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

[Christian Mertes]

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


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