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

Wed Sep 11 11:13:07 CEST 2019

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 <mertes using 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 <mertes using in.tum.de
>>> <mailto:mertes using 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: mertes using in.tum.de <mailto:mertes using 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 using r-project.org <mailto:Bioc-devel using 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: mertes using 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 using 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
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