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

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Joey Hess 2015-08-27 14:21:40 -07:00
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### Please describe the problem.
subj -- happens for sync and merge commands at least
[[!format sh """
$> git annex sync --help
git-annex: Not in a git repository.
$> git annex merge --help
git-annex: Not in a git repository.
$> git annex version
git-annex version: 5.20150819+gitgc587698-1~ndall+1
build flags: Assistant Webapp Webapp-secure Pairing Testsuite S3 WebDAV Inotify DBus DesktopNotify XMPP DNS Feeds Quvi TDFA Database
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
"""]]
### 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)
YES -- lots of luck ;)

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### Please describe the problem.
All the new wonderful SHA3_* backends are gone from the Linux AMD64 build of 5.20150825-g7826f84. They exist in the i386 version (5.20150824-g8529cb2), though. It's probably compiled without Cryptonite support or something.
### What steps will reproduce the problem?
Everything involving any of the SHA3_* backends result in an "unknown backend SHA3_*" error with the amd64 build (5.20150825-g7826f84). The i386 version (5.20150824-g8529cb2) works.
wget https://github.com/sunny256/utils/raw/master/tests/ga-fsck-size-files/annex-backends.tar.gz
tar xzf annex-backends.tar.gz
cd annex-backends
git annex fsck
results in
[snip]
fsck SHA384.txt (checksum...)
ok
fsck SHA384E.txt (checksum...)
ok
skipping SHA3_224.txt (unknown backend SHA3_224)
skipping SHA3_224E.txt (unknown backend SHA3_224E)
skipping SHA3_256.txt (unknown backend SHA3_256)
skipping SHA3_256E.txt (unknown backend SHA3_256E)
skipping SHA3_384.txt (unknown backend SHA3_384)
skipping SHA3_384E.txt (unknown backend SHA3_384E)
skipping SHA3_512.txt (unknown backend SHA3_512)
skipping SHA3_512E.txt (unknown backend SHA3_512E)
fsck SHA512.txt (checksum...)
ok
fsck SHA512E.txt (checksum...)
ok
[snip]
fsck WORM.txt ok
(recording state in git...)
### What version of git-annex are you using? On what operating system?
Newest official builds from downloads.kitenet.net . Debian GNU/Linux all the way.
### 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)
Oh, yes. It rules. :) One of the most important programs I use because I have all my valuable stuff in it. My files have never been safer.

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### Please describe the problem.
On windows, fails getting files with the following error : "rsync: Failed to exec ssh: No such file or directory". The server runs gitolite. I've tested from a Linux client, and it works.
$ git annex get big\ file
get big file (from origin...) rsync: Failed to exec ssh: No such file or directory (2)
rsync error: error in IPC code (code 14) at /home/lapo/package/rsync-3.0.9-1/src/rsync-3.0.9/pipe.c(84) [Receiver=3.0.9]
rsync: connection unexpectedly closed (0 bytes received so far) [Receiver]
rsync error: error in IPC code (code 14) at /home/lapo/package/rsync-3.0.9-1/src/rsync-3.0.9/io.c(605) [Receiver=3.0.9]
rsync failed -- run git annex again to resume file transfer
Unable to access these remotes: origin
Try making some of these repositories available:
dc8840b6-c0ec-4166-adcc-f821f3ee0216 -- olivier@myhost:~/git/whatever/testing
f8ef7445-2ccc-4871-a95a-7e4325fc763d -- gitolite3@aserver:~/repositories/testing.git [origin]
failed
git-annex: get: 1 failed
### What steps will reproduce the problem?
'git clone' from a repo containing a big file, then git annex init locally, then git get for the file contained in the repo
### What version of git-annex are you using? On what operating system?
* Git for windows, from http://git-scm.com/downloads (referenced from https://git-annex.branchable.com/install/Windows/), i.e. Git 2.5.0
* Git annex gotten from https://downloads.kitenet.net/git-annex/windows/current/ as of 2015-08-19 08:43 (GitAnnexDistribution {distributionUrl = "https://downloads.kitenet.net/git-annex/windows/current/git-annex-installer.exe", distributionKey = Key {keyName = "76e06059fe0146d228578a1eef42d92f94f4d89b5b00798f317083f90a73e006.exe", keyBackendName = "SHA256E", keySize = Just 24420678, keyMtime = Nothing, keyChunkSize = Nothing, keyChunkNum = Nothing}, distributionVersion = "5.20150819", distributionReleasedate = 2015-08-24 21:24:56.240184 UTC, distributionUrgentUpgrade = Nothing})
### 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)
Yes :-) Only on linux so far and trying on windows now :-/

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[[!comment format=mdwn
username="OlivierBerger"
subject="Using --debug gives this"
date="2015-08-27T14:26:54Z"
content="""
Here's a transcript of the --debug output (edited to mask file name and servername)
[[!format sh \"\"\"
# If you can, paste a complete transcript of the problem occurring here.
# If the problem is with the git-annex assistant, paste in .git/annex/daemon.log
$ git annex get big\ file --debug
[2015-08-27 16:21:36.8295694] read: git [\"--git-dir=.git\",\"--work-tree=.\",\"--literal-pathspecs\",\"-c\",\"core.bare=false\",\"ls-files\",\"--cached\",\"-z\",\"--\",\"big file\"]
get big file [2015-08-27 16:21:36.8495982] read: git [\"--git-dir=.git\",\"--work-tree=.\",\"--literal-pathspecs\",\"-c\",\"core.bare=false\",\"show-ref\",\"git-annex\"]
[2015-08-27 16:21:36.8796414] process done ExitSuccess
[2015-08-27 16:21:36.8796414] read: git [\"--git-dir=.git\",\"--work-tree=.\",\"--literal-pathspecs\",\"-c\",\"core.bare=false\",\"show-ref\",\"--hash\",\"refs/heads/git-annex\"]
[2015-08-27 16:21:36.8996702] process done ExitSuccess
[2015-08-27 16:21:36.8996702] read: git [\"--git-dir=.git\",\"--work-tree=.\",\"--literal-pathspecs\",\"-c\",\"core.bare=false\",\"log\",\"refs/heads/git-annex..f98a471b32f963a0bf816800d766690d53ef150d\",\"-n1\",\"--pretty=%H\"]
[2015-08-27 16:21:36.919699] process done ExitSuccess
[2015-08-27 16:21:36.9297134] read: git [\"--git-dir=.git\",\"--work-tree=.\",\"--literal-pathspecs\",\"-c\",\"core.bare=false\",\"log\",\"refs/heads/git-annex..15e7ab1f3b70629db852f8565bf988b25af02ec6\",\"-n1\",\"--pretty=%H\"]
[2015-08-27 16:21:36.9497422] process done ExitSuccess
[2015-08-27 16:21:36.9497422] read: git [\"--git-dir=.git\",\"--work-tree=.\",\"--literal-pathspecs\",\"-c\",\"core.bare=false\",\"log\",\"refs/heads/git-annex..1e04e80b99361e5b516d3a266bbc7b1d1478dff5\",\"-n1\",\"--pretty=%H\"]
[2015-08-27 16:21:36.9897998] process done ExitSuccess
[2015-08-27 16:21:36.9897998] chat: git [\"--git-dir=.git\",\"--work-tree=.\",\"--literal-pathspecs\",\"-c\",\"core.bare=false\",\"cat-file\",\"--batch\"]
(from origin...) [2015-08-27 16:21:37.0098286] read: rsync [\"--progress\",\"--inplace\",\"-e\",\"'ssh' '-T' 'gitolite3@server' 'git-annex-shell ''sendkey'' ''/~/testing'' ''--debug'' ''SHA256E-s264620717--23e70aae588a049d52909cd68067cf2885429ae557f52e3f2d6033260c3ad9ea.mp4'' --uuid f8ef7445-2ccc-4871-a95a-7e4325fc763d ''--'' ''remoteuuid=8fb9f88a-1105-4278-aa85-7b5c78a0e0e5'' ''direct=1'' ''associatedfile=big file'' ''--'''\",\"--\",\"dummy:\",\".git/annex/tmp/SHA256E-s264620717--23e70aae588a049d52909cd68067cf2885429ae557f52e3f2d6033260c3ad9ea.mp4\"]
rsync: Failed to exec ssh: No such file or directory (2)
rsync error: error in IPC code (code 14) at /home/lapo/package/rsync-3.0.9-1/src/rsync-3.0.9/pipe.c(84) [Receiver=3.0.9]
rsync: writefd_unbuffered failed to write 4 bytes to socket [Receiver]: Broken pipe (32)
rsync error: error in IPC code (code 14) at /home/lapo/package/rsync-3.0.9-1/src/rsync-3.0.9/io.c(1532) [Receiver=3.0.9]
[2015-08-27 16:21:37.0799294] process done ExitFailure 14
# End of transcript or log.
\"\"\"]]
"""]]

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[[!comment format=mdwn
username="OlivierBerger"
subject="git 2.5 for windows seems the culprit whereas mysygit 1.9 works"
date="2015-08-27T15:02:14Z"
content="""
I've removed Git for windows 2.5, and installed the latest msysgit 1.9, and it seems that this works much better.
However, I have to invoke git-annex from the command-line through its full path with :
\"C:\Program Files\Git\cmd\git-annex.exe\" get .
I guess this gives hope :-)
"""]]

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[[!comment format=mdwn
username="edward"
subject="I've ended up with lots of staged deletes"
date="2015-08-27T08:29:55Z"
content="""
I have the same problem with another annex. I ran the webapp using `git annex webapp` in the annex on my laptop hard drive. It seemed to update and sync with the annex on my external USB drive, but now when I run `git status` in the annex directory on the drive it has staged lots of deletes. I don't understand what is going on here. Both annexes are in indirect mode.
On branch master
Your branch is behind 'origin/master' by 61 commits, and can be fast-forwarded.
(use \"git pull\" to update your local branch)
Changes to be committed:
(use \"git reset HEAD <file>...\" to unstage)
deleted: 4angle_tech_ltd/032-570247_20150312-074413_30313.pdf
deleted: 4angle_tech_ltd/032-570247_20150312_09486613.pdf
deleted: android/RUU_PRIMO_U_ICS_40A_HTC_Europe_2.22.401.1_Radio_20.76.30.0835U_3831.19.00.120_release_273801_signed.exe
deleted: article/Fukuyama-End-of-history-article.pdf
deleted: article/The Selling of the Avocado - Health - The Atlantic.html
The symlinks and the data are still on the disk, as is the data that the symlinks point to.
$ ls 4angle_tech_ltd -l
total 8
lrwxrwxrwx 1 edward edward 197 Mar 15 08:39 032-570247_20150312-074413_30313.pdf -> ../.git/annex/objects/qM/mj/SHA256E-s21598--efb39974c5253d8059f0fe991c1b76aba8455d8439eefd6cd8943503f85109c0.pdf/SHA256E-s21598--efb39974c5253d8059f0fe991c1b76aba8455d8439eefd6cd8943503f85109c0.pdf
lrwxrwxrwx 1 edward edward 197 Mar 15 08:39 032-570247_20150312_09486613.pdf -> ../.git/annex/objects/JX/XP/SHA256E-s93692--8e88ca5071bc2155acfe16a41c9c6b756fecc6515cfb7907105dd1a83e73f57a.pdf/SHA256E-s93692--8e88ca5071bc2155acfe16a41c9c6b756fecc6515cfb7907105dd1a83e73f57a.pdf
$
"""]]

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### Please describe the problem.
Currently if download stalls the whole 'annex get' stalls -- I have been watching the terminal with 0% for an hour now ;)
You could test that on http://github.com/datalad/mlbooks annex, just get
G.James_D.Witten_T.Hastie_R.Tibshirani-An_Introduction_to_Statistical_Learning_with_Applications_in_R.pdf
original url for the file is http://www-bcf.usc.edu/~gareth/ISL/ISLR%20Fourth%20Printing.pdf
and wgetting works for me on some boxes but not on the other, forgot why so
### What version of git-annex are you using? On what operating system?
5.20150706+gitgefc3bcd-1~ndall+1 and tried in clean debian sid docker with 5.20150812-2

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[[!comment format=mdwn
username="edward"
subject="Same problem"
date="2015-08-27T09:24:38Z"
content="""
I think I'm having the same problem. See my comments on [[bugs/git annex sync deleted a bunch of files (not expected)]]
I've run `git annex sync` or `git annex webapp` on the laptop annex, then `git annex sync` on the external drive. I'm pretty sure some of the syncs have been interrupted. Does it help to see the .git/config from the external drive?
[core]
repositoryformatversion = 0
filemode = true
bare = false
logallrefupdates = true
[remote \"origin\"]
url = /home/edward/annex
fetch = +refs/heads/*:refs/remotes/origin/*
annex-uuid = 38d109c9-7f5f-47cd-b15a-7b2beac22c64
[branch \"master\"]
remote = origin
merge = refs/heads/master
[annex]
uuid = 822dec0f-a0d3-42f6-b0dc-a47b6bf91944
version = 5
[remote \"x230\"]
url = /home/edward/annex
fetch = +refs/heads/*:refs/remotes/x230/*
annex-uuid = 38d109c9-7f5f-47cd-b15a-7b2beac22c64
Observations about my config, I have `bare = false`, which is correct. Do you think it is a problem that I have two remotes, `\"origin\"` and `\"x230\"` pointing at the same location?
"""]]