[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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