[Bioc-devel] Failing to build vignette because of problems with ImageMagick
Andrzej Oleś
@ndrzej@o|e@ @end|ng |rom gm@||@com
Wed Oct 9 12:55:28 CEST 2019
Hi Vince,
I briefly communicated with Martin regarding this issue a few days ago. The
ImageMagick convert tool called by BiocStyle through a knitr figure
cropping hook can certainly be improved, as pointed out by Yihui in the in
the GitHub issue linked by Christian. This is something I will look into.
However, I don't think that your failing builds are related to BiocStyle. I
can only second on what Herve has already mentioned here: the observed
convert messages are picked up as warnings by 'R CMD build' and they don't
actually cause the build to fail.
Cheers,
Andrzej
On Wed, Oct 9, 2019 at 12:10 PM Vincent Carey <stvjc using channing.harvard.edu>
wrote:
> Just wondering whether this has been followed up. I am still seeing build
> errors for
> windows related to this.
>
> On Tue, Sep 17, 2019 at 10:20 AM Christian Mertes <mertes using in.tum.de>
> wrote:
>
> > I just came across this issue on rmarkdown which links the same problem
> to
> > BiocStyle.
> > The post is from Nov 2017.
> >
> > https://github.com/rstudio/rmarkdown/issues/1207
> >
> > Maybe this helps to understand the underlying problem?
> >
> > It was suggested to check this in BiocStyle:
> >
> > Have you reported to the authors of BiocStyle? It seems they enabled the
> > *knitr* hook knitr::hook_pdfcrop unconditionally (i.e. without checking
> > if ImageMagick has been installed).
> >
> > Best,
> >
> > Christian
> > On 9/11/19 5:50 PM, Pages, Herve wrote:
> >
> > New to me too. But it seems that knitr suggests magick, which itself has
> >
> > SystemRequirements: ImageMagick++: ImageMagick-c++-devel (rpm) or
> > libmagick++-dev (deb)
> >
> > Don't know when this knitr dep on magick was introduced tough... Bummer!
> >
> > H.
> >
> > On 9/11/19 06:13, Kasper Daniel Hansen wrote:
> >
> > Yeah, does this imply that the render operation uses (or tries to use)
> > ImageMagick? That's news to me, but I am not following this closely.
> >
> > On Wed, Sep 11, 2019 at 5:21 AM Pages, Herve <hpages using fredhutch.org
> <mailto:hpages using fredhutch.org> <hpages using fredhutch.org>> wrote:
> >
> > On 9/11/19 00:50, Vincent Carey wrote:
> > > I seem to be running into a similar problem with BiocOncoTK on
> > windows
> > >
> > > The build report for tokay1 shows:
> > >
> > > Loading required package: ontologyIndex
> > > Invalid Parameter - /figure-html
> > > Warning in shell(paste(c(cmd, args), collapse = " ")) :
> > > 'convert "BiocOncoTK_files/figure-html/lkgbm-1.png" -trim
> > > "BiocOncoTK_files/figure-html/lkgbm-1.png"' execution failed with
> > > error code 4
> > > Invalid Parameter - /figure-html
> > >
> > > The figure code is introduced with ```{r
> > lkgbm,fig=TRUE,message=FALSE}
> > > ... the 'convert' process is not requested by me
> > >
> > > Is the fig=TRUE problematic for windows? It seems unnecessary.
> >
> > Not sure what's going on. A few observations:
> >
> > a) About 500 software packages use fig=TRUE.
> >
> > b) The convert warning is just a warning. The actual error in the
> case
> > of BiocOncoTK is:
> >
> > Error: processing vignette 'BiocOncoTK.Rmd' failed with
> diagnostics:
> > argument is of length zero
> >
> > Note that the ndexr vignette also fails with this error on tokay1
> > only but it doesn't have the convert warning (this vignette does not
> > use
> > 'fig' at all). So it's not clear to me that the "argument is of
> length
> > zero" error is related to the convert warning.
> >
> > c) The devel build report shows the convert warning for 4 other
> > packages
> > (CAGEfightR, CATALYST, CTDquerier, specL) but each of them actually
> > fails with a different error message:
> >
> > CAGEfightR:
> > colData(object1) not identical to colData(object2)
> >
> > CATALYST:
> > no slot of name "reducedDims" for this object of class
> "daFrame"
> >
> > CTDquerier:
> > bfcadd() failed; see warnings()
> >
> > specL:
> > pandoc.exe: Out of memory
> >
> > These errors don't seem related to the convert warning either.
> >
> > So I'm wondering: could it be that the convert warning is actually
> > common but we generally don't see it because 'R CMD build' doesn't
> > report warnings? And that we just happen to see the warning when 'R
> CMD
> > build' fails to build a vignette.
> >
> > We'll investigate more.
> >
> > H.
> >
> >
> > >
> > > On Tue, Sep 10, 2019 at 11:35 AM Christian Mertes
> > <mertes using in.tum.de <mailto:mertes using in.tum.de> <mertes using in.tum.de>>
> wrote:
> > >
> > >> Thanks a lot for the info! So from my understanding we dont use
> any
> > >> trimming or editing function from ImageMagick directly. I think
> > this is
> > >> rather knitr based since we just include png files in the
> vignette.
> > >>
> > >> I guess it was an hickup since now the error is gone over night.
> > >>
> > >> Best regards,
> > >>
> > >> Christian
> > >>
> > >> On 9/9/19 4:34 PM, Kasper Daniel Hansen wrote:
> > >>> You don't declare any systems requirements for ImageMagick
> > (doing so
> > >>> will probably not solve your problem, but you really should).
> > >>>
> > >>> Alternatively you could look into using the tools provided by
> the
> > >>> magick package, which wraps ImageMagick.
> > >>>
> > >>> But it looks like you're editing PNG files for your vignette. I
> > would
> > >>> really recommend not doing so. It introduces a system
> > dependency which
> > >>> is just going to increase headaches on your end, for (perhaps)
> > no real
> > >>> tangible benefits. If you're trimming PNGs, you should be able
> to
> > >>> achieve the same effect when using the png device(s) in R, and
> that
> > >>> will make everything more portable anyway.
> > >>>
> > >>> On Mon, Sep 9, 2019 at 9:42 AM Christian Mertes
> > <mertes using in.tum.de <mailto:mertes using in.tum.de> <mertes using in.tum.de>
> > >>> <mailto:mertes using in.tum.de <mertes using in.tum.de> <mailto:
> mertes using in.tum.de> <mertes using in.tum.de>>> wrote:
> > >>>
> > >>> Dear BioC team,
> > >>>
> > >>> I just noticed that our package is failing on the
> > bioconductor build
> > >>> system during the build of the vignette on Windows and on
> > MacOS
> > >>> platforms.
> > >>>
> > >>> From the error I would guess its a problem with the
> > installation
> > >>> of the
> > >>> ImageMagick package. Please correct me if Im wrong.
> > >>>
> > >>> It goes through on travis and appveyor. Any suggestions?
> > >>>
> > >>> Here are some links to the build logs:
> > >>>
> > >>>
> >
> https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.riken.jp_checkResults_3.9_bioc-2DLATEST_OUTRIDER_&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=EwnHWfrov-A-kbkOeSotrFEWVXwIUuSJog3NysTJUnE&s=NA7UQNLz8lFT9bIMHiFka2iUJDarMgfT0uW36-nO9og&e=
> > >>>
> >
> https://urldefense.proofpoint.com/v2/url?u=https-3A__travis-2Dci.org_gagneurlab_OUTRIDER&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=EwnHWfrov-A-kbkOeSotrFEWVXwIUuSJog3NysTJUnE&s=lf9cL5c-plgiqIP3Hx6Eht_Ataw3bG3x3rP7gi79flg&e=
> > >>>
> >
> https://urldefense.proofpoint.com/v2/url?u=https-3A__ci.appveyor.com_project_c-2Dmertes_OUTRIDER&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=EwnHWfrov-A-kbkOeSotrFEWVXwIUuSJog3NysTJUnE&s=l-gS-eeyNnK7JCEdHKIUQifQoI40TZZXQox80MniKEA&e=
> > >>>
> > >>> Best,
> > >>>
> > >>> Christian
> > >>>
> > >>> PS: the error message on the bioc build system:
> > >>>
> > >>>
> > >>
> >
> ##############################################################################
> > >>>
> > >>
> >
> ##############################################################################
> > >>> ###
> > >>> ### Running command:
> > >>> ###
> > >>> ### chmod a+r OUTRIDER -R &&
> > >>> C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD build
> > >>> --keep-empty-dirs --no-resave-data OUTRIDER
> > >>> ###
> > >>>
> > >>
> >
> ##############################################################################
> > >>>
> > >>
> >
> ##############################################################################
> > >>>
> > >>>
> > >>> * checking for file 'OUTRIDER/DESCRIPTION' ... OK
> > >>> * preparing 'OUTRIDER':
> > >>> * checking DESCRIPTION meta-information ... OK
> > >>> * cleaning src
> > >>> * installing the package to build vignettes
> > >>> * creating vignettes ... ERROR
> > >>> --- re-building 'OUTRIDER.Rnw' using knitr
> > >>> Invalid Parameter - /deVsOutlier-1.png"
> > >>> Warning in shell(paste(c(cmd, args), collapse = " ")) :
> > >>> 'convert "figure/deVsOutlier-1.png" -trim
> > >>> "figure/deVsOutlier-1.png"' execution failed with error
> code 4
> > >>> 229 genes did not passed the filter due to zero counts.
> > This is
> > >>> 22.9% of the genes.
> > >>> Sat Sep 07 01:16:53 2019: SizeFactor estimation ...
> > >>> Sat Sep 07 01:16:53 2019: Controlling for confounders ...
> > >>> Using estimated q with: 23
> > >>> Sat Sep 07 01:16:53 2019: Using the autoencoder
> > implementation for
> > >>> controlling.
> > >>> Sat Sep 07 01:17:52 2019: Used the autoencoder
> > implementation for
> > >>> controlling.
> > >>> Sat Sep 07 01:17:52 2019: P-value calculation ...
> > >>> Sat Sep 07 01:17:52 2019: Zscore calculation ...
> > >>> Invalid Parameter - /quick_guide-1.png"
> > >>> Warning in shell(paste(c(cmd, args), collapse = " ")) :
> > >>> 'convert "figure/quick_guide-1.png" -trim
> > >>> "figure/quick_guide-1.png"' execution failed with error
> code 4
> > >>> Quitting from lines 222-232 (OUTRIDER.Rnw)
> > >>> Error: processing vignette 'OUTRIDER.Rnw' failed with
> > diagnostics:
> > >>> no lines available in input
> > >>> --- failed re-building 'OUTRIDER.Rnw'
> > >>>
> > >>> SUMMARY: processing the following file failed:
> > >>> 'OUTRIDER.Rnw'
> > >>>
> > >>> Error: Vignette re-building failed.
> > >>> Execution halted
> > >>>
> > >>> --
> > >>>
> > >>> Christian Mertes
> > >>> PhD Student / Lab Administrator
> > >>> Gagneur lab
> > >>>
> > >>> Computational Genomics
> > >>> I12 - Bioinformatics Department
> > >>> Technical University Munich
> > >>> Boltzmannstr. 3
> > >>> 85748 Garching, Germany
> > >>>
> > >>> Mail: mertes using in.tum.de <mailto:mertes using in.tum.de> <
> mertes using in.tum.de>
> > <mailto:mertes using in.tum.de <mertes using in.tum.de> <mailto:mertes using in.tum.de>
> <mertes using in.tum.de>>
> > >>> Phone: +49-89-289-19416
> > >>>
> >
> https://urldefense.proofpoint.com/v2/url?u=http-3A__gagneurlab.in.tum.de&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=EwnHWfrov-A-kbkOeSotrFEWVXwIUuSJog3NysTJUnE&s=Xm9xiIrQ9GfPE9Y2UAWzyudbqri57cp7CBlr9xFyU_g&e=
> > >>>
> > >>>
> > >>> [[alternative HTML version deleted]]
> > >>>
> > >>> _______________________________________________
> > >>> Bioc-devel using r-project.org <mailto:Bioc-devel using r-project.org> <
> Bioc-devel using r-project.org>
> > <mailto:Bioc-devel using r-project.org <Bioc-devel using r-project.org> <mailto:
> Bioc-devel using r-project.org> <Bioc-devel using r-project.org>>
> > mailing
> > >>> list
> > >>>
> >
> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=EwnHWfrov-A-kbkOeSotrFEWVXwIUuSJog3NysTJUnE&s=o9t9FYXG8jComIN3q8qZEwZCYCkvfK8dX3iNC03q4DA&e=
> > >>>
> > >>>
> > >>>
> > >>> --
> > >>> Best,
> > >>> Kasper
> > >>
> > >> --
> > >>
> > >> Christian Mertes
> > >> PhD Student / Lab Administrator
> > >> Gagneur lab
> > >>
> > >> Computational Genomics
> > >> I12 - Bioinformatics Department
> > >> Technical University Munich
> > >> Boltzmannstr. 3
> > >> 85748 Garching, Germany
> > >>
> > >> Mail: mertes using in.tum.de <mailto:mertes using in.tum.de> <
> mertes using in.tum.de>
> > >> Phone: +49-89-289-19416
> > >>
> >
> https://urldefense.proofpoint.com/v2/url?u=http-3A__gagneurlab.in.tum.de&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=EwnHWfrov-A-kbkOeSotrFEWVXwIUuSJog3NysTJUnE&s=Xm9xiIrQ9GfPE9Y2UAWzyudbqri57cp7CBlr9xFyU_g&e=
> > >>
> > >>
> > >> [[alternative HTML version deleted]]
> > >>
> > >> _______________________________________________
> > >> Bioc-devel using r-project.org <mailto:Bioc-devel using r-project.org> <
> Bioc-devel using r-project.org>
> > mailing list
> > >>
> >
> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=EwnHWfrov-A-kbkOeSotrFEWVXwIUuSJog3NysTJUnE&s=o9t9FYXG8jComIN3q8qZEwZCYCkvfK8dX3iNC03q4DA&e=
> > >>
> > >
> >
> > --
> > Hervé Pagès
> >
> > Program in Computational Biology
> > Division of Public Health Sciences
> > Fred Hutchinson Cancer Research Center
> > 1100 Fairview Ave. N, M1-B514
> > P.O. Box 19024
> > Seattle, WA 98109-1024
> >
> > E-mail: hpages using fredhutch.org <mailto:hpages using fredhutch.org> <
> hpages using fredhutch.org>
> > Phone: (206) 667-5791
> > Fax: (206) 667-1319
> > _______________________________________________
> > Bioc-devel using r-project.org <mailto:Bioc-devel using r-project.org> <
> Bioc-devel using r-project.org> mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> > <
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> >
> >
> >
> >
> > --
> > Best,
> > Kasper
> >
> > --
> >
> > Christian Mertes
> > PhD Student / Lab Administrator
> > Gagneur lab
> >
> > Computational Genomics
> > I12 - Bioinformatics Department
> > Technical University Munich
> > Boltzmannstr. 3
> > 85748 Garching, Germany
> >
> > Mail: mertes using in.tum.de
> > Phone: +49-89-289-19416http://gagneurlab.in.tum.de
> >
> >
>
> --
> The information in this e-mail is intended only for th...{{dropped:10}}
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