* using log directory ‘/data/gannet/ripley/R/packages/tests-noLD/ALA4R.Rcheck’ * using R Under development (unstable) (2021-07-22 r80654) * 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 ... NOTE Package suggested but not available for checking: ‘phytools’ * 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 ... [9s/11s] 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 ... [17s/21s] 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’ [17s/45s] [17s/46s] OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking re-building of vignette outputs ... [20s/31s] WARNING Error(s) in re-building vignettes: --- re-building ‘ALA4R.Rmd’ using rmarkdown Installing package into '/data/gannet/ripley/R/packages/tests-noLD/ALA4R.Rcheck' (as 'lib' is unspecified) also installing the dependencies 'fastmatch', 'phangorn' trying URL 'http://cran.us.r-project.org/src/contrib/fastmatch_1.1-0.tar.gz' Content type 'application/x-gzip' length 14290 bytes (13 KB) ================================================== downloaded 13 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/phytools_0.7-80.tar.gz' Content type 'application/x-gzip' length 328187 bytes (320 KB) ================================================== downloaded 320 KB * installing *source* package ‘fastmatch’ ... ** package ‘fastmatch’ successfully unpacked and MD5 sums checked ** using staged installation ** libs make[2]: Entering directory '/tmp/RtmpU5KFIv/working_dir/RtmpV2irzs/R.INSTALL21492fa0924/fastmatch/src' gcc -I"/data/gannet/ripley/R/R-devel-noLD/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-noLD/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 In file included from fasthash.c:19: common.h:13:17: error: conflicting types for ‘R_xlen_t’ 13 | typedef R_len_t R_xlen_t; | ^~~~~~~~ In file included from common.h:8, from fasthash.c:19: /data/gannet/ripley/R/R-devel-noLD/include/Rinternals.h:72:23: note: previous declaration of ‘R_xlen_t’ was here 72 | typedef ptrdiff_t R_xlen_t; | ^~~~~~~~ make[2]: *** [/data/gannet/ripley/R/R-devel-noLD/etc/Makeconf:168: fasthash.o] Error 1 make[2]: Leaving directory '/tmp/RtmpU5KFIv/working_dir/RtmpV2irzs/R.INSTALL21492fa0924/fastmatch/src' ERROR: compilation failed for package ‘fastmatch’ * removing ‘/data/gannet/ripley/R/packages/tests-noLD/ALA4R.Rcheck/fastmatch’ ERROR: dependency ‘fastmatch’ is not available for package ‘phangorn’ * removing ‘/data/gannet/ripley/R/packages/tests-noLD/ALA4R.Rcheck/phangorn’ ERROR: dependency ‘phangorn’ is not available for package ‘phytools’ * removing ‘/data/gannet/ripley/R/packages/tests-noLD/ALA4R.Rcheck/phytools’ The downloaded source packages are in '/tmp/RtmpU5KFIv/working_dir/RtmpDZw31r/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 'phytools' --- 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, 1 NOTE See ‘/data/gannet/ripley/R/packages/tests-noLD/ALA4R.Rcheck/00check.log’ for details. Time 2:52.25, 97.44 + 9.64