[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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