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List:       bioc-devel
Subject:    Re: [Bioc-devel] NAMESPACE issue in bumphunter
From:       Leonardo Collado Torres <lcollado () jhu ! edu>
Date:       2016-03-24 21:50:44
Message-ID: CAP8VEO7CjC-gnEvo1DCZWd_KUxS6zxjRQvWavOpow4EgXYf_xA () mail ! gmail ! com
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My svn account doesn't have permission to write on the bumphunter
package, which is what I tried before emailing the patch. Or are you
saying that if I use the Git mirrors, `git svn dcommit` won't complain
about the permission issue?

On Thu, Mar 24, 2016 at 5:04 PM, Dan Tenenbaum <dtenenba@fredhutch.org> wrote:
> Please make the change yourself using the git mirrors.
>
> https://bioconductor.org/developers/how-to/git-mirrors/
>
> Dan
>
>
> ----- Original Message -----
>> From: "lcollado" <lcollado@jhu.edu>
>> To: "bioc-devel" <bioc-devel@r-project.org>
>> Cc: "Rafael Irizarry" <rafa@jimmy.harvard.edu>
>> Sent: Thursday, March 24, 2016 1:59:02 PM
>> Subject: [Bioc-devel] NAMESPACE issue in bumphunter
>
>> Hi,
>>
>> I found a NAMESPACE issue in bumphunter version 1.11.3 as reported at
>> https://github.com/ririzarr/bumphunter/issues/7 with the proposed fix
>> at
>> https://github.com/lcolladotor/bumphunter/commit/4093a628ecd81ace3a26511b82d2c3ca47849d33
>> However the bumphunter GitHub repository is outdated versus the
>> version available in Bioc-devel as I reported at
>> https://github.com/ririzarr/bumphunter/issues/9. I can recognize that
>> it stopped being in sync once the git-svn-bridge stopped working.
>> Which is why I'm sending here a SVN diff file with the patch that can
>> fix this small issue.
>>
>> The patch reads:
>>
>>
>> Index: DESCRIPTION
>> ===================================================================
>> --- DESCRIPTION (revision 115247)
>> +++ DESCRIPTION (working copy)
>> @@ -1,5 +1,5 @@
>> Package: bumphunter
>> -Version: 1.11.3
>> +Version: 1.11.4
>> Title: Bump Hunter
>> Description: Tools for finding bumps in genomic data
>> Authors@R: c(person(c("Rafael", "A."), "Irizarry", role = c("cre","aut"), email
>> Index: NAMESPACE
>> ===================================================================
>> --- NAMESPACE (revision 115247)
>> +++ NAMESPACE (working copy)
>> @@ -19,6 +19,7 @@
>> importFrom(GenomicRanges, GRanges, makeGRangesFromDataFrame)
>> importMethodsFrom(GenomicRanges, sort)
>> importFrom(locfit, locfit)
>> +importFrom(locfit, lp)
>> importFrom(utils, data, packageDescription)
>> importFrom(parallel, mclapply, stopCluster)
>> importFrom(GenomicFeatures, exonsBy, cdsBy, transcriptsBy)
>>
>>
>>
>>
>> Best,
>> Leonardo
>>
>> Leonardo Collado Torres, PhD Candidate
>> Department of Biostatistics
>> Johns Hopkins University
>> Bloomberg School of Public Health
>> Website: http://lcolladotor.github.io/about.html
>>
>> _______________________________________________
>> Bioc-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel

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