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
