[Bioc-devel] EXTERNAL: Rcwl problems reported in the Multiple platform build/check report for BioC 3.9

Pages, Herve hp@ge@ @end|ng |rom |redhutch@org
Mon Oct 21 19:07:47 CEST 2019 

Hi Qiang,

Any reason why you use:

   UnsupportedPlatforms: win64, win32

and not just:

   UnsupportedPlatforms: win

in your .BBSoptions file?

Also make sure to have a line terminator:

   hpages using spectre:~/RcwlPipelines$ file .BBSoptions
   .BBSoptions: ASCII text, with no line terminators

The lack of line terminator might be breaking the code that parses the file.

Thanks,
H.


On 10/21/19 09:23, Hu, Qiang wrote:
> Hi,
> 
> My packages, Rcwl and RcwlPipelines got building error from the windows machine. But those two packages have a BBSoption file to skip the windows system and the packages didn't be checked in the tokay1 before. Could you help to check it?
> 
> Thanks,
> Qiang
> ________________________________
> From: Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of Hu, Qiang <Qiang.Hu using RoswellPark.org>
> Sent: Friday, April 26, 2019 2:47 PM
> To: bioc-devel using r-project.org <bioc-devel using r-project.org>
> Subject: Re: [Bioc-devel] EXTERNAL: Rcwl problems reported in the Multiple platform build/check report for BioC 3.9
> 
> Hi all,
> 
> 
> Could you please help to check whether the required python package "cwltool" is installed and works in malbec2 and celaya2?
> 
> Here is part of the error log in malbec2:
> 
> $cwltool --version
> 
> ...
> 
> pkg_resources.DistributionNotFound: The 'pyparsing' distribution was not found and is required by rdflib
> ...
> It seems the cwltool doesn't work properly.
> 
> For elaya2, the required cwltool is not installed.
> 
> 
> Thanks,
> Qiang
> 
> 
> ________________________________
> From: BBS-noreply using bioconductor.org <BBS-noreply using bioconductor.org>
> Sent: Friday, April 26, 2019 2:16:38 PM
> To: Hu, Qiang
> Subject: EXTERNAL: Rcwl problems reported in the Multiple platform build/check report for BioC 3.9
> 
> [This is an automatically generated email. Please don't reply.]
> 
> Hi Rcwl maintainer,
> 
> According to the Multiple platform build/check report for BioC 3.9,
> the Rcwl package has the following problem(s):
> 
>    o ERROR for 'R CMD INSTALL' on malbec2. See the details here:
>        https://urldefense.proofpoint.com/v2/url?u=https-3A__master.bioconductor.org_checkResults_3.9_bioc-2DLATEST_Rcwl_malbec2-2Dinstall.html&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=X2NATaD0oIGctOMxPDYt-MnQoQpmUOkzXzFRdn-6zhA&s=8jgPoOfCnzRwXCi7faEKLCkTzzcfbX8ywB_szlBJ1U4&e=
> 
>    o ERROR for 'R CMD build' on malbec2. See the details here:
>        https://urldefense.proofpoint.com/v2/url?u=https-3A__master.bioconductor.org_checkResults_3.9_bioc-2DLATEST_Rcwl_malbec2-2Dbuildsrc.html&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=X2NATaD0oIGctOMxPDYt-MnQoQpmUOkzXzFRdn-6zhA&s=LXm1HJPGIDQVwrCOyV5oG6BT4ls6w07CEwQ7QsQly2o&e=
> 
> Please take the time to address this by committing and pushing
> changes to your package at git.bioconductor.org
> 
> Notes:
> 
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-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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