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

Fri Apr 10 02:59:25 CEST 2020

Thanks Michael!

I verified that building regionReport works with ggbio 1.35.2
https://github.com/tengfei/ggbio/commit/6bc94f45e6479b01287e25140821f239f1a7f92d
on linux OS and I updated the gist at
https://gist.github.com/lcolladotor/b7585962082263b377c02fa4451f27e6
with a file linux_regionReport_build_ggbio_1.35.2.txt that has all the
relevant output. I also added a
linux_reprex_derfinderPlot_output_ggbio_1.35.2.txt that shows the
issues with validObject(hg19IdeogramCyto) from biovizBase.

My guess is that the linux OS had ggbio 1.35.1 from
https://github.com/tengfei/ggbio/commit/e385a446fc8a255515fbaba818ae59ef240d494f
that is one commit prior to
https://github.com/tengfei/ggbio/commit/930e521bfe0967f5095583c69f655fa571e3fa42
which fixes this issue and was maybe the ggbio 1.35.1 version I
installed on my macOS. This makes sense to me (and I'll keep a mental
note to check commit history in the future when OS reports differ),
but if have other possible explanations for the OS discrepancies
please let me know.

Thanks again for the speedy fix!! =)

Best,
Leo

On Thu, Apr 9, 2020 at 4:41 PM Michael Lawrence
<lawrence.michael using gene.com> wrote:
>
> 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
>
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