This happens every few days. Several repositories are not restarted after the backup task. The log does not seem to contain anything useful other than a message about not being able to restart.
I am using version 3.2.2.
One of the repositories is called MBCS_Git and I am providing snippets of the log that pertain to that repository:
2014-02-18 01:00:00,916 INFO [quartzScheduler_Worker-8 backup-1392706800017] fisheye MessageLoggingProgressMonitor-update - Shutting down repository MBCS_Git...
2014-02-18 01:00:00,916 INFO [quartzScheduler_Worker-8 backup-1392706800017] fisheye RepositoryHandle-stop - STOP requested on MBCS_Git
2014-02-18 01:00:10,226 DEBUG [IncrementalPinger5 MBCS_Git] fisheye LoggingProcessMonitor-onAfterFinished - Finished process: git ls-remote --heads d:\git\mbcscentral_c took 13394ms
2014-02-18 01:00:10,226 DEBUG [IncrementalPinger5 MBCS_Git] fisheye LoggingProcessMonitor-onBeforeStart - Starting process: git fetch d:\git\mbcscentral_c +refs/heads/*:refs/heads/*
2014-02-18 01:00:12,521 DEBUG [IncrementalPinger1 WinGL] fisheye LoggingProcessMonitor-onAfterFinished - Finished process: git fetch d:\git\WinGL +refs/*:refs/* took 13450ms
2014-02-18 01:00:12,521 DEBUG [IncrementalPinger1 WinGL] fisheye LoggingProcessMonitor-onBeforeStart - Starting process: git branch --verbose --no-abbrev
2014-02-18 01:00:12,549 DEBUG [IncrementalPinger1 WinGL] fisheye LoggingProcessMonitor-onAfterFinished - Finished process: git branch --verbose --no-abbrev took 28ms
2014-02-18 01:00:12,549 DEBUG [IncrementalPinger1 WinGL] fisheye LoggingProcessMonitor-onBeforeStart - Starting process: git ls-remote --heads d:\git\WinGL
2014-02-18 01:00:19,227 DEBUG [IncrementalPinger3 MbcsCentralWeb] fisheye LoggingProcessMonitor-onAfterFinished - Finished process: git ls-remote --heads d:\git\MbcsCentralWeb took 11190ms
2014-02-18 01:00:19,227 DEBUG [IncrementalPinger3 MbcsCentralWeb] fisheye LoggingProcessMonitor-onBeforeStart - Starting process: git fetch d:\git\MbcsCentralWeb +refs/heads/*:refs/heads/*
2014-02-18 01:00:20,614 DEBUG [notificationManager1 ] fisheye DefaultNotificationManager-processNotifications - Processing notifications
2014-02-18 01:00:21,414 WARN [quartzScheduler_Worker-8 backup-1392706800017] fisheye MessageLoggingProgressMonitor-update - Unable to stop FishEye repository MBCS_Git. Caches included in this backup may not be consistent. If the problem persists, try stopping the repositories manually, before backup.
2014-02-18 01:00:23,806 DEBUG [IncrementalPinger5 MBCS_Git] fisheye LoggingProcessMonitor-onAfterFinished - Finished process: git fetch d:\git\mbcscentral_c +refs/heads/*:refs/heads/* took 13580ms
2014-02-18 01:00:23,807 DEBUG [IncrementalPinger5 MBCS_Git] fisheye LoggingProcessMonitor-onBeforeStart - Starting process: git ls-remote --tags d:\git\mbcscentral_c
2014-02-18 01:00:32,187 INFO [quartzScheduler_Worker-8 backup-1392706800017] fisheye MessageLoggingProgressMonitor-update - Restarted repository MbcsMain
2014-02-18 01:00:32,187 DEBUG [FE-CacheWarmer ] fisheye RepositoryHandle-acquire - acquire engine on MbcsMain, count=1, waited 0 ms to acquire.
2014-02-18 01:00:32,187 WARN [quartzScheduler_Worker-8 backup-1392706800017] fisheye MessageLoggingProgressMonitor-update - Unable to restart repository MBCS_Git
2014-02-18 01:00:32,187 WARN [quartzScheduler_Worker-8 backup-1392706800017] fisheye FishEyeCacheBackup$SaverImpl-backup - Unable to restart repository MBCS_Git
2014-02-18 01:00:32,187 WARN [quartzScheduler_Worker-8 backup-1392706800017] fisheye MessageLoggingProgressMonitor-update - The process cannot access the file because another process has locked a portion of the file
2014-02-18 01:00:32,189 INFO [quartzScheduler_Worker-8 backup-1392706800017] fisheye MessageLoggingProgressMonitor-update - Backup failed
2014-02-18 01:00:32,189 ERROR [quartzScheduler_Worker-8 backup-1392706800017] fisheye BackupJob-execute - Error performing backup: The process cannot access the file because another process has locked a portion of the file
2014-02-18 01:00:37,395 DEBUG [IncrementalPinger5 MBCS_Git] fisheye LoggingProcessMonitor-onAfterFinished - Finished process: git ls-remote --tags d:\git\mbcscentral_c took 13588ms
2014-02-18 01:00:37,396 DEBUG [IncrementalPinger5 MBCS_Git] fisheye LoggingProcessMonitor-onBeforeStart - Starting process: git show-ref -d --tags
2014-02-18 01:00:37,458 DEBUG [IncrementalPinger5 MBCS_Git] fisheye LoggingProcessMonitor-onAfterFinished - Finished process: git show-ref -d --tags took 62ms
2014-02-18 01:00:37,458 DEBUG [IncrementalPinger5 MBCS_Git] fisheye RepositoryStatus-setMessage - Status change [MBCS_Git]: Updated from d:\git\mbcscentral_c
2014-02-18 01:00:37,458 INFO [IncrementalPinger5 MBCS_Git] fisheye BaseRepositoryScanner-ping - processing MBCS_Git
2014-02-18 01:00:37,458 DEBUG [IncrementalPinger5 MBCS_Git] fisheye LifecycleRepositoryScanner-doSlurpTransaction - Rolling back cache changes
2014-02-18 01:00:37,458 INFO [IncrementalPinger5 MBCS_Git] fisheye BaseRepositoryScanner-ping - done slurp for /MBCS_Git time = 0ms
2014-02-18 01:00:37,458 DEBUG [IncrementalPinger5 ] fisheye RepositoryHandle-release - release engine on MBCS_Git, count=0 waited 0 ms to release
2014-02-18 01:00:37,458 DEBUG [IncrementalPinger5 ] fisheye RepositoryHandle-tryToBeginStopProcedure - STOPPING MBCS_Git
2014-02-18 01:00:37,458 DEBUG [IncrementalPinger5 ] fisheye InfinityDbHandle-close - closing c:\fisheye_data\var\cache\MBCS_Git\revcache\data.bin
2014-02-18 01:00:37,995 DEBUG [IncrementalPinger5 ] fisheye RepositoryEngine-forceClose - Closed engine MBCS_Git
2014-02-18 01:03:33,754 DEBUG [qtp8303200-15359 ] fisheye ProfilingServletFilter-logRequest - start request GET /login?origUrl=%2Fbrowse%2FMBCS_Git%2FMbcsCentral.iw9%3F%2540annm%3Dblame%26r%3D9d8009b%26r%3De084411ac745017e4b60aebb3b500f8ce03d818d nosession
2014-02-18 01:03:33,769 DEBUG [qtp8303200-15359 ] fisheye ProfilingServletFilter-logRequest - end request GET /login?origUrl=%2Fbrowse%2FMBCS_Git%2FMbcsCentral.iw9%3F%2540annm%3Dblame%26r%3D9d8009b%26r%3De084411ac745017e4b60aebb3b500f8ce03d818d nosession 200
2014-02-18 01:07:21,142 DEBUG [qtp8303200-15363 ] fisheye ProfilingServletFilter-logRequest - start request GET /login?origUrl=%2Fbrowse%2FMBCS_Git%2FEomReorg_2.dtp%3Fr%3D651f64c30c23c9cc58ace0ce22284035cbab08ce%26r%3D9d8009bae0f4a1670c5c6f4b1c18ac21099894d5%26r%3D44e326114e577cb87d0c1791d8af36eee8841773 nosession
2014-02-18 01:07:21,157 DEBUG [qtp8303200-15363 ] fisheye ProfilingServletFilter-logRequest - end request GET /login?origUrl=%2Fbrowse%2FMBCS_Git%2FEomReorg_2.dtp%3Fr%3D651f64c30c23c9cc58ace0ce22284035cbab08ce%26r%3D9d8009bae0f4a1670c5c6f4b1c18ac21099894d5%26r%3D44e326114e577cb87d0c1791d8af36eee8841773 nosession 200