[Bioc-devel] Policies regarding forked packages

Thu Nov 7 22:37:57 CET 2024

Dear Lori,

In light of the time burden that the Bioconductor core team has: Does this
project for "a maintainer validity check " require specific permissions or
internal expertise?
Could someone from the community contribute or help to get it done
(hopefully sooner)?

For instance with Henrik, we have a website that warns when CRAN packages
are about to be archived (https://www.cranhaven.org/).
If Bioconductor considers these Orphaned packages and removes them in the
following release it could be something I (we) would be interested in.

Best,

Lluís

On Thu, 7 Nov 2024 at 14:26, Kern, Lori via Bioc-devel <
bioc-devel using r-project.org> wrote:

> FWIW: Bioconductor does follow CRAN policy except we do not change or have
> a tag for "orphaned" packages.   We consider an unmaintained package that
> is failing in this category so anything that is up for deprecation/removal
> and if someone is trying to reach the maintainer and they remain
> unresponsive or we find the email is no longer active but currently don't
> have a maintainer validity check.  A maintainer validity check is on my
> list of projects for the next year and hope to have better policy around it
> soon.
>
>
> https://contributions.bioconductor.org/package-end-of-life-policy.html#orphaned-packages
>
>
>
>
> Lori Shepherd - Kern
>
> Bioconductor Core Team
>
> Roswell Park Comprehensive Cancer Center
>
> Department of Biostatistics & Bioinformatics
>
> Elm & Carlton Streets
>
> Buffalo, New York 14263
>
> ________________________________
> From: Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of Henrik
> Bengtsson <henrik.bengtsson using gmail.com>
> Sent: Friday, November 1, 2024 2:26 PM
> To: Alexey Sergushichev <alsergbox using gmail.com>
> Cc: bioc-devel using r-project.org <bioc-devel using r-project.org>
> Subject: Re: [Bioc-devel] Policies regarding forked packages
>
> FWIW, the CRAN Repository Policies
> (
> https://secure-web.cisco.com/1lFLAjnYOFY0iw8-RCsn0CycoLWJ7yncfpzjgM9_-zAA7aiTvwczvM67cgvFZ4GE_4qOadaK8tib68GD4jJsSzxLrlnchDLgqtAg4SY_VhYvBLGAq3xzI1bqRbeFs_Wdx5NT1IYTvlDPZB7jNPoKZVn3LIk-MsYeDYd_CSmXoplpbNo2heLRd8etXaMiQh251Ba4H-DpzyOX128gItwSOrxdlgnF6noPMqIYC7EF3uzZO3jcx-boQ7rU0sfiTy2G1MHBAvSz-aGa2V24RniqhcJJe8ioqWZQ7M9dhsTBzHj_9Z4eicYWAsuCLPr63IhE_/https%3A%2F%2Fcran.r-project.org%2Fweb%2Fpackages%2Fpolicies.html)
> has the below
> regarding "takeovers". Maybe Bioconductor can borrow from this.
>
> "Packages should be named in a way that does not conflict
> (irrespective of case) with any current or past CRAN package (the
> Archive area can be consulted), nor any current Bioconductor package.
> Package maintainers give the right to use that package name to CRAN
> when they submit, so the CRAN team may orphan a package and allow
> another maintainer to take it over. Package names on CRAN are
> persistent and in general it is not permitted to change a package’s
> name.
>
> When a new maintainer wishes to take over a package, this should be
> accompanied by the written agreement of the previous maintainer
> (unless the package has been formally orphaned)."
>
> This covers takeover of a package that has been orphaned.  CRAN uses:
>
> Maintainer: ORPHANED
>
> to formally mark a package orphaned, e.g.
>
> https://secure-web.cisco.com/13bPQMOH7vYOL3tkcwP8YsKVHhxYAi-_qMdXVUp_qnCexURbwdeCtcpeHDhOGNNmKgtx9ZrhPPJzxBnYYyTXeLRrEiPJG0TWmUfWil_IEMo5DT6hkm52HifGoOmgu3NTRILuC_UjrnwUOS_1KkHeK-zsWZPqJ6wT27l3oqomhRrMMK9zUvaGIsg5V6Aes-O9ZfHpZQLm44TKh3u5-VrJHhfsJnXtVxaDGNNCcoaiK9JWSupt4N9Rgyu91XuSX2_6MvSF0umN4H3QdVDQRqBwL1xPB3KEWGZXiH_HquucBVoirCY7r1JnFGBg_EjhATDhK/https%3A%2F%2Fgithub.com%2Fsearch%3Fq%3Dorg%253Acran%2BMaintainer%253A%2BORPHANED%26type%3Dcode
>
> R CMD check with _R_CHECK_ORPHANED_=true gives an alert (NOTE or
> WARNING?) package that directly or indirectly depend on an orphaned
> package.
>
> The CRAN Policies doesn't say how and when CRAN decides to orphan a
> package.  My guess is that they might do it when they noticed that the
> maintainer does not respond to their requests, or the maintainer's
> email address bounces. OTH, we
> (
> https://secure-web.cisco.com/1Uo28vF0edpjufYoVBsf08d-s_m1lgQu29amlCN4Bw04UZfdXVT0mu-irJ8Pfba_U0fv9tSw0r8dJ7IXZABXee25b9fUJVSyZjWnLXGlnoMTCyKb20Kpy2XqyfLt6RdAJdCUc1yGWgrjj5_gH-uG89OOIBmKfijO-CCx4bUtdzyvwAeqv98LYzc0Otv-NAM-GPgS74s82UzHf0BItYTfhbCn8VXZaFA5OLulo9jrXeOGJtIgbKAj0o4cWRZG1yjmL73CuLTFyXf0sXRNp7XcJweD0dXKbeTKfs-BX0sJFKwYgDPSaxG5GAV6tkkUL7vbx/https%3A%2F%2Fwww.cranhaven.org%2Fdashboard-live.html)
> also see that they end
> up archiving all-OK packages when the maintainer does not respond,
> e.g.
> https://secure-web.cisco.com/1oQcIGmdeKDwxBE2MAS1XRBgVmHYnBWoBrQFFI24Pho6qDqiGRUgt9WYvinAVhPGHG6NTpx8l7DDbliafVxvwdZMIzCL27BVYUfFrr9mhqVGBLUgkHKOoRL5TG5hWitqXoe13wiArGXQ4FIW3xlr2cwEZNqDfBJo6fnePLRhSRt4eDfN_eBhU8H5Z1uH6S9SwZhDRrpRnWznFTbVeXqRA19aVhNJvy8Sa6oMBWwCdFZWyhMrMLO97CGoDZ0PIlDjA-ThypkTYR2rk4r-RUBmbM4_UtTp0ZwrbVAH8D_Xdf5ZOovdFgfK4Z526YQVVE8Z1/https%3A%2F%2Fcran.r-project.org%2Fpackage%3DSACCR
>
> Although not explicitly stated, CRAN has the power to orphan a
> package, and *orphaned* packages can be taken over per the above
> policies. They don't write anything explicit about taking over
> *archived*, non-orphaned packages, but I guess that can declare a
> package that has been archived for a "long time" to be orphaned, and
> thereby allow someone to take it over.
>
> /Henrik
>
> On Fri, Nov 1, 2024 at 9:46 AM Alexey Sergushichev <alsergbox using gmail.com>
> wrote:
> >
> > Hi,
> >
> > I also would add that it could make sense to rename your fork. I
> understand
> > this is a normal practice in open source software, that you start a new
> > project by forking an old one, but unless you have an explicit permission
> > to use the original package name, I'm not sure using it is ethically or
> > legally correct. When you have your own package name, the MIT licence
> > allows you to use the old code.
> >
> > Best,
> > Aexey
> >
> > On Fri, Nov 1, 2024 at 11:06 AM Leonardo Collado Torres <
> > lcolladotor using gmail.com> wrote:
> >
> > > Hi,
> > >
> > > I'm not from Bioconductor core. Just a heads up that they've been busy
> > > with the BioC 3.20 release that was just recently completed
> > >
> https://secure-web.cisco.com/1KwanelqCXoWA9jhcSMq6Lw7JRw6V22t1PzRed4ifaS9ljY-KuJ6w--5ok1pJPIbvlSs6Z3Xmha-hucV4w_sxaiG41GCnkASu6bVZGVAmePPyb_5foWkAUVgkxbT0HSCC26A6WK9-AEJ6ZPewhEpblQfREkAifg7URU0C5koN2APBEqpj7Wioq8j363yHg0czxV8hJ7GhbDskLpSv_myPMBq-TyWDbpar_zCEhmNDH9gXEOvMQbRJF_89z5KbxzXz_0IpQ1tkpBC_wvgGTaLo7XrZDJ3suqS_FVF-4cDsU5KnfNNW7I8aXH8en6gvSEYl/https%3A%2F%2Fbioconductor.org%2Fnews%2Fbioc_3_20_release%2F
> > >
> > > From the sideline, it seems that you are doing a great service to the
> > > community by keeping your fork in working conditions. From
> > >
> https://secure-web.cisco.com/16QJgaBGzigF48ApScNzJunsbZ0qi5uoBRlYb7OwBdiUA91VMDYCrNNiIwwhcdzV6Hfrfo0JpNnZFSzUBmKcFHq2xZgVlvCjt94ytZl7YcR0FeLitPNOohFVvFrAMwjIkKbOox2syFq3GA46UWlvWP4hF5YSt-Ti4zwk-G_WBICaXmZUpl3FzNj2QieE6_5ohHShw5S3xmawhuuRzo5qAZ20bQheQuW532OwuIZo4yFISZY3U4QWCoV6bBGESq7l8WGVxksdTI3PodwzeD2OAcbVGvYQC4DThmHwtCXQf2jD457eYQ7iEd6849IrlrhrU/https%3A%2F%2Fgithub.com%2FBioconductor%2FContributions%2Fissues%2Fnew
> I don't see
> > > any specific info about your question. Searching "fork" at
> > >
> https://secure-web.cisco.com/18_IoJdbkdcvGIYJZicUOiMXM-JIMvXs7mRoXvf0LOSJcNEiQvvQLL5irziBm1DeAVPqqccn8gvnKyQBLWdcB3d_shhIca6_iID6W4ra0s9raQNhKW5h1lggRd-2oVUFd8-1l2bj2-psl_mf5z2ycAGgqqb79a61qlyDbO1XFrWb6tdgUEBoqxGhyeDpsDy9BivOAx8CO73tQmrosV7G3MeQ4TRRV9jiRWhiIK-ztHRwuIW9tPXVrUzdOUcSp6Gj_3UT7WXmv8DyLU7ZCGc_7si7Q-GsvDKsX_lrhugPQkTYVaoE9HjZeg82UYXsxbsI6/https%3A%2F%2Fcontributions.bioconductor.org%2Findex.html
> also didn't lead me
> > > to any relevant results.
> > >
> > > Best,
> > > Leo
> > >
> > > Leonardo Collado Torres, Ph. D.
> > > Investigator, LIEBER INSTITUTE for BRAIN DEVELOPMENT
> > > Assistant Professor, Department of Biostatistics
> > > Johns Hopkins Bloomberg School of Public Health
> > > 855 N. Wolfe St., Room 382
> > > Baltimore, MD 21205
> > > lcolladotor.github.io
> > > lcolladotor using gmail.com
> > >
> > > Leonardo Collado Torres, Ph. D.
> > > Investigator, LIEBER INSTITUTE for BRAIN DEVELOPMENT
> > > Assistant Professor, Department of Biostatistics
> > > Johns Hopkins Bloomberg School of Public Health
> > > 855 N. Wolfe St., Room 382
> > > Baltimore, MD 21205
> > > lcolladotor.github.io
> > > lcolladotor using gmail.com
> > >
> > >
> > >
> > > On Mon, Oct 28, 2024 at 9:39 AM Ali Sajid Imami
> > > <ali.sajid.imami using gmail.com> wrote:
> > > >
> > > > Hi,
> > > >
> > > > I have a question about your policies regarding forked packages.
> There
> > > is a package that some of our other packages depend on and is of
> interest
> > > to the Bioconductor community that our lab did not create. However, the
> > > package was never submitted to CRAN or BioConductor, and the original
> > > authors are not reachable. It has not been updated in over 7 years, and
> > > consequently, it does not build. It is, however, licensed under the MIT
> > > license. To ensure our build systems and analysis pipelines keep
> working,
> > > we forked this package a while back and have been maintaining that
> fork.
> > > What is the policy regarding submitting this package to Bioconductor?
> Our
> > > lab is well-versed in the package’s codebase, and we would be able to
> both
> > > maintain it indefinitely and be able to address any comments from the
> > > BioConductor community.
> > > >
> > > >
> > > >
> > > >
> > > >
> > > > ------------------------
> > > > Regards,
> > > > Dr. Ali Sajid Imami
> > > > LinkedIn <
> https://secure-web.cisco.com/1iAVv9_vvcnEbJDz_JcWRp3GlBPeXyoGXZIrq8ExyYGaqL3Glo4zrXYZwNMTgxgVC6AXb9Ga3Q4kxn7enATe5-8yHaEvlccLowJX0NntxOxFt5DqUVNQbo98QPE_c-DjVijgSm9k4rSNL5GhFKFZsoAQj2Wy-XFIYqxtLxlS3PA0VGEyZYwrmAMAgTfuhECI-VSB3geNBXBkbSD8a_Aw5XL0-fH_9SNZ4qse-EaypV1aO21i0Od_x5m-ZSZ6qFml4q1Ru0-3MzFuSpoFDnPk1E-9aM7k5JLiC0YBJ9O_5T9LgFkq20pzvQi0Ss8ZbPyp2/https%3A%2F%2Fpk.linkedin.com%2Fpub%2Fali-sajid-imami%2F50%2F956%2F2a6
> >
> > > >
> > > > Out of the night that covers me,
> > > >       Black as the pit from pole to pole,
> > > > I thank whatever gods may be
> > > >       For my unconquerable soul.
> > > >
> > > > It matters not how strait the gate,
> > > >       How charged with punishments the scroll,
> > > > I am the master of my fate,
> > > >       I am the captain of my soul.”
> > > >
> > > > Invictus by William Ernest Henley
> > > >
> > > >
> > > >         [[alternative HTML version deleted]]
> > > >
> > > > _______________________________________________
> > > > Bioc-devel using r-project.org mailing list
> > > >
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> > >
> >
> >         [[alternative HTML version deleted]]
> >
> > _______________________________________________
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