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

Dan Tenenbaum dtenenba at fhcrc.org
Thu May 22 03:59:09 CEST 2014 


----- Original Message -----
> From: "Kasper Daniel Hansen" <kasperdanielhansen at gmail.com>
> To: "Dan Tenenbaum" <dtenenba at fhcrc.org>
> Cc: bioc-devel at r-project.org, "Sean Davis" <sdavis2 at mail.nih.gov>, "Hector Corrada Bravo" <hcorrada at gmail.com>
> Sent: Wednesday, May 21, 2014 6:15:50 PM
> Subject: Re: [Bioc-devel] Bioconductor git-svn bridge is available
> 
> 
> All it says is
> 
> "An error occurred creating the git-svn bridge."
> 
> 
> Safari 7.0.3 on OS X Mavericks
> 
> 
> 
> 
> I know nothing about debugging html / javascript stuff, but there is
> nothing reported in the "error console" in Safari.
> 
> 
> This is for re-creating a bridge that used to exist: minfi.
> 
> 

The issue has been fixed and your bridge has been created. Thanks for the report.
Dan


> Best,
> Kasper
> 
> 
> 
> On Wed, May 21, 2014 at 9:08 PM, Dan Tenenbaum < dtenenba at fhcrc.org >
> wrote:
> 
> 
> 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
> > > > > 
> > > > > 
> > > > > 
> > > > > 
> > > > > --
> > > > > The Wellcome Trust Sanger Institute is operated by Genome
> > > > > Research
> > > > > Limited, a charity registered in England with number 1021457
> > > > > and a
> > > > > company registered in England with number 2742969, whose
> > > > > registered
> > > > > office is 215 Euston Road, London, NW1 2BE.
> > > > > 
> > > > > _______________________________________________
> > > > > Bioc-devel at r-project.org mailing list
> > > > > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> > > > 
> > > > _______________________________________________
> > > > Bioc-devel at r-project.org mailing list
> > > > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> > > > 
> > > 
> > > _______________________________________________
> > > 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
> > 
> > 
> 
>

More information about the Bioc-devel mailing list