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List: bioc-devel
Subject: Re: [Bioc-devel] Incorrect version of package MSstatsTMT in Bioconductor 3.10
From: ting huang <thuang0703 () gmail ! com>
Date: 2019-10-31 23:47:18
Message-ID: E636C00A-FDE5-4C94-80D7-3BAC78B6AC3A () gmail ! com
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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@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@husky.neu.edu>
> Date: Sat May 4 16:12:18 2019 -0400
>
> Update version bump
>
> commit 21273e6d818ed70fd258a9574700cc0f53ce0b8b
> Author: Ting Huang <huang.tin@husky.neu.edu>
> Date: Thu Aug 22 01:08:03 2019 -0400
>
> Add global normalization
>
> commit d98e5a84473f0d3d505b9cc7edeed2c169361648
> Author: Ting Huang <huang.tin@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@r-project.org on behalf of hpages@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@spectre:~/sandbox/MSstatsTMT$ git status
> On branch master
> Your branch is up-to-date with 'origin/master'.
> nothing to commit, working directory clean
> hpages@spectre:~/sandbox/MSstatsTMT$ git log
> commit 8597c7bd033b5690013604317490f8cca1507185
> Author: Nitesh Turaga <nitesh.turaga@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@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@husky.neu.edu>
> Date: Sat May 4 16:12:18 2019 -0400
>
> Fix version number
>
> commit d401543723af97fb2204bd91a58677e649b391f2
> Author: Ting Huang <huang.tin@husky.neu.edu>
> Date: Sat May 4 14:36:40 2019 -0400
>
> bug fix: my bug fix
>
> commit 76d20aabeb8a2990c7ca794aea4ffb4633239c56
> Author: Ting Huang <huang.tin@husky.neu.edu>
> Date: Sat May 4 14:11:32 2019 -0400
>
> bug fix: my bug fix
>
> commit 3b5924216f9d82867696d978adb735d69f765593
> Author: Ting Huang <huang.tin@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@r-project.org mailing list
> > https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo \
> > _bioc-2Ddevel&d=DwIFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSX \
> > AJJKaaPhzWA&m=UTF1FgVr08NqiYrWipNdjYVk7sr6fhyDedfbva_FOF8&s=NN6x1AClUMXzcjoQSrE24IrJ63mBCMao1t6gaLBOtkQ&e=
> >
>
> --
> Hervé Pagès
>
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M1-B514
> P.O. Box 19024
> Seattle, WA 98109-1024
>
> E-mail: hpages@fredhutch.org
> Phone: (206) 667-5791
> Fax: (206) 667-1319
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>
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