[Bioc-devel] Code quality and bug reports

Obenchain, Valerie Valerie.Obenchain at roswellpark.org
Fri Jan 6 18:56:04 CET 2017

On 01/04/2017 07:53 AM, Lluís Revilla wrote:
> Dear Guangchuang and all,
> Quality of the packages has been a preoccupation of the project from
> the  beginning  (see
> https://stat.ethz.ch/pipermail/bioc-devel/2014-May/005810.html for
> more references and other discussions about bug reports.) Despite not
> being in a goal of the project, it is necessary to do a reproducible
> research, which it is a goal: "To further scientific understanding by
> producing high-quality documentation and reproducible research.".
> Although it seems that this discussion appears periodically
> Bioconductor I don't know any solution in the project.
> I have never submitted a package to Bioconductor or CRAN, and I am
> quite new to R (and is my first mail to the list), but one thing that
> I keep thinking (before publishing a package) is the maintainability
> of it. I don't know how much time/desires will I have to dedicate to a
> package (if it is accepted) in the future, but at the same time I want
> to make useful code to be used in further research beyond my own
> project.
> However the Bioconductor core team may be already too busy to deal
> with the issues of all packages. Maybe it would be better to bring
> CRAN's policy to orphan packages (see:
> https://cran.r-project.org/src/contrib/Orphaned/README):

Bioconductor does have a system for dealing with orphaned packages
called End of Life:


Deprecated packages have a strikethrough the name on the build reports,
e.g., the saps package,



> "Possible reasons for orphanizing a package:
> 1) The current maintainer actively wants to orphanize the package,
>    e.g., due to no longer having time or interest to act as package
>    maintainer.
> 2) Emails sent to the current maintainer by the CRAN admins bounced, or
>    were not answered for longer periods of time.
> "
> Example of an orhpan package is clusterRepro.
> To orphanize a package the current maintainer could post it here on
> the devel list and ask for a maintainer on the support site, and it is
> his/her decision to whom is passed the responsibility.
> Otherwise, maybe the limit of time without answering mails/posts in
> support could be 3 months/6 months. (I don't know the CRAN decision
> when not answering mails)
> Once the orphaned status is reached maybe however who wants could send
> patches or take the maintenance of the package for another 3 months or
> more.
> This status would not make bugs easier to fix or control, but could
> mark that a package is not in the best maintenance status.
> Hope this helps,
> Lluís
> ----
> Date: Wed, 4 Jan 2017 15:38:53 +0800
> From: "Yu, Guangchuang" <gcyu at connect.hku.hk>
> To: bioc-devel <bioc-devel at r-project.org>
> Subject: [Bioc-devel] report package issue to Bioconductor
> Message-ID:
>         <CAEF2yOdEQ9LOA3nFbLBvNddtLTKMZ-YiVkCf7UMJRRpfQP7Lmw at mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
> Dear all,
> Some packages never updated after they publish a paper, and they just
> ignore bug report.
> I think we need somewhere, maybe on github, to post code review and
> Bioconductor core team can take action if maintainer fail to fix issue.
> Here is a quick look of the CorMut package:
> https://gist.github.com/GuangchuangYu/91b3396c7e49ab42c565a9cda3c35e18.
> There should be more issues than I can found with quick look of the source
> code.
> Best wishes,
> Guangchuang
> ?
> --
> --~--~---------~--~----~------------~-------~--~----~
> Guangchuang Yu, PhD Candidate
> State Key Laboratory of Emerging Infectious Diseases
> School of Public Health
> The University of Hong Kong
> Hong Kong SAR, China
> www: https://guangchuangyu.github.io
> -~----------~----~----~----~------~----~------~--~---
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel

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