[Bioc-devel] Failing to build vignette because of problems with ImageMagick
Vincent Carey
@tvjc @end|ng |rom ch@nn|ng@h@rv@rd@edu
Wed Oct 9 12:10:15 CEST 2019
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
> _______________________________________________
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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
>
>
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