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

Christian Mertes merte@ @end|ng |rom |n@tum@de
Tue Sep 17 16:20:50 CEST 2019


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>> 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>> 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>
>>      >>> <mailto: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>
>>     <mailto: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>
>>     <mailto: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 <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=
>>      >>
>>      >
>>
>>     -- 
>>     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>
>>     Phone:  (206) 667-5791
>>     Fax:    (206) 667-1319
>>     _______________________________________________
>>     Bioc-devel using r-project.org <mailto:Bioc-devel using r-project.org> mailing list
>>     https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>     <https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwMFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=qBjqQdm_Q-bhQUa33Z-YE1bQ5xJfX8otPPeI27_GX4M&s=H-n3b1cvm3MrMIgggesOcfGgWnqj-mEmcaOyGjO5dPM&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
http://gagneurlab.in.tum.de


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