[R-sig-Debian] Unable to install some R packages in Ubuntu 20.04--internal compiler error: Segmentation fault

[George N. White III]

On Fri, 23 Apr 2021 at 00:29, Dirk Eddelbuettel <edd using debian.org> wrote:

>
> On 22 April 2021 at 18:43, Mazin Abdelghany wrote:
>
> | [...] 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.
>

I agree this is almost certainly the reason building packages fails.  I
have seen this
before (my interests include ocean remote sensing where Python and R are
often used
at different stages in a workflow).   In addition to compilers, there can
be problems with
differing dynamic library and python module versions, or the data files
used by some
libraries.  Some users conclude that "R doesn't work".  Such conflicts,
however, easily
avoided by using an environment manager such as John Furlani's Environment
Modules[1] (has a long history and was included in SGI IRIX64 decades ago)
or the
more recent Lua Mod[2].  Both are available as Ubuntu packages.  There are
others
(see the Wikipedia articles on Environment Modules).

[1] John L. Furlani, Modules: Providing a Flexible User Environment
<http://modules.sourceforge.net/docs/Modules-Paper.pdf> *Proceedings of the
Fifth Large Installation Systems Administration Conference (LISA V)*,
pp. 141–152, San Diego, CA, September 30 - October 3, 1991.
[2] https://www.tacc.utexas.edu/research-development/tacc-projects/lmod,
"Modern Scientific Software Management Using EasyBuild and Lmod," M.
Geimer, K. Hoste, and R. McLay, Proceedings of the First International
Workshop on HPC User Support Tools, HUST '14, Nov. 2014.
dx.doi.org/10.1109/HUST.2014.8.

-- 
George N. White III

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