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

Mon Jan 2 23:12:41 CET 2017

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.sh and 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.sh and 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

-- 
IPB Halle                    AG Massenspektrometrie & Bioinformatik
Dr. Steffen Neumann          http://www.IPB-Halle.DE
Weinberg 3                   Tel. +49 (0) 345 5582 - 1470
06120 Halle                       +49 (0) 345 5582 - 0           
sneumann(at)IPB-Halle.DE     Fax. +49 (0) 345 5582 - 1409