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

Fri Nov 3 12:48:19 CET 2017

It can take up to 24 hours for the results to show in the build report.  Please check again today and let us know if it is not reflected in the Friday build report.

Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

________________________________
From: Bioc-devel <bioc-devel-bounces at r-project.org> on behalf of kushal kumar dey <kshldey at gmail.com>
Sent: Thursday, November 2, 2017 6:52:56 PM
To: Turaga, Nitesh
Cc: bioc-devel at r-project.org
Subject: Re: [Bioc-devel] Package update not showing on Bioc 3.6 webpage

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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>> >> 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
>

--
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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