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Bug 543 - mpicbg submodule not available
mpicbg submodule not available
Status: RESOLVED FIXED
Product: Fiji
Classification: Unclassified
Component: Other
unspecified
PC Linux
: P3 normal
Assigned To: ImageJ Bugs Mailing List
Depends on:
Blocks:
 
Reported: 2013-01-04 15:15 CST by Stephan Saalfeld
Modified: 2013-01-14 10:44 CST
1 user (show)

See Also:
Description Stephan Saalfeld 2013-01-04 15:15:37 CST 
Hi,

I just tried to confirm that Fiji's mpicbg submodule is not built correctly as reported by Preibisch and that TrakEM2 is bot built correctly as noticed by myself recently.  To file a noise free bug-report, I cloned a fresh Fiji repository and executed

git submodule init modules/TrakEM2
git submodule update modules/TrakEM2

which instantiates a pre-maven commit ((a83aa97...)) of TrakEM2 in modules/TrakEM2 ... fine.

git submodule init modules/mpicbg
git submodule update modules/mpicbg

says

fatal: Not a git repository: ../.git/modules/modules/mpicbg
Unable to fetch in submodule path 'modules/mpicbg'

despite that it should fetch the mpicbg submodule at something close to master.  This is not the bug that I wanted to report (Fiji doesn't build mpicbg and TrakEM2) but most likely something on the lane.

I would be absolutely grateful for any expert advice what all that means and how to untangle it.

Best,
Stephan
Comment 1 Johannes Schindelin 2013-01-04 16:14:02 CST 
Works for me...

$ git clone git://github.com/fiji/fiji
Cloning into 'fiji'...
remote: Counting objects: 80340, done.
remote: Compressing objects: 100% (22491/22491), done.
remote: Total 80340 (delta 50880), reused 79272 (delta 49949)
Receiving objects: 100% (80340/80340), 212.85 MiB | 1.80 MiB/s, done.
Resolving deltas: 100% (50880/50880), done.
$ cd fiji
$ git submodule update --init modules/TrakEM2
Submodule 'TrakEM2' (ssh://mob@repo.or.cz/srv/git/trakem2.git) registered for path 'modules/TrakEM2'
Cloning into 'modules/TrakEM2'...
The authenticity of host 'repo.or.cz (195.113.20.142)' can't be established.
RSA key fingerprint is 07:7a:5c:6c:39:b3:ac:a9:e5:70:5d:41:ba:a6:37:04.
Are you sure you want to continue connecting (yes/no)? yes
Warning: Permanently added 'repo.or.cz,195.113.20.142' (RSA) to the list of known hosts.
remote: Counting objects: 31221, done.
remote: Compressing objects: 100% (5479/5479), done.
remote: Total 31221 (delta 21394), reused 31221 (delta 21394)
Receiving objects: 100% (31221/31221), 11.71 MiB | 2.36 MiB/s, done.
Resolving deltas: 100% (21394/21394), done.
Submodule path 'modules/TrakEM2': checked out 'a83aa977e4768f570dd0c6e0d5d588e91
96fd66e'
$ git submodule update --init modules/mpicbg
Submodule 'mpicbg' (ssh://contrib@fiji.sc/srv/git/mpicbg.git) registered for path 'modules/mpicbg'
Cloning into 'modules/mpicbg'...
remote: Counting objects: 4946, done.
remote: Compressing objects: 100% (1799/1799), done.
remote: Total 4946 (delta 3168), reused 4637 (delta 3055)
Receiving objects: 100% (4946/4946), 1.10 MiB | 751 KiB/s, done.
Resolving deltas: 100% (3168/3168), done.
Submodule path 'modules/mpicbg': checked out 'e982ec5bd30c8dbe3a478e021ad577521490ae3e'

FWIW a83aa977 changes VectorString/pom.xml, so it is a post-Mavenization commit.

The error message suggest that the Fiji repository was checked out with submodules earlier, using an older Git version, then the mpicbg directory was (re-)moved and the submodule re-initialized with a newer Git. For whatever reason, someone found it more sensible to have the .git/ directory of submodules in the .git/ directory of the superproject in a recent Git, and whether a submodule is checked out or not is determined by looking at the .git/config of the superproject (so it still thinks that mpicbg is checked out, that's my guess).
Comment 2 Stephan Saalfeld 2013-01-14 10:32:18 CST 
Thanks for the comment and fixing the other build issue.  Something in the git rep was dirty due to intermediate network outages.