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

Catherine Ross c@ther|nem@ro@@ @end|ng |rom m@||@utoronto@c@
Wed Feb 17 00:06:01 CET 2021


I’m running the following Github R-CMD-check workflow file on my package repository.

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?


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