Hi Vivek, Make sure you are using the appropriate version of R.
Your appveyor code says you're using 3.4.4. https://ci.appveyor.com/project/vivekbhr/icetea#L22 Add a chunk like: ``` environment: global: ... matrix: - R_VERSION: devel ``` after your "global:" tag under the "environment:" field. Regards, Marcel On 03/29/2018 02:39 PM, Vivek Bhardwaj wrote: > 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. > This email message may contain legally privileged and/or...{{dropped:4}} _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel