[Bioc-devel] 'OUTRIDER' Bioconductor package

[Christian Mertes]

Thanks Martin for the hint. Then let's hope that it will vanish 
automatically with the next build.

Am 10/12/2019 um 3:06 AM schrieb Martin Morgan:
> I think this is an error in BiocParallel that has been corrected (in v. 1.19.4) but not yet propagated through the build system and report.
>
> Martin
>
> On 10/11/19, 7:33 PM, "Bioc-devel on behalf of Christian Mertes" <bioc-devel-bounces using r-project.org on behalf of mertes using in.tum.de> wrote:
>
>      Dear Bioc Team,
>      
>      I noticed already the error and I'm not completely sure why this is
>      happening. On appveyor it is going through with no problems. I never
>      call the function mcparallel but I did register MulticoreParams() in the
>      vignette which could caused the problem. But I'm puzzled why it works on
>      appveyor and not on Bioconductor.
>      
>      I did removed now the MutlicoreParam call. So lets see if it solved the
>      problem.
>      
>      Best,
>      Christian
>      
>      Link to appveyor log from the specific commit:
>      https://ci.appveyor.com/project/c-mertes/outrider/builds/27915255
>      This is the error from BioConductor for the same commit:
>      
>      * 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
>      Warning in MulticoreParam(2) :
>         MulticoreParam() not supported on Windows, use SnowParam()
>      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.
>      Fri Oct 11 01:01:13 2019: SizeFactor estimation ...
>      Fri Oct 11 01:01:13 2019: Controlling for confounders ...
>      Using estimated q with: 23
>      Fri Oct 11 01:01:13 2019: Using the autoencoder implementation for
>      controlling.
>      Quitting from lines 180-200 (OUTRIDER.Rnw)
>      Error: processing vignette 'OUTRIDER.Rnw' failed with diagnostics:
>      'mcparallel' is not an exported object from 'namespace:parallel'
>      --- failed re-building 'OUTRIDER.Rnw'
>      
>      
>      Am 10/11/2019 um 7:33 PM schrieb Interdonato, Kayla:
>      >
>      > The next Bioconductor release 3.10 is scheduled for October 30^th .
>      > The current
>      >
>      > Bioc 3.9 release branch will be frozen Tuesday October 15^th . There
>      > will be no
>      >
>      > opportunities to commit or correct the release 3.9 branch after the
>      > freeze.
>      >
>      > We like to make an effort to have all Bioconductor packages building and
>      >
>      > checking without ERROR or TIMEOUT in both release and devel versions.
>      > It seems
>      >
>      > your package is producing an ERROR for the Windows builder in the release
>      >
>      > version of Bioconductor.
>      >
>      > Release build report -
>      > https://bioconductor.org/checkResults/3.9/bioc-LATEST/OUTRIDER/
>      >
>      > Could you please investigate and make the necessary changes by Tuesday.
>      >
>      > If you need any assistance please feel free to ask questions at
>      >
>      > bioc-devel using r-project.org <mailto:bioc-devel using r-project.org>.
>      >
>      > Thank you,
>      >
>      > *Kayla E. Interdonato, MS*
>      >
>      > Programmer/Analyst
>      >
>      > Bioconductor Core Team
>      >
>      > Roswell Park Cancer Institute
>      >
>      > Department of Biostatistics & Bioinformatics
>      >
>      > (716)845-1300 x4621
>      >
>      >
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>      --
>      *Christian Mertes* | PhD Student / Lab Administrator
>      
>      *Gagneur Lab* - Computational Genomics
>      I12 - Department of Informatics
>      Technical University of Munich
>      Boltzmannstr. 3, 85748 Garching, Germany
>      
>      mertes using in.tum.de <mailto:mertes using in.tum.de> | http://gagneurlab.in.tum.de
>      
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-- 
*Christian Mertes* | PhD Student / Lab Administrator

*Gagneur Lab* - Computational Genomics
I12 - Department of Informatics
Technical University of Munich
Boltzmannstr. 3, 85748 Garching, Germany

mertes using in.tum.de <mailto:mertes using in.tum.de> | http://gagneurlab.in.tum.de

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