] 820 | static unsigned long int total_NFC = 0UL, subtotal_NFC = 0UL; | ^~~~~~~~~ match_pdict_utils.c:819:40: warning: unused variable ‘NFC’ [-Wunused-variable] 819 | unsigned long int ndup, nloci, NFC; // NFC = Number of Flank Comparisons | ^~~ match_pdict_utils.c:819:33: warning: unused variable ‘nloci’ [-Wunused-variable] 819 | unsigned long int ndup, nloci, NFC; // NFC = Number of Flank Comparisons | ^~~~~ match_pdict_utils.c:819:27: warning: unused variable ‘ndup’ [-Wunused-variable] 819 | unsigned long int ndup, nloci, NFC; // NFC = Number of Flank Comparisons | ^~~~ match_pdict_utils.c: At top level: match_pdict_utils.c:261:13: warning: ‘match_headtail_by_loc’ defined but not used [-Wunused-function] 261 | static void match_headtail_by_loc(const HeadTail *headtail, | ^~~~~~~~~~~~~~~~~~~~~ gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c replace_letter_at.c -o replace_letter_at.o In file included from /data/gannet/ripley/R/R-devel/include/Rdefines.h:41, from /tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include/S4Vectors_defines.h:18, from /tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include/IRanges_defines.h:18, from ../inst/include/Biostrings_defines.h:18, from Biostrings.h:1, from match_pdict_Twobit.c:10: In function ‘Twobit_asLIST’, inlined from ‘build_Twobit’ at match_pdict_Twobit.c:145:2: match_pdict_Twobit.c:75:27: warning: ‘twobit_sign2pos’ may be used uninitialized [-Wmaybe-uninitialized] 75 | PROTECT(ans_elt = new_XInteger_from_tag("XInteger", twobit_sign2pos)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /data/gannet/ripley/R/R-devel/include/Rinternals.h:366:36: note: in definition of macro ‘PROTECT’ 366 | #define PROTECT(s) Rf_protect(s) | ^ match_pdict_Twobit.c: In function ‘build_Twobit’: match_pdict_Twobit.c:110:19: note: ‘twobit_sign2pos’ was declared here 110 | SEXP ans, twobit_sign2pos; | ^~~~~~~~~~~~~~~ match_pdict_ACtree2.c: In function ‘split_and_move_pointers’: match_pdict_ACtree2.c:1031:17: warning: variable ‘node0’ set but not used [-Wunused-but-set-variable] 1031 | ACnode *node0, *node1, *node2; | ^~~~~ match_pdict_ACtree2.c: In function ‘merge_pointers’: match_pdict_ACtree2.c:1076:17: warning: variable ‘node0’ set but not used [-Wunused-but-set-variable] 1076 | ACnode *node0, *node1, *node2; | ^~~~~ match_pattern_indels.c:7:13: warning: ‘test_match_pattern_indels’ defined but not used [-Wunused-function] 7 | static void test_match_pattern_indels(const char *p, const char *s, | ^~~~~~~~~~~~~~~~~~~~~~~~~ letter_frequency.c: In function ‘XStringSet_two_way_letter_frequency’: letter_frequency.c:957:48: warning: unused variable ‘x_pos’ [-Wunused-variable] 957 | int x_width, y_width, x_length, *ans_mat, i, x_pos; | ^~~~~ match_pdict_ACtree2.c: At top level: match_pdict_ACtree2.c:602:21: warning: ‘a_nice_max_nodeextbuf_nelt’ defined but not used [-Wunused-function] 602 | static unsigned int a_nice_max_nodeextbuf_nelt(int nnodes) | ^~~~~~~~~~~~~~~~~~~~~~~~~~ match_pdict_ACtree2.c:139:13: warning: ‘debug_node_counting_functions’ defined but not used [-Wunused-function] 139 | static void debug_node_counting_functions(int maxdepth) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c strutils.c -o strutils.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c translate.c -o translate.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c unstrsplit_methods.c -o unstrsplit_methods.o XStringSet_class.c: In function ‘new_XStringSet_from_CHARACTER’: XStringSet_class.c:124:17: warning: ‘lkup_len’ may be used uninitialized [-Wmaybe-uninitialized] 124 | _copy_CHARSXP_to_Chars_holder(&ans_elt_holder, x_elt, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 125 | INTEGER(start)[i], lkup0, lkup_len); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ XStringSet_class.c:103:22: note: ‘lkup_len’ was declared here 103 | int ans_len, lkup_len, i; | ^~~~~~~~ gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c utils.c -o utils.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c xscat.c -o xscat.o read_fastq_files.c: In function ‘parse_FASTQ_file’: read_fastq_files.c:408:28: warning: ‘dont_load’ may be used uninitialized [-Wmaybe-uninitialized] 408 | if (dont_load || loader->new_qualid_hook == NULL) | ^ read_fastq_files.c:311:26: note: ‘dont_load’ was declared here 311 | lineinrecno, dont_load; | ^~~~~~~~~ In file included from /data/gannet/ripley/R/R-devel/include/Rdefines.h:41, from /tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include/S4Vectors_defines.h:18, from /tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include/IRanges_defines.h:18, from ../inst/include/Biostrings_defines.h:18, from Biostrings.h:1, from xscat.c:1: xscat.c: In function ‘XString_xscat’: /data/gannet/ripley/R/R-devel/include/Rdefines.h:91:33: warning: ‘ans_length’ may be used uninitialized [-Wmaybe-uninitialized] 91 | #define NEW_RAW(n) Rf_allocVector(RAWSXP,n) | ^~~~~~~~~~~~~~~~~~~~~~~~ /data/gannet/ripley/R/R-devel/include/Rinternals.h:366:36: note: in definition of macro ‘PROTECT’ 366 | #define PROTECT(s) Rf_protect(s) | ^ xscat.c:38:27: note: in expansion of macro ‘NEW_RAW’ 38 | PROTECT(ans_tag = NEW_RAW(ans_length)); | ^~~~~~~ xscat.c:18:20: note: ‘ans_length’ was declared here 18 | int nargs, ans_length, tag_offset, j; | ^~~~~~~~~~ xscat.c:52:23: warning: ‘ans_classname’ may be used uninitialized [-Wmaybe-uninitialized] 52 | PROTECT(ans = new_XRaw_from_tag(ans_classname, ans_tag)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /data/gannet/ripley/R/R-devel/include/Rinternals.h:366:36: note: in definition of macro ‘PROTECT’ 366 | #define PROTECT(s) Rf_protect(s) | ^ xscat.c:20:21: note: ‘ans_classname’ was declared here 20 | const char *ans_classname; | ^~~~~~~~~~~~~ utils.c: In function ‘_get_twobit_signature’: utils.c:157:16: warning: ‘twobit_sign’ may be used uninitialized [-Wmaybe-uninitialized] 157 | return twobit_sign; | ^~~~~~~~~~~ utils.c:150:16: note: ‘twobit_sign’ was declared here 150 | int i, twobit_sign; | ^~~~~~~~~~~ utils.c: In function ‘_get_twobit_signature_at’: utils.c:174:16: warning: ‘twobit_sign’ may be used uninitialized [-Wmaybe-uninitialized] 174 | return twobit_sign; | ^~~~~~~~~~~ utils.c:164:19: note: ‘twobit_sign’ was declared here 164 | int i, j, twobit_sign; | ^~~~~~~~~~~ xscat.c: In function ‘XStringSet_xscat’: /data/gannet/ripley/R/R-devel/include/Rdefines.h:85:33: warning: ‘ans_length’ may be used uninitialized [-Wmaybe-uninitialized] 85 | #define NEW_INTEGER(n) Rf_allocVector(INTSXP,n) | ^~~~~~~~~~~~~~~~~~~~~~~~ /data/gannet/ripley/R/R-devel/include/Rinternals.h:366:36: note: in definition of macro ‘PROTECT’ 366 | #define PROTECT(s) Rf_protect(s) | ^ xscat.c:91:29: note: in expansion of macro ‘NEW_INTEGER’ 91 | PROTECT(ans_width = NEW_INTEGER(ans_length)); | ^~~~~~~~~~~ xscat.c:66:39: note: ‘ans_length’ was declared here 66 | int nargs, *arg_lengths, *ii, ans_length, i, j, *width; | ^~~~~~~~~~ xscat.c:108:23: warning: ‘ans_element_type’ may be used uninitialized [-Wmaybe-uninitialized] 108 | PROTECT(ans = _alloc_XStringSet(ans_element_type, ans_width)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /data/gannet/ripley/R/R-devel/include/Rinternals.h:366:36: note: in definition of macro ‘PROTECT’ 366 | #define PROTECT(s) Rf_protect(s) | ^ xscat.c:68:21: note: ‘ans_element_type’ was declared here 68 | const char *ans_element_type; | ^~~~~~~~~~~~~~~~ In function ‘vcount_PDict3Parts_XStringSet’, inlined from ‘vmatch_PDict3Parts_XStringSet’ at match_pdict.c:508:10: match_pdict.c:419:33: warning: ‘ans_col’ may be used uninitialized [-Wmaybe-uninitialized] 419 | ans_col += tb_length; | ~~~~~~~~^~~~~~~~~~~~ match_pdict.c: In function ‘vmatch_PDict3Parts_XStringSet’: match_pdict.c:392:65: note: ‘ans_col’ was declared here 392 | int tb_length, S_length, collapse0, i, j, match_count, *ans_col; | ^~~~~~~ In function ‘vcount_XStringSet_XStringSet’, inlined from ‘vmatch_XStringSet_XStringSet’ at match_pdict.c:542:10: match_pdict.c:470:41: warning: ‘ans_elt’ may be used uninitialized [-Wmaybe-uninitialized] 470 | ans_elt += P_length; | ~~~~~~~~^~~~~~~~~~~ match_pdict.c: In function ‘vmatch_XStringSet_XStringSet’: match_pdict.c:441:64: note: ‘ans_elt’ was declared here 441 | int P_length, S_length, collapse0, i, j, match_count, *ans_elt; | ^~~~~~~ make[2]: Target 'all' not remade because of errors. make[2]: Leaving directory '/tmp/Rtmp7CAajn/working_dir/RtmpyUIR7f/R.INSTALL371fe514215431/Biostrings/src' ERROR: compilation failed for package ‘Biostrings’ * removing ‘/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/Biostrings’ ERROR: dependency ‘Biostrings’ is not available for package ‘Rsamtools’ Perhaps try a variation of: install.packages('Biostrings') * removing ‘/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/Rsamtools’ The downloaded source packages are in '/tmp/Rtmp7CAajn/working_dir/RtmpjyO0Wr/downloaded_packages' 'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package = "BiocManager")' for details. Replacement repositories: CRAN: file:///data/gannet/ripley/R Bioconductor version 3.23 (BiocManager 1.30.27), R Under development (unstable) (2026-03-03 r89531) Installing package(s) 'limma' also installing the dependency 'statmod' trying URL 'https://bioconductor.org/packages/3.23/bioc/src/contrib/limma_3.67.0.tar.gz' Content type 'application/x-gzip' length 2849446 bytes (2.7 MB) ================================================== downloaded 2.7 MB * installing *source* package ‘statmod’ ... ** this is package ‘statmod’ version ‘1.5.1’ ** package ‘statmod’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc (GCC) 15.2.1 20260123 (Red Hat 15.2.1-7)’ using Fortran compiler: ‘GNU Fortran (GCC) 15.2.1 20260123 (Red Hat 15.2.1-7)’ make[2]: Entering directory '/tmp/Rtmp7CAajn/working_dir/Rtmpqoum7w/R.INSTALL3723e331793876/statmod/src' gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c expectedDeviance.c -o expectedDeviance.o gfortran -fpic -g -O2 -mtune=native -Wall -pedantic -c gaussq2.f -o gaussq2.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c init.c -o init.o gcc -shared -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -L/usr/local/lib64 -o statmod.so expectedDeviance.o gaussq2.o init.o -lgfortran -lm -lquadmath make[2]: Leaving directory '/tmp/Rtmp7CAajn/working_dir/Rtmpqoum7w/R.INSTALL3723e331793876/statmod/src' make[2]: Entering directory '/tmp/Rtmp7CAajn/working_dir/Rtmpqoum7w/R.INSTALL3723e331793876/statmod/src' make[2]: Leaving directory '/tmp/Rtmp7CAajn/working_dir/Rtmpqoum7w/R.INSTALL3723e331793876/statmod/src' installing to /tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/00LOCK-statmod/00new/statmod/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (statmod) * installing *source* package ‘limma’ ... ** this is package ‘limma’ version ‘3.67.0’ ** using staged installation ** libs using C compiler: ‘gcc (GCC) 15.2.1 20260123 (Red Hat 15.2.1-7)’ make[2]: Entering directory '/tmp/Rtmp7CAajn/working_dir/Rtmp0NPDHD/R.INSTALL372ba8637c08bc/limma/src' gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c init.c -o init.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c normexp.c -o normexp.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c weighted_lowess.c -o weighted_lowess.o normexp.c: In function ‘fit_saddle_nelder_mead’: normexp.c:166:78: warning: ISO C forbids passing argument 9 of ‘nmmin’ between function pointer and ‘void *’ [-Wpedantic] 166 | nmmin(3, par, parsOut, Fmin, normexp_m2loglik_saddle, fail, abstol, intol, &ex, alpha, beta, gamma, trace, fncount, maxit); | ^~~ In file included from normexp.c:13: /data/gannet/ripley/R/R-devel/include/R_ext/Applic.h:72:58: note: expected ‘void *’ but argument is of type ‘void (*)(void)’ 72 | int *fail, double abstol, double intol, void *ex, | ~~~~~~^~ gcc -shared -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -L/usr/local/lib64 -o limma.so init.o normexp.o weighted_lowess.o make[2]: Leaving directory '/tmp/Rtmp7CAajn/working_dir/Rtmp0NPDHD/R.INSTALL372ba8637c08bc/limma/src' make[2]: Entering directory '/tmp/Rtmp7CAajn/working_dir/Rtmp0NPDHD/R.INSTALL372ba8637c08bc/limma/src' make[2]: Leaving directory '/tmp/Rtmp7CAajn/working_dir/Rtmp0NPDHD/R.INSTALL372ba8637c08bc/limma/src' installing to /tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/00LOCK-limma/00new/limma/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (limma) The downloaded source packages are in '/tmp/Rtmp7CAajn/working_dir/RtmpjyO0Wr/downloaded_packages' 'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package = "BiocManager")' for details. Replacement repositories: CRAN: file:///data/gannet/ripley/R Bioconductor version 3.23 (BiocManager 1.30.27), R Under development (unstable) (2026-03-03 r89531) Installing package(s) 'HTSFilter' also installing the dependencies 'SparseArray', 'DelayedArray', 'locfit', 'SummarizedExperiment', 'edgeR', 'DESeq2' trying URL 'https://bioconductor.org/packages/3.23/bioc/src/contrib/SparseArray_1.11.10.tar.gz' trying URL 'https://bioconductor.org/packages/3.23/bioc/src/contrib/DelayedArray_0.37.0.tar.gz' trying URL 'https://bioconductor.org/packages/3.23/bioc/src/contrib/SummarizedExperiment_1.41.1.tar.gz' trying URL 'https://bioconductor.org/packages/3.23/bioc/src/contrib/edgeR_4.9.4.tar.gz' trying URL 'https://bioconductor.org/packages/3.23/bioc/src/contrib/DESeq2_1.51.6.tar.gz' trying URL 'https://bioconductor.org/packages/3.23/bioc/src/contrib/HTSFilter_1.51.0.tar.gz' * installing *source* package ‘SparseArray’ ... ** this is package ‘SparseArray’ version ‘1.11.10’ ** using staged installation ** libs using C compiler: ‘gcc (GCC) 15.2.1 20260123 (Red Hat 15.2.1-7)’ make[2]: Entering directory '/tmp/Rtmp7CAajn/working_dir/RtmpGjLroL/R.INSTALL374074593c8157/SparseArray/src' gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c ExtendableJaggedArray.c -o ExtendableJaggedArray.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c IRanges_stubs.c -o IRanges_stubs.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c OPBufTree.c -o OPBufTree.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c R_init_SparseArray.c -o R_init_SparseArray.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c Rvector_summarization.c -o Rvector_summarization.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c Rvector_utils.c -o Rvector_utils.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c S4Vectors_stubs.c -o S4Vectors_stubs.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c SBT_utils.c -o SBT_utils.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c SVT_SparseArray_class.c -o SVT_SparseArray_class.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c SparseArray_Arith_methods.c -o SparseArray_Arith_methods.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c SparseArray_Compare_methods.c -o SparseArray_Compare_methods.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c SparseArray_Complex_methods.c -o SparseArray_Complex_methods.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c SparseArray_Logic_methods.c -o SparseArray_Logic_methods.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c SparseArray_Math_methods.c -o SparseArray_Math_methods.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c SparseArray_abind.c -o SparseArray_abind.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c SparseArray_aperm.c -o SparseArray_aperm.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c SparseArray_dim_tuning.c -o SparseArray_dim_tuning.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c SparseArray_matrixStats.c -o SparseArray_matrixStats.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c SparseArray_misc_methods.c -o SparseArray_misc_methods.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c SparseArray_subassignment.c -o SparseArray_subassignment.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c SparseArray_subsetting.c -o SparseArray_subsetting.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c SparseArray_summarization.c -o SparseArray_summarization.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c SparseMatrix_mult.c -o SparseMatrix_mult.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c SparseVec.c -o SparseVec.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c SparseVec_Arith.c -o SparseVec_Arith.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c SparseVec_Compare.c -o SparseVec_Compare.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c SparseVec_Logic.c -o SparseVec_Logic.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c SparseVec_Math.c -o SparseVec_Math.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c SparseVec_dotprod.c -o SparseVec_dotprod.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c SparseVec_subassignment.c -o SparseVec_subassignment.o Rvector_utils.c: In function ‘_fill_Rvector_block_with_val’: Rvector_utils.c:245:43: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration] 245 | _set_elts_to_val(TYPEOF(Rvector), DATAPTR(Rvector), | ^~~~~~~ | DATAPTR_RO Rvector_utils.c:245:43: error: passing argument 2 of ‘_set_elts_to_val’ makes pointer from integer without a cast [-Wint-conversion] 245 | _set_elts_to_val(TYPEOF(Rvector), DATAPTR(Rvector), | ^~~~~~~~~~~~~~~~ | | | int Rvector_utils.c:99:45: note: expected ‘void *’ but argument is of type ‘int’ 99 | void _set_elts_to_val(SEXPTYPE Rtype, void *x, R_xlen_t offset, R_xlen_t n, | ~~~~~~^ Rvector_utils.c: In function ‘_fill_Rvector_block_with_zeros’: Rvector_utils.c:263:34: error: passing argument 2 of ‘_set_elts_to_zero’ makes pointer from integer without a cast [-Wint-conversion] 263 | _set_elts_to_zero(Rtype, DATAPTR(Rvector), block_offset, block_len); | ^~~~~~~~~~~~~~~~ | | | int Rvector_utils.c:122:46: note: expected ‘void *’ but argument is of type ‘int’ 122 | void _set_elts_to_zero(SEXPTYPE Rtype, void *x, R_xlen_t offset, R_xlen_t n) | ~~~~~~^ Rvector_utils.c: In function ‘_fill_Rvector_block_with_ones’: Rvector_utils.c:271:43: error: passing argument 2 of ‘_set_elts_to_one’ makes pointer from integer without a cast [-Wint-conversion] 271 | _set_elts_to_one(TYPEOF(Rvector), DATAPTR(Rvector), | ^~~~~~~~~~~~~~~~ | | | int Rvector_utils.c:137:45: note: expected ‘void *’ but argument is of type ‘int’ 137 | void _set_elts_to_one(SEXPTYPE Rtype, void *x, R_xlen_t offset, R_xlen_t n) | ~~~~~~^ Rvector_utils.c: In function ‘_fill_Rvector_block_with_minus_one’: Rvector_utils.c:280:49: error: passing argument 2 of ‘_set_elts_to_minus_one’ makes pointer from integer without a cast [-Wint-conversion] 280 | _set_elts_to_minus_one(TYPEOF(Rvector), DATAPTR(Rvector), | ^~~~~~~~~~~~~~~~ | | | int Rvector_utils.c:159:51: note: expected ‘void *’ but argument is of type ‘int’ 159 | void _set_elts_to_minus_one(SEXPTYPE Rtype, void *x, | ~~~~~~^ Rvector_utils.c: In function ‘_fill_Rvector_block_with_NA’: Rvector_utils.c:296:32: error: passing argument 2 of ‘_set_elts_to_NA’ makes pointer from integer without a cast [-Wint-conversion] 296 | _set_elts_to_NA(Rtype, DATAPTR(Rvector), block_offset, block_len); | ^~~~~~~~~~~~~~~~ | | | int Rvector_utils.c:184:44: note: expected ‘void *’ but argument is of type ‘int’ 184 | void _set_elts_to_NA(SEXPTYPE Rtype, void *x, R_xlen_t offset, R_xlen_t n) | ~~~~~~^ Rvector_utils.c: In function ‘_fill_Rvector_subset_with_zeros’: Rvector_utils.c:463:43: error: passing argument 2 of ‘_set_selected_elts_to_zero’ makes pointer from integer without a cast [-Wint-conversion] 463 | _set_selected_elts_to_zero(Rtype, DATAPTR(Rvector), | ^~~~~~~~~~~~~~~~ | | | int Rvector_utils.c:365:55: note: expected ‘void *’ but argument is of type ‘int’ 365 | void _set_selected_elts_to_zero(SEXPTYPE Rtype, void *x, | ~~~~~~^ Rvector_utils.c: In function ‘_fill_Rvector_subset_with_ones’: Rvector_utils.c:473:52: error: passing argument 2 of ‘_set_selected_elts_to_one’ makes pointer from integer without a cast [-Wint-conversion] 473 | _set_selected_elts_to_one(TYPEOF(Rvector), DATAPTR(Rvector), | ^~~~~~~~~~~~~~~~ | | | int Rvector_utils.c:397:54: note: expected ‘void *’ but argument is of type ‘int’ 397 | void _set_selected_elts_to_one(SEXPTYPE Rtype, void *x, | ~~~~~~^ In file included from SparseMatrix_mult.c:14: SparseVec.h: In function ‘toSparseVec’: SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration] 125 | sv.nzvals = DATAPTR(nzvals); | ^~~~~~~ | DATAPTR_RO SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion] 125 | sv.nzvals = DATAPTR(nzvals); | ^ In file included from SparseVec.c:4: SparseVec.h: In function ‘toSparseVec’: SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration] 125 | sv.nzvals = DATAPTR(nzvals); | ^~~~~~~ | DATAPTR_RO SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion] 125 | sv.nzvals = DATAPTR(nzvals); | ^ In file included from SparseArray_Math_methods.c:7: SparseVec.h: In function ‘toSparseVec’: SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration] 125 | sv.nzvals = DATAPTR(nzvals); | ^~~~~~~ | DATAPTR_RO SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion] 125 | sv.nzvals = DATAPTR(nzvals); | ^ In file included from SparseArray_Logic_methods.c:7: SparseVec.h: In function ‘toSparseVec’: SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration] 125 | sv.nzvals = DATAPTR(nzvals); | ^~~~~~~ | DATAPTR_RO SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion] 125 | sv.nzvals = DATAPTR(nzvals); | ^ In file included from leaf_utils.h:6, from R_init_SparseArray.c:6: SparseVec.h: In function ‘toSparseVec’: SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration] 125 | sv.nzvals = DATAPTR(nzvals); | ^~~~~~~ | DATAPTR_RO SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion] 125 | sv.nzvals = DATAPTR(nzvals); | ^ In file included from SparseArray_Compare_methods.c:7: SparseVec.h: In function ‘toSparseVec’: SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration] 125 | sv.nzvals = DATAPTR(nzvals); | ^~~~~~~ | DATAPTR_RO SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion] 125 | sv.nzvals = DATAPTR(nzvals); | ^ In file included from leaf_utils.h:6, from SparseArray_Complex_methods.c:6: SparseVec.h: In function ‘toSparseVec’: SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration] 125 | sv.nzvals = DATAPTR(nzvals); | ^~~~~~~ | DATAPTR_RO SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion] 125 | sv.nzvals = DATAPTR(nzvals); | ^ make[2]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: SparseVec.o] Error 1 gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c SparseVec_subsetting.c -o SparseVec_subsetting.o In file included from SparseVec_dotprod.h:4, from SparseVec_dotprod.c:4: SparseVec.h: In function ‘toSparseVec’: SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration] 125 | sv.nzvals = DATAPTR(nzvals); | ^~~~~~~ | DATAPTR_RO SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion] 125 | sv.nzvals = DATAPTR(nzvals); | ^ make[2]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: SparseArray_Math_methods.o] Error 1 gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c XVector_stubs.c -o XVector_stubs.o In file included from leaf_utils.h:6, from ExtendableJaggedArray.c:8: SparseVec.h: In function ‘toSparseVec’: SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration] 125 | sv.nzvals = DATAPTR(nzvals); | ^~~~~~~ | DATAPTR_RO make[2]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: SparseArray_Logic_methods.o] Error 1 gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c argcheck_utils.c -o argcheck_utils.o SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion] 125 | sv.nzvals = DATAPTR(nzvals); | ^ SparseMatrix_mult.c: At top level: SparseMatrix_mult.c:346:13: warning: ‘crossprod2_doublemat_doubleSV’ defined but not used [-Wunused-function] 346 | static void crossprod2_doublemat_doubleSV( | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SparseMatrix_mult.c:306:13: warning: ‘crossprod2_doubleSV_doublemat’ defined but not used [-Wunused-function] 306 | static void crossprod2_doubleSV_doublemat( | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from leaf_utils.h:6, from SparseArray_aperm.c:16: SparseVec.h: In function ‘toSparseVec’: SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration] 125 | sv.nzvals = DATAPTR(nzvals); | ^~~~~~~ | DATAPTR_RO SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion] 125 | sv.nzvals = DATAPTR(nzvals); | ^ In file included from SparseVec_Logic.h:6, from SparseVec_Logic.c:4: SparseVec.h: In function ‘toSparseVec’: SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration] 125 | sv.nzvals = DATAPTR(nzvals); | ^~~~~~~ | DATAPTR_RO SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion] 125 | sv.nzvals = DATAPTR(nzvals); | ^ In file included from SparseArray_matrixStats.c:15: SparseVec.h: In function ‘toSparseVec’: SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration] 125 | sv.nzvals = DATAPTR(nzvals); | ^~~~~~~ | DATAPTR_RO make[2]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: Rvector_utils.o] Error 1 SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion] 125 | sv.nzvals = DATAPTR(nzvals); | ^ gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c coerceVector2.c -o coerceVector2.o make[2]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: SparseMatrix_mult.o] Error 1 gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c leaf_utils.c -o leaf_utils.o In file included from leaf_utils.h:6, from SparseArray_misc_methods.c:8: SparseVec.h: In function ‘toSparseVec’: SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration] 125 | sv.nzvals = DATAPTR(nzvals); | ^~~~~~~ | DATAPTR_RO SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion] 125 | sv.nzvals = DATAPTR(nzvals); | ^ In file included from leaf_utils.h:6, from SparseArray_dim_tuning.c:7: SparseVec.h: In function ‘toSparseVec’: SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration] 125 | sv.nzvals = DATAPTR(nzvals); | ^~~~~~~ | DATAPTR_RO SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion] 125 | sv.nzvals = DATAPTR(nzvals); | ^ make[2]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: R_init_SparseArray.o] Error 1 gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c misc_utils.c -o misc_utils.o In file included from leaf_utils.h:6, from SparseArray_abind.c:11: SparseVec.h: In function ‘toSparseVec’: SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration] 125 | sv.nzvals = DATAPTR(nzvals); | ^~~~~~~ | DATAPTR_RO SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion] 125 | sv.nzvals = DATAPTR(nzvals); | ^ In file included from leaf_utils.h:6, from SparseArray_summarization.c:12: SparseVec.h: In function ‘toSparseVec’: SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration] 125 | sv.nzvals = DATAPTR(nzvals); | ^~~~~~~ | DATAPTR_RO SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion] 125 | sv.nzvals = DATAPTR(nzvals); | ^ SparseArray_matrixStats.c: In function ‘C_colStats_SVT’: SparseArray_matrixStats.c:275:26: error: passing argument 6 of ‘REC_colStats_SVT’ makes pointer from integer without a cast [-Wint-conversion] 275 | DATAPTR(ans), ans_Rtype, | ^~~~~~~~~~~~ | | | int SparseArray_matrixStats.c:203:23: note: expected ‘void *’ but argument is of type ‘int’ 203 | void *out, SEXPTYPE out_Rtype, | ~~~~~~^~~ In file included from leaf_utils.h:6, from SparseArray_subassignment.c:13: SparseVec.h: In function ‘toSparseVec’: SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration] 125 | sv.nzvals = DATAPTR(nzvals); | ^~~~~~~ | DATAPTR_RO SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion] 125 | sv.nzvals = DATAPTR(nzvals); | ^ make[2]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: SparseArray_Complex_methods.o] Error 1 gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c randomSparseArray.c -o randomSparseArray.o SparseArray_matrixStats.c: In function ‘C_rowStats_SVT’: SparseArray_matrixStats.c:1178:25: error: passing argument 8 of ‘SVT_rowMinsMaxs’ makes pointer from integer without a cast [-Wint-conversion] 1178 | DATAPTR(ans), LENGTH(ans), ans_Rtype, | ^~~~~~~~~~~~ | | | int SparseArray_matrixStats.c:966:23: note: expected ‘void *’ but argument is of type ‘int’ 966 | void *out, R_xlen_t out_len, SEXPTYPE out_Rtype, | ~~~~~~^~~ make[2]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: SparseArray_Compare_methods.o] Error 1 gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c readSparseCSV.c -o readSparseCSV.o In file included from SparseVec_Compare.h:6, from SparseVec_Compare.c:4: SparseVec.h: In function ‘toSparseVec’: SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration] 125 | sv.nzvals = DATAPTR(nzvals); | ^~~~~~~ | DATAPTR_RO SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion] 125 | sv.nzvals = DATAPTR(nzvals); | ^ In file included from leaf_utils.h:6, from SVT_SparseArray_class.c:9: SparseVec.h: In function ‘toSparseVec’: SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration] 125 | sv.nzvals = DATAPTR(nzvals); | ^~~~~~~ | DATAPTR_RO SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion] 125 | sv.nzvals = DATAPTR(nzvals); | ^ In file included from SparseArray_Arith_methods.c:7: SparseVec.h: In function ‘toSparseVec’: SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration] 125 | sv.nzvals = DATAPTR(nzvals); | ^~~~~~~ | DATAPTR_RO SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion] 125 | sv.nzvals = DATAPTR(nzvals); | ^ make[2]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: SparseVec_Logic.o] Error 1 gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c rowsum_methods.c -o rowsum_methods.o In file included from leaf_utils.h:6, from SBT_utils.c:7: SparseVec.h: In function ‘toSparseVec’: SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration] 125 | sv.nzvals = DATAPTR(nzvals); | ^~~~~~~ | DATAPTR_RO SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion] 125 | sv.nzvals = DATAPTR(nzvals); | ^ In file included from SparseVec_subassignment.h:6, from SparseVec_subassignment.c:4: SparseVec.h: In function ‘toSparseVec’: make[2]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: SparseVec_dotprod.o] Error 1 gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c sparseMatrix_utils.c -o sparseMatrix_utils.o SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration] 125 | sv.nzvals = DATAPTR(nzvals); | ^~~~~~~ | DATAPTR_RO SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion] 125 | sv.nzvals = DATAPTR(nzvals); | ^ SparseArray_aperm.c: In function ‘spray_integer_leaf’: SparseArray_aperm.c:724:28: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 724 | nzvals_p = (const type *) DATAPTR(nzvals); \ | ^ SparseArray_aperm.c:746:39: note: in expansion of macro ‘FUNDEF_spray_leaf’ 746 | static inline void spray_integer_leaf FUNDEF_spray_leaf(int) | ^~~~~~~~~~~~~~~~~ SparseArray_aperm.c: In function ‘spray_double_leaf’: SparseArray_aperm.c:724:28: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 724 | nzvals_p = (const type *) DATAPTR(nzvals); \ | ^ SparseArray_aperm.c:747:38: note: in expansion of macro ‘FUNDEF_spray_leaf’ 747 | static inline void spray_double_leaf FUNDEF_spray_leaf(double) | ^~~~~~~~~~~~~~~~~ make[2]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: SparseArray_matrixStats.o] Error 1 gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c test.c -o test.o SparseArray_aperm.c: In function ‘spray_complex_leaf’: SparseArray_aperm.c:724:28: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 724 | nzvals_p = (const type *) DATAPTR(nzvals); \ | ^ SparseArray_aperm.c:748:39: note: in expansion of macro ‘FUNDEF_spray_leaf’ 748 | static inline void spray_complex_leaf FUNDEF_spray_leaf(Rcomplex) | ^~~~~~~~~~~~~~~~~ SparseArray_aperm.c: In function ‘spray_raw_leaf’: SparseArray_aperm.c:724:28: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 724 | nzvals_p = (const type *) DATAPTR(nzvals); \ | ^ SparseArray_aperm.c:749:35: note: in expansion of macro ‘FUNDEF_spray_leaf’ 749 | static inline void spray_raw_leaf FUNDEF_spray_leaf(Rbyte) | ^~~~~~~~~~~~~~~~~ make[2]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: SparseArray_dim_tuning.o] Error 1 gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include' -I'/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c thread_control.c -o thread_control.o make[2]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: SparseArray_summarization.o] Error 1 make[2]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: SparseArray_misc_methods.o] Error 1 In file included from leaf_utils.h:6, from SparseArray_subsetting.c:14: SparseVec.h: In function ‘toSparseVec’: SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration] 125 | sv.nzvals = DATAPTR(nzvals); | ^~~~~~~ | DATAPTR_RO SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion] 125 | sv.nzvals = DATAPTR(nzvals); | ^ In file included from SparseVec_Arith.h:6, from SparseVec_Arith.c:4: SparseVec.h: In function ‘toSparseVec’: SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration] 125 | sv.nzvals = DATAPTR(nzvals); | ^~~~~~~ | DATAPTR_RO SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion] 125 | sv.nzvals = DATAPTR(nzvals); | ^ make[2]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: SparseArray_abind.o] Error 1 make[2]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: ExtendableJaggedArray.o] Error 1 Rvector_summarization.c:1370:12: warning: ‘count_NA_list_elts’ defined but not used [-Wunused-function] 1370 | static int count_NA_list_elts(SEXP x) | ^~~~~~~~~~~~~~~~~~ Rvector_summarization.c:1360:12: warning: ‘any_NA_list_elt’ defined but not used [-Wunused-function] 1360 | static int any_NA_list_elt(SEXP x) | ^~~~~~~~~~~~~~~ In file included from SparseVec_Math.h:6, from SparseVec_Math.c:4: SparseVec.h: In function ‘toSparseVec’: SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration] 125 | sv.nzvals = DATAPTR(nzvals); | ^~~~~~~ | DATAPTR_RO SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion] 125 | sv.nzvals = DATAPTR(nzvals); | ^ make[2]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: SparseArray_aperm.o] Error 1 make[2]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: SparseArray_subassignment.o] Error 1 make[2]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: SparseVec_subassignment.o] Error 1 make[2]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: SparseArray_Arith_methods.o] Error 1 SparseArray_subsetting.c: In function ‘REC_subset_SVT_as_SVT’: SparseArray_subsetting.c:843:26: warning: comparison between pointer and integer 843 | if (offs != i2 || ans_elt != subSVT) | ^~ make[2]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: SparseVec_Compare.o] Error 1 make[2]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: SVT_SparseArray_class.o] Error 1 In file included from SparseVec_subsetting.h:6, from SparseVec_subsetting.c:4: SparseVec.h: In function ‘toSparseVec’: SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration] 125 | sv.nzvals = DATAPTR(nzvals); | ^~~~~~~ | DATAPTR_RO SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion] 125 | sv.nzvals = DATAPTR(nzvals); | ^ make[2]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: SparseVec_Math.o] Error 1 make[2]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: SBT_utils.o] Error 1 make[2]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: SparseArray_subsetting.o] Error 1 make[2]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: SparseVec_subsetting.o] Error 1 In file included from leaf_utils.h:6, from randomSparseArray.c:6: SparseVec.h: In function ‘toSparseVec’: SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration] 125 | sv.nzvals = DATAPTR(nzvals); | ^~~~~~~ | DATAPTR_RO SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion] 125 | sv.nzvals = DATAPTR(nzvals); | ^ make[2]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: SparseVec_Arith.o] Error 1 In file included from leaf_utils.h:6, from readSparseCSV.c:10: SparseVec.h: In function ‘toSparseVec’: SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration] 125 | sv.nzvals = DATAPTR(nzvals); | ^~~~~~~ | DATAPTR_RO SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion] 125 | sv.nzvals = DATAPTR(nzvals); | ^ make[2]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: randomSparseArray.o] Error 1 In file included from leaf_utils.h:6, from rowsum_methods.c:9: SparseVec.h: In function ‘toSparseVec’: SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration] 125 | sv.nzvals = DATAPTR(nzvals); | ^~~~~~~ | DATAPTR_RO SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion] 125 | sv.nzvals = DATAPTR(nzvals); | ^ make[2]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: readSparseCSV.o] Error 1 In file included from leaf_utils.h:6, from leaf_utils.c:4: SparseVec.h: In function ‘toSparseVec’: SparseVec.h:125:37: error: implicit declaration of function ‘DATAPTR’; did you mean ‘DATAPTR_RO’? [-Wimplicit-function-declaration] 125 | sv.nzvals = DATAPTR(nzvals); | ^~~~~~~ | DATAPTR_RO SparseVec.h:125:35: error: assignment to ‘void *’ from ‘int’ makes pointer from integer without a cast [-Wint-conversion] 125 | sv.nzvals = DATAPTR(nzvals); | ^ make[2]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: rowsum_methods.o] Error 1 leaf_utils.c: In function ‘_make_leaf_from_two_arrays’: leaf_utils.c:132:24: error: passing argument 1 of ‘memcpy’ makes pointer from integer without a cast [-Wint-conversion] 132 | memcpy(DATAPTR(ans_nzvals), nzvals_p, Rtype_size * nzcount); | ^~~~~~~~~~~~~~~~~~~ | | | int In file included from /usr/include/features.h:524, from /usr/include/bits/libc-header-start.h:33, from /usr/include/string.h:26, from /data/gannet/ripley/R/R-devel/include/R_ext/RS.h:34, from /data/gannet/ripley/R/R-devel/include/Rdefines.h:38, from leaf_utils.h:4: /usr/include/bits/string_fortified.h:26:1: note: expected ‘void *’ but argument is of type ‘int’ 26 | __NTH (memcpy (void *__restrict __dest, const void *__restrict __src, | ^~~~~ make[2]: *** [/data/gannet/ripley/R/R-devel/etc/Makeconf:190: leaf_utils.o] Error 1 make[2]: Target 'all' not remade because of errors. make[2]: Leaving directory '/tmp/Rtmp7CAajn/working_dir/RtmpGjLroL/R.INSTALL374074593c8157/SparseArray/src' ERROR: compilation failed for package ‘SparseArray’ * removing ‘/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/SparseArray’ * installing *source* package ‘locfit’ ... ** this is package ‘locfit’ version ‘1.5-9.12’ ** package ‘locfit’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc (GCC) 15.2.1 20260123 (Red Hat 15.2.1-7)’ make[2]: Entering directory '/tmp/Rtmp7CAajn/working_dir/Rtmpzx72rl/R.INSTALL37413970f69828/locfit/src' gcc -std=gnu17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c S_enter.c -o S_enter.o gcc -std=gnu17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c band.c -o band.o gcc -std=gnu17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c dbinom.c -o dbinom.o gcc -std=gnu17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c dens_haz.c -o dens_haz.o gcc -std=gnu17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c dens_int.c -o dens_int.o gcc -std=gnu17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c dens_odi.c -o dens_odi.o gcc -std=gnu17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c density.c -o density.o gcc -std=gnu17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c ev_atree.c -o ev_atree.o gcc -std=gnu17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c ev_interp.c -o ev_interp.o gcc -std=gnu17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c ev_kdtre.c -o ev_kdtre.o gcc -std=gnu17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c ev_main.c -o ev_main.o gcc -std=gnu17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c ev_sphere.c -o ev_sphere.o gcc -std=gnu17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c ev_trian.c -o ev_trian.o gcc -std=gnu17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c family.c -o family.o gcc -std=gnu17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c fitted.c -o fitted.o gcc -std=gnu17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c frend.c -o frend.o gcc -std=gnu17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c lf_adap.c -o lf_adap.o gcc -std=gnu17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c lf_dercor.c -o lf_dercor.o gcc -std=gnu17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c lf_fitfun.c -o lf_fitfun.o gcc -std=gnu17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c lf_nbhd.c -o lf_nbhd.o gcc -std=gnu17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c lf_robust.c -o lf_robust.o gcc -std=gnu17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c lf_vari.c -o lf_vari.o gcc -std=gnu17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c lf_wdiag.c -o lf_wdiag.o gcc -std=gnu17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c lfstr.c -o lfstr.o gcc -std=gnu17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c locfit.c -o locfit.o gcc -std=gnu17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c m_chol.c -o m_chol.o gcc -std=gnu17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c m_eigen.c -o m_eigen.o gcc -std=gnu17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c m_icirc.c -o m_icirc.o gcc -std=gnu17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c m_imont.c -o m_imont.o gcc -std=gnu17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c m_isimp.c -o m_isimp.o In file included from /data/gannet/ripley/R/R-devel/include/R.h:70, from local.h:12, from lf_dercor.c:18: /data/gannet/ripley/R/R-devel/include/R_ext/Boolean.h:66:16: warning: ISO C does not support specifying ‘enum’ underlying types before C23 [-Wpedantic] 66 | typedef enum :int { FALSE = 0, TRUE } Rboolean; // so NOT NA | ^ In file included from /data/gannet/ripley/R/R-devel/include/R.h:70, from local.h:12, from ev_main.c:6: /data/gannet/ripley/R/R-devel/include/R_ext/Boolean.h:66:16: warning: ISO C does not support specifying ‘enum’ underlying types before C23 [-Wpedantic] 66 | typedef enum :int { FALSE = 0, TRUE } Rboolean; // so NOT NA | ^ In file included from /data/gannet/ripley/R/R-devel/include/R.h:70, from local.h:12, from fitted.c:15: /data/gannet/ripley/R/R-devel/include/R_ext/Boolean.h:66:16: warning: ISO C does not support specifying ‘enum’ underlying types before C23 [-Wpedantic] 66 | typedef enum :int { FALSE = 0, TRUE } Rboolean; // so NOT NA | ^ In file included from /data/gannet/ripley/R/R-devel/include/R.h:70, from local.h:12, from family.c:6: /data/gannet/ripley/R/R-devel/include/R_ext/Boolean.h:66:16: warning: ISO C does not support specifying ‘enum’ underlying types before C23 [-Wpedantic] 66 | typedef enum :int { FALSE = 0, TRUE } Rboolean; // so NOT NA | ^ In file included from /data/gannet/ripley/R/R-devel/include/R.h:70, from local.h:12, from frend.c:6: /data/gannet/ripley/R/R-devel/include/R_ext/Boolean.h:66:16: warning: ISO C does not support specifying ‘enum’ underlying types before C23 [-Wpedantic] 66 | typedef enum :int { FALSE = 0, TRUE } Rboolean; // so NOT NA | ^ In file included from /data/gannet/ripley/R/R-devel/include/R.h:70, from local.h:12, from dens_odi.c:19: /data/gannet/ripley/R/R-devel/include/R_ext/Boolean.h:66:16: warning: ISO C does not support specifying ‘enum’ underlying types before C23 [-Wpedantic] 66 | typedef enum :int { FALSE = 0, TRUE } Rboolean; // so NOT NA | ^ In file included from /data/gannet/ripley/R/R-devel/include/R.h:70, from local.h:12, from S_enter.c:14: /data/gannet/ripley/R/R-devel/include/R_ext/Boolean.h:66:16: warning: ISO C does not support specifying ‘enum’ underlying types before C23 [-Wpedantic] 66 | typedef enum :int { FALSE = 0, TRUE } Rboolean; // so NOT NA | ^ In file included from /data/gannet/ripley/R/R-devel/include/R.h:70, from m_eigen.c:6: /data/gannet/ripley/R/R-devel/include/R_ext/Boolean.h:66:16: warning: ISO C does not support specifying ‘enum’ underlying types before C23 [-Wpedantic] 66 | typedef enum :int { FALSE = 0, TRUE } Rboolean; // so NOT NA | ^ In file included from /data/gannet/ripley/R/R-devel/include/R.h:70, from local.h:12, from lfstr.c:24: /data/gannet/ripley/R/R-devel/include/R_ext/Boolean.h:66:16: warning: ISO C does not support specifying ‘enum’ underlying types before C23 [-Wpedantic] 66 | typedef enum :int { FALSE = 0, TRUE } Rboolean; // so NOT NA | ^ In file included from /data/gannet/ripley/R/R-devel/include/R.h:70, from local.h:12, from ev_atree.c:10: /data/gannet/ripley/R/R-devel/include/R_ext/Boolean.h:66:16: warning: ISO C does not support specifying ‘enum’ underlying types before C23 [-Wpedantic] 66 | typedef enum :int { FALSE = 0, TRUE } Rboolean; // so NOT NA | ^ In file included from /data/gannet/ripley/R/R-devel/include/R.h:70, from m_imont.c:13: /data/gannet/ripley/R/R-devel/include/R_ext/Boolean.h:66:16: warning: ISO C does not support specifying ‘enum’ underlying types before C23 [-Wpedantic] 66 | typedef enum :int { FALSE = 0, TRUE } Rboolean; // so NOT NA | ^ In file included from /data/gannet/ripley/R/R-devel/include/R.h:70, from local.h:12, from band.c:6: /data/gannet/ripley/R/R-devel/include/R_ext/Boolean.h:66:16: warning: ISO C does not support specifying ‘enum’ underlying types before C23 [-Wpedantic] 66 | typedef enum :int { FALSE = 0, TRUE } Rboolean; // so NOT NA | ^ In file included from /data/gannet/ripley/R/R-devel/include/R.h:70, from local.h:12, from locfit.c:6: /data/gannet/ripley/R/R-devel/include/R_ext/Boolean.h:66:16: warning: ISO C does not support specifying ‘enum’ underlying types before C23 [-Wpedantic] 66 | typedef enum :int { FALSE = 0, TRUE } Rboolean; // so NOT NA | ^ In file included from /data/gannet/ripley/R/R-devel/include/R.h:70, from local.h:12, from dens_haz.c:25: /data/gannet/ripley/R/R-devel/include/R_ext/Boolean.h:66:16: warning: ISO C does not support specifying ‘enum’ underlying types before C23 [-Wpedantic] 66 | typedef enum :int { FALSE = 0, TRUE } Rboolean; // so NOT NA | ^ In file included from /data/gannet/ripley/R/R-devel/include/R.h:70, from local.h:12, from ev_trian.c:6: /data/gannet/ripley/R/R-devel/include/R_ext/Boolean.h:66:16: warning: ISO C does not support specifying ‘enum’ underlying types before C23 [-Wpedantic] 66 | typedef enum :int { FALSE = 0, TRUE } Rboolean; // so NOT NA | ^ In file included from /data/gannet/ripley/R/R-devel/include/R.h:70, from local.h:12, from lf_fitfun.c:23: /data/gannet/ripley/R/R-devel/include/R_ext/Boolean.h:66:16: warning: ISO C does not support specifying ‘enum’ underlying types before C23 [-Wpedantic] 66 | typedef enum :int { FALSE = 0, TRUE } Rboolean; // so NOT NA | ^ In file included from /data/gannet/ripley/R/R-devel/include/R.h:70, from local.h:12, from lf_robust.c:26: /data/gannet/ripley/R/R-devel/include/R_ext/Boolean.h:66:16: warning: ISO C does not support specifying ‘enum’ underlying types before C23 [-Wpedantic] 66 | typedef enum :int { FALSE = 0, TRUE } Rboolean; // so NOT NA | ^ In file included from /data/gannet/ripley/R/R-devel/include/R.h:70, from local.h:12, from ev_interp.c:6: /data/gannet/ripley/R/R-devel/include/R_ext/Boolean.h:66:16: warning: ISO C does not support specifying ‘enum’ underlying types before C23 [-Wpedantic] 66 | typedef enum :int { FALSE = 0, TRUE } Rboolean; // so NOT NA | ^ In file included from /data/gannet/ripley/R/R-devel/include/R.h:70, from local.h:12, from lf_nbhd.c:11: /data/gannet/ripley/R/R-devel/include/R_ext/Boolean.h:66:16: warning: ISO C does not support specifying ‘enum’ underlying types before C23 [-Wpedantic] 66 | typedef enum :int { FALSE = 0, TRUE } Rboolean; // so NOT NA | ^ In file included from /data/gannet/ripley/R/R-devel/include/R.h:70, from local.h:12, from dens_int.c:21: /data/gannet/ripley/R/R-devel/include/R_ext/Boolean.h:66:16: warning: ISO C does not support specifying ‘enum’ underlying types before C23 [-Wpedantic] 66 | typedef enum :int { FALSE = 0, TRUE } Rboolean; // so NOT NA | ^ In file included from /data/gannet/ripley/R/R-devel/include/R.h:70, from local.h:12, from lf_adap.c:13: /data/gannet/ripley/R/R-devel/include/R_ext/Boolean.h:66:16: warning: ISO C does not support specifying ‘enum’ underlying types before C23 [-Wpedantic] 66 | typedef enum :int { FALSE = 0, TRUE } Rboolean; // so NOT NA | ^ In file included from /data/gannet/ripley/R/R-devel/include/R.h:70, from local.h:12, from ev_sphere.c:9: /data/gannet/ripley/R/R-devel/include/R_ext/Boolean.h:66:16: warning: ISO C does not support specifying ‘enum’ underlying types before C23 [-Wpedantic] 66 | typedef enum :int { FALSE = 0, TRUE } Rboolean; // so NOT NA | ^ In file included from /data/gannet/ripley/R/R-devel/include/R.h:70, from local.h:12, from density.c:6: /data/gannet/ripley/R/R-devel/include/R_ext/Boolean.h:66:16: warning: ISO C does not support specifying ‘enum’ underlying types before C23 [-Wpedantic] 66 | typedef enum :int { FALSE = 0, TRUE } Rboolean; // so NOT NA | ^ In file included from /data/gannet/ripley/R/R-devel/include/R.h:70, from local.h:12, from ev_kdtre.c:11: /data/gannet/ripley/R/R-devel/include/R_ext/Boolean.h:66:16: warning: ISO C does not support specifying ‘enum’ underlying types before C23 [-Wpedantic] 66 | typedef enum :int { FALSE = 0, TRUE } Rboolean; // so NOT NA | ^ In file included from /data/gannet/ripley/R/R-devel/include/R.h:70, from local.h:12, from lf_wdiag.c:12: /data/gannet/ripley/R/R-devel/include/R_ext/Boolean.h:66:16: warning: ISO C does not support specifying ‘enum’ underlying types before C23 [-Wpedantic] 66 | typedef enum :int { FALSE = 0, TRUE } Rboolean; // so NOT NA | ^ In file included from /data/gannet/ripley/R/R-devel/include/R.h:70, from local.h:12, from lf_vari.c:11: /data/gannet/ripley/R/R-devel/include/R_ext/Boolean.h:66:16: warning: ISO C does not support specifying ‘enum’ underlying types before C23 [-Wpedantic] 66 | typedef enum :int { FALSE = 0, TRUE } Rboolean; // so NOT NA | ^ m_icirc.c: In function ‘integ_disc’: m_icirc.c:115:14: warning: ‘nr’ may be used uninitialized [-Wmaybe-uninitialized] 115 | for (j=0; jnew_qualid_hook == NULL) | ^ read_fastq_files.c:311:26: note: ‘dont_load’ was declared here 311 | lineinrecno, dont_load; | ^~~~~~~~~ In function ‘vcount_PDict3Parts_XStringSet’, inlined from ‘vmatch_PDict3Parts_XStringSet’ at match_pdict.c:508:10: match_pdict.c:419:33: warning: ‘ans_col’ may be used uninitialized [-Wmaybe-uninitialized] 419 | ans_col += tb_length; | ~~~~~~~~^~~~~~~~~~~~ match_pdict.c: In function ‘vmatch_PDict3Parts_XStringSet’: match_pdict.c:392:65: note: ‘ans_col’ was declared here 392 | int tb_length, S_length, collapse0, i, j, match_count, *ans_col; | ^~~~~~~ In function ‘vcount_XStringSet_XStringSet’, inlined from ‘vmatch_XStringSet_XStringSet’ at match_pdict.c:542:10: match_pdict.c:470:41: warning: ‘ans_elt’ may be used uninitialized [-Wmaybe-uninitialized] 470 | ans_elt += P_length; | ~~~~~~~~^~~~~~~~~~~ match_pdict.c: In function ‘vmatch_XStringSet_XStringSet’: match_pdict.c:441:64: note: ‘ans_elt’ was declared here 441 | int P_length, S_length, collapse0, i, j, match_count, *ans_elt; | ^~~~~~~ In file included from /data/gannet/ripley/R/R-devel/include/Rdefines.h:41, from /tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/S4Vectors/include/S4Vectors_defines.h:18, from /tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/IRanges/include/IRanges_defines.h:18, from ../inst/include/Biostrings_defines.h:18, from Biostrings.h:1, from xscat.c:1: xscat.c: In function ‘XString_xscat’: /data/gannet/ripley/R/R-devel/include/Rdefines.h:91:33: warning: ‘ans_length’ may be used uninitialized [-Wmaybe-uninitialized] 91 | #define NEW_RAW(n) Rf_allocVector(RAWSXP,n) | ^~~~~~~~~~~~~~~~~~~~~~~~ /data/gannet/ripley/R/R-devel/include/Rinternals.h:366:36: note: in definition of macro ‘PROTECT’ 366 | #define PROTECT(s) Rf_protect(s) | ^ xscat.c:38:27: note: in expansion of macro ‘NEW_RAW’ 38 | PROTECT(ans_tag = NEW_RAW(ans_length)); | ^~~~~~~ xscat.c:18:20: note: ‘ans_length’ was declared here 18 | int nargs, ans_length, tag_offset, j; | ^~~~~~~~~~ xscat.c:52:23: warning: ‘ans_classname’ may be used uninitialized [-Wmaybe-uninitialized] 52 | PROTECT(ans = new_XRaw_from_tag(ans_classname, ans_tag)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /data/gannet/ripley/R/R-devel/include/Rinternals.h:366:36: note: in definition of macro ‘PROTECT’ 366 | #define PROTECT(s) Rf_protect(s) | ^ xscat.c:20:21: note: ‘ans_classname’ was declared here 20 | const char *ans_classname; | ^~~~~~~~~~~~~ xscat.c: In function ‘XStringSet_xscat’: /data/gannet/ripley/R/R-devel/include/Rdefines.h:85:33: warning: ‘ans_length’ may be used uninitialized [-Wmaybe-uninitialized] 85 | #define NEW_INTEGER(n) Rf_allocVector(INTSXP,n) | ^~~~~~~~~~~~~~~~~~~~~~~~ /data/gannet/ripley/R/R-devel/include/Rinternals.h:366:36: note: in definition of macro ‘PROTECT’ 366 | #define PROTECT(s) Rf_protect(s) | ^ xscat.c:91:29: note: in expansion of macro ‘NEW_INTEGER’ 91 | PROTECT(ans_width = NEW_INTEGER(ans_length)); | ^~~~~~~~~~~ xscat.c:66:39: note: ‘ans_length’ was declared here 66 | int nargs, *arg_lengths, *ii, ans_length, i, j, *width; | ^~~~~~~~~~ xscat.c:108:23: warning: ‘ans_element_type’ may be used uninitialized [-Wmaybe-uninitialized] 108 | PROTECT(ans = _alloc_XStringSet(ans_element_type, ans_width)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /data/gannet/ripley/R/R-devel/include/Rinternals.h:366:36: note: in definition of macro ‘PROTECT’ 366 | #define PROTECT(s) Rf_protect(s) | ^ xscat.c:68:21: note: ‘ans_element_type’ was declared here 68 | const char *ans_element_type; | ^~~~~~~~~~~~~~~~ utils.c: In function ‘_get_twobit_signature’: utils.c:157:16: warning: ‘twobit_sign’ may be used uninitialized [-Wmaybe-uninitialized] 157 | return twobit_sign; | ^~~~~~~~~~~ utils.c:150:16: note: ‘twobit_sign’ was declared here 150 | int i, twobit_sign; | ^~~~~~~~~~~ utils.c: In function ‘_get_twobit_signature_at’: utils.c:174:16: warning: ‘twobit_sign’ may be used uninitialized [-Wmaybe-uninitialized] 174 | return twobit_sign; | ^~~~~~~~~~~ utils.c:164:19: note: ‘twobit_sign’ was declared here 164 | int i, j, twobit_sign; | ^~~~~~~~~~~ make[2]: Target 'all' not remade because of errors. make[2]: Leaving directory '/tmp/Rtmp7CAajn/working_dir/RtmpvLS3J4/R.INSTALL3757a45cdec9e/Biostrings/src' ERROR: compilation failed for package ‘Biostrings’ * removing ‘/tmp/Rtmp7CAajn/RLIBS_33e6b03dd45874/Biostrings’ The downloaded source packages are in '/tmp/Rtmp7CAajn/working_dir/RtmpjyO0Wr/downloaded_packages' Saving _problems/test-inDAGO_shiny-26.R [ FAIL 1 | WARN 25 | SKIP 0 | PASS 0 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-inDAGO_shiny.R:26:3'): Shiny app is generated ────────────────── Error in `inDAGO()`: The following packages are not installed: ShortRead, rtracklayer, Rsamtools, HTSFilter, Biostrings. To enable all the features of inDAGO install with: if (!requireNamespace('BiocManager', quietly=TRUE)) install.packages('BiocManager') BiocManager::install(c("ShortRead", "rtracklayer", "Rsamtools", "HTSFilter", "Biostrings")) Backtrace: ▆ 1. ├─testthat::expect_s3_class(inDAGO(), "shiny.appobj") at test-inDAGO_shiny.R:26:3 2. │ └─testthat::quasi_label(enquo(object)) 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 4. └─inDAGO::inDAGO() [ FAIL 1 | WARN 25 | SKIP 0 | PASS 0 ] Error: ! Test failures. Execution halted * checking PDF version of manual ... OK * checking HTML version of manual ... OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 1 ERROR See ‘/data/gannet/ripley/R/packages/tests-Suggests/inDAGO.Rcheck/00check.log’ for details. Command exited with non-zero status 1 Time 26:12.36, 2041.68 + 131.21