Hi Martin Thanks for the quick reply. I think that would have been the real issue most probably. I fixed it, though the build still failed, but this time it might be due to build cache or other issues with appveyor? A unit test that was fixed earlier also keeps failing on appveyor.
My travis build <https://travis-ci.org/vivekbhr/icetea>. My appveyor build <https://ci.appveyor.com/project/vivekbhr/icetea>. I am developing on R-3.5 and Bioc3.7 on my local linux system (travis is also using that for linux/mac), but our sysadmin didn't install the devel version on the windows therefore I have to use the older one there for testing. Thanks for the comment on biocparallel. I would try this. Best, Vivek On 03/29/2018 03:23 PM, Martin Morgan wrote: > Hi Vivek... > > On 03/29/2018 08:39 AM, Vivek Bhardwaj wrote: >> Dear All >> >> I have travis and appveyor CI running for my upcoming package in >> development. I find that the appveyor CI fails for the function >> `GenomicAlignments::summarizeOverlaps`, which is called by one of the >> functions in my package. It doesn't recognize the BPPARAM argument >> (appveyor build is here >> <https://ci.appveyor.com/project/vivekbhr/icetea>). The same function >> passes on my local windows system. >> > > I would guess that the underlying reason is a difference in package > versions. > > I'd also guess that the problem is at > https://github.com/vivekbhr/icetea/blob/master/R/detect_diffTSS.R#L125 > , where summarizeOverlaps hands off the BPPARAM to ResizeReads via > ..., which is then passed to GenomicRanges::resize where the function > is not expecting an argument named BPPARAM. Probably simply replace l > 131 with > > GenomicRanges::resize(reads, width = width, fix=fix) > > Remember that your new package will be added to the 'devel' version of > Bioconductor, so you should be building and testing on R-3.5 / Bioc 3.7. > > There seem to be several calls to bplapply in your code; it might pay > to start the parallel back-end at the top of your function, as > mentioned in https://support.bioconductor.org/p/107303/#107322 > > Martin > >> *appveyor windows build : * >> >> R version 3.4.4 Patched (2018-03-19 r74453) >> Platform: i386-w64-mingw32/i386 (32-bit) >> Running under: Windows Server 2012 R2 x64 (build 9600) >> >> *my local windows info : * >> >> R version 3.4.3 (2017-11-30) >> Platform: x86_64-w64-mingw32/x64 (64-bit) >> Running under: Windows 7 x64 (build 7601) Service Pack 1 >> >> Has anyone encountered this issue? The call to bplapply works in other >> functions of the package so I am not sure if this is coming directly >> from biocparallel. >> >> >> Best Wishes >> Vivek >> >> -------- >> >> *Vivek Bhardwaj* >> PhD Candidate | International Max Planck Research School >> Max Planck Institute of Immunobiology and Epigenetics >> Stübeweg 51, Freiburg >> E-mail: bhard...@ie-freiburg.mpg.de >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioc-devel@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/bioc-devel >> > > > 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. -- Best Wishes Vivek -------- *Vivek Bhardwaj* PhD Candidate | International Max Planck Research School Max Planck Institute of Immunobiology and Epigenetics Stübeweg 51, Freiburg E-mail: bhard...@ie-freiburg.mpg.de Tel: +49-761-5108-472 Website: https://vivekbhr.github.io [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel