[Bioc-devel] error pushing changes

Wed Feb 6 17:20:28 CET 2019

Hi Marta,

That’s good to know that nothing is awry as far as versions go. 

There is no active web hook once a package is accepted, the web hook is for building and checking while the package is going through the submission process. 

Once it is accepted into Bioconductor, we just have the package registered on the build machines so that the developers and core team can check if it builds successfully on the devel and RELEASE branches. 

Best,

Nitesh 

> On Feb 6, 2019, at 11:07 AM, Marta Hidalgo <marta.hidalgo using outlook.es> wrote:
> 
> Hi Nitesh, 
> 
> Thank you so much for your help. I think I have managed not to mess it up again. 
> Btw, I have a small question regarding the webhook that should be added to the github repository when submitting a package: is this webhook still necessary once the package has been acepted?
> 
> Well, thanks again for your help, 
> Best, 
> 
> Marta
> 
> Marta Hidalgo 
> 
> De: Turaga, Nitesh <Nitesh.Turaga using RoswellPark.org>
> Enviado: miércoles, 30 de enero de 2019 18:27
> Para: Marta Hidalgo
> Cc: Bioc-devel; Morgan, Martin
> Asunto: Re: [Bioc-devel] error pushing changes
>  
> Hi Marta,
> 
> I have fixed your repository in the Bioconductor repo. git using git.bioconductor.org:packages/hipathia.git
> 
> Please follow this document exactly as is, to sync your GitHub repository (http://bioconductor.org/developers/how-to/git/sync-existing-repositories/). If you are having issues with this, feel free to reach out in this thread. It’s easier to point to the correct git resources, than to fix the versions. 
> 
> As a precaution in the future, do not merge the ‘master’ branch into ‘RELEASE_X_Y’ that is the issue which caused the version numbering to go bad. 
> 
> Best,
> 
> Nitesh
> 
> 
> > On Jan 30, 2019, at 5:00 AM, Marta Hidalgo <marta.hidalgo using outlook.es> wrote:
> > 
> > Hi Nitesh,
> > 
> > Thank you for your quick answer and sorry for the trouble.
> > Yes please, I think I'll need some help to fix this. Can you give me some instructions?
> > 
> > Thank you again!
> > 
> > Marta
> > 
> > ________________________________
> > 
> > Marta Hidalgo
> > 
> > 
> > ________________________________
> > De: Nitesh Turaga <nturaga using alumni.cmu.edu>
> > Enviado: miércoles, 30 de enero de 2019 1:36
> > Para: Bioc-devel; Morgan, Martin
> > Cc: marta.hidalgo using outlook.es
> > Asunto: Re: error pushing changes
> > 
> > Hi Marta,
> > 
> > There are a few issues with your repository. Let’s take a look at your commit history.
> > 
> > t/hipathia (RELEASE_3_8)❯❯❯ git log —oneline
> > d93efc9 (HEAD -> RELEASE_3_8, origin/RELEASE_3_8) Fixing bug in Wilcoxon test
> > bd245a5 fixing version number in NEWS file
> > bdfe551 fixing version number after merging
> > 33addfa bumping version and updating NEWS file
> > 2331dac Merge branch 'RELEASE_3_8' of git.bioconductor.org<http://git.bioconductor.org>:packages/hipathia
> > 4686268 Fixing bug in get_pathways_summary when comp is ordered
> > f5e8ef4 minor adding to vignette
> > b96521e bump x.y.z versions to odd y after creation of RELEASE_3_8 branch
> > f7bc056 bump x.y.z versions to even y prior to creation of RELEASE_3_8 branch
> > 
> > The commit b96521e is not supposed to exist on the RELEASE_3_8 branch. It is supposed to be only in the devel (master) branch of your repository. So when you merged, you seem to have merged the master branch into RELEASE_3_8.
> > 
> > So, your RELEASE_3_8 versioning is wrong. As shown, below, your RELEASE_3_8 should just be incrementing after commit f7bc056 where the version number was set by the core team as Version: 1.2.0. The next one should be 1.2.1 and 1.2.2 and so on. The ‘y’ in the x.y.z should always be even.
> > 
> > /t/hipathia(RELEASE_3_8) ❯❯❯ git show f7bc056
> > commit f7bc056e55a220b8bea8793a9b3b375c0ab66e7a
> > Author: vobencha <vobencha using gmail.com<mailto:vobencha using gmail.com>>
> > ...
> >    bump x.y.z versions to even y prior to creation of RELEASE_3_8 branch
> > ….
> > -Version: 1.1.3
> > +Version: 1.2.0
> > 
> > When you pushed, the current version of your repository in RELEASE_3_8 is being shown as 1.3.1. This is not allowed. I’m investigating how you were able to even pass through the commit hook with the bad version number, but the commit below should have been an indicator that something is seriously going wrong. Particularly the highlighted bits below where there are three version numbers which are being changed, moving ‘y’ from odd to even. The developer should never ever touch the ‘y’ version of number, only the ‘z’.
> > 
> > /t/hipathia(RELEASE_3_8) ❯❯❯ git show bdfe551514f0cf33798c45ae0475ff42eb4285e8
> > commit bdfe551514f0cf33798c45ae0475ff42eb4285e8
> > Merge: 33addfa b96521e
> > Author: Marta R. Hidalgo <marta.hidalgo using outlook.es<mailto:marta.hidalgo using outlook.es>>
> > Date:   Mon Dec 17 11:14:39 2018 +0100
> > 
> >    fixing version number after merging
> > 
> > diff --cc DESCRIPTION
> > index 7b35af2,24c9d19..491fbd6
> > --- a/DESCRIPTION
> > +++ b/DESCRIPTION
> > @@@ -1,6 -1,6 +1,6 @@@
> >  Package: hipathia
> >  Title: HiPathia: High-throughput Pathway Analysis
> > - Version: 1.2.1
> > -Version: 1.3.0
> > ++Version: 1.3.1
> > 
> > You will have to fix your last few commits. I can help you revert it back to the previous release, and we can go from there. Please let me know how you want to proceed.
> > 
> > Best,
> > 
> > Nitesh
> > 
> > 
> > 
> > On Jan 29, 2019, at 4:24 PM, Martin Morgan <mtmorgan.bioc using gmail.com<mailto:mtmorgan.bioc using gmail.com>> wrote:
> > 
> > Hi Nitesh -- can you help Marta please? Thanks, Martin
> > 
> > 
> > 
> > On 1/29/19, 12:20 PM, "Marta Hidalgo" <marta.hidalgo using outlook.es<mailto:marta.hidalgo using outlook.es>> wrote:
> > 
> > 
> >   Hi,
> > 
> > 
> >   I'm trying to push some changes to the RELEASE_3_8 branch of package Hipathia and I'm getting the following error:
> > 
> > 
> >   Agent admitted failure to sign using the key.
> >   Total 0 (delta 0), reused 0 (delta 0)
> > 
> >   remote: Error: Illegal version bump from '1.3.1' to '1.3.2'. Check
> > 
> >   remote: http://bioconductor.org/developers/how-to/version-numbering/
> > 
> >   remote: for details
> > 
> >   To git using git.bioconductor.org<mailto:git using git.bioconductor.org>:packages/hipathia.git
> > 
> >    ! [remote rejected] RELEASE_3_8 -> RELEASE_3_8 (pre-receive hook declined)
> > 
> >   error: s'ha fallat en pujar algunes referències a 'git using git.bioconductor.org<mailto:git using git.bioconductor.org>:packages/hipathia.git'
> > 
> > 
> > 
> >   What can I do to solve it?
> >   Thank you in advance,
> > 
> > 
> >   Marta
> > 
> > 
> > 
> > 
> >   ________________________________________
> >   Marta Hidalgo
> > 
> > 
> > 
> > 
> > 
> > 
> > 
> >        [[alternative HTML version deleted]]
> > 
> > _______________________________________________
> > Bioc-devel using 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.

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.