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

[Christian Mertes]

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
Phone: +49-89-289-19416
http://gagneurlab.in.tum.de


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