[Bioc-devel] Code quality and bug reports

Wed Jan 18 17:52:02 CET 2017

Hi,

On 01/14/2017 03:01 AM, Lluís Revilla wrote:
> Dear Valerie and all,
>
> If I understood the page you kindly linked correctly, a package is deprecated:
> 1) When it fails to build and check (unless it is fixed).
> 2) When the maintainer asks for it.
> 3) If the maintainer is unresponsive (I assume when a mail is not
> delivered) and(/or?) doesn't answers questions about the package (How
> is this tracked? Which is the threshold for unanswered questions, 1
> year? )
We contact maintainers when a package fails on the build system. There
isn't a set rule on the number of times contacted with no response
because there are so many exceptions, e.g., transferred maintainer ship,
away from email due to travel, etc. I'd say the average number of
contacts is 3 before getting the final 2 week notice.

>
> In some packages, it seems the maintainers receive the mails, and the
> packages build and past the daily checks of Bioconductor, but there
> are bugs and issues with those packages that are left unanswered and
> unsolved in support.bioconductor.org. Those packages that are still
> functional and used but don't receive maintenance are then kept ? How
> should the community help to solve those issues?
A primary motivation for implementing badges on the landing pages was to
provide the "maintenance status" you mention below. The badge stats give
an idea of how active the maintainer is (posts, commits, coverage) as
well as the level of use by others (downloads). The 'posts' badge shows
support site activity over that past 6 months in terms of 4 fields:
tagged questions / average answers per question / average comments per
question / accepted answers.

The CorMut package has no tagged questions:

  http://www.bioconductor.org/packages/3.5/bioc/html/CorMut.html

If Guangchuang had asked questions on the support site instead of
posting comments in a gist there would be a number of tagged questions
with no answers. This would give other users some data to go on - an
unresponsive maintainer of a package with no unit tests. In contrast, a
package like edgeR has an average of 1 answer and 3 comments for every
question asked:

  http://www.bioconductor.org/packages/3.5/bioc/html/edgeR.html

We don't have a system in place to remove packages from the repo based
on unanswered questions or bug reports. Ideally the combination of badge
stats and input from others on the support site (i.e., 'what package
would you recommend for ...') is sufficient to get direction on actively
maintained and well-thought-of packages.

If there are suggestions for improving the badges please let us know.
There may also be parts of the package review process that could be
improved such as requiring unit tests instead of suggesting them. But
again, having unit tests does not guarantee that all (or the most
important) aspects of the package are tested.

Valerie

> Thanks,
>
> Lluís
>
> On 6 January 2017 at 18:56, Obenchain, Valerie
> <Valerie.Obenchain at roswellpark.org> wrote:
>> 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:
>>
>>   http://www.bioconductor.org/developers/package-end-of-life/
>>
>> Deprecated packages have a strikethrough the name on the build reports,
>> e.g., the saps package,
>>
>>   http://www.bioconductor.org/checkResults/devel/bioc-LATEST/
>>
>>
>> Valerie
>>
>>> "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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