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
wrote:
> Hello,
> I'm trying to update documentation for the
> https://bioconductor.org/packages/devel/data/annotation/html/CTCF.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://bioconductor.org/checkResults/3.16/data-annotation-LATEST/CTCF/.
> 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]]
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
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Re: [Bioc-devel] CTCF annotation package's vignette not updating
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/
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 on behalf of Vincent Carey
Sent: Sunday, October 30, 2022 9:13 PM
To: Mikhail Dozmorov
Cc: bioc-devel
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
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]]
>
> ___
> Bioc-devel@r-project.org mailing list
> https://secure-web.cisco.com/1mueWKL3AMBjbkUJbDAqpWGLMWD-5Jsb_WUCt5eZZyzaY9qAg0iypSVjgckFNG0n3vlDSi5njIeMnl3aDgga-H4koSxK-E0Om-GewGInXGSWP8lQROFryCUI29Rds3DBhKrKKIyGrWI_3ZIHJynixzUzhU1pMpa3Kz1NIcEoCMvGXPfHCmBCCQa2A011_wb7rqUXGvevN9fYOBQBj6ILBcyBWfDAw2MA6GG9UOVa8tkotsOI4wWiZ8zkNj5lTx16Qa0KFb4JI1dvPyjye-WtMQBXCfFAOSKEGkHVjZJYJN3WP36NiiuDr7A0jY9JYfu5R/https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel
>
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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.
According to guidelines
https://contributions.bioconductor.org/versionnum.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.
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
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/
>
> 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 on behalf of
> Vincent Carey
> *Sent:* Sunday, October 30, 2022 9:13 PM
> *To:* Mikhail Dozmorov
> *Cc:* bioc-devel
> *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.dozmo...@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]]
> >
> > ___
> > Bioc-devel@r-project.org mailing list
> >
> https://secure-web.cisco.com/1mueWKL3AMBjbkUJbDAqpWGLMWD-5Jsb_WUCt5eZZyzaY9qAg0iypSVjgckFNG0n3vlDSi5njIeMnl3aDgga-H4koSxK-E0Om-GewGInXGSWP8lQROFryCUI29Rds3DBhKrKKIyGrWI_3ZIHJynixzUzhU1pMpa3Kz1NIcEoCMvGXPfHCmBCCQa2A011_wb7rqUXGvevN9fYOBQBj6ILBcyBWfDAw2MA6GG9UOVa8tkotsOI4wWiZ8zkNj5lTx16Qa0KFb4JI1dvPyjye-WtMQBXCfFAOSKEGkHVjZJYJN3WP36NiiuDr7A0jY9JYfu5R/https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel
> >
>
> --
> The information in this e-mail is intended only for th...{{dropped:25}}
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Re: [Bioc-devel] CTCF annotation package's vignette not updating
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 Sent: Friday, November 11, 2022 10:30 AM To: bioc-devel ; Kern, Lori 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_vpuxp5oQkGvnXhB Ht1LRrVhbr4fUR6pgnkYtuFn-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 mailto:lori.sheph...@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 mailto:bioc-devel-boun...@r-project.org>> on behalf of Vincent Carey mailto:st...@channing.harvard.edu>> Sent: Sunday, October 30, 2022 9:13 PM To: Mikhail Dozmorov mailto:mikhail.dozmo...@gmail.com>> Cc: bioc-devel mailto:bioc-devel@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 mailto:mikhail.dozmo...@gmail.com>&g
Re: [Bioc-devel] CTCF annotation package's vignette not updating
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 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 > *Sent:* Friday, November 11, 2022 10:30 AM > *To:* bioc-devel ; Kern, Lori > > *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 > 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_dkLC3zXUlQ4ElQR8EwtgBUh
