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 <mer...@in.tum.de > <mailto:mer...@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: mer...@in.tum.de <mailto:mer...@in.tum.de> > Phone: +49-89-289-19416 > http://gagneurlab.in.tum.de > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-devel@r-project.org <mailto:Bioc-devel@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: mer...@in.tum.de Phone: +49-89-289-19416 http://gagneurlab.in.tum.de [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
