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.b...@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+pengyang0...@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-boun...@r-project.org on behalf of p...@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.tur...@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.tur...@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 <pengyang0...@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-boun...@r-project.org> on behalf of
> py11 <p...@rice.edu>
> Sent: Wednesday, January 15, 2020 7:46 PM
> To: bioc-devel@r-project.org <bioc-devel@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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