Merge branch 'master' of ssh://git-annex.branchable.com
This commit is contained in:
Joey Hess
commit
aaa59cce8c
4 changed files with 2132 additions and 0 deletions
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[[!comment format=mdwn
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username="ilovezfs"
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avatar="http://cdn.libravatar.org/avatar/f2b3954cf2ed0a551de9a49d3b6a64d0"
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subject="pipe: resource exhausted (Too many open files)"
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date="2017-07-30T16:05:10Z"
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content="""
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Hi Joey,
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Yes, I can work around that particular failure by tweaking constraints.
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In particular,
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--allow-newer=\"sandi:base\" --allow-newer=\"aws:time\"
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I also first need to \"cabal install Cabal<1.25\" because git-annex seems
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to have a compatibility problem with Cabal-2.0.0.2. The error with
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Cabal-2.0.0.2 is
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[[!format sh \"\"\"
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Building executable 'git-annex' for git-annex-6.20170520..
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Build/BuildVersion.hs:1:1: error:
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File name does not match module name:
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Saw: ‘Main’
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Expected: ‘Build.BuildVersion’
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1 | {- Outputs the version of git-annex that was built, for use by
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| ^
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cabal: Leaving directory '.'
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cabal: Error: some packages failed to install:
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git-annex-6.20170520-3mbb3kAWTlXI0EMervIo66 failed during the building phase.
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The exception was:
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ExitFailure 1
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\"\"\"]]
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But, once I've installed the lower version of Cabal, and tweaked the
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constraints for sandi and for aws, git-annex does build successfully.
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However, at that point a more serious issue comes up when I run \"git
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annex test\" and here is the full log:
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https://gist.github.com/ilovezfs/d430f589d87d7f7237591cd51b2b94cb
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Here is a snippet:
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[[!format sh \"\"\"
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From ../../.t/tmprepo53
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* [new branch] git-annex -> r2/git-annex
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* [new branch] master -> r2/master
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* [new branch] synced/master -> r2/synced/master
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conflictor/subfile
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conflictor.variant-cc12
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conflictor/subfile
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conflictor.variant-cc12
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OK (3.27s)
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conflict resolution symlink bit: OK
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conflict resolution (uncommitted local file): FAIL (0.49s)
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sync failed in r1
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conflict resolution (removed file): FAIL
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Exception: git: createProcess: runInteractiveProcess: pipe: resource exhausted (Too many open files)
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conflict resolution (nonannexed file): FAIL
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Exception: git: createProcess: runInteractiveProcess: pipe: resource exhausted (Too many open files)
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conflict resolution (nonannexed symlink): FAIL (0.03s)
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git annex init failed
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conflict resolution (mixed locked and unlocked file): FAIL
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Exception: git: createProcess: runInteractiveProcess: pipe: resource exhausted (Too many open files)
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map: FAIL
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Exception: git: createProcess: runInteractiveProcess: pipe: resource exhausted (Too many open files)
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\"\"\"]]
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"""]]
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2004
doc/bugs/Tests_fail_on_Windows_10.mdwn
Normal file
2004
doc/bugs/Tests_fail_on_Windows_10.mdwn
Normal file
File diff suppressed because it is too large
Load diff
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### Please describe the problem.
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subject
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### What steps will reproduce the problem?
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repo from http://datasets.datalad.org/workshops/nih-2017/ds000114/derivatives/freesurfer/
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### What version of git-annex are you using? On what operating system?
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6.20170525+gitge1cf095ae-1~ndall+1
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### Please provide any additional information below.
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[[!format sh """
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[student3@helix freesurfer]$ 'git' '-c' 'receive.autogc=0' '-c' 'gc.auto=0' 'annex' 'get' '--debug' '--json' '--json-progress' 'sub-01/label/lh.aparc.a2009s.annot'
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[2017-07-30 09:33:42.479678681] read: git ["--git-dir=.git","--work-tree=.","--literal-pathspecs","ls-files","--cached","-z","--","sub-01/label/lh.aparc.a2009s.annot"]
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[2017-07-30 09:33:42.501443872] read: git ["--git-dir=.git","--work-tree=.","--literal-pathspecs","show-ref","git-annex"]
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[2017-07-30 09:33:42.523673251] process done ExitSuccess
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[2017-07-30 09:33:42.523765181] read: git ["--git-dir=.git","--work-tree=.","--literal-pathspecs","show-ref","--hash","refs/heads/git-annex"]
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[2017-07-30 09:33:42.544559473] process done ExitSuccess
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[2017-07-30 09:33:42.553475534] chat: git ["--git-dir=.git","--work-tree=.","--literal-pathspecs","cat-file","--batch"]
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[2017-07-30 09:33:42.554641292] chat: git ["--git-dir=.git","--work-tree=.","--literal-pathspecs","cat-file","--batch-check=%(objectname) %(objecttype) %(objectsize)"]
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[2017-07-30 09:33:42.591306199] call: curl ["-sS","-f","-L","-C","-","-#","-o","/scratch/nih-2017/ds000114/derivatives/freesurfer/.git/annex/tmp/MD5E-s831572--7437ad482af573329af54386a15007fe","https://dl.dropbox.com/s/85yms1fl56pq7io/lh.aparc.a2009s.annot?dl=0","--user-agent","git-annex/6.20170525+gitge1cf095ae-1~ndall+1"]
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curl: (77) error setting certificate verify locations:
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CAfile: /etc/ssl/certs/ca-certificates.crt
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CApath: /etc/ssl/certs
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[2017-07-30 09:33:42.693467186] process done ExitFailure 77
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{"command":"get","wanted":[{"here":false,"uuid":"00000000-0000-0000-0000-000000000001","description":"web"},{"here":false,"uuid":"5e47b3f3-f09c-4969-8885-920a49ff8a45","description":"yoh@smaug:/mnt/btrfs/datasets/datalad/crawl/workshops/nih-workshop-2017/ds000114/derivatives/freesurfer"}],"note":"Try making some of these repositories available:\n\t00000000-0000-0000-0000-000000000001 -- web\n \t5e47b3f3-f09c-4969-8885-920a49ff8a45 -- yoh@smaug:/mnt/btrfs/datasets/datalad/crawl/workshops/nih-workshop-2017/ds000114/derivatives/freesurfer\n","skipped":[],"success":false,"key":"MD5E-s831572--7437ad482af573329af54386a15007fe","file":"sub-01/label/lh.aparc.a2009s.annot"}
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git-annex: get: 1 failed
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[student3@helix freesurfer]$ 'git' '-c' 'receive.autogc=0' '-c' 'gc.auto=0' 'annex' 'get' '--json' '--json-progress' 'sub-01/label/lh.aparc.a2009s.annot'
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curl: (77) error setting certificate verify locations:
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CAfile: /etc/ssl/certs/ca-certificates.crt
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CApath: /etc/ssl/certs
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{"command":"get","wanted":[{"here":false,"uuid":"00000000-0000-0000-0000-000000000001","description":"web"},{"here":false,"uuid":"5e47b3f3-f09c-4969-8885-920a49ff8a45","description":"yoh@smaug:/mnt/btrfs/datasets/datalad/crawl/workshops/nih-workshop-2017/ds000114/derivatives/freesurfer"}],"note":"Try making some of these repositories available:\n\t00000000-0000-0000-0000-000000000001 -- web\n \t5e47b3f3-f09c-4969-8885-920a49ff8a45 -- yoh@smaug:/mnt/btrfs/datasets/datalad/crawl/workshops/nih-workshop-2017/ds000114/derivatives/freesurfer\n","skipped":[],"success":false,"key":"MD5E-s831572--7437ad482af573329af54386a15007fe","file":"sub-01/label/lh.aparc.a2009s.annot"}
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git-annex: get: 1 failed
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while works fine without:
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[student3@helix freesurfer]$ 'git' '-c' 'receive.autogc=0' '-c' 'gc.auto=0' 'annex' 'get' 'sub-01/label/lh.aparc.a2009s.annot'
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get sub-01/label/lh.aparc.a2009s.annot (from web...)
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/scratch/nih-2017/ds000114/ 100%[===========================================>] 812.08K --.-KB/s in 0.08s
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2017-07-30 09:34:02 URL:https://dl.dropboxusercontent.com/s/85yms1fl56pq7io/lh.aparc.a2009s.annot?dl=0 [831572/831572] -> "/scratch/nih-2017/ds000114/derivatives/freesurfer/.git/annex/tmp/MD5E-s831572--7437ad482af573329af54386a15007fe" [1]
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(checksum...)
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(recording state in git...)
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"""]]
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[[!meta author=yoh]]
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@ -0,0 +1,11 @@
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[[!comment format=mdwn
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username="yarikoptic"
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avatar="http://cdn.libravatar.org/avatar/f11e9c84cb18d26a1748c33b48c924b4"
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subject="issue seems to be out there"
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date="2017-07-31T15:03:41Z"
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content="""
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[https://github.com/datalad/datalad/issues/1678](https://github.com/datalad/datalad/issues/1678)
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git annex standalone is quite recent so those manpage workarounds should be in place
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"""]]
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