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@rob:~$ docker run --rm -ti rocker/r-bspm:20.04 bash
root@6f02540917d0:/# apt update -qq # refresh indices
71 packages can be upgraded. Run 'apt list --upgradable' to see them.
root@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@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 | e...@debian.org

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