Hi, I went to google again and maybe https://github.com/phw/peek/issues/112#issuecomment-296690302 is the answer? It would require someone with access to the Linux builder to check this particular ImageMagick config XML file.
I had linked to this thread earlier https://stat.ethz.ch/pipermail/bioc-devel/2020-April/016538.html though back then I mentioned that it could be a disk space issue. That was before the more recent thread about that ended with ggbio being bumpted to 1.35.2 (for which using Bioconductor's devel docker revealed the problem). I also just asked on Twitter https://twitter.com/fellgernon/status/1253502433231343617?s=20 to see if anyone has seen a similar error. Best, Leo On Thu, Apr 23, 2020 at 9:36 PM Leonardo Collado Torres <lcollado...@gmail.com> wrote: > > 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
