[BioLib-dev] GSL

[Pjotr Prins]

The tree looks sane to me - as it is now. The renaming is there
biolib_gsl. Your branch on your machine is probably dirty now. But the
ones on github are fine. Destroy all the branches with the dirty
patch (after making a backup). Pull your github master branch and
update from my libsequence branch. Everything should by hunky dory.

Pj.

On Mon, Aug 10, 2009 at 04:18:51PM -0400, Xin Shuai wrote:
> Then ,do I have to throw out that commit?
> 
> On Mon, Aug 10, 2009 at 4:09 PM, Pjotr Prins <pjotr.public14 at thebird.nl>wrote:
> 
> > All great :-)
> >
> > On Mon, Aug 10, 2009 at 03:33:51PM -0400, Xin Shuai wrote:
> > > Hi, Pjotr:  I checked my file permission set up in my machine and it is
> > > alright. So I don't need to change the unmask.
> > >
> > >   Regarding to the bad commit,
> > > I think I forgot to tell you one thing. During the process of
> > > modifying the CMake files to include gsl linking, I found you named
> > > all the dependent library with a biolib_ prefix: biolib_core, biolib_R.
> > So I
> > > renamed ./gsl directory to ./biolib_gsl directory. Otherwise, your cmake
> > > setup cannot find the gsl dynamic library. So when I commit, the .gsl/
> > > directory with all its 644 mode files are deleted and a new directory
> > > ./biolib_gsl is added.
> > >
> > >  This is not the first time I do this. At the beginning, when I compile
> > the
> > > libsequence library, I handle it similarly: I changed the
> > > ./clibs/libsequence to ./clibs/libsequence-1.6.6. Otherwise, your cmake
> > > setup cannot find correct path.
> > >
> > > So is there anything I missed?
> > >
> > >
> > > On Mon, Aug 10, 2009 at 1:06 PM, Pjotr Prins <pjotr.public14 at thebird.nl
> > >wrote:
> > >
> > > > Hi Xin,
> > > >
> > > > This was a bit painful, but arguably my mistake. You can pull from my
> > > > branch now without problems. You may have to revert your own branch
> > > > to your github master first: to throw out the reintroduced patch.
> > > >
> > > > Note you have later put it new files with the wrong permissions. See
> > > > the patch:
> > > >
> > > >  c92151cdc3db8b353534532baee4c70dc5a2583e
> > > >
> > > > it includes a number of 755 permissions. When you create a new file
> > > > on your machine:
> > > >
> > > >  touch test.me
> > > >  ls -l test.me
> > > >
> > > > what are its permissions? It should be 644 or -rw-r--r--. If they are
> > > > 755 (rwxr-xr-x) you may need to change the umask on your machine:
> > > >
> > > >  umask 022
> > > >
> > > > See Internet resources on how to manage that.
> > > >
> > > > Pj.
> > > >
> > > > On Mon, Aug 10, 2009 at 06:02:07PM +0200, Pjotr Prins wrote:
> > > > > I think your master branch is clean. I'll work from there.
> > > > >
> > > > > Pj.
> > > > >
> > > > > On Mon, Aug 10, 2009 at 11:01:40AM +0200, Pjotr Prins wrote:
> > > > > > Hi Xin,
> > > > > >
> > > > > > On Fri, Aug 07, 2009 at 04:14:29PM -0400, Xin Shuai wrote:
> > > > > > > I have already modified related .cmake files and tested it. It
> > looked
> > > > fine.If
> > > > > > > only the problem of my last email is solved, I think I can update
> > the
> > > > > > > cmake-support submodule.
> > > > > >
> > > > > > Good job :-). I can build libsequence and compile Python bindings
> > > > > > now. Cool stuff. Now the final step before merging into
> > > > > > release_candidate. After updating from my tree:
> > > > > >
> > > > > >   git pull pjotr libsequence
> > > > > >   git submodule update
> > > > > >
> > > > > > add a working 'integration' test to the Python module. When you do:
> > > > > >
> > > > > >   cd src/mappings/swig/python/libsequence
> > > > > >   cmake .
> > > > > >   make
> > > > > >   make test
> > > > > >
> > > > > > you'll see   1/  1 Testing TestPythonlibsequence         ***Failed
> > > > > >
> > > > > > the output is in Testing/Temporary/LastTest.log.
> > > > > >
> > > > > > Currently ../test/test_libsequence.py consists of your doctests.
> > They
> > > > > > are bound to be elaborate. A biolib integration test merely makes
> > sure
> > > > > > the build system did not fail - so it usually has a few simple
> > tests.
> > > > > >
> > > > > > Rename your current doctest to ../test/doctest_libsequence.py
> > > > > >
> > > > > > and create a new short test (see test_example.py) that confirms the
> > > > > > libraries are linked together and the mapping just works. Same for
> > > > > > the Perl module.
> > > > > >
> > > > > > Once that test passes I'll merge into release_candidate so Mark
> > (and
> > > > > > perhaps others) can start testing.
> > > > > >
> > > > > > Pj.
> > > > > >
> > > > > > P.S. I had to revert some changes in cmake-support. Not sure why
> > you
> > > > > > changed those, but I think this is correct.
> > > > > >
> > > > > > _______________________________________________
> > > > > > BioLib-dev mailing list
> > > > > > BioLib-dev at lists.open-bio.org
> > > > > > http://lists.open-bio.org/mailman/listinfo/biolib-dev
> > > >
> > >
> > >
> > >
> > > --
> > > Xin Shuai (David)
> > > PhD of Complex System in School of Informatics
> > > Indiana University Bloomington
> > > 812-606-8019
> >
> 
> 
> 
> -- 
> Xin Shuai (David)
> PhD of Complex System in School of Informatics
> Indiana University Bloomington
> 812-606-8019