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

A few new pieces of information with this feedback:

First,
Opening R in the terminal window by running
R
And then typing
install.packages("utf8")
threw the error that I noted above.

Running
sudo apt install r-cran-utf8
in the terminal works to install the package

Second,
I have never used conda to do anything with R. I installed conda as the
package and environment manager for python, which I use for projects
outside of R. I checked and my install of miniconda does not contain an R
installation. Because miniconda is installed on my system, the PATH
variable is changed to the below:
/home/mazin/miniconda3/condabin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin

Using Dirk's suggestion, I installed the package bspm, which solved the
issue for me.
Running: (1) bspm::enable() within R and then install.packages() worked. I
then, as written in its documentation, enabled bspm system-wide by default,
including suppressMessages(bspm::enable()) in the Rprofile.site file.

Thanks all,
Mazin

On Mon, Apr 19, 2021 at 11:28 AM Dirk Eddelbuettel <edd at debian.org>
wrote:
>
> 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]]
> |
> | _______________________________________________
> | R-SIG-Debian mailing list
> | R-SIG-Debian at r-project.org
> | https://stat.ethz.ch/mailman/listinfo/r-sig-debian
>
> --
> https://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org
>
	[[alternative HTML version deleted]]

On 22 April 2021 at 18:43, Mazin Abdelghany wrote:
|  A few new pieces of information with this feedback:
| 
| First,
| Opening R in the terminal window by running
| R
| And then typing
| install.packages("utf8")
| threw the error that I noted above.
| 
| Running
| sudo apt install r-cran-utf8
| in the terminal works to install the package
| 
| Second,
| I have never used conda to do anything with R. I installed conda as the
| package and environment manager for python, which I use for projects
| outside of R. I checked and my install of miniconda does not contain an R
| installation. Because miniconda is installed on my system, the PATH
| variable is changed to the below:
|
/home/mazin/miniconda3/condabin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin

That likely puts a compiler _ahead_ in the path meaning that when R calls a
compiler to install a package from source it may get _an incompatible_ one.

Which would explain your issues.
 
| Using Dirk's suggestion, I installed the package bspm, which solved the
| issue for me.
| Running: (1) bspm::enable() within R and then install.packages() worked. I
| then, as written in its documentation, enabled bspm system-wide by default,
| including suppressMessages(bspm::enable()) in the Rprofile.site file.

That is indeed very nice as it gets you _binaries_ so it skips the need for
binaries -- which helps as your ability to create binaries appears to be
brokeb by conda or miniconda.

Dirk

| Thanks all,
| Mazin
| 
| On Mon, Apr 19, 2021 at 11:28 AM Dirk Eddelbuettel <edd at debian.org>
wrote:
| 
| >
| > 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]]
| > |
| > | _______________________________________________
| > | R-SIG-Debian mailing list
| > | R-SIG-Debian at r-project.org
| > | https://stat.ethz.ch/mailman/listinfo/r-sig-debian
| >
| > --
| > https://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org
| >
| 
| 	[[alternative HTML version deleted]]
| 
| _______________________________________________
| R-SIG-Debian mailing list
| R-SIG-Debian at r-project.org
| https://stat.ethz.ch/mailman/listinfo/r-sig-debian

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