Troubleshooting Bioconductor GitHub mirror setup

bioc-mirror-troubleshoot.md

# (1) Using existing repo
git clone git@github.com:PeteHaitch/GenomicTuples.git
cd GenomicTuples
curl -O https://raw.githubusercontent.com/Bioconductor/mirror/master/update_remotes.sh
bash update_remotes.sh
# Bump Version and Date in DESCRIPTION (v1.5.2)
# NOTE: Version isn't up-to-date with SVN; why?
git add DESCRIPTION
git commit -m "Bump version number"
git push
git checkout devel
git svn rebase
# So far, so good. But now comes a horrendous pile of merge conflicts.
git merge master --log
# Auto-merging DESCRIPTION
# CONFLICT (content): Merge conflict in DESCRIPTION
# Automatic merge failed; fix conflicts and then commit the result.
# Resolved conflict using v1.5.2
Committing to https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GenomicTuples ...

ERROR from SVN:
URL access forbidden for unknown reason: Access to '/bioconductor/!svn/me' forbidden
W: 19dd1bf054944b290c5e85e271dd0a88122dd8a5 and refs/remotes/git-svn-devel differ, using rebase:
:100644 100644 1a46140ad99aa9c4d53786a2ed96b4465bd3a888 a5d33afd7fd2508a7a83ccc315f34a702cdaabac M	DESCRIPTION
First, rewinding head to replay your work on top of it...
Applying: Initial commit.
Using index info to reconstruct a base tree...
<stdin>:170: trailing whitespace.
#' 
<stdin>:172: trailing whitespace.
#' 
<stdin>:174: trailing whitespace.
#' 
<stdin>:185: trailing whitespace.
#' Compute the IPD of genomic tuples stored in a \code{\link{GTuples}} or 
<stdin>:187: trailing whitespace.
#' 
warning: squelched 629 whitespace errors
warning: 634 lines add whitespace errors.
Falling back to patching base and 3-way merge...
Auto-merging src/compareGTuples.cpp
CONFLICT (add/add): Merge conflict in src/compareGTuples.cpp
Auto-merging src/allTuplesSorted.cpp
CONFLICT (add/add): Merge conflict in src/allTuplesSorted.cpp
Auto-merging src/RcppExports.cpp
CONFLICT (add/add): Merge conflict in src/RcppExports.cpp
Auto-merging src/IPD.cpp
CONFLICT (add/add): Merge conflict in src/IPD.cpp
Auto-merging man/intra-tuple-methods.Rd
CONFLICT (add/add): Merge conflict in man/intra-tuple-methods.Rd
Auto-merging man/findOverlaps-methods.Rd
CONFLICT (add/add): Merge conflict in man/findOverlaps-methods.Rd
Auto-merging man/GenomicTuples-package.Rd
CONFLICT (add/add): Merge conflict in man/GenomicTuples-package.Rd
Auto-merging man/GTuplesList-class.Rd
CONFLICT (add/add): Merge conflict in man/GTuplesList-class.Rd
Auto-merging man/GTuples-comparison.Rd
CONFLICT (add/add): Merge conflict in man/GTuples-comparison.Rd
Auto-merging man/GTuples-class.Rd
CONFLICT (add/add): Merge conflict in man/GTuples-class.Rd
Auto-merging TODO.Rmd
CONFLICT (add/add): Merge conflict in TODO.Rmd
Auto-merging R/nearest-methods.R
CONFLICT (add/add): Merge conflict in R/nearest-methods.R
Auto-merging R/mapCoords-methods.R
CONFLICT (add/add): Merge conflict in R/mapCoords-methods.R
Auto-merging R/intra-tuple-methods.R
CONFLICT (add/add): Merge conflict in R/intra-tuple-methods.R
Auto-merging R/inter-tuple-methods.R
CONFLICT (add/add): Merge conflict in R/inter-tuple-methods.R
Auto-merging R/findOverlaps-methods.R
CONFLICT (add/add): Merge conflict in R/findOverlaps-methods.R
Auto-merging R/coverage-methods.R
CONFLICT (add/add): Merge conflict in R/coverage-methods.R
Auto-merging R/RcppExports.R
CONFLICT (add/add): Merge conflict in R/RcppExports.R
Auto-merging R/GenomicTuples.R
CONFLICT (add/add): Merge conflict in R/GenomicTuples.R
Auto-merging R/GTuplesList-class.R
CONFLICT (add/add): Merge conflict in R/GTuplesList-class.R
Auto-merging R/GTuples-comparison.R
CONFLICT (add/add): Merge conflict in R/GTuples-comparison.R
Auto-merging R/GTuples-class.R
CONFLICT (add/add): Merge conflict in R/GTuples-class.R
Auto-merging R/AllUtilities.R
CONFLICT (add/add): Merge conflict in R/AllUtilities.R
Auto-merging R/AllGenerics.R
CONFLICT (add/add): Merge conflict in R/AllGenerics.R
Auto-merging NAMESPACE
CONFLICT (add/add): Merge conflict in NAMESPACE
Auto-merging DESCRIPTION
CONFLICT (add/add): Merge conflict in DESCRIPTION
Auto-merging .gitignore
CONFLICT (add/add): Merge conflict in .gitignore
Auto-merging .Rbuildignore
CONFLICT (add/add): Merge conflict in .Rbuildignore
Failed to merge in the changes.
Patch failed at 0001 Initial commit.
The copy of the patch that failed is found in:
   /Users/hickey/Desktop/GenomicTuples/.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: 1

# (2) Using a fork of the repo hosted on bioconductor-mirror
git clone git@github.com:PeteHaitch/GenomicTuples-1.git
cd GenomicTuples-1
curl -O https://raw.githubusercontent.com/Bioconductor/mirror/master/update_remotes.sh
bash update_remotes.sh
# Bump Version and Date in DESCRIPTION (v1.5.2)
git add DESCRIPTION
git commit -m "Bump version number"
git push
git checkout devel 
# error: pathspec 'devel' did not match any file(s) known to git.