Re: [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 .
> My appveyor build .
>
> 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
>>> ). 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: bhard...@ie-freiburg.mpg.de
>>>
>>> [[alternative HTML version deleted]]
>>>
>>> ___
>>> Bioc-devel@r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>
>>
>> This email message may contain legally privileged and/or confidential 
>> information.  If you are not the intended recipient(s), or the 
>> employee or agent responsible for the delivery of this message to the 
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>> copying, distribution, or use of this email message is prohibited.  If 
>> you have received this message in error, please notify the sender 
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>



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Re: [Bioc-devel] appveyor CI failing with biocparam

[Vivek Bhardwaj]

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 .
My appveyor build .

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
>> ). 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: bhard...@ie-freiburg.mpg.de
>>
>> [[alternative HTML version deleted]]
>>
>> ___
>> Bioc-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>
>
> This email message may contain legally privileged and/or confidential 
> information.  If you are not the intended recipient(s), or the 
> employee or agent responsible for the delivery of this message to the 
> intended recipient(s), you are hereby notified that any disclosure, 
> copying, distribution, or use of this email message is prohibited.  If 
> you have received this message in error, please notify the sender 
> immediately by e-mail and delete this email message from your 
> computer. Thank you.


-- 

Best Wishes
Vivek



*Vivek Bhardwaj*
PhD Candidate | International Max Planck Research School
Max Planck Institute of Immunobiology and Epigenetics
Stübeweg 51, Freiburg
E-mail: bhard...@ie-freiburg.mpg.de
Tel: +49-761-5108-472
Website: https://vivekbhr.github.io

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Re: [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
). 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: bhard...@ie-freiburg.mpg.de

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