I just came across this issue on rmarkdown which links the same problem to BiocStyle. The post is from Nov 2017.
https://github.com/rstudio/rmarkdown/issues/1207 Maybe this helps to understand the underlying problem? It was suggested to check this in BiocStyle: Have you reported to the authors of BiocStyle? It seems they enabled the *knitr* hook |knitr::hook_pdfcrop| unconditionally (i.e. without checking if ImageMagick has been installed). Best, Christian On 9/11/19 5:50 PM, Pages, Herve wrote: > New to me too. But it seems that knitr suggests magick, which itself has > > SystemRequirements: ImageMagick++: ImageMagick-c++-devel (rpm) or > libmagick++-dev (deb) > > Don't know when this knitr dep on magick was introduced tough... Bummer! > > H. > > On 9/11/19 06:13, Kasper Daniel Hansen wrote: >> Yeah, does this imply that the render operation uses (or tries to use) >> ImageMagick? That's news to me, but I am not following this closely. >> >> On Wed, Sep 11, 2019 at 5:21 AM Pages, Herve <hpa...@fredhutch.org >> <mailto:hpa...@fredhutch.org>> wrote: >> >> On 9/11/19 00:50, Vincent Carey wrote: >> > 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. >> >> Not sure what's going on. A few observations: >> >> a) About 500 software packages use fig=TRUE. >> >> b) The convert warning is just a warning. The actual error in the case >> of BiocOncoTK is: >> >> Error: processing vignette 'BiocOncoTK.Rmd' failed with diagnostics: >> argument is of length zero >> >> Note that the ndexr vignette also fails with this error on tokay1 >> only but it doesn't have the convert warning (this vignette does not >> use >> 'fig' at all). So it's not clear to me that the "argument is of length >> zero" error is related to the convert warning. >> >> c) The devel build report shows the convert warning for 4 other >> packages >> (CAGEfightR, CATALYST, CTDquerier, specL) but each of them actually >> fails with a different error message: >> >> CAGEfightR: >> colData(object1) not identical to colData(object2) >> >> CATALYST: >> no slot of name "reducedDims" for this object of class "daFrame" >> >> CTDquerier: >> bfcadd() failed; see warnings() >> >> specL: >> pandoc.exe: Out of memory >> >> These errors don't seem related to the convert warning either. >> >> So I'm wondering: could it be that the convert warning is actually >> common but we generally don't see it because 'R CMD build' doesn't >> report warnings? And that we just happen to see the warning when 'R CMD >> build' fails to build a vignette. >> >> We'll investigate more. >> >> H. >> >> >> > >> > On Tue, Sep 10, 2019 at 11:35 AM Christian Mertes >> <mer...@in.tum.de <mailto:mer...@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 >> <mer...@in.tum.de <mailto:mer...@in.tum.de> >> >>> <mailto: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: >> >>> >> >>> >> >> 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: mer...@in.tum.de <mailto:mer...@in.tum.de> >> <mailto:mer...@in.tum.de <mailto:mer...@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]] >> >>> >> >>> _______________________________________________ >> >>> Bioc-devel@r-project.org <mailto:Bioc-devel@r-project.org> >> <mailto:Bioc-devel@r-project.org <mailto:Bioc-devel@r-project.org>> >> mailing >> >>> list >> >>> >> >> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=EwnHWfrov-A-kbkOeSotrFEWVXwIUuSJog3NysTJUnE&s=o9t9FYXG8jComIN3q8qZEwZCYCkvfK8dX3iNC03q4DA&e= >> >>> >> >>> >> >>> >> >>> -- >> >>> 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 <mailto:mer...@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]] >> >> >> >> _______________________________________________ >> >> Bioc-devel@r-project.org <mailto:Bioc-devel@r-project.org> >> mailing list >> >> >> >> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=EwnHWfrov-A-kbkOeSotrFEWVXwIUuSJog3NysTJUnE&s=o9t9FYXG8jComIN3q8qZEwZCYCkvfK8dX3iNC03q4DA&e= >> >> >> > >> >> -- >> Hervé Pagès >> >> Program in Computational Biology >> Division of Public Health Sciences >> Fred Hutchinson Cancer Research Center >> 1100 Fairview Ave. N, M1-B514 >> P.O. Box 19024 >> Seattle, WA 98109-1024 >> >> E-mail: hpa...@fredhutch.org <mailto:hpa...@fredhutch.org> >> Phone: (206) 667-5791 >> Fax: (206) 667-1319 >> _______________________________________________ >> Bioc-devel@r-project.org <mailto:Bioc-devel@r-project.org> mailing list >> https://stat.ethz.ch/mailman/listinfo/bioc-devel >> >> <https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwMFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=qBjqQdm_Q-bhQUa33Z-YE1bQ5xJfX8otPPeI27_GX4M&s=H-n3b1cvm3MrMIgggesOcfGgWnqj-mEmcaOyGjO5dPM&e=> >> >> >> >> -- >> 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