[Bioc-devel] CTCF annotation package's vignette not updating

Mon Nov 14 15:29:59 CET 2022

Thank you, Lori. My understanding, a version bump for a data package won't
trigger rebuild, but this branching process will.

I'm still confused how to version data package updates (e.g., vignettes).
Any attempt to bump version results in "Error: Illegal version bump" when
pushing. Changes without version bump can be pushed. And, will probably be
propagated by the manual branching process. Here is another example when
the old vignette results in error when used in 3.16, but the new one is not
showing up
https://bioconductor.org/checkResults/3.16/data-annotation-LATEST/excluderanges/.
I'll wait, hopefully this branching process will resolve these issues.
It'll be great to clarify in the documentation.

Thanks again,
Mikhail

On Mon, Nov 14, 2022 at 7:19 AM Kern, Lori <Lori.Shepherd using roswellpark.org>
wrote:

> Annotation packages are slightly different - we don't automatically bump
> the versions of annotations at release as it implies annotations were
> updated when most of the time they are not.
>
> We also have not reimplemented the auto process of git hosted annotations
> as we have to branch the annotations as part of the release process. Due to
> the large number of packages that could be affected, we normally wait a
> week or so to branch to allow the other release updates to settle.
>
> We plan to do this branching process today or tomorrow.  After that time,
> changes pushed to the git hosted annotation packages will be reflected in
> weekly reports.
>
> I'm very sorry for the confusion and delay.
>
>
>
> Lori Shepherd - Kern
>
> Bioconductor Core Team
>
> Roswell Park Comprehensive Cancer Center
>
> Department of Biostatistics & Bioinformatics
>
> Elm & Carlton Streets
>
> Buffalo, New York 14263
> ------------------------------
> *From:* Mikhail Dozmorov <mikhail.dozmorov using gmail.com>
> *Sent:* Friday, November 11, 2022 10:30 AM
> *To:* bioc-devel <bioc-devel using r-project.org>; Kern, Lori
> <Lori.Shepherd using RoswellPark.org>
> *Subject:* Re: [Bioc-devel] CTCF annotation package's vignette not
> updating
>
> It must be very simple, but I'm still unable to trigger the build -
> confused by version numbering. CTCF had version 0.99.5 in BioC 3.15,
> https://bioconductor.org/packages/3.15/data/annotation/html/CTCF.html
> <https://secure-web.cisco.com/11SfcSGs4ZZwaIIwBqVkHeQD6vQ8L-EJ5yHoT-kyvApm8alpLidSDiL4dpxaUEApgk359bfZjYIJnfJLV-c_YbnCzFkDwEEpVMv6lst_Oxdsa4EMp0-K2yXrzvHIsOQaKsAyjLVjMdRcUfPlooUlkpbtPGeGk81FwgdAtctb74YrUyO7x7tlC-7vQPLXX1SGXV99macucJ99MPrxbBMmmBpvSvdEsQudyWeteavNitEWej_yK4apKO5Ot2oi1j32naCXToK9HKsA-DjZQFUK1lpOr2x1NohQhZTn2ukhmsqMLF-M0s4K6rOU_zvBVXtZc/https%3A%2F%2Fbioconductor.org%2Fpackages%2F3.15%2Fdata%2Fannotation%2Fhtml%2FCTCF.html>.
> According to guidelines
> https://contributions.bioconductor.org/versionnum.html
> <https://secure-web.cisco.com/1Ji55I99uGIxLYNCvStQt1WLoOMNm3ZlCvvBpZT093MnuWH5JDV98LX-tjZCKkauABSUs-PUD1bJlS7SIA5ANgYIKfmqqlTnUiQJsPANwECE0UjzRHeGoIwZu6-NluMMVycKpTGWO0wepCTpSBd99AdwzoFofsPvkSDj1ZxARHX4o1RQ1Wa-_cvUpW4l3CZwIu1b_Qy2W9mWOeSUODPqZCg1mNzVUnWZhy_vpuxp5oQkGvnXhBHt1LRrVhbr4fUR6pgnkYtuFn-N0ufZ_zLR2AoRdqYVNMZNLZ0EazjAX2Qj2rJqMIuLVrDdQC8ynzAFR/https%3A%2F%2Fcontributions.bioconductor.org%2Fversionnum.html>,
> its version should be 1.0.0 in the next release, 3.16. But it shows 0.99.9,
> https://bioconductor.org/packages/release/data/annotation/html/CTCF.html
> <https://secure-web.cisco.com/1-HAas6uKczMa97dum6aDLNdzsZnXMYuveFVQxWaxDoh9rvacjeTs3WMAt0O-eooA8Q7FqZn9iArd1OukmW3s91CU0iBR52XyqSRfCUtGeJbBX7uVq2jyBBXnaAXhmCTwlyhs86eAyt3a0VjEgCmIh2VN1_EmtOvLuLAOmsq_h1IHeTluYvlnIdeaZJ2-eTf-39PvyLmko3WIhjQx1tMFS0J8TJUHZp0q83bFllBFnVJb-cTOPHxc_FXC1qc2xtJ8sSi-T3G0QqzGZVd6jROteWJoI-mo7RBbkqDpmqcsDvVWJ0nGqYl8Z4ywmNAyb63w/https%3A%2F%2Fbioconductor.org%2Fpackages%2Frelease%2Fdata%2Fannotation%2Fhtml%2FCTCF.html>.
> Incrementing "the z" part has no effect, even after waiting for Wednesday's
> report update. Other attempts like setting the version to 1.0.0 fail with
> "remote: Error: Illegal version bump" when pushing to the "RELEASE_3_16"
> branch. Which version number should I set to trigger the build?
>
> Thanks,
> Mikhail
>
> On Mon, Oct 31, 2022 at 7:22 AM Kern, Lori <Lori.Shepherd using roswellpark.org>
> wrote:
>
> Please remember that once accepted the packages are only built and
> propagated on a particular schedule and not on demand.  Annotation packages
> that are in git are updated once a week. The schedule of the builds of
> different packages can be found:
>
> http://bioconductor.org/checkResults/
> <http://secure-web.cisco.com/1cfqN3qMzaLQA1lWYolkIbhsv9WGMpsY66OEXdCIPzSd1yNFbBP6GSHrkzH7a9yKpkLvDUgpLeoHt_xuDF1W8xb-NbGK05m_bZCoi13PBtWmot0DSpYuEF0PxvfawZShy7WegFieevp6sGsT50v99SlhnhoufX6iwmLZdEpJxaUeuLZiDzDdzzuZQQipr73iDYOuHbMudvWrZiLm72n9kCzo73oAgvq42bBuYOVQ7GEgJIU9Z0jeK1EcWFF6WYcvDQzQ1-y4HY4nFhD_dkLC3zXUlQ4ElQR8EwtgBUhfHH1NRuEqg-Q64ozC7mMgJdHA_/http%3A%2F%2Fbioconductor.org%2FcheckResults%2F>
>
> Vince is also correct.  You will still be able to update 3.16 but after
> tomorrow it would have to be done on the RELEASE_3_16 branch and master
> (3.17) branch.
>
> Cheers,
>
> 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
> Vincent Carey <stvjc using channing.harvard.edu>
> *Sent:* Sunday, October 30, 2022 9:13 PM
> *To:* Mikhail Dozmorov <mikhail.dozmorov using gmail.com>
> *Cc:* bioc-devel <bioc-devel using r-project.org>
> *Subject:* Re: [Bioc-devel] CTCF annotation package's vignette not
> updating
>
> Maybe I am wrong Mikhail but I think you have about 6 months to enhance the
> documentation of your package in 3.16.
>
> On Sun, Oct 30, 2022 at 7:54 PM Mikhail Dozmorov <
> mikhail.dozmorov using gmail.com>
> wrote:
>
> > Hello,
> > I'm trying to update documentation for the
> >
> https://secure-web.cisco.com/1p7VBteo2CRqcBZV-zNncaSH__4Q_rsUE7Tn2Jkq-yeqpCers_iPa5A4EytZziK_btn-kss-FCaAzY0CSPldbZubwnGgPQgU04BMpStqnTNklfw-_ddCnIOgtYwUAN6qdYRlypSYHUwSyBtC6gWj1hXZNcs55UpZ06-GtOnl0Lj9HrD_1VTmnUwEd5Q4iw4n-1jo6Z_u2Mfz-XXVjbbdRDbyVRbcybt2rJuElNK_pBimikAbulhNN-cB7Qi-FU22CPGSd2aflxOQ9NbzZ8zsTw5vmru5HNLzAizCcaBesTCiYcIgbNaEhmmQR4MHK060c/https%3A%2F%2Fbioconductor.org%2Fpackages%2Fdevel%2Fdata%2Fannotation%2Fhtml%2FCTCF.html
> > package so it can be shown in the 3.16 release. Pushed to bioc master
> > twice, with version bump. But the build is not triggered
> >
> https://secure-web.cisco.com/1sBV614NyVTESrurr0us0eF9hlgOxwbnKgjdZcAZHH3VbS8lsHGGEBUiZTaHOxgv8Fv2pVah4r-j1Roi7k0KRBrVF6DeQMeM43DlY5Ua4ovtWWhIWA6iy2CLp7SCH2VMVeL2h_jHVb8hOvDVA37A4Uz7QjD_tb7UWK5L4pemedIxxWDpoCQzaueRv4O-fjjz2gB4eqI8IrXNibaWEXrT0F0K7-QcTFZLpSsVP1OFHSCZKQw1rIA2vOjMSxZqEZlftwz_3SW507U8Z6rxaklHUWNOrX_SQK8F4x20XwQctLWVDW9RO2o2_pHumKAErweRB/https%3A%2F%2Fbioconductor.org%2FcheckResults%2F3.16%2Fdata-annotation-LATEST%2FCTCF%2F
> > It
> > may be due to the 3.16 release schedule or something very simple, but I'm
> > trying to meet the October 31 1:30 pm EST deadline and running out of
> ideas
> > what to do to update the package.
> > Thanks,
> > Mikhail
> >
> >         [[alternative HTML version deleted]]
> >
> > _______________________________________________
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