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

[Martin Morgan]

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
    > _______________________________________________
    > Bioc-devel using r-project.org mailing list
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