[Bioc-devel] DeMixT issue
py11
py11 @end|ng |rom r|ce@edu
Mon Jan 20 21:11:39 CET 2020
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
> > >
> > > _______________________________________________
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> > >
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