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-boun...@r-project.org on behalf of mer...@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@r-project.org <mailto:bioc-devel@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 > > > > > > This email message may contain legally privileged and/or confidential > > information. If you are not the intended recipient(s), or the employee > > or agent responsible for the delivery of this message to the intended > > recipient(s), you are hereby notified that any disclosure, copying, > > distribution, or use of this email message is prohibited. If you have > > received this message in error, please notify the sender immediately > > by e-mail and delete this email message from your computer. Thank you. > -- > *Christian Mertes* | PhD Student / Lab Administrator > > *Gagneur Lab* - Computational Genomics > I12 - Department of Informatics > Technical University of Munich > Boltzmannstr. 3, 85748 Garching, Germany > > mer...@in.tum.de <mailto:mer...@in.tum.de> | http://gagneurlab.in.tum.de > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > -- *Christian Mertes* | PhD Student / Lab Administrator *Gagneur Lab* - Computational Genomics I12 - Department of Informatics Technical University of Munich Boltzmannstr. 3, 85748 Garching, Germany mer...@in.tum.de <mailto:mer...@in.tum.de> | http://gagneurlab.in.tum.de [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel