[Bioc-devel] 'OUTRIDER' Bioconductor package

Martin Morgan mtmorg@n@b|oc @end|ng |rom gm@||@com
Sat Oct 12 03:06:26 CEST 2019

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.


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 
    Link to appveyor log from the specific commit: 
    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 
    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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