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

[Vincent Carey]

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.


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:
> >
> >     http://bioconductor.riken.jp/checkResults/3.9/bioc-LATEST/OUTRIDER/
> >     https://travis-ci.org/gagneurlab/OUTRIDER
> >     https://ci.appveyor.com/project/c-mertes/OUTRIDER
> >
> >     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
> >     http://gagneurlab.in.tum.de
> >
> >
> >             [[alternative HTML version deleted]]
> >
> >     _______________________________________________
> >     Bioc-devel using r-project.org <mailto:Bioc-devel using r-project.org> mailing
> >     list
> >     https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
> >
> >
> > --
> > 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
>
>
>         [[alternative HTML version deleted]]
>
> _______________________________________________
> Bioc-devel using r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

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