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 http://eikke.com/importing-a-git-tree-into-a-subversion-repository/ 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 Bioconductor). The result is that, in contrast to the SVN trunk (version 1.1.3; https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/TVTB/DESCRIPTION) the Bioconductor-mirror of my package shows version 0.1.7 of my package, with largely pre-dates its addition to Bioconductor ( https://github.com/Bioconductor-mirror/TVTB/blob/master/DESCRIPTION). 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 http://bioconductor.org/developers/how-to/git-mirrors/ 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 messages: $git svn dcommit --add-author-from Committing to https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/TVTB ... M appveyor.yml ERROR from SVN: Item is out of date: Item '/trunk/madman/Rpacks/TVTB/appveyor.yml' is out of date W: 533e40cfd8c74fa1d525cf6b4a7fc1e016f07e09 and refs/remotes/git-svn-devel differ, using rebase: :040000 040000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 Bioconductor-mirror. 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 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! Kevin [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
