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

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 at 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 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:

     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 at in.tum.de <mailto:mertes at 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]]

--

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
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]]