[Bioc-devel] Request upstream pull --force of sanitized master branch

[Leonardo Collado Torres]

Thanks for fixing this Nitesh and Sam!

I wrote that R check and forgot that it depended on the Gencode url. I
had to fix this too for recount
https://github.com/leekgroup/recount/commit/056e81c326143e3748b452988ac15a6bed3b035e.

Best,
Leo


On Mon, Nov 5, 2018 at 3:14 PM Turaga, Nitesh
<Nitesh.Turaga using roswellpark.org> wrote:
>
> Hi Sam,
>
> I fixed the RELEASE_3_8 branch as well. There was a minor discrepancy in the commit history for RELEASE_3_8 though, (which I fixed in git.bioconductor.org/packages/bumphunter) so you should resync RELEASE_3_8 in rafalab/bumphunter.
>
> The commit history on rafalab/bumphunter:RELEASE_3_8 looks like this,
>
> 7437f04 Apply interval bugfix to sanitized master branch
> ****a58c60a bump x.y.z versions to odd y after creation of RELEASE_3_8 branch****
> 3d4f308 bump x.y.z versions to even y prior to creation of RELEASE_3_8 branch
>
> The commit showing "bump x.y.z versions to odd y after creation of RELEASE_3_8 branch”  should not be in the RELEASE_3_8 branch. The version number in the RELEASE_3_8 branch should have an “even” Y, in the X.Y.Z version numbering scheme.
>
> After fixing your RELEASE_3_8 branch now looks like this,
>
> 96fd715 Bump version after cherry-picking bug fix,
> ac34111 Apply interval bugfix to sanitized master branch
> 3d4f308 bump x.y.z versions to even y prior to creation of RELEASE_3_8 branch
>
> Please sync your RELEASE_3_8 branch on GitHub as well. “bumphunter" should now build on RELEASE_3_8 if the fix works.
>
> NOTE: After a push is made it can take up to 48 hours for it to
> appear on the build report and landing pages - i.e. we do one pull,
> build, check, propagate in 24 hours - so if your commit was after the pull
> for the day it wont be until the following day
>
>
> Best,
>
> Nitesh
>
>
> > On Nov 5, 2018, at 2:56 PM, Samuela Pollack <spollack using jimmy.harvard.edu> wrote:
> >
> > Hi Nitesh,
> >
> > I have fixed the commit history for rafalab/bumphunter RELEASE_3_8 branch, and request synchronization with Bioconductor RELEASE_3_8. We need this, because bumphunter is not building on RELEASE_3_8, due to an obsolete URL in one of the tests.
> >
> > thanks,
> >
> > - Sam
> >
> >
> > On 11/5/18 7:56 AM, Turaga, Nitesh wrote:
> >>         External Email - Use Caution
> >>
> >> Hi Sam,
> >>
> >> I have updated your “master” branch on git.bioconductor.com to reflect what you have on GitHub, at https://github.com/rafalab/bumphunter.  You will not get the duplicate commit error when you push to the master branch anymore.
> >>
> >> However, RELEASE_3_8 still has duplicate commits in the history. You could follow the same procedure as you did for the master branch, and de-duplicate the commit history for RELEASE_3_8. You should invest time in this only if you think there will be any changes made to the release branch. If not, then this is not an issue. If you do choose to follow through with RELEASE_3_8 as well, please reply to this thread when you have made the de-duplication changes and added the branch to your GitHub repository.
> >>
> >> Best regards,
> >>
> >> Nitesh
> >>
> >>> On Nov 2, 2018, at 5:09 PM, Samuela Pollack <spollack using jimmy.harvard.edu> wrote:
> >>>
> >>> Dear Bioconductor,
> >>>
> >>> I believe I have removed all duplicate commits from the bumphunter package. The main branch in rafalab/bumphunter incorporates the new commit history. It passes 'library(devtools); build("."); install(); check("."); BiocCheck(".")'
> >>>
> >>> I am contacting you in accordance with item 6 of the instructions at this URL: http://bioconductor.org/developers/how-to/git/resolve-duplicate-commits/
> >>>
> >>> - Sam
> >>>
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