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@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 unresponsive or we find the email is no longer active but currently don't 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-boun...@r-project.org> on behalf of Henrik > Bengtsson <henrik.bengts...@gmail.com> > Sent: Friday, November 1, 2024 2:26 PM > To: Alexey Sergushichev <alserg...@gmail.com> > Cc: bioc-devel@r-project.org <bioc-devel@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 <alserg...@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 < > > lcollado...@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 > > > lcollado...@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 > > > lcollado...@gmail.com > > > > > > > > > > > > On Mon, Oct 28, 2024 at 9:39 AM Ali Sajid Imami > > > <ali.sajid.im...@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@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@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@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@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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