[Bioc-devel] appveyor CI failing with biocparam

[Martin Morgan]

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: bhardwaj at ie-freiburg.mpg.de
> 
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