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

[Nitesh Turaga]

I think point #2 is the bigger issue. We are pressed for time as far as reviews go, and I’m happy to try and get sparrow reviewed, but cannot promise time for sparrow.shiny.

You are welcome to submit though, but there is no guarantee that I will be assigned to the package for review.



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

> On Oct 5, 2021, at 9:53 AM, Steve Lianoglou <slianoglou using gmail.com> wrote:
> 
> You are having it ;) I’m the one assigned to your package.
> 
> Oh, sweet!
> 
> My last commit looks like it has resulted in a successful build across the board, so I guess the hard part begins now: sorry in advance for any headaches this particular review may cause ;-)
> 
> It would be great if I could add as an additional package to this review the "sibling" package {sparrow.shiny} of shiny modules and an app that enables users to interactively explore gsea results that are produced by {sparrow}.
> 
> My reservations are these -- assuming the main {sparrow} package you are now reviewing looks good for acceptance into bioc and release:
> 
> 1. Would any snafu's that arise in reviewing {sparrow.shiny} potentially hold back {sparrow}'s inclusion into the upcoming bioc release?
> 
> 2. We are now past the official deadline of new package submission, so don't want to try and take advantage of your time in this way.
> 
> Thanks again for your feedback and time,
> -steve
>  
> > 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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