[Bioc-devel] appveyor CI failing with biocparam

[Marcel Ramos]

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: bhardwaj at ie-freiburg.mpg.de
>>>
>>>     [[alternative HTML version deleted]]
>>>
>>> _______________________________________________
>>> Bioc-devel at r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>
>>
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