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List: bioc-devel
Subject: Re: [Bioc-devel] DeMixT issue
From: Martin Morgan <mtmorgan.bioc () gmail ! com>
Date: 2020-01-24 8:30:23
Message-ID: BN8PR04MB5522B476627E6EABC801D654F90E0 () BN8PR04MB5522 ! namprd04 ! prod ! outlook ! com
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Just as before (https://github.com/Bioconductor/Contributions/issues/853#issuecomment-496776719), \
you pushed your changes AFTER the nightly build started. Compare the 'Snapshot Date: \
2020-01-22 16:45:20 -0500 (Wed, 22 Jan 2020)' with the date of your commit
DeMixT RELEASE_3_10$ git log
commit e4e3f547d28e1e23015715f5c417de3cc8a0a37d (HEAD -> RELEASE_3_10, \
origin/RELEASE_3_10)
Merge: 5e4f45c b3e094b
Author: pengyang0411 <pengyang0411@gmail.com>
Date: Wed Jan 22 21:24:07 2020 -0600
...
ALSO REMEMBER (as mentioned in \
https://github.com/Bioconductor/Contributions/issues/1343#issuecomment-574858510) \
THAT THE RELEASE BRANCH IS MEANT FOR BUG FIXES ONLY, so that your users have a \
consistent experience. You made major changes in the devel branch, and then ported \
those major changes to the release branch, ruining any of your users' existing work \
flows and reproducible research. It is 'too late' to reverse this; in the future only \
incorporate bug fixes in the release branch.
Martin Morgan
Bioconductor
On 1/23/20, 11:09 PM, "py11" <py11@rice.edu> wrote:
Hi Lori,
I just pushed my new updated package into RELEASE_3_10 with version
1.2.3(old one was 1.2.1); however, I didn't see the change in release
version as well as no build report update in the following link,
http://bioconductor.org/checkResults/release/bioc-LATEST/DeMixT/
may I know how should address this issue? In the mean time, I
successfully pushed version 1.3.3 into devel branch and has built
successfully.
Thanks,
Peng
Quoting "Shepherd, Lori" <Lori.Shepherd@roswellpark.org>:
> We noticed the build report has not been updated since Fri Jan 17th.
> We have corrected the issue and there should be a new report today
> or tomorrow.
>
> Cheers,
>
>
> Lori Shepherd
>
> 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@r-project.org> on behalf of
> Shepherd, Lori <Lori.Shepherd@RoswellPark.org>
> Sent: Tuesday, January 21, 2020 9:06 AM
> To: py11 <py11@rice.edu>; Martin Morgan <mtmorgan.bioc@gmail.com>
> Cc: bioc-devel@r-project.org <bioc-devel@r-project.org>
> Subject: Re: [Bioc-devel] DeMixT issue
>
> The current version on devel is 1.3.2 which is what is consistent
> with what is in
> git@git.bioconductor.org:packages/DeMixT.git
>
> If you would like updates you need to update your version to 1.3.3
> in the next round of changes.
>
>
> As Martin said previously, the landing page will not update until
> you have a successful build. You can see from the build report,
> the package is still timing out using version 1.3.2
> http://bioconductor.org/checkResults/devel/bioc-LATEST/DeMixT/
> Therefore the landing page remains at 1.3.1
>
> Cheers
>
>
>
> Lori Shepherd
>
> 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@r-project.org> on behalf of
> py11 <py11@rice.edu>
> Sent: Monday, January 20, 2020 3:11 PM
> To: Martin Morgan <mtmorgan.bioc@gmail.com>
> Cc: bioc-devel@r-project.org <bioc-devel@r-project.org>
> Subject: Re: [Bioc-devel] DeMixT issue
>
> Hello,
>
> I pushed my updated package into biconductor master branch on Jan
> 18th; however, I still didn't see the version change in devel branch
> as follow:
>
> https://bioconductor.org/packages/devel/bioc/html/DeMixT.html
>
> May I ask where can I find the build report for the latest update?
>
> Thanks,
> Peng
>
> Quoting Martin Morgan <mtmorgan.bioc@gmail.com>:
>
>> The package is always built from the current git repository,
>> regardless of version. So your package will build.
>>
>> A successfully built package (passing install / build / check) is
>> only 'pushed' to the public repository if the version is different
>> (higher) than the current published repository. Your original 1.3.2
>> version has not built successfully, it has not been pushed. If your
>> new 1.3.2 version builds successfully, it will be pushed.
>>
>> BUT the best practice is simply to increment the version, so that
>> there is no confusion -- in the previous paragraph I had to say
>> 'your original 1.3.2 version' and 'your new 1.3.2 version', but it
>> would have been much clearer to say version 1.3.2 and 1.3.3.
>>
>> Martin
>>
>> On 1/18/20, 5:39 PM, "py11" <py11@rice.edu> wrote:
>>
>> Hi Martin,
>>
>> Thank you very much for the detailed report. I have noticed in
>> the report
>>
>> https://bioconductor.org/checkResults/devel/bioc-LATEST/DeMixT/
>>
>> the build failed due to check out of time. I re-arrange the examples
>> in my Rd file, which guarantee the run time of R CMD check lower than
>> 10 mins. So I pushed the package again into bioconductor with version
>> 1.3.2 again. And my question is, is 1.3.2 the right version that I am
>> using for and will it be built in the following night?
>>
>> Note the current devel version in our package page is 1.3.1 as shown
>> in link below:
>>
>> https://bioconductor.org/packages/devel/bioc/html/DeMixT.html
>>
>> Thanks,
>> Peng
>>
>>
>>
>> Quoting Martin Morgan <mtmorgan.bioc@gmail.com>:
>>
>> > I see
>> >
>> > DeMixT master$ grep Version DESCRIPTION
>> > Version: 1.3.2
>> >
>> > Which is fine.
>> >
>> > Remember that accepted Bioconductor packages are *built nightly*
>> > rather than on commit. This ensures that the current version of your
>> > package is working with the current version of all other packages in
>> > the Bioconductor ecosystem, and that that other Bioconductor
>> > packages that may depend on your package are working with it.
>> >
>> > Look at the build report for your package
>> >
>> > https://bioconductor.org/checkResults/devel/bioc-LATEST/DeMixT/
>> >
>> > Note the publication date, which is when the last nightly build
>> > completed and the build report created
>> >
>> > This page was generated on 2020-01-15 11:54:40 -0500 (Wed,
>> 15 Jan 2020).
>> >
>> > Note the Snapshot date, the date and time when a clone of your
>> > repository was made to start the nightly build
>> >
>> > Snapshot Date: 2020-01-14 16:46:51 -0500 (Tue, 14 Jan 2020)
>> >
>> > Finally, note from your repository the date of your last commit
>> >
>> > DeMixT master$ git log -n 1
>> > commit e86bea0d14ac39f3d019f8aed3612747acabb55f
>> > Author: pengyang0411
>> <57335942+pengyang0411@users.noreply.github.com>
>> > Date: Wed Jan 15 14:27:55 2020 -0600
>> >
>> > Your commit was after the most recent nightly build started, so the
>> > changes have not yet been incorporated into the build. Wait for the
>> > next nightly build (starting at about 5pm Eastern time, ending
>> > Tomorrow at about noon US eastern time) to see your changes
>> > incorporated into the build system.
>> >
>> > If the build is successful, then the blue 'light' at the extreme
>> > right of the report will change to 'green', indicating that a new
>> > version has been built. This will then trigger an update of your
>> > package landing page
>> >
>> > https://bioconductor.org/packages/devel/DeMixT
>> >
>> > A similar process occurs for the release branch, with the report and
>> > landing page at
>> >
>> > https://bioconductor.org/checkResults/release/bioc-LATEST/DeMixT/
>> > https://bioconductor.org/packages/release/DeMixT
>> >
>> > Martin
>> >
>> > On 1/15/20, 9:34 PM, "Bioc-devel on behalf of py11"
>> > <bioc-devel-bounces@r-project.org on behalf of py11@rice.edu> wrote:
>> >
>> > Hi Nitesh,
>> >
>> > Thank you very much for detailed explanation. Since there
>> is a major
>> > change in our package, we decided to bump version from
>> 1.3.1 to 1.5.0
>> > under devel branch. I did push repository from local machine into
>> > bioconductor from 1.3.1 --> 1.4.0 and the second try was
>> from 1.3.1
>> > --> 1.5.0; but both of these two 'push' have been rejected
>> with error:
>> > Illegal version bump from '1.3.1' to '1.4.0' and Illegal
>> version bump
>> > from '1.3.1' to '1.5.0'.
>> >
>> > However, my last try was from 1.3.1 --> 1.3.2 and it
>> succeed. I just
>> > double checked all the files in
>> updatedremote/upstream/master has been
>> > updated.
>> >
>> > I apologize for making it inconvenience since I just took
>> over the job
>> > to maintain the package, and thanks again for the help.
>> >
>> > Best,
>> > Peng
>> >
>> > Quoting "Turaga, Nitesh" <Nitesh.Turaga@roswellpark.org>:
>> >
>> > > Hi Peng,
>> > >
>> > > I was looking through your version bumps, and it looks a little
>> > > off-track I have to say. The version bumps you should
>> have in your
>> > > repository should be following the order(from the commit below)
>> > > should be 1.3.0 --> 1.3.1 --> 1.3.2 and so on.
>> > >
>> > > commit c358f5e7d8564423fb60abea7024b01068046ea8
>> > > Author: Nitesh Turaga <nitesh.turaga@gmail.com>
>> > > Date: 2019-10-29 13:43:32 -0400
>> > >
>> > > bump x.y.z version to odd y after creation of
>> RELEASE_3_10 branch
>> > >
>> > > diff --git a/DESCRIPTION b/DESCRIPTION
>> > > index c922ad7..8fff467 100644
>> > > --- a/DESCRIPTION
>> > > +++ b/DESCRIPTION
>> > > @@ -2,7 +2,7 @@ Package: DeMixT
>> > > Title: Cell type-specific deconvolution of heterogeneous
>> > tumor samples with
>> > > two or three components using expression data
>> from RNAseq
>> > > or microarray platforms
>> > > -Version: 1.2.0
>> > > +Version: 1.3.0
>> > >
>> > >
>> > > But it seems like this order has been lost somehow and
>> you started
>> > > with 1.4.0 and 1.5.0. I'm actually surprised you were
>> able to push
>> > > up these changes to the repository as the git hook should have
>> > > prevented you from making 1.3.0 --> 1.4.0. An important
>> question is,
>> > > did you "push" your commits to the Bioconductor git repository
>> > > after accumulating multiple commits on your local machine?
>> > >
>> > > This commit should have been declined by the hook,
>> > >
>> > > commit c17654aa8f76e36faf143deedf0495619567459a
>> > > Author: pengyang0411 <pengyang0411@gmail.com>
>> > > Date: Sun Jan 12 22:26:37 2020 -0600
>> > >
>> > > update to v1.4.0
>> > >
>> > > diff --git a/DESCRIPTION b/DESCRIPTION
>> > > index 62a7290..9b5a6b8 100644
>> > > --- a/DESCRIPTION
>> > > +++ b/DESCRIPTION
>> > > @@ -1,7 +1,7 @@
>> > > Package: DeMixT
>> > > Title: Cell type-specific deconvolution of heterogeneous tumor
>> > > samples with two or three
>> > > components using expression data from RNAseq or
>> > microarray platforms
>> > > -Version: 1.3.0
>> > > +Version: 1.4.0
>> > > Date: 2020-01-06
>> > >
>> > > And you have this
>> commit(7fa3d1b4e97a48112634452ac752a9fed8ade493)
>> > > taking it to 1.5.0 and then this one
>> > > (f5c7fdc25ed18dc21f16f02bdc20a1805efa2b50) to 1.5.1.
>> > >
>> > > We'll have to figure out a way to fix your version
>> numbers. But as
>> > > far as the build report goes, if you pushed all your commits in
>> > > today, then you'll have to wait for the nightly builders
>> to produce
>> > > the build report tomorrow.
>> > >
>> > > We'll get back to you on a path forward.
>> > >
>> > > Best,
>> > >
>> > > Nitesh
>> > >
>> > >
>> > > ________________________________
>> > > From: Bioc-devel <bioc-devel-bounces@r-project.org> on behalf of
>> > > py11 <py11@rice.edu>
>> > > Sent: Wednesday, January 15, 2020 7:46 PM
>> > > To: bioc-devel@r-project.org <bioc-devel@r-project.org>
>> > > Subject: [Bioc-devel] DeMixT issue
>> > >
>> > > Hi Bioconductor team,
>> > >
>> > > I just pushed the latest version from 1.3.1 to 1.3.2 into devel
>> > > branch; however, there is no changes on the DeMixT website in
>> > > biocondoctor,
>> > > https://bioconductor.org/packages/devel/bioc/html/DeMixT.html
>> > >
>> > > Can you help me update it or is there anything I can do?
>> > >
>> > > Thanks,
>> > > Peng
>> > >
>> > > _______________________________________________
>> > > Bioc-devel@r-project.org mailing list
>> > > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>> > >
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