[Bioc-devel] DeMixT issue
py11
py11 @end|ng |rom r|ce@edu
Sat Jan 18 23:39:13 CET 2020
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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