[Bioc-devel] Bioconductor git-svn bridge is available
Ilari Scheinin
ilari.scheinin at gmail.com
Fri May 23 21:24:23 CEST 2014
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.
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
>>>>>
>>>>
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>>>>
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>>>
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>>
>>
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