Hello all, I recently installed R onto my Ubuntu 20.04 install using the instructions here: https://cran.r-project.org/bin/linux/ubuntu/. R works as expected.
However, while some packages have installed without issue (e.g., R.matlab), there are many packages that have not been able to install. Each failed install throws a very similar error message. As an example, install.packages("utf8") throws: ``` during GIMPLE pass: ccp as_utf8.c: In function ‘rutf8_as_utf8’: as_utf8.c:128:1: internal compiler error: Segmentation fault 128 | } | ^ Please submit a full bug report, with preprocessed source if appropriate. See <file:///usr/share/doc/gcc-9/README.Bugs> for instructions. make: *** [/usr/lib/R/etc/Makeconf:172: as_utf8.o] Error 1 ERROR: compilation failed for package ‘utf8’ ``` As another example, install.packages("fansi") throws: ``` during GIMPLE pass: ccp nchar.c: In function ‘FANSI_nzchar’: nchar.c:85:1: internal compiler error: Segmentation fault 85 | } | ^ Please submit a full bug report, with preprocessed source if appropriate. See <file:///usr/share/doc/gcc-9/README.Bugs> for instructions. make: *** [/usr/lib/R/etc/Makeconf:172: nchar.o] Error 1 ERROR: compilation failed for package ‘fansi’ ``` I have tried reinstalling gcc-9, which has not helped. I had found that the PATH in Sys.getenv("PATH") was pointing to a miniconda3 install on my system, so updated that to /usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/usr/lib/rstudio/bin/postback, which also has not helped. I posted a question to: https://answers.launchpad.net/ubuntu/+question/696623 and it was suggested that I use gcc-10 instead of gcc-9. I edited /usr/lib/R/etc/Makeconf and replaced CC=-std=gnu99 with CC=gcc-10. This resolved the issue and the packages that were throwing these errors were able to be installed. After posting the question to Stackoverflow, it was made clear that this was not a solution rather an obtuse workaround. It was recommended that I send the question here for help. Output of gcc -v: ``` Using built-in specs. COLLECT_GCC=gcc COLLECT_LTO_WRAPPER=/usr/lib/gcc/x86_64-linux-gnu/9/lto-wrapper OFFLOAD_TARGET_NAMES=nvptx-none:hsa OFFLOAD_TARGET_DEFAULT=1 Target: x86_64-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Ubuntu 9.3.0-17ubuntu1~20.04' --with-bugurl=file:///usr/share/doc/gcc-9/README.Bugs --enable-languages=c,ada,c++,go,brig,d,fortran,objc,obj-c++,gm2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-9 --program-prefix=x86_64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-vtable-verify --enable-plugin --enable-default-pie --with-system-zlib --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-werror --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-offload-targets=nvptx-none=/build/gcc-9-HskZEa/gcc-9-9.3.0/debian/tmp-nvptx/usr,hsa --without-cuda-driver --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu Thread model: posix gcc version 9.3.0 (Ubuntu 9.3.0-17ubuntu1~20.04) ``` Output of sessionInfo() in R: ``` R version 4.0.5 (2021-03-31) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 20.04.2 LTS Matrix products: default BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so.3 locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] compiler_4.0.5 tools_4.0.5 ``` Thanks all for your help and advice. Best, Mazin [[alternative HTML version deleted]] _______________________________________________ R-SIG-Debian mailing list R-SIG-Debian@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-debian