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 -- 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 Phone: (206) 667-5791 Fax: (206) 667-1319 _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
