[Bioc-devel] Code quality and bug reports

Lluís Revilla lluis.revilla at gmail.com
Wed Jan 4 16:51:25 CET 2017

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

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:

"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

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

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,


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
        <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:

There should be more issues than I can found with quick look of the source

Best wishes,
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

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