[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 14:17:52 CEST 2019
On Wed, Oct 9, 2019 at 6:55 AM Andrzej Oleś <andrzej.oles using gmail.com> wrote:
> 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.
>
Thank you Andrzej ... I missed this point. Because it is a
platform-specific failure (no prob on linux or mac)
I assumed that this event was the problem. I will look more closely at a
windows build attempt.
>
> 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
>> > <
>> 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=>
>> <
>> 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: +49-89-289-19416http://gagneurlab.in.tum.de
>> >
>> >
>>
>> --
>> The information in this e-mail is intended only for t...{{dropped:27}}
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