[Bioc-devel] Request to reverse package deprecation (and support pushing changes)
Responded to the slack message as well but so it is documented on the mailing list. If the package was deprecated, yes you must request undeprecation here. The package was failing for over 6 months without updates or efforts to fix. We will only undeprecate once the package is building cleanly on our build system. You must fix the package on the RELEASE_3_18 branch as it is not included in the devel branch because it is set for removal in devel. Please push changes to the RELEASE_3_18 branch on git.bioconductor.org. For more information see http://contributions.bioconductor.org/git-version-control.html The large file hook seems to be giving an ERROR. I'm tyring to track down the ERROR in the output that is displayed for the hook but am currently having trouble reproducing the ERROR. I can work with you off list to track this down. It would seem however that something might be triggering the large file hook (a file over 5MB?) which is not allowed. 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 L Rutter <lindsayannerutter at gmail.com>
Sent: Thursday, November 9, 2023 7:02 PM
To: bioc-devel at r-project.org <bioc-devel at r-project.org>
Subject: [Bioc-devel] Request to reverse package deprecation (and support pushing changes)
Sent: Thursday, November 9, 2023 7:02 PM
To: bioc-devel at r-project.org <bioc-devel at r-project.org>
Subject: [Bioc-devel] Request to reverse package deprecation (and support pushing changes)
Good afternoon: I'm the maintainer for the Bioconductor package "bigPint", located here <https://secure-web.cisco.com/1ApAPx9S-2yczYKQ03XR4AtcgTsAPS9L6XmenyOsVcYCK5nBvOFdTP6onxb9mo3VhmBCrYHKbzq7u4EhGJXWyQDXfhFb9KdpScw1wPZUZsZpAVIz6DBJC8_aeIXYoz7JAVwRx6lMvxCnrIlShLWBsB2IYnh6lO8tHIv871ql-43EYLVGJGL8obZtEbKSNPJ4oIjDDXfiTXp0YS1YVwfBvP9e_WAJ1ANIXopVXediYuOeoPnU5dtB5XZMZsI7ZdZHY4vnUMk9CYqRBIQgUELE6X3LjJ8DNHAgBygiO5gFk0alWPH9m0feCQcC9snj8l79J/https%3A%2F%2Fwww.bioconductor.org%2Fpackages%2Frelease%2Fbioc%2Fhtml%2FbigPint.html>. I've recently tried to push changes I made to resolve ERRORS in my package by the command " git push upstream devel". However, this has led to an ERROR, which I am pasting beneath my signature below. I see in Bioc-devel mail archives (here <https://secure-web.cisco.com/1-uTVZXFGQ6MB25AHEj1FiYfo1d7WmHRQW3b5j2KJZZGazdZr5Go7Dccn69vaJtK4atfifMZDsplXigJxuq9UNaf5Xj1rIoG2HGB8KwvmWsC9HZqv5wVi4vn1asFBLIel5pIz-f7FvCzkRQJTNTQQmOA9JWw-EsZl6Yuz6xe9CoFr05K8s9aMfuZU3KW-hG0Zn8XILJ9b9x_5WbaF-AVp5FU4isJYWEUumP53U-BgkLKhzfCQAw1a4IHALbR9c3T0LkBBh1qMqOo95yvRg59KcMwWkAcB4qXKc_El23JB2WCFT3dFUIR65fidq-sUEixx/https%3A%2F%2Fwww.mail-archive.com%2Fbioc-devel%40r-project.org%2Fmsg14325.html>) that this error can be something on the Bioconductor developer side. I also see that my package has been deprecated, and, when seeking support for this error on the bioc_git Slack channel, it was suggested to me to send a message here asking for my package to be undeprecated. I apologize for the inconvenience, and thank you for any assistance you can provide. Kind regards, Lindsay Enumerating objects: 114, done. Counting objects: 100% (96/96), done. Delta compression using up to 4 threads Compressing objects: 100% (50/50), done. Writing objects: 100% (72/72), 12.06 KiB | 3.01 MiB/s, done. Total 72 (delta 53), reused 27 (delta 21), pack-reused 0 remote: fatal: Not a valid object name f7c29bb3d981eb1080813b334bdc3731e6cd9b4d:"\033\033" remote: Traceback (most recent call last): remote: File "hooks/pre-receive.h00-pre-receive-hook-software", line 93, in <module> remote: apply_hooks(hooks_dict) remote: File "hooks/pre-receive.h00-pre-receive-hook-software", line 76, in apply_hooks remote: prevent_large_files(oldrev, newrev, refname) remote: File "/home/git/.gitolite/local/hooks/repo-specific/prevent_large_files.py", line 42, in prevent_large_files remote: newrev + ":" + fl.decode()]) remote: File "/usr/lib/python3.5/subprocess.py", line 626, in check_output remote: **kwargs).stdout remote: File "/usr/lib/python3.5/subprocess.py", line 708, in run remote: output=stdout, stderr=stderr) remote: subprocess.CalledProcessError: Command '['git', 'cat-file', '-s', 'f7c29bb3d981eb1080813b334bdc3731e6cd9b4d:"\\033\\033"']' returned non-zero exit status 128 To git.bioconductor.org:packages/bigPint.git ! [remote rejected] devel -> devel (pre-receive hook declined) error: failed to push some refs to 'git.bioconductor.org:packages/bigPint.git' [[alternative HTML version deleted]] _______________________________________________ Bioc-devel at r-project.org mailing list https://secure-web.cisco.com/1G6F6Wmh5x6hk_mLERm4RNJ8apyyz3wCRzqtN7CRL_gYOvvM2uP9eVJG61kSLgA0PegfOI9wVZQ09Fr3mgt-M0gIfEk-a_VH3zRSxPD9cKoh5S603X163319X-a6v4raJBKEl6Azz5T27clQe9p30F6se5onyem50NtVX1yGEQicVvT6fDLZLqMKdLtxQ75FFKpsRaXOH2XeDer7WNg-bRZ_3v5pRxOFerBMH_O-LCdT7Jdax9TVO_d_Fge9R7caX4gq2y3xk8LN1EeufFT-BejBdJH8ymh-jwi6R37FhrPc4C7RkwguuQ0ebh1enL2hZ/https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited. If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you.