[Bioc-devel] Failing to build vignette because of problems with ImageMagick
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 <hpages at fredhutch.org
<mailto:hpages at 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
<mertes at in.tum.de <mailto:mertes at 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 at in.tum.de <mailto:mertes at in.tum.de>
>>> <mailto:mertes at in.tum.de <mailto:mertes at 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 at in.tum.de <mailto:mertes at in.tum.de>
<mailto:mertes at in.tum.de <mailto:mertes at 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 at r-project.org <mailto:Bioc-devel at r-project.org>
<mailto:Bioc-devel at r-project.org <mailto:Bioc-devel at 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 at in.tum.de <mailto:mertes at 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 at r-project.org <mailto:Bioc-devel at r-project.org>
mailing list
>>
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>>
>
--
Herv? Pag?s
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: hpages at fredhutch.org <mailto:hpages at fredhutch.org>
Phone:? (206) 667-5791
Fax:? ? (206) 667-1319
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--
Best,
Kasper
Herv? Pag?s 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: hpages at fredhutch.org Phone: (206) 667-5791 Fax: (206) 667-1319