From 117c009f234d5f15b3b6963cef1f8523627355d9 Mon Sep 17 00:00:00 2001 From: aragilar Date: Thu, 16 May 2019 06:27:23 +0000 Subject: [PATCH 1/9] --- doc/bugs/Show_current_config_of_special_remote.mdwn | 9 +++++++++ 1 file changed, 9 insertions(+) create mode 100644 doc/bugs/Show_current_config_of_special_remote.mdwn diff --git a/doc/bugs/Show_current_config_of_special_remote.mdwn b/doc/bugs/Show_current_config_of_special_remote.mdwn new file mode 100644 index 0000000000..aaa36680bf --- /dev/null +++ b/doc/bugs/Show_current_config_of_special_remote.mdwn @@ -0,0 +1,9 @@ +### Please describe the problem. +There appears to be no way of getting the current configuration of special remotes (e.g. url, keyid). Maybe there should be git-annex-showremote (or similar). + +### What steps will reproduce the problem? +Configure the special remote (e.g. webdav), and then forget what settings you specified ;) + +### What version of git-annex are you using? On what operating system? +7.20190129-3 (Debian) + From 1a33402476c52a8f117fe1f807b19e4ae3e97a2f Mon Sep 17 00:00:00 2001 From: derobert Date: Thu, 16 May 2019 08:12:45 +0000 Subject: [PATCH 2/9] Added a comment --- .../comment_1_3886d242006fbc6928685bfeaaf93d70._comment | 8 ++++++++ 1 file changed, 8 insertions(+) create mode 100644 doc/bugs/Show_current_config_of_special_remote/comment_1_3886d242006fbc6928685bfeaaf93d70._comment diff --git a/doc/bugs/Show_current_config_of_special_remote/comment_1_3886d242006fbc6928685bfeaaf93d70._comment b/doc/bugs/Show_current_config_of_special_remote/comment_1_3886d242006fbc6928685bfeaaf93d70._comment new file mode 100644 index 0000000000..2539e907d3 --- /dev/null +++ b/doc/bugs/Show_current_config_of_special_remote/comment_1_3886d242006fbc6928685bfeaaf93d70._comment @@ -0,0 +1,8 @@ +[[!comment format=mdwn + username="derobert" + avatar="http://cdn.libravatar.org/avatar/05b48b72766177b3b0a6ff4afdb70790" + subject="comment 1" + date="2019-05-16T08:12:45Z" + content=""" +Did you try `git-annex info «remote»` (where «remote» could be the name or the UUID). +"""]] From bea10be73c9b169b89ae5d705e8b579acd53a170 Mon Sep 17 00:00:00 2001 From: aragilar Date: Thu, 16 May 2019 08:26:28 +0000 Subject: [PATCH 3/9] Added a comment --- .../comment_2_bf5f08276435a95f0c3822ef99655f67._comment | 8 ++++++++ 1 file changed, 8 insertions(+) create mode 100644 doc/bugs/Show_current_config_of_special_remote/comment_2_bf5f08276435a95f0c3822ef99655f67._comment diff --git a/doc/bugs/Show_current_config_of_special_remote/comment_2_bf5f08276435a95f0c3822ef99655f67._comment b/doc/bugs/Show_current_config_of_special_remote/comment_2_bf5f08276435a95f0c3822ef99655f67._comment new file mode 100644 index 0000000000..a8e791fe64 --- /dev/null +++ b/doc/bugs/Show_current_config_of_special_remote/comment_2_bf5f08276435a95f0c3822ef99655f67._comment @@ -0,0 +1,8 @@ +[[!comment format=mdwn + username="aragilar" + avatar="http://cdn.libravatar.org/avatar/7390f7c0dd07d43ca827a5446b65c102" + subject="comment 2" + date="2019-05-16T08:26:28Z" + content=""" +Weird, I tried that on the same remote on a different system, and it gave what I wanted... I'll have to work out why that didn't work the first time. Thanks @derobert! +"""]] From 33c16fd93691734d2fe566486f3188ee80633f3f Mon Sep 17 00:00:00 2001 From: Ilya_Shlyakhter Date: Thu, 16 May 2019 18:36:44 +0000 Subject: [PATCH 4/9] reported still seeing errors with git-annex-add --- ...eing_errors_with_parallel_git-annex-add.mdwn | 17 +++++++++++++++++ 1 file changed, 17 insertions(+) create mode 100644 doc/bugs/still_seeing_errors_with_parallel_git-annex-add.mdwn diff --git a/doc/bugs/still_seeing_errors_with_parallel_git-annex-add.mdwn b/doc/bugs/still_seeing_errors_with_parallel_git-annex-add.mdwn new file mode 100644 index 0000000000..282cb558d1 --- /dev/null +++ b/doc/bugs/still_seeing_errors_with_parallel_git-annex-add.mdwn @@ -0,0 +1,17 @@ +It seems that the [[issue with parallel git-annex-add|bugs/withOtherTmp_file_escapes]] is not yet quite fixed; I'm seeing it in the git-annex version 7.20190507-g0c2cc3d . Repeating the git-annex-add command succeeds in adding the files that failed the first time. + +[[!format sh """ +add benchmarks/rabies200/analysis-FK7BF7Q0761xKv6V3z3gzZgK/benchmark_variants/v1.23.0_spades-3.13.0-trinity-metaspades-01/inputs-local.json +git-annex: .git/annex/othertmp/inge11793-2931: rename: permission denied (Permission denied) +failed +add benchmarks/rabies200/analysis-FK7BKGj0761VgPb22550gfBX/benchmark_variants/v1.23.0_spades-3.13.0-trinity-metaspades-01/inputs-local.json +git-annex: .git/annex/othertmp/inge11793-3330: rename: permission denied (Permission denied) +failed +git-annex: add: 2 failed +"""]] + +### 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) + +git-annex has become an essential tool for organizing my bioinformatics data analyses. It scales well to large repos. It lets me keep track of analyses without +locking myself into any specific cloud platform. It lets me quickly free up space on demand by moving data to cheaper storage, with the assurance that nothing will get lost. +Thanks @joeyh for all your work on it. From d803c1c3310bad52d75e962539e14233e258f0fe Mon Sep 17 00:00:00 2001 From: Ilya_Shlyakhter Date: Fri, 17 May 2019 17:51:25 +0000 Subject: [PATCH 5/9] reported issue with git-annex-init silently overwriting repo description --- ..._overwrites_existing_repo_description.mdwn | 20 +++++++++++++++++++ 1 file changed, 20 insertions(+) create mode 100644 doc/bugs/git-annex-init_with_no_args_overwrites_existing_repo_description.mdwn diff --git a/doc/bugs/git-annex-init_with_no_args_overwrites_existing_repo_description.mdwn b/doc/bugs/git-annex-init_with_no_args_overwrites_existing_repo_description.mdwn new file mode 100644 index 0000000000..52885b300f --- /dev/null +++ b/doc/bugs/git-annex-init_with_no_args_overwrites_existing_repo_description.mdwn @@ -0,0 +1,20 @@ +### Please describe the problem. +The man page for [[`git-annex-init`|git-annex-init]] suggests that it is idempotent. But, when run with no args, it will overwrite an existing repo description with an automatically-generated one. Same for [[`git-annex-describe`|git-annex-describe]]. + +### What version of git-annex are you using? On what operating system? +(master_env_v135_py36) 13:44 [r2] $ git annex version +git-annex version: 7.20190507-g0c2cc3d +build flags: Assistant Webapp Pairing S3 WebDAV Inotify DBus DesktopNotify TorrentParser MagicMime Feeds Testsuite +dependency versions: aws-0.21.1 bloomfilter-2.0.1.0 cryptonite-0.25 DAV-1.3.3 feed-1.0.1.0 ghc-8.4.2 http-client-0.5.14 persistent-sq\ +lite-2.9.2 torrent-10000.1.1 uuid-1.3.13 yesod-1.6.0 +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 BLAKE2B256E BLAKE2B256 BLAKE2B512E BLAKE2B512 BLAKE2B160E BLAKE2B160 BLA\ +KE2B224E BLAKE2B224 BLAKE2B384E BLAKE2B384 BLAKE2S256E BLAKE2S256 BLAKE2S160E BLAKE2S160 BLAKE2S224E BLAKE2S224 BLAKE2SP256E BLAKE2SP\ +256 BLAKE2SP224E BLAKE2SP224 SHA1E SHA1 MD5E MD5 WORM URL +remote types: git gcrypt p2p S3 bup directory rsync web bittorrent webdav adb tahoe glacier ddar hook external +operating system: linux x86_64 +supported repository versions: 5 7 +upgrade supported from repository versions: 0 1 2 3 4 5 6 +local repository version: 5 +(master_env_v135_py36) 13:47 [r2] $ uname -a +Linux ip-172-31-90-58.ec2.internal 4.14.114-105.126.amzn2.x86_64 #1 SMP Tue May 7 02:26:40 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux From c70f344af4b942deb40d8d1c0db4097dde7e59ca Mon Sep 17 00:00:00 2001 From: ply Date: Fri, 17 May 2019 20:55:48 +0000 Subject: [PATCH 6/9] Added a comment --- ..._4462c0640e11e20a8655743ecc78eaaa._comment | 76 +++++++++++++++++++ 1 file changed, 76 insertions(+) create mode 100644 doc/forum/git-annex__58___openFile__58___resource_busy___40__file_is_locked__41__/comment_3_4462c0640e11e20a8655743ecc78eaaa._comment diff --git a/doc/forum/git-annex__58___openFile__58___resource_busy___40__file_is_locked__41__/comment_3_4462c0640e11e20a8655743ecc78eaaa._comment b/doc/forum/git-annex__58___openFile__58___resource_busy___40__file_is_locked__41__/comment_3_4462c0640e11e20a8655743ecc78eaaa._comment new file mode 100644 index 0000000000..ae97acc298 --- /dev/null +++ b/doc/forum/git-annex__58___openFile__58___resource_busy___40__file_is_locked__41__/comment_3_4462c0640e11e20a8655743ecc78eaaa._comment @@ -0,0 +1,76 @@ +[[!comment format=mdwn + username="ply" + avatar="http://cdn.libravatar.org/avatar/1270501a59ed4a4042366b00295fe236" + subject="comment 3" + date="2019-05-17T20:55:48Z" + content=""" +Hello, I have similar problem, but with exFAT on macOS 10.13.6. Output is not stripped, it's no filename there: + +``` +$ git annex info --fast --debug +[2019-05-17 22:42:09.997466] read: git [\"--git-dir=.git\",\"--work-tree=.\",\"--literal-pathspecs\",\"show-ref\",\"git-annex\"] +[2019-05-17 22:42:12.914831] process done ExitSuccess +[2019-05-17 22:42:12.915017] read: git [\"--git-dir=.git\",\"--work-tree=.\",\"--literal-pathspecs\",\"show-ref\",\"--hash\",\"refs/heads/git-annex\"] +[2019-05-17 22:42:12.953171] process done ExitSuccess +[2019-05-17 22:42:12.953815] read: git [\"--git-dir=.git\",\"--work-tree=.\",\"--literal-pathspecs\",\"log\",\"refs/heads/git-annex..a0409bc558f0ed6679bf591e80f9782f1cd81da3\",\"--pretty=%H\",\"-n1\"] +[2019-05-17 22:42:12.995305] process done ExitSuccess +[2019-05-17 22:42:12.996023] chat: git [\"--git-dir=.git\",\"--work-tree=.\",\"--literal-pathspecs\",\"hash-object\",\"-w\",\"--stdin-paths\",\"--no-filters\"] +[2019-05-17 22:42:13.014492] chat: git [\"--git-dir=.git\",\"--work-tree=.\",\"--literal-pathspecs\",\"cat-file\",\"--batch\"] +[2019-05-17 22:42:13.029075] chat: git [\"--git-dir=.git\",\"--work-tree=.\",\"--literal-pathspecs\",\"cat-file\",\"--batch-check=%(objectname) %(objecttype) %(objectsize)\"] +[2019-05-17 22:42:13.043862] feed: git [\"--git-dir=.git\",\"--work-tree=.\",\"--literal-pathspecs\",\"update-index\",\"-z\",\"--index-info\"] +[2019-05-17 22:42:13.050909] read: git [\"--git-dir=.git\",\"--work-tree=.\",\"--literal-pathspecs\",\"diff-index\",\"--raw\",\"-z\",\"-r\",\"--no-renames\",\"-l0\",\"--cached\",\"refs/heads/git-annex\",\"--\"] +[2019-05-17 22:42:14.066638] process done ExitSuccess +[2019-05-17 22:42:14.08207] process done ExitSuccess +[2019-05-17 22:42:14.090912] feed: git [\"--git-dir=.git\",\"--work-tree=.\",\"--literal-pathspecs\",\"update-index\",\"-z\",\"--index-info\"] +[2019-05-17 22:42:15.852868] process done ExitSuccess +(recording state in git...) +[2019-05-17 22:42:15.868392] read: git [\"--git-dir=.git\",\"--work-tree=.\",\"--literal-pathspecs\",\"write-tree\"] +[2019-05-17 22:42:17.763573] process done ExitSuccess +[2019-05-17 22:42:17.763746] chat: git [\"--git-dir=.git\",\"--work-tree=.\",\"--literal-pathspecs\",\"commit-tree\",\"20ab70e8f50d62cc8d9657eaaff71cce88dfaa21\",\"--no-gpg-sign\",\"-p\",\"refs/heads/git-annex\"] +[2019-05-17 22:42:17.800472] process done ExitSuccess +[2019-05-17 22:42:17.800747] call: git [\"--git-dir=.git\",\"--work-tree=.\",\"--literal-pathspecs\",\"update-ref\",\"refs/heads/git-annex\",\"e0259808f7fbed2ce7cf0d8080dabb8d208c0da1\"] +[2019-05-17 22:42:17.867585] process done ExitSuccess + +git-annex: openFile: resource busy (file is locked) +failed +[2019-05-17 22:42:17.870299] process done ExitSuccess +[2019-05-17 22:42:17.875024] process done ExitSuccess +[2019-05-17 22:42:17.886388] process done ExitSuccess +``` + +I tried `sudo dtruss -f git annex info --fast --debug`, and this is an excerpt from the terminal: + +``` +82503/0x1b0045: write(0x2, \"[2019-05-17 22:29:55.91659] process done ExitSuccess\n\0\", 0x35) = 53 0 +82503/0x1b0045: mkdir(\".git/annex\0\", 0x1FF, 0x0) = -1 Err#17 +82503/0x1b0045: stat64(\".git/annex\0\", 0x4200038E40, 0x0) = 0 0 +82503/0x1b0045: getpid(0x0, 0x0, 0x0) = 82503 0 +82503/0x1b0045: open(\".git/annex/index.lck82503-2.tmp\0\", 0x20A06, 0x180) = 13 0 +82503/0x1b0045: fstat64(0xD, 0x420004D050, 0x0) = 0 0 +82503/0x1b0045: stat64(\".git/annex\0\", 0x420004D1D0, 0x0) = 0 0 +82503/0x1b0045: mkdir(\".git/annex\0\", 0x1FF, 0x0) = -1 Err#17 +82503/0x1b0045: stat64(\".git/annex\0\", 0x420004D3A0, 0x0) = 0 0 +82503/0x1b0045: open(\".git/annex/index.lck82503-3.tmp\0\", 0x20A06, 0x180) = 21 0 +82503/0x1b0045: fstat64(0x15, 0x420004D580, 0x0) = 0 0 +82503/0x1b0045: close(0xC) = 0 0 +82503/0x1b0045: poll(0x7FFEEC5CC810, 0x1, 0x0) = 1 0 +82503/0x1b0045: write(0x1, \"\n\0\", 0x1) = 1 0 +82503/0x1b0045: poll(0x7FFEEC5CC810, 0x1, 0x0) = 1 0 +82503/0x1b0045: write(0x2, \"git-annex: openFile: resource busy (file is locked)\n\0\", 0x34) = 52 0 +``` + +Removing `.git/annex/*.lck*` hadn't helped. + +I use git-annex version 7.20190322 from Homebrew: + +``` +build flags: Assistant Webapp Pairing S3(multipartupload)(storageclasses) WebDAV FsEvents TorrentParser MagicMime Feeds Testsuite +dependency versions: aws-0.19 bloomfilter-2.0.1.0 cryptonite-0.25 DAV-1.3.3 feed-1.0.1.0 ghc-8.2.2 http-client-0.5.14 persistent-sqlite-2.6.4 torrent-10000.1.1 uuid-1.3.13 yesod-1.4.5 +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 BLAKE2B256E BLAKE2B256 BLAKE2B512E BLAKE2B512 BLAKE2B160E BLAKE2B160 BLAKE2B224E BLAKE2B224 BLAKE2B384E BLAKE2B384 BLAKE2S256E BLAKE2S256 BLAKE2S160E BLAKE2S160 BLAKE2S224E BLAKE2S224 BLAKE2SP256E BLAKE2SP256 BLAKE2SP224E BLAKE2SP224 SHA1E SHA1 MD5E MD5 WORM URL +remote types: git gcrypt p2p S3 bup directory rsync web bittorrent webdav adb tahoe glacier ddar hook external +operating system: darwin x86_64 +supported repository versions: 5 7 +upgrade supported from repository versions: 0 1 2 3 4 5 6 +local repository version: 7 +``` +"""]] From 02a3160ca547248db51a7ddbdf6d6f995c51c2ce Mon Sep 17 00:00:00 2001 From: "branchable@bafd175a4b99afd6ed72501042e364ebd3e0c45e" Date: Sat, 18 May 2019 19:46:09 +0000 Subject: [PATCH 7/9] Added a comment: .profile doesn't take effect --- .../comment_4_d8cec7fae740e82c5da1da47037e2da6._comment | 9 +++++++++ 1 file changed, 9 insertions(+) create mode 100644 doc/bugs/Android_install_doesn__39__t_permanently_add_to___36__PATH/comment_4_d8cec7fae740e82c5da1da47037e2da6._comment diff --git a/doc/bugs/Android_install_doesn__39__t_permanently_add_to___36__PATH/comment_4_d8cec7fae740e82c5da1da47037e2da6._comment b/doc/bugs/Android_install_doesn__39__t_permanently_add_to___36__PATH/comment_4_d8cec7fae740e82c5da1da47037e2da6._comment new file mode 100644 index 0000000000..2c9ce281a0 --- /dev/null +++ b/doc/bugs/Android_install_doesn__39__t_permanently_add_to___36__PATH/comment_4_d8cec7fae740e82c5da1da47037e2da6._comment @@ -0,0 +1,9 @@ +[[!comment format=mdwn + username="branchable@bafd175a4b99afd6ed72501042e364ebd3e0c45e" + nickname="branchable" + avatar="http://cdn.libravatar.org/avatar/ae41dba34ee6000056f00793c695be75" + subject=".profile doesn't take effect" + date="2019-05-18T19:46:09Z" + content=""" +Ah, interesting. Very odd that the install script doesn't do that directly. I do have the same contents in my `~/.profile`, but Termux happily ignores it, so `$PATH` is unaltered. Does it really work for you? What version of Termux do you have? +"""]] From b7a8264c2f4f23527cf8d425bc68ce97d3a0142b Mon Sep 17 00:00:00 2001 From: "anthony@2b89f08c5c67f83d920fe464d7363db8f45cec20" Date: Sun, 19 May 2019 08:39:09 +0000 Subject: [PATCH 8/9] Added a comment --- .../comment_5_3eafb2258ac0c8c4e18a3f4591728b32._comment | 9 +++++++++ 1 file changed, 9 insertions(+) create mode 100644 doc/bugs/Android_install_doesn__39__t_permanently_add_to___36__PATH/comment_5_3eafb2258ac0c8c4e18a3f4591728b32._comment diff --git a/doc/bugs/Android_install_doesn__39__t_permanently_add_to___36__PATH/comment_5_3eafb2258ac0c8c4e18a3f4591728b32._comment b/doc/bugs/Android_install_doesn__39__t_permanently_add_to___36__PATH/comment_5_3eafb2258ac0c8c4e18a3f4591728b32._comment new file mode 100644 index 0000000000..f0a0dd8721 --- /dev/null +++ b/doc/bugs/Android_install_doesn__39__t_permanently_add_to___36__PATH/comment_5_3eafb2258ac0c8c4e18a3f4591728b32._comment @@ -0,0 +1,9 @@ +[[!comment format=mdwn + username="anthony@2b89f08c5c67f83d920fe464d7363db8f45cec20" + nickname="anthony" + avatar="http://cdn.libravatar.org/avatar/5d9fb1b0dd5ae1428c4c5b7df8d26bf2" + subject="comment 5" + date="2019-05-19T08:39:09Z" + content=""" +I have the latest from the Play store on one device and the latest from F-Droid on the other. Is it possible you have a bash_profile or bash_login? If so, then I believe bash won't read profile. +"""]] From 06bc46eaa2f03401e031eb49c3e93f261b9651bd Mon Sep 17 00:00:00 2001 From: "branchable@bafd175a4b99afd6ed72501042e364ebd3e0c45e" Date: Sun, 19 May 2019 10:05:27 +0000 Subject: [PATCH 9/9] Added a comment: it's zsh --- .../comment_6_dd74b3b5a15b6b9f21f3835da134cd5a._comment | 9 +++++++++ 1 file changed, 9 insertions(+) create mode 100644 doc/bugs/Android_install_doesn__39__t_permanently_add_to___36__PATH/comment_6_dd74b3b5a15b6b9f21f3835da134cd5a._comment diff --git a/doc/bugs/Android_install_doesn__39__t_permanently_add_to___36__PATH/comment_6_dd74b3b5a15b6b9f21f3835da134cd5a._comment b/doc/bugs/Android_install_doesn__39__t_permanently_add_to___36__PATH/comment_6_dd74b3b5a15b6b9f21f3835da134cd5a._comment new file mode 100644 index 0000000000..a98c4ff2ee --- /dev/null +++ b/doc/bugs/Android_install_doesn__39__t_permanently_add_to___36__PATH/comment_6_dd74b3b5a15b6b9f21f3835da134cd5a._comment @@ -0,0 +1,9 @@ +[[!comment format=mdwn + username="branchable@bafd175a4b99afd6ed72501042e364ebd3e0c45e" + nickname="branchable" + avatar="http://cdn.libravatar.org/avatar/ae41dba34ee6000056f00793c695be75" + subject="it's zsh" + date="2019-05-19T10:05:27Z" + content=""" +I figured it out - I changed my default shell to `zsh`, which doesn't read `.profile`. IMHO the installation should also set up `.zprofile` in the same way. +"""]]