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Bug 2505 - remove symbolic links from svn repository
| Status | CLOSED FIXED |
| Reported | 2014-03-19 16:01:00 +0100 |
| Modified | 2016-06-14 16:14:45 +0200 |
| Product: | FieldTrip |
| Component: | core |
| Version: | unspecified |
| Hardware: | PC |
| Operating System: | Mac OS |
| Importance: | P3 normal |
| Assigned to: | Robert Oostenveld |
| URL: | |
| Tags: | |
| Depends on: | |
| Blocks: | |
| See also: |
Robert Oostenveld - 2014-03-19 16:01:59 +0100
On 19 Mar 2014, at 15:08, Johanna Zumer wrote: I have a Linux Ubuntu VMware guest running on a Windows 7 host. The host has 2 harddrives (250 GB SSD on C:\ and 2 TB SATA on D:\). Both the Windows OS as well as VMware run on the C drive. When I run within Linux VM on the /home/zumerj path the svn checkout, then it all works fine. However, I would like to put the code on the C or D drive (mounted on the VM) so that I can see it when I'm not running the VM. But if I run a separate svn checkout from within Linux VM on /mnt/hgfs/D which is the mounted D drive, I get this error: svn: In directory 'fieldtrip_svn/realtime/bin/glnxa64' svn: Can't create symbolic link 'fieldtrip_svn/realtime/bin/glnxa64/libtia.so.1.0.tmp': Operation not supported And then I have to 'svn cleanup' and then: svn: Failed to add file 'realtime/bin/glnxa64/libtia.so.1.0.0': an unversioned file of the same name already exists so I remove it and 'svn update' and it restores it, but then complains about other files all within that subdirectory. I've tried removing the whole fieldtrip folder and doing a fresh checkout but it's happened several times now, and never fully gets through. (Sorry, I forget now what the final error is that I couldn't get past).
Robert Oostenveld - 2014-05-07 15:18:37 +0200
hmm, these symbolic links indeed don't work on windows. I found these lrwxr-xr-x 1 roboos staff 15 Apr 17 2013 libtia.so -> libtia.so.1.0.0 lrwxr-xr-x 1 roboos staff 15 Apr 17 2013 libtia.so.1 -> libtia.so.1.0.0 lrwxr-xr-x 1 roboos staff 15 Apr 17 2013 libtia.so.1.0 -> libtia.so.1.0.0 -rwxr-xr-x 1 roboos staff 1473185 Apr 17 2013 libtia.so.1.0.0 but don't understand why the same file needs to be present 4 times. It would be only used by tia2ft. roboos@mentat001> ldd tia2ft ./tia2ft: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.14' not found (required by ./libtia.so.1) linux-vdso.so.1 => (0x00007fffbc3ff000) libpthread.so.0 => /lib64/libpthread.so.0 (0x00000033ace00000) libboost_thread.so.1.42.0 => not found libboost_system.so.1.42.0 => not found libboost_program_options.so.1.42.0 => not found libtia.so.1 => ./libtia.so.1 (0x00007f698e06d000) libstdc++.so.6 => /usr/lib64/libstdc++.so.6 (0x00000033b3200000) libm.so.6 => /lib64/libm.so.6 (0x00000033ad200000) libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00000033b2e00000) libc.so.6 => /lib64/libc.so.6 (0x00000033ac600000) /lib64/ld-linux-x86-64.so.2 (0x00000033ac200000) I have tried cleaning it up, please try again roboos@mentat001> svn commit Deleting glnxa64/libtia.so Replacing glnxa64/libtia.so.1 Deleting glnxa64/libtia.so.1.0 Deleting glnxa64/libtia.so.1.0.0 Committed revision 9471.
Robert Oostenveld - 2014-05-14 20:08:49 +0200
closed several of my bugs that have been resolved
Johanna - 2014-06-19 14:59:00 +0200
Sorry for the late reply, but I have tested this, and it now works. Thank you!
Johanna - 2016-01-20 18:45:30 +0100
Hi Robert, I've been having new problems with svn (and I think a symbolic link). I checked out a fresh copy of FT and the error is svn: In directory 'fieldtrip_svn/contrib/nutmegtrip/private' svn: Can't create symbolic link 'fieldtrip_svn/contrib/nutmegtrip/private/parameterselection.m.tmp': Operation not supported I then try 'svn update' and get this error: svn: Working copy 'contrib/nutmegtrip/private' locked svn: run 'svn cleanup' to remove locks (type 'svn help cleanup' for details) I then 'svn cleanup' and then 'svn update' again, and get this error: svn: Failed to add file 'contrib/nutmegtrip/private/nmt_ts_intervalpower.m': an unversioned file of the same name already exists [I cc Sarang so he is aware of the problem for symbolic links (though I know he's on holiday now until March, and so he probably won't respond!)] I'm not exactly sure what's going on here, or whether this is the same issue as this original bug, but as it seemed closely related, I reopened this one. Thank you, JOhanna
Robert Oostenveld - 2016-01-21 14:52:50 +0100
(In reply to Johanna from comment #4) You are right, there are a number of symbolic links here: mac011> pwd /Users/roboos/matlab/fieldtrip/contrib/nutmegtrip/private mac011> ls -al total 88 drwxr-xr-x 11 roboos staff 374 Nov 20 08:53 . drwxr-xr-x 14 roboos staff 476 Nov 20 08:53 .. lrwxr-xr-x 1 roboos staff 31 Nov 20 08:53 atlas_lookup.m -> ../../../private/atlas_lookup.m -rw-r--r-- 1 roboos staff 9815 Nov 18 08:50 freezeColors.m lrwxr-xr-x 1 roboos staff 28 Nov 20 08:53 getdimord.m -> ../../../private/getdimord.m lrwxr-xr-x 1 roboos staff 28 Nov 20 08:53 getdimsiz.m -> ../../../private/getdimsiz.m -rw-r--r-- 1 roboos staff 251 Nov 18 08:50 nmt_coord_diff.m -rw-r--r-- 1 roboos staff 129 Nov 18 08:50 nmt_rownorm.m -rw-r--r-- 1 roboos staff 309 Nov 18 08:50 nmt_ts_intervalpower.m lrwxr-xr-x 1 roboos staff 37 Nov 20 08:53 parameterselection.m -> ../../../private/parameterselection.m -rwxr-xr-x 1 roboos staff 3611 Nov 18 08:50 unfreezeColors.m Rather than symlinks, this should have been implemented according to http://www.fieldtriptoolbox.org/development/svn#how_to_maintain_two_copies_of_the_same_file --- I removed the symlinks in commit 11089. Then I did mac011> svn copy ../../../private/atlas_lookup.m . A atlas_lookup.m mac011> svn copy ../../../private/getdimord.m . A getdimord.m mac011> svn copy ../../../private/getdimsiz.m . A getdimsiz.m mac011> svn copy ../../../private/parameterselection.m . A parameterselection.m mac011> svn propget autosync *.m getdimord.m - true getdimsiz.m - true parameterselection.m - true here I notice that atlas_lookup.m does not yet have autosync=true. This sets it to both: mac011> svn propset autosync true atlas_lookup.m property 'autosync' set on 'atlas_lookup.m' mac011> svn propset autosync true ../../../private/atlas_lookup.m property 'autosync' set on '/Users/roboos/matlab/fieldtrip/private/atlas_lookup.m' And this finalizes it: mac011> svn commit . ../../../private/atlas_lookup.m Adding contrib/nutmegtrip/private/atlas_lookup.m Adding contrib/nutmegtrip/private/getdimord.m Adding contrib/nutmegtrip/private/getdimsiz.m Adding contrib/nutmegtrip/private/parameterselection.m Sending private/atlas_lookup.m Committed revision 11090. --------- PS note that due to bug 3049 (migrate from svn to github) in the future a different solution is needed. Probably a github web hook that calls a shell script.