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

Thu Nov 2 23:52:56 CET 2017

Hi Nitesh,

It seems that the bug fixes I made to my software are still not updated in
the Bioconductor page. I bumped the version to 1.4.1 but I still find the
version to be 1.4.0

https://www.bioconductor.org/packages/3.6/bioc/html/CountClust.html

Didn't the build go through?

Thanks

Kushal

On 1 November 2017 at 16:45, kushal kumar dey <kshldey at gmail.com> wrote:

> 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/ho
>> w-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/OI4nc8NE0sL4COb6uNaBI
>> URhJoSyisz8i8/KWum0xFhav7ouDpMoZz0lgnlRaIYIRquJx0R44ojDcsN45
>> TBR8Rna4PNBscVJEsbonD0k3wi2OBySgwxTzL5aZl99HzuAzthAPzFuskZDH
>> ahws9sPUtWMxioI6D5ZktVOb/QJbDJdFHFPXcd8l90wRJN0eGJXX9excJBDU
>> 57ufEgDBx9vGv85GTwJjP4UQYLyjDIap2CbrdC+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 <+1%20312-709-0680> | kkdey at uchicago.edu
>> >>
>> >>      [[alternative HTML version deleted]]
>> >>
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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
>

-- 
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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