[Bioc-devel] Incorrect version of package MSstatsTMT in Bioconductor 3.10

Fri Nov 1 00:47:18 CET 2019

Thanks very much for the detailed explanation. That’s exactly what I did before. Now I see the problem. 

Best,
Ting

> On Oct 31, 2019, at 4:13 PM, Martin Morgan <mtmorgan.bioc using gmail.com> wrote:
> 
> On the 3_9 branch I see
> 
> commit c1382c3f7a0e3872cb66d077f9572b2b9618ecec (HEAD -> RELEASE_3_9, origin/RELEASE_3_9)
> Author: Ting Huang <huang.tin using husky.neu.edu>
> Date:   Sat May 4 16:12:18 2019 -0400
> 
>    Update version bump
> 
> commit 21273e6d818ed70fd258a9574700cc0f53ce0b8b
> Author: Ting Huang <huang.tin using husky.neu.edu>
> Date:   Thu Aug 22 01:08:03 2019 -0400
> 
>    Add global normalization
> 
> commit d98e5a84473f0d3d505b9cc7edeed2c169361648
> Author: Ting Huang <huang.tin using husky.neu.edu>
> Date:   Sat May 4 16:12:18 2019 -0400
> 
>    Update version bump
> 
> where it looks like there was a commit in August, and then a commit from earlier was re-applied. The August commit has
> 
> git show 21273e6d818ed70fd258a9574700cc0f53ce0b8b
> ...
> -Version: 1.2.5
> -Date: 2019-06-18
> +Version: 1.3.7
> +Date: 2019-08-15
> 
> Remember that the 3.9 branch is the 'release' branch, where the 'y' version of x.y.z should be even. So probably you tried to push this to the repository, but were told the version number was bad, so you changed it by re-applying the earlier commit
> 
> git show c1382c3f7a0e3872cb66d077f9572b2b9618ecec
> ...
> -Version: 1.3.7
> +Version: 1.2.7
> 
> So the 3.9 branch has an August commit.
> 
> But remember that Bioconductor always has a current release branch, and a devel (master) branch. The devel (master) branch always gives rise to the next release. So your August commit on the 3.9 branch did not propagate to the 3.10 branch.
> -----+-----3.9.              -----+----- 3.10
> /                                   /
> +-----+-----+-----+-----+-----+ devel / master
> 
> I guess your August commit was a 'new feature' ('add global normalization') so should have been added to the devel (master) branch.
> 
> You could re-apply the august commit to the 3.10 branch, and also to devel / master.
> 
> Martin
> 
> On 10/31/19, 3:52 PM, "Bioc-devel on behalf of Pages, Herve" <bioc-devel-bounces using r-project.org on behalf of hpages using fredhutch.org> wrote:
> 
>    Hi Ting,
> 
>    We don't roll back anything. We just take whatever is in 
>    https://git.bioconductor.org/packages/MSstatsTMT and build that.
>    I don't see any commit from August in the RELEASE_3_10 branch there:
> 
>    hpages using spectre:~/sandbox/MSstatsTMT$ git status
>    On branch master
>    Your branch is up-to-date with 'origin/master'.
>    nothing to commit, working directory clean
>    hpages using spectre:~/sandbox/MSstatsTMT$ git log
>    commit 8597c7bd033b5690013604317490f8cca1507185
>    Author: Nitesh Turaga <nitesh.turaga using gmail.com>
>    Date:   Tue Oct 29 13:43:20 2019 -0400
> 
>         bump x.y.z version to odd y after creation of RELEASE_3_10 branch
> 
>    commit 10bd72b5b331be9085401ea2d294f8906bd0992d
>    Author: Nitesh Turaga <nitesh.turaga using gmail.com>
>    Date:   Tue Oct 29 13:11:24 2019 -0400
> 
>         bump x.y.z version to even y prior to creation of RELEASE_3_10 branch
> 
>    commit f8fa7784468e4494678379c6fbe2ea86bb5a412a
>    Author: Ting Huang <huang.tin using husky.neu.edu>
>    Date:   Sat May 4 16:12:18 2019 -0400
> 
>         Fix version number
> 
>    commit d401543723af97fb2204bd91a58677e649b391f2
>    Author: Ting Huang <huang.tin using husky.neu.edu>
>    Date:   Sat May 4 14:36:40 2019 -0400
> 
>         bug fix: my bug fix
> 
>    commit 76d20aabeb8a2990c7ca794aea4ffb4633239c56
>    Author: Ting Huang <huang.tin using husky.neu.edu>
>    Date:   Sat May 4 14:11:32 2019 -0400
> 
>         bug fix: my bug fix
> 
>    commit 3b5924216f9d82867696d978adb735d69f765593
>    Author: Ting Huang <huang.tin using husky.neu.edu>
>    Date:   Sat May 4 14:09:28 2019 -0400
> 
>         Update version number
> 
>    etc...
> 
>    If you've committed something in August, make sure to push your changes 
>    to git.bioconductor.org in addition to GitHub. See our collections of 
>    HOWTO documents for how to do this:
> 
>       https://bioconductor.org/developers/how-to/git/
> 
>    Hope this helps.
> 
>    Best,
>    H.
> 
> 
>    On 10/31/19 12:31, ting huang wrote:
>> Dear Bioc-Team,
>> 
>> I’m the developer of package MSstatsTMT. Today I tried to install MSstatsTMT from the new released Bioconductor 3.10. But it was found that the version of MSstatsTMT is rolled back.
>> 
>> My last commit to MSstatsTMT is 2019 Aug 15 and the version in Bioconductor 3.9 is 1.2.7. However the new version MSstatsTMT 1.4.0 in Bioconductor 3.10 showed the last commit is 2019 May 4. Somehow MSstatsTMT was rolled back to an old version in Bioconductor 3.10. Any clue on why this happened?
>> 
>> Many thanks and best regards,
>> Ting
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> 
>    -- 
>    Hervé Pagès
> 
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