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' @ error/registry.c/GetImageRegistry/202 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. Best, Leo [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 http://lcolladotor.github.io _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
