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

kushal kumar dey kshldey at gmail.com
Wed Nov 1 19:23:59 CET 2017

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

*(or you mis-spelled the reponame)*

You can check the branch I want to push on my Github


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!


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

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