Please describe the problem.
Not able to successfully git-annex sync with a remote due to a git fatal. Caused by masters diverging?
What steps will reproduce the problem?
git-annex sync, or, letting the assistant try.
What version of git-annex are you using? On what operating system?
git-annex version: 5.20131221+b1 on my laptop git-annex version: 5.20131224-g6ca5271 on the remote server
Please provide any additional information below.
Output of a manual git-annex sync in the directory:
greg@x200s:~/Documents$ git-annex sync commit (Recording state in git...) Copyright Office/Orphan Works/ARROW/170409_ARROW_Leaflet.pdf: unmerged (783afced6bc43138373fda43edfda0c33be36525) Copyright Office/Orphan Works/ARROW/ARROWproject_results1.pdf: unmerged (b536e5f3d93e7905e05510f26db1f743e9eae16e) Copyright Office/Orphan Works/ARROW/ARROWproject_results1.ppt: unmerged (5543049b8940cc5702d37aff18b03c67d9c8374d) Copyright Office/Orphan Works/ARROW/ARROWstandardPresent2010.pdf: unmerged (54d751bc98cb5da29d3d568856b74675e842072e) Copyright Office/Orphan Works/ARROW/ARROWstandardPresent2010.ppt: unmerged (efe0e94b51eccb9a6a0c352f4a210bd5a6105050) Copyright Office/Orphan Works/ARROW/ARROWtrifoldMAR2011.pdf: unmerged (b52ff16178e29261fe00a518c23610a3b0826482) Copyright Office/Orphan Works/Documentation/20110531/Documentation.doc.odt: unmerged (1348d5f42f7e34706407f7936f4fb0438e4b8ffa) Copyright Office/Orphan Works/Documentation/AAPpublishers.pdf: unmerged (3f448a03d31a38adb095e3031e4ee13771d22d70) Copyright Office/Orphan Works/Documentation/Documentation.doc: unmerged (265fdff7787f560e3ba20789a12e15ffb165ec7f) Copyright Office/Orphan Works/Documentation/Documentation.pdf: unmerged (7a9ff92663ed42b42b9baaefaf4721499d18d82d) ... fatal: git-write-tree: error building trees git-annex: failed to read sha from git write-tree
- the partial daemon log from the assistant running in that directory on the laptop and
- the output of git fsck on the remote.
git-annex repair on the laptop and the server:
greg@x200s:~/Documents$ git-annex repair Running git fsck ... No problems found. ok
How I ended up fixing it:
greg@x200s:~/Documents$ killall git-annex greg@x200s:~/Documents$ git-annex indirect blah............... indirect ok ok greg@x200s:~/Documents$ git status On branch master Your branch and 'rose/master' have diverged, and have 294 and 1 different commit each, respectively. (use "git pull" to merge the remote branch into yours) Untracked files: (use "git add <file>..." to include in what will be committed) .gitrefs/ nothing added to commit but untracked files present (use "git add" to track) greg@x200s:~/Documents$ git pull Merge made by the 'recursive' strategy. Copyright Office/Orphan Works/staging/reporting/process_report.txt.2 | 1 + Copyright Office/Orphan Works/staging/reporting/with-title.xls | 1 + Copyright Office/Orphan Works/staging/with-title.xls | 1 + Copyright Office/Orphan Works/worker_emails.txt | 1 + git.fsck.log | 1 + 5 files changed, 5 insertions(+) create mode 120000 Copyright Office/Orphan Works/staging/reporting/process_report.txt.2 create mode 120000 Copyright Office/Orphan Works/staging/reporting/with-title.xls create mode 120000 Copyright Office/Orphan Works/staging/with-title.xls create mode 120000 Copyright Office/Orphan Works/worker_emails.txt create mode 120000 git.fsck.log greg@x200s:~/Documents$ git-annex sync commit ok pull rose Already up-to-date. ok push rose Counting objects: 1658, done. Delta compression using up to 2 threads. Compressing objects: 100% (904/904), done. Writing objects: 100% (1604/1604), 138.97 KiB | 0 bytes/s, done. Total 1604 (delta 892), reused 1298 (delta 688) To email@example.com:/home/greg/Documents/ f1d206e..e836b9b master -> synced/master ok greg@x200s:~/Documents$
I restarted the assistant and the daemon.log looks good.
After sync'ing on the server, it appears that this has been the case for quite some time (based off of what symlinks were created).
Lastly: Joey, this is probably what caused that weird behavior in the webapp where it showed the bad transfer each day after the fsck at noon. I never diagnosed that more but I bet I won't see it tomorrow.