[Bioc-devel] Problem with git-mirror

Kevin RUE kevinrue67 at gmail.com
Fri Nov 4 17:01:02 CET 2016

Dear all,

Apologies for the confusing email below, but I'm not sure anymore which
information can save the day. I'll provide all the information necessary to
fix the situation!

I think I've turned my GitHub/svn/GitHub-mirror repositories into a huge
plate of spaghetti after encountering successively pretty much all the
issues listed out at http://bioconductor.org/developers/how-to/git-mirrors/

After two successful commits and pushes on the devel and release branch of
my package, the situation started with the error message "Unable to
determine upstream SVN information from HEAD history." when running "git
svn dcommit", as described at

Following the instructions on that page, I somehow managed to push my
latest code onto the Bioconductor SVN (TVTB verson 1.1.3) before all hell
broke lose.

I must have done something wrong with either a rebase or a merge step
because it also seems that it reapplied pretty much every commit since the
creation of my own GitHub repository (with predates acceptance to
The result is that, in contrast to the SVN trunk (version 1.1.3;
the Bioconductor-mirror of my package shows version 0.1.7 of my package,
with largely pre-dates its addition to Bioconductor (

After failing to fix the situation, I tried starting fresh (losing the
commit history prior addition to Bioconductor) by renaming my original
GitHub repository to "TVTB-original" (
https://github.com/kevinrue/TVTB-original) and creating a fresh fork from
the Bioconductor-mirror, so that I would fall back into the "*Scenario 2:
Set Up Your Own GitHub Repository*" described at

But now, following to the letter the process to push to SVN, it fails at
the "git svn dcommit --add-author-from" step with errors and CONFLICT

$git svn dcommit --add-author-from
Committing to
https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/TVTB ...
    M    appveyor.yml
Item is out of date: Item '/trunk/madman/Rpacks/TVTB/appveyor.yml' is out
of date
W: 533e40cfd8c74fa1d525cf6b4a7fc1e016f07e09 and refs/remotes/git-svn-devel
differ, using rebase:
:040000 040000 e1ff243efb925d24ba3823445035f91714c8d718
36e542cde3260307a1378870ff42c3975cd99a4e M    inst
First, rewinding head to replay your work on top of it...
Applying: Applied all changes more recent than the Bioconductor-mirror.
Using index info to reconstruct a base tree...
M    .Rbuildignore
M    .gitignore


.git/rebase-apply/patch:4788: trailing whitespace.
| Platforms |  OS  | R CMD check | Coverage |
.git/rebase-apply/patch:4807: trailing whitespace.
The value of this information is truly revealed when
.git/rebase-apply/patch:20559: trailing whitespace.
    + affecting the genomic ranges to import from the VCF file
.git/rebase-apply/patch:20574: trailing whitespace.
To reduce the burden of repetition during programming, and to
.git/rebase-apply/patch:20696: trailing whitespace.
(both extending the virtual class `VCF`) of the
warning: squelched 32 whitespace errors
warning: 37 lines add whitespace errors.
Falling back to patching base and 3-way merge...
Auto-merging man/TVTBParam-class.Rd
CONFLICT (add/add): Merge conflict in man/TVTBParam-class.Rd
Auto-merging man/Genotypes-class.Rd
CONFLICT (add/add): Merge conflict in man/Genotypes-class.Rd
CONFLICT (rename/delete): inst/misc/subset_moderate_samples.R deleted in
Applied all changes more recent than the Bioconductor-mirror. and renamed
in 6be1d3b971a54854350105f00f09b794d108ae6d. Version
6be1d3b971a54854350105f00f09b794d108ae6d of
inst/misc/subset_moderate_samples.R left in tree.
Auto-merging appveyor.yml
CONFLICT (add/add): Merge conflict in appveyor.yml
Auto-merging DESCRIPTION
CONFLICT (content): Merge conflict in DESCRIPTION
error: Failed to merge in the changes.
Patch failed at 0001 Applied all changes more recent than the
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

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

I'm really lost how to restore a sane state and re-synchronise my code on
all of (my GitHub), (Bioconductor SVN trunk), (Bioconductor-mirror).

Thanks in advance for advice!

	[[alternative HTML version deleted]]

More information about the Bioc-devel mailing list