[Bioc-devel] Cannot reproduce a regionReport 1.21.7 error on the Bioc 3.11 Linux builder

Leonardo Collado Torres |co||@dotor @end|ng |rom gm@||@com
Fri Apr 24 03:36:08 CEST 2020

Hi Bioc-devel,

I'm having trouble with my regionReport package on the Bioc-devel
(3.11) Linux builds. Two weeks ago, using the Bioconductor devel
docker I was able to reproduce an error that was solved by ggbio
bumping their version number to 1.35.2 as described in [1]. I've tried
my best to reproduce the error shown at [2] which is:

Quitting from lines 224-229 (basicExploration.Rmd)
Error: processing vignette 'regionReport.Rmd' failed with diagnostics:
R: unable to get registry ID `cache:hosts' @

Recently [3], I bumped the regionReport version to 1.21.7 where I
explicitly asked for ggbio 1.35.2 to be available. I suspected that
the Linux builder still had version ggbio 1.35.1 installed. But that
did not resolve the issue as the current build report is for
regionReport version 1.21.7 and there's no error about ggbio 1.21.7
not being available. Hm... the required versions for the dependencies
does get checked at R CMD build (or even install), right?

At [4] you can see that regionReport 1.21.7 can be successfully
checked against Bioconductor devel's docker. This uses GitHub actions
that has 7 GB of RAM available [5]. The memory resources (7GB vs 2.5
GB? [6]), disk space (14 GB vs ?) and some system dependencies are the
only differences I can think of (installed through [7], none seem to
me to be related from what I see at [8]) besides the Linux builder
differences vs the Bioconductor devel docker (dunno what they are).

If you have any suggestions, please let me know.


[1] https://stat.ethz.ch/pipermail/bioc-devel/2020-April/016538.html
[2] https://master.bioconductor.org/checkResults/3.11/bioc-LATEST/regionReport/malbec2-buildsrc.html
[3] https://github.com/leekgroup/regionReport/commit/5e7d956f71011f8551f2431f5af0e212d04be9f1
[4] https://github.com/leekgroup/regionReport/runs/604161822?check_suite_focus=true#step:8:98
[5] https://help.github.com/en/actions/reference/virtual-environments-for-github-hosted-runners#supported-runners-and-hardware-resources
[6] https://github.com/Bioconductor/Contributions/issues/1389#issuecomment-605024369
2.5 GB is used for the 32-bit windows Single Package Builder.
[7] https://github.com/leekgroup/regionReport/runs/604161822?check_suite_focus=true#step:6:2
[8] https://github.com/leekgroup/regionReport/runs/604161822?check_suite_focus=true#step:6:167

Leonardo Collado Torres, Ph. D., Research Scientist
Lieber Institute for Brain Development
855 N Wolfe St, Suite 300
Baltimore, MD 21205

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