R SIG Debian - Apr 2021 - Unable to install some R packages in Ubuntu 20.04--internal compiler error: Segmentation fault

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]]

Hi Mazin,

On 19 April 2021 at 10:24, Mazin Abdelghany wrote:
| 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?
| ```

Weird. I have been on Ubuntu for most of its existence, and tend to compile
(on my main development machine) all packages directly from CRAN.

These packages _definitely_ install normally, so would need some extra
details.

| 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

Ahhhhhhhhhhhhh. That is extra detail. And ... not a good idea in general.

Mixing conda and normal installations is NOT a good idea. You also did not
mention above that you switched to conda.

| 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.

As I menionted when you asked on StackOverflow, that was not a good
suggestion. The compiler has nothing to do with this but you generally may
run into issue mixing conda and normal use.

My recommendation and preference would be to stay away from conda -- as I
never used (or needed) it. Maybe others can help you with it.

If you read the README for Ubuntu and CRAN, check out the hint about the
PPA. You can even couple it with the (very clever) 'bspm' package and
then
_normal R installations will give you binaries_.  Demo in the r-bspm:20.04
container follows:

edd at rob:~$ docker run --rm -ti rocker/r-bspm:20.04 bash
root at 6f02540917d0:/# apt update -qq # refresh indices
71 packages can be upgraded. Run 'apt list --upgradable' to see them.
root at 6f02540917d0:/# Rscript -e 'install.packages(c("utf8",
"fansi"))'
Loading required package: utils
Tracing function "install.packages" in package "utils"
Install system packages as root...
Reading package lists... Done
Building dependency tree        
Reading state information... Done
Hit http://archive.ubuntu.com/ubuntu focal InRelease
Hit http://security.ubuntu.com/ubuntu focal-security InRelease
Hit http://ppa.launchpad.net/c2d4u.team/c2d4u4.0+/ubuntu focal InRelease
Hit http://archive.ubuntu.com/ubuntu focal-updates InRelease
Hit http://archive.ubuntu.com/ubuntu focal-backports InRelease
Hit http://ppa.launchpad.net/edd/r-4.0/ubuntu focal InRelease
Hit http://ppa.launchpad.net/marutter/rrutter4.0/ubuntu focal InRelease
Fetched 0 B in 0s (0 B/s)
Reading package lists... Done    
Building dependency tree          
Reading state information... Done
Get:1 http://ppa.launchpad.net/c2d4u.team/c2d4u4.0+/ubuntu focal/main amd64
r-cran-fansi amd64 0.4.2-1cran1.2004.0 [176 kB]
Get:2 http://ppa.launchpad.net/c2d4u.team/c2d4u4.0+/ubuntu focal/main amd64
r-cran-utf8 amd64 1.2.1-1cran1.2004.0 [122 kB]
Fetched 298 kB in 0s (0 B/s)
Selecting previously unselected package r-cran-fansi.
(Reading database ... 20588 files and directories currently installed.)
Preparing to unpack .../r-cran-fansi_0.4.2-1cran1.2004.0_amd64.deb ...
Unpacking r-cran-fansi (0.4.2-1cran1.2004.0) ...
Selecting previously unselected package r-cran-utf8.
Preparing to unpack .../r-cran-utf8_1.2.1-1cran1.2004.0_amd64.deb ...
Unpacking r-cran-utf8 (1.2.1-1cran1.2004.0) ...
Setting up r-cran-fansi (0.4.2-1cran1.2004.0) ...
Setting up r-cran-utf8 (1.2.1-1cran1.2004.0) ...
root at 6f02540917d0:/#

You could do the same via 'sudo apt install r-cran-utf8 r-cran-fansi'
without
'bspm' if you just set up the PPA.

Good luck,  Dirk


 
| 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]]
| 
| _______________________________________________
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-- 
https://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org