[Bioc-devel] appveyor CI failing with biocparam
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
St?beweg 51, Freiburg
E-mail: bhardwaj at ie-freiburg.mpg.de
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Best Wishes Vivek -------- *Vivek Bhardwaj* PhD Candidate | International Max Planck Research School Max Planck Institute of Immunobiology and Epigenetics St?beweg 51, Freiburg E-mail: bhardwaj at ie-freiburg.mpg.de Tel: +49-761-5108-472 Website: https://vivekbhr.github.io [[alternative HTML version deleted]]