[Bioc-devel] DeMixT issue

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 at 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 at r-project.org on behalf of py11 at 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 at 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 at 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 at 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 at r-project.org> on behalf of
    > py11 <py11 at rice.edu>
    > Sent: Wednesday, January 15, 2020 7:46 PM
    > To: bioc-devel at r-project.org <bioc-devel at 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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