[Bioc-devel] DeMixT issue
Martin Morgan
mtmorg@n@b|oc @end|ng |rom gm@||@com
Fri Jan 24 09:30:23 CET 2020
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 using 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 using 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 using 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 using r-project.org> on behalf of
> Shepherd, Lori <Lori.Shepherd using RoswellPark.org>
> Sent: Tuesday, January 21, 2020 9:06 AM
> To: py11 <py11 using rice.edu>; Martin Morgan <mtmorgan.bioc using gmail.com>
> Cc: bioc-devel using r-project.org <bioc-devel using 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 using 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 using r-project.org> on behalf of
> py11 <py11 using rice.edu>
> Sent: Monday, January 20, 2020 3:11 PM
> To: Martin Morgan <mtmorgan.bioc using gmail.com>
> Cc: bioc-devel using r-project.org <bioc-devel using 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 using 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 using 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 using 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 using 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 using r-project.org on behalf of py11 using 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 using 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 using 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 using 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 using r-project.org> on behalf of
>> > > py11 <py11 using rice.edu>
>> > > Sent: Wednesday, January 15, 2020 7:46 PM
>> > > To: bioc-devel using r-project.org <bioc-devel using 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 using r-project.org mailing list
>> > > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>> > >
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