[Bioc-devel] Bioconductor git-svn bridge is available
Dan Tenenbaum
dtenenba at fhcrc.org
Fri May 23 21:41:11 CEST 2014
Hi Ilari,
----- Original Message -----
> From: "Ilari Scheinin" <ilari.scheinin at gmail.com>
> To: bioc-devel at r-project.org
> Sent: Friday, May 23, 2014 12:24:23 PM
> Subject: Re: [Bioc-devel] Bioconductor git-svn bridge is available
>
> I’m also having issues with my bridges. It seems that they always
> “die" after the initial sync (which for me is always a Git win).
> After awhile when I commit again to GitHub, nothing happens on the
> SVN, and I end up deleting the bridges and re-creating them. This
> always does the trick, but when I commit the next time, it’s the
> same thing again.
>
> I thought the problem was maybe with the webhook, so I went to double
> check it. I noticed that GitHub has probably updated these settings,
> since in the bridge documentation it says:
>
> > Leave "Payload version" alone (it should be
> > "application/vnd.github-v3+form")
>
> But it looks like nowadays the setting is called “Content type” and
> options are “application/json” and
> “application/x-www-form-urlencoded” (which I have selected).
>
> Otherwise everything looks to be ok (“Just the push event”, “Active”,
> and the new option “Secret” is empty), and under “Recent Deliveries”
> I do see that the hook has indeed been triggered by my commits. So,
> I guess there must be something wrong with the bridge itself. Both
> my repositories (QDNAseq and QDNAseq-release) are organization ones,
> if that makes a difference. I don’t really know what else I could do
> to debug this. Maybe there could be some kind of logging that was
> visible to the bridge owners.
>
I apologize for the problems. Github keeps changing the format of the push hooks they send, and they don't seem to document these in a consistent way. However, I've made my code more robust in that it recognizes the variations that I have seen so far.
So, if you go to the settings page for your repos (the page you were on before) and go down to "Recent deliveries", and expand (click on "...") the deliveries corresponding to your recent git commits, then click "Redeliver", this will send the message to the bridge that there is a new commit, and this time the bridge should handle it properly.
I'll update the documentation with the changed verbiage on that page.
Thanks,
Dan
> Ilari
>
>
> On 22.5.2014, at 3.59, Dan Tenenbaum <dtenenba at fhcrc.org> wrote:
>
> >
> >
> > ----- 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]]
> >>>
> >>> _______________________________________________
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> >>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >>>
> >>>
> >>
> >>
> >
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