[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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