[Bioc-devel] regionReport error leads to ggbio & biovizBase issues, confusingly not on all OS though

[Michael Lawrence]

I bumped the version of ggbio which should propagate a recent fix.

Michael

On Thu, Apr 9, 2020 at 7:11 AM Leonardo Collado Torres <
lcolladotor using gmail.com> wrote:

> Hi BioC-devel,
>
> I was able to trace a regionReport error back to ggbio & biovizBase.
> However, I'm completely clueless as to why (a) it only appears in some
> OS (though this has changed over time) and (b) it does not seem to be
> a problem with derfinderPlot on the build reports for the same OS.
>
>
>
> ## Short version
>
> library('ggbio')
> data(hg19IdeogramCyto, package = 'biovizBase')
> p.ideo <- plotIdeogram(hg19IdeogramCyto, 'chr21')
> tracks(p.ideo)
>
> This code on linux leads to 3 warnings from plotIdeogram() and an
> error from tracks(). Also, validObject(hg19IdeogramCyto) fails (this
> also fails on macOS).
>
> One warning (about seqlengths) and validObject() can be fixed with:
>
> hg19IdeogramCytoFixed <- updateObject(hg19IdeogramCyto)
>     seqlengths(hg19IdeogramCytoFixed) <-
> seqlengths(getChromInfoFromUCSC('hg19', as.Seqinfo =
> TRUE))[seqlevels(hg19IdeogramCytoFixed)]
>
>
> This code is currently run from derfinderPlot::plotCluster() and for
> some reason, the examples don't fail.
>
>
>
> ## Long version
>
> My package regionReport has been failing for a while with the same
> error on Bioc-release (3.10) and bioc-devel (3.11). I've been watching
> the fails for a while and it's mostly:
>
> * linux on 3.10, occasionally Windows
> * linux on 3.11
>
> Right now, it's only linux on both 3.10 and 3.11.
>
> The error always is:
>
> Quitting from lines 224-229 (basicExploration.Rmd)
> Error in magick_image_trim(image, fuzz) :
>   R: unable to get registry ID `cache:hosts' @
> error/registry.c/GetImageRegistry/202
> Calls: render ... <Anonymous> -> assert_image -> <Anonymous> ->
> magick_image_trim
>
>
> A while back, I reported that I couldn't reproduce this on 3.10 on
> Windows (when it was failing). I've looked at the magick package and
> it didn't seem to be the issue
> mhttps://
> github.com/ropensci/magick/search?q=magick_image_trim&unscoped_q=magick_image_trim
> .
>
> After getting R 4.0.0 setup on my macOS, I also couldn't reproduce it.
> So I finally looked at Nitesh's work on dockers at
> http://bioconductor.org/help/docker/
>
>  docker run \
>      -e PASSWORD=bioc \
>      -p 8787:8787 \
>      bioconductor/bioconductor_docker:devel
>
> There I could reproduce the build problem from regionReport and got a
> more detailed error message. Using an interactive session where I ran
> the internal code piece by piece, I got to the biovizBase + ggbio
> error.
>
> derfinderPlot::plotCluster(), which is also a package I made, runs the
> exact same code and has not failed at all on both bioc-release (3.10)
> and devel (3.11) all this time. I would have expected derfinderPlot to
> fail also (in which case it would have provided a more informative
> error than the one hidden by rmarkdown in regionReport's build
> reports). If I run the example for derfinderPlot::plotCluster() on
> linux it does fail, however this was not picked up by the BioC build
> report. Hence why I'm even more confused.
>
> Anyway, hopefully fixing the ggbio/biovizBase issue will fix
> derfinderPlot::plotCluster() and in turn regionReport.
>
> As to the inconsistencies across OS or between the BioC build report
> output for derfinderPlot and what I see on linux, I have no idea
> though.
>
>
> ## Gist with details
>
> I have a Gist with all the output logs and the R session information
> at https://gist.github.com/lcolladotor/b7585962082263b377c02fa4451f27e6.
> Here's the brief description for each file.
>
> * macOS_regionReport_build.txt: runs R CMD build for regionReport
> without a problem
> * linux_regionReport_build.txt: fails to run R CMD build for
> regionReport and provides more details and the BioC build report. This
> is where we can start to see errors related to the ideograms. I
> thought that fixing this would only involve a updateObject() call at
> this point.
> * reprex_ggbio_code.R: smallest code I have for reproducing this issue
> * macOS_reprex_ggbio_output.txt: runs without errors (though it still
> has warnings about seqlengths and other ggbio parts)
> * linux_reprex_ggbio_output.txt: fails to run the small reprex
> * reprex_derfinderPlot_code.R: runs the example for
> derfinderPlot::plotCluster()
> * macOS_reprex_derfinderPlot_output.txt: similar story to
> macOS_reprex_ggbio_output.txt:
> * linux_reprex_derfinderPlot_output.txt: the example fails here too!
> Which makes me even more confused. I mean, it's consistent with
> regionReport and the ggbio reprex. However, I then don't understand
> why this hasn't failed in the BioC builds.
>
>
>
> Best,
> Leo
>
>
> 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
>
>
> On Tue, Mar 17, 2020 at 6:35 PM Leonardo Collado Torres
> <lcolladotor using gmail.com> wrote:
> >
> > Hi BioC-devel,
> >
> > I spent some time yesterday getting my Windows laptop ready to debug a
> > Windows OS-only issue in regionReport (bioc-release 3.10), but
> > ultimately I couldn't reproduce it. Since the error seems to be some
> > type of cache, I bumped the version number but it still failed today
> > and it then also failed on bioc-devel (3.11) on Linux (as well as
> > Windows).
> >
> > ## Bioc-release (3.10) Windows is the only that fails
> >
> > 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
> > --- failed re-building ‘regionReport.Rmd’
> >
> > similarly
> >
> > Quitting from lines 224-229 (basicExploration.Rmd)
> > Error in magick_image_trim(image, fuzz) :
> >   R: unable to get registry ID `cache:hosts' @
> > error/registry.c/GetImageRegistry/202
> > Calls: render ... <Anonymous> -> assert_image -> <Anonymous> ->
> > magick_image_trim
> >
> >
> > ## Bioc-devel (3.11) Linux and Windows fails
> >
> >
> http://bioconductor.org/checkResults/release/bioc-LATEST/regionReport/malbec1-buildsrc.html
> >
> > However, I see at
> >
> http://bioconductor.org/checkResults/devel/bioc-LATEST/regionReport/malbec2-buildsrc.html
> > that the error appeared today also on the Linux bioc-devel builder.
> >
> > ## Google
> >
> > Searching for the error message led me to
> > https://github.com/phw/peek/issues/112 which talks about disk space
> > running out for ImageMagick. Do you think that this is something that
> > is affecting the builders too? Do you have any suggestions I could
> > try?
> >
> > Best,
> > Leo
>
> _______________________________________________
> Bioc-devel using r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>


-- 
Michael Lawrence
Senior Scientist, Bioinformatics and Computational Biology
Genentech, A Member of the Roche Group
Office +1 (650) 225-7760
michafla using gene.com

Join Genentech on LinkedIn | Twitter | Facebook | Instagram | YouTube

	[[alternative HTML version deleted]]