[Bioc-devel] R-CMD-check fails on ubuntu-20.04 (release)

[Catherine Ross]

Hi Robert, Martin,

Thank you both for your responses!

I wasn’t able to recreate the issue on the Ubuntu docker image (only when you try to fail do you not fail… ), but adding the line `sudo apt-get install -y libglpk-dev` to my Github Action workflow did the trick.

Catherine

On Feb 16, 2021, at 7:39 PM, Martin Morgan <mtmorgan.bioc using gmail.com<mailto:mtmorgan.bioc using gmail.com>> wrote:

EXTERNAL EMAIL:

The key is that libglpk.so.40 cannot be loaded.

I'm guessing that igraph was installed from the RStudio package manager as a 'binary'. The RSPM had a libglpk installed when the igraph binary was built, so the binary package expects this library to be available. It was not on the image where the installation failed.

The solution is to arrange for libglpk to be installed on whatever image you are using  for your CI, maybe sudo apt-get install -y libglpk-dev.

Several interesting points.

Binary packages are installed, but unlike source packages R does not try to load them after they are installed, somehow assuming that the installation was correct. So the igraph failure is not apparent until later.

igraph's dependency on libglpk is optional, so if you'd installed it from source rather than from RSPM this would not have been an issue.

This issue came up immediately before the Bioc2020 annual conference, where the bioconductor/bioconductor_docker:devel image did not have libglpk because the rocker base image did not use RSPM at the time the Bioconductor docker file was created; it was introduced as an upstream change that was picked up when bioconductor/bioconductor_docker:devel image was rebuilt from source.

Martin Morgan

On 2/16/21, 7:01 PM, "Bioc-devel on behalf of Robert M. Flight" <bioc-devel-bounces using r-project.org<mailto:bioc-devel-bounces using r-project.org> on behalf of rflight79 using gmail.com<mailto:rflight79 using gmail.com>> wrote:

   Hi Catherine,

   It looks like igraph is not installed, which RCy3 depends on. This seems
   odd, because my own package categoryCompare depends on RCy3 and igraph, and
   it is building fine in the Bioconductor release and dev.

   I would see if you can recreate this issue locally on the Ubuntu docker
   image, or even use another github repo that just tries to install igraph or
   RCy3 on Ubuntu-release. igraph is still on CRAN, so it should be able to
   install.

   Regards,

   -Robert

   On Tue, Feb 16, 2021 at 6:10 PM Catherine Ross <
   catherinem.ross using mail.utoronto.ca<mailto:catherinem.ross using mail.utoronto.ca>> wrote:

Hello,

I’m running the following Github R-CMD-check workflow file on my package
repository.
https://github.com/r-lib/actions/tree/master/examples#standard-ci-workflow

It passes on 3/4 operating systems — windows-latest (release),
macOS-latest (release), ubuntu-20.04 (devel) — but fails on ubuntu-20.04
(release).
I get the following error at the ‘Install dependencies’ section:

* installing *source* package ‘RCy3’ ... ** using staged installation ** R
** inst ** byte-compile and prepare package for lazy loading Error in
dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object
'/home/runner/work/_temp/Library/igraph/libs/igraph.so': libglpk.so.40:
cannot open shared object file: No such file or directory Calls:
<Anonymous> ... asNamespace -> loadNamespace -> library.dynam -> dyn.load
Execution halted ERROR: lazy loading failed for package ‘RCy3’ * removing
‘/home/runner/work/_temp/Library/RCy3’

Then this error during ‘Check’:

Run options(crayon.enabled = TRUE) ── R CMD build
───────────────────────────────────────────────────────────────── *
checking for file ‘/home/runner/work/FEDUP/FEDUP/DESCRIPTION’ ... OK *
preparing ‘FEDUP’: * checking DESCRIPTION meta-information ... OK *
installing the package to build vignettes
----------------------------------- ERROR: dependency ‘RCy3’ is not
available for package ‘FEDUP’ * removing
‘/tmp/RtmpQdTGMd/Rinst3f8b26ef4bf5/FEDUP’
----------------------------------- ERROR: package installation failed
Error: Error in proc$get_built_file() : Build process failed Calls:
<Anonymous> ... build_package -> with_envvar -> force -> <Anonymous>
Execution halted Error: Process completed with exit code 1.

I run into no issues when running devtools::check() locally on my system
(macOS Big Sur 11.2).

Any ideas on how to fix this issue?

Thanks,
Catherine

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