[Bioc-devel] Bioconductor git-svn bridge is available

Dan Tenenbaum dtenenba at fhcrc.org
Thu May 22 03:08:11 CEST 2014 

Hi Kasper,

----- Original Message -----
> From: "Kasper Daniel Hansen" <kasperdanielhansen at gmail.com>
> To: "Hector Corrada Bravo" <hcorrada at gmail.com>
> Cc: "Dan Tenenbaum" <dtenenba at fhcrc.org>, bioc-devel at r-project.org, "Sean Davis" <sdavis2 at mail.nih.gov>
> Sent: Wednesday, May 21, 2014 4:50:59 PM
> Subject: Re: [Bioc-devel] Bioconductor git-svn bridge is available
> 
> 
> I am trying to re-create my git-svn bridges, but the website throws
> an error when I do it. Not sure why. I am trying to let svn win.
> 

What is the error?

Also, what is your OS (+ version + distro) and browser ( + version)? I have a report that there are are problems creating bridges on Linux using firefox and chrome but that it worked for this user with firefox on windows (and for me on Mac with several browsers). I'll do some testing.


If there is a javascript console available, can you see if there is an error there? If not, no worries, just let me know what config you're using.

Dan



> 
> Best,
> Kasper
> 
> 
> 
> On Mon, May 12, 2014 at 1:41 PM, Hector Corrada Bravo <
> hcorrada at gmail.com > wrote:
> 
> 
> Another use case where this is useful is that newer packages may
> still need
> to use the 'devel' BioC branch as something of a 'release' branch
> since a
> natural release cycle is faster than the BioC cycle (I think of the
> BioC
> devel branch that way for some packages).
> 
> This way the master branch on git can be the 'no guarantees' branch,
> and
> another branch on git is synchronized with the devel branch on svn.
> 
> 
> 
> 
> On Mon, May 12, 2014 at 1:26 PM, Dan Tenenbaum < dtenenba at fhcrc.org >
> wrote:
> 
> > 
> > 
> > ----- Original Message -----
> > > From: "Henrik Bengtsson" < hb at biostat.ucsf.edu >
> > > To: "Moritz Gerstung" < mg14 at sanger.ac.uk >
> > > Cc: bioc-devel at r-project.org , "Sean Davis" <
> > > sdavis2 at mail.nih.gov >
> > > Sent: Monday, May 12, 2014 10:19:15 AM
> > > Subject: Re: [Bioc-devel] Bioconductor git-svn bridge is
> > > available
> > > 
> > > On Mon, May 12, 2014 at 1:32 AM, Moritz Gerstung <
> > > mg14 at sanger.ac.uk >
> > > wrote:
> > > > Hi all
> > > > 
> > > > Following Kasper's idea from a couple of months ago: Would it
> > > > be
> > > > possible to have the git-svn bridge synchronise a branch other
> > > > than master?
> > > > 
> > > > If so, one could use the git subtree command,
> > > > 
> > > > git subtree split -P minfi -b biocsvn
> > > > 
> > > > to create a branch 'biocsvn' only containing minfi directory
> > > > [package]. This branch would then be synchronised over the
> > > > git-svn
> > > > bridge. Changes in the biocsvn branch can be merged back into
> > > > the
> > > > master branch and the correct directory with
> > > > 
> > > > git subtree merge -P minfi biocsvn
> > > > 
> > > > I would also fancy a directory structure as Kasper suggested,
> > > > where
> > > > the actual R package is a subdirectory. This would allow for
> > > > placing extra files such as README.md or Makefile into the root
> > > > directory and other project related data which shouldn't go
> > > > into
> > > > the package, but may be useful, in other directories. As a side
> > > > effect one can also screw up the git master branch without
> > > > breaking the devel repository.
> > > 
> > > Just a FYI: Using .Rbuildignore you can still add Makefile and
> > > other
> > > files to the repository that won't go into the package
> > > build/install/check/distro/.... This works regardless of
> > > Subversion
> > > of Git.
> > > 
> > 
> > 
> > Right. But if you wanted to structure your repo like this:
> > 
> > - README
> > - package/
> > DESCRIPTION
> > etc
> > - otherstuff/
> > 
> > where the actual R package is in the 'package' directory, then
> > .Rbuildignore would not help.
> > 
> > This (I think) is what the original request was about.
> > 
> > Dan
> > 
> > 
> > 
> > > /Henrik
> > > 
> > > 
> > > > 
> > > > I'm not a git guru, so maybe I'm missing something here, but it
> > > > seems feasible.
> > > > 
> > > > Cheers,
> > > > 
> > > > Moritz
> > > > 
> > > > PS. Resent as it bounced from list before.
> > > > 
> > > > 
> > > > On 21 Feb 2014, at 17:00, Kasper Daniel Hansen
> > > > < kasperdanielhansen at gmail.com > wrote:
> > > > 
> > > >> Thanks everyone, it was worth a question.
> > > >> 
> > > >> Perhaps I will figure out how to use submodules.
> > > >> 
> > > >> Kasper
> > > >> 
> > > >> 
> > > >> On Fri, Feb 21, 2014 at 11:45 AM, Dan Tenenbaum
> > > >> < dtenenba at fhcrc.org > wrote:
> > > >> 
> > > >>> 
> > > >>> 
> > > >>> ----- Original Message -----
> > > >>>> From: "Sean Davis" < sdavis2 at mail.nih.gov >
> > > >>>> To: "Kasper Daniel Hansen" < kasperdanielhansen at gmail.com >
> > > >>>> Cc: bioc-devel at r-project.org , "Dan Tenenbaum"
> > > >>>> < dtenenba at fhcrc.org >
> > > >>>> Sent: Friday, February 21, 2014 7:08:21 AM
> > > >>>> Subject: Re: [Bioc-devel] Fwd: Bioconductor git-svn bridge
> > > >>>> is
> > > >>>> available
> > > >>>> 
> > > >>>> 
> > > >>>> 
> > > >>>> I doubt this is possible given the atomic nature of a git
> > > >>>> repository.
> > > >>>> You might look at using a second git repository and
> > > >>>> including
> > > >>>> the
> > > >>>> minfi package as a git submodule of that second repository.
> > > >>>> Then,
> > > >>>> you can keep things in sync, but the minfi repository
> > > >>>> remains
> > > >>>> atomic.
> > > >>>> 
> > > >>> 
> > > >>> I think Sean is correct.
> > > >>> Dan
> > > >>> 
> > > >>> 
> > > >>>> Sean
> > > >>>> On Feb 21, 2014 9:44 AM, "Kasper Daniel Hansen" <
> > > >>>> kasperdanielhansen at gmail.com > wrote:
> > > >>>> 
> > > >>>> 
> > > >>>> Question: is it possible to synchronize a subset of a github
> > > >>>> repos?
> > > >>>> For
> > > >>>> minfi, I would like my github to be
> > > >>>> 
> > > >>>> minfi-devel
> > > >>>> /minfi
> > > >>>> OTHER SCRIPTS
> > > >>>> 
> > > >>>> where OTHER SCRIPTS could be notes or test scripts I use for
> > > >>>> internal
> > > >>>> development. I then only want to synchronize the
> > > >>>> minfi-devel/minfi
> > > >>>> directory with Bioc.
> > > >>>> 
> > > >>>> Kasper
> > > >>>> 
> > > >>>> 
> > > >>>> On Sun, Feb 9, 2014 at 9:55 AM, Kasper Daniel Hansen <
> > > >>>> kasperdanielhansen at gmail.com > wrote:
> > > >>>> 
> > > >>>>> Seems to work for me; I have now populated my github repo.
> > > >>>>> 
> > > >>>>> Thanks for the help,
> > > >>>>> Kasper
> > > >>>>> 
> > > >>>>> 
> > > >>>>> On Sun, Feb 9, 2014 at 2:35 AM, Dan Tenenbaum <
> > > >>>>> dtenenba at fhcrc.org
> > > >>>>>> wrote:
> > > >>>>> 
> > > >>>>>> This should be fixed now.
> > > >>>>>> Thanks.
> > > >>>>>> Dan
> > > >>>>>> 
> > > >>>>>> 
> > > >>>>>> ----- Original Message -----
> > > >>>>>>> From: "Kasper Daniel Hansen" <
> > > >>>>>>> kasperdanielhansen at gmail.com >
> > > >>>>>>> To: "Dan Tenenbaum" < dtenenba at fhcrc.org >
> > > >>>>>>> Cc: bioc-devel at r-project.org
> > > >>>>>>> Sent: Saturday, February 8, 2014 7:07:44 PM
> > > >>>>>>> Subject: Re: [Bioc-devel] Fwd: Bioconductor git-svn
> > > >>>>>>> bridge is
> > > >>>>>>> available
> > > >>>>>>> 
> > > >>>>>>> 
> > > >>>>>>> 
> > > >>>>>>> Yes, see screenshot
> > > >>>>>>> 
> > > >>>>>>> 
> > > >>>>>>> (I do know I have a whitespace in front of the github url
> > > >>>>>>> and
> > > >>>>>>> I
> > > >>>>>>> get a
> > > >>>>>>> note and I fixed it.
> > > >>>>>>> 
> > > >>>>>>> 
> > > >>>>>>> Kasper
> > > >>>>>>> 
> > > >>>>>>> 
> > > >>>>>>> On Sat, Feb 8, 2014 at 9:56 PM, Dan Tenenbaum <
> > > >>>>>>> dtenenba at fhcrc.org >
> > > >>>>>>> wrote:
> > > >>>>>>> 
> > > >>>>>>> 
> > > >>>>>>> 
> > > >>>>>>> https://github.com/kasperdanielhansen/minfi
> > > >>>>>>> 
> > > >>>>>>> 
> > > >>>>>> 
> > > >>>>> 
> > > >>>>> 
> > > >>>> 
> > > >>>> [[alternative HTML version deleted]]
> > > >>>> 
> > > >>>> _______________________________________________
> > > >>>> Bioc-devel at r-project.org mailing list
> > > >>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> > > >>>> 
> > > >>> 
> > > >> 
> > > >> [[alternative HTML version deleted]]
> > > >> 
> > > >> _______________________________________________
> > > >> Bioc-devel at r-project.org mailing list
> > > >> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> > > > 
> > > > 
> > > > 
> > > > 
> > > > --
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> > > > and a
> > > > company registered in England with number 2742969, whose
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> > > > 
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> > 
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