Re: [Bioc-devel] DeMixT issue
Wait 24 hours and check the build report http://bioconductor.org/checkResults/ The updated versions will not show up in today's build report as they were pushed to git too late but should appear in tomorrow's build report. Any changes before 4:45 PM EST will not be included in the nightly build and will be in the following days report. If you do not want to wait that long - You can always try cloning your package down directly from git.bioconductor.org into a new temporary directory and checking the versions. git clone g...@git.bioconductor.org:packages/DeMixT.git For What Its Worth - I do see the version changes in both release and devel. Cheers, Lori Shepherd Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 From: Bioc-devel on behalf of p...@rice.edu Sent: Wednesday, February 5, 2020 1:04 AM To: bioc-devel@r-project.org Subject: [Bioc-devel] DeMixT issue Hi Bioconductor team, I just pushed DeMixT package from 1.3.3 to 1.3.4 into level branch and 1.2.3 to 1.2.4 into release branch since I found a bug in the package. Since I am very new to git, may I know how can I verify the change of log? Besides, is there anyway that I can notice the change to users? Thanks, Peng [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited. If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you. [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] DeMixT issue
Hi Bioconductor team, I just pushed DeMixT package from 1.3.3 to 1.3.4 into level branch and 1.2.3 to 1.2.4 into release branch since I found a bug in the package. Since I am very new to git, may I know how can I verify the change of log? Besides, is there anyway that I can notice the change to users? Thanks, Peng [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] DeMixT issue
Just as before (https://github.com/Bioconductor/Contributions/issues/853#issuecomment-496776719), you pushed your changes AFTER the nightly build started. Compare the 'Snapshot Date: 2020-01-22 16:45:20 -0500 (Wed, 22 Jan 2020)' with the date of your commit DeMixT RELEASE_3_10$ git log commit e4e3f547d28e1e23015715f5c417de3cc8a0a37d (HEAD -> RELEASE_3_10, origin/RELEASE_3_10) Merge: 5e4f45c b3e094b Author: pengyang0411 Date: Wed Jan 22 21:24:07 2020 -0600 ... ALSO REMEMBER (as mentioned in https://github.com/Bioconductor/Contributions/issues/1343#issuecomment-574858510) THAT THE RELEASE BRANCH IS MEANT FOR BUG FIXES ONLY, so that your users have a consistent experience. You made major changes in the devel branch, and then ported those major changes to the release branch, ruining any of your users' existing work flows and reproducible research. It is 'too late' to reverse this; in the future only incorporate bug fixes in the release branch. Martin Morgan Bioconductor On 1/23/20, 11:09 PM, "py11" wrote: Hi Lori, I just pushed my new updated package into RELEASE_3_10 with version 1.2.3(old one was 1.2.1); however, I didn't see the change in release version as well as no build report update in the following link, http://bioconductor.org/checkResults/release/bioc-LATEST/DeMixT/ may I know how should address this issue? In the mean time, I successfully pushed version 1.3.3 into devel branch and has built successfully. Thanks, Peng Quoting "Shepherd, Lori" : > We noticed the build report has not been updated since Fri Jan 17th. > We have corrected the issue and there should be a new report today > or tomorrow. > > Cheers, > > > Lori Shepherd > > Bioconductor Core Team > > Roswell Park Comprehensive Cancer Center > > Department of Biostatistics & Bioinformatics > > Elm & Carlton Streets > > Buffalo, New York 14263 > > > From: Bioc-devel on behalf of > Shepherd, Lori > Sent: Tuesday, January 21, 2020 9:06 AM > To: py11 ; Martin Morgan > Cc: bioc-devel@r-project.org > Subject: Re: [Bioc-devel] DeMixT issue > > The current version on devel is 1.3.2 which is what is consistent > with what is in > g...@git.bioconductor.org:packages/DeMixT.git > > If you would like updates you need to update your version to 1.3.3 > in the next round of changes. > > > As Martin said previously, the landing page will not update until > you have a successful build. You can see from the build report, > the package is still timing out using version 1.3.2 > http://bioconductor.org/checkResults/devel/bioc-LATEST/DeMixT/ > Therefore the landing page remains at 1.3.1 > > Cheers > > > > Lori Shepherd > > Bioconductor Core Team > > Roswell Park Comprehensive Cancer Center > > Department of Biostatistics & Bioinformatics > > Elm & Carlton Streets > > Buffalo, New York 14263 > > ____________ > From: Bioc-devel on behalf of > py11 > Sent: Monday, January 20, 2020 3:11 PM > To: Martin Morgan > Cc: bioc-devel@r-project.org > Subject: Re: [Bioc-devel] DeMixT issue > > 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 : > >> 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. >>
Re: [Bioc-devel] DeMixT issue
Hi Lori, I just pushed my new updated package into RELEASE_3_10 with version 1.2.3(old one was 1.2.1); however, I didn't see the change in release version as well as no build report update in the following link, http://bioconductor.org/checkResults/release/bioc-LATEST/DeMixT/ may I know how should address this issue? In the mean time, I successfully pushed version 1.3.3 into devel branch and has built successfully. Thanks, Peng Quoting "Shepherd, Lori" : We noticed the build report has not been updated since Fri Jan 17th. We have corrected the issue and there should be a new report today or tomorrow. Cheers, Lori Shepherd Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 From: Bioc-devel on behalf of Shepherd, Lori Sent: Tuesday, January 21, 2020 9:06 AM To: py11 ; Martin Morgan Cc: bioc-devel@r-project.org Subject: Re: [Bioc-devel] DeMixT issue The current version on devel is 1.3.2 which is what is consistent with what is in g...@git.bioconductor.org:packages/DeMixT.git If you would like updates you need to update your version to 1.3.3 in the next round of changes. As Martin said previously, the landing page will not update until you have a successful build. You can see from the build report, the package is still timing out using version 1.3.2 http://bioconductor.org/checkResults/devel/bioc-LATEST/DeMixT/ Therefore the landing page remains at 1.3.1 Cheers Lori Shepherd Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 From: Bioc-devel on behalf of py11 Sent: Monday, January 20, 2020 3:11 PM To: Martin Morgan Cc: bioc-devel@r-project.org Subject: Re: [Bioc-devel] DeMixT issue 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 : 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" 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 : > 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 > >
Re: [Bioc-devel] DeMixT issue
We noticed the build report has not been updated since Fri Jan 17th. We have corrected the issue and there should be a new report today or tomorrow. Cheers, Lori Shepherd Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 From: Bioc-devel on behalf of Shepherd, Lori Sent: Tuesday, January 21, 2020 9:06 AM To: py11 ; Martin Morgan Cc: bioc-devel@r-project.org Subject: Re: [Bioc-devel] DeMixT issue The current version on devel is 1.3.2 which is what is consistent with what is in g...@git.bioconductor.org:packages/DeMixT.git If you would like updates you need to update your version to 1.3.3 in the next round of changes. As Martin said previously, the landing page will not update until you have a successful build. You can see from the build report, the package is still timing out using version 1.3.2 http://bioconductor.org/checkResults/devel/bioc-LATEST/DeMixT/ Therefore the landing page remains at 1.3.1 Cheers Lori Shepherd Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 From: Bioc-devel on behalf of py11 Sent: Monday, January 20, 2020 3:11 PM To: Martin Morgan Cc: bioc-devel@r-project.org Subject: Re: [Bioc-devel] DeMixT issue 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 : > 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" 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 : > > > 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...@us
Re: [Bioc-devel] DeMixT issue
The current version on devel is 1.3.2 which is what is consistent with what is in g...@git.bioconductor.org:packages/DeMixT.git If you would like updates you need to update your version to 1.3.3 in the next round of changes. As Martin said previously, the landing page will not update until you have a successful build. You can see from the build report, the package is still timing out using version 1.3.2 http://bioconductor.org/checkResults/devel/bioc-LATEST/DeMixT/ Therefore the landing page remains at 1.3.1 Cheers Lori Shepherd Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 From: Bioc-devel on behalf of py11 Sent: Monday, January 20, 2020 3:11 PM To: Martin Morgan Cc: bioc-devel@r-project.org Subject: Re: [Bioc-devel] DeMixT issue 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 : > 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" 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 : > > > 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 >
Re: [Bioc-devel] DeMixT issue
ucceed. 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" :
>
> > 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
> > 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
> > 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 on behalf of
> > py11
> > Sent: Wednesday, January 15, 2020 7:46 PM
> > To: 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
> >
> > ___
> > Bioc-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
> >
> > This email message may contain legally privileged and/or
> > confidential information. If you are not the intended
recipient(s),
> > or the employee or agent responsible for the delivery of this
> > message to the intended recipient(s), you are hereby
notified that
> > any disclosure, copying, distribution, or use of this
email message
> > is prohibited. If you have received this message in
error, please
> > notify the sender immediately by e-mail and delete this email
> > message from your computer. Thank you.
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] DeMixT issue
> after accumulating multiple commits on your local machine?
>
> This commit should have been declined by the hook,
>
> commit c17654aa8f76e36faf143deedf0495619567459a
> Author: pengyang0411
> 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 on behalf of
> py11
> Sent: Wednesday, January 15, 2020 7:46 PM
> To: 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
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
>
> This email message may contain legally privileged and/or
> confidential information. If you are not the intended recipient(s),
> or the employee or agent responsible for the delivery of this
> message to the intended recipient(s), you are hereby notified that
> any disclosure, copying, distribution, or use of this email message
> is prohibited. If you have received this message in error, please
> notify the sender immediately by e-mail and delete this email
> message from your computer. Thank you.
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] DeMixT issue
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" : 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 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 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 on behalf of py11 Sent: Wednesday, January 15, 2020 7:46 PM To: 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 ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited. If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you. ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] DeMixT issue
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 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 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 on behalf of py11 Sent: Wednesday, January 15, 2020 7:46 PM To: 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 ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited. If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you. [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[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 ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
