[Bioc-devel] hypeR Bioconductor package

[Nitesh Turaga]

The release branch has been frozen. http://bioconductor.org/developers/release-schedule/

Best,



Nitesh Turaga
Scientist II, Department of Data Science,
Bioconductor Core Team Member
Dana Farber Cancer Institute

> On Oct 25, 2021, at 10:28 AM, Federico, Anthony, Nicholas <anfed using bu.edu> wrote:
> 
> Hi Nitesh,
> 
> Any idea why this isn’t working?
> 
> ❯ git push upstream master:RELEASE_3_13 
> 
> Enumerating objects: 7, done.
> Counting objects: 100% (7/7), done.
> Delta compression using up to 4 threads
> Compressing objects: 100% (4/4), done.
> Writing objects: 100% (4/4), 383 bytes | 383.00 KiB/s, done.
> Total 4 (delta 3), reused 0 (delta 0), pack-reused 0
> 
> remote: Error: Illegal version bump from '1.8.0' to '2.0.0'.
> remote: 
> remote: Check http://bioconductor.org/developers/how-to/version-numbering/
> remote: for details.
> remote: 
> To git.bioconductor.org:packages/hypeR.git
> ! [remote rejected] master -> RELEASE_3_13 (pre-receive hook declined)
> error: failed to push some refs to 'git.bioconductor.org:packages/hypeR.git’
> 
> My understanding was an even “y” in x.y.z version was all that was required for pushing to release branches.
> 
> Anthony
> 
>> On Oct 13, 2021, at 9:40 AM, Federico, Anthony, Nicholas <anfed using bu.edu> wrote:
>> 
>> Hi Nitesh,
>> 
>> So it seems my key is ok:
>> 
>> ssh -T git using git.bioconductor.org returns:
>> R W    packages/hypeR
>> 
>> Do I need to create a new RELEASE branch on the upstream repository?
>> 
>> I noticed on the hypeR main repo, there is RELEASE_3_9 and RELEASE_3_10 - but they stopped ~ 2 years ago. 
>> 
>> Anthony
>> 
>>> On Oct 9, 2021, at 10:09 AM, Federico, Anthony, Nicholas <anfed using bu.edu> wrote:
>>> 
>>> I’ll try with a new key and let you know if it worked.
>>> 
>>> Anthony
>>> 
>>>> On Oct 9, 2021, at 10:08 AM, Anthony Federico <anfed using bu.edu> wrote:
>>>> 
>>>> Here is what I get:
>>>> 
>>>> ❯ git remote -v
>>>> origin  https://github.com/montilab/hypeR.git (fetch)
>>>> origin  https://github.com/montilab/hypeR.git (push)
>>>> upstream        git using git.bioconductor.org:packages/hypeR.git (fetch)
>>>> upstream        git using git.bioconductor.org:packages/hypeR.git (push)
>>>> 
>>>> Anthony
>>>> 
>>>>> On Oct 8, 2021, at 4:45 PM, Nitesh Turaga <nturaga.bioc using gmail.com> wrote:
>>>>> 
>>>>> Hi,
>>>>> 
>>>>> What is your upstream remote set as?
>>>>> 
>>>>> 	git remote -v
>>>>> 
>>>>> Please send results. It might just be you are using the wrong SSH key. A good solution is to try with a new SSH key on your BiocCredentials app.
>>>>> 
>>>>> Best,
>>>>> 
>>>>> Nitesh
>>>>> 
>>>>> 
>>>>> Nitesh Turaga
>>>>> Scientist II, Department of Data Science,
>>>>> Bioconductor Core Team Member
>>>>> Dana Farber Cancer Institute
>>>>> 
>>>>>> On Oct 8, 2021, at 10:34 AM, Federico, Anthony, Nicholas <anfed using bu.edu> wrote:
>>>>>> 
>>>>>> So here are my notes for this when pushing changes:
>>>>>> 
>>>>>> # Sync with bioconductor dev branch
>>>>>> git fetch --all
>>>>>> git checkout master
>>>>>> git merge upstream/master
>>>>>> git push upstream master
>>>>>> 
>>>>>> This worked for a while (past 3 years) but then at some point the Bioconductor branch on hypeR stopped getting updated. It seems like that last time it worked was in May of this year.
>>>>>> 
>>>>>> https://bioconductor.org/checkResults/release/bioc-LATEST/hypeR/
>>>>>> Snapshot Date: 2021-10-07 04:50:01 -0400 (Thu, 07 Oct 2021)
>>>>>> git_url: https://git.bioconductor.org/packages/hypeR
>>>>>> git_branch: RELEASE_3_13
>>>>>> git_last_commit: 23b7217
>>>>>> git_last_commit_date: 2021-05-19 12:41:30 -0400 (Wed, 19 May 2021)
>>>>>> 
>>>>>> Sorry for the confusion, my understanding of how to merge things upstream may just be lacking.
>>>>>> 
>>>>>> Anthony
>>>>>> 
>>>>>>> On Oct 6, 2021, at 11:11 AM, Nitesh Turaga <nturaga.bioc using gmail.com> wrote:
>>>>>>> 
>>>>>>> What are you trying exactly?
>>>>>>> 
>>>>>>> Please send the exact commands. 
>>>>>>> 
>>>>>>> Check -  http://bioconductor.org/developers/how-to/git/ and the FAQ http://bioconductor.org/developers/how-to/git/faq/.
>>>>>>> 
>>>>>>> Best,
>>>>>>> 
>>>>>>> Nitesh
>>>>>>> 
>>>>>>> 
>>>>>>> 
>>>>>>> 
>>>>>>> On Wed, Oct 6, 2021, 4:38 AM Federico, Anthony, Nicholas <anfed using bu.edu> wrote:
>>>>>>> Hi,
>>>>>>> 
>>>>>>> I think I need some help, I somehow lost the ability to update the Bioc branch for hypeR. The GitHub main branch is passing my tests locally but whatever I try never seems to update the BioC servers.
>>>>>>> 
>>>>>>> Anthony
>>>>>>> 
>>>>>>>> On Oct 4, 2021, at 7:43 PM, nturaga.bioc using gmail.com wrote:
>>>>>>>> 
>>>>>>>> hypeR Bioconductor Package Notification
>>>>>>>> 
>>>>>>>> Nitesh Turaga1
>>>>>>>> 
>>>>>>>> 1Dana Farber Cancer Institute, Boston, MA, USA
>>>>>>>> 
>>>>>>>> October 04, 2021
>>>>>>>> 
>>>>>>>> Package: hypeR
>>>>>>>> 
>>>>>>>> Hi Anthony Federico,
>>>>>>>> 
>>>>>>>> I am contacting you concerning the hypeR package, on the release and devel branch of Bioconductor, for which you are listed as the maintainer.
>>>>>>>> 
>>>>>>>> The latest build/check report shows that your package is failing on one or more platforms. Please resolve the issues before the next Bioconductor release for your package’s continued inclusion in Bioconductor.
>>>>>>>> 
>>>>>>>> https://bioconductor.org/checkResults/release/bioc-LATEST/hypeR/https://bioconductor.org/checkResults/devel/bioc-LATEST/hypeR/
>>>>>>>> 
>>>>>>>> Please let me know if you have any questions.
>>>>>>>> 
>>>>>>>> Regards,
>>>>>>>> 
>>>>>>>> Nitesh
>>>>>>>> 
>>>>>>>> Bioconductor Core Team 
>>>>>>>> Scientist II 
>>>>>>>> Dana Farber Cancer Institute 
>>>>>>>> Data Science 
>>>>>>>> Boston, MA
>>>>>>>> 
>>>>>>> 
>>>>>> 
>>>>> 
>>>> 
>>> 
>> 
>