[Bioc-devel] Failing to build vignette because of problems with ImageMagick

Kasper Daniel Hansen k@@perd@n|e|h@n@en @end|ng |rom gm@||@com
Wed Sep 11 15:13:25 CEST 2019


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> 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>
> 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>> 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>
> >>>      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>
> 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
> >> 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 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
> Phone:  (206) 667-5791
> Fax:    (206) 667-1319
> _______________________________________________
> Bioc-devel using r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>


-- 
Best,
Kasper

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