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

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 at in.tum.de
<mailto:mertes at 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 at in.tum.de <mailto:mertes at in.tum.de>
    Phone: +49-89-289-19416
    http://gagneurlab.in.tum.de


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