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Merge branch 'master' of ssh://git-annex.branchable.com

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Joey Hess 2018-11-23 15:19:54 -04:00
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### Please describe the problem.
get annex sync fails with rsync error saying that the remote is not accessible.
(root cause git annex did not work on my storage machine which causes the client to complain that it can not download objects but I couldn't figure out how to change the title.)
rerunning the rsync command gives
[[!format sh """
rsync -vvv "--progress" "--inplace" "--perms" "-e" "'ssh' 'jwiklund@born' '-S' '.git/annex/ssh/jwiklund@born' '-o' 'ControlMaster=auto' '-o' 'ControlPersist=yes' '-T' 'git-annex-shell ''sendkey'' ''/store/backup/Documents.annex.1'' ''--debug'' ''SHA256E-xxx.org'' --uuid xxx ''--'' ''remoteuuid=xxx'' ''unlocked='' ''direct='' ''associatedfile=tools.org'' ''--'''" "--" "dummy:" ".git/annex/tmp/SHA256E-xxx.org"
opening connection using: ssh x@y -S .git/annex/ssh/x@y -o ControlMaster=auto -o ControlPersist=yes -T "git-annex-shell 'sendkey' '/path' '--debug' 'SHA256E-xxx.org' --uuid 36c1cd35-bac3-485f-bfaa-e2bb29e25957 '--' 'remoteuuid=yyy' 'unlocked=' 'direct=' 'associatedfile=tools.org' '--'" dummy rsync --server --sender -vvvpe.Lsfx --inplace . . (18 args)
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]
[Receiver] _exit_cleanup(code=2, file=compat.c, line=176): about to call exit(2)
"""]]
which seems to tell me something is wrong with rsync (the man page references invalid .bashrc but that was not it).
trying to run the command git-annex-shell on that host gives
[[!format sh """
git-annex-shell
rm: loadlocale.c:129: _nl_intern_locale_data: Assertion `cnt < (sizeof (_nl_value_type_LC_TIME) / sizeof (_nl_value_type_LC_TIME[0]))' failed.
Aborted (core dumped)
rm: loadlocale.c:129: _nl_intern_locale_data: Assertion `cnt < (sizeof (_nl_value_type_LC_TIME) / sizeof (_nl_value_type_LC_TIME[0]))' failed.
Aborted (core dumped)
"""]]
Seems to indicate something is wrong with the locale (on that machine), setting it to c fixes the problem.
[[!format sh """
echo $LANG
en_US.UTF-8
set LANG=c
git-annex-shell
"""]]
Actually investigating this shows that git annex it self crashes with this locale for some reason
[[!format sh """
git-annex version
rm: loadlocale.c:129: _nl_intern_locale_data: Assertion `cnt < (sizeof (_nl_value_type_LC_TIME) / sizeof (_nl_value_type_LC_TIME[0]))' failed.
Aborted (core dumped)
rm: loadlocale.c:129: _nl_intern_locale_data: Assertion `cnt < (sizeof (_nl_value_type_LC_TIME) / sizeof (_nl_value_type_LC_TIME[0]))' failed.
Aborted (core dumped)
"""]]
I made it work by adding `status --is-interactive; or set -x LANG c` to my `.config/fish/config.fish` but maybe someone else runs into this.
### What steps will reproduce the problem?
git-annex sync with against a remote host with a broken LANG git-annex combination.
actually `git-annex` breaks on that host.
### What version of git-annex are you using? On what operating system?
Breaking on OS is Ubuntu 14.04.5 LTS
It works on Ubuntu 16.04.5 LTS
[[!format sh """
git-annex version: 7.20181106-g6ba6c6b53
build flags: Assistant Webapp Pairing S3(multipartupload)(storageclasses) WebDAV Inotify DBus DesktopNotify TorrentParser MagicMime Feeds Testsuite
dependency versions: aws-0.19 bloomfilter-2.0.1.0 cryptonite-0.25 DAV-1.3.2 feed-1.0.0.0 ghc-8.2.2 http-client-0.5.13 persistent-sqlite-2.8.1.2 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 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: linux x86_64
supported repository versions: 5 7
upgrade supported from repository versions: 0 1 2 3 4 5 6
"""]]
### Please provide any additional information below.
(I installed the latest release while writing this report, and it worked the first time, then it started crashing again):
[[!format sh """
$ echo $LANG
en_US.UTF-8
$ git-annex version
git-annex version: 7.20181106-g6ba6c6b53
build flags: Assistant Webapp Pairing S3(multipartupload)(storageclasses) WebDAV Inotify DBus DesktopNotify TorrentParser MagicMime Feeds Testsuite
dependency versions: aws-0.19 bloomfilter-2.0.1.0 cryptonite-0.25 DAV-1.3.2 feed-1.0.0.0 ghc-8.2.2 http-client-0.5.13 persistent-sqlite-2.8.1.2 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 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: linux x86_64
supported repository versions: 5 7
upgrade supported from repository versions: 0 1 2 3 4 5 6
$ git-annex version
rm: loadlocale.c:129: _nl_intern_locale_data: Assertion `cnt < (sizeof (_nl_value_type_LC_TIME) / sizeof (_nl_value_type_LC_TIME[0]))' failed.
Aborted (core dumped)
rm: loadlocale.c:129: _nl_intern_locale_data: Assertion `cnt < (sizeof (_nl_value_type_LC_TIME) / sizeof (_nl_value_type_LC_TIME[0]))' failed.
Aborted (core dumped)
rm: loadlocale.c:129: _nl_intern_locale_data: Assertion `cnt < (sizeof (_nl_value_type_LC_TIME) / sizeof (_nl_value_type_LC_TIME[0]))' failed.
Aborted (core dumped)
$ set -x LANG c
$ git-annex version
git-annex version: 7.20181106-g6ba6c6b53
build flags: Assistant Webapp Pairing S3(multipartupload)(storageclasses) WebDAV Inotify DBus DesktopNotify TorrentParser MagicMime Feeds Testsuite
dependency versions: aws-0.19 bloomfilter-2.0.1.0 cryptonite-0.25 DAV-1.3.2 feed-1.0.0.0 ghc-8.2.2 http-client-0.5.13 persistent-sqlite-2.8.1.2 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 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: linux x86_64
supported repository versions: 5 7
upgrade supported from repository versions: 0 1 2 3 4 5 6
"""]]
### 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 worked well for more than a year now :) happy user.

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### Please describe the problem.
I'm using a special directory remote for one of my annex repository. This directory is slow (because it's a FUSE-mounted directory), so I decided to symlink /SPECIALREMOTEDIRECTORY/tmp/ to another drive (as tmp/ is just used during the copy operations). However it doesn't work as expected as git-annex seems unable to copy anything from /SPECIALREMOTEDIRECTORY/tmp/ to /SPECIALREMOTEDIRECTORY/.
git annex copy --to special_dir myfile
copy mlyfile (to special_dir...)
100% 288 MiB 26 MiB/s 0s
/SPECIALREMOTEDIRECTORY/annex/k/tmp/GPGHMACSHA1--800acc67c0803274ed67cea51a1f0df75c225621/: renamePath:rename: unsupported operation (Cross-device link)
git-annex: copy: 1 failed
ls -l /SPECIALREMOTEDIRECTORY/annex/k/
drwx------ 1 TroisSinges wheel 167 22 nov 17:49 fe5
drwx------ 1 TroisSinges wheel 167 22 nov 17:53 ff5
lrwx------ 1 TroisSinges wheel 18 23 nov 08:04 tmp -> /Users/TroisSinges/tmp
### What version of git-annex are you using? On what operating system?
git-annex version: 7.20181105 (via Homebrew)
MacOS High Sierra 10.13.6
### 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)
Of course! git-annex is totally amazing in order to manage big collections of files. I'm using it for my videos, and for my photos as well (thousands of files), on Linux and MacOS. Thank you very much for this awesome tool!

8
doc/bugs/special_directory_remotes__58___git_annex_copy_fails_if_tmp__47___is_a_symbolic_link_to_another_device/comment_1_a96a560b46a24148b5e21695c899c728._comment Normal file
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[[!comment format=mdwn
username="TroisSinges"
avatar="http://cdn.libravatar.org/avatar/43f6eb327d2da6cb5bc6d55740e1ed78"
subject="comment 1"
date="2018-11-23T07:33:55Z"
content="""
Found [this bug](https://github.com/commercialhaskell/hindent/issues/170) in another tool, I think it's the same root cause.
"""]]

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I am using git-annex to set up a file distribution system with git commands as the interface. I have configured a unix user account with .ssh key so that calls to the git remote are authenticated automatically. I have set the ownership and permissions for that user account. I can ssh into the remote with that account no problem. But when I run `git annex get` to retrieve the source data from the annex, I get a typical permissions error. I have tried `chown'ing` and `chmod'ing` many combinations, but always get the same error.
Looking for help to diagnose and fix this issue. Let me know if there are other commands I can run to hone in.
> git ls-remote
Warning: No xauth data; using fake authentication data for X11 forwarding.
From username@distro.myserver.edu:/path/to/remote/repo/.git
f4d9c5e4735f4c6b057d0c43090c80c09b7ab9ae HEAD
49b3b4c81c3ce78443bb00c594cce51a4fa2c034 refs/heads/git-annex
f4d9c5e4735f4c6b057d0c43090c80c09b7ab9ae refs/heads/master
> git remote -v
origin username@distro.myserver.edu:/path/to/remote/repo/.git (fetch)
origin username@distro.myserver.edu:/path/to/remote/repo/.git (push)
> git annex get sub-STJ82860572941V0120181112132504070/dwi/sub-STJ82860572941V0120181112132504070_dwi__dup-10.nii.gz
get sub-STJ82860572941V0120181112132504070/dwi/sub-STJ82860572941V0120181112132504070_dwi__dup-10.nii.gz (not available)
Try making some of these repositories available:
fcfe03d6-3638-4ae2-baca-67c4c28e74bb -- username@myserver:/path/to/remote/annex
failed
git-annex: get: 1 failed
Cross post: https://stackoverflow.com/questions/53418582/permissions-error-with-ssh-key-authentication-to-remote-git-annex-get-file