On Wed, Oct 9, 2019 at 6:55 AM Andrzej Oleś <andrzej.o...@gmail.com> wrote:
> Hi Vince, > > I briefly communicated with Martin regarding this issue a few days ago. > The ImageMagick convert tool called by BiocStyle through a knitr figure > cropping hook can certainly be improved, as pointed out by Yihui in the in > the GitHub issue linked by Christian. This is something I will look into. > However, I don't think that your failing builds are related to BiocStyle. I > can only second on what Herve has already mentioned here: the observed > convert messages are picked up as warnings by 'R CMD build' and they don't > actually cause the build to fail. > Thank you Andrzej ... I missed this point. Because it is a platform-specific failure (no prob on linux or mac) I assumed that this event was the problem. I will look more closely at a windows build attempt. > > Cheers, > Andrzej > > On Wed, Oct 9, 2019 at 12:10 PM Vincent Carey <st...@channing.harvard.edu> > wrote: > >> Just wondering whether this has been followed up. I am still seeing build >> errors for >> windows related to this. >> >> On Tue, Sep 17, 2019 at 10:20 AM Christian Mertes <mer...@in.tum.de> >> wrote: >> >> > 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> <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> <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> <mer...@in.tum.de> >> > >>> <mailto:mer...@in.tum.de <mer...@in.tum.de> <mailto: >> mer...@in.tum.de> <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> < >> mer...@in.tum.de> >> > <mailto:mer...@in.tum.de <mer...@in.tum.de> <mailto: >> mer...@in.tum.de> <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> < >> Bioc-devel@r-project.org> >> > <mailto:Bioc-devel@r-project.org <Bioc-devel@r-project.org> >> <mailto:Bioc-devel@r-project.org> <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> < >> 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> < >> 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> < >> hpa...@fredhutch.org> >> > Phone: (206) 667-5791 >> > Fax: (206) 667-1319 >> > _______________________________________________ >> > Bioc-devel@r-project.org <mailto:Bioc-devel@r-project.org> < >> 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=> >> < >> 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: +49-89-289-19416http://gagneurlab.in.tum.de >> > >> > >> >> -- >> The information in this e-mail is intended only for t...{{dropped:27}} _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
