[Bioc-devel] 'OUTRIDER' Bioconductor package
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
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
> 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 -
> 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*
> 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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