[Bioc-devel] Policies regarding forked packages
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, Llu?s On Thu, 7 Nov 2024 at 14:26, Kern, Lori via Bioc-devel <
bioc-devel at 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and if someone is trying to reach the maintainer and they remain unresponsive or we find the email is no longer active but currently don't have a maintainer validity check.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 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 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.? 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