[Bioc-devel] Package update not showing on Bioc 3.6 webpage

Wed Nov 1 22:45:35 CET 2017

Thanks so much for the help.  I did manage to push with the SSH protocol.
Will wait till the next build to see if it went through.

Best

Kushal

On 1 November 2017 at 16:18, Turaga, Nitesh <Nitesh.Turaga at roswellpark.org>
wrote:

> Hi Kushal,
>
> You also need to use the “SSH” protocol, and not the “HTTPS” protocol.
>
> Your upstream should be git at git.bioconductor.org:packages/CountClust
>
> Best,
>
> Nitesh
>
> > On Nov 1, 2017, at 5:06 PM, Turaga, Nitesh <Nitesh.Turaga at RoswellPark.org>
> wrote:
> >
> > Hi Kushal,
> >
> > Can you please try,
> >
> >       ssh -T git at git.bioconductor.org -v
> >
> >
> > Are you using the correct private key to your corresponding public key
> on our machine?
> >
> > If not, please check the FAQ section bioconductor.org/developers/
> how-to/git/faq/ point#15. You can set up a config file to use the correct
> private key.
> >
> > A snippet of your public key on our machine is,
> >
> > ssh-rsa AAAAB3NzaC1yc2EAAAADAQABAAACAQC8EgObkc/
> OI4nc8NE0sL4COb6uNaBIURhJoSyisz8i8/KWum0xFhav7ouDpMoZz0lgnlRaIYIR
> quJx0R44ojDcsN45TBR8Rna4PNBscVJEsbonD0k3wi2OBySgwxTzL5aZl99H
> zuAzthAPzFuskZDHahws9sPUtWMxioI6D5ZktVOb/QJbDJdFHFPXcd8l90wRJN0eGJXX9ex
> cJBDU57ufEgDBx9vGv85GTwJjP4UQYLyjDIap2CbrdC+7nJ95fa7YcNUj2znVFcrNnkW9
> >
> > Best,
> >
> > Nitesh
> >
> >
> >> On Nov 1, 2017, at 2:23 PM, kushal kumar dey <kshldey at gmail.com> wrote:
> >>
> >> Hi Herve,
> >>
> >> Thanks for clarifying on the matter. I followed your instructions and
> did *git
> >> cherry-pick* to make the following changes
> >>
> >> - fix a bug in one of the functions
> >> - add a citation
> >> - fix the readme
> >>
> >> I bumped the version number from 1.4.0 to 1.4.1 and tried to push to the
> >> release branch, but I when I run the command,
> >>
> >> git push upstream RELEASE_3_6
> >>
> >> I meet with the following error
> >>
> >> *fatal: remote error: FATAL: W any packages/CountClust nobody DENIED by
> >> fallthru*
> >>
> >> *(or you mis-spelled the reponame)*
> >>
> >>
> >> You can check the branch I want to push on my Github
> >>
> >>
> >>
> >> *https://github.com/kkdey/CountClust/tree/RELEASE_3_6
> >> <https://github.com/kkdey/CountClust/tree/RELEASE_3_6>*
> >>
> >>
> >> This is my output from *git remote -v *
> >>
> >> *origin https://github.com/kkdey/CountClust.git
> >> <https://github.com/kkdey/CountClust.git> (fetch)*
> >>
> >> *origin https://github.com/kkdey/CountClust.git
> >> <https://github.com/kkdey/CountClust.git> (push)*
> >>
> >> *upstream https://git.bioconductor.org/packages/CountClust
> >> <https://git.bioconductor.org/packages/CountClust> (fetch)*
> >>
> >> *upstream https://git.bioconductor.org/packages/CountClust
> >> <https://git.bioconductor.org/packages/CountClust> (push)*
> >>
> >>
> >> Can you please let me know what I am doing wrong here and how I can
> update
> >> the release version?
> >>
> >>
> >> Thank you so much!
> >>
> >>
> >> Kushal
> >>
> >>
> >>
> >>
> >>
> >> On 30 October 2017 at 17:50, Hervé Pagès <hpages at fredhutch.org> wrote:
> >>
> >>> Hi Kushal,
> >>>
> >>> If you push changes without bumping the version of your package,
> >>> the update won't propagate.
> >>>
> >>> You only bumped the version to 1.5.1 today so you need to wait
> >>> about 24 hours before seeing this reflected on the landing page
> >>> for CountClust.
> >>>
> >>> Also please note that you did the version bump plus a few other
> >>> commits (6 commits in total) in master today **after** we created
> >>> the RELEASE_3_6 branch so these changes will only propagate to
> >>> BioC 3.7 (the new devel version of BioC, starting tomorrow).
> >>> If you want these changes to also propagate to the BioC 3.6 release
> >>> you'll need to push them to the RELEASE_3_6 branch. This is
> >>> typically done with 'git cherry-pick' as documented here:
> >>>
> >>>
> >>> https://bioconductor.org/developers/how-to/git/bug-fix-in-
> >>> release-and-devel/
> >>>
> >>> Cheers,
> >>> H.
> >>>
> >>>
> >>> On 10/30/2017 02:41 PM, kushal kumar dey wrote:
> >>>
> >>>> Hi all,
> >>>>
> >>>> I am the author and maintainer of the CountClust package. I recently
> >>>> submitted an update (version 1.5.1) to the package through
> >>>> Bioconductor Git  and I can access this updated version when I clone
> the
> >>>> source repository
> >>>>
> >>>> git clone https://urldefense.proofpoint.
> com/v2/url?u=https-3A__git.bio
> >>>> conductor.org_packages_CountClust&d=DwICAg&c=eRAMFD45gAfqt84
> >>>> VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=-x3S
> >>>> 8Sl0fsASITg_-ULMYIykoPk6Y0PqK2NoRjC43iA&s=YBM0DldFbCkrEBnHaB
> >>>> n5X8-jb1yhm_GmSUWL6SIGLmo&e=
> >>>>
> >>>> However, the updated version is not available in the official
> Bioconductor
> >>>> 3.6 page, which still shows the version 1.3.0.
> >>>>
> >>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__www.bio
> >>>> conductor.org_packages_3.6_bioc_html_CountClust.html&d=DwICA
> >>>> g&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvS
> >>>> XAJJKaaPhzWA&m=-x3S8Sl0fsASITg_-ULMYIykoPk6Y0PqK2NoRjC43iA&
> >>>> s=UfPX4T5l4JBfXBumCcQ-5YOm59i_xfX2OEILrQ3I2u0&e=
> >>>>
> >>>> Can you please let me know if the page has not been updated for the
> >>>> packages yet or if I would need to do something at my end to update
> the
> >>>> version reported on the page?
> >>>>
> >>>> Thanks so much
> >>>>
> >>>>
> >>> --
> >>> Hervé Pagès
> >>>
> >>> Program in Computational Biology
> >>> Division of Public Health Sciences
> >>> Fred Hutchinson Cancer Research Ce
> >>> <https://maps.google.com/?q=n+Cancer+Research+Ce&entry=gmail&source=g
> >nter
> >>> 1100 Fairview Ave. N, M1-B514
> >>> P.O. Box 19024
> >>> Seattle, WA 98109-1024
> >>>
> >>> E-mail: hpages at fredhutch.org
> >>> Phone:  (206) 667-5791
> >>> Fax:    (206) 667-1319
> >>>
> >>
> >>
> >>
> >> --
> >> Kushal K. Dey
> >> Graduate Student
> >> 5 th Year, Department of Statistics
> >> University of Chicago
> >> Contact: +1 312-709-0680 | kkdey at uchicago.edu
> >>
> >>      [[alternative HTML version deleted]]
> >>
> >> _______________________________________________
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> >> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
> >
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-- 
Kushal K. Dey
Graduate Student
5 th Year, Department of Statistics
University of Chicago
Contact: +1 312-709-0680 | kkdey at uchicago.edu

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