[Bioc-devel] Request to reverse package deprecation (and support pushing changes)

[Kern, Lori]

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 using r-project.org> on behalf of L Rutter <lindsayannerutter using gmail.com>
Sent: Thursday, November 9, 2023 7:02 PM
To: bioc-devel using r-project.org <bioc-devel using 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 using 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.
	[[alternative HTML version deleted]]