'Re: [Bioc-devel] EXTERNAL: Rcwl problems reported in the Multiple platform build/check report for Bi'

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List:       bioc-devel
Subject:    Re: [Bioc-devel] EXTERNAL: Rcwl problems reported in the Multiple platform build/check report for Bi
From:       "Hu, Qiang" <Qiang.Hu () RoswellPark ! org>
Date:       2019-10-21 17:57:18
Message-ID: BN6PR12MB142776F7D58A1EDD1B15CCE599690 () BN6PR12MB1427 ! namprd12 ! prod ! outlook ! com
[Download RAW message or body]

Hi Herve,

Thanks! just updated the file.

Thanks,
Qiang
________________________________
From: Pages, Herve <hpages@fredhutch.org>
Sent: Monday, October 21, 2019 1:07 PM
To: Hu, Qiang <Qiang.Hu@RoswellPark.org>; bioc-devel@r-project.org \
                <bioc-devel@r-project.org>
Subject: Re: [Bioc-devel] EXTERNAL: Rcwl problems reported in the Multiple platform \
build/check report for BioC 3.9

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@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@r-project.org> on behalf of Hu, Qiang \
>                 <Qiang.Hu@RoswellPark.org>
> Sent: Friday, April 26, 2019 2:47 PM
> To: bioc-devel@r-project.org <bioc-devel@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@bioconductor.org <BBS-noreply@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_checkRe \
> sults_3.9_bioc-2DLATEST_Rcwl_malbec2-2Dinstall.html&d=DwICAg&c=eRAMFD45gAfqt84VtBcfh \
> Q&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_checkRe \
> sults_3.9_bioc-2DLATEST_Rcwl_malbec2-2Dbuildsrc.html&d=DwICAg&c=eRAMFD45gAfqt84VtBcf \
> hQ&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:
> 
> * This was the status of your package at the time this email was sent to you.
> Given that the online report is updated daily (in normal conditions) you
> could see something different when you visit the URL(s) above, especially if
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--
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpages@fredhutch.org
Phone:  (206) 667-5791
Fax:    (206) 667-1319

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