Dear IFB team,
We are currently encountering a compilation error while attempting to install the R package pak.
Below is the error we receive for sknafo account while working on cross_species_prof_scn project:
trying URL 'https://cran.rstudio.com/src/contrib/pak_0.8.0.tar.gz'
Content type 'application/x-gzip' length 2046894 bytes (2.0 MB)
==================================================
downloaded 2.0 MB
* installing *source* package ‘pak’ ...
** package ‘pak’ successfully unpacked and MD5 sums checked
** using staged installation
** Running ./configure
** libs
Current platform: x86_64-conda-linux-gnu
Build platform:
Target platform:
Compiling R6
Compiling cli
sh: 1: x86_64-conda-linux-gnu-cc: not found
make[1]: Entering directory '/tmp/Rtmpn5HhMi/R.INSTALL292caa25bb9fe8/pak/src/library/cli/src'
x86_64-conda-linux-gnu-cc -I"/shared/ifbstor1/software/miniconda/envs/r-4.4.1/lib/R/include" -DNDEBUG -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /shared/ifbstor1/software/miniconda/envs/r-4.4.1/include -I/shared/ifbstor1/software/miniconda/envs/r-4.4.1/include -Wl,-rpath-link,/shared/ifbstor1/software/miniconda/envs/r-4.4.1/lib -fvisibility=hidden -I../inst/include -fpic -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /shared/ifbstor1/software/miniconda/envs/r-4.4.1/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1720307580853/work=/usr/local/src/conda/r-base-4.4.1 -fdebug-prefix-map=/shared/ifbstor1/software/miniconda/envs/r-4.4.1=/usr/local/src/conda-prefix -c ansi.c -o ansi.o
/bin/sh: 1: x86_64-conda-linux-gnu-cc: not found
make[1]: *** [/shared/ifbstor1/software/miniconda/envs/r-4.4.1/lib/R/etc/Makeconf:197: ansi.o] Error 127
make[1]: Leaving directory '/tmp/Rtmpn5HhMi/R.INSTALL292caa25bb9fe8/pak/src/library/cli/src'
ERROR: compilation failed for package ‘cli’
Error in install_one(pkg, lib = lib) : FAILED
Calls: install_embedded_main -> install_all -> install_one
Execution halted
installing via 'install.libs.R' to /shared/home/sknafo/R/x86_64-conda-linux-gnu-library/4.4/00LOCK-pak/00new/pak
Error in eval(ei, envir) : Compilation failed.
* removing ‘/shared/home/sknafo/R/x86_64-conda-linux-gnu-library/4.4/pak’
The downloaded source packages are in
'/tmp/Rtmppxzxdw/downloaded_packages'
Error in library(pak) : there is no package called 'pak'
It appears that the compiler (x86_64-conda-linux-gnu-cc) is not found.
NB: This problem is only encountered when working under the sknafo account, whereas from the syoujilabadi account it works without any issues.
Common project : cross_species_prof_scn
Any suggestions or guidance on how to resolve this error would be greatly appreciated. Thank you in advance for your assistance.
Kind regards,
S.