[Bioc-devel] Policies regarding forked packages
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and if someone is trying to reach the maintainer and they remain unresponsive or we find the email is no longer active but currently don't have a maintainer validity check.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 at r-project.org> on behalf of Henrik Bengtsson <henrik.bengtsson at gmail.com>
Sent: Friday, November 1, 2024 2:26 PM
To: Alexey Sergushichev <alsergbox at gmail.com>
Cc: bioc-devel at r-project.org <bioc-devel at r-project.org>
Subject: Re: [Bioc-devel] Policies regarding forked packages
Sent: Friday, November 1, 2024 2:26 PM
To: Alexey Sergushichev <alsergbox at gmail.com>
Cc: bioc-devel at r-project.org <bioc-devel at 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 at 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 at 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 at 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 at gmail.com > > > > > > > > On Mon, Oct 28, 2024 at 9:39?AM Ali Sajid Imami > > <ali.sajid.imami at 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 at r-project.org mailing list > > > https://secure-web.cisco.com/1IQfs-Stth6Wjg0edLp34UAoMwRC_lwJLMJ3hyHF4D65K-IlLZv6uUG_aBVTw8Ry_usfHzSz9iVX_5o5A8PQIt-incyCg21BH4phTIyHSyT7r1UxKCWObUgj0JjfrwowWJlQaS66MeJ0F9bi5GvP3_kAqSVy1DCg_Q4am9sn28jq4KwkkpWNfA9SHhDK_tlX5wVV71nJDOLFqCkoBx6FRJREitJM5g67dUsNEXcH-QvaoqtBbC1mUxgeQ4XNkORALjT4M8NuSYHJVjBj_Uf_FcaAsZDd-bPmSA5ihdhch3hi6F1oiSLCm0AElpFGh8NBL/https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel > > > > _______________________________________________ > > Bioc-devel at r-project.org mailing list > > https://secure-web.cisco.com/1IQfs-Stth6Wjg0edLp34UAoMwRC_lwJLMJ3hyHF4D65K-IlLZv6uUG_aBVTw8Ry_usfHzSz9iVX_5o5A8PQIt-incyCg21BH4phTIyHSyT7r1UxKCWObUgj0JjfrwowWJlQaS66MeJ0F9bi5GvP3_kAqSVy1DCg_Q4am9sn28jq4KwkkpWNfA9SHhDK_tlX5wVV71nJDOLFqCkoBx6FRJREitJM5g67dUsNEXcH-QvaoqtBbC1mUxgeQ4XNkORALjT4M8NuSYHJVjBj_Uf_FcaAsZDd-bPmSA5ihdhch3hi6F1oiSLCm0AElpFGh8NBL/https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-devel at r-project.org mailing list > https://secure-web.cisco.com/1IQfs-Stth6Wjg0edLp34UAoMwRC_lwJLMJ3hyHF4D65K-IlLZv6uUG_aBVTw8Ry_usfHzSz9iVX_5o5A8PQIt-incyCg21BH4phTIyHSyT7r1UxKCWObUgj0JjfrwowWJlQaS66MeJ0F9bi5GvP3_kAqSVy1DCg_Q4am9sn28jq4KwkkpWNfA9SHhDK_tlX5wVV71nJDOLFqCkoBx6FRJREitJM5g67dUsNEXcH-QvaoqtBbC1mUxgeQ4XNkORALjT4M8NuSYHJVjBj_Uf_FcaAsZDd-bPmSA5ihdhch3hi6F1oiSLCm0AElpFGh8NBL/https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel _______________________________________________ Bioc-devel at r-project.org mailing list https://secure-web.cisco.com/1IQfs-Stth6Wjg0edLp34UAoMwRC_lwJLMJ3hyHF4D65K-IlLZv6uUG_aBVTw8Ry_usfHzSz9iVX_5o5A8PQIt-incyCg21BH4phTIyHSyT7r1UxKCWObUgj0JjfrwowWJlQaS66MeJ0F9bi5GvP3_kAqSVy1DCg_Q4am9sn28jq4KwkkpWNfA9SHhDK_tlX5wVV71nJDOLFqCkoBx6FRJREitJM5g67dUsNEXcH-QvaoqtBbC1mUxgeQ4XNkORALjT4M8NuSYHJVjBj_Uf_FcaAsZDd-bPmSA5ihdhch3hi6F1oiSLCm0AElpFGh8NBL/https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel This email message may contain legally privileged and/or confidential information. 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