[Bioc-devel] Don't have git access to my newly submitted git package

[Nitesh Turaga]

Hi Steve,

You are having it ;) I’m the one assigned to your package.

Best,

Nitesh



Nitesh Turaga
Scientist II, Department of Data Science,
Bioconductor Core Team Member
Dana Farber Cancer Institute

> On Oct 4, 2021, at 5:42 PM, Steve Lianoglou <slianoglou using gmail.com> wrote:
> 
> Hi Nitesh,
> 
> Thanks for working on this ... I've been able to push some changes I've made up to the upstream/master, so I think we should be ok for now.
> 
> Waiting till the next cycle is fine if you think that is the best approach. 
> 
> In all honesty, I'd prefer to attach the associated "shiny add-on package" to be reviewed with the main sparrow package I submitted last week, but I don't want to overwhelm the reviewers. Perhaps this is a conversation I can have directly with the person assigned to review my package via the github issues?
> 
> Thanks!
> -steve
>  
> > On Oct 1, 2021, at 5:52 PM, Steve Lianoglou <slianoglou using gmail.com> wrote:
> > 
> > Hello folks,
> > 
> > I think I may have a similar problem accessing the git repos as was
> > reported by Henrik back in August:
> > https://marc.info/?l=bioc-devel&m=162937494630582&w=2
> > 
> > My recently submitted package (sparrow) was just accepted for review:
> > https://github.com/Bioconductor/Contributions/issues/2342
> > 
> > I added the upstream bioc git repos, and have activated my account under:
> > https://git.bioconductor.org/BiocCredentials/profile/
> > 
> > I have also confirmed that the public ssh-rsa key under my bioc profile is
> > the one I have in ~/.ssh/id_rsa.pub
> > 
> > I want to start whacking away at the code so that the package passes on the
> > bioc build servers, but when I try to push a small change to the upstream
> > repo, I get this:
> > 
> > ```
> > $ git push upstream main
> > FATAL: W any packages/sparrow s.lianoglou DENIED by fallthru
> > (or you mis-spelled the reponame)
> > fatal: Could not read from remote repository.
> > 
> > Please make sure you have the correct access rights
> > and the repository exists.
> > ```
> > 
> > I went in to see what's cooking via ssh and see that I only have read
> > access to the sparrow repository:
> > 
> > ```
> > $ ssh -T git using git.bioconductor.org | grep -E "sparrow"
> > R   packages/sparrow
> > ```
> > 
> > But I can also see that I have write access to some repositories I
> > contributed to back in the day when I was a graduate student (ohhh good
> > times):
> > 
> > ```
> > $ ssh -T git using git.bioconductor.org | grep -E "^ R W"
> > R W packages/GenomicRanges
> > R W packages/Gviz
> > R W packages/IRanges
> > ```
> > 
> > Is this likely something going wrong on my side, or is there something
> > cooking on the bioc side?
> > 
> > Lastly, I would also like to submit a second "sibling" package along
> > sparrow that (only) enhances sparrow by adding shiny modules and a full
> > shiny app to explore GSEA results.
> > 
> > I planned on doing that following the instructions here:
> > https://github.com/Bioconductor/Contributions#submitting-related-packages
> > 
> > But maybe I should wait until the next cycle (happy to do that)?
> > 
> > There is a package in bioc (gCrisprTools) with an update that relies on
> > some mojo in my sparrow package and don't want to jeopardize sparrow's
> > consideration for this release cycle by adding another package for review
> > on top of that.
> > 
> > https://stat.ethz.ch/pipermail/bioc-devel/2021-August/018402.html
> > 
> > Thanks in advance for your time and guidance,
> > -steve
> > 
> >       [[alternative HTML version deleted]]
> > 
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