[Bioc-devel] appveyor CI failing with biocparam
bhardwaj at ie-freiburg.mpg.de
Thu Mar 29 20:39:07 CEST 2018
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
Thanks for the comment on biocparallel. I would try this.
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
> I'd also guess that the problem is at
> , 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
>> *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 Bhardwaj*
>> PhD Candidate | International Max Planck Research School
>> Max Planck Institute of Immunobiology and Epigenetics
>> Stübeweg 51, Freiburg
>> E-mail: bhardwaj at ie-freiburg.mpg.de
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PhD Candidate | International Max Planck Research School
Max Planck Institute of Immunobiology and Epigenetics
Stübeweg 51, Freiburg
E-mail: bhardwaj at ie-freiburg.mpg.de
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