* using log directory ‘/data/gannet/ripley/R/packages/tests-Suggests/ALA4R.Rcheck’ * using R Under development (unstable) (2021-07-28 r80671) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-stop-on-test-error’ * checking for file ‘ALA4R/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘ALA4R’ version ‘1.9.1’ * 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 ‘ALA4R’ can be installed ... OK * checking package directory ... OK * checking ‘build’ 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 R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... 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 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 ... [11s/11s] 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 contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ [11s/31s] [12s/31s] OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking re-building of vignette outputs ... [254s/285s] WARNING Error(s) in re-building vignettes: --- re-building ‘ALA4R.Rmd’ using rmarkdown Installing packages into '/tmp/Rtmpy0wbVY/RLIBS_3258c769b7f455' (as 'lib' is unspecified) also installing the dependencies 'colorspace', 'fansi', 'pkgconfig', 'cli', 'crayon', 'utf8', 'farver', 'labeling', 'munsell', 'RColorBrewer', 'viridisLite', 'tmvnsim', 'fastmatch', 'igraph', 'quadprog', 'ellipsis', 'generics', 'lifecycle', 'rlang', 'tibble', 'tidyselect', 'vctrs', 'pillar', 'gtable', 'isoband', 'scales', 'withr', 'clusterGeneration', 'coda', 'combinat', 'expm', 'mnormt', 'numDeriv', 'phangorn', 'plotrix', 'scatterplot3d', 'purrr', 'permute' trying URL 'http://cran.us.r-project.org/src/contrib/colorspace_2.0-2.tar.gz' Content type 'application/x-gzip' length 2196563 bytes (2.1 MB) ================================================== downloaded 2.1 MB trying URL 'http://cran.us.r-project.org/src/contrib/fansi_0.5.0.tar.gz' Content type 'application/x-gzip' length 301724 bytes (294 KB) ================================================== downloaded 294 KB trying URL 'http://cran.us.r-project.org/src/contrib/pkgconfig_2.0.3.tar.gz' Content type 'application/x-gzip' length 6080 bytes ================================================== downloaded 6080 bytes trying URL 'http://cran.us.r-project.org/src/contrib/cli_3.0.1.tar.gz' Content type 'application/x-gzip' length 225589 bytes (220 KB) ================================================== downloaded 220 KB trying URL 'http://cran.us.r-project.org/src/contrib/crayon_1.4.1.tar.gz' Content type 'application/x-gzip' length 35769 bytes (34 KB) ================================================== downloaded 34 KB trying URL 'http://cran.us.r-project.org/src/contrib/utf8_1.2.2.tar.gz' Content type 'application/x-gzip' length 240327 bytes (234 KB) ================================================== downloaded 234 KB trying URL 'http://cran.us.r-project.org/src/contrib/farver_2.1.0.tar.gz' Content type 'application/x-gzip' length 1281864 bytes (1.2 MB) ================================================== downloaded 1.2 MB trying URL 'http://cran.us.r-project.org/src/contrib/labeling_0.4.2.tar.gz' Content type 'application/x-gzip' length 10156 bytes ================================================== downloaded 10156 bytes trying URL 'http://cran.us.r-project.org/src/contrib/munsell_0.5.0.tar.gz' Content type 'application/x-gzip' length 182653 bytes (178 KB) ================================================== downloaded 178 KB trying URL 'http://cran.us.r-project.org/src/contrib/RColorBrewer_1.1-2.tar.gz' Content type 'application/x-gzip' length 11532 bytes (11 KB) ================================================== downloaded 11 KB trying URL 'http://cran.us.r-project.org/src/contrib/viridisLite_0.4.0.tar.gz' Content type 'application/x-gzip' length 1267080 bytes (1.2 MB) ================================================== downloaded 1.2 MB trying URL 'http://cran.us.r-project.org/src/contrib/tmvnsim_1.0-2.tar.gz' Content type 'application/x-gzip' length 6052 bytes ================================================== downloaded 6052 bytes trying URL 'http://cran.us.r-project.org/src/contrib/fastmatch_1.1-3.tar.gz' Content type 'application/x-gzip' length 14887 bytes (14 KB) ================================================== downloaded 14 KB trying URL 'http://cran.us.r-project.org/src/contrib/igraph_1.2.6.tar.gz' Content type 'application/x-gzip' length 2715500 bytes (2.6 MB) ================================================== downloaded 2.6 MB trying URL 'http://cran.us.r-project.org/src/contrib/quadprog_1.5-8.tar.gz' Content type 'application/x-gzip' length 36141 bytes (35 KB) ================================================== downloaded 35 KB trying URL 'http://cran.us.r-project.org/src/contrib/ellipsis_0.3.2.tar.gz' Content type 'application/x-gzip' length 8066 bytes ================================================== downloaded 8066 bytes trying URL 'http://cran.us.r-project.org/src/contrib/generics_0.1.0.tar.gz' Content type 'application/x-gzip' length 117834 bytes (115 KB) ================================================== downloaded 115 KB trying URL 'http://cran.us.r-project.org/src/contrib/lifecycle_1.0.0.tar.gz' Content type 'application/x-gzip' length 83389 bytes (81 KB) ================================================== downloaded 81 KB trying URL 'http://cran.us.r-project.org/src/contrib/rlang_0.4.11.tar.gz' Content type 'application/x-gzip' length 861727 bytes (841 KB) ================================================== downloaded 841 KB trying URL 'http://cran.us.r-project.org/src/contrib/tibble_3.1.3.tar.gz' Content type 'application/x-gzip' length 694155 bytes (677 KB) ================================================== downloaded 677 KB trying URL 'http://cran.us.r-project.org/src/contrib/tidyselect_1.1.1.tar.gz' Content type 'application/x-gzip' length 92088 bytes (89 KB) ================================================== downloaded 89 KB trying URL 'http://cran.us.r-project.org/src/contrib/vctrs_0.3.8.tar.gz' Content type 'application/x-gzip' length 782608 bytes (764 KB) ================================================== downloaded 764 KB trying URL 'http://cran.us.r-project.org/src/contrib/pillar_1.6.1.tar.gz' Content type 'application/x-gzip' length 1111747 bytes (1.1 MB) ================================================== downloaded 1.1 MB trying URL 'http://cran.us.r-project.org/src/contrib/gtable_0.3.0.tar.gz' Content type 'application/x-gzip' length 368081 bytes (359 KB) ================================================== downloaded 359 KB trying URL 'http://cran.us.r-project.org/src/contrib/isoband_0.2.5.tar.gz' Content type 'application/x-gzip' length 1671911 bytes (1.6 MB) ================================================== downloaded 1.6 MB trying URL 'http://cran.us.r-project.org/src/contrib/scales_1.1.1.tar.gz' Content type 'application/x-gzip' length 515201 bytes (503 KB) ================================================== downloaded 503 KB trying URL 'http://cran.us.r-project.org/src/contrib/withr_2.4.2.tar.gz' Content type 'application/x-gzip' length 94283 bytes (92 KB) ================================================== downloaded 92 KB trying URL 'http://cran.us.r-project.org/src/contrib/clusterGeneration_1.3.7.tar.gz' Content type 'application/x-gzip' length 56528 bytes (55 KB) ================================================== downloaded 55 KB trying URL 'http://cran.us.r-project.org/src/contrib/coda_0.19-4.tar.gz' Content type 'application/x-gzip' length 74239 bytes (72 KB) ================================================== downloaded 72 KB trying URL 'http://cran.us.r-project.org/src/contrib/combinat_0.0-8.tar.gz' Content type 'application/x-gzip' length 9197 bytes ================================================== downloaded 9197 bytes trying URL 'http://cran.us.r-project.org/src/contrib/expm_0.999-6.tar.gz' Content type 'application/x-gzip' length 151884 bytes (148 KB) ================================================== downloaded 148 KB trying URL 'http://cran.us.r-project.org/src/contrib/mnormt_2.0.2.tar.gz' Content type 'application/x-gzip' length 50606 bytes (49 KB) ================================================== downloaded 49 KB trying URL 'http://cran.us.r-project.org/src/contrib/numDeriv_2016.8-1.1.tar.gz' Content type 'application/x-gzip' length 76053 bytes (74 KB) ================================================== downloaded 74 KB trying URL 'http://cran.us.r-project.org/src/contrib/phangorn_2.7.1.tar.gz' Content type 'application/x-gzip' length 1975903 bytes (1.9 MB) ================================================== downloaded 1.9 MB trying URL 'http://cran.us.r-project.org/src/contrib/plotrix_3.8-1.tar.gz' Content type 'application/x-gzip' length 317856 bytes (310 KB) ================================================== downloaded 310 KB trying URL 'http://cran.us.r-project.org/src/contrib/scatterplot3d_0.3-41.tar.gz' Content type 'application/x-gzip' length 460912 bytes (450 KB) ================================================== downloaded 450 KB trying URL 'http://cran.us.r-project.org/src/contrib/purrr_0.3.4.tar.gz' Content type 'application/x-gzip' length 375062 bytes (366 KB) ================================================== downloaded 366 KB trying URL 'http://cran.us.r-project.org/src/contrib/permute_0.9-5.tar.gz' Content type 'application/x-gzip' length 400033 bytes (390 KB) ================================================== downloaded 390 KB trying URL 'http://cran.us.r-project.org/src/contrib/ape_5.5.tar.gz' Content type 'application/x-gzip' length 1751486 bytes (1.7 MB) ================================================== downloaded 1.7 MB trying URL 'http://cran.us.r-project.org/src/contrib/dplyr_1.0.7.tar.gz' Content type 'application/x-gzip' length 852103 bytes (832 KB) ================================================== downloaded 832 KB trying URL 'http://cran.us.r-project.org/src/contrib/ggplot2_3.3.5.tar.gz' Content type 'application/x-gzip' length 3063309 bytes (2.9 MB) ================================================== downloaded 2.9 MB trying URL 'http://cran.us.r-project.org/src/contrib/jpeg_0.1-9.tar.gz' Content type 'application/x-gzip' length 18596 bytes (18 KB) ================================================== downloaded 18 KB trying URL 'http://cran.us.r-project.org/src/contrib/maps_3.3.0.tar.gz' Content type 'application/x-gzip' length 2493744 bytes (2.4 MB) ================================================== downloaded 2.4 MB trying URL 'http://cran.us.r-project.org/src/contrib/mapdata_2.3.0.tar.gz' Content type 'application/x-gzip' length 13619287 bytes (13.0 MB) ================================================== downloaded 13.0 MB trying URL 'http://cran.us.r-project.org/src/contrib/maptools_1.1-1.tar.gz' Content type 'application/x-gzip' length 1586925 bytes (1.5 MB) ================================================== downloaded 1.5 MB trying URL 'http://cran.us.r-project.org/src/contrib/phytools_0.7-80.tar.gz' Content type 'application/x-gzip' length 328187 bytes (320 KB) ================================================== downloaded 320 KB trying URL 'http://cran.us.r-project.org/src/contrib/tidyr_1.1.3.tar.gz' Content type 'application/x-gzip' length 707909 bytes (691 KB) ================================================== downloaded 691 KB trying URL 'http://cran.us.r-project.org/src/contrib/vegan_2.5-7.tar.gz' Content type 'application/x-gzip' length 2074611 bytes (2.0 MB) ================================================== downloaded 2.0 MB * installing *source* package ‘colorspace’ ... ** package ‘colorspace’ successfully unpacked and MD5 sums checked ** using staged installation ** libs make[1]: Entering directory '/tmp/Rtmpy0wbVY/working_dir/RtmpEsKqeK/R.INSTALL32896e7f799030/colorspace/src' gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c colorspace.c -o colorspace.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c init.c -o init.o gcc -shared -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -fpic -L/usr/local/lib64 -o colorspace.so colorspace.o init.o make[1]: Leaving directory '/tmp/Rtmpy0wbVY/working_dir/RtmpEsKqeK/R.INSTALL32896e7f799030/colorspace/src' make[1]: Entering directory '/tmp/Rtmpy0wbVY/working_dir/RtmpEsKqeK/R.INSTALL32896e7f799030/colorspace/src' make[1]: Leaving directory '/tmp/Rtmpy0wbVY/working_dir/RtmpEsKqeK/R.INSTALL32896e7f799030/colorspace/src' installing to /tmp/Rtmpy0wbVY/RLIBS_3258c769b7f455/00LOCK-colorspace/00new/colorspace/libs ** R ** data *** moving datasets to lazyload DB ** demo ** 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 (colorspace) * installing *source* package ‘fansi’ ... ** package ‘fansi’ successfully unpacked and MD5 sums checked ** using staged installation ** libs make[1]: Entering directory '/tmp/Rtmpy0wbVY/working_dir/RtmpSXQ2rV/R.INSTALL328bde447954c5/fansi/src' gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c assumptions.c -o assumptions.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c has.c -o has.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c nchar.c -o nchar.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c rnchar.c -o rnchar.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c state.c -o state.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c strip.c -o strip.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c strsplit.c -o strsplit.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c tabs.c -o tabs.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c tohtml.c -o tohtml.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c unhandled.c -o unhandled.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c unique.c -o unique.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c utf8.c -o utf8.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c utils.c -o utils.o utils.c: In function ‘FANSI_find_esc’: utils.c:193:47: warning: ‘x_found_end’ may be used uninitialized in this function [-Wmaybe-uninitialized] 193 | .start=x_found_start, .len=(x_found_end - x_found_start), | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ utils.c:193:47: warning: ‘x_found_start’ may be used uninitialized in this function [-Wmaybe-uninitialized] gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c wrap.c -o wrap.o gcc -shared -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -fpic -L/usr/local/lib64 -o fansi.so assumptions.o has.o init.o nchar.o read.o rnchar.o state.o strip.o strsplit.o tabs.o tohtml.o unhandled.o unique.o utf8.o utils.o wrap.o make[1]: Leaving directory '/tmp/Rtmpy0wbVY/working_dir/RtmpSXQ2rV/R.INSTALL328bde447954c5/fansi/src' make[1]: Entering directory '/tmp/Rtmpy0wbVY/working_dir/RtmpSXQ2rV/R.INSTALL328bde447954c5/fansi/src' make[1]: Leaving directory '/tmp/Rtmpy0wbVY/working_dir/RtmpSXQ2rV/R.INSTALL328bde447954c5/fansi/src' installing to /tmp/Rtmpy0wbVY/RLIBS_3258c769b7f455/00LOCK-fansi/00new/fansi/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 (fansi) * installing *source* package ‘pkgconfig’ ... ** package ‘pkgconfig’ 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 (pkgconfig) * installing *source* package ‘cli’ ... ** package ‘cli’ successfully unpacked and MD5 sums checked ** using staged installation ** libs make[1]: Entering directory '/tmp/Rtmpy0wbVY/working_dir/RtmpSqduYf/R.INSTALL328c9c42db2495/cli/src' gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c cleancall.c -o cleancall.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c errors.c -o errors.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c progress-altrep.c -o progress-altrep.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c progress.c -o progress.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c thread.c -o thread.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c tty.c -o tty.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c win-utf8.c -o win-utf8.o gcc -shared -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -fpic -L/usr/local/lib64 -o cli.so cleancall.o errors.o init.o progress-altrep.o progress.o thread.o tty.o win-utf8.o make[1]: Leaving directory '/tmp/Rtmpy0wbVY/working_dir/RtmpSqduYf/R.INSTALL328c9c42db2495/cli/src' make[1]: Entering directory '/tmp/Rtmpy0wbVY/working_dir/RtmpSqduYf/R.INSTALL328c9c42db2495/cli/src' make[1]: Leaving directory '/tmp/Rtmpy0wbVY/working_dir/RtmpSqduYf/R.INSTALL328c9c42db2495/cli/src' installing to /tmp/Rtmpy0wbVY/RLIBS_3258c769b7f455/00LOCK-cli/00new/cli/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** 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 (cli) * installing *source* package ‘crayon’ ... ** package ‘crayon’ 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 (crayon) * installing *source* package ‘utf8’ ... ** package ‘utf8’ successfully unpacked and MD5 sums checked ** using staged installation ** libs make[1]: Entering directory '/tmp/Rtmpy0wbVY/working_dir/RtmpSbrq1u/R.INSTALL328ed748ca3837/utf8/src' gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -Iutf8lite/src -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c as_utf8.c -o as_utf8.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -Iutf8lite/src -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c bytes.c -o bytes.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -Iutf8lite/src -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c context.c -o context.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -Iutf8lite/src -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c init.c -o init.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -Iutf8lite/src -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c render.c -o render.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -Iutf8lite/src -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c render_table.c -o render_table.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -Iutf8lite/src -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c string.c -o string.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -Iutf8lite/src -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c text.c -o text.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -Iutf8lite/src -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c utf8_encode.c -o utf8_encode.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -Iutf8lite/src -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c utf8_format.c -o utf8_format.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -Iutf8lite/src -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c utf8_normalize.c -o utf8_normalize.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -Iutf8lite/src -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c utf8_valid.c -o utf8_valid.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -Iutf8lite/src -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c utf8_width.c -o utf8_width.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -Iutf8lite/src -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c util.c -o util.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -Iutf8lite/src -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c utf8lite/src/array.c -o utf8lite/src/array.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -Iutf8lite/src -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c utf8lite/src/char.c -o utf8lite/src/char.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -Iutf8lite/src -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c utf8lite/src/encode.c -o utf8lite/src/encode.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -Iutf8lite/src -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c utf8lite/src/error.c -o utf8lite/src/error.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -Iutf8lite/src -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c utf8lite/src/escape.c -o utf8lite/src/escape.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -Iutf8lite/src -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c utf8lite/src/graph.c -o utf8lite/src/graph.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -Iutf8lite/src -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c utf8lite/src/graphscan.c -o utf8lite/src/graphscan.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -Iutf8lite/src -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c utf8lite/src/normalize.c -o utf8lite/src/normalize.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -Iutf8lite/src -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c utf8lite/src/render.c -o utf8lite/src/render.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -Iutf8lite/src -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c utf8lite/src/text.c -o utf8lite/src/text.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -Iutf8lite/src -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c utf8lite/src/textassign.c -o utf8lite/src/textassign.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -Iutf8lite/src -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c utf8lite/src/textiter.c -o utf8lite/src/textiter.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -Iutf8lite/src -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c utf8lite/src/textmap.c -o utf8lite/src/textmap.o gcc-ar rcs libcutf8lite.a utf8lite/src/array.o utf8lite/src/char.o utf8lite/src/encode.o utf8lite/src/error.o utf8lite/src/escape.o utf8lite/src/graph.o utf8lite/src/graphscan.o utf8lite/src/normalize.o utf8lite/src/render.o utf8lite/src/text.o utf8lite/src/textassign.o utf8lite/src/textiter.o utf8lite/src/textmap.o gcc -shared -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -fpic -L/usr/local/lib64 -o utf8.so as_utf8.o bytes.o context.o init.o render.o render_table.o string.o text.o utf8_encode.o utf8_format.o utf8_normalize.o utf8_valid.o utf8_width.o util.o -L. -lcutf8lite make[1]: Leaving directory '/tmp/Rtmpy0wbVY/working_dir/RtmpSbrq1u/R.INSTALL328ed748ca3837/utf8/src' make[1]: Entering directory '/tmp/Rtmpy0wbVY/working_dir/RtmpSbrq1u/R.INSTALL328ed748ca3837/utf8/src' make[1]: Leaving directory '/tmp/Rtmpy0wbVY/working_dir/RtmpSbrq1u/R.INSTALL328ed748ca3837/utf8/src' installing to /tmp/Rtmpy0wbVY/RLIBS_3258c769b7f455/00LOCK-utf8/00new/utf8/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 (utf8) * installing *source* package ‘farver’ ... ** package ‘farver’ successfully unpacked and MD5 sums checked ** using staged installation ** libs make[1]: Entering directory '/tmp/Rtmpy0wbVY/working_dir/RtmpafmELH/R.INSTALL328fbb16d6563/farver/src' g++ -std=gnu++11 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c ColorSpace.cpp -o ColorSpace.o g++ -std=gnu++11 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c Comparison.cpp -o Comparison.o g++ -std=gnu++11 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c Conversion.cpp -o Conversion.o g++ -std=gnu++11 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c encode.cpp -o encode.o encode.cpp: In function ‘int double2int(double)’: encode.cpp:22:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 22 | return reinterpret_cast(d); | ^ g++ -std=gnu++11 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c farver.cpp -o farver.o g++ -std=gnu++11 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c init.cpp -o init.o g++ -std=gnu++11 -shared -L/usr/local/lib64 -o farver.so ColorSpace.o Comparison.o Conversion.o encode.o farver.o init.o make[1]: Leaving directory '/tmp/Rtmpy0wbVY/working_dir/RtmpafmELH/R.INSTALL328fbb16d6563/farver/src' make[1]: Entering directory '/tmp/Rtmpy0wbVY/working_dir/RtmpafmELH/R.INSTALL328fbb16d6563/farver/src' make[1]: Leaving directory '/tmp/Rtmpy0wbVY/working_dir/RtmpafmELH/R.INSTALL328fbb16d6563/farver/src' installing to /tmp/Rtmpy0wbVY/RLIBS_3258c769b7f455/00LOCK-farver/00new/farver/libs ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** 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 (farver) * installing *source* package ‘labeling’ ... ** package ‘labeling’ 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 (labeling) * installing *source* package ‘RColorBrewer’ ... ** package ‘RColorBrewer’ 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 (RColorBrewer) * installing *source* package ‘viridisLite’ ... ** package ‘viridisLite’ 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 ** 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 (viridisLite) * installing *source* package ‘tmvnsim’ ... ** package ‘tmvnsim’ successfully unpacked and MD5 sums checked ** using staged installation ** libs make[1]: Entering directory '/tmp/Rtmpy0wbVY/working_dir/RtmphimAaU/R.INSTALL32921162e805d9/tmvnsim/src' gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c Fortran2CWrapper.c -o Fortran2CWrapper.o gfortran -fno-optimize-sibling-calls -fpic -g -O2 -mtune=native -Wall -pedantic -c tmvnghk.f90 -o tmvnghk.o gcc -shared -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -fpic -L/usr/local/lib64 -o tmvnsim.so Fortran2CWrapper.o tmvnghk.o -L/data/gannet/ripley/R/R-devel/lib -lRlapack -L/data/gannet/ripley/R/R-devel/lib -lRblas -lgfortran -lm -lquadmath -lgfortran -lm -lquadmath make[1]: Leaving directory '/tmp/Rtmpy0wbVY/working_dir/RtmphimAaU/R.INSTALL32921162e805d9/tmvnsim/src' make[1]: Entering directory '/tmp/Rtmpy0wbVY/working_dir/RtmphimAaU/R.INSTALL32921162e805d9/tmvnsim/src' make[1]: Leaving directory '/tmp/Rtmpy0wbVY/working_dir/RtmphimAaU/R.INSTALL32921162e805d9/tmvnsim/src' installing to /tmp/Rtmpy0wbVY/RLIBS_3258c769b7f455/00LOCK-tmvnsim/00new/tmvnsim/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 (tmvnsim) * installing *source* package ‘fastmatch’ ... ** package ‘fastmatch’ successfully unpacked and MD5 sums checked ** using staged installation ** libs make[1]: Entering directory '/tmp/Rtmpy0wbVY/working_dir/Rtmpue8B3h/R.INSTALL32925854a4e0eb/fastmatch/src' gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c ctapply.c -o ctapply.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c fasthash.c -o fasthash.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c fastmatch.c -o fastmatch.o gcc -shared -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -fpic -L/usr/local/lib64 -o fastmatch.so ctapply.o fasthash.o fastmatch.o make[1]: Leaving directory '/tmp/Rtmpy0wbVY/working_dir/Rtmpue8B3h/R.INSTALL32925854a4e0eb/fastmatch/src' make[1]: Entering directory '/tmp/Rtmpy0wbVY/working_dir/Rtmpue8B3h/R.INSTALL32925854a4e0eb/fastmatch/src' make[1]: Leaving directory '/tmp/Rtmpy0wbVY/working_dir/Rtmpue8B3h/R.INSTALL32925854a4e0eb/fastmatch/src' installing to /tmp/Rtmpy0wbVY/RLIBS_3258c769b7f455/00LOCK-fastmatch/00new/fastmatch/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 (fastmatch) * installing *source* package ‘quadprog’ ... ** package ‘quadprog’ successfully unpacked and MD5 sums checked ** using staged installation ** libs make[1]: Entering directory '/tmp/Rtmpy0wbVY/working_dir/RtmpfMVntf/R.INSTALL3292a714f90dbd/quadprog/src' gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic -g -O2 -mtune=native -Wall -pedantic -msse2 -mfpmath=sse -fpic -g -O2 -mtune=native -Wall -pedantic -c aind.f -o aind.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c init.c -o init.o gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic -g -O2 -mtune=native -Wall -pedantic -msse2 -mfpmath=sse -fpic -g -O2 -mtune=native -Wall -pedantic -c solve.QP.compact.f -o solve.QP.compact.o solve.QP.compact.f:254:3: 254 | 72 if (nvl .EQ. 0) then | 1 Warning: Label 72 at (1) defined but not used [-Wunused-label] solve.QP.compact.f:302:2: 302 | 7 t1inf = .FALSE. | 1 Warning: Label 7 at (1) defined but not used [-Wunused-label] gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic -g -O2 -mtune=native -Wall -pedantic -msse2 -mfpmath=sse -fpic -g -O2 -mtune=native -Wall -pedantic -c solve.QP.f -o solve.QP.o solve.QP.f:245:3: 245 | 72 if (nvl .EQ. 0) then | 1 Warning: Label 72 at (1) defined but not used [-Wunused-label] solve.QP.f:293:2: 293 | 7 t1inf = .FALSE. | 1 Warning: Label 7 at (1) defined but not used [-Wunused-label] gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic -g -O2 -mtune=native -Wall -pedantic -msse2 -mfpmath=sse -fpic -g -O2 -mtune=native -Wall -pedantic -c util.f -o util.o gcc -shared -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -fpic -L/usr/local/lib64 -o quadprog.so aind.o init.o solve.QP.compact.o solve.QP.o util.o -L/data/gannet/ripley/R/R-devel/lib -lRblas -lgfortran -lm -lquadmath -lgfortran -lm -lquadmath make[1]: Leaving directory '/tmp/Rtmpy0wbVY/working_dir/RtmpfMVntf/R.INSTALL3292a714f90dbd/quadprog/src' make[1]: Entering directory '/tmp/Rtmpy0wbVY/working_dir/RtmpfMVntf/R.INSTALL3292a714f90dbd/quadprog/src' make[1]: Leaving directory '/tmp/Rtmpy0wbVY/working_dir/RtmpfMVntf/R.INSTALL3292a714f90dbd/quadprog/src' installing to /tmp/Rtmpy0wbVY/RLIBS_3258c769b7f455/00LOCK-quadprog/00new/quadprog/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 (quadprog) * installing *source* package ‘generics’ ... ** package ‘generics’ 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 (generics) * installing *source* package ‘rlang’ ... ** package ‘rlang’ successfully unpacked and MD5 sums checked ** using staged installation ** libs make[1]: Entering directory '/tmp/Rtmpy0wbVY/working_dir/RtmpQiMAxL/R.INSTALL32934c5a597144/rlang/src' gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I./lib/ -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c capture.c -o capture.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I./lib/ -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c export.c -o export.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I./lib/ -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c internal.c -o internal.o In file included from ./lib/rlang.h:83, from internal/arg.c:1, from internal.c:1: internal/eval-tidy.c: In function ‘rlang_tilde_eval’: ./lib/env.h:33:10: warning: ‘top’ may be used uninitialized in this function [-Wmaybe-uninitialized] 33 | return ENCLOS(env); | ^~~~~~~~~~~ In file included from internal.c:8: internal/eval-tidy.c:417:9: note: ‘top’ was declared here 417 | sexp* top; | ^~~ gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I./lib/ -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c lib.c -o lib.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I./lib/ -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c version.c -o version.o gcc -shared -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -fpic -L/usr/local/lib64 -o rlang.so capture.o export.o internal.o lib.o version.o make[1]: Leaving directory '/tmp/Rtmpy0wbVY/working_dir/RtmpQiMAxL/R.INSTALL32934c5a597144/rlang/src' make[1]: Entering directory '/tmp/Rtmpy0wbVY/working_dir/RtmpQiMAxL/R.INSTALL32934c5a597144/rlang/src' make[1]: Leaving directory '/tmp/Rtmpy0wbVY/working_dir/RtmpQiMAxL/R.INSTALL32934c5a597144/rlang/src' installing to /tmp/Rtmpy0wbVY/RLIBS_3258c769b7f455/00LOCK-rlang/00new/rlang/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** 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 (rlang) * installing *source* package ‘gtable’ ... ** package ‘gtable’ 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 (gtable) * installing *source* package ‘isoband’ ... ** package ‘isoband’ successfully unpacked and MD5 sums checked ** using staged installation ** libs make[1]: Entering directory '/tmp/Rtmpy0wbVY/working_dir/RtmpAClx1G/R.INSTALL3293d021dd3b59/isoband/src' g++ -std=gnu++11 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -Itestthat -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c clip-lines.cpp -o clip-lines.o g++ -std=gnu++11 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -Itestthat -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c init.cpp -o init.o g++ -std=gnu++11 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -Itestthat -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c isoband.cpp -o isoband.o g++ -std=gnu++11 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -Itestthat -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c polygon.cpp -o polygon.o g++ -std=gnu++11 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -Itestthat -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c separate-polygons.cpp -o separate-polygons.o g++ -std=gnu++11 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -Itestthat -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c test-clip-lines.cpp -o test-clip-lines.o g++ -std=gnu++11 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -Itestthat -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c test-runner.cpp -o test-runner.o g++ -std=gnu++11 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -Itestthat -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c test-separate-polygons.cpp -o test-separate-polygons.o g++ -std=gnu++11 -shared -L/usr/local/lib64 -o isoband.so clip-lines.o init.o isoband.o polygon.o separate-polygons.o test-clip-lines.o test-runner.o test-separate-polygons.o make[1]: Leaving directory '/tmp/Rtmpy0wbVY/working_dir/RtmpAClx1G/R.INSTALL3293d021dd3b59/isoband/src' make[1]: Entering directory '/tmp/Rtmpy0wbVY/working_dir/RtmpAClx1G/R.INSTALL3293d021dd3b59/isoband/src' make[1]: Leaving directory '/tmp/Rtmpy0wbVY/working_dir/RtmpAClx1G/R.INSTALL3293d021dd3b59/isoband/src' installing to /tmp/Rtmpy0wbVY/RLIBS_3258c769b7f455/00LOCK-isoband/00new/isoband/libs ** 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 ** 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 (isoband) * installing *source* package ‘withr’ ... ** package ‘withr’ 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 (withr) ERROR: dependency ‘MASS’ is not available for package ‘clusterGeneration’ * removing ‘/tmp/Rtmpy0wbVY/RLIBS_3258c769b7f455/clusterGeneration’ * installing *source* package ‘coda’ ... ** package ‘coda’ successfully unpacked and MD5 sums checked ** using staged installation ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (coda) * installing *source* package ‘combinat’ ... ** package ‘combinat’ 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 (combinat) ERROR: dependency ‘Matrix’ is not available for package ‘expm’ * removing ‘/tmp/Rtmpy0wbVY/RLIBS_3258c769b7f455/expm’ * installing *source* package ‘numDeriv’ ... ** package ‘numDeriv’ 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 (numDeriv) * installing *source* package ‘plotrix’ ... ** package ‘plotrix’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data ** demo ** 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 (plotrix) * installing *source* package ‘scatterplot3d’ ... ** package ‘scatterplot3d’ 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 (scatterplot3d) * installing *source* package ‘permute’ ... ** package ‘permute’ successfully unpacked and MD5 sums checked ** using staged installation ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (permute) ERROR: dependency ‘nlme’ is not available for package ‘ape’ * removing ‘/tmp/Rtmpy0wbVY/RLIBS_3258c769b7f455/ape’ * installing *source* package ‘jpeg’ ... ** package ‘jpeg’ successfully unpacked and MD5 sums checked ** using staged installation ** libs make[1]: Entering directory '/tmp/Rtmpy0wbVY/working_dir/RtmpMpIFAU/R.INSTALL32973b348a688c/jpeg/src' gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c write.c -o write.o gcc -shared -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -fpic -L/usr/local/lib64 -o jpeg.so read.o reg.o write.o -ljpeg make[1]: Leaving directory '/tmp/Rtmpy0wbVY/working_dir/RtmpMpIFAU/R.INSTALL32973b348a688c/jpeg/src' make[1]: Entering directory '/tmp/Rtmpy0wbVY/working_dir/RtmpMpIFAU/R.INSTALL32973b348a688c/jpeg/src' make[1]: Leaving directory '/tmp/Rtmpy0wbVY/working_dir/RtmpMpIFAU/R.INSTALL32973b348a688c/jpeg/src' installing to /tmp/Rtmpy0wbVY/RLIBS_3258c769b7f455/00LOCK-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 ‘maps’ ... ** package ‘maps’ successfully unpacked and MD5 sums checked ** using staged installation checking for gawk... gawk configure: creating ./config.status config.status: creating src/Makefile ** libs ** arch - make[1]: Entering directory '/tmp/Rtmpy0wbVY/working_dir/Rtmp6ECExB/R.INSTALL329787606295e6/maps/src' make -f "/data/gannet/ripley/R/R-devel/etc/Makeconf" -f Makefile init.o mapclip.o mapget.o smooth.o thin.o make[2]: Entering directory '/tmp/Rtmpy0wbVY/working_dir/Rtmp6ECExB/R.INSTALL329787606295e6/maps/src' gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c mapclip.c -o mapclip.o mapclip.c: In function ‘map_clip_poly’: mapclip.c:123:12: warning: ‘position’ may be used uninitialized in this function [-Wmaybe-uninitialized] 123 | if (position > 0) { /*we finished (and thus also started) inside the region, */ | ^ gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c mapget.c -o mapget.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c smooth.c -o smooth.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c thin.c -o thin.o make[2]: Leaving directory '/tmp/Rtmpy0wbVY/working_dir/Rtmp6ECExB/R.INSTALL329787606295e6/maps/src' "/data/gannet/ripley/R/R-devel/bin/R" CMD SHLIB -o maps.so init.o mapclip.o mapget.o smooth.o thin.o make[2]: Entering directory '/tmp/Rtmpy0wbVY/working_dir/Rtmp6ECExB/R.INSTALL329787606295e6/maps/src' gcc -shared -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -fpic -L/usr/local/lib64 -o maps.so init.o mapclip.o mapget.o smooth.o thin.o make[2]: Leaving directory '/tmp/Rtmpy0wbVY/working_dir/Rtmp6ECExB/R.INSTALL329787606295e6/maps/src' make[2]: Entering directory '/tmp/Rtmpy0wbVY/working_dir/Rtmp6ECExB/R.INSTALL329787606295e6/maps/src' make[2]: Leaving directory '/tmp/Rtmpy0wbVY/working_dir/Rtmp6ECExB/R.INSTALL329787606295e6/maps/src' make -f "/data/gannet/ripley/R/R-devel/etc/Makeconf" -f Makefile Gmake make[2]: Entering directory '/tmp/Rtmpy0wbVY/working_dir/Rtmp6ECExB/R.INSTALL329787606295e6/maps/src' gcc -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -I/usr/local/include -L/usr/local/lib64 Gmake.c -o Gmake make[2]: Leaving directory '/tmp/Rtmpy0wbVY/working_dir/Rtmp6ECExB/R.INSTALL329787606295e6/maps/src' make -f "/data/gannet/ripley/R/R-devel/etc/Makeconf" -f Makefile Lmake make[2]: Entering directory '/tmp/Rtmpy0wbVY/working_dir/Rtmp6ECExB/R.INSTALL329787606295e6/maps/src' gcc -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -I/usr/local/include -L/usr/local/lib64 Lmake.c -o Lmake make[2]: Leaving directory '/tmp/Rtmpy0wbVY/working_dir/Rtmp6ECExB/R.INSTALL329787606295e6/maps/src' make -f "/data/gannet/ripley/R/R-devel/etc/Makeconf" -f Makefile world2.line make[2]: Entering directory '/tmp/Rtmpy0wbVY/working_dir/Rtmp6ECExB/R.INSTALL329787606295e6/maps/src' Converting world to world2 gawk -f ./convert.awk < world.line > world2.line Creating legacy world2 database gawk -f ./legacy_convert.awk < legacy_world.line > legacy_world2.line make[2]: Leaving directory '/tmp/Rtmpy0wbVY/working_dir/Rtmp6ECExB/R.INSTALL329787606295e6/maps/src' make -f "/data/gannet/ripley/R/R-devel/etc/Makeconf" -f Makefile county.L state.L usa.L nz.L world.L world2.L italy.L france.L state.vbm.L state.carto.L legacy_world.L legacy_world2.L lakes.L make[2]: Entering directory '/tmp/Rtmpy0wbVY/working_dir/Rtmp6ECExB/R.INSTALL329787606295e6/maps/src' ./Lmake 0 s b county.line county.linestats ../inst/mapdata/county.L ./Lmake 0 s b state.line state.linestats ../inst/mapdata/state.L ./Lmake 0 s b usa.line usa.linestats ../inst/mapdata/usa.L ./Lmake 0 s b nz.line nz.linestats ../inst/mapdata/nz.L ./Lmake 0 s b world.line world.linestats ../inst/mapdata/world.L ./Lmake 0 s b world2.line world2.linestats ../inst/mapdata/world2.L ./Lmake 0 s b italy.line italy.linestats ../inst/mapdata/italy.L ./Lmake 0 s b france.line france.linestats ../inst/mapdata/france.L ./Lmake 0 p b state.vbm.line state.vbm.linestats ../inst/mapdata/state.vbm.L ./Lmake 0 p b state.carto.line state.carto.linestats ../inst/mapdata/state.carto.L ./Lmake 0 s b legacy_world.line legacy_world.linestats ../inst/mapdata/legacy_world.L ./Lmake 0 s b legacy_world2.line legacy_world2.linestats ../inst/mapdata/legacy_world2.L ./Lmake 0 s b lakes.line lakes.linestats ../inst/mapdata/lakes.L make[2]: Leaving directory '/tmp/Rtmpy0wbVY/working_dir/Rtmp6ECExB/R.INSTALL329787606295e6/maps/src' make -f "/data/gannet/ripley/R/R-devel/etc/Makeconf" -f Makefile county.G state.G usa.G nz.G world.G world2.G italy.G france.G state.vbm.G state.carto.G legacy_world.G legacy_world2.G lakes.G make[2]: Entering directory '/tmp/Rtmpy0wbVY/working_dir/Rtmp6ECExB/R.INSTALL329787606295e6/maps/src' ./Gmake b county.gon county.gonstats ../inst/mapdata/county.G ../inst/mapdata/county.L ./Gmake b state.gon state.gonstats ../inst/mapdata/state.G ../inst/mapdata/state.L ./Gmake b usa.gon usa.gonstats ../inst/mapdata/usa.G ../inst/mapdata/usa.L ./Gmake b nz.gon nz.gonstats ../inst/mapdata/nz.G ../inst/mapdata/nz.L ./Gmake b world.gon world.gonstats ../inst/mapdata/world.G ../inst/mapdata/world.L ./Gmake b world2.gon world2.gonstats ../inst/mapdata/world2.G ../inst/mapdata/world2.L ./Gmake b italy.gon italy.gonstats ../inst/mapdata/italy.G ../inst/mapdata/italy.L ./Gmake b france.gon france.gonstats ../inst/mapdata/france.G ../inst/mapdata/france.L ./Gmake b state.vbm.gon state.vbm.gonstats ../inst/mapdata/state.vbm.G ../inst/mapdata/state.vbm.L ./Gmake b state.carto.gon state.carto.gonstats ../inst/mapdata/state.carto.G ../inst/mapdata/state.carto.L ./Gmake b legacy_world.gon legacy_world.gonstats ../inst/mapdata/legacy_world.G ../inst/mapdata/legacy_world.L ./Gmake b legacy_world2.gon legacy_world2.gonstats ../inst/mapdata/legacy_world2.G ../inst/mapdata/legacy_world2.L ./Gmake b lakes.gon lakes.gonstats ../inst/mapdata/lakes.G ../inst/mapdata/lakes.L make[2]: Leaving directory '/tmp/Rtmpy0wbVY/working_dir/Rtmp6ECExB/R.INSTALL329787606295e6/maps/src' make -f "/data/gannet/ripley/R/R-devel/etc/Makeconf" -f Makefile county.N state.N usa.N nz.N world.N world2.N italy.N france.N state.vbm.N state.carto.N legacy_world.N legacy_world2.N lakes.N make[2]: Entering directory '/tmp/Rtmpy0wbVY/working_dir/Rtmp6ECExB/R.INSTALL329787606295e6/maps/src' make[2]: Leaving directory '/tmp/Rtmpy0wbVY/working_dir/Rtmp6ECExB/R.INSTALL329787606295e6/maps/src' make[1]: Leaving directory '/tmp/Rtmpy0wbVY/working_dir/Rtmp6ECExB/R.INSTALL329787606295e6/maps/src' installing to /tmp/Rtmpy0wbVY/RLIBS_3258c769b7f455/00LOCK-maps/00new/maps/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 (maps) ERROR: dependency ‘foreign’ is not available for package ‘maptools’ * removing ‘/tmp/Rtmpy0wbVY/RLIBS_3258c769b7f455/maptools’ * installing *source* package ‘munsell’ ... ** package ‘munsell’ 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 ** 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 (munsell) ERROR: dependency ‘Matrix’ is not available for package ‘igraph’ * removing ‘/tmp/Rtmpy0wbVY/RLIBS_3258c769b7f455/igraph’ * installing *source* package ‘ellipsis’ ... ** package ‘ellipsis’ successfully unpacked and MD5 sums checked ** using staged installation ** libs make[1]: Entering directory '/tmp/Rtmpy0wbVY/working_dir/Rtmp26urRu/R.INSTALL329954e67ec04/ellipsis/src' gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c dots.c -o dots.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c init.c -o init.o gcc -shared -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -fpic -L/usr/local/lib64 -o ellipsis.so dots.o init.o make[1]: Leaving directory '/tmp/Rtmpy0wbVY/working_dir/Rtmp26urRu/R.INSTALL329954e67ec04/ellipsis/src' make[1]: Entering directory '/tmp/Rtmpy0wbVY/working_dir/Rtmp26urRu/R.INSTALL329954e67ec04/ellipsis/src' make[1]: Leaving directory '/tmp/Rtmpy0wbVY/working_dir/Rtmp26urRu/R.INSTALL329954e67ec04/ellipsis/src' installing to /tmp/Rtmpy0wbVY/RLIBS_3258c769b7f455/00LOCK-ellipsis/00new/ellipsis/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 (ellipsis) * installing *source* package ‘lifecycle’ ... ** package ‘lifecycle’ 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 (lifecycle) * installing *source* package ‘mnormt’ ... ** package ‘mnormt’ successfully unpacked and MD5 sums checked ** using staged installation ** libs make[1]: Entering directory '/tmp/Rtmpy0wbVY/working_dir/RtmpUAEC4k/R.INSTALL3299bc5981fc69/mnormt/src' gfortran -fno-optimize-sibling-calls -fpic -g -O2 -mtune=native -Wall -pedantic -c biv-nt.f -o biv-nt.o biv-nt.f:371:11: 371 | hs = sign( one, dh - r*dk ) | 1 Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion] biv-nt.f:372:11: 372 | ks = sign( one, dk - r*dh ) | 1 Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion] gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c mnormt_init.c -o mnormt_init.o gfortran -fno-optimize-sibling-calls -fpic -g -O2 -mtune=native -Wall -pedantic -c sadmvnt.f -o sadmvnt.o sadmvnt.f:977:3: 977 | 10 END DO | 1 Warning: Label 10 at (1) defined but not used [-Wunused-label] sadmvnt.f:81:15: 81 | INFORM = MVNNIT( N, CORREL, LOWER, UPPER, INFIN, INFIS, D, E ) | 1 Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion] sadmvnt.f:218:38: 218 | IF ( MINCLS .LT. 0 ) SBRGNS = WORK(LENWRK) | 1 Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion] sadmvnt.f:276:21: 276 | RGNCLS = RGNCLS*(MESH(DIVAXN)+1)/MESH(DIVAXN) | 1 Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion] sadmvnt.f:277:21: 277 | NWRGNS = NWRGNS*(MESH(DIVAXN)+1)/MESH(DIVAXN) | 1 Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion] sadmvnt.f:1275:24: 1275 | POINTS = PONTRS(SUBTMP) | 1 Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion] sadmvnt.f:1276:24: 1276 | POINTP = PONTRS(SUBTMP+1) | 1 Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion] sadmvnt.f:1284:21: 1284 | POINTS = PONTRS(SUBTMP) | 1 Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion] sadmvnt.f:1304:21: 1304 | POINTS = PONTRS(SUBTMP) | 1 Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion] sadmvnt.f:325:15: 325 | TOP = PONTRS(1) | 1 Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion] sadmvnt.f:332:21: 332 | RGNCLS = RGNCLS*MESH(I) | 1 Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion] sadmvnt.f:337:18: 337 | RGNCLS = RGNCLS*(MESH(DIVAXN)+1)/MESH(DIVAXN) | 1 Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion] sadmvnt.f:1586:3: 1586 | 10 END DO | 1 Warning: Label 10 at (1) defined but not used [-Wunused-label] sadmvnt.f:1433:15: 1433 | INFORM = MVTNIT( N, NU, CORREL, LOWER, UPPER, INFIN, INFIS, D, E ) | 1 Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion] sadmvnt.f:1662:72: 1662 | & /( 1 + BMIN**2/(NU+I-1) )**( (NU+I-2)/TWO ) | ^ Warning: ‘bmin’ may be used uninitialized in this function [-Wmaybe-uninitialized] sadmvnt.f:1659:72: 1659 | & /( 1 + AMIN**2/(NU+I-1) )**( (NU+I-2)/TWO ) | ^ Warning: ‘amin’ may be used uninitialized in this function [-Wmaybe-uninitialized] sadmvnt.f:1128:31: 1128 | INTEGER S, IXCHNG, LXCHNG, I, L | ^ Warning: ‘lxchng’ may be used uninitialized in this function [-Wmaybe-uninitialized] sadmvnt.f:805:72: 805 | END | ^ Warning: ‘__result_bvn’ may be used uninitialized in this function [-Wmaybe-uninitialized] sadmvnt.f:763:35: 763 | DOUBLE PRECISION FUNCTION BVN ( LOWER, UPPER, INFIN, CORREL ) | ^ note: ‘__result_bvn’ was declared here sadmvnt.f:1045:72: 1045 | IF ( INFI(I) .EQ. 0 ) Y(I) = BMIN | ^ Warning: ‘bmin’ may be used uninitialized in this function [-Wmaybe-uninitialized] sadmvnt.f:1046:72: 1046 | IF ( INFI(I) .EQ. 1 ) Y(I) = AMIN | ^ Warning: ‘amin’ may be used uninitialized in this function [-Wmaybe-uninitialized] gfortran -fno-optimize-sibling-calls -fpic -g -O2 -mtune=native -Wall -pedantic -c tvpack.f -o tvpack.o tvpack.f:459:14: 459 | HS = SIGN( ONE, DH - R*DK ) | 1 Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion] tvpack.f:460:14: 460 | KS = SIGN( ONE, DK - R*DH ) | 1 Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion] tvpack.f:126:52: 126 | DOUBLE PRECISION ONE, ZRO, EPS, ZROS(3), HS(3), TVT | 1 Warning: Unused variable ‘hs’ declared at (1) [-Wunused-variable] tvpack.f:126:45: 126 | DOUBLE PRECISION ONE, ZRO, EPS, ZROS(3), HS(3), TVT | 1 Warning: Unused variable ‘zros’ declared at (1) [-Wunused-variable] tvpack.f:286:72: 286 | END | ^ Warning: ‘fin’ may be used uninitialized in this function [-Wmaybe-uninitialized] tvpack.f:262:58: 262 | DOUBLE PRECISION EI(NL), AI(NL), BI(NL), FI(NL), FIN, ERR, KRNRDT | ^ note: ‘fin’ was declared here gcc -shared -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -fpic -L/usr/local/lib64 -o mnormt.so biv-nt.o mnormt_init.o sadmvnt.o tvpack.o -lgfortran -lm -lquadmath make[1]: Leaving directory '/tmp/Rtmpy0wbVY/working_dir/RtmpUAEC4k/R.INSTALL3299bc5981fc69/mnormt/src' make[1]: Entering directory '/tmp/Rtmpy0wbVY/working_dir/RtmpUAEC4k/R.INSTALL3299bc5981fc69/mnormt/src' make[1]: Leaving directory '/tmp/Rtmpy0wbVY/working_dir/RtmpUAEC4k/R.INSTALL3299bc5981fc69/mnormt/src' installing to /tmp/Rtmpy0wbVY/RLIBS_3258c769b7f455/00LOCK-mnormt/00new/mnormt/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 (mnormt) * installing *source* package ‘purrr’ ... ** package ‘purrr’ successfully unpacked and MD5 sums checked ** using staged installation ** libs make[1]: Entering directory '/tmp/Rtmpy0wbVY/working_dir/Rtmpii2TFy/R.INSTALL329a0e243bf5b3/purrr/src' gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c backports.c -o backports.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c coerce.c -o coerce.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c conditions.c -o conditions.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c flatten.c -o flatten.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c map.c -o map.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c pluck.c -o pluck.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c transpose.c -o transpose.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c utils.c -o utils.o gcc -shared -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -fpic -L/usr/local/lib64 -o purrr.so backports.o coerce.o conditions.o flatten.o init.o map.o pluck.o transpose.o utils.o make[1]: Leaving directory '/tmp/Rtmpy0wbVY/working_dir/Rtmpii2TFy/R.INSTALL329a0e243bf5b3/purrr/src' make[1]: Entering directory '/tmp/Rtmpy0wbVY/working_dir/Rtmpii2TFy/R.INSTALL329a0e243bf5b3/purrr/src' make[1]: Leaving directory '/tmp/Rtmpy0wbVY/working_dir/Rtmpii2TFy/R.INSTALL329a0e243bf5b3/purrr/src' installing to /tmp/Rtmpy0wbVY/RLIBS_3258c769b7f455/00LOCK-purrr/00new/purrr/libs ** 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 ** 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 (purrr) * installing *source* package ‘mapdata’ ... ** package ‘mapdata’ successfully unpacked and MD5 sums checked ** using staged installation checking for gawk... gawk configure: creating ./config.status config.status: creating src/Makefile ** libs ** arch - make[1]: Entering directory '/tmp/Rtmpy0wbVY/working_dir/RtmpN7182g/R.INSTALL329a8129a040a8/mapdata/src' make -f "/data/gannet/ripley/R/R-devel/etc/Makeconf" -f Makefile Gmake make[2]: Entering directory '/tmp/Rtmpy0wbVY/working_dir/RtmpN7182g/R.INSTALL329a8129a040a8/mapdata/src' gcc -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -I/usr/local/include -L/usr/local/lib64 Gmake.c -o Gmake make[2]: Leaving directory '/tmp/Rtmpy0wbVY/working_dir/RtmpN7182g/R.INSTALL329a8129a040a8/mapdata/src' make -f "/data/gannet/ripley/R/R-devel/etc/Makeconf" -f Makefile Lmake make[2]: Entering directory '/tmp/Rtmpy0wbVY/working_dir/RtmpN7182g/R.INSTALL329a8129a040a8/mapdata/src' gcc -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -I/usr/local/include -L/usr/local/lib64 Lmake.c -o Lmake make[2]: Leaving directory '/tmp/Rtmpy0wbVY/working_dir/RtmpN7182g/R.INSTALL329a8129a040a8/mapdata/src' make -f "/data/gannet/ripley/R/R-devel/etc/Makeconf" -f Makefile world2Lores.line world2Hires.line make[2]: Entering directory '/tmp/Rtmpy0wbVY/working_dir/RtmpN7182g/R.INSTALL329a8129a040a8/mapdata/src' Converting worldLores to world2Lores gawk -f ./convert.awk < worldLores.line > world2Lores.line Converting worldHires to world2Hires gawk -f ./convert.awk < worldHires.line > world2Hires.line make[2]: Leaving directory '/tmp/Rtmpy0wbVY/working_dir/RtmpN7182g/R.INSTALL329a8129a040a8/mapdata/src' make -f "/data/gannet/ripley/R/R-devel/etc/Makeconf" -f Makefile china.L japan.L nzHires.L rivers.L worldHires.L world2Hires.L worldLores.L world2Lores.L make[2]: Entering directory '/tmp/Rtmpy0wbVY/working_dir/RtmpN7182g/R.INSTALL329a8129a040a8/mapdata/src' ./Lmake 0 s b china.line china.linestats ../inst/mapdata/china.L ./Lmake 0 s b japan.line japan.linestats ../inst/mapdata/japan.L ./Lmake 0 s b nzHires.line nzHires.linestats ../inst/mapdata/nzHires.L ./Lmake 0 s b rivers.line rivers.linestats ../inst/mapdata/rivers.L ./Lmake 0 s b worldHires.line worldHires.linestats ../inst/mapdata/worldHires.L ./Lmake 0 s b world2Hires.line world2Hires.linestats ../inst/mapdata/world2Hires.L ./Lmake 0 s b worldLores.line worldLores.linestats ../inst/mapdata/worldLores.L ./Lmake 0 s b world2Lores.line world2Lores.linestats ../inst/mapdata/world2Lores.L make[2]: Leaving directory '/tmp/Rtmpy0wbVY/working_dir/RtmpN7182g/R.INSTALL329a8129a040a8/mapdata/src' make -f "/data/gannet/ripley/R/R-devel/etc/Makeconf" -f Makefile china.G japan.G nzHires.G rivers.G worldHires.G world2Hires.G worldLores.G world2Lores.G make[2]: Entering directory '/tmp/Rtmpy0wbVY/working_dir/RtmpN7182g/R.INSTALL329a8129a040a8/mapdata/src' ./Gmake b china.gon china.gonstats ../inst/mapdata/china.G ../inst/mapdata/china.L ./Gmake b japan.gon japan.gonstats ../inst/mapdata/japan.G ../inst/mapdata/japan.L ./Gmake b nzHires.gon nzHires.gonstats ../inst/mapdata/nzHires.G ../inst/mapdata/nzHires.L ./Gmake b rivers.gon rivers.gonstats ../inst/mapdata/rivers.G ../inst/mapdata/rivers.L ./Gmake b worldHires.gon worldHires.gonstats ../inst/mapdata/worldHires.G ../inst/mapdata/worldHires.L ./Gmake b world2Hires.gon world2Hires.gonstats ../inst/mapdata/world2Hires.G ../inst/mapdata/world2Hires.L ./Gmake b worldLores.gon worldLores.gonstats ../inst/mapdata/worldLores.G ../inst/mapdata/worldLores.L ./Gmake b world2Lores.gon world2Lores.gonstats ../inst/mapdata/world2Lores.G ../inst/mapdata/world2Lores.L make[2]: Leaving directory '/tmp/Rtmpy0wbVY/working_dir/RtmpN7182g/R.INSTALL329a8129a040a8/mapdata/src' make -f "/data/gannet/ripley/R/R-devel/etc/Makeconf" -f Makefile china.N japan.N nzHires.N rivers.N worldHires.N world2Hires.N worldLores.N world2Lores.N make[2]: Entering directory '/tmp/Rtmpy0wbVY/working_dir/RtmpN7182g/R.INSTALL329a8129a040a8/mapdata/src' make[2]: Leaving directory '/tmp/Rtmpy0wbVY/working_dir/RtmpN7182g/R.INSTALL329a8129a040a8/mapdata/src' make[1]: Leaving directory '/tmp/Rtmpy0wbVY/working_dir/RtmpN7182g/R.INSTALL329a8129a040a8/mapdata/src' ** 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 (mapdata) ERROR: dependencies ‘MASS’, ‘cluster’, ‘mgcv’ are not available for package ‘vegan’ * removing ‘/tmp/Rtmpy0wbVY/RLIBS_3258c769b7f455/vegan’ * installing *source* package ‘vctrs’ ... ** package ‘vctrs’ successfully unpacked and MD5 sums checked ** using staged installation ** libs make[1]: Entering directory '/tmp/Rtmpy0wbVY/working_dir/RtmpelgO9S/R.INSTALL329bd41e74ac41/vctrs/src' gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c altrep-rle.c -o altrep-rle.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c arg-counter.c -o arg-counter.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c arg.c -o arg.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c bind.c -o bind.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c c-unchop.c -o c-unchop.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c c.c -o c.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c callables.c -o callables.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c cast-bare.c -o cast-bare.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c cast-dispatch.c -o cast-dispatch.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c cast.c -o cast.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c compare.c -o compare.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c complete.c -o complete.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c conditions.c -o conditions.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c dictionary.c -o dictionary.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c dim.c -o dim.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c equal.c -o equal.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c fields.c -o fields.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c fill.c -o fill.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c group.c -o group.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c growable.c -o growable.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c hash.c -o hash.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c init.c -o init.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c names.c -o names.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c order-groups.c -o order-groups.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c order-radix.c -o order-radix.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c order-sortedness.c -o order-sortedness.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c order-transform.c -o order-transform.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c order-truelength.c -o order-truelength.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c poly-op.c -o poly-op.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c proxy-restore.c -o proxy-restore.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c proxy.c -o proxy.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c ptype2-dispatch.c -o ptype2-dispatch.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c rep.c -o rep.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c runs.c -o runs.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c shape.c -o shape.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c size-common.c -o size-common.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c size.c -o size.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c slice-array.c -o slice-array.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c slice-assign-array.c -o slice-assign-array.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c slice-assign.c -o slice-assign.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c slice-chop.c -o slice-chop.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c slice.c -o slice.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c split.c -o split.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c subscript-loc.c -o subscript-loc.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c subscript.c -o subscript.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c translate.c -o translate.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c type-data-frame.c -o type-data-frame.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c type-date-time.c -o type-date-time.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c type-factor.c -o type-factor.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c type-info.c -o type-info.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c type-tibble.c -o type-tibble.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c type.c -o type.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c type2.c -o type2.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c typeof2-s3.c -o typeof2-s3.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c typeof2.c -o typeof2.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c unspecified.c -o unspecified.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c utils-dispatch.c -o utils-dispatch.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c utils-rlang.c -o utils-rlang.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c utils.c -o utils.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c version.c -o version.o gcc -shared -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -fpic -L/usr/local/lib64 -o vctrs.so altrep-rle.o arg-counter.o arg.o bind.o c-unchop.o c.o callables.o cast-bare.o cast-dispatch.o cast.o compare.o complete.o conditions.o dictionary.o dim.o equal.o fields.o fill.o group.o growable.o hash.o init.o names.o order-groups.o order-radix.o order-sortedness.o order-transform.o order-truelength.o poly-op.o proxy-restore.o proxy.o ptype2-dispatch.o rep.o runs.o shape.o size-common.o size.o slice-array.o slice-assign-array.o slice-assign.o slice-chop.o slice.o split.o subscript-loc.o subscript.o translate.o type-data-frame.o type-date-time.o type-factor.o type-info.o type-tibble.o type.o type2.o typeof2-s3.o typeof2.o unspecified.o utils-dispatch.o utils-rlang.o utils.o version.o make[1]: Leaving directory '/tmp/Rtmpy0wbVY/working_dir/RtmpelgO9S/R.INSTALL329bd41e74ac41/vctrs/src' make[1]: Entering directory '/tmp/Rtmpy0wbVY/working_dir/RtmpelgO9S/R.INSTALL329bd41e74ac41/vctrs/src' make[1]: Leaving directory '/tmp/Rtmpy0wbVY/working_dir/RtmpelgO9S/R.INSTALL329bd41e74ac41/vctrs/src' installing to /tmp/Rtmpy0wbVY/RLIBS_3258c769b7f455/00LOCK-vctrs/00new/vctrs/libs ** 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 ** 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 (vctrs) * installing *source* package ‘scales’ ... ** package ‘scales’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** 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 (scales) ERROR: dependencies ‘ape’, ‘igraph’, ‘Matrix’ are not available for package ‘phangorn’ * removing ‘/tmp/Rtmpy0wbVY/RLIBS_3258c769b7f455/phangorn’ * installing *source* package ‘tidyselect’ ... ** package ‘tidyselect’ 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 (tidyselect) * installing *source* package ‘pillar’ ... ** package ‘pillar’ 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 (pillar) ERROR: dependencies ‘ape’, ‘clusterGeneration’, ‘expm’, ‘MASS’, ‘nlme’, ‘phangorn’ are not available for package ‘phytools’ * removing ‘/tmp/Rtmpy0wbVY/RLIBS_3258c769b7f455/phytools’ * installing *source* package ‘tibble’ ... ** package ‘tibble’ successfully unpacked and MD5 sums checked ** using staged installation ** libs make[1]: Entering directory '/tmp/Rtmpy0wbVY/working_dir/RtmpCS2xFh/R.INSTALL329e3a39d20801/tibble/src' gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c attributes.c -o attributes.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c coerce.c -o coerce.o gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -c matrixToDataFrame.c -o matrixToDataFrame.o gcc -shared -g -O2 -Wall -pedantic -mtune=native -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -fpic -L/usr/local/lib64 -o tibble.so attributes.o coerce.o init.o matrixToDataFrame.o make[1]: Leaving directory '/tmp/Rtmpy0wbVY/working_dir/RtmpCS2xFh/R.INSTALL329e3a39d20801/tibble/src' make[1]: Entering directory '/tmp/Rtmpy0wbVY/working_dir/RtmpCS2xFh/R.INSTALL329e3a39d20801/tibble/src' make[1]: Leaving directory '/tmp/Rtmpy0wbVY/working_dir/RtmpCS2xFh/R.INSTALL329e3a39d20801/tibble/src' installing to /tmp/Rtmpy0wbVY/RLIBS_3258c769b7f455/00LOCK-tibble/00new/tibble/libs ** 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 ** 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 (tibble) * installing *source* package ‘dplyr’ ... ** package ‘dplyr’ successfully unpacked and MD5 sums checked ** using staged installation ** libs make[1]: Entering directory '/tmp/Rtmpy0wbVY/working_dir/RtmpQQz5Sz/R.INSTALL329e8d7de44637/dplyr/src' g++ -std=gnu++14 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c chop.cpp -o chop.o g++ -std=gnu++14 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c filter.cpp -o filter.o g++ -std=gnu++14 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c funs.cpp -o funs.o g++ -std=gnu++14 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c group_by.cpp -o group_by.o g++ -std=gnu++14 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c group_data.cpp -o group_data.o g++ -std=gnu++14 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c imports.cpp -o imports.o g++ -std=gnu++14 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c init.cpp -o init.o g++ -std=gnu++14 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c mask.cpp -o mask.o g++ -std=gnu++14 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c mutate.cpp -o mutate.o g++ -std=gnu++14 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c slice.cpp -o slice.o g++ -std=gnu++14 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c summarise.cpp -o summarise.o g++ -std=gnu++14 -shared -L/usr/local/lib64 -o dplyr.so chop.o filter.o funs.o group_by.o group_data.o imports.o init.o mask.o mutate.o slice.o summarise.o make[1]: Leaving directory '/tmp/Rtmpy0wbVY/working_dir/RtmpQQz5Sz/R.INSTALL329e8d7de44637/dplyr/src' make[1]: Entering directory '/tmp/Rtmpy0wbVY/working_dir/RtmpQQz5Sz/R.INSTALL329e8d7de44637/dplyr/src' make[1]: Leaving directory '/tmp/Rtmpy0wbVY/working_dir/RtmpQQz5Sz/R.INSTALL329e8d7de44637/dplyr/src' installing to /tmp/Rtmpy0wbVY/RLIBS_3258c769b7f455/00LOCK-dplyr/00new/dplyr/libs ** R ** data *** moving datasets to lazyload DB ** 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 ** 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 (dplyr) ERROR: dependencies ‘MASS’, ‘mgcv’ are not available for package ‘ggplot2’ * removing ‘/tmp/Rtmpy0wbVY/RLIBS_3258c769b7f455/ggplot2’ * installing *source* package ‘tidyr’ ... ** package ‘tidyr’ successfully unpacked and MD5 sums checked ** using staged installation ** libs make[1]: Entering directory '/tmp/Rtmpy0wbVY/working_dir/RtmpICk09T/R.INSTALL329f1575f13cbe/tidyr/src' g++ -std=gnu++11 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmpy0wbVY/RLIBS_3258c769b7f455/cpp11/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c cpp11.cpp -o cpp11.o g++ -std=gnu++11 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmpy0wbVY/RLIBS_3258c769b7f455/cpp11/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c fill.cpp -o fill.o g++ -std=gnu++11 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmpy0wbVY/RLIBS_3258c769b7f455/cpp11/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c melt.cpp -o melt.o g++ -std=gnu++11 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/tmp/Rtmpy0wbVY/RLIBS_3258c769b7f455/cpp11/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c simplifyPieces.cpp -o simplifyPieces.o g++ -std=gnu++11 -shared -L/usr/local/lib64 -o tidyr.so cpp11.o fill.o melt.o simplifyPieces.o make[1]: Leaving directory '/tmp/Rtmpy0wbVY/working_dir/RtmpICk09T/R.INSTALL329f1575f13cbe/tidyr/src' make[1]: Entering directory '/tmp/Rtmpy0wbVY/working_dir/RtmpICk09T/R.INSTALL329f1575f13cbe/tidyr/src' make[1]: Leaving directory '/tmp/Rtmpy0wbVY/working_dir/RtmpICk09T/R.INSTALL329f1575f13cbe/tidyr/src' installing to /tmp/Rtmpy0wbVY/RLIBS_3258c769b7f455/00LOCK-tidyr/00new/tidyr/libs ** R ** data *** moving datasets to lazyload DB ** 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 ** 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 (tidyr) The downloaded source packages are in '/tmp/Rtmpy0wbVY/working_dir/RtmpG6ffSm/downloaded_packages' Attaching package: 'dplyr' The following objects are masked from 'package:stats': filter, lag The following objects are masked from 'package:base': intersect, setdiff, setequal, union Quitting from lines 153-155 (ALA4R.Rmd) Error: processing vignette 'ALA4R.Rmd' failed with diagnostics: there is no package called 'ape' --- failed re-building ‘ALA4R.Rmd’ SUMMARY: processing the following file failed: ‘ALA4R.Rmd’ Error: Vignette re-building failed. Execution halted * checking PDF 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 WARNING See ‘/data/gannet/ripley/R/packages/tests-Suggests/ALA4R.Rcheck/00check.log’ for details. Time 6:09.37, 290.14 + 28.62