From ea57543394a4ce3d63685794c038c4dd3e68fa0b Mon Sep 17 00:00:00 2001 From: ellis Date: Wed, 9 Mar 2016 19:15:10 +0000 Subject: [PATCH 01/88] Added a comment --- .../comment_7_505d70bad4ebe33fedd9066bc96fa92d._comment | 7 +++++++ 1 file changed, 7 insertions(+) create mode 100644 doc/bugs/git-annex:_failed_to_lock_content/comment_7_505d70bad4ebe33fedd9066bc96fa92d._comment diff --git a/doc/bugs/git-annex:_failed_to_lock_content/comment_7_505d70bad4ebe33fedd9066bc96fa92d._comment b/doc/bugs/git-annex:_failed_to_lock_content/comment_7_505d70bad4ebe33fedd9066bc96fa92d._comment new file mode 100644 index 0000000000..b90c1a624a --- /dev/null +++ b/doc/bugs/git-annex:_failed_to_lock_content/comment_7_505d70bad4ebe33fedd9066bc96fa92d._comment @@ -0,0 +1,7 @@ +[[!comment format=mdwn + username="ellis" + subject="comment 7" + date="2016-03-09T19:15:10Z" + content=""" +Thanks, Joey, much appreciated! +"""]] From 7ca35b766f637f88787c7e8da61e6a961b350d70 Mon Sep 17 00:00:00 2001 From: "https://me.yahoo.com/a/EbvxpTI_xP9Aod7Mg4cwGhgjrCrdM5s-#7c0f4" Date: Thu, 10 Mar 2016 04:36:12 +0000 Subject: [PATCH 02/88] Added a comment --- ...ent_12_d499a2f44e8ee2f39ee959f4d6373570._comment | 13 +++++++++++++ 1 file changed, 13 insertions(+) create mode 100644 doc/bugs/git-annex:_content_is_locked__while_trying_to_move_under_NFS_and_pidlock/comment_12_d499a2f44e8ee2f39ee959f4d6373570._comment diff --git a/doc/bugs/git-annex:_content_is_locked__while_trying_to_move_under_NFS_and_pidlock/comment_12_d499a2f44e8ee2f39ee959f4d6373570._comment b/doc/bugs/git-annex:_content_is_locked__while_trying_to_move_under_NFS_and_pidlock/comment_12_d499a2f44e8ee2f39ee959f4d6373570._comment new file mode 100644 index 0000000000..5ab7c9e118 --- /dev/null +++ b/doc/bugs/git-annex:_content_is_locked__while_trying_to_move_under_NFS_and_pidlock/comment_12_d499a2f44e8ee2f39ee959f4d6373570._comment @@ -0,0 +1,13 @@ +[[!comment format=mdwn + username="https://me.yahoo.com/a/EbvxpTI_xP9Aod7Mg4cwGhgjrCrdM5s-#7c0f4" + subject="comment 12" + date="2016-03-10T04:36:12Z" + content=""" +so -- shouldn't annex at least upon init sense if repo is under nfs? if to be done platform independent way then it could do smth like + +[[!format sh \"\"\" +python -c 'from glob import glob; import os; f=open(\".tmp-test\", \"w\"); os.unlink(\".tmp-test\"); assert(not glob(\".nfs*\"))' +\"\"\"]] + +somewhere under .git/annex/tmp .. so if .nfs* file gets generated -- under nfs. Seems to work for me in limited set of tests -- assertion fails all the time under NFS ;) +"""]] From 11a5985389f341780f4df9f50688ec913a5fed48 Mon Sep 17 00:00:00 2001 From: "https://me.yahoo.com/a/EbvxpTI_xP9Aod7Mg4cwGhgjrCrdM5s-#7c0f4" Date: Thu, 10 Mar 2016 15:16:33 +0000 Subject: [PATCH 03/88] --- ...O_permissions_are_stalking_me_somehow.mdwn | 55 +++++++++++++++++++ 1 file changed, 55 insertions(+) create mode 100644 doc/bugs/R__47__O_permissions_are_stalking_me_somehow.mdwn diff --git a/doc/bugs/R__47__O_permissions_are_stalking_me_somehow.mdwn b/doc/bugs/R__47__O_permissions_are_stalking_me_somehow.mdwn new file mode 100644 index 0000000000..df480901d0 --- /dev/null +++ b/doc/bugs/R__47__O_permissions_are_stalking_me_somehow.mdwn @@ -0,0 +1,55 @@ +### Please describe the problem. + +I have got data which I was trying to add to an existing annex. Unfortunately I have missed first that some files were not having write permissions so initial 'annex add' failed with similar to below messages, so I have pruned misctmp, adjusted permissions and have tried to add again -- but the same error keeps coming back + +[[!format sh """ +% chmod +w -R S1/DDA-Freeviewing/surf2anat + +% ls -l S1/DDA-Freeviewing/surf2anat/S1_run1_lh* +-rw-r----- 2 yoh retino 241147956 Feb 28 21:46 S1/DDA-Freeviewing/surf2anat/S1_run1_lh_process_surf.nii.gz + +% rm -rf .git/annex/misctmp/* +zsh: sure you want to delete all the files in /mnt/datasets/mikemp/data-annex/.git/annex/misctmp [yn]? y + +% git annex add S1/DDA-Freeviewing/surf2anat/S1_run1_lh_process_surf.nii.gz +add S1/DDA-Freeviewing/surf2anat/S1_run1_lh_process_surf.nii.gz +git-annex: .git/annex/misctmp/S1_run1_lh1804289383846930886: rename: permission denied (Permission denied) +failed +git-annex: add: 1 failed + +% ls -l S1/DDA-Freeviewing/surf2anat/S1_run1_lh* +-r--r----- 2 yoh retino 241147956 Feb 28 21:46 S1/DDA-Freeviewing/surf2anat/S1_run1_lh_process_surf.nii.gz + +% git annex version +git-annex version: 6.20160307+gitgb095561-1~ndall+1 +build flags: Assistant Webapp Pairing Testsuite S3(multipartupload)(storageclasses) WebDAV Inotify DBus DesktopNotify XMPP ConcurrentOutput TorrentParser MagicMime Feeds Quvi +key/value backends: SHA256E SHA256 SHA512E SHA512 SHA224E SHA224 SHA384E SHA384 SHA3_256E SHA3_256 SHA3_512E SHA3_512 SHA3_224E SHA3_224 SHA3_384E SHA3_384 SKEIN256E SKEIN256 SKEIN512E SKEIN512 SHA1E SHA1 MD5E MD5 WORM URL +remote types: git gcrypt S3 bup directory rsync web bittorrent webdav tahoe glacier ddar hook external +local repository version: 5 +supported repository versions: 5 6 +upgrade supported from repository versions: 0 1 2 4 5 + + +% rm -rf .git/annex/misctmp/* +zsh: sure you want to delete all the files in /mnt/datasets/mikemp/data-annex/.git/annex/misctmp [yn]? y + +% chmod +w -R S1/DDA-Freeviewing/surf2anat + +% git annex add --debug S1/DDA-Freeviewing/surf2anat/S1_run1_lh_process_surf.nii.gz +[2016-03-10 10:15:22.578786] read: git ["--git-dir=.git","--work-tree=.","--literal-pathspecs","ls-files","--others","--exclude-standard","-z","--","S1/DDA-Freeviewing/surf2anat/S1_run1_lh_process_surf.nii.gz"] +[2016-03-10 10:15:22.583854] chat: git ["--git-dir=.git","--work-tree=.","--literal-pathspecs","check-attr","-z","--stdin","annex.backend","annex.numcopies","annex.largefiles","--"] +[2016-03-10 10:15:22.584443] read: git ["--version"] +[2016-03-10 10:15:22.588703] process done ExitSuccess +add S1/DDA-Freeviewing/surf2anat/S1_run1_lh_process_surf.nii.gz [2016-03-10 10:15:23.186056] read: sha256sum [".git/annex/misctmp/S1_run1_lh1804289383846930886"] +[2016-03-10 10:15:24.611133] process done ExitSuccess + +git-annex: .git/annex/misctmp/S1_run1_lh1804289383846930886: rename: permission denied (Permission denied) +failed +[2016-03-10 10:15:24.648808] read: git ["--git-dir=.git","--work-tree=.","--literal-pathspecs","diff","--name-only","--diff-filter=T","-z","--","S1/DDA-Freeviewing/surf2anat/S1_run1_lh_process_surf.nii.gz"] +git-annex: add: 1 failed +% ls -l .git/annex/misctmp/S1_run1_lh1804289383846930886 +-r--r----- 2 yoh retino 241147956 Feb 28 21:46 .git/annex/misctmp/S1_run1_lh1804289383846930886 + +"""]] + +[[!meta author=yoh]] From 662fc7fc75331d8c9cba8a2af1fbf0a86a701215 Mon Sep 17 00:00:00 2001 From: Horus Date: Thu, 10 Mar 2016 21:40:31 +0000 Subject: [PATCH 04/88] --- doc/forum/Autostart_the_assistant.mdwn | 9 +++++++++ 1 file changed, 9 insertions(+) create mode 100644 doc/forum/Autostart_the_assistant.mdwn diff --git a/doc/forum/Autostart_the_assistant.mdwn b/doc/forum/Autostart_the_assistant.mdwn new file mode 100644 index 0000000000..06439750e9 --- /dev/null +++ b/doc/forum/Autostart_the_assistant.mdwn @@ -0,0 +1,9 @@ +Hello, + +I'm using the Arch git-annex package: https://www.archlinux.org/packages/community/x86_64/git-annex/ + +Checking the autostart checkbox in the assistant's web interface has no effect. There is no git-annex desktop file in ~/.config/autostart/ or alike. Neither is one contained in the package, however in the tarball I haven't found either. + +How does autostarting the assistant works? + +Best Thanks! From c20e8d17db6a6037743bbf4ba9347982483287ac Mon Sep 17 00:00:00 2001 From: "mark@6b90344cdab3158eacb94a3944460d138afc9bef" Date: Thu, 10 Mar 2016 22:46:42 +0000 Subject: [PATCH 05/88] --- ...t_copy_fails_with_absolute_path_on_mavericks.mdwn | 12 ++++++++++++ 1 file changed, 12 insertions(+) create mode 100644 doc/bugs/Git_copy_fails_with_absolute_path_on_mavericks.mdwn diff --git a/doc/bugs/Git_copy_fails_with_absolute_path_on_mavericks.mdwn b/doc/bugs/Git_copy_fails_with_absolute_path_on_mavericks.mdwn new file mode 100644 index 0000000000..5704bf1ccc --- /dev/null +++ b/doc/bugs/Git_copy_fails_with_absolute_path_on_mavericks.mdwn @@ -0,0 +1,12 @@ +### Please describe the problem. + +git-annex version: 6.20160126 + +Problem happens on Mavericks, not on Yosemite with same version. + +Can do a relative or absolute path on a git annex add. + +But on the git annex copy to an S3 remote, if I use an absolute path for the file descriptor (e.g. /Users/name/git_directory/test.txt) it will not report an error, but will also not print the "copied..." string. A subsequent call with a relative path (e.g. test.txt) will work, show the copied message and indeed show up on S3. + + +Good news: It's working great on Yosemite! From 26405c107a147c41a16c818645fa032aafffd503 Mon Sep 17 00:00:00 2001 From: Joey Hess Date: Fri, 11 Mar 2016 19:55:27 -0400 Subject: [PATCH 06/88] devblog --- .../day_372__adjusted_branches_improved.mdwn | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) create mode 100644 doc/devblog/day_372__adjusted_branches_improved.mdwn diff --git a/doc/devblog/day_372__adjusted_branches_improved.mdwn b/doc/devblog/day_372__adjusted_branches_improved.mdwn new file mode 100644 index 0000000000..ce91693f4b --- /dev/null +++ b/doc/devblog/day_372__adjusted_branches_improved.mdwn @@ -0,0 +1,18 @@ +After a real brain-bender of a day, I have commit propigation from the +adjusted branch back to the original branch working, without needing to +reverse adjust the whole tree. This is faster, but the really nice thing +is that it makes individual adjustments simpler to write. + +In fact, it's so simple that I took 10 minutes just now to implement a second +adjustment! + +[[!format haskell """ +adjustTreeItem HideMissingAdjustment h ti@(TreeItem _ _ s) = do + mk <- catKey s + case mk of + Just k -> ifM (inAnnex k) + ( return (Just ti) + , return Nothing + ) + Nothing -> return (Just ti) +"""]] From b1b80e6decf8bdb7adefed41b659a25272c735ba Mon Sep 17 00:00:00 2001 From: Richard Hartmann Date: Sat, 12 Mar 2016 15:13:46 +0100 Subject: [PATCH 07/88] Typo --- doc/devblog/day_372__adjusted_branches_improved.mdwn | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/devblog/day_372__adjusted_branches_improved.mdwn b/doc/devblog/day_372__adjusted_branches_improved.mdwn index ce91693f4b..625169eafd 100644 --- a/doc/devblog/day_372__adjusted_branches_improved.mdwn +++ b/doc/devblog/day_372__adjusted_branches_improved.mdwn @@ -1,4 +1,4 @@ -After a real brain-bender of a day, I have commit propigation from the +After a real brain-bender of a day, I have commit propagation from the adjusted branch back to the original branch working, without needing to reverse adjust the whole tree. This is faster, but the really nice thing is that it makes individual adjustments simpler to write. From b02f813ed8e31a93ff2154238398f9e22b8b90bc Mon Sep 17 00:00:00 2001 From: Joey Hess Date: Sat, 12 Mar 2016 12:35:41 -0400 Subject: [PATCH 08/88] bump process version in stack.yaml Newer version than current lts has is needed on windows --- stack.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/stack.yaml b/stack.yaml index cb7a573a30..5f202e71d0 100644 --- a/stack.yaml +++ b/stack.yaml @@ -23,3 +23,4 @@ resolver: lts-5.5 extra-deps: - mountpoints-1.0.1 - disk-free-space-0.1.0.1 +- process-1.3.0.0 From 7125a1fb27c354b26d56a7b3bac9094c5f5d6e8c Mon Sep 17 00:00:00 2001 From: Joey Hess Date: Sat, 12 Mar 2016 12:57:18 -0400 Subject: [PATCH 09/88] rename files containing : This is mostly to let the repo check out on windows w/o using cygwin's git. 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doc/forum/bainstorming:_git_annex_push___38___pull/comment_1_3a0bf74b51586354b7a91f8b43472376._comment rename to doc/forum/bainstorming__58___git_annex_push___38___pull/comment_1_3a0bf74b51586354b7a91f8b43472376._comment diff --git a/doc/forum/bainstorming:_git_annex_push___38___pull/comment_2_b02ca09914e788393c01196686f95831._comment b/doc/forum/bainstorming__58___git_annex_push___38___pull/comment_2_b02ca09914e788393c01196686f95831._comment similarity index 100% rename from doc/forum/bainstorming:_git_annex_push___38___pull/comment_2_b02ca09914e788393c01196686f95831._comment rename to doc/forum/bainstorming__58___git_annex_push___38___pull/comment_2_b02ca09914e788393c01196686f95831._comment diff --git a/doc/forum/comprehension_question:_repository_vs._working_copy_in_direct_mode.mdwn b/doc/forum/comprehension_question__58___repository_vs._working_copy_in_direct_mode.mdwn similarity index 100% rename from doc/forum/comprehension_question:_repository_vs._working_copy_in_direct_mode.mdwn rename to doc/forum/comprehension_question__58___repository_vs._working_copy_in_direct_mode.mdwn diff --git a/doc/forum/comprehension_question:_repository_vs._working_copy_in_direct_mode/comment_1_a6b4db0cefa439f72b97089d48dfacbd._comment b/doc/forum/comprehension_question__58___repository_vs._working_copy_in_direct_mode/comment_1_a6b4db0cefa439f72b97089d48dfacbd._comment similarity index 100% rename from doc/forum/comprehension_question:_repository_vs._working_copy_in_direct_mode/comment_1_a6b4db0cefa439f72b97089d48dfacbd._comment rename to doc/forum/comprehension_question__58___repository_vs._working_copy_in_direct_mode/comment_1_a6b4db0cefa439f72b97089d48dfacbd._comment diff --git a/doc/forum/error:_refs__47__heads__47__git-annex_does_not_point_to_a_valid_object__33__.mdwn b/doc/forum/error__58___refs__47__heads__47__git-annex_does_not_point_to_a_valid_object__33__.mdwn similarity index 100% rename from doc/forum/error:_refs__47__heads__47__git-annex_does_not_point_to_a_valid_object__33__.mdwn rename to doc/forum/error__58___refs__47__heads__47__git-annex_does_not_point_to_a_valid_object__33__.mdwn diff --git a/doc/forum/error:_refs__47__heads__47__git-annex_does_not_point_to_a_valid_object__33__/comment_1_d370b044da3bfebf9e4c90ce1e243587._comment b/doc/forum/error__58___refs__47__heads__47__git-annex_does_not_point_to_a_valid_object__33__/comment_1_d370b044da3bfebf9e4c90ce1e243587._comment similarity index 100% rename from doc/forum/error:_refs__47__heads__47__git-annex_does_not_point_to_a_valid_object__33__/comment_1_d370b044da3bfebf9e4c90ce1e243587._comment rename to doc/forum/error__58___refs__47__heads__47__git-annex_does_not_point_to_a_valid_object__33__/comment_1_d370b044da3bfebf9e4c90ce1e243587._comment diff --git a/doc/forum/fail_to_git_annex_add_some_files:_getFileStatus:_does_not_exist__40__v_3.20111231__41__.mdwn 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doc/forum/fail_to_git_annex_add_some_files__58___getFileStatus__58___does_not_exist__40__v_3.20111231__41__/comment_1_990197bf01351dc1ccbe1940d5084adb._comment diff --git a/doc/forum/fail_to_git_annex_add_some_files:_getFileStatus:_does_not_exist__40__v_3.20111231__41__/comment_2_3bb1d21b7f0d0bd6d59190ae9d246d46._comment b/doc/forum/fail_to_git_annex_add_some_files__58___getFileStatus__58___does_not_exist__40__v_3.20111231__41__/comment_2_3bb1d21b7f0d0bd6d59190ae9d246d46._comment similarity index 100% rename from doc/forum/fail_to_git_annex_add_some_files:_getFileStatus:_does_not_exist__40__v_3.20111231__41__/comment_2_3bb1d21b7f0d0bd6d59190ae9d246d46._comment rename to doc/forum/fail_to_git_annex_add_some_files__58___getFileStatus__58___does_not_exist__40__v_3.20111231__41__/comment_2_3bb1d21b7f0d0bd6d59190ae9d246d46._comment diff --git a/doc/forum/fail_to_git_annex_add_some_files:_getFileStatus:_does_not_exist__40__v_3.20111231__41__/comment_3_692f268218690437138ae0540c879425._comment b/doc/forum/fail_to_git_annex_add_some_files__58___getFileStatus__58___does_not_exist__40__v_3.20111231__41__/comment_3_692f268218690437138ae0540c879425._comment similarity index 100% rename from doc/forum/fail_to_git_annex_add_some_files:_getFileStatus:_does_not_exist__40__v_3.20111231__41__/comment_3_692f268218690437138ae0540c879425._comment rename to doc/forum/fail_to_git_annex_add_some_files__58___getFileStatus__58___does_not_exist__40__v_3.20111231__41__/comment_3_692f268218690437138ae0540c879425._comment diff --git a/doc/forum/fatal:_Out_of_memory__63___mmap_failed:_No_such_file_or_directory.mdwn b/doc/forum/fatal__58___Out_of_memory__63___mmap_failed__58___No_such_file_or_directory.mdwn similarity index 100% rename from doc/forum/fatal:_Out_of_memory__63___mmap_failed:_No_such_file_or_directory.mdwn rename to doc/forum/fatal__58___Out_of_memory__63___mmap_failed__58___No_such_file_or_directory.mdwn diff --git a/doc/forum/fatal:_Out_of_memory__63___mmap_failed:_No_such_file_or_directory/comment_1_d98a155fa01d10ecff9058d79290156d._comment b/doc/forum/fatal__58___Out_of_memory__63___mmap_failed__58___No_such_file_or_directory/comment_1_d98a155fa01d10ecff9058d79290156d._comment similarity index 100% rename from doc/forum/fatal:_Out_of_memory__63___mmap_failed:_No_such_file_or_directory/comment_1_d98a155fa01d10ecff9058d79290156d._comment rename to doc/forum/fatal__58___Out_of_memory__63___mmap_failed__58___No_such_file_or_directory/comment_1_d98a155fa01d10ecff9058d79290156d._comment diff --git a/doc/forum/fatal:_Out_of_memory__63___mmap_failed:_No_such_file_or_directory/comment_2_3b9ea7a1254ac5b50a5ab59cd331ec3f._comment b/doc/forum/fatal__58___Out_of_memory__63___mmap_failed__58___No_such_file_or_directory/comment_2_3b9ea7a1254ac5b50a5ab59cd331ec3f._comment similarity index 100% rename from doc/forum/fatal:_Out_of_memory__63___mmap_failed:_No_such_file_or_directory/comment_2_3b9ea7a1254ac5b50a5ab59cd331ec3f._comment rename to doc/forum/fatal__58___Out_of_memory__63___mmap_failed__58___No_such_file_or_directory/comment_2_3b9ea7a1254ac5b50a5ab59cd331ec3f._comment diff --git a/doc/forum/fatal:_Out_of_memory__63___mmap_failed:_No_such_file_or_directory/comment_3_5ee300034819c5825c676cd7e3af659f._comment b/doc/forum/fatal__58___Out_of_memory__63___mmap_failed__58___No_such_file_or_directory/comment_3_5ee300034819c5825c676cd7e3af659f._comment similarity index 100% rename from doc/forum/fatal:_Out_of_memory__63___mmap_failed:_No_such_file_or_directory/comment_3_5ee300034819c5825c676cd7e3af659f._comment rename to doc/forum/fatal__58___Out_of_memory__63___mmap_failed__58___No_such_file_or_directory/comment_3_5ee300034819c5825c676cd7e3af659f._comment diff --git 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b/doc/forum/git-annex__58___map__58___1_failed/comment_1_35ff3256e823ab8cfc53276a2123ad5f._comment similarity index 100% rename from doc/forum/git-annex:_map:_1_failed/comment_1_35ff3256e823ab8cfc53276a2123ad5f._comment rename to doc/forum/git-annex__58___map__58___1_failed/comment_1_35ff3256e823ab8cfc53276a2123ad5f._comment diff --git a/doc/forum/git-annex:_map:_1_failed/comment_2_b0826073ebbd2847f4ab0d9bdba2dce5._comment b/doc/forum/git-annex__58___map__58___1_failed/comment_2_b0826073ebbd2847f4ab0d9bdba2dce5._comment similarity index 100% rename from doc/forum/git-annex:_map:_1_failed/comment_2_b0826073ebbd2847f4ab0d9bdba2dce5._comment rename to doc/forum/git-annex__58___map__58___1_failed/comment_2_b0826073ebbd2847f4ab0d9bdba2dce5._comment diff --git a/doc/forum/git:___39__annex__39___is_not_a_git_command_error_after_installing.mdwn b/doc/forum/git__58_____39__annex__39___is_not_a_git_command_error_after_installing.mdwn similarity index 100% rename from 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doc/walkthrough/quiet_please:_When_git-annex_seems_to_skip_files.mdwn rename to doc/walkthrough/quiet_please__58___When_git-annex_seems_to_skip_files.mdwn diff --git a/doc/walkthrough/removing_files:_When_things_go_wrong.mdwn b/doc/walkthrough/removing_files__58___When_things_go_wrong.mdwn similarity index 100% rename from doc/walkthrough/removing_files:_When_things_go_wrong.mdwn rename to doc/walkthrough/removing_files__58___When_things_go_wrong.mdwn diff --git a/doc/walkthrough/transferring_files:_When_things_go_wrong.mdwn b/doc/walkthrough/transferring_files__58___When_things_go_wrong.mdwn similarity index 100% rename from doc/walkthrough/transferring_files:_When_things_go_wrong.mdwn rename to doc/walkthrough/transferring_files__58___When_things_go_wrong.mdwn From c483e11cb3ec9309a228e605b07adb43254abe0b Mon Sep 17 00:00:00 2001 From: Richard Hartmann Date: Thu, 10 Mar 2016 23:43:18 +0100 Subject: [PATCH 10/88] Bump standards version (cherry picked from commit 6efa2492bb0c34279f535e79228016555bdb915c) --- debian/control | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/debian/control b/debian/control index 21c7a8bcef..e77a8b7ffe 100644 --- a/debian/control +++ b/debian/control @@ -85,7 +85,7 @@ Build-Depends: openssh-client, git-remote-gcrypt (>= 0.20130908-6), Maintainer: Richard Hartmann -Standards-Version: 3.9.6 +Standards-Version: 3.9.7 Vcs-Git: git://git.kitenet.net/git-annex Homepage: http://git-annex.branchable.com/ XS-Testsuite: autopkgtest From 2eae70353d442cffe2f7a41061f654f4e968b7e0 Mon Sep 17 00:00:00 2001 From: Joey Hess Date: Sat, 12 Mar 2016 13:45:31 -0400 Subject: [PATCH 11/88] remove note about cygwin git --- doc/install/Windows.mdwn | 3 --- 1 file changed, 3 deletions(-) diff --git a/doc/install/Windows.mdwn b/doc/install/Windows.mdwn index 5063b275ba..d32a790b4d 100644 --- a/doc/install/Windows.mdwn +++ b/doc/install/Windows.mdwn @@ -35,8 +35,5 @@ Once the prerequisites are installed, run: cd gitannex build -Note that git from Cygwin is able to clone git-annex's git repository; -Regular git for Windows cannot due to some characters in filenames. - (To build the git-annex installer, you also need to install the NullSoft installer system.) From 348105debceef44f829cda794b1c8df099d66cdf Mon Sep 17 00:00:00 2001 From: Joey Hess Date: Sat, 12 Mar 2016 13:47:31 -0400 Subject: [PATCH 12/88] fix links --- doc/walkthrough.mdwn | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/doc/walkthrough.mdwn b/doc/walkthrough.mdwn index 94889864aa..22c94d570f 100644 --- a/doc/walkthrough.mdwn +++ b/doc/walkthrough.mdwn @@ -9,18 +9,18 @@ A walkthrough of the basic features of git-annex. walkthrough/renaming_files walkthrough/getting_file_content walkthrough/syncing - walkthrough/transferring_files:_When_things_go_wrong + walkthrough/transferring_files__58___When_things_go_wrong walkthrough/removing_files - walkthrough/removing_files:_When_things_go_wrong + walkthrough/removing_files__58___When_things_go_wrong walkthrough/modifying_annexed_files walkthrough/using_ssh_remotes walkthrough/using_special_remotes walkthrough/moving_file_content_between_repositories - walkthrough/quiet_please:_When_git-annex_seems_to_skip_files + walkthrough/quiet_please__58___When_git-annex_seems_to_skip_files walkthrough/using_tags_and_branches walkthrough/unused_data - walkthrough/fsck:_verifying_your_data - walkthrough/fsck:_when_things_go_wrong + walkthrough/fsck__58___verifying_your_data + walkthrough/fsck__58___when_things_go_wrong walkthrough/backups walkthrough/automatically_managing_content walkthrough/more From 8b653bf9ef6ae1e1f9e72b92a1a963b0013d2e17 Mon Sep 17 00:00:00 2001 From: Joey Hess Date: Sat, 12 Mar 2016 13:51:25 -0400 Subject: [PATCH 13/88] remove danging comment with * in its filename --- ...ment_1_6227a28cd0c848cc1479d17fd48d37d5._comment | 13 ------------- 1 file changed, 13 deletions(-) delete mode 100644 doc/forum/Can__39__t_create_remote_for_Goo*/comment_1_6227a28cd0c848cc1479d17fd48d37d5._comment diff --git a/doc/forum/Can__39__t_create_remote_for_Goo*/comment_1_6227a28cd0c848cc1479d17fd48d37d5._comment b/doc/forum/Can__39__t_create_remote_for_Goo*/comment_1_6227a28cd0c848cc1479d17fd48d37d5._comment deleted file mode 100644 index cdfb24685a..0000000000 --- a/doc/forum/Can__39__t_create_remote_for_Goo*/comment_1_6227a28cd0c848cc1479d17fd48d37d5._comment +++ /dev/null @@ -1,13 +0,0 @@ -[[!comment format=mdwn - username="joey" - subject="""comment 1""" - date="2015-03-16T17:43:44Z" - content=""" -Ok, the problem here is that Aws.S3.Core.StorageClass currently only -offers Standard | ReducedRedundancy | Glacier. - -To support this google thing, the library needs to be expanded. -I have filed a request for that here: - - -"""]] From 92877bb5d064f7122d6c1118b0ffe918cd84117f Mon Sep 17 00:00:00 2001 From: Joey Hess Date: Sat, 12 Mar 2016 13:57:07 -0400 Subject: [PATCH 14/88] windows git seems to fail to checkout foo.../bar ; rename --- ...WARNING__58___linker__58__git-annex_has_text_relocations.mdwn} | 0 .../comment_1_fee360353f0b46aab6ee7a902c0837bb._comment | 0 .../{lost_in_walkthrough....mdwn => lost_in_walkthrough.mdwn} | 0 .../comment_1_51b703b961ca762f0359e1c169f1ee75._comment | 0 .../comment_2_a9de0401a103bdd4401ba2d5983dc54a._comment | 0 5 files changed, 0 insertions(+), 0 deletions(-) rename doc/forum/{WARNING__58___linker__58__git-annex_has_text_relocations....mdwn => WARNING__58___linker__58__git-annex_has_text_relocations.mdwn} (100%) rename doc/forum/{WARNING__58___linker__58__git-annex_has_text_relocations... => WARNING__58___linker__58__git-annex_has_text_relocations}/comment_1_fee360353f0b46aab6ee7a902c0837bb._comment (100%) rename doc/forum/{lost_in_walkthrough....mdwn => lost_in_walkthrough.mdwn} (100%) rename doc/forum/{lost_in_walkthrough... => lost_in_walkthrough}/comment_1_51b703b961ca762f0359e1c169f1ee75._comment (100%) rename doc/forum/{lost_in_walkthrough... => lost_in_walkthrough}/comment_2_a9de0401a103bdd4401ba2d5983dc54a._comment (100%) diff --git a/doc/forum/WARNING__58___linker__58__git-annex_has_text_relocations....mdwn b/doc/forum/WARNING__58___linker__58__git-annex_has_text_relocations.mdwn similarity index 100% rename from doc/forum/WARNING__58___linker__58__git-annex_has_text_relocations....mdwn rename to doc/forum/WARNING__58___linker__58__git-annex_has_text_relocations.mdwn diff --git a/doc/forum/WARNING__58___linker__58__git-annex_has_text_relocations.../comment_1_fee360353f0b46aab6ee7a902c0837bb._comment b/doc/forum/WARNING__58___linker__58__git-annex_has_text_relocations/comment_1_fee360353f0b46aab6ee7a902c0837bb._comment similarity index 100% rename from doc/forum/WARNING__58___linker__58__git-annex_has_text_relocations.../comment_1_fee360353f0b46aab6ee7a902c0837bb._comment rename to doc/forum/WARNING__58___linker__58__git-annex_has_text_relocations/comment_1_fee360353f0b46aab6ee7a902c0837bb._comment diff --git a/doc/forum/lost_in_walkthrough....mdwn b/doc/forum/lost_in_walkthrough.mdwn similarity index 100% rename from doc/forum/lost_in_walkthrough....mdwn rename to doc/forum/lost_in_walkthrough.mdwn diff --git a/doc/forum/lost_in_walkthrough.../comment_1_51b703b961ca762f0359e1c169f1ee75._comment b/doc/forum/lost_in_walkthrough/comment_1_51b703b961ca762f0359e1c169f1ee75._comment similarity index 100% rename from doc/forum/lost_in_walkthrough.../comment_1_51b703b961ca762f0359e1c169f1ee75._comment rename to doc/forum/lost_in_walkthrough/comment_1_51b703b961ca762f0359e1c169f1ee75._comment diff --git a/doc/forum/lost_in_walkthrough.../comment_2_a9de0401a103bdd4401ba2d5983dc54a._comment b/doc/forum/lost_in_walkthrough/comment_2_a9de0401a103bdd4401ba2d5983dc54a._comment similarity index 100% rename from doc/forum/lost_in_walkthrough.../comment_2_a9de0401a103bdd4401ba2d5983dc54a._comment rename to doc/forum/lost_in_walkthrough/comment_2_a9de0401a103bdd4401ba2d5983dc54a._comment From e191f127eb0727ce08a1399813ee700788f2af53 Mon Sep 17 00:00:00 2001 From: "susetux@ed6f4e20192c3eae018e1fc6442bf993d41b3848" Date: Sun, 13 Mar 2016 11:16:09 +0000 Subject: [PATCH 15/88] --- ...v5_repo_to_an_always_unlocked_v6_repo.mdwn | 22 +++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 doc/forum/converting_a_v5_repo_to_an_always_unlocked_v6_repo.mdwn diff --git a/doc/forum/converting_a_v5_repo_to_an_always_unlocked_v6_repo.mdwn b/doc/forum/converting_a_v5_repo_to_an_always_unlocked_v6_repo.mdwn new file mode 100644 index 0000000000..4eec48138a --- /dev/null +++ b/doc/forum/converting_a_v5_repo_to_an_always_unlocked_v6_repo.mdwn @@ -0,0 +1,22 @@ +Hi, +I'm trying to convert a v5 classic, symlink repository into a v6 always unloked repository. + + +I'm trying to follow along with: +but something goes wrong in the process, so I'm sure I'm missing something. +The repository is about 600G to start with and I don't have another 600G of free space on disk, so I'm going with thin mode: + +1. git annex upgrade +2. git config annex.thin true +3. git annex fix +4. git annex unlock + +It's all good to this point. Everything gets unlocked and is fine. +Then I try to commit the changes with "git annex sync" and the process seems to take +and incredibly long time (hours) and then ends up running out of space. I check the repository with "du -sh" +and it's almost double the size. Is there a reason for this? Is there a way to avoid this duplication of data. Shouldn't annex.thin do the trick? +Should I not have done the sync thing? (I need to sync with other repos too after the migration is done) + +Is there a correct way to migrate my repo to an always unlocked one which won't require hours of time and take all that disk space? + +thanks a lot, daniel From a1765ecf8cfa2a44ffd3aabf3d144ef1d961d83f Mon Sep 17 00:00:00 2001 From: "susetux@ed6f4e20192c3eae018e1fc6442bf993d41b3848" Date: Sun, 13 Mar 2016 11:19:39 +0000 Subject: [PATCH 16/88] --- ...onverting_a_v5_repo_to_an_always_unlocked_v6_repo.mdwn | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/doc/forum/converting_a_v5_repo_to_an_always_unlocked_v6_repo.mdwn b/doc/forum/converting_a_v5_repo_to_an_always_unlocked_v6_repo.mdwn index 4eec48138a..7c42094fa0 100644 --- a/doc/forum/converting_a_v5_repo_to_an_always_unlocked_v6_repo.mdwn +++ b/doc/forum/converting_a_v5_repo_to_an_always_unlocked_v6_repo.mdwn @@ -12,8 +12,12 @@ The repository is about 600G to start with and I don't have another 600G of free 4. git annex unlock It's all good to this point. Everything gets unlocked and is fine. -Then I try to commit the changes with "git annex sync" and the process seems to take -and incredibly long time (hours) and then ends up running out of space. I check the repository with "du -sh" +Then I try to commit the changes with: + + git annex sync + +The process seems to take +and incredibly long time (several hours) and then ends up running out of space. I check the repository with "du -sh" and it's almost double the size. Is there a reason for this? Is there a way to avoid this duplication of data. Shouldn't annex.thin do the trick? Should I not have done the sync thing? (I need to sync with other repos too after the migration is done) From b28f32e47f4c6b3b2003194fe62c95ae013ac5d7 Mon Sep 17 00:00:00 2001 From: "susetux@ed6f4e20192c3eae018e1fc6442bf993d41b3848" Date: Sun, 13 Mar 2016 11:20:49 +0000 Subject: [PATCH 17/88] --- .../converting_a_v5_repo_to_an_always_unlocked_v6_repo.mdwn | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/doc/forum/converting_a_v5_repo_to_an_always_unlocked_v6_repo.mdwn b/doc/forum/converting_a_v5_repo_to_an_always_unlocked_v6_repo.mdwn index 7c42094fa0..11ff6116b0 100644 --- a/doc/forum/converting_a_v5_repo_to_an_always_unlocked_v6_repo.mdwn +++ b/doc/forum/converting_a_v5_repo_to_an_always_unlocked_v6_repo.mdwn @@ -19,8 +19,7 @@ Then I try to commit the changes with: The process seems to take and incredibly long time (several hours) and then ends up running out of space. I check the repository with "du -sh" and it's almost double the size. Is there a reason for this? Is there a way to avoid this duplication of data. Shouldn't annex.thin do the trick? -Should I not have done the sync thing? (I need to sync with other repos too after the migration is done) -Is there a correct way to migrate my repo to an always unlocked one which won't require hours of time and take all that disk space? +Is there a correct and faster way to migrate my repo to an always unlocked one which won't require hours of time and take all that disk space? thanks a lot, daniel From bef922be213cb075d1200580a537d904573f5f29 Mon Sep 17 00:00:00 2001 From: "susetux@ed6f4e20192c3eae018e1fc6442bf993d41b3848" Date: Sun, 13 Mar 2016 11:28:17 +0000 Subject: [PATCH 18/88] --- .../converting_a_v5_repo_to_an_always_unlocked_v6_repo.mdwn | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/forum/converting_a_v5_repo_to_an_always_unlocked_v6_repo.mdwn b/doc/forum/converting_a_v5_repo_to_an_always_unlocked_v6_repo.mdwn index 11ff6116b0..77731fefe2 100644 --- a/doc/forum/converting_a_v5_repo_to_an_always_unlocked_v6_repo.mdwn +++ b/doc/forum/converting_a_v5_repo_to_an_always_unlocked_v6_repo.mdwn @@ -4,7 +4,7 @@ I'm trying to convert a v5 classic, symlink repository into a v6 always unloked I'm trying to follow along with: but something goes wrong in the process, so I'm sure I'm missing something. -The repository is about 600G to start with and I don't have another 600G of free space on disk, so I'm going with thin mode: +The repository is about 600G to start with on a ext4 filesystem, and I don't have another 600G of free space on disk, so I'm going with thin mode: 1. git annex upgrade 2. git config annex.thin true From 0d9f3bdae07ac067af942606b2b56a9ef06390ae Mon Sep 17 00:00:00 2001 From: "susetux@ed6f4e20192c3eae018e1fc6442bf993d41b3848" Date: Sun, 13 Mar 2016 11:32:35 +0000 Subject: [PATCH 19/88] --- ...nverting_a_v5_repo_to_an_always_unlocked_v6_repo.mdwn | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/doc/forum/converting_a_v5_repo_to_an_always_unlocked_v6_repo.mdwn b/doc/forum/converting_a_v5_repo_to_an_always_unlocked_v6_repo.mdwn index 77731fefe2..40735383ae 100644 --- a/doc/forum/converting_a_v5_repo_to_an_always_unlocked_v6_repo.mdwn +++ b/doc/forum/converting_a_v5_repo_to_an_always_unlocked_v6_repo.mdwn @@ -20,6 +20,15 @@ The process seems to take and incredibly long time (several hours) and then ends up running out of space. I check the repository with "du -sh" and it's almost double the size. Is there a reason for this? Is there a way to avoid this duplication of data. Shouldn't annex.thin do the trick? +This is also strange: with "git annex info" I get + + local annex keys: 3572 + local annex size: 933.19 gigabytes + annexed files in working tree: 0 + size of annexed files in working tree: 0 bytes + +the annex size should be about 540G and why are there no annexed files in the working tree? + Is there a correct and faster way to migrate my repo to an always unlocked one which won't require hours of time and take all that disk space? thanks a lot, daniel From 48b2357963a9a2932db58ace4c8b6f7546cacb2b Mon Sep 17 00:00:00 2001 From: karl Date: Sun, 13 Mar 2016 16:01:03 +0000 Subject: [PATCH 20/88] --- doc/todo/immediate_stream-to-sync.mdwn | 9 +++++++++ 1 file changed, 9 insertions(+) create mode 100644 doc/todo/immediate_stream-to-sync.mdwn diff --git a/doc/todo/immediate_stream-to-sync.mdwn b/doc/todo/immediate_stream-to-sync.mdwn new file mode 100644 index 0000000000..919651df50 --- /dev/null +++ b/doc/todo/immediate_stream-to-sync.mdwn @@ -0,0 +1,9 @@ +git-annex is really great for secure distributed archival, but it's missing a piece of the reliability portion: when data is generated and saved a system may crash before finishing, and some data may be lost, before the add is initiated. + +If there were a way to add a file at the same time as writing it -- and then at the same time stream that live data to a remote -- it would increase the utility of git-add for such uses as storing live recording and logfiles. + +I imagine e.g. + +$ cat /proc/kmsg | git annex addstreamsync livelogs/kernel-log-$(date) + +and kmsg would be streamed to enough remotes to meet numcopies, and hashed live . If possible, if the system then crashed and even the entire source repo was lost, the remote would have some incomplete file and be able to complete the add properly at next sync. Hashing the data at the same time as generating it would also speed adding any new file. From 82f7582f8f323cbd432df95bbafbc821984358fa Mon Sep 17 00:00:00 2001 From: torpidus Date: Sun, 13 Mar 2016 19:18:39 +0000 Subject: [PATCH 21/88] removed --- ...messed_up_annex_by_using_git_checkout.mdwn | 40 ------------------- 1 file changed, 40 deletions(-) delete mode 100644 doc/tips/messed_up_annex_by_using_git_checkout.mdwn diff --git a/doc/tips/messed_up_annex_by_using_git_checkout.mdwn b/doc/tips/messed_up_annex_by_using_git_checkout.mdwn deleted file mode 100644 index f9b2eb63c4..0000000000 --- a/doc/tips/messed_up_annex_by_using_git_checkout.mdwn +++ /dev/null @@ -1,40 +0,0 @@ -Hello. Linux experienced user here, but with no development or git experience ever. This directly leads me to my biggest trouble with git-annex because I constantly suffer from misunderstanding each and everything. That being said, my problem is the following: I had the terrible idea to have my .thunderbird directory synchronized over several machines, leading the thunderbird profile to total corruption because after a few weeks I finally managed to have multiple machines accessing it. As I started trying to recover, things got worse and this is my last seek for help before starting over by creating the repositories from scratch. - -What I did: - -1. I did some research on how to recover an old state of the repo, which should not have been a problem because there is a "full backup" repo. I came across this [1] page and the pain started with me looking for my wanted commit to roll-back in "git log" and then did some tries in the way something like, "git checkout -b old-state4 012345678". - -2. Of course this recovered the whole repo and not only thunderbird, so I used a file synchronizer to put everything else back into place after the action. - -3. Unfortunately, the "branches" seem to have been messed up and the repos are no longer in sync. - -This is what the machine says that I have used to create the mess: - - [2016-03-08 19:15:26.915116] Pusher: Syncing with host123 - (recording state in git...) - To ssh://user@10.0.0.1/mnt/foo/bar - d35c699..fed0636 git-annex -> synced/git-annex - a44bfb2..818b7b5 annex/direct/old_state4 -> synced/old_state4 - -This is what another machine says: - - [2016-03-08 21:17:48.649949] Pusher: Syncing with host123 - (recording state in git...) - To ssh://user@10.0.0.1/mnt/foo/bar - - 423f50f..4c8fad8 annex/direct/master -> q/annex/direct/master - 2a67458..fed0636 git-annex -> host123/git-annex - 6a1076b..4c8fad8 master -> host123/master - 7f55414..818b7b5 old_state4 -> host123/old_state4 - -Long story, short... - -I apologize for being a total git noob while at the same time performing git magic leading into a total desaster. -However, I hope someone can give me a hint what to do to have the "old_state4" solved? - -Also, I really would like to get used to the git internals but since git is quite powerful, I always get overwhelmed because the tutorials out there are either developer-focused (which I'm not in the correct target group) or they simply cover each and everything (which is of no use because I don't want to administrate a GitHub repo but a private git-annex for my files and documents). - -Thank you so much! - - -[1] http://stackoverflow.com/questions/4114095/revert-git-repo-to-a-previous-commit From 1d81caedfe7e6e089578f87c23d8c36967cf7edd Mon Sep 17 00:00:00 2001 From: torpidus Date: Sun, 13 Mar 2016 19:19:13 +0000 Subject: [PATCH 22/88] --- ...messed_up_annex_by_using_git_checkout.mdwn | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 doc/forum/messed_up_annex_by_using_git_checkout.mdwn diff --git a/doc/forum/messed_up_annex_by_using_git_checkout.mdwn b/doc/forum/messed_up_annex_by_using_git_checkout.mdwn new file mode 100644 index 0000000000..f9b2eb63c4 --- /dev/null +++ b/doc/forum/messed_up_annex_by_using_git_checkout.mdwn @@ -0,0 +1,40 @@ +Hello. Linux experienced user here, but with no development or git experience ever. This directly leads me to my biggest trouble with git-annex because I constantly suffer from misunderstanding each and everything. That being said, my problem is the following: I had the terrible idea to have my .thunderbird directory synchronized over several machines, leading the thunderbird profile to total corruption because after a few weeks I finally managed to have multiple machines accessing it. As I started trying to recover, things got worse and this is my last seek for help before starting over by creating the repositories from scratch. + +What I did: + +1. I did some research on how to recover an old state of the repo, which should not have been a problem because there is a "full backup" repo. I came across this [1] page and the pain started with me looking for my wanted commit to roll-back in "git log" and then did some tries in the way something like, "git checkout -b old-state4 012345678". + +2. Of course this recovered the whole repo and not only thunderbird, so I used a file synchronizer to put everything else back into place after the action. + +3. Unfortunately, the "branches" seem to have been messed up and the repos are no longer in sync. + +This is what the machine says that I have used to create the mess: + + [2016-03-08 19:15:26.915116] Pusher: Syncing with host123 + (recording state in git...) + To ssh://user@10.0.0.1/mnt/foo/bar + d35c699..fed0636 git-annex -> synced/git-annex + a44bfb2..818b7b5 annex/direct/old_state4 -> synced/old_state4 + +This is what another machine says: + + [2016-03-08 21:17:48.649949] Pusher: Syncing with host123 + (recording state in git...) + To ssh://user@10.0.0.1/mnt/foo/bar + + 423f50f..4c8fad8 annex/direct/master -> q/annex/direct/master + 2a67458..fed0636 git-annex -> host123/git-annex + 6a1076b..4c8fad8 master -> host123/master + 7f55414..818b7b5 old_state4 -> host123/old_state4 + +Long story, short... + +I apologize for being a total git noob while at the same time performing git magic leading into a total desaster. +However, I hope someone can give me a hint what to do to have the "old_state4" solved? + +Also, I really would like to get used to the git internals but since git is quite powerful, I always get overwhelmed because the tutorials out there are either developer-focused (which I'm not in the correct target group) or they simply cover each and everything (which is of no use because I don't want to administrate a GitHub repo but a private git-annex for my files and documents). + +Thank you so much! + + +[1] http://stackoverflow.com/questions/4114095/revert-git-repo-to-a-previous-commit From 8f362565a8e69073c7fd77faf17994e83b12680d Mon Sep 17 00:00:00 2001 From: Horus Date: Mon, 14 Mar 2016 08:18:50 +0000 Subject: [PATCH 23/88] Added a comment --- .../comment_1_a5421711102fb1649d98d916e5ced86b._comment | 7 +++++++ 1 file changed, 7 insertions(+) create mode 100644 doc/forum/Autostart_the_assistant/comment_1_a5421711102fb1649d98d916e5ced86b._comment diff --git a/doc/forum/Autostart_the_assistant/comment_1_a5421711102fb1649d98d916e5ced86b._comment b/doc/forum/Autostart_the_assistant/comment_1_a5421711102fb1649d98d916e5ced86b._comment new file mode 100644 index 0000000000..88ad0fc3ad --- /dev/null +++ b/doc/forum/Autostart_the_assistant/comment_1_a5421711102fb1649d98d916e5ced86b._comment @@ -0,0 +1,7 @@ +[[!comment format=mdwn + username="Horus" + subject="comment 1" + date="2016-03-14T08:18:49Z" + content=""" +Bump that, since a vast number of ancient posts somehow were resurrected... +"""]] From 1df49506c4989f53d75bb7ec11926bbe8c8f18a4 Mon Sep 17 00:00:00 2001 From: Joey Hess Date: Mon, 14 Mar 2016 13:13:56 -0400 Subject: [PATCH 24/88] Correct git-annex info to include unlocked files in v6 repository. An unlocked present file does not have a pointer file in the worktree, so info skipped counting it. It may be that unused was also affected by the problem, but it seemed not to be in my tests. I think because of the use of the associatedFilesFilter. This fix slows down both info and unused a little bit, since they have to query the contents of files from git, but only when handling unlocked files. --- Annex/Link.hs | 4 +++- Command/Unused.hs | 6 ++---- debian/changelog | 1 + 3 files changed, 6 insertions(+), 5 deletions(-) diff --git a/Annex/Link.hs b/Annex/Link.hs index 40e56f23ef..629e77d7f2 100644 --- a/Annex/Link.hs +++ b/Annex/Link.hs @@ -159,7 +159,9 @@ formatPointer :: Key -> String formatPointer k = toInternalGitPath (pathSeparator:objectDir keyFile k) ++ "\n" -{- Checks if a file is a pointer to a key. -} +{- Checks if a worktree file is a pointer to a key. + - + - Unlocked files whose content is present are not detected by this. -} isPointerFile :: FilePath -> IO (Maybe Key) isPointerFile f = catchDefaultIO Nothing $ do b <- L.take maxPointerSz <$> L.readFile f diff --git a/Command/Unused.hs b/Command/Unused.hs index b6f3e93b6d..8040dc21ac 100644 --- a/Command/Unused.hs +++ b/Command/Unused.hs @@ -27,6 +27,7 @@ import qualified Remote import qualified Annex.Branch import Annex.Link import Annex.CatFile +import Annex.WorkTree import Types.RefSpec import Git.Types import Git.Sha @@ -215,10 +216,7 @@ withKeysReferenced' mdir initial a = do Just dir -> inRepo $ LsFiles.inRepo [dir] go v [] = return v go v (f:fs) = do - mk <- getM id - [ isAnnexLink f - , liftIO (isPointerFile f) - ] + mk <- lookupFile f case mk of Nothing -> go v fs Just k -> do diff --git a/debian/changelog b/debian/changelog index fc01dbdafa..e2c13be40c 100644 --- a/debian/changelog +++ b/debian/changelog @@ -12,6 +12,7 @@ git-annex (6.20160230) UNRELEASED; urgency=medium * Fix OSX dmg to include libraries needed by bundled gpg, lost in last release. * Always try to thaw content, even when annex.crippledfilesystem is set. + * Correct git-annex info to include unlocked files in v6 repository. -- Joey Hess Mon, 29 Feb 2016 13:00:30 -0400 From 7398fc36f2206253c5b1fbecb205d80f9c2be78f Mon Sep 17 00:00:00 2001 From: Joey Hess Date: Mon, 14 Mar 2016 13:26:26 -0400 Subject: [PATCH 25/88] response --- ..._e08eb54547bfd4dbfcc79a5a4a529647._comment | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 doc/forum/converting_a_v5_repo_to_an_always_unlocked_v6_repo/comment_1_e08eb54547bfd4dbfcc79a5a4a529647._comment diff --git a/doc/forum/converting_a_v5_repo_to_an_always_unlocked_v6_repo/comment_1_e08eb54547bfd4dbfcc79a5a4a529647._comment b/doc/forum/converting_a_v5_repo_to_an_always_unlocked_v6_repo/comment_1_e08eb54547bfd4dbfcc79a5a4a529647._comment new file mode 100644 index 0000000000..362609f524 --- /dev/null +++ b/doc/forum/converting_a_v5_repo_to_an_always_unlocked_v6_repo/comment_1_e08eb54547bfd4dbfcc79a5a4a529647._comment @@ -0,0 +1,35 @@ +[[!comment format=mdwn + username="joey" + subject="""comment 1""" + date="2016-03-14T16:48:33Z" + content=""" +Thank you for trying v6 unlocked mode; do note that it's still somewhat +experimental. + +`git annex info` doesn't report correctly on unlocked files, which is why +it has 0 in two places in the output you showed. I have just committed a +fix for that problem. + +I don't know what would cause the unexpectedly small "local annex size". +That should correspond to `du -hsc .git/annex/objects`; if it does then you +seem to have fewer annexed objects than you expect for some reason. + +The behavior on sync sounds kind of like git commit is checking the whole +contents of files into git, bypassing the annex. I don't know how that +could happen, barring a misconfiguration, but it's at least the first thing +to check. Check for gigabytes of data in .git/objects/ to see if that +is the case. + +If the above isn't the problem, can you see if the files in the work tree +have a link count of 2? For example: + + $ ls -l + -rw-r--r-- 2 joey joey 30 Mar 14 12:49 foo + ^ + +If you don't see link count of 2, something has caused the annex.thin not +to take effect. One possibility would be if the `git annex sync` merged in +changes that moved a lot of files around. When that happens, git checks out +the updated work tree, and git-annex currently is not able to preserve +annex.thin in that case. +"""]] From 6bc44d5d16206a3fd6df84d3a250880c7783bbd5 Mon Sep 17 00:00:00 2001 From: Joey Hess Date: Mon, 14 Mar 2016 13:30:25 -0400 Subject: [PATCH 26/88] comment --- ...omment_1_04f33895f6451690372595c576be2811._comment | 11 +++++++++++ 1 file changed, 11 insertions(+) create mode 100644 doc/forum/messed_up_annex_by_using_git_checkout/comment_1_04f33895f6451690372595c576be2811._comment diff --git a/doc/forum/messed_up_annex_by_using_git_checkout/comment_1_04f33895f6451690372595c576be2811._comment b/doc/forum/messed_up_annex_by_using_git_checkout/comment_1_04f33895f6451690372595c576be2811._comment new file mode 100644 index 0000000000..cd480bc153 --- /dev/null +++ b/doc/forum/messed_up_annex_by_using_git_checkout/comment_1_04f33895f6451690372595c576be2811._comment @@ -0,0 +1,11 @@ +[[!comment format=mdwn + username="joey" + subject="""comment 1""" + date="2016-03-14T17:27:17Z" + content=""" +You don't seem to really say what the problem is, but I guess it has +something to do with this `old_state4` branch which you have made. + +Maybe check what `git branch` shows to see if that branch is checked out, +and if so, `git checkout master` to get back to the master branch. +"""]] From dc2da86939ad54ef1394f9e15bbf32e410a3816d Mon Sep 17 00:00:00 2001 From: Joey Hess Date: Mon, 14 Mar 2016 13:38:41 -0400 Subject: [PATCH 27/88] comment --- ..._2f0c74aba502533b85b922ea81ded70d._comment | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 doc/bugs/Git_copy_fails_with_absolute_path_on_mavericks/comment_1_2f0c74aba502533b85b922ea81ded70d._comment diff --git a/doc/bugs/Git_copy_fails_with_absolute_path_on_mavericks/comment_1_2f0c74aba502533b85b922ea81ded70d._comment b/doc/bugs/Git_copy_fails_with_absolute_path_on_mavericks/comment_1_2f0c74aba502533b85b922ea81ded70d._comment new file mode 100644 index 0000000000..e538a75c62 --- /dev/null +++ b/doc/bugs/Git_copy_fails_with_absolute_path_on_mavericks/comment_1_2f0c74aba502533b85b922ea81ded70d._comment @@ -0,0 +1,23 @@ +[[!comment format=mdwn + username="joey" + subject="""comment 1""" + date="2016-03-14T17:34:21Z" + content=""" +Using absolute paths to files is an unusual thing to do with git in my +experience. But, git does seem to support it, at least some of the time. + +I think that git-annex's support for it comes down to what `git ls-files` +does. For example: + + joey@darkstar:~/tmp/me> git ls-files ~/tmp/me/foo + foo + +Since git-annex uses git ls-files, it sees a relative file and so +all or most all git-annex commands can work with the absolute file input. + +Does git ls-files convert the absolute path to a relative path +when you run it on the Mavericks system? + +What version of git is installed on the Mavericks system? Is +git-annex installed from the git-annex app, or from homebrew, or how? +"""]] From 5633e8ed50fd8757ca2ca1ff513a2d08427ac1b3 Mon Sep 17 00:00:00 2001 From: Joey Hess Date: Mon, 14 Mar 2016 13:50:47 -0400 Subject: [PATCH 28/88] comment --- ..._df70bd0f5caab43503a3c9d805323289._comment | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 doc/forum/Autostart_the_assistant/comment_2_df70bd0f5caab43503a3c9d805323289._comment diff --git a/doc/forum/Autostart_the_assistant/comment_2_df70bd0f5caab43503a3c9d805323289._comment b/doc/forum/Autostart_the_assistant/comment_2_df70bd0f5caab43503a3c9d805323289._comment new file mode 100644 index 0000000000..3bad9e467b --- /dev/null +++ b/doc/forum/Autostart_the_assistant/comment_2_df70bd0f5caab43503a3c9d805323289._comment @@ -0,0 +1,35 @@ +[[!comment format=mdwn + username="joey" + subject="""comment 2""" + date="2016-03-14T17:41:38Z" + content=""" +The way autostart works is, the repository gets listed in +`~/.config/git-annex/autostart` -- setting up that file is all that +the webapp preferences does. + +`git annex assistant --autostart` looks at that files and gets the +assistant running in each listed repository. + +Now, something has to take care of running that command when the system +starts or you log in or whatever. At this point it gets OS dependant. + +For example, on Debian, this is handled by the git-annex package containing +`/etc/xdg/autostart/git-annex.desktop` + +Sounds like they may have left this file out of the Arch package. + +git-annex's `make install` handles building that desktop file. It only +generates it if run as root, or with DESTDIR set. One or the other should +normally be the case when building a package. + +Here's the content of `/etc/xdg/autostart/git-annex.desktop` + + [Desktop Entry] + Type=Application + Version=1.0 + Name=Git Annex Assistant + Comment=Autostart + Terminal=false + Exec=/usr/bin/git-annex assistant --autostart + Categories= +"""]] From 11d31f53bf2198f3f20e783f750273619c0d25e4 Mon Sep 17 00:00:00 2001 From: Joey Hess Date: Mon, 14 Mar 2016 13:55:57 -0400 Subject: [PATCH 29/88] comment --- ...mment_1_9e4ba1e03a89c219c5e62280757311ba._comment | 12 ++++++++++++ 1 file changed, 12 insertions(+) create mode 100644 doc/bugs/R__47__O_permissions_are_stalking_me_somehow/comment_1_9e4ba1e03a89c219c5e62280757311ba._comment diff --git a/doc/bugs/R__47__O_permissions_are_stalking_me_somehow/comment_1_9e4ba1e03a89c219c5e62280757311ba._comment b/doc/bugs/R__47__O_permissions_are_stalking_me_somehow/comment_1_9e4ba1e03a89c219c5e62280757311ba._comment new file mode 100644 index 0000000000..6e77495297 --- /dev/null +++ b/doc/bugs/R__47__O_permissions_are_stalking_me_somehow/comment_1_9e4ba1e03a89c219c5e62280757311ba._comment @@ -0,0 +1,12 @@ +[[!comment format=mdwn + username="joey" + subject="""comment 1""" + date="2016-03-14T17:53:32Z" + content=""" +A file's permissions cannot prevent it being renamed; so I diagnose some +kind of directory permission problem. + +(Also AFAICS git-annex add deals with files whose permissions don't allow +being read by turning on the read bit. And it should never need the write +bit. I can `chmod 000 foo; git annex add foo` and it succeeds..) +"""]] From f2772f469af21a2853667527349cb1983c25c485 Mon Sep 17 00:00:00 2001 From: Joey Hess Date: Mon, 14 Mar 2016 15:54:46 -0400 Subject: [PATCH 30/88] followup --- Annex/HashObject.hs | 54 +++++++++++++++++++ ..._3233c29405da296360d57af7d5eb418d._comment | 46 ++++++++++++++++ 2 files changed, 100 insertions(+) create mode 100644 Annex/HashObject.hs create mode 100644 doc/bugs/__39__add__39___results_in_max_cpu__44___long_run_and_huge_repo/comment_1_3233c29405da296360d57af7d5eb418d._comment diff --git a/Annex/HashObject.hs b/Annex/HashObject.hs new file mode 100644 index 0000000000..aa8c2a1746 --- /dev/null +++ b/Annex/HashObject.hs @@ -0,0 +1,54 @@ +{- git hash-object interface, with handle automatically stored in the Annex monad + - + - Copyright 2016 Joey Hess + - + - Licensed under the GNU GPL version 3 or higher. + -} + +module Annex.HashObject ( + hashFile, + hashBlob, + hashObjectHandle, + hashObjectStop, +) where + +import qualified Data.ByteString.Lazy as L +import qualified Data.Map as M +import System.PosixCompat.Types + +import Annex.Common +import qualified Git +import qualified Git.HashObject +import qualified Annex +import Git.Types +import Git.FilePath +import qualified Git.Ref +import Annex.Link + +hashObjectHandle :: Annex Git.HashObject.HashObjectHandle +hashObjectHandle = maybe startup return =<< Annex.getState Annex.hashobjecthandle + where + startup = do + inRepo $ Git.hashObjectStart + Annex.changeState $ \s -> s { Annex.hashobjecthandle = Just h } + return h + +hashObjectStop :: Annex () +hashObjectStop = maybe noop stop =<< Annex.hashobjecthandle + where + stop h = do + liftIO $ Git.hashObjectStop h + Annex.changeState $ \s -> s { Annex.hashobjecthandle = Nothing } + +hashFile :: FilePath -> Annex Sha +hashFile f = do + h <- hashObjectHandle + Git.HashObject.hashFile h f + +{- Note that the content will be written to a temp file. + - So it may be faster to use Git.HashObject.hashObject for large + - blob contents. -} +hashBlob :: String -> Annex Sha +hashBlob content = do + h <- hashObjectHandle + Git.HashObject.hashFile h content diff --git a/doc/bugs/__39__add__39___results_in_max_cpu__44___long_run_and_huge_repo/comment_1_3233c29405da296360d57af7d5eb418d._comment b/doc/bugs/__39__add__39___results_in_max_cpu__44___long_run_and_huge_repo/comment_1_3233c29405da296360d57af7d5eb418d._comment new file mode 100644 index 0000000000..4bd283aa22 --- /dev/null +++ b/doc/bugs/__39__add__39___results_in_max_cpu__44___long_run_and_huge_repo/comment_1_3233c29405da296360d57af7d5eb418d._comment @@ -0,0 +1,46 @@ +[[!comment format=mdwn + username="joey" + subject="""comment 1""" + date="2016-03-14T17:59:08Z" + content=""" +If I've done the math right, 5 files per second over 3 hours is only 2000 files. +The size of the files does matter, since git-annex has to read them all. +You said the repo grew to 28 gb; does that mean you added 2000 files +totalling 28 gb in size? + +I can add 2000 tiny files (5 bytes each) in 2 seconds on a SSD on Linux. + +By using a FAT filesystem, you've forced git-annex to use direct mode. +Direct mode can be a little slower, but not a great deal. Adding 2000 files +to a direct mode repo takes around 11 seconds here. (I did a little +optimisation and sped that up to 7 seconds.) + +Doing the same benchmark on a removable USB stick with a FAT filesystem +was still not slow; 7 seconds again. + +But then I had linux mount that FAT filesystem sync (so, it flushes each +file write to disk, not buffering them), and I start getting closer to your +slow speed; benchmark took 53 minutes. + +So, I think the slow speed you're seeing is quite likely due to a +combination of, in order from most to least important: + +1. Synchronous writes to your disk drive. Fixable in linux by eg, running + "mount -o remount,async /path/to/repo" and there's probably something + similar for OSX. +2. External drive being slow to access. (And if a spinning disk, slow to + seek.) +3. git-annex using direct mode on FAT + +Also there is a fair amount of faff that git-annex does when adding a file +around calling rename, stat, mkdir, etc multiple times. It may be possible +to optimize some of that to get at some speedup on synchronous disks. +But, I'd not expect more than a few percentage points speedup from such +optimisation. + +One other possiblity is you could be hitting an edge case where direct mode's +performace is bad. One known such edge case is if you have a lot of files +that all have the same content. For example, I made 2000 files that were +all empty; adding them to a direct mode repository gets slower and slower +to the point it's spending 10 or more seconds per file. +"""]] From 88a4a6f396fa0f31793dd21aef9e12ff9696e30f Mon Sep 17 00:00:00 2001 From: Joey Hess Date: Mon, 14 Mar 2016 15:58:46 -0400 Subject: [PATCH 31/88] Sped up git-annex add in direct mode and v6 by using git hash-object --batch. Speeds up hashSymlink and hashPointerFile. --- Annex.hs | 3 +++ Annex/Concurrent.hs | 2 ++ Annex/HashObject.hs | 19 ++++++------------- Annex/Link.hs | 12 +++--------- Annex/View.hs | 20 +++++++++----------- debian/changelog | 2 ++ 6 files changed, 25 insertions(+), 33 deletions(-) diff --git a/Annex.hs b/Annex.hs index 6a3d0cebb8..fe68027769 100644 --- a/Annex.hs +++ b/Annex.hs @@ -42,6 +42,7 @@ import qualified Git import qualified Git.Config import Annex.Fixup import Git.CatFile +import Git.HashObject import Git.CheckAttr import Git.CheckIgnore import qualified Git.Hook @@ -106,6 +107,7 @@ data AnnexState = AnnexState , branchstate :: BranchState , repoqueue :: Maybe Git.Queue.Queue , catfilehandles :: M.Map FilePath CatFileHandle + , hashobjecthandle :: Maybe HashObjectHandle , checkattrhandle :: Maybe CheckAttrHandle , checkignorehandle :: Maybe (Maybe CheckIgnoreHandle) , forcebackend :: Maybe String @@ -151,6 +153,7 @@ newState c r = AnnexState , branchstate = startBranchState , repoqueue = Nothing , catfilehandles = M.empty + , hashobjecthandle = Nothing , checkattrhandle = Nothing , checkignorehandle = Nothing , forcebackend = Nothing diff --git a/Annex/Concurrent.hs b/Annex/Concurrent.hs index d5809df457..ee19d4766b 100644 --- a/Annex/Concurrent.hs +++ b/Annex/Concurrent.hs @@ -11,6 +11,7 @@ import Annex.Common import Annex import Annex.CatFile import Annex.CheckAttr +import Annex.HashObject import Annex.CheckIgnore import qualified Annex.Queue @@ -64,4 +65,5 @@ mergeState st = do closehandles = do catFileStop checkAttrStop + hashObjectStop checkIgnoreStop diff --git a/Annex/HashObject.hs b/Annex/HashObject.hs index aa8c2a1746..16f7414076 100644 --- a/Annex/HashObject.hs +++ b/Annex/HashObject.hs @@ -12,38 +12,31 @@ module Annex.HashObject ( hashObjectStop, ) where -import qualified Data.ByteString.Lazy as L -import qualified Data.Map as M -import System.PosixCompat.Types - import Annex.Common -import qualified Git import qualified Git.HashObject import qualified Annex import Git.Types -import Git.FilePath -import qualified Git.Ref -import Annex.Link hashObjectHandle :: Annex Git.HashObject.HashObjectHandle hashObjectHandle = maybe startup return =<< Annex.getState Annex.hashobjecthandle where startup = do - inRepo $ Git.hashObjectStart + h <- inRepo $ Git.HashObject.hashObjectStart Annex.changeState $ \s -> s { Annex.hashobjecthandle = Just h } return h hashObjectStop :: Annex () -hashObjectStop = maybe noop stop =<< Annex.hashobjecthandle +hashObjectStop = maybe noop stop =<< Annex.getState Annex.hashobjecthandle where stop h = do - liftIO $ Git.hashObjectStop h + liftIO $ Git.HashObject.hashObjectStop h Annex.changeState $ \s -> s { Annex.hashobjecthandle = Nothing } + return () hashFile :: FilePath -> Annex Sha hashFile f = do h <- hashObjectHandle - Git.HashObject.hashFile h f + liftIO $ Git.HashObject.hashFile h f {- Note that the content will be written to a temp file. - So it may be faster to use Git.HashObject.hashObject for large @@ -51,4 +44,4 @@ hashFile f = do hashBlob :: String -> Annex Sha hashBlob content = do h <- hashObjectHandle - Git.HashObject.hashFile h content + liftIO $ Git.HashObject.hashBlob h content diff --git a/Annex/Link.hs b/Annex/Link.hs index 629e77d7f2..b191bce6fe 100644 --- a/Annex/Link.hs +++ b/Annex/Link.hs @@ -18,11 +18,11 @@ module Annex.Link where import Annex.Common import qualified Annex -import qualified Git.HashObject import qualified Git.UpdateIndex import qualified Annex.Queue import Git.Types import Git.FilePath +import Annex.HashObject import qualified Data.ByteString.Lazy as L import Data.Int @@ -105,12 +105,7 @@ addAnnexLink linktarget file = do {- Injects a symlink target into git, returning its Sha. -} hashSymlink :: LinkTarget -> Annex Sha -hashSymlink linktarget = inRepo $ Git.HashObject.hashObject BlobObject $ - toInternalGitPath linktarget - -hashSymlink' :: Git.HashObject.HashObjectHandle -> LinkTarget -> Annex Sha -hashSymlink' h linktarget = liftIO $ Git.HashObject.hashBlob h $ - toInternalGitPath linktarget +hashSymlink linktarget = hashBlob (toInternalGitPath linktarget) {- Stages a symlink to an annexed object, using a Sha of its target. -} stageSymlink :: FilePath -> Sha -> Annex () @@ -120,8 +115,7 @@ stageSymlink file sha = {- Injects a pointer file content into git, returning its Sha. -} hashPointerFile :: Key -> Annex Sha -hashPointerFile key = inRepo $ Git.HashObject.hashObject BlobObject $ - formatPointer key +hashPointerFile key = hashBlob (formatPointer key) {- Stages a pointer file, using a Sha of its content -} stagePointerFile :: FilePath -> Sha -> Annex () diff --git a/Annex/View.hs b/Annex/View.hs index 14c3eccad2..0078c2cad1 100644 --- a/Annex/View.hs +++ b/Annex/View.hs @@ -19,7 +19,7 @@ import qualified Git.LsFiles import qualified Git.Ref import Git.UpdateIndex import Git.Sha -import Git.HashObject +import Annex.HashObject import Git.Types import Git.FilePath import Annex.WorkTree @@ -340,38 +340,36 @@ applyView' mkviewedfile getfilemetadata view = do (l, clean) <- inRepo $ Git.LsFiles.inRepo [top] liftIO . nukeFile =<< fromRepo gitAnnexViewIndex uh <- withViewIndex $ inRepo Git.UpdateIndex.startUpdateIndex - hasher <- inRepo hashObjectStart forM_ l $ \f -> do relf <- getTopFilePath <$> inRepo (toTopFilePath f) - go uh hasher relf =<< lookupFile f + go uh relf =<< lookupFile f liftIO $ do - hashObjectStop hasher void $ stopUpdateIndex uh void clean genViewBranch view where genviewedfiles = viewedFiles view mkviewedfile -- enables memoization - go uh hasher f (Just k) = do + go uh f (Just k) = do metadata <- getCurrentMetaData k let metadata' = getfilemetadata f `unionMetaData` metadata forM_ (genviewedfiles f metadata') $ \fv -> do f' <- fromRepo $ fromTopFilePath $ asTopFilePath fv - stagesymlink uh hasher f' =<< calcRepo (gitAnnexLink f' k) - go uh hasher f Nothing + stagesymlink uh f' =<< calcRepo (gitAnnexLink f' k) + go uh f Nothing | "." `isPrefixOf` f = do s <- liftIO $ getSymbolicLinkStatus f if isSymbolicLink s - then stagesymlink uh hasher f =<< liftIO (readSymbolicLink f) + then stagesymlink uh f =<< liftIO (readSymbolicLink f) else do - sha <- liftIO $ Git.HashObject.hashFile hasher f + sha <- hashFile f let blobtype = if isExecutable (fileMode s) then ExecutableBlob else FileBlob liftIO . Git.UpdateIndex.streamUpdateIndex' uh =<< inRepo (Git.UpdateIndex.stageFile sha blobtype f) | otherwise = noop - stagesymlink uh hasher f linktarget = do - sha <- hashSymlink' hasher linktarget + stagesymlink uh f linktarget = do + sha <- hashSymlink linktarget liftIO . Git.UpdateIndex.streamUpdateIndex' uh =<< inRepo (Git.UpdateIndex.stageSymlink f sha) diff --git a/debian/changelog b/debian/changelog index e2c13be40c..d5b98c1927 100644 --- a/debian/changelog +++ b/debian/changelog @@ -13,6 +13,8 @@ git-annex (6.20160230) UNRELEASED; urgency=medium lost in last release. * Always try to thaw content, even when annex.crippledfilesystem is set. * Correct git-annex info to include unlocked files in v6 repository. + * Sped up git-annex add in direct mode and v6 by using + git hash-object --batch. -- Joey Hess Mon, 29 Feb 2016 13:00:30 -0400 From 00d9da353482e5ebb2995b59235af730c1b91618 Mon Sep 17 00:00:00 2001 From: Joey Hess Date: Mon, 14 Mar 2016 16:12:55 -0400 Subject: [PATCH 32/88] use hash-object --batch Handle was plumbed through, but not used. --- Annex/Branch.hs | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Annex/Branch.hs b/Annex/Branch.hs index 6ef778801e..a46a90ee9a 100644 --- a/Annex/Branch.hs +++ b/Annex/Branch.hs @@ -564,7 +564,7 @@ performTransitionsLocked jl ts neednewlocalbranch transitionedrefs = do -- transitions on it. return () ChangeFile content' -> do - sha <- inRepo $ hashObject BlobObject content' + sha <- liftIO $ hashBlob hasher content' Annex.Queue.addUpdateIndex $ Git.UpdateIndex.pureStreamer $ Git.UpdateIndex.updateIndexLine sha FileBlob (asTopFilePath file) apply rest hasher file content' trustmap From a27faf699965f3d175fd1eb1de7e6768ca48c8d4 Mon Sep 17 00:00:00 2001 From: Joey Hess Date: Mon, 14 Mar 2016 16:19:27 -0400 Subject: [PATCH 33/88] fix build of this --- git-union-merge.hs | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/git-union-merge.hs b/git-union-merge.hs index 31c71ba729..6930640452 100644 --- a/git-union-merge.hs +++ b/git-union-merge.hs @@ -44,5 +44,5 @@ main = do _ <- Git.Index.override $ tmpIndex g setup g Git.UnionMerge.merge aref bref g - _ <- Git.Branch.commit "union merge" newref [aref, bref] g + _ <- Git.Branch.commit Git.Branch.ManualCommit False "union merge" newref [aref, bref] g cleanup g From 2d234de78152cd6dd7fe4e69e25ad8321f7266ce Mon Sep 17 00:00:00 2001 From: Joey Hess Date: Mon, 14 Mar 2016 16:23:22 -0400 Subject: [PATCH 34/88] Sped up git-annex merge by using git hash-object --batch. This does mean that it has to write out temp files containing updated objects for the merge. So may use more disk space, and disk IO, but that should generally win out over needing to launch N separate git hash-object processes. --- Annex/Branch.hs | 6 ++++-- Git/UnionMerge.hs | 35 +++++++++++++++++++---------------- debian/changelog | 1 + 3 files changed, 24 insertions(+), 18 deletions(-) diff --git a/Annex/Branch.hs b/Annex/Branch.hs index a46a90ee9a..d6735be883 100644 --- a/Annex/Branch.hs +++ b/Annex/Branch.hs @@ -50,6 +50,7 @@ import Git.Types import Git.FilePath import Annex.CatFile import Annex.Perms +import Annex.HashObject (hashObjectHandle) import Logs import Logs.Transitions import Logs.Trust.Pure @@ -342,8 +343,9 @@ genIndex g = Git.UpdateIndex.streamUpdateIndex g mergeIndex :: JournalLocked -> [Git.Ref] -> Annex () mergeIndex jl branches = do prepareModifyIndex jl - h <- catFileHandle - inRepo $ \g -> Git.UnionMerge.mergeIndex h g branches + hashhandle <- hashObjectHandle + ch <- catFileHandle + inRepo $ \g -> Git.UnionMerge.mergeIndex hashhandle ch g branches {- Removes any stale git lock file, to avoid git falling over when - updating the index. diff --git a/Git/UnionMerge.hs b/Git/UnionMerge.hs index bb42e7cc51..9ae8295ae2 100644 --- a/Git/UnionMerge.hs +++ b/Git/UnionMerge.hs @@ -30,12 +30,14 @@ import Git.FilePath -} merge :: Ref -> Ref -> Repo -> IO () merge x y repo = do - h <- catFileStart repo + hashhandle <- hashObjectStart repo + ch <- catFileStart repo streamUpdateIndex repo [ lsTree x repo - , mergeTrees x y h repo + , mergeTrees x y hashhandle ch repo ] - catFileStop h + catFileStop ch + hashObjectStop hashhandle {- Merges a list of branches into the index. Previously staged changes in - the index are preserved (and participate in the merge). @@ -45,17 +47,18 @@ merge x y repo = do - harder to calculate a single union merge involving all the refs, as well - as the index. -} -mergeIndex :: CatFileHandle -> Repo -> [Ref] -> IO () -mergeIndex h repo bs = forM_ bs $ \b -> - streamUpdateIndex repo [mergeTreeIndex b h repo] +mergeIndex :: HashObjectHandle -> CatFileHandle -> Repo -> [Ref] -> IO () +mergeIndex hashhandle ch repo bs = forM_ bs $ \b -> + streamUpdateIndex repo [mergeTreeIndex b hashhandle ch repo] {- For merging two trees. -} -mergeTrees :: Ref -> Ref -> CatFileHandle -> Repo -> Streamer -mergeTrees (Ref x) (Ref y) h = doMerge h $ "diff-tree":diffOpts ++ [x, y, "--"] +mergeTrees :: Ref -> Ref -> HashObjectHandle -> CatFileHandle -> Repo -> Streamer +mergeTrees (Ref x) (Ref y) hashhandle ch = doMerge hashhandle ch + ("diff-tree":diffOpts ++ [x, y, "--"]) {- For merging a single tree into the index. -} -mergeTreeIndex :: Ref -> CatFileHandle -> Repo -> Streamer -mergeTreeIndex (Ref r) h = doMerge h $ +mergeTreeIndex :: Ref -> HashObjectHandle -> CatFileHandle -> Repo -> Streamer +mergeTreeIndex (Ref r) hashhandle ch = doMerge hashhandle ch $ "diff-index" : diffOpts ++ ["--cached", r, "--"] diffOpts :: [String] @@ -63,26 +66,26 @@ diffOpts = ["--raw", "-z", "-r", "--no-renames", "-l0"] {- Streams update-index changes to perform a merge, - using git to get a raw diff. -} -doMerge :: CatFileHandle -> [String] -> Repo -> Streamer -doMerge ch differ repo streamer = do +doMerge :: HashObjectHandle -> CatFileHandle -> [String] -> Repo -> Streamer +doMerge hashhandle ch differ repo streamer = do (diff, cleanup) <- pipeNullSplit (map Param differ) repo go diff void $ cleanup where go [] = noop - go (info:file:rest) = mergeFile info file ch repo >>= + go (info:file:rest) = mergeFile info file hashhandle ch >>= maybe (go rest) (\l -> streamer l >> go rest) go (_:[]) = error $ "parse error " ++ show differ {- Given an info line from a git raw diff, and the filename, generates - a line suitable for update-index that union merges the two sides of the - diff. -} -mergeFile :: String -> FilePath -> CatFileHandle -> Repo -> IO (Maybe String) -mergeFile info file h repo = case filter (/= nullSha) [Ref asha, Ref bsha] of +mergeFile :: String -> FilePath -> HashObjectHandle -> CatFileHandle -> IO (Maybe String) +mergeFile info file hashhandle h = case filter (/= nullSha) [Ref asha, Ref bsha] of [] -> return Nothing (sha:[]) -> use sha shas -> use - =<< either return (\s -> hashObject BlobObject (unlines s) repo) + =<< either return (\s -> hashBlob hashhandle (unlines s)) =<< calcMerge . zip shas <$> mapM getcontents shas where [_colonmode, _bmode, asha, bsha, _status] = words info diff --git a/debian/changelog b/debian/changelog index d5b98c1927..80d07cb773 100644 --- a/debian/changelog +++ b/debian/changelog @@ -15,6 +15,7 @@ git-annex (6.20160230) UNRELEASED; urgency=medium * Correct git-annex info to include unlocked files in v6 repository. * Sped up git-annex add in direct mode and v6 by using git hash-object --batch. + * Sped up git-annex merge by using git hash-object --batch. -- Joey Hess Mon, 29 Feb 2016 13:00:30 -0400 From a2b668a8f69e7267f4a548c1f2013285fd8f1636 Mon Sep 17 00:00:00 2001 From: Joey Hess Date: Mon, 14 Mar 2016 16:29:19 -0400 Subject: [PATCH 35/88] reuse annex's HashObjectHandle --- Annex/Branch.hs | 25 +++++++++++-------------- 1 file changed, 11 insertions(+), 14 deletions(-) diff --git a/Annex/Branch.hs b/Annex/Branch.hs index d6735be883..32aef28a9b 100644 --- a/Annex/Branch.hs +++ b/Annex/Branch.hs @@ -45,12 +45,12 @@ import qualified Git.Branch import qualified Git.UnionMerge import qualified Git.UpdateIndex import Git.LsTree (lsTreeParams) -import Git.HashObject +import qualified Git.HashObject +import Annex.HashObject import Git.Types import Git.FilePath import Annex.CatFile import Annex.Perms -import Annex.HashObject (hashObjectHandle) import Logs import Logs.Transitions import Logs.Trust.Pure @@ -425,11 +425,10 @@ stageJournal jl = withIndex $ do let dir = gitAnnexJournalDir g (jlogf, jlogh) <- openjlog liftIO $ fileEncoding jlogh - withJournalHandle $ \jh -> do - h <- hashObjectStart g + h <- hashObjectHandle + withJournalHandle $ \jh -> Git.UpdateIndex.streamUpdateIndex g [genstream dir h jh jlogh] - hashObjectStop h return $ cleanup dir jlogh jlogf where genstream dir h jh jlogh streamer = do @@ -439,7 +438,7 @@ stageJournal jl = withIndex $ do Just file -> do unless (dirCruft file) $ do let path = dir file - sha <- hashFile h path + sha <- Git.HashObject.hashFile h path hPutStrLn jlogh file streamer $ Git.UpdateIndex.updateIndexLine sha FileBlob (asTopFilePath $ fileJournal file) @@ -551,13 +550,11 @@ performTransitionsLocked jl ts neednewlocalbranch transitionedrefs = do run changers = do trustmap <- calcTrustMap <$> getRaw trustLog fs <- branchFiles - hasher <- inRepo hashObjectStart forM_ fs $ \f -> do content <- getRaw f - apply changers hasher f content trustmap - liftIO $ hashObjectStop hasher - apply [] _ _ _ _ = return () - apply (changer:rest) hasher file content trustmap = + apply changers f content trustmap + apply [] _ _ _ = return () + apply (changer:rest) file content trustmap = case changer file content trustmap of RemoveFile -> do Annex.Queue.addUpdateIndex @@ -566,12 +563,12 @@ performTransitionsLocked jl ts neednewlocalbranch transitionedrefs = do -- transitions on it. return () ChangeFile content' -> do - sha <- liftIO $ hashBlob hasher content' + sha <- hashBlob content' Annex.Queue.addUpdateIndex $ Git.UpdateIndex.pureStreamer $ Git.UpdateIndex.updateIndexLine sha FileBlob (asTopFilePath file) - apply rest hasher file content' trustmap + apply rest file content' trustmap PreserveFile -> - apply rest hasher file content trustmap + apply rest file content trustmap checkBranchDifferences :: Git.Ref -> Annex () checkBranchDifferences ref = do From bd4ad3d2e83ae9a5a0c57daaf620ecf58208b799 Mon Sep 17 00:00:00 2001 From: Joey Hess Date: Mon, 14 Mar 2016 16:37:55 -0400 Subject: [PATCH 36/88] comment --- ...ent_5_46acb9fbbd5ef19f65115723888f3eb6._comment | 14 ++++++++++++++ 1 file changed, 14 insertions(+) create mode 100644 doc/walkthrough/unused_data/comment_5_46acb9fbbd5ef19f65115723888f3eb6._comment diff --git a/doc/walkthrough/unused_data/comment_5_46acb9fbbd5ef19f65115723888f3eb6._comment b/doc/walkthrough/unused_data/comment_5_46acb9fbbd5ef19f65115723888f3eb6._comment new file mode 100644 index 0000000000..2e8af7ff55 --- /dev/null +++ b/doc/walkthrough/unused_data/comment_5_46acb9fbbd5ef19f65115723888f3eb6._comment @@ -0,0 +1,14 @@ +[[!comment format=mdwn + username="joey" + subject="""comment 5""" + date="2016-03-14T20:33:13Z" + content=""" +Tom, it should suffice for your colleague to pull the new +version from you, and then run `git annex unused` to find unused files. + +Now, if you have other branches or tags pointing at older versions +of the data, those files will still be considered to be used, even if +the current version doesn't use them. There's a new +`--used-refspec` option for [[git-annex unused|git-annex-unused]] that +you can use to specify which branches to consider to be used. +"""]] From 3a86cdf3e629eb3364b4ac2bea893eac40b10c06 Mon Sep 17 00:00:00 2001 From: Joey Hess Date: Mon, 14 Mar 2016 16:39:39 -0400 Subject: [PATCH 37/88] comment --- .../comment_2_ff7cbdf93f0be5886f212bdd411efb5b._comment | 9 +++++++++ 1 file changed, 9 insertions(+) create mode 100644 doc/design/adjusted_branches/comment_2_ff7cbdf93f0be5886f212bdd411efb5b._comment diff --git a/doc/design/adjusted_branches/comment_2_ff7cbdf93f0be5886f212bdd411efb5b._comment b/doc/design/adjusted_branches/comment_2_ff7cbdf93f0be5886f212bdd411efb5b._comment new file mode 100644 index 0000000000..6a3502997e --- /dev/null +++ b/doc/design/adjusted_branches/comment_2_ff7cbdf93f0be5886f212bdd411efb5b._comment @@ -0,0 +1,9 @@ +[[!comment format=mdwn + username="joey" + subject="""comment 2""" + date="2016-03-14T20:38:09Z" + content=""" +Yes, lots of things are possible with this. Filtering to only annexed files +probably. May be some hairyness around updating the branch when files are +got or dropped. Matching a preferred content expression, maybe.. +"""]] From 231a914018b6b3e36f898110e21b558cdd034953 Mon Sep 17 00:00:00 2001 From: Joey Hess Date: Mon, 14 Mar 2016 16:42:29 -0400 Subject: [PATCH 38/88] comment --- ...ment_1_396b436e5fec8fc492d9595afa5f6a85._comment | 13 +++++++++++++ 1 file changed, 13 insertions(+) create mode 100644 doc/bugs/duplicate_progress_reports_in_parallel___39__get__39__/comment_1_396b436e5fec8fc492d9595afa5f6a85._comment diff --git a/doc/bugs/duplicate_progress_reports_in_parallel___39__get__39__/comment_1_396b436e5fec8fc492d9595afa5f6a85._comment b/doc/bugs/duplicate_progress_reports_in_parallel___39__get__39__/comment_1_396b436e5fec8fc492d9595afa5f6a85._comment new file mode 100644 index 0000000000..567c494adf --- /dev/null +++ b/doc/bugs/duplicate_progress_reports_in_parallel___39__get__39__/comment_1_396b436e5fec8fc492d9595afa5f6a85._comment @@ -0,0 +1,13 @@ +[[!comment format=mdwn + username="joey" + subject="""comment 1""" + date="2016-03-14T20:40:45Z" + content=""" +Is this git-annex built with the ConcurrentOutput flag? + +It kind of looks like it; if so the only thing that looks wrong +is there are for some reason two copies of each progress line for each +file. + +I don't see this in my testing.. +"""]] From 13f4af5d3328f2a7025f8e2318faed3fcff6c9bf Mon Sep 17 00:00:00 2001 From: Joey Hess Date: Mon, 14 Mar 2016 16:45:27 -0400 Subject: [PATCH 39/88] typo --- debian/changelog | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/debian/changelog b/debian/changelog index 80d07cb773..3bb289298a 100644 --- a/debian/changelog +++ b/debian/changelog @@ -14,8 +14,8 @@ git-annex (6.20160230) UNRELEASED; urgency=medium * Always try to thaw content, even when annex.crippledfilesystem is set. * Correct git-annex info to include unlocked files in v6 repository. * Sped up git-annex add in direct mode and v6 by using - git hash-object --batch. - * Sped up git-annex merge by using git hash-object --batch. + git hash-object --stdin-paths. + * Sped up git-annex merge by using git hash-object --stdin-paths. -- Joey Hess Mon, 29 Feb 2016 13:00:30 -0400 From 31480a54e24cb6056e0bb776aff5a16a09754c38 Mon Sep 17 00:00:00 2001 From: Joey Hess Date: Mon, 14 Mar 2016 16:47:32 -0400 Subject: [PATCH 40/88] close --- doc/todo/optimise_git-annex_merge.mdwn | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/doc/todo/optimise_git-annex_merge.mdwn b/doc/todo/optimise_git-annex_merge.mdwn index 91d18ebd77..ff2da32095 100644 --- a/doc/todo/optimise_git-annex_merge.mdwn +++ b/doc/todo/optimise_git-annex_merge.mdwn @@ -8,6 +8,9 @@ Instead, I'd like a way to stream multiple objects into git using stdin. Sometime, should look at either extending git-hash-object to support that, or possibly look at using git-fast-import instead. +> Well, I went with git hash-object --stdin-paths despite it needing to read from +> temp files. --[[Joey]] + --- `git-annex merge` also runs `git show` once per file that needs to be @@ -21,3 +24,5 @@ There is already a Git.CatFile library that can do this easily. --[[Joey]] Merging used to use memory proportional to the size of the diff. It now streams data, running in constant space. This probably sped it up a lot, as there's much less allocation and GC action. --[[Joey]] + +[[done]] From 834b0ac2d95d5ef9890d97ffca92e7e4fbd7ac0a Mon Sep 17 00:00:00 2001 From: Joey Hess Date: Mon, 14 Mar 2016 16:53:14 -0400 Subject: [PATCH 41/88] devblog --- doc/devblog/day_373__away.mdwn | 6 ++++++ 1 file changed, 6 insertions(+) create mode 100644 doc/devblog/day_373__away.mdwn diff --git a/doc/devblog/day_373__away.mdwn b/doc/devblog/day_373__away.mdwn new file mode 100644 index 0000000000..e8761b4e2c --- /dev/null +++ b/doc/devblog/day_373__away.mdwn @@ -0,0 +1,6 @@ +Caught up with a few last things today, before I leave for +[a week in Boston](http://joeyh.name/trips/2016/boston/). + +Converted several places that ran git hash-object repeatedly to feed data +to a running process. This sped up git-annex add in direct mode and with +v6 unlocked files, by up to 2x. From 199b0d1dd85d500bea5900b2ad8e681f447d2ae2 Mon Sep 17 00:00:00 2001 From: "https://me.yahoo.com/a/EbvxpTI_xP9Aod7Mg4cwGhgjrCrdM5s-#7c0f4" Date: Mon, 14 Mar 2016 21:05:06 +0000 Subject: [PATCH 42/88] Added a comment --- ...2_1c348653d630e40e2ff87b7f6c159b35._comment | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) create mode 100644 doc/bugs/duplicate_progress_reports_in_parallel___39__get__39__/comment_2_1c348653d630e40e2ff87b7f6c159b35._comment diff --git a/doc/bugs/duplicate_progress_reports_in_parallel___39__get__39__/comment_2_1c348653d630e40e2ff87b7f6c159b35._comment b/doc/bugs/duplicate_progress_reports_in_parallel___39__get__39__/comment_2_1c348653d630e40e2ff87b7f6c159b35._comment new file mode 100644 index 0000000000..6e326e59e4 --- /dev/null +++ b/doc/bugs/duplicate_progress_reports_in_parallel___39__get__39__/comment_2_1c348653d630e40e2ff87b7f6c159b35._comment @@ -0,0 +1,18 @@ +[[!comment format=mdwn + username="https://me.yahoo.com/a/EbvxpTI_xP9Aod7Mg4cwGhgjrCrdM5s-#7c0f4" + subject="comment 2" + date="2016-03-14T21:05:06Z" + content=""" +FWIW it was \"stock\" debian/neurodebian build so whatever default or flags you impose in debian/rules -- they were it ;) + +[[!format sh \"\"\" +neurodebian@smaug ..annex/6.20160213+gitg9597a21-1~ndall+1 % grep Concur git-annex_6.20160213+gitg9597a21-1~ndall+1_amd64.build +[178 of 534] Compiling Messages.Concurrent ( Messages/Concurrent.hs, dist/build/git-annex/git-annex-tmp/Messages/Concurrent.o ) +[239 of 534] Compiling Annex.Concurrent ( Annex/Concurrent.hs, dist/build/git-annex/git-annex-tmp/Annex/Concurrent.o ) +build flags: Assistant Webapp Pairing Testsuite S3(multipartupload) WebDAV Inotify DBus DesktopNotify XMPP ConcurrentOutput TorrentParser MagicMime Feeds Quvi +build flags: Assistant Webapp Pairing Testsuite S3(multipartupload) WebDAV Inotify DBus DesktopNotify XMPP ConcurrentOutput TorrentParser MagicMime Feeds Quvi +build flags: Assistant Webapp Pairing Testsuite S3(multipartupload) WebDAV Inotify DBus DesktopNotify XMPP ConcurrentOutput TorrentParser MagicMime Feeds Quvi +build flags: Assistant Webapp Pairing Testsuite S3(multipartupload) WebDAV Inotify DBus DesktopNotify XMPP ConcurrentOutput TorrentParser MagicMime Feeds Quvi + +\"\"\"]] +"""]] From 786643dbf48c52642dfb6f247c14c7671c215e02 Mon Sep 17 00:00:00 2001 From: "https://me.yahoo.com/a/EbvxpTI_xP9Aod7Mg4cwGhgjrCrdM5s-#7c0f4" Date: Mon, 14 Mar 2016 21:10:56 +0000 Subject: [PATCH 43/88] Added a comment --- ..._4600a48aa4c00102b2974c1ae18f6db7._comment | 52 +++++++++++++++++++ 1 file changed, 52 insertions(+) create mode 100644 doc/bugs/duplicate_progress_reports_in_parallel___39__get__39__/comment_3_4600a48aa4c00102b2974c1ae18f6db7._comment diff --git a/doc/bugs/duplicate_progress_reports_in_parallel___39__get__39__/comment_3_4600a48aa4c00102b2974c1ae18f6db7._comment b/doc/bugs/duplicate_progress_reports_in_parallel___39__get__39__/comment_3_4600a48aa4c00102b2974c1ae18f6db7._comment new file mode 100644 index 0000000000..4acf1465bd --- /dev/null +++ b/doc/bugs/duplicate_progress_reports_in_parallel___39__get__39__/comment_3_4600a48aa4c00102b2974c1ae18f6db7._comment @@ -0,0 +1,52 @@ +[[!comment format=mdwn + username="https://me.yahoo.com/a/EbvxpTI_xP9Aod7Mg4cwGhgjrCrdM5s-#7c0f4" + subject="comment 3" + date="2016-03-14T21:10:56Z" + content=""" +just rechecked with freshier version: + +[[!format sh \"\"\" +% git clone https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/repo/freesurfer.git +Cloning into 'freesurfer'... +Checking connectivity... done. +% cd freesurfer +% git annex get -J 5 . +(merging origin/git-annex origin/synced/git-annex into git-annex...) +get BrainstemSS/AtlasDump.mgz (from origin...) (checksum...) ok +get BrainstemSS/AtlasMesh.gz (from origin...) +get GEMS/data/CurrentMeshCollection30.gz + not enough free space, need 2.94 MB more (use --force to override this check or adjust annex.diskreserve) + + Unable to access these remotes: origin + + Try making some of these repositories available: + 14311777-6106-4ba8-8356-2bfb0d198b64 -- zkaufman@sand:/autofs/space/sand_001/users/zkaufman/temp/stable.sync/dev.git + 58892d74-dae0-4bd1-a160-011e82d201f2 -- sand trunk + 6d0bc2d9-c184-445c-82d0-b5c56c5bf5d9 -- zkaufman@gust.nmr.mgh.harvard.edu:/autofs/space/sand_001/users/zkaufman/freesurfer_lion/trunk/dev + 739a31b2-febf-43ee-be59-713bdaa01a06 -- sand-sync + 9240fb38-adbe-4bfe-847a-bdd98d570f75 -- [origin] + ba0b9401-2821-41d2-b9fc-f3319dc053e3 -- sand stable6 + d018cb1b-c841-48b8-ba50-11b686a5c6ad +failed +get BrainstemSS/mac_osx/segmentSubject.app/Contents/Resources/membrane.icns (from origin...) (checksum...) ok +get BrainstemSS/AtlasMesh.gz (from origin...) +.... +get BrainstemSS/AtlasMesh.gz (from origin...) +19% 336.0KB/s 4s +19% 336.0KB/s 4s +get BrainstemSS/linux_x86_64/SegmentSubject.bin (from origin...) +10% 640.0KB/s 9s +10% 640.0KB/s 9s +get BrainstemSS/mac_osx/segmentSubject.app/Contents/MacOS/segmentSubject (from origin...) +18% 864.0KB/s 4s +18% 864.0KB/s 4s +get distribution/average/Buckner_JNeurophysiol11_MNI152/Buckner2011_7Networks_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz (from origin +...) +get distribution/average/Buckner_JNeurophysiol11_MNI152/Buckner2011_7Networks_MNI152_FreeSurferConformed1mm_TightMask.nii.gz (from origin +...) +^C +% git annex version +git-annex version: 6.20160307+gitgb095561-1~ndall+1 +... +\"\"\"]] +"""]] From 91de23966a4c093d6cba2c791bbfc29673f653d8 Mon Sep 17 00:00:00 2001 From: "https://christian.amsuess.com/chrysn" Date: Tue, 15 Mar 2016 07:58:08 +0000 Subject: [PATCH 44/88] new issue with sharedRepository introdcued in 5.20151208 --- ...pository_lead_to_permissionDenied_in_fsck.mdwn | 15 +++++++++++++++ 1 file changed, 15 insertions(+) create mode 100644 doc/bugs/mode_changes_for_sharedRepository_lead_to_permissionDenied_in_fsck.mdwn diff --git a/doc/bugs/mode_changes_for_sharedRepository_lead_to_permissionDenied_in_fsck.mdwn b/doc/bugs/mode_changes_for_sharedRepository_lead_to_permissionDenied_in_fsck.mdwn new file mode 100644 index 0000000000..c1e1d9e177 --- /dev/null +++ b/doc/bugs/mode_changes_for_sharedRepository_lead_to_permissionDenied_in_fsck.mdwn @@ -0,0 +1,15 @@ +### Please describe the problem. + +When a repository created shared pre 5.20151208 is fsck'd, it spews error messages a la `setFileMode: permission denied (Operation not permitted)` and fails the fsck. + +This seems to be due to the change in file permissions introduced in [[news/5.20151208]] ("When core.sharedRepository is set, annex object files are not made mode 444, since that prevents a user other than the file owner from locking them. Instead, a mode such as 664 is used in this case."). The error message is unclear to a user, though, and does IMO not constitute an error to fail over. + +IMO, failure to set the mode due to ownership issues should be ignored in fsck, and when a user other than the original owner tries to lock a file, they should be presented with an error message a la "Please run `git annex fsck --fast` as to fix the file's permissions". As an alternative or additionally, fsck could show a warning (maybe even an error) that running an additional fsck as all of the other users (explicit list would be nice) to fix all file permissions. + +### Workarounds + +The issue can be resolved for a repository by + +### What version of git-annex are you using? On what operating system? + +This was observed on a git-annex remote pushed to via ssh on debian sid, with pushes from various git-annex versions over the past years. From 7b84c2fef4906cd8e690cf6c00ec924f6991b2be Mon Sep 17 00:00:00 2001 From: Horus Date: Tue, 15 Mar 2016 08:53:15 +0000 Subject: [PATCH 45/88] Added a comment --- ..._42de896f64adb49c60ec3f7e0aeebda6._comment | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) create mode 100644 doc/forum/Autostart_the_assistant/comment_3_42de896f64adb49c60ec3f7e0aeebda6._comment diff --git a/doc/forum/Autostart_the_assistant/comment_3_42de896f64adb49c60ec3f7e0aeebda6._comment b/doc/forum/Autostart_the_assistant/comment_3_42de896f64adb49c60ec3f7e0aeebda6._comment new file mode 100644 index 0000000000..3f23c03e54 --- /dev/null +++ b/doc/forum/Autostart_the_assistant/comment_3_42de896f64adb49c60ec3f7e0aeebda6._comment @@ -0,0 +1,19 @@ +[[!comment format=mdwn + username="Horus" + subject="comment 3" + date="2016-03-15T08:53:14Z" + content=""" +I use the Arch package, it is built / installed like that + + runhaskell Setup configure -O --prefix=/usr --docdir=\"/usr/share/doc/${pkgname}\" \ + -fcryptonite -fnetwork-uri -f-ekg -fconcurrentoutput -ftorrentparser \ + -ftestsuite -f-androidsplice -f-android -fproduction -fpairing -fwebapp \ + -fassistant -fwebdav -fs3 -f-benchmark -fdbus -fxmpp -fmagicmime + runhaskell Setup build + + runhaskell Setup copy --destdir=\"${pkgdir}\" + +Seem to be no classical make install involved. I try to peek your build system, but I know way to little about Haskell. + +Is there a way to get all the generated desktop files? Maybe add them to the prebuilt tarball? +"""]] From 784cb2463b161d3220d5cb9eee96e504c5620f4e Mon Sep 17 00:00:00 2001 From: "susetux@ed6f4e20192c3eae018e1fc6442bf993d41b3848" Date: Tue, 15 Mar 2016 14:14:47 +0000 Subject: [PATCH 46/88] Added a comment: re --- ..._85946916ac9c2a19c0d65e2b1a3e5832._comment | 21 +++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 doc/forum/converting_a_v5_repo_to_an_always_unlocked_v6_repo/comment_2_85946916ac9c2a19c0d65e2b1a3e5832._comment diff --git a/doc/forum/converting_a_v5_repo_to_an_always_unlocked_v6_repo/comment_2_85946916ac9c2a19c0d65e2b1a3e5832._comment b/doc/forum/converting_a_v5_repo_to_an_always_unlocked_v6_repo/comment_2_85946916ac9c2a19c0d65e2b1a3e5832._comment new file mode 100644 index 0000000000..4c8f1b2387 --- /dev/null +++ b/doc/forum/converting_a_v5_repo_to_an_always_unlocked_v6_repo/comment_2_85946916ac9c2a19c0d65e2b1a3e5832._comment @@ -0,0 +1,21 @@ +[[!comment format=mdwn + username="susetux@ed6f4e20192c3eae018e1fc6442bf993d41b3848" + nickname="susetux" + subject="re" + date="2016-03-15T14:14:47Z" + content=""" +Hi, thanks for your quick feedback! + +So, I've investigated a bit and this is what I found: + +1. hardlinks are there: both \"ls -l\" and \"find -samefile\" report that most files (I haven't checked all of them though) are hardlinked, as expected, in the annex. So annex.thin is doing something. +2. \"du -shc .git/annex/objects\" has the same size of the same command given on the whole annex, as expected (du counts hard links only once, so it makes sense). It gives about 933G. +3. 900G is well above what it should be: 530G of the indirect annex. +4. This size is also reported in git annex info: \"local annex size: 933.19 gigabytes\" +5. I tried locking the files again (and git annex fix), but the annex remained oversized. + +I currently deleted the annex and restored from a backup because I couldn't afford to keep it in an inconsistent state. +It seems like this problem can be consistently reproduced. I had the same problem on a smaller annex (200G) which took a long time to commit and also inflated during the process. At the end of the process (it had enough space to finish) the size shrinked again, although it was still bigger than the original. I also tried with a test annex and random data a the problem seemed to still be there. + + +"""]] From 4f171baa894bd2647f83420abde4f74fc64f02d7 Mon Sep 17 00:00:00 2001 From: openmedi Date: Wed, 16 Mar 2016 21:05:31 +0000 Subject: [PATCH 47/88] --- ...nex_assistant_atempts_to_repair__44___but_never_finishes.mdwn | 1 + 1 file changed, 1 insertion(+) create mode 100644 doc/forum/git-annex_assistant_atempts_to_repair__44___but_never_finishes.mdwn diff --git a/doc/forum/git-annex_assistant_atempts_to_repair__44___but_never_finishes.mdwn b/doc/forum/git-annex_assistant_atempts_to_repair__44___but_never_finishes.mdwn new file mode 100644 index 0000000000..ecfb0771cf --- /dev/null +++ b/doc/forum/git-annex_assistant_atempts_to_repair__44___but_never_finishes.mdwn @@ -0,0 +1 @@ +I'm using git-annex (git-annex-6.20160126 from homebrew) on osx and for a while now, it claims that it tries to repair my annex-dir on my osx machine, even though it never finishes (or fails) to do so. I'm not sure what's causing this and I also tried to use `git annex repair`, but this didn't help either (it ran forever but never finishes). I tried to run `git annex fsck` and saw that some larger video files were only in one other place and therefore couldn't be droped, which I think I fixed by doing `git annex add` then `git annex sync` and finally `git annex copy --auto -to $Remote. I'm not sure how to proceed, the log file doesn't seem to tell me a whole lot either. It just tells me for some of my files "Unable to lock down 1 copy of file that is required to safely drop it." and tries to do that stuff over and over and over… or at least that's what I guess happens. From 5845622c28f9358fc3d38828f18283f27926bafe Mon Sep 17 00:00:00 2001 From: openmedi Date: Wed, 16 Mar 2016 21:16:07 +0000 Subject: [PATCH 48/88] --- ...ex_assistant_atempts_to_repair__44___but_never_finishes.mdwn | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/forum/git-annex_assistant_atempts_to_repair__44___but_never_finishes.mdwn b/doc/forum/git-annex_assistant_atempts_to_repair__44___but_never_finishes.mdwn index ecfb0771cf..75ba03dd32 100644 --- a/doc/forum/git-annex_assistant_atempts_to_repair__44___but_never_finishes.mdwn +++ b/doc/forum/git-annex_assistant_atempts_to_repair__44___but_never_finishes.mdwn @@ -1 +1 @@ -I'm using git-annex (git-annex-6.20160126 from homebrew) on osx and for a while now, it claims that it tries to repair my annex-dir on my osx machine, even though it never finishes (or fails) to do so. I'm not sure what's causing this and I also tried to use `git annex repair`, but this didn't help either (it ran forever but never finishes). I tried to run `git annex fsck` and saw that some larger video files were only in one other place and therefore couldn't be droped, which I think I fixed by doing `git annex add` then `git annex sync` and finally `git annex copy --auto -to $Remote. I'm not sure how to proceed, the log file doesn't seem to tell me a whole lot either. It just tells me for some of my files "Unable to lock down 1 copy of file that is required to safely drop it." and tries to do that stuff over and over and over… or at least that's what I guess happens. +I'm using git-annex (git-annex-6.20160126 from homebrew) on osx and for a while now, it claims that it tries to repair my annex-dir on my osx machine, even though it never finishes (or fails) to do so. I'm not sure what's causing this and I also tried to use `git annex repair`, but this didn't help either (it ran forever but never finishes). I tried to run `git annex fsck` and saw that some larger video files were only in one other place and therefore couldn't be droped, which I think I fixed by doing `git annex add` then `git annex sync` and finally `git annex copy --auto -to $Remote`. I'm not sure how to proceed, the log file doesn't seem to tell me a whole lot either. It just tells me for some of my files "Unable to lock down 1 copy of file that is required to safely drop it." and tries to repair that stuff over and over and over… or at least that's what I guess happens. From 0d541a3a23f7935b19eaf6116b781c6be71c40a1 Mon Sep 17 00:00:00 2001 From: torpidus Date: Wed, 16 Mar 2016 22:04:30 +0000 Subject: [PATCH 49/88] --- ...protocol_mismatch_due_to_encfs_folder.mdwn | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 doc/forum/rsync_protocol_mismatch_due_to_encfs_folder.mdwn diff --git a/doc/forum/rsync_protocol_mismatch_due_to_encfs_folder.mdwn b/doc/forum/rsync_protocol_mismatch_due_to_encfs_folder.mdwn new file mode 100644 index 0000000000..c3667a2b69 --- /dev/null +++ b/doc/forum/rsync_protocol_mismatch_due_to_encfs_folder.mdwn @@ -0,0 +1,24 @@ +One of my repositories worked just fine for months, until I have decided to put an encfs folder within it. Encfs is encrypting folders and files, resulting in weird file and folder names. However, rsync just seems to fail. + + +This has already been a topic here a few times, for example [1] and [2]. + +Unfortunately, I have not been lucky enough to recover the situation by the hints given. + + +What I did to investigate is that I have re-run one of the shell commands stuck client-side and appended --debug to gain a deeper look. This is the output: + + $ /opt/git-annex/2016-01-14/exe/ssh --library-path /opt/git-annex/2016-01-14//etc/ld.so.conf.d:/opt/git-annex/2016-01-14//usr/lib/x86_64-linux-gnu/gconv:/opt/git-annex/2016-01-14//usr/lib/x86_64-linux-gnu/audit:/opt/git-annex/2016-01-14//usr/lib:/opt/git-annex/2016-01-14//usr/lib/x86_64-linux-gnu:/opt/git-annex/2016-01-14//lib64:/opt/git-annex/2016-01-14//lib/x86_64-linux-gnu: /opt/git-annex/2016-01-14/shimmed/ssh/ssh -S .git/annex/ssh/user@10.0.0.1 -o ControlMaster=auto -o ControlPersist=yes -T user@10.0.0.1 git-annex-shell 'recvkey' '/mnt/path/to/share/' 'SHA256E-s262670--e004c6e3f87ad2b5d74d206de85de5449c9f263d83e6ef1c87ffb03be8b7e725' --debug --uuid e34522e4-1dab-459c-b295-1fe41e7692e4 '--' 'remoteuuid=07820aec-e2a3-4c60-bd57-b39b7213e056' 'unlocked=1' 'direct=1' 'associatedfile=.encfs_folder/CMG23xCwkemocE-Gq9WHpO-n/1vqfTkJChNm5CgjBsZ--,9r,ZOcSBTxE-Ogz5ytA8R23st52LWf4d9MjRref56VhbEB/4ezakoEn8dqOT8s,K4X,ueSs' '--' dummy rsync --server -pe.Lsfx --log-format=X --inplace . . + [2016-03-16 22:52:18.922914] transfer start + [2016-03-16 22:52:18.949417] call: rsync ["--server","-t","--inplace","-e.Lsf",".","../../mnt/path/to/share/.git/annex/tmp/SHA256E-s262670--e004c6e3f87ad2b5d74d206de85de5449c9f263d83e6ef1c87ffb03be8b7e725"] + protocol version mismatch -- is your shell clean? + (see the rsync man page for an explanation) + rsync error: protocol incompatibility (code 2) at compat.c(176) [Receiver=3.1.1] + [2016-03-16 22:59:05.890987] process done ExitFailure 2 + [2016-03-16 22:59:05.899506] transfer done + +What can I do other than to just move the encfs outside my repository, which is of course the least favorable option for me to do? + +[1] + +[2] From e029eb8b61be3490a3cc55d70eff18ef776eafe0 Mon Sep 17 00:00:00 2001 From: torpidus Date: Wed, 16 Mar 2016 22:23:26 +0000 Subject: [PATCH 50/88] Added a comment --- ...ent_6_26d444afe2edea3500f80bb5c62ba491._comment | 14 ++++++++++++++ 1 file changed, 14 insertions(+) create mode 100644 doc/forum/Ssh_remote_on_NAS/comment_6_26d444afe2edea3500f80bb5c62ba491._comment diff --git a/doc/forum/Ssh_remote_on_NAS/comment_6_26d444afe2edea3500f80bb5c62ba491._comment b/doc/forum/Ssh_remote_on_NAS/comment_6_26d444afe2edea3500f80bb5c62ba491._comment new file mode 100644 index 0000000000..af180a980c --- /dev/null +++ b/doc/forum/Ssh_remote_on_NAS/comment_6_26d444afe2edea3500f80bb5c62ba491._comment @@ -0,0 +1,14 @@ +[[!comment format=mdwn + username="torpidus" + subject="comment 6" + date="2016-03-16T22:23:26Z" + content=""" +Hello Fabio, +I came across this posting from you one year ago. Since I'm also using a QNAP NAS for hosting several of my git-annex repos, it would be very valuable to hear some details about your setup. My setup currently consists of a virtual machine hosted on the NAS with an ordinary linux, nothing special. Would love to have git-annex installed on the NAS operating system rather, which is unfortunately not that easy. + + +Even in case you may not have been able to solve the issue described in this thread, can you maybe tell for example how you solved the issue of the QNAP operating system purging self-installed software? Or how you managed to let the pre-installed SSH daemon let other users than \"admin\" log-in? + + +Probably we're the first ones ever trying this, so it would be very useful to collect all about QNAP NAS and the usage of git-annex on these devices. +"""]] From c12602187143e2089a6dab1d99ca863f73f692af Mon Sep 17 00:00:00 2001 From: nanotech Date: Thu, 17 Mar 2016 08:39:37 +0000 Subject: [PATCH 51/88] Added a comment --- .../comment_3_4026607087a9da2759f841e59aadfcdc._comment | 9 +++++++++ 1 file changed, 9 insertions(+) create mode 100644 doc/bugs/MacOSX__58___archive_folders_not_working_as_expected/comment_3_4026607087a9da2759f841e59aadfcdc._comment diff --git a/doc/bugs/MacOSX__58___archive_folders_not_working_as_expected/comment_3_4026607087a9da2759f841e59aadfcdc._comment b/doc/bugs/MacOSX__58___archive_folders_not_working_as_expected/comment_3_4026607087a9da2759f841e59aadfcdc._comment new file mode 100644 index 0000000000..ae32c97888 --- /dev/null +++ b/doc/bugs/MacOSX__58___archive_folders_not_working_as_expected/comment_3_4026607087a9da2759f841e59aadfcdc._comment @@ -0,0 +1,9 @@ +[[!comment format=mdwn + username="nanotech" + subject="comment 3" + date="2016-03-17T08:39:36Z" + content=""" +I think this is the same bug as [Moved files are not picked up by the assistant on OS X](https://git-annex.branchable.com/bugs/Moved_files_are_not_picked_up_by_the_assistant_on_OS_X/). To reproduce, run the first transcript there but drop the file before moving it. + +FSEvents fails to produce add events for dangling symlinks (), although it does produce removal events. Recompiling and using Kqueue with git-annex instead seems to detect dangling symlinks and add them correctly. +"""]] From 91341559f7b6e1f9c03c67982116e4407f0effd8 Mon Sep 17 00:00:00 2001 From: nanotech Date: Thu, 17 Mar 2016 09:02:41 +0000 Subject: [PATCH 52/88] --- .../stack_build_Setup.hs_dependencies.mdwn | 56 +++++++++++++++++++ 1 file changed, 56 insertions(+) create mode 100644 doc/bugs/stack_build_Setup.hs_dependencies.mdwn diff --git a/doc/bugs/stack_build_Setup.hs_dependencies.mdwn b/doc/bugs/stack_build_Setup.hs_dependencies.mdwn new file mode 100644 index 0000000000..1e9fc431f8 --- /dev/null +++ b/doc/bugs/stack_build_Setup.hs_dependencies.mdwn @@ -0,0 +1,56 @@ +### Please describe the problem. + +`stack build` on a fresh clone of git-annex at e029eb8b fails with + + git-annex-6.20160229: configure + + Utility/FileSystemEncoding.hs:30:18: + Could not find module ‘Data.Hash.MD5’ + Use -v to see a list of the files searched for. + + Utility/FileSystemEncoding.hs:32:8: + Could not find module ‘Data.Bits.Utils’ + Perhaps you meant + Data.BitUtil + Data.Bits.Lens (from lens-4.13@lens_IUJoiaRWYAQ6ieqgqTJZ5D) + Use -v to see a list of the files searched for. + + Utility/FileSystemEncoding.hs:34:8: + Could not find module ‘Data.List.Utils’ + Perhaps you meant + Data.BitUtil + Data.List.Lens (from lens-4.13@lens_IUJoiaRWYAQ6ieqgqTJZ5D) + Data.List.Split (from split-0.2.3@split_CDzOynTh4l8Ahg1HaWUL4Z) + Use -v to see a list of the files searched for. + + Utility/Process.hs:53:8: + Could not find module ‘System.Log.Logger’ + Perhaps you meant + System.Log.FastLogger (from fast-logger-2.4.1@fastl_1adi3bwIxvVE3Gyx2Jy1k0) + Use -v to see a list of the files searched for. + + Utility/SafeCommand.hs:14:8: + Could not find module ‘Data.String.Utils’ + Perhaps you meant + Data.String.UTF8 (from utf8-string-1.0.1.1@utf8s_L8eKHa7Iv9q7FVKUYW6u4b) + Use -v to see a list of the files searched for. + +### What steps will reproduce the problem? + +`stack build` + +### What version of git-annex are you using? On what operating system? + +e029eb8b, OS X 10.10.5. + +### Please provide any additional information below. + +These are apparently dependencies of `Setup.hs`. Adding + + explicit-setup-deps: + "*": true + +to `stack.yaml` [(as described here)](https://github.com/commercialhaskell/stack/blob/a59997d5db963bba403119843340688ee25e2c6f/doc/yaml_configuration.md#explicit-setup-deps) +fixes the error and builds git-annex successfully. + +### Have you had any luck using git-annex before? (Sometimes we get tired of reading bug reports all day and a lil' positive end note does wonders) From 75838ad7ba41384f1e68700a32fcace180311b02 Mon Sep 17 00:00:00 2001 From: "https://me.yahoo.com/a/EbvxpTI_xP9Aod7Mg4cwGhgjrCrdM5s-#7c0f4" Date: Thu, 17 Mar 2016 21:16:41 +0000 Subject: [PATCH 53/88] Initiated page for a "datalad" user to join both yoh and mih pages --- doc/users/datalad.mdwn | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 doc/users/datalad.mdwn diff --git a/doc/users/datalad.mdwn b/doc/users/datalad.mdwn new file mode 100644 index 0000000000..1aad07cf69 --- /dev/null +++ b/doc/users/datalad.mdwn @@ -0,0 +1,23 @@ +TODOs for DataLad +================= + +[[!inline pages="todo/* and !todo/done and !link(todo/done) and +(author(yoh) or author(mih))" sort=mtime feeds=no actions=yes archive=yes show=0]] + +Done +---- + +[[!inline pages="todo/* and !todo/done and link(todo/done) and +(author(yoh) or author(mih))" feeds=no actions=yes archive=yes show=0]] + +My bugs +======= + +[[!inline pages="bugs/* and !bugs/done and !link(bugs/done) and +(author(yoh) or author(mih))" sort=mtime feeds=no actions=yes archive=yes show=0 template=buglist]] + +Fixed +----- + +[[!inline pages="bugs/* and !bugs/done and link(bugs/done) and +(author(yoh) or author(mih))" feeds=no actions=yes archive=yes show=0 template=buglist]] From eae56e9df31e17fb55f6664ac468d4b8b298480b Mon Sep 17 00:00:00 2001 From: "https://me.yahoo.com/a/EbvxpTI_xP9Aod7Mg4cwGhgjrCrdM5s-#7c0f4" Date: Thu, 17 Mar 2016 21:17:15 +0000 Subject: [PATCH 54/88] Added page for mih user --- doc/users/mih.mdwn | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 doc/users/mih.mdwn diff --git a/doc/users/mih.mdwn b/doc/users/mih.mdwn new file mode 100644 index 0000000000..1a0327a400 --- /dev/null +++ b/doc/users/mih.mdwn @@ -0,0 +1,23 @@ +My todos +======== + +[[!inline pages="todo/* and !todo/done and !link(todo/done) and +author(mih)" sort=mtime feeds=no actions=yes archive=yes show=0]] + +Done +---- + +[[!inline pages="todo/* and !todo/done and link(todo/done) and +author(mih)" feeds=no actions=yes archive=yes show=0]] + +My bugs +======= + +[[!inline pages="bugs/* and !bugs/done and !link(bugs/done) and +author(mih)" sort=mtime feeds=no actions=yes archive=yes show=0 template=buglist]] + +Fixed +----- + +[[!inline pages="bugs/* and !bugs/done and link(bugs/done) and +author(mih)" feeds=no actions=yes archive=yes show=0 template=buglist]] From b418bed8d7232771eafccc2cb86a4474a3722b6d Mon Sep 17 00:00:00 2001 From: Joey Hess Date: Thu, 17 Mar 2016 23:08:39 -0400 Subject: [PATCH 55/88] tracking bug --- doc/bugs/git_security_fix.mdwn | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) create mode 100644 doc/bugs/git_security_fix.mdwn diff --git a/doc/bugs/git_security_fix.mdwn b/doc/bugs/git_security_fix.mdwn new file mode 100644 index 0000000000..3c25f49450 --- /dev/null +++ b/doc/bugs/git_security_fix.mdwn @@ -0,0 +1,18 @@ +git had some remotely exploitable security holes announced recently +(CVE-2016-2324, CVE-2016-2315) + +git-annex builds that bundle git need to be updated. + +status of autobuilds: + +* Linux is fixed (all builds) +* OSX pending +* Windows waiting on updated release of git for Windows +* Android is fixed (git build is untested) + +status of released builds: + +* Linux is vulnerable +* OSX is vulnerable +* Windows is vulnerable +* Android is vulnerable From b482cb9d9003c87d41fd940e8a351afe512df7e0 Mon Sep 17 00:00:00 2001 From: Joey Hess Date: Thu, 17 Mar 2016 23:14:37 -0400 Subject: [PATCH 56/88] Fix build with stack 0.1.6 which needs explicit-setup-deps. --- debian/changelog | 1 + doc/bugs/stack_build_Setup.hs_dependencies.mdwn | 4 ++++ stack.yaml | 2 ++ 3 files changed, 7 insertions(+) diff --git a/debian/changelog b/debian/changelog index 3bb289298a..d5c0461a66 100644 --- a/debian/changelog +++ b/debian/changelog @@ -16,6 +16,7 @@ git-annex (6.20160230) UNRELEASED; urgency=medium * Sped up git-annex add in direct mode and v6 by using git hash-object --stdin-paths. * Sped up git-annex merge by using git hash-object --stdin-paths. + * Fix build with stack 0.1.6 which needs explicit-setup-deps. -- Joey Hess Mon, 29 Feb 2016 13:00:30 -0400 diff --git a/doc/bugs/stack_build_Setup.hs_dependencies.mdwn b/doc/bugs/stack_build_Setup.hs_dependencies.mdwn index 1e9fc431f8..3cbcfa82ee 100644 --- a/doc/bugs/stack_build_Setup.hs_dependencies.mdwn +++ b/doc/bugs/stack_build_Setup.hs_dependencies.mdwn @@ -54,3 +54,7 @@ to `stack.yaml` [(as described here)](https://github.com/commercialhaskell/stack fixes the error and builds git-annex successfully. ### Have you had any luck using git-annex before? (Sometimes we get tired of reading bug reports all day and a lil' positive end note does wonders) + +> Ok, added that. I am not sure if older version of stack will stumble over +> the new field; if so I suppose the user can comment it out or upgrade +> stack. [[done]] --[[Joey]] diff --git a/stack.yaml b/stack.yaml index 5f202e71d0..622e37b118 100644 --- a/stack.yaml +++ b/stack.yaml @@ -24,3 +24,5 @@ extra-deps: - mountpoints-1.0.1 - disk-free-space-0.1.0.1 - process-1.3.0.0 +explicit-setup-deps: + "*": true From edbd46943f89d5992c785b8af0d26b64e337374d Mon Sep 17 00:00:00 2001 From: Joey Hess Date: Thu, 17 Mar 2016 23:20:50 -0400 Subject: [PATCH 57/88] update --- doc/bugs/stack_build_Setup.hs_dependencies.mdwn | 9 ++++++--- stack.yaml | 2 +- 2 files changed, 7 insertions(+), 4 deletions(-) diff --git a/doc/bugs/stack_build_Setup.hs_dependencies.mdwn b/doc/bugs/stack_build_Setup.hs_dependencies.mdwn index 3cbcfa82ee..0805272591 100644 --- a/doc/bugs/stack_build_Setup.hs_dependencies.mdwn +++ b/doc/bugs/stack_build_Setup.hs_dependencies.mdwn @@ -55,6 +55,9 @@ fixes the error and builds git-annex successfully. ### Have you had any luck using git-annex before? (Sometimes we get tired of reading bug reports all day and a lil' positive end note does wonders) -> Ok, added that. I am not sure if older version of stack will stumble over -> the new field; if so I suppose the user can comment it out or upgrade -> stack. [[done]] --[[Joey]] +> Looks like older versions of stack work too with files with +> this field in it. But, this broke stack 1.0.4 building some +> dependencies (eg, process), so I instead set only "git-annex: true" +> so building deps won't be affected. +> +> [[done]] --[[Joey]] diff --git a/stack.yaml b/stack.yaml index 622e37b118..a03db5cc0f 100644 --- a/stack.yaml +++ b/stack.yaml @@ -25,4 +25,4 @@ extra-deps: - disk-free-space-0.1.0.1 - process-1.3.0.0 explicit-setup-deps: - "*": true + git-annex: true From 39165d4bf76e618c95b18e4636ae18f4e869db7b Mon Sep 17 00:00:00 2001 From: Joey Hess Date: Thu, 17 Mar 2016 23:22:28 -0400 Subject: [PATCH 58/88] update android git to 2.8.0.rc3, fixing recent security holes --- standalone/android/Makefile | 4 ++-- standalone/android/git.patch | 20 ++++++++++---------- 2 files changed, 12 insertions(+), 12 deletions(-) diff --git a/standalone/android/Makefile b/standalone/android/Makefile index 261259bf41..6f49b495f6 100644 --- a/standalone/android/Makefile +++ b/standalone/android/Makefile @@ -49,8 +49,8 @@ $(GIT_ANNEX_ANDROID_SOURCETREE)/busybox/build-stamp: busybox_config $(GIT_ANNEX_ANDROID_SOURCETREE)/git/build-stamp: git.patch # This is a known-good version that the patch works with. - cat git.patch | (cd $(GIT_ANNEX_ANDROID_SOURCETREE)/git && git reset --hard f9dc5d65ca31cb79893e1296efe37727bf58f3f3 && git am) - cd $(GIT_ANNEX_ANDROID_SOURCETREE)/git && $(MAKE) install NO_OPENSSL=1 NO_GETTEXT=1 NO_GECOS_IN_PWENT=1 NO_GETPASS=1 NO_NSEC=1 NO_MKDTEMP=1 NO_PTHREADS=1 NO_PERL=1 NO_CURL=1 NO_EXPAT=1 NO_TCLTK=1 NO_ICONV=1 HAVE_CLOCK_GETTIME= prefix= DESTDIR=installed-tree + cat git.patch | (cd $(GIT_ANNEX_ANDROID_SOURCETREE)/git && git reset --hard d9c691a759d62cef53a6cc11864a2ef4b0829244 && git am) + cd $(GIT_ANNEX_ANDROID_SOURCETREE)/git && $(MAKE) install NO_OPENSSL=1 NO_GETTEXT=1 NO_GECOS_IN_PWENT=1 NO_GETPASS=1 NO_NSEC=1 NO_MKDTEMP=1 NO_PTHREADS=1 NO_PERL=1 NO_CURL=1 NO_EXPAT=1 NO_TCLTK=1 NO_ICONV=1 HAVE_CLOCK_GETTIME= HAVE_GETDELIM= prefix= DESTDIR=installed-tree touch $@ $(GIT_ANNEX_ANDROID_SOURCETREE)/rsync/build-stamp: rsync.patch diff --git a/standalone/android/git.patch b/standalone/android/git.patch index ecf095849d..ec81aaaeb4 100644 --- a/standalone/android/git.patch +++ b/standalone/android/git.patch @@ -1,4 +1,4 @@ -From 6134cc328f513e32895462e884487513b28029ba Mon Sep 17 00:00:00 2001 +From e0fffe80a8815e64dbc1d690c79bf006651c7642 Mon Sep 17 00:00:00 2001 From: Joey Hess Date: Wed, 13 Aug 2014 13:50:56 -0400 Subject: [PATCH] avoid using of chmod on android when changing config @@ -10,17 +10,17 @@ implentations, all total shite. 1 file changed, 4 insertions(+) diff --git a/config.c b/config.c -index 058505c..16854b2 100644 +index 9ba40bc..a350638 100644 --- a/config.c +++ b/config.c -@@ -1634,12 +1634,14 @@ int git_config_set_multivar_in_file(const char *config_filename, - MAP_PRIVATE, in_fd, 0); +@@ -2124,12 +2124,14 @@ int git_config_set_multivar_in_file_gently(const char *config_filename, close(in_fd); + in_fd = -1; + /* not on android - if (chmod(lock->filename, st.st_mode & 07777) < 0) { + if (chmod(get_lock_file_path(lock), st.st_mode & 07777) < 0) { error("chmod on %s failed: %s", - lock->filename, strerror(errno)); + get_lock_file_path(lock), strerror(errno)); ret = CONFIG_NO_WRITE; goto out_free; } @@ -28,14 +28,14 @@ index 058505c..16854b2 100644 if (store.seen == 0) store.seen = 1; -@@ -1813,11 +1815,13 @@ int git_config_rename_section_in_file(const char *config_filename, +@@ -2329,11 +2331,13 @@ int git_config_rename_section_in_file(const char *config_filename, fstat(fileno(config_file), &st); + /* not on android - if (chmod(lock->filename, st.st_mode & 07777) < 0) { + if (chmod(get_lock_file_path(lock), st.st_mode & 07777) < 0) { ret = error("chmod on %s failed: %s", - lock->filename, strerror(errno)); + get_lock_file_path(lock), strerror(errno)); goto out; } + */ @@ -43,5 +43,5 @@ index 058505c..16854b2 100644 while (fgets(buf, sizeof(buf), config_file)) { int i; -- -2.1.0.rc1 +2.1.4 From 204dbf597d46a2f0100497967787f03c56be682c Mon Sep 17 00:00:00 2001 From: Joey Hess Date: Thu, 17 Mar 2016 23:42:45 -0400 Subject: [PATCH 59/88] well, that broke the i386ancient autobuilder. revert --- debian/changelog | 1 - .../stack_build_Setup.hs_dependencies.mdwn | 18 +++++++++++++----- stack.yaml | 2 -- 3 files changed, 13 insertions(+), 8 deletions(-) diff --git a/debian/changelog b/debian/changelog index d5c0461a66..3bb289298a 100644 --- a/debian/changelog +++ b/debian/changelog @@ -16,7 +16,6 @@ git-annex (6.20160230) UNRELEASED; urgency=medium * Sped up git-annex add in direct mode and v6 by using git hash-object --stdin-paths. * Sped up git-annex merge by using git hash-object --stdin-paths. - * Fix build with stack 0.1.6 which needs explicit-setup-deps. -- Joey Hess Mon, 29 Feb 2016 13:00:30 -0400 diff --git a/doc/bugs/stack_build_Setup.hs_dependencies.mdwn b/doc/bugs/stack_build_Setup.hs_dependencies.mdwn index 0805272591..0dcc6f7ea4 100644 --- a/doc/bugs/stack_build_Setup.hs_dependencies.mdwn +++ b/doc/bugs/stack_build_Setup.hs_dependencies.mdwn @@ -55,9 +55,17 @@ fixes the error and builds git-annex successfully. ### Have you had any luck using git-annex before? (Sometimes we get tired of reading bug reports all day and a lil' positive end note does wonders) -> Looks like older versions of stack work too with files with -> this field in it. But, this broke stack 1.0.4 building some -> dependencies (eg, process), so I instead set only "git-annex: true" -> so building deps won't be affected. +> I tried enabling this, and it broke build on my i386ancient autobuilder, +> which uses stack 1.0.4.2. Strange build failure +> both building git-annex and also its dependencies (eg, process): + + /usr/bin/ld: cannot find -ltinfo + +> Which seems to be libtinfo, part of the ncurses library. Which is weird, +> AFAIK git-annex does not use ncurses at all. > -> [[done]] --[[Joey]] +> I tried weakening the setting from `*` to `git-annex: true`, which +> lets the build deps get built, but building git-annex still fails with +> above error. +> +> --[[Joey]] diff --git a/stack.yaml b/stack.yaml index a03db5cc0f..5f202e71d0 100644 --- a/stack.yaml +++ b/stack.yaml @@ -24,5 +24,3 @@ extra-deps: - mountpoints-1.0.1 - disk-free-space-0.1.0.1 - process-1.3.0.0 -explicit-setup-deps: - git-annex: true From d594fc0146f733f4b0470ce88fba999dd095b590 Mon Sep 17 00:00:00 2001 From: "luukhendrix9@f5b077cf0dfcfec03c5f00e5df3c00279ef5c477" Date: Fri, 18 Mar 2016 13:44:20 +0000 Subject: [PATCH 60/88] --- ...ers_in_pairing_message__59___ignoring.mdwn | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 doc/forum/_illegal_control_characters_in_pairing_message__59___ignoring.mdwn diff --git a/doc/forum/_illegal_control_characters_in_pairing_message__59___ignoring.mdwn b/doc/forum/_illegal_control_characters_in_pairing_message__59___ignoring.mdwn new file mode 100644 index 0000000000..5d39ec77f8 --- /dev/null +++ b/doc/forum/_illegal_control_characters_in_pairing_message__59___ignoring.mdwn @@ -0,0 +1,40 @@ +Currently I am trying to synchronize two folders between my NAS and my main computer. On both machines I can access the web app. However, once I try to pair these machines with a secret phrase I get the following error: + +illegal control characters in pairing message; ignoring + +The log on one machine is: + +[2016-03-18 14:25:16.861132] main: Pairing in progress +Generating public/private rsa key pair. +Your identification has been saved in /var/folders/_v/hkf9zbqs0bgd2vcnmr_qnlgm0000gn/T/git-annex-keygenN92651/key. +Your public key has been saved in /var/folders/_v/hkf9zbqs0bgd2vcnmr_qnlgm0000gn/T/git-annex-keygenN92651/key.pub. +The key fingerprint is: +SHA256:beyV1f5MKFGaaH9p1CRMPmaVcYAmOyc/lhp7HCw668M username@iMac.home +The key's randomart image is: ++---[RSA 2048]----+ +| +=o*| +| ..o=.B.| +| o++ B o| +| ++..B = | +| S +*=.= o| +| oo.B+ o.| +| . ..B o o| +| E o o | +| .o+ . | ++----[SHA256]-----+ +[2016-03-18 14:25:26.442301] main: Pairing in progress + + illegal control characters in pairing message; ignoring + + illegal control characters in pairing message; ignoring + + illegal control characters in pairing message; ignoring + + illegal control characters in pairing message; ignoring + +While on the other machine I get: + +[2016-03-18 14:25:35 CET] main: Pairing with username@iMac.home:~/Desktop/annex in progress + + + From 4fc3a79ea6e4a9a4ed7ab7c6447292b8adbe88ab Mon Sep 17 00:00:00 2001 From: Joey Hess Date: Fri, 18 Mar 2016 11:28:11 -0400 Subject: [PATCH 61/88] update --- doc/bugs/git_security_fix.mdwn | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/doc/bugs/git_security_fix.mdwn b/doc/bugs/git_security_fix.mdwn index 3c25f49450..559f392cf7 100644 --- a/doc/bugs/git_security_fix.mdwn +++ b/doc/bugs/git_security_fix.mdwn @@ -6,13 +6,13 @@ git-annex builds that bundle git need to be updated. status of autobuilds: * Linux is fixed (all builds) -* OSX pending +* OSX pending (host is moving) * Windows waiting on updated release of git for Windows * Android is fixed (git build is untested) status of released builds: -* Linux is vulnerable +* Linux is fixed (all builds) * OSX is vulnerable * Windows is vulnerable -* Android is vulnerable +* Android is fixed (git build is untested) From d8b8984b9bc0fbc38d5c5ec955b512a43370b7bf Mon Sep 17 00:00:00 2001 From: Joey Hess Date: Fri, 18 Mar 2016 11:30:46 -0400 Subject: [PATCH 62/88] prep release --- debian/changelog | 4 ++-- git-annex.cabal | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/debian/changelog b/debian/changelog index 3bb289298a..185ad685fb 100644 --- a/debian/changelog +++ b/debian/changelog @@ -1,4 +1,4 @@ -git-annex (6.20160230) UNRELEASED; urgency=medium +git-annex (6.20160318) unstable; urgency=medium * metadata: Added -r to remove all current values of a field. * Fix data loss that can occur when annex.pidlock is set in a repository. @@ -17,7 +17,7 @@ git-annex (6.20160230) UNRELEASED; urgency=medium git hash-object --stdin-paths. * Sped up git-annex merge by using git hash-object --stdin-paths. - -- Joey Hess Mon, 29 Feb 2016 13:00:30 -0400 + -- Joey Hess Fri, 18 Mar 2016 11:30:36 -0400 git-annex (6.20160229) unstable; urgency=medium diff --git a/git-annex.cabal b/git-annex.cabal index 9630948b16..1b3ce4b040 100644 --- a/git-annex.cabal +++ b/git-annex.cabal @@ -1,5 +1,5 @@ Name: git-annex -Version: 6.20160229 +Version: 6.20160318 Cabal-Version: >= 1.8 License: GPL-3 Maintainer: Joey Hess From 63d87261f389834a5032f69cbedbe9ba1da5603e Mon Sep 17 00:00:00 2001 From: Joey Hess Date: Fri, 18 Mar 2016 11:34:26 -0400 Subject: [PATCH 63/88] comment --- ...nt_1_99975a677f832c410050ba721be6d904._comment | 15 +++++++++++++++ 1 file changed, 15 insertions(+) create mode 100644 doc/forum/_illegal_control_characters_in_pairing_message__59___ignoring/comment_1_99975a677f832c410050ba721be6d904._comment diff --git a/doc/forum/_illegal_control_characters_in_pairing_message__59___ignoring/comment_1_99975a677f832c410050ba721be6d904._comment b/doc/forum/_illegal_control_characters_in_pairing_message__59___ignoring/comment_1_99975a677f832c410050ba721be6d904._comment new file mode 100644 index 0000000000..0ebe49ec5b --- /dev/null +++ b/doc/forum/_illegal_control_characters_in_pairing_message__59___ignoring/comment_1_99975a677f832c410050ba721be6d904._comment @@ -0,0 +1,15 @@ +[[!comment format=mdwn + username="joey" + subject="""comment 1""" + date="2016-03-18T15:31:17Z" + content=""" +This probably has something to do with the hostname of the other host than +the one that displays the error. Or possibly with the name of the user on +that host, or the directory on that host where the git-annex repository is. + +Can you share that information, or at least the parts of it that are not +regular alphabet characters? + +(There's also an outside possibility it could have found a control +character in the ssh public key, but I don't see how.) +"""]] From ff9f3508d9d5187383e3f5713eee58c3798377ec Mon Sep 17 00:00:00 2001 From: Joey Hess Date: Fri, 18 Mar 2016 11:35:40 -0400 Subject: [PATCH 64/88] add news item for git-annex 6.20160318 --- doc/news/version_6.20160114.mdwn | 59 -------------------------------- doc/news/version_6.20160318.mdwn | 18 ++++++++++ 2 files changed, 18 insertions(+), 59 deletions(-) delete mode 100644 doc/news/version_6.20160114.mdwn create mode 100644 doc/news/version_6.20160318.mdwn diff --git a/doc/news/version_6.20160114.mdwn b/doc/news/version_6.20160114.mdwn deleted file mode 100644 index f6ba0ebcf5..0000000000 --- a/doc/news/version_6.20160114.mdwn +++ /dev/null @@ -1,59 +0,0 @@ -git-annex 6.20160114 released with [[!toggle text="these changes"]] -[[!toggleable text=""" -"hexapodia as the key insight" - -* Added v6 repository mode, but v5 is still the default for now. -* unlock, lock: In v6 mode, unlocking a file changes it from a symlink to a - pointer file, and this change can be committed to the git repository. - For details, see http://git-annex.branchable.com/tips/unlocked\_files/ -* The upgrade to version 6 is not done fully automatically yet, because - upgrading a direct mode repository to version 6 will prevent old - versions of git-annex from working in other clones of that repository. - For details, see http://git-annex.branchable.com/upgrades/ -* init: --version parameter added to control which supported repository - version to use. -* init, upgrade: Configure .git/info/attributes to use git-annex - as a smudge filter. In v6 repository mode, this makes git add - add files to the annex in unlocked mode, unless overridden by - annex.largefiles configuration. -* assistant: In v6 mode, adds files in unlocked mode, so they can - continue to be modified. -* Added annex.thin setting, which makes unlocked files in v6 repositories - be hard linked to their content, instead of a copy. This saves disk - space but means any modification of an unlocked file will lose the local - (and possibly only) copy of the old version. -* Enable annex.thin by default on upgrade from direct mode to v6, since - direct mode made the same tradeoff. -* fix: Adjusts unlocked files as configured by annex.thin. -* persistent-sqlite is now a hard build dependency, since v6 repository - mode needs it. -* status: On crippled filesystems, was displaying M for all annexed files - that were present. Probably caused by a change to what git status - displays in this situation. Fixed by treating files git thinks are - modified the same as typechanged files. -* addurl: Added --batch and --with-files options. -* addurl: Support --json, particularly useful in --batch mode. -* addurl: Refuse to overwrite any existing, non-annexed file. -* Debian: Adjust build dependencies for webapp, DAV. Now available on - mips, mipsel, but temporarily removed armel since build is failing - there. -* info: Fix "backend usage" numbers, which were counting present keys - twice. -* info --json: Improve json for "backend usage", using a nested object - with fields for each backend instead of the previous weird nested lists. - This may break existing parsers of this json output, if there were any. -* whereis --json: Make url list be included in machine-parseable form. -* test: Added --keep-failures option. -* unused: Bug fix when a new file was added to the annex, and then - removed (but not git rmed). git still has the add staged in this case, - so the content should not be unused and was wrongly treated as such. -* migrate: Copy over metadata to new key. -* rekey: No longer copies over urls from the old to the new key. - It makes sense for migrate to do that, but not for this low-level - (and little used) plumbing command to. -* view: Fix crash in non-unicode capable locale when entering a view - of metadata containing a slash or backslash. -* When annex.http-headers is used to set the User-Agent header, avoid - sending User-Agent: git-annex -* Windows: Fix rsync cross-drive hack to work with msys2 rsync. - Thanks, Pieter Kitslaar."""]] diff --git a/doc/news/version_6.20160318.mdwn b/doc/news/version_6.20160318.mdwn new file mode 100644 index 0000000000..7277d06963 --- /dev/null +++ b/doc/news/version_6.20160318.mdwn @@ -0,0 +1,18 @@ +git-annex 6.20160318 released with [[!toggle text="these changes"]] +[[!toggleable text=""" + * metadata: Added -r to remove all current values of a field. + * Fix data loss that can occur when annex.pidlock is set in a repository. + * Fix bug preventing moving files to/from a repository with annex.pidlock set. + * Fix shared lock file FD leak. + * Fix metadata hook behavior when multiple files are added at once. + Thanks, Klaus Ethgen. + * Added dependencies on haskell mountpoints and disk-free-space + libraries, removing FFI code from git-annex. + * dropkey: Add --batch and --json. + * Fix OSX dmg to include libraries needed by bundled gpg, + lost in last release. + * Always try to thaw content, even when annex.crippledfilesystem is set. + * Correct git-annex info to include unlocked files in v6 repository. + * Sped up git-annex add in direct mode and v6 by using + git hash-object --stdin-paths. + * Sped up git-annex merge by using git hash-object --stdin-paths."""]] \ No newline at end of file From 1889abd8746070bea4641492e8aec0dea8da8eac Mon Sep 17 00:00:00 2001 From: Joey Hess Date: Fri, 18 Mar 2016 11:46:03 -0400 Subject: [PATCH 65/88] update --- doc/bugs/git_security_fix.mdwn | 6 +++--- doc/devblog/day_374__security_fix.mdwn | 4 ++++ 2 files changed, 7 insertions(+), 3 deletions(-) create mode 100644 doc/devblog/day_374__security_fix.mdwn diff --git a/doc/bugs/git_security_fix.mdwn b/doc/bugs/git_security_fix.mdwn index 559f392cf7..3ce6c4b073 100644 --- a/doc/bugs/git_security_fix.mdwn +++ b/doc/bugs/git_security_fix.mdwn @@ -7,12 +7,12 @@ status of autobuilds: * Linux is fixed (all builds) * OSX pending (host is moving) -* Windows waiting on updated release of git for Windows +* Windows does not bundle git * Android is fixed (git build is untested) status of released builds: * Linux is fixed (all builds) -* OSX is vulnerable -* Windows is vulnerable +* OSX is **vulnerable** +* Windows does not bundle git * Android is fixed (git build is untested) diff --git a/doc/devblog/day_374__security_fix.mdwn b/doc/devblog/day_374__security_fix.mdwn new file mode 100644 index 0000000000..c1d20bbdf1 --- /dev/null +++ b/doc/devblog/day_374__security_fix.mdwn @@ -0,0 +1,4 @@ +Pushed out a git-annex release this morning mostly because of the recent +[[bugs/git_security_fix]]. Several git-annex builds bundle a copy of git and +needed to be updated. Note that the OSX autobuilder is temporarily down and +so it's not been updated yet -- hopefully soon. From e03c42aaa174d50388e295e43a2352c4acb6992c Mon Sep 17 00:00:00 2001 From: openmedi Date: Sat, 19 Mar 2016 17:08:19 +0000 Subject: [PATCH 66/88] Added a comment --- .../comment_1_a12892b2881969ddd6faa92d860e1bc8._comment | 7 +++++++ 1 file changed, 7 insertions(+) create mode 100644 doc/forum/git-annex_assistant_atempts_to_repair__44___but_never_finishes/comment_1_a12892b2881969ddd6faa92d860e1bc8._comment diff --git a/doc/forum/git-annex_assistant_atempts_to_repair__44___but_never_finishes/comment_1_a12892b2881969ddd6faa92d860e1bc8._comment b/doc/forum/git-annex_assistant_atempts_to_repair__44___but_never_finishes/comment_1_a12892b2881969ddd6faa92d860e1bc8._comment new file mode 100644 index 0000000000..92a3f70b7d --- /dev/null +++ b/doc/forum/git-annex_assistant_atempts_to_repair__44___but_never_finishes/comment_1_a12892b2881969ddd6faa92d860e1bc8._comment @@ -0,0 +1,7 @@ +[[!comment format=mdwn + username="openmedi" + subject="comment 1" + date="2016-03-19T17:08:19Z" + content=""" +I added an old external hdd to my setup and now it seems to be working again. I assume, that a lot of my remotes stoped working, or only working sometimes. I guess I have to use `testremote` and go from there… +"""]] From d9657c0449afb1501a27545dbdcfd477b9bb9542 Mon Sep 17 00:00:00 2001 From: "divergentdave@5c17d06f6d67c6f157b76a4cc95ca764b7d2f899" Date: Mon, 21 Mar 2016 04:13:15 +0000 Subject: [PATCH 67/88] Added a comment --- .../comment_2_041fe2a545b48acd2c9d15eb2ac2b34f._comment | 8 ++++++++ 1 file changed, 8 insertions(+) create mode 100644 doc/bugs/Android__58___use___47__data__47____8230___for_git-annex.home__63__/comment_2_041fe2a545b48acd2c9d15eb2ac2b34f._comment diff --git a/doc/bugs/Android__58___use___47__data__47____8230___for_git-annex.home__63__/comment_2_041fe2a545b48acd2c9d15eb2ac2b34f._comment b/doc/bugs/Android__58___use___47__data__47____8230___for_git-annex.home__63__/comment_2_041fe2a545b48acd2c9d15eb2ac2b34f._comment new file mode 100644 index 0000000000..486d1843ff --- /dev/null +++ b/doc/bugs/Android__58___use___47__data__47____8230___for_git-annex.home__63__/comment_2_041fe2a545b48acd2c9d15eb2ac2b34f._comment @@ -0,0 +1,8 @@ +[[!comment format=mdwn + username="divergentdave@5c17d06f6d67c6f157b76a4cc95ca764b7d2f899" + nickname="divergentdave" + subject="comment 2" + date="2016-03-21T04:13:15Z" + content=""" +Each app has one subfolder inside /data that is private to that app (and user) alone. Generally, you can't read or enumerate /data itself. There is a function in the Java API to get the current app's internal storage folder, see https://developer.android.com/reference/android/content/Context.html#getFilesDir%28%29. +"""]] From 0dbcc7d6e85f3d59ed9efe2c5b5578d4c21d9394 Mon Sep 17 00:00:00 2001 From: "divergentdave@5c17d06f6d67c6f157b76a4cc95ca764b7d2f899" Date: Mon, 21 Mar 2016 05:04:58 +0000 Subject: [PATCH 68/88] --- .../Android_chroot_stuck_in_Cabal_hell.mdwn | 20 +++++++++++++++++++ 1 file changed, 20 insertions(+) create mode 100644 doc/bugs/Android_chroot_stuck_in_Cabal_hell.mdwn diff --git a/doc/bugs/Android_chroot_stuck_in_Cabal_hell.mdwn b/doc/bugs/Android_chroot_stuck_in_Cabal_hell.mdwn new file mode 100644 index 0000000000..1587d4a667 --- /dev/null +++ b/doc/bugs/Android_chroot_stuck_in_Cabal_hell.mdwn @@ -0,0 +1,20 @@ +### Please describe the problem. +I'm trying to get an Android development environment set up, but I am running into conflicting library versions inside of the chroot. The package installation script now finishes, but I run into a link-time error during `cabal configure` because it is pulling in two different versions of the unix package for some reason. Please let me know if there is any information I can get from my build environment that would help diagnosing the issue. + +### What steps will reproduce the problem? +Run `buildchroot`, `install-haskell-packages`, `make android` + +### What version of git-annex are you using? On what operating system? +Attempting to build from source, cross-compiling for Android on Debian Jessie. + +### Please provide any additional information below. + +[[!format sh """ +Linking ./dist/setup/setup ... +/usr/lib/ghc/unix-2.6.0.1/libHSunix-2.6.0.1.a(execvpe.o): In function `pPrPr_disableITimers': +(.text+0x300): multiple definition of `pPrPr_disableITimers' +/home/builder/.cabal/lib/i386-linux-ghc-7.6.3/unix-2.7.1.0/libHSunix-2.7.1.0.a(ghcrts.o):ghcrts.c:(.text+0x0): first defined here +collect2: error: ld returned 1 exit status +Makefile:225: recipe for target 'android' failed +make: *** [android] Error 1 +"""]] From c4fb70038f6053a4f43ddc7c1631ddd8f28326f8 Mon Sep 17 00:00:00 2001 From: Tobias Date: Mon, 21 Mar 2016 10:14:27 +0000 Subject: [PATCH 69/88] --- doc/forum/web-browser_for_the_repository.mdwn | 10 ++++++++++ 1 file changed, 10 insertions(+) create mode 100644 doc/forum/web-browser_for_the_repository.mdwn diff --git a/doc/forum/web-browser_for_the_repository.mdwn b/doc/forum/web-browser_for_the_repository.mdwn new file mode 100644 index 0000000000..40a332b6e8 --- /dev/null +++ b/doc/forum/web-browser_for_the_repository.mdwn @@ -0,0 +1,10 @@ +Hi! + +I am a teacher and I would like to organize my school-files with git-annex in combination with a wiki. In the wiki I would like to outline lessons with included pictures (and links) of work-sheets etc. git-annex would help me to transfer and organize all the files. + +Now I'm searching for a web-browser for a git-annex-repository, like the source-browser of trac (or gitweb). Actually I would really like to use trac (or dokuwiki) for my school-project. I tried trac with a bare-annex-repos, but it only shows the hash-links. In the web-assistent of annex I couldn't find such a feature. + + +Is there any web-browser for a git-annex-repository? + +-- Tobias From 43713b1972e8dfc3e7ab3b0081adf7a09b34d08d Mon Sep 17 00:00:00 2001 From: Joey Hess Date: Mon, 21 Mar 2016 10:43:24 -0400 Subject: [PATCH 70/88] fix typo --- debian/control | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/debian/control b/debian/control index e77a8b7ffe..e144f78d88 100644 --- a/debian/control +++ b/debian/control @@ -31,7 +31,7 @@ Build-Depends: libghc-stm-dev (>= 2.3), libghc-dbus-dev (>= 0.10.7) [linux-any], libghc-fdo-notify-dev (>= 0.3) [linux-any], - libghc-yesod-dev (>= 1.2.6.1) [i386 amd64 arm64 armhf kfreebsd-amd64 kfreebsd-i386 mips mips64el mipsel powerpc ppc64el s390x] + libghc-yesod-dev (>= 1.2.6.1) [i386 amd64 arm64 armhf kfreebsd-amd64 kfreebsd-i386 mips mips64el mipsel powerpc ppc64el s390x], libghc-yesod-core-dev (>= 1.2.19) [i386 amd64 arm64 armhf kfreebsd-i386 kfreebsd-amd64 mips mips64el mipsel powerpc ppc64el s390x], libghc-yesod-form-dev (>= 1.3.15) [i386 amd64 arm64 armhf kfreebsd-i386 kfreebsd-amd64 mips mips64el mipsel powerpc ppc64el s390x], libghc-yesod-static-dev (>= 1.2.4) [i386 amd64 arm64 armhf kfreebsd-i386 kfreebsd-amd64 mips mips64el mipsel powerpc ppc64el s390x], @@ -42,7 +42,7 @@ Build-Depends: libghc-warp-tls-dev [i386 amd64 arm64 armhf kfreebsd-i386 kfreebsd-amd64 mips mips64el mipsel powerpc ppc64el s390x], libghc-wai-dev [i386 amd64 arm64 armhf kfreebsd-i386 kfreebsd-amd64 mips mips64el mipsel powerpc ppc64el s390x], libghc-wai-extra-dev [i386 amd64 arm64 armhf kfreebsd-i386 kfreebsd-amd64 mips mips64el mipsel powerpc ppc64el s390x], - libghc-dav-dev (>= 1.0) + libghc-dav-dev (>= 1.0), libghc-persistent-dev, libghc-persistent-template-dev, libghc-persistent-sqlite-dev, From 55315a3a581ad45515e5c1c11cc590e0aa6edaeb Mon Sep 17 00:00:00 2001 From: Kalle Date: Mon, 21 Mar 2016 21:02:58 +0000 Subject: [PATCH 71/88] Added a comment: Different solution --- .../comment_1_1f8e7e54e9f377417cd672d66ae9bd9d._comment | 9 +++++++++ 1 file changed, 9 insertions(+) create mode 100644 doc/forum/web-browser_for_the_repository/comment_1_1f8e7e54e9f377417cd672d66ae9bd9d._comment diff --git a/doc/forum/web-browser_for_the_repository/comment_1_1f8e7e54e9f377417cd672d66ae9bd9d._comment b/doc/forum/web-browser_for_the_repository/comment_1_1f8e7e54e9f377417cd672d66ae9bd9d._comment new file mode 100644 index 0000000000..32296609a0 --- /dev/null +++ b/doc/forum/web-browser_for_the_repository/comment_1_1f8e7e54e9f377417cd672d66ae9bd9d._comment @@ -0,0 +1,9 @@ +[[!comment format=mdwn + username="Kalle" + subject="Different solution" + date="2016-03-21T21:02:57Z" + content=""" +Hi + +Are you able to install git-annex on the server? If so perhaps switching the server repo to **direct mode** will work. Then you should be able to use any directory listing method you like. My guess is that you need to make sure the file listing software is configured to ignore `.git` directories. I've never used TRAC so can't tell if this is possible or required. +"""]] From 0266c28614f4c6ad12dbd00a1088ec47fe143001 Mon Sep 17 00:00:00 2001 From: Tobias Date: Mon, 21 Mar 2016 21:28:57 +0000 Subject: [PATCH 72/88] Added a comment: bare repository in direct mode --- .../comment_2_551d5bb2d24212de65720d796365177f._comment | 9 +++++++++ 1 file changed, 9 insertions(+) create mode 100644 doc/forum/web-browser_for_the_repository/comment_2_551d5bb2d24212de65720d796365177f._comment diff --git a/doc/forum/web-browser_for_the_repository/comment_2_551d5bb2d24212de65720d796365177f._comment b/doc/forum/web-browser_for_the_repository/comment_2_551d5bb2d24212de65720d796365177f._comment new file mode 100644 index 0000000000..dfee3959e5 --- /dev/null +++ b/doc/forum/web-browser_for_the_repository/comment_2_551d5bb2d24212de65720d796365177f._comment @@ -0,0 +1,9 @@ +[[!comment format=mdwn + username="Tobias" + subject="bare repository in direct mode" + date="2016-03-21T21:28:57Z" + content=""" +It is not possible to put a bare repository in direct mode. I tried it and it did not work. + +Tobias +"""]] From 309e16fc369668a55010a1ea9a8f1690a04fc4dd Mon Sep 17 00:00:00 2001 From: "b@526b37d9a821b5f9ce4e48014422239233ded155" Date: Mon, 21 Mar 2016 22:47:43 +0000 Subject: [PATCH 73/88] Added a comment: Fetch files from two (or more) remotes simultaneously? --- .../comment_4_44dcb42a011cc203655bccca06de2e10._comment | 8 ++++++++ 1 file changed, 8 insertions(+) create mode 100644 doc/git-annex-copy/comment_4_44dcb42a011cc203655bccca06de2e10._comment diff --git a/doc/git-annex-copy/comment_4_44dcb42a011cc203655bccca06de2e10._comment b/doc/git-annex-copy/comment_4_44dcb42a011cc203655bccca06de2e10._comment new file mode 100644 index 0000000000..abd34e5978 --- /dev/null +++ b/doc/git-annex-copy/comment_4_44dcb42a011cc203655bccca06de2e10._comment @@ -0,0 +1,8 @@ +[[!comment format=mdwn + username="b@526b37d9a821b5f9ce4e48014422239233ded155" + nickname="b" + subject="Fetch files from two (or more) remotes simultaneously?" + date="2016-03-21T22:47:42Z" + content=""" +Let's assume that user has two slow remotes. Is it possible to fetch the data from both to at least partially speed-up the process? +"""]] From 7948110134af191d5ac1613b57e00657cd8c58b5 Mon Sep 17 00:00:00 2001 From: Robie Basak Date: Wed, 23 Mar 2016 03:42:13 +0000 Subject: [PATCH 74/88] ddar remote: fix ssh calls sshOptions is now designed for working out ssh options only, and may insert the extra options it is given to the middle. So it is incorrect to call it with the remote parameters at the end. Instead, append them to its return value. This half regressed in 5be7ba7, and presumably regressed fully when sshOptions was changed some time later. --- Remote/Ddar.hs | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/Remote/Ddar.hs b/Remote/Ddar.hs index 4a46fe15ce..8758949c9c 100644 --- a/Remote/Ddar.hs +++ b/Remote/Ddar.hs @@ -122,8 +122,8 @@ ddarRemoteCall :: DdarRepo -> Char -> [CommandParam] -> Annex (String, [CommandP ddarRemoteCall ddarrepo cmd params | ddarLocal ddarrepo = return ("ddar", localParams) | otherwise = do - os <- sshOptions (host, Nothing) (ddarRepoConfig ddarrepo) remoteParams - return ("ssh", os) + os <- sshOptions (host, Nothing) (ddarRepoConfig ddarrepo) [] + return ("ssh", os ++ remoteParams) where (host, ddarrepo') = splitRemoteDdarRepo ddarrepo localParams = Param [cmd] : Param (ddarRepoLocation ddarrepo) : params @@ -158,8 +158,8 @@ ddarDirectoryExists ddarrepo Left _ -> Right False Right status -> Right $ isDirectory status | otherwise = do - ps <- sshOptions (host, Nothing) (ddarRepoConfig ddarrepo) params - exitCode <- liftIO $ safeSystem "ssh" ps + ps <- sshOptions (host, Nothing) (ddarRepoConfig ddarrepo) [] + exitCode <- liftIO $ safeSystem "ssh" (ps ++ params) case exitCode of ExitSuccess -> return $ Right True ExitFailure 1 -> return $ Right False From 589ff4ebbb7686c0a889edfd9b57208fd81cd3e5 Mon Sep 17 00:00:00 2001 From: Joey Hess Date: Wed, 23 Mar 2016 11:42:49 -0400 Subject: [PATCH 75/88] changelog --- debian/changelog | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/debian/changelog b/debian/changelog index 185ad685fb..eed11e4f8e 100644 --- a/debian/changelog +++ b/debian/changelog @@ -1,3 +1,10 @@ +git-annex (6.20160319) UNRELEASED; urgency=medium + + * ddar remote: fix ssh calls + Thanks, Robie Basak + + -- Joey Hess Wed, 23 Mar 2016 11:42:36 -0400 + git-annex (6.20160318) unstable; urgency=medium * metadata: Added -r to remove all current values of a field. From ecc5480828af363ed5359e9d8e6898d867ac8fce Mon Sep 17 00:00:00 2001 From: Kalle Date: Wed, 23 Mar 2016 21:22:16 +0000 Subject: [PATCH 76/88] Added a comment --- .../comment_3_d410df4b7160f17e3846674c3e0e9368._comment | 9 +++++++++ 1 file changed, 9 insertions(+) create mode 100644 doc/forum/web-browser_for_the_repository/comment_3_d410df4b7160f17e3846674c3e0e9368._comment diff --git a/doc/forum/web-browser_for_the_repository/comment_3_d410df4b7160f17e3846674c3e0e9368._comment b/doc/forum/web-browser_for_the_repository/comment_3_d410df4b7160f17e3846674c3e0e9368._comment new file mode 100644 index 0000000000..c84959a570 --- /dev/null +++ b/doc/forum/web-browser_for_the_repository/comment_3_d410df4b7160f17e3846674c3e0e9368._comment @@ -0,0 +1,9 @@ +[[!comment format=mdwn + username="Kalle" + subject="comment 3" + date="2016-03-23T21:22:15Z" + content=""" +A normal direct mode repo with git annex installed on the server should give you a synced directory structure of files that you can browse with most directory listing software/modules and download files. + +Are you looking to enable something beyond browsing and downloading the files? +"""]] From e16ba65caf190faf15e9c9419b2c7898126a88f2 Mon Sep 17 00:00:00 2001 From: anarcat Date: Thu, 24 Mar 2016 14:15:06 +0000 Subject: [PATCH 77/88] Added a comment: git remote --- .../comment_8_eedf260df630192b49557bfc84c9ce82._comment | 7 +++++++ 1 file changed, 7 insertions(+) create mode 100644 doc/special_remotes/ipfs/comment_8_eedf260df630192b49557bfc84c9ce82._comment diff --git a/doc/special_remotes/ipfs/comment_8_eedf260df630192b49557bfc84c9ce82._comment b/doc/special_remotes/ipfs/comment_8_eedf260df630192b49557bfc84c9ce82._comment new file mode 100644 index 0000000000..62a67913cd --- /dev/null +++ b/doc/special_remotes/ipfs/comment_8_eedf260df630192b49557bfc84c9ce82._comment @@ -0,0 +1,7 @@ +[[!comment format=mdwn + username="anarcat" + subject="git remote" + date="2016-03-24T14:15:06Z" + content=""" +there is now a [git remote for IPFS](https://github.com/cryptix/git-remote-ipfs). I *believe* it suffers from the same problem as all files within ipfs, namely that the contents are duplicated inside the repo. However, it certainly make for an interesting decentralised way of sharing metadata. --[[anarcat]] +"""]] From 74fbef73c894a3f81983afb2b2fa61d249a958fb Mon Sep 17 00:00:00 2001 From: "185.16.53.225" <185.16.53.225@web> Date: Thu, 24 Mar 2016 16:01:43 +0000 Subject: [PATCH 78/88] poll vote (Same as for regular git-annex. ~/annex/) --- doc/design/assistant/polls/Android_default_directory.mdwn | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/design/assistant/polls/Android_default_directory.mdwn b/doc/design/assistant/polls/Android_default_directory.mdwn index 3febc95a15..b2b22a20b6 100644 --- a/doc/design/assistant/polls/Android_default_directory.mdwn +++ b/doc/design/assistant/polls/Android_default_directory.mdwn @@ -4,4 +4,4 @@ Same as the desktop webapp, users will be able to enter a directory they want the first time they run it, but to save typing on android, anything that gets enough votes will be included in a list of choices as well. -[[!poll open=yes expandable=yes 73 "/sdcard/annex" 6 "Whole /sdcard" 8 "DCIM directory (photos and videos only)" 2 "Same as for regular git-annex. ~/annex/"]] +[[!poll open=yes expandable=yes 73 "/sdcard/annex" 6 "Whole /sdcard" 8 "DCIM directory (photos and videos only)" 3 "Same as for regular git-annex. ~/annex/"]] From 541ac227b7cf41c1aef44682c5380b2db2648c88 Mon Sep 17 00:00:00 2001 From: Tobias Date: Fri, 25 Mar 2016 15:24:22 +0000 Subject: [PATCH 79/88] Added a comment: History --- .../comment_4_d06217403bf53a713b845bbc9ca8b962._comment | 7 +++++++ 1 file changed, 7 insertions(+) create mode 100644 doc/forum/web-browser_for_the_repository/comment_4_d06217403bf53a713b845bbc9ca8b962._comment diff --git a/doc/forum/web-browser_for_the_repository/comment_4_d06217403bf53a713b845bbc9ca8b962._comment b/doc/forum/web-browser_for_the_repository/comment_4_d06217403bf53a713b845bbc9ca8b962._comment new file mode 100644 index 0000000000..e0ce7359bc --- /dev/null +++ b/doc/forum/web-browser_for_the_repository/comment_4_d06217403bf53a713b845bbc9ca8b962._comment @@ -0,0 +1,7 @@ +[[!comment format=mdwn + username="Tobias" + subject="History" + date="2016-03-25T15:24:21Z" + content=""" +I'm not only interested in the current state of the files but also in a browser for the revisions. Therefore I need a \"real\" repository-browser. +"""]] From b476204254da64c7224f33634e78c331789a4940 Mon Sep 17 00:00:00 2001 From: "freewheelinfranks@f936f2e420801f565d39e40036c0a22c71a79425" Date: Sun, 27 Mar 2016 00:56:57 +0000 Subject: [PATCH 80/88] --- doc/forum/Androd__58___Cabal-hell.mdwn | 32 ++++++++++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 doc/forum/Androd__58___Cabal-hell.mdwn diff --git a/doc/forum/Androd__58___Cabal-hell.mdwn b/doc/forum/Androd__58___Cabal-hell.mdwn new file mode 100644 index 0000000000..e31b1b0dce --- /dev/null +++ b/doc/forum/Androd__58___Cabal-hell.mdwn @@ -0,0 +1,32 @@ +I tried to build the Android app according to the instructions on [the install page](https://git-annex.branchable.com/install/Android/). + +But during step 2 (In the chroot, run install-haskell-packages) cabal fails to handle the dependencies correctly. So I tried to change the standalone/android/cabal.config file to update all the dependencies, but this had me running into something I think is unresolvable in another package's +dependencies. Eventually I had the following output: + + # ./standalone/android/install-haskell-packages + Downloading the latest package list from hackage.haskell.org + Skipping download: Local and remote files match. + /home/repo/git-annex /home/repo/git-annex/standalone/android + Resolving dependencies... + cabal: Could not resolve dependencies: + trying: git-annex-6.20160318 (user goal) + trying: persistent-template-2.1.6/installed-08b... (dependency of + git-annex-6.20160318) + next goal: monad-control (dependency of git-annex-6.20160318) + rejecting: monad-control-1.0.0.5/installed-cac..., 1.0.0.5, 1.0.0.4, 1.0.0.3, + 1.0.0.2, 1.0.0.1, 1.0.0.0, 0.3.3.1, 0.3.3.0, 0.3.2.3 (global constraint + requires ==0.3.2.2) + rejecting: monad-control-0.3.2.2 (conflict: persistent-template => + monad-control==1.0.0.5/installed-cac...) + rejecting: monad-control-0.3.2.1, 0.3.2, 0.3.1.4, 0.3.1.3, 0.3.1.2, 0.3.1.1, + 0.3.1, 0.3.0.1, 0.3, 0.2.0.3, 0.2.0.2, 0.2.0.1, 0.2, 0.1 (global constraint + requires ==0.3.2.2) + +This tells me that the package persistent-template depends on the package monad-control at a version of 1.0.0.5. So I look at the [persistent-template hackage page](https://hackage.haskell.org/package/persistent-template-2.1.6) and see that it lists its dependency on monad-control as: + + monad-control (>=0.2 && <1.1) + +And I don't think that's possible to resolve. + +All I wanted to do was change the icons on the Android package, so if you'll just accept the changed +icons folder, I can submit the patch without testing the Android build, but currently I'm unable to build the Android port of git-annex. From 61ad36c67d3d33c9e27a3f38544607bfc583c554 Mon Sep 17 00:00:00 2001 From: "freewheelinfranks@f936f2e420801f565d39e40036c0a22c71a79425" Date: Sun, 27 Mar 2016 00:57:44 +0000 Subject: [PATCH 81/88] removed --- doc/forum/Androd__58___Cabal-hell.mdwn | 32 -------------------------- 1 file changed, 32 deletions(-) delete mode 100644 doc/forum/Androd__58___Cabal-hell.mdwn diff --git a/doc/forum/Androd__58___Cabal-hell.mdwn b/doc/forum/Androd__58___Cabal-hell.mdwn deleted file mode 100644 index e31b1b0dce..0000000000 --- a/doc/forum/Androd__58___Cabal-hell.mdwn +++ /dev/null @@ -1,32 +0,0 @@ -I tried to build the Android app according to the instructions on [the install page](https://git-annex.branchable.com/install/Android/). - -But during step 2 (In the chroot, run install-haskell-packages) cabal fails to handle the dependencies correctly. So I tried to change the standalone/android/cabal.config file to update all the dependencies, but this had me running into something I think is unresolvable in another package's -dependencies. Eventually I had the following output: - - # ./standalone/android/install-haskell-packages - Downloading the latest package list from hackage.haskell.org - Skipping download: Local and remote files match. - /home/repo/git-annex /home/repo/git-annex/standalone/android - Resolving dependencies... - cabal: Could not resolve dependencies: - trying: git-annex-6.20160318 (user goal) - trying: persistent-template-2.1.6/installed-08b... (dependency of - git-annex-6.20160318) - next goal: monad-control (dependency of git-annex-6.20160318) - rejecting: monad-control-1.0.0.5/installed-cac..., 1.0.0.5, 1.0.0.4, 1.0.0.3, - 1.0.0.2, 1.0.0.1, 1.0.0.0, 0.3.3.1, 0.3.3.0, 0.3.2.3 (global constraint - requires ==0.3.2.2) - rejecting: monad-control-0.3.2.2 (conflict: persistent-template => - monad-control==1.0.0.5/installed-cac...) - rejecting: monad-control-0.3.2.1, 0.3.2, 0.3.1.4, 0.3.1.3, 0.3.1.2, 0.3.1.1, - 0.3.1, 0.3.0.1, 0.3, 0.2.0.3, 0.2.0.2, 0.2.0.1, 0.2, 0.1 (global constraint - requires ==0.3.2.2) - -This tells me that the package persistent-template depends on the package monad-control at a version of 1.0.0.5. So I look at the [persistent-template hackage page](https://hackage.haskell.org/package/persistent-template-2.1.6) and see that it lists its dependency on monad-control as: - - monad-control (>=0.2 && <1.1) - -And I don't think that's possible to resolve. - -All I wanted to do was change the icons on the Android package, so if you'll just accept the changed -icons folder, I can submit the patch without testing the Android build, but currently I'm unable to build the Android port of git-annex. From f3148c431313b33c7160155413a48735ded31967 Mon Sep 17 00:00:00 2001 From: "freewheelinfranks@f936f2e420801f565d39e40036c0a22c71a79425" Date: Sun, 27 Mar 2016 00:58:22 +0000 Subject: [PATCH 82/88] --- doc/forum/Android__58___Cabal_hell.mdwn | 32 +++++++++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 doc/forum/Android__58___Cabal_hell.mdwn diff --git a/doc/forum/Android__58___Cabal_hell.mdwn b/doc/forum/Android__58___Cabal_hell.mdwn new file mode 100644 index 0000000000..e31b1b0dce --- /dev/null +++ b/doc/forum/Android__58___Cabal_hell.mdwn @@ -0,0 +1,32 @@ +I tried to build the Android app according to the instructions on [the install page](https://git-annex.branchable.com/install/Android/). + +But during step 2 (In the chroot, run install-haskell-packages) cabal fails to handle the dependencies correctly. So I tried to change the standalone/android/cabal.config file to update all the dependencies, but this had me running into something I think is unresolvable in another package's +dependencies. Eventually I had the following output: + + # ./standalone/android/install-haskell-packages + Downloading the latest package list from hackage.haskell.org + Skipping download: Local and remote files match. + /home/repo/git-annex /home/repo/git-annex/standalone/android + Resolving dependencies... + cabal: Could not resolve dependencies: + trying: git-annex-6.20160318 (user goal) + trying: persistent-template-2.1.6/installed-08b... (dependency of + git-annex-6.20160318) + next goal: monad-control (dependency of git-annex-6.20160318) + rejecting: monad-control-1.0.0.5/installed-cac..., 1.0.0.5, 1.0.0.4, 1.0.0.3, + 1.0.0.2, 1.0.0.1, 1.0.0.0, 0.3.3.1, 0.3.3.0, 0.3.2.3 (global constraint + requires ==0.3.2.2) + rejecting: monad-control-0.3.2.2 (conflict: persistent-template => + monad-control==1.0.0.5/installed-cac...) + rejecting: monad-control-0.3.2.1, 0.3.2, 0.3.1.4, 0.3.1.3, 0.3.1.2, 0.3.1.1, + 0.3.1, 0.3.0.1, 0.3, 0.2.0.3, 0.2.0.2, 0.2.0.1, 0.2, 0.1 (global constraint + requires ==0.3.2.2) + +This tells me that the package persistent-template depends on the package monad-control at a version of 1.0.0.5. So I look at the [persistent-template hackage page](https://hackage.haskell.org/package/persistent-template-2.1.6) and see that it lists its dependency on monad-control as: + + monad-control (>=0.2 && <1.1) + +And I don't think that's possible to resolve. + +All I wanted to do was change the icons on the Android package, so if you'll just accept the changed +icons folder, I can submit the patch without testing the Android build, but currently I'm unable to build the Android port of git-annex. From 7fc51f338c127e2df12fadb6eb538fb8bbe0ed50 Mon Sep 17 00:00:00 2001 From: "https://openid.stackexchange.com/user/27ceb3c5-0762-42b8-8f8a-ed21c284748f" Date: Mon, 28 Mar 2016 08:32:45 +0000 Subject: [PATCH 83/88] Added a comment: why not mimetypes for preferred content? --- .../comment_3_bf44404de52b00ff4e4f1effd4cef336._comment | 8 ++++++++ 1 file changed, 8 insertions(+) create mode 100644 doc/devblog/day_360__annex.largefiles_mimetype/comment_3_bf44404de52b00ff4e4f1effd4cef336._comment diff --git a/doc/devblog/day_360__annex.largefiles_mimetype/comment_3_bf44404de52b00ff4e4f1effd4cef336._comment b/doc/devblog/day_360__annex.largefiles_mimetype/comment_3_bf44404de52b00ff4e4f1effd4cef336._comment new file mode 100644 index 0000000000..e7f4f40549 --- /dev/null +++ b/doc/devblog/day_360__annex.largefiles_mimetype/comment_3_bf44404de52b00ff4e4f1effd4cef336._comment @@ -0,0 +1,8 @@ +[[!comment format=mdwn + username="https://openid.stackexchange.com/user/27ceb3c5-0762-42b8-8f8a-ed21c284748f" + nickname="g" + subject="why not mimetypes for preferred content?" + date="2016-03-28T08:32:45Z" + content=""" +Why does matching by mimetype only make sense for annex.largefiles, but not for preferred content expressions? Sorry if this is a stupid question, but it seems it would in fact be quite useful to easily express that, for example, a certain repo have a preference for my photos and not my music files (though both should be considered large files) +"""]] From 891fdf7eaacbf462977f06cd673563e06b761b28 Mon Sep 17 00:00:00 2001 From: "http://svario.it/gioele" Date: Mon, 28 Mar 2016 09:58:25 +0000 Subject: [PATCH 84/88] --- .../wishlist__58___Unix_time_in_git_annex_log.mdwn | 14 ++++++++++++++ 1 file changed, 14 insertions(+) create mode 100644 doc/todo/wishlist__58___Unix_time_in_git_annex_log.mdwn diff --git a/doc/todo/wishlist__58___Unix_time_in_git_annex_log.mdwn b/doc/todo/wishlist__58___Unix_time_in_git_annex_log.mdwn new file mode 100644 index 0000000000..706686f621 --- /dev/null +++ b/doc/todo/wishlist__58___Unix_time_in_git_annex_log.mdwn @@ -0,0 +1,14 @@ +Could `git annex log` show the modification times using the Unix time instead of human-readable timestamps? + +This is an example of the output of `git annex log`: + +``` ++ 2014-10-27 01:00:18 ev-2014.pdf | 50083bd6-7e20-4356-a32f-a1dde07de441 -- penn +``` + +If the timestamp were in Unix time, it would be easier to process in a mechanical way. Unix time would also avoid having to guess what is the correct timezone for the timestamp. + +``` ++ 1414368018 ev-2014.pdf | 50083bd6-7e20-4356-a32f-a1dde07de441 -- penn +``` + From a60fbce82633c57ae405f126c2cc169abea98673 Mon Sep 17 00:00:00 2001 From: Joey Hess Date: Mon, 28 Mar 2016 09:21:37 -0400 Subject: [PATCH 85/88] comment --- ...ment_1_34e869c1092f2885f54f627fb77a6057._comment | 13 +++++++++++++ 1 file changed, 13 insertions(+) create mode 100644 doc/forum/Android__58___Cabal_hell/comment_1_34e869c1092f2885f54f627fb77a6057._comment diff --git a/doc/forum/Android__58___Cabal_hell/comment_1_34e869c1092f2885f54f627fb77a6057._comment b/doc/forum/Android__58___Cabal_hell/comment_1_34e869c1092f2885f54f627fb77a6057._comment new file mode 100644 index 0000000000..e96bdf2222 --- /dev/null +++ b/doc/forum/Android__58___Cabal_hell/comment_1_34e869c1092f2885f54f627fb77a6057._comment @@ -0,0 +1,13 @@ +[[!comment format=mdwn + username="joey" + subject="""comment 1""" + date="2016-03-28T13:20:06Z" + content=""" +The android packages are all pinned at old versions, so the build is +supposed to be reproducible using those versions. Diverging certainly +invites cabal hell. + +Any chance you could show the original failure? + +I could probably integrate new icons if you want to just submit them. +"""]] From 53a1a38aeb32e386392a6b606c779fd1da7e65a4 Mon Sep 17 00:00:00 2001 From: Joey Hess Date: Mon, 28 Mar 2016 09:23:53 -0400 Subject: [PATCH 86/88] comment --- ...ment_4_70c337d91f8d0458927c111763041118._comment | 13 +++++++++++++ 1 file changed, 13 insertions(+) create mode 100644 doc/devblog/day_360__annex.largefiles_mimetype/comment_4_70c337d91f8d0458927c111763041118._comment diff --git a/doc/devblog/day_360__annex.largefiles_mimetype/comment_4_70c337d91f8d0458927c111763041118._comment b/doc/devblog/day_360__annex.largefiles_mimetype/comment_4_70c337d91f8d0458927c111763041118._comment new file mode 100644 index 0000000000..51bff84886 --- /dev/null +++ b/doc/devblog/day_360__annex.largefiles_mimetype/comment_4_70c337d91f8d0458927c111763041118._comment @@ -0,0 +1,13 @@ +[[!comment format=mdwn + username="joey" + subject="""comment 4""" + date="2016-03-28T13:22:35Z" + content=""" +For the simple reason that git-annex doesn't know the mime type of a file +before it downloads a copy. + +There are some more complicated reasons involving preferred content +expressions needing to evaluate the same way in different repos, which +can be on different computers with different versions of the magic +database, etc. +"""]] From 2ba851ff5d81f886bc858a764b77804b32600996 Mon Sep 17 00:00:00 2001 From: Joey Hess Date: Mon, 28 Mar 2016 12:51:16 -0400 Subject: [PATCH 87/88] OSX build updated for security fix; old obsolete builds for older versions removed as they contain vulnerable git --- doc/bugs/git_security_fix.mdwn | 6 ++++-- doc/install/OSX.mdwn | 2 -- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/doc/bugs/git_security_fix.mdwn b/doc/bugs/git_security_fix.mdwn index 3ce6c4b073..43b3f505f7 100644 --- a/doc/bugs/git_security_fix.mdwn +++ b/doc/bugs/git_security_fix.mdwn @@ -6,13 +6,15 @@ git-annex builds that bundle git need to be updated. status of autobuilds: * Linux is fixed (all builds) -* OSX pending (host is moving) +* OSX is fixed * Windows does not bundle git * Android is fixed (git build is untested) status of released builds: * Linux is fixed (all builds) -* OSX is **vulnerable** +* OSX is fixed (yosemite only; old builds vulnerable so removed) * Windows does not bundle git * Android is fixed (git build is untested) + +[[done]] --[[Joey]] diff --git a/doc/install/OSX.mdwn b/doc/install/OSX.mdwn index b1ff1cc854..6b333dd7d0 100644 --- a/doc/install/OSX.mdwn +++ b/doc/install/OSX.mdwn @@ -4,8 +4,6 @@ For easy installation, use the prebuilt app bundle. * 10.11 El Capitan / 10.10 Yosemite / 10.9 Mavericks: [git-annex.dmg](https://downloads.kitenet.net/git-annex/OSX/current/10.10_Yosemite/git-annex.dmg) -* 10.8.2 Mountain Lion: [git-annex.dmg.bz2](https://downloads.kitenet.net/git-annex/OSX/current/10.8.2_Mountain_Lion/git-annex.dmg.bz2) **warning: not being updated any longer** -* 10.7.5 Lion: [git-annex.dmg](https://downloads.kitenet.net/git-annex/OSX/current/10.7.5_Lion/git-annex.dmg) **warning: not being updated any longer** To run the [[git-annex_assistant|/assistant]], just install the app, look for the icon, and start it up. From 2fd7cc4bfe02b6b331d5bd8990c660ee78fa4036 Mon Sep 17 00:00:00 2001 From: "https://me.yahoo.com/a/EbvxpTI_xP9Aod7Mg4cwGhgjrCrdM5s-#7c0f4" Date: Tue, 29 Mar 2016 13:27:39 +0000 Subject: [PATCH 88/88] --- ..._operating_on_a_clone_with_submodules.mdwn | 60 +++++++++++++++++++ 1 file changed, 60 insertions(+) create mode 100644 doc/bugs/awkward_error_from_annex_whenever_operating_on_a_clone_with_submodules.mdwn diff --git a/doc/bugs/awkward_error_from_annex_whenever_operating_on_a_clone_with_submodules.mdwn b/doc/bugs/awkward_error_from_annex_whenever_operating_on_a_clone_with_submodules.mdwn new file mode 100644 index 0000000000..720b0c0698 --- /dev/null +++ b/doc/bugs/awkward_error_from_annex_whenever_operating_on_a_clone_with_submodules.mdwn @@ -0,0 +1,60 @@ +### Please describe the problem. + +git annex init fails on a clone of a sub sub module from a git repo + +### What steps will reproduce the problem? + +This is the archive with sample repo which is used in example below +[http://www.onerussian.com/tmp/repl_submodule.tgz] + + +### What version of git-annex are you using? On what operating system? + +6.20160307+gitgb095561-1~ndall+1 + +[[!format sh """ +> tar -xzf repl_submodule.tgz + +> ls -ld datalad_temp_testrepo_Lb8lMD +drwx------ 5 yoh yoh 180 Mar 29 09:06 datalad_temp_testrepo_Lb8lMD/ + +> git clone datalad_temp_testrepo_Lb8lMD/sub1/sub1 +Cloning into 'sub1'... +done. + +> cd sub1 +INFO.txt sub1/ sub2/ test-annex.dat@ test.dat + +> git annex init +init fatal: Could not switch to '/sub1/': No such file or directory +ok +(recording state in git...) + +> cat .git/config +[core] + repositoryformatversion = 0 + filemode = true + bare = false + logallrefupdates = true +[remote "origin"] + url = /tmp/datalad_temp_testrepo_Lb8lMD/sub1/sub1 + fetch = +refs/heads/*:refs/remotes/origin/* +[branch "master"] + remote = origin + merge = refs/heads/master +[annex] + uuid = 7293cd84-98c5-4f8c-b1ff-1c4fadd90ba3 + version = 5 + +> git annex --debug init 2>&1 | grep -3 "Could not" +[2016-03-29 09:22:21.786669] read: git ["config","--null","--list"] +[2016-03-29 09:22:21.792047] process done ExitSuccess +[2016-03-29 09:22:21.792158] read: git ["--git-dir=../datalad_temp_testrepo_Lb8lMD/sub1/sub1/.git","--work-tree=/sub1/sub1","--literal-pathspecs","show-ref","git-annex"] +fatal: Could not switch to '/sub1/': No such file or directory +[2016-03-29 09:22:21.797597] process done ExitFailure 128 +ok +[2016-03-29 09:22:21.800514] chat: git ["--git-dir=.git","--work-tree=.","--literal-pathspecs","hash-object","-w","--stdin-paths","--no-filters"] + +"""]] + +[[!meta author=yoh]]