Thanks Hervé, I also found this tweet by John Muschelli useful for this situation https://twitter.com/StrictlyStat/status/1103303028751372289 where he suggests using suppressWarnings(RNGversion("3.5.0"))
That's what I did for example in https://github.com/leekgroup/derfinderHelper/commit/c2c756d6e1f6c3da219073a6c36c2b475453ecf1 to resolve the issue with derfinderHelper. Best, Leo On Mon, Apr 8, 2019 at 6:40 PM Pages, Herve <hpa...@fredhutch.org> wrote: > > Dear developers, > > As reported on this list in March > (https://stat.ethz.ch/pipermail/bioc-devel/2019-March/014776.html) the > sample() function has changed in recent R-devel. This change breaks the 19 > following Bioconductor software packages: > > - cicero > - clipper > - clusterExperiment > - CMA > - CNVPanelizer > - derfinder > - derfinderHelper > - flowQB > - mAPKLA > - MCbiclust > - Melissa > - metaseqR > - nucleoSim > - onlineFDR > - PathNet > - phyloseq > - SPONGE > - treeio > - trena > > > For all these packages (except for the CMA package), the change to sample() > breaks the unit tests where sample() is used to generate random data as input > to the test. Since sample() generates different random numbers in R 3.6 > (compared to R 3.5, with the seed set to the same value), the input to the > test now is different and so is its output, so comparison to the old expected > result now fails. The fix is to simply modify the expected result to match > the new output. > > If you maintain one of the above package, please fix your package as soon as > possible. > > Keep in mind that all Bioconductor packages will need to pass 'R CMD build' > and 'R CMD check' with no error in order to be included in the next > Bioconductor release, scheduled for Tuesday April 30. Note that Bioconductor > 3.9 will be based on R 3.6 (scheduled to be released on Friday April 26) so > please make sure to use a recent version of R devel when testing/fixing your > package. > > See our release schedule: > > https://bioconductor.org/developers/release-schedule/ > > and this recent announcement on this list: > > https://stat.ethz.ch/pipermail/bioc-devel/2019-April/014832.html > > Thank you for your ongoing contribution to Bioconductor. > > Cheers, > > H. > > > -- > Hervé Pagès > > Program in Computational Biology > Division of Public Health Sciences > Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N, M1-B514 > P.O. Box 19024 > Seattle, WA 98109-1024 > > E-mail: hpa...@fredhutch.org<mailto:hpa...@fredhutch.org> > Phone: (206) 667-5791 > Fax: (206) 667-1319 > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
