[Bioc-devel] Problem pushing new versions of xcms via git svn dcommit

Wed Jan 4 07:54:47 CET 2017

Hi Steffen and Laurent,

one problem with xcms is that the 'devel' branch on sneumann/xcms is the real 'master' branch. I would suggest to create a new branch on github, e.g. 'biocdevel' and to link that one to the BioC svn (means also that update_remotes.sh can not be user right away - the svn remote should be added manually). That way development can still be performed on sneumann/xcms devel branch and once stuff should be pushed to BioC devel could be merged into biocdevel and committed to svn using the git svn dcommit. I think that having the devel branch both for development via github and as the link to BioC svn is problematic.

One last thing: I experienced lots of out-of-sync problems in ensembldb, apparently because many individual commits were committed "too fast" to svn and thus the github-mirror went out-of-sync. For ensembldb I am now basically merging the commits from my master branch as a single commit to devel using "git merge --squash". I thus loose part of the history, but since github master contains the full history I'm fine with lacking it on BioC svn.

cheers, jo

On 3 Jan 2017, at 22:10, Laurent Gatto <lg390 at cam.ac.uk<mailto:lg390 at cam.ac.uk>> wrote:

Hi Steffen,

The usual

 Commit to git as normal, when you want to push your commits to svn
   1. `git checkout devel` to switch to the devel branch. (use release-X.X for
         release branches)
   2. `git svn rebase` to get the latest SVN changes.
   3. `git merge master --log` to merge your changes from the master branch
         or skip this step and work directly on the current branch.
   4. `git svn dcommit --add-author-from` to sync and commit
         your changes to svn.

worked out for me. Your latest commit #4b68af1d156b73 and #a03fba48f82b7
(updated NEWS file) have now been comitted to hedgehog.

I am not sure what is going on for you, but when I desperate with
git/git-svn, right before the nervous breakdown, I go for the 'have you
tried to turn it on and off again' solution, which generally works:

1) make sure you have comitted/pushed to Github and have a backup of any
  files/dir you gitignore
2) rm -rf mzR
3) git clone git at github.com<mailto:git at github.com>:sneumann/mzR.git
4) use update_remotes.sh

Let me know if there's anything I can help with.

Best wishes,

Laurent

On  2 January 2017 22:12, Steffen Neumann wrote:

Hi all,and a happy new year!

I am experiencing a lot of frustration getting changes from github
pushed to BioC svn, and that includes some fixes for build issues
in packages depending on xcms. I have tried several options:

1) git svn checkout, git remote add, git merge and git svn dcommit.
2) git clone github repo, update_remotes.shand git svn rebase

both of which seem to fail due to the same reason,
which seems to be somewhere around

https://github.com/sneumann/xcms/commit/f9be4f4f23c49f56074670658bc9665e093c8f83
Author: Steffen Neumann <sneumann at ipb-halle.de>
Date:Fri Apr 1 14:09:29 2016 +0200
Add automatic repair for "m/z sort assumption violated !" error in findPeaks (centWave)

I fail to fix these issues, and I am pretty frustrated
since I fell into the git-svn tarpit not for the first time,
it seems to be not fool-proof :-(

Below are the details, hoping for help.

Yours,
Steffen

1) git svn checkout, git remote add, git merge and git svn dcommit.

So, I have a fresh

sneumann at acryl /vol/R/BioC/devel/xcms3 $ git svn checkout https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/xcms

Then I add the github remote:

sneumann at acryl /vol/R/BioC/devel/xcms3/xcms (master) $ git remote add origin git at github.com:sneumann/xcms.git
sneumann at acryl /vol/R/BioC/devel/xcms3/xcms (master) $ git fetch --tags
remote: Counting objects: 1475, done.
[...]
>From github.com:sneumann/xcms
* [new branch]devel-> origin/devel
* [new branch]master-> origin/master
* [new branch]xcms3-> origin/xcms3

The devel branch is what I use to be in sync with BioC-SVN:

sneumann at acryl /vol/R/BioC/devel/xcms3/xcms (master) $ git checkout devel
Branch devel set up to track remote branch devel from origin.
Switched to a new branch 'devel'

sneumann at acryl /vol/R/BioC/devel/xcms3/xcms (devel) $ git merge origin/xcms3
Updating a4421c3..a112206
Fast-forward
DESCRIPTION|6 +-
NAMESPACE|48 ++-
R/AllGenerics.R|38 +-
[...]
vignettes/new_functionality.org|88 ++++-
41 files changed, 4890 insertions(+), 2250 deletions(-)

sneumann at acryl /vol/R/BioC/devel/xcms3/xcms (devel) $ git svn dcommit
Committing to https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/xcms ...
D R/00Generics.R

ERROR from SVN:
Filesystem has no item: '/bioconductor/!svn/txr/125556-1/trunk/madman/Rpacks/xcms/R/00Generics.R' path not found
W: a1122065a96cf6e69088417d82fe987cda188cd5 and refs/remotes/git-svn differ, using rebase:
:100644 100644 d36b142908ab4507e95d495d3ec450008a210e8f a3f97d8f779d878b86a73d534415e679415e90f3 M DESCRIPTION
:100755 100755 a58677bbe186fea1447948c7286bc47d04735efc fe69bdd2e969a906fac87d4bddd64bd90258f0cd M NAMESPACE
:040000 040000 2f5317b4c96f1d267b43ef8deba1532df6cb56db c760aa2196632e99c0e0e59ed9700b27cb001fa3 M R
:040000 040000 45a9a220d96c3cdabe03cd8792dfc9628f058dab e89e65a3eb7db9d6590c12b8fb94306811557789 M inst
:040000 040000 8284909b39e4d90eb957aadc26f92a8df9907cb2 125b7635684f73f65185aea52a7564c11bf187c5 M man
:040000 040000 da9a1c166e3df0c13cd3ea61e44356039b649cd2 dbee4fedf371d6570b91cc7f50fe930294eac1f2 M vignettes
First, rewinding head to replay your work on top of it...
Applying: Add automatic repair for "m/z sort assumption violated !" error in findPeaks (centWave)
Using index info to reconstruct a base tree...
A R/xcmsRaw.R
.git/rebase-apply/patch:37: trailing whitespace.
scan <- getScan(object, scan=i)
.git/rebase-apply/patch:82: trailing whitespace.
xr at env$mz[1:length(o)] <- scan[o, "mz"]
.git/rebase-apply/patch:83: trailing whitespace.
xr at env$intensity[1:length(o)] <- scan[o, "intensity"]
.git/rebase-apply/patch:88: trailing whitespace.

.git/rebase-apply/patch:90: new blank line at EOF.
+
warning: 5 lines add whitespace errors.
Falling back to patching base and 3-way merge...
Auto-merging inst/unitTests/runit.findPeaksCentWave.R
CONFLICT (add/add): Merge conflict in inst/unitTests/runit.findPeaksCentWave.R
CONFLICT (modify/delete): R/xcmsRaw.R deleted in 4c6815a9b4f985658f19824dde21748e49b5dad0 and modified in Add automatic repair for "m/z sort assumption violated !" error in findPeaks (centWave). Version Add automatic repair for "m/z sort assumption violated !" error in findPeaks (centWave) of R/xcmsRaw.R left in tree.
error: Failed to merge in the changes.
Patch failed at 0001 Add automatic repair for "m/z sort assumption violated !" error in findPeaks (centWave)
The copy of the patch that failed is found in: .git/rebase-apply/patch

When you have resolved this problem, run "git rebase --continue".
If you prefer to skip this patch, run "git rebase --skip" instead.
To check out the original branch and stop rebasing, run "git rebase --abort".

rebase refs/remotes/git-svn: command returned error: 128

-----------------------------------------------------------------------------

2) git clone github repo, update_remotes.shand git svn rebase

sneumann at acryl /vol/R/BioC/devel/xcms3 $ git clone git at github.com:sneumann/xcms.git
Cloning into 'xcms'...
remote: Counting objects: 6343, done.
remote: Compressing objects: 100% (188/188), done.
remote: Total 6343 (delta 124), reused 0 (delta 0), pack-reused 6155
Receiving objects: 100% (6343/6343), 3.74 MiB | 1.39 MiB/s, done.
Resolving deltas: 100% (4806/4806), done.
Checking connectivity... done.

sneumann at acryl /vol/R/BioC/devel/xcms3 $ cd xcms
sneumann at acryl /vol/R/BioC/devel/xcms3/xcms (devel) $ ../update_remotes.sh
Enter passphrase for key '/home/sneumann/.ssh/id_rsa':
devel already exists, create a custom branch to track bioc/master with
`git branch --track NEW_NAME bioc/master`
Commit to git as normal, when you want to push your commits to svn
1. `git checkout devel` to switch to the devel branch. (use release-X.X for
release branches)
2. `git svn rebase` to get the latest SVN changes.
3. `git merge master --log` to merge your changes from the master branch
or skip this step and work directly on the current branch.
4. `git svn dcommit --add-author-from` to sync and commit
your changes to svn.

sneumann at acryl /vol/R/BioC/devel/xcms3/xcms (devel) $ git branch --track biocmaster bioc/master
Branch biocmaster set up to track remote branch master from bioc.

sneumann at acryl /vol/R/BioC/devel/xcms3/xcms (devel) $ git svn rebase
Migrating from a git-svn v1 layout...
Data from a previous version of git-svn exists, but
.git/svn
(required for this version (2.7.4) of git-svn) does not exist.
Done migrating from a git-svn v1 layout
Rebuilding .git/svn/refs/remotes/git-svn-devel/.rev_map.bc3139a8-67e5-0310-9ffc-ced21a209358 ...
r11695 = 612044c47521e079cf31425550729010d9654abc
[...]
r125419 = 4c6815a9b4f985658f19824dde21748e49b5dad0
Done rebuilding .git/svn/refs/remotes/git-svn-devel/.rev_map.bc3139a8-67e5-0310-9ffc-ced21a209358

First, rewinding head to replay your work on top of it...
Applying: Add automatic repair for "m/z sort assumption violated !" error in findPeaks (centWave)
Using index info to reconstruct a base tree...
A R/xcmsRaw.R
.git/rebase-apply/patch:37: trailing whitespace.
scan <- getScan(object, scan=i)
.git/rebase-apply/patch:82: trailing whitespace.
xr at env$mz[1:length(o)] <- scan[o, "mz"]
.git/rebase-apply/patch:83: trailing whitespace.
xr at env$intensity[1:length(o)] <- scan[o, "intensity"]
.git/rebase-apply/patch:88: trailing whitespace.

.git/rebase-apply/patch:90: new blank line at EOF.
+
warning: 5 lines add whitespace errors.
Falling back to patching base and 3-way merge...
Auto-merging inst/unitTests/runit.findPeaksCentWave.R
CONFLICT (add/add): Merge conflict in inst/unitTests/runit.findPeaksCentWave.R
CONFLICT (modify/delete): R/xcmsRaw.R deleted in 4c6815a9b4f985658f19824dde21748e49b5dad0 and modified in Add automatic repair for "m/z sort assumption violated !" error in findPeaks (centWave). Version Add automatic repair for "m/z sort assumption violated !" error in findPeaks (centWave) of R/xcmsRaw.R left in tree.
error: Failed to merge in the changes.
Patch failed at 0001 Add automatic repair for "m/z sort assumption violated !" error in findPeaks (centWave)
The copy of the patch that failed is found in: .git/rebase-apply/patch

When you have resolved this problem, run "git rebase --continue".
If you prefer to skip this patch, run "git rebase --skip" instead.
To check out the original branch and stop rebasing, run "git rebase --abort".

rebase refs/remotes/git-svn-devel: command returned error: 128

--
Laurent Gatto | @lgatt0
http://cpu.sysbiol.cam.ac.uk/
http://lgatto.github.io/

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