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

From: "Moritz Gerstung" <mg14 at sanger.ac.uk>
To: "Kasper Daniel Hansen" <kasperdanielhansen at gmail.com>
Cc: "Dan Tenenbaum" <dtenenba at fhcrc.org>, bioc-devel at r-project.org, "Sean Davis" <sdavis2 at mail.nih.gov>
Sent: Monday, May 12, 2014 1:32:38 AM
Subject: Re: [Bioc-devel] Bioconductor git-svn bridge is available

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.

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]]

	[[alternative HTML version deleted]]

--
 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.

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.

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]]

      [[alternative HTML version deleted]]

--
 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.

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.

/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]]

      [[alternative HTML version deleted]]

--
 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.

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.

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]]

[[alternative HTML version deleted]]

--
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.

[[alternative HTML version deleted]]

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.

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]]

[[alternative HTML version deleted]]

--
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.

[[alternative HTML version deleted]]

Leave "Payload version" alone (it should be "application/vnd.github-v3+form")

----- 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]]

[[alternative HTML version deleted]]

--
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.

[[alternative HTML version deleted]]

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.

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]]

[[alternative HTML version deleted]]

--
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.

[[alternative HTML version deleted]]