[BioLib-dev] GSL

[Pjotr Prins]

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.
> > 
> > _______________________________________________
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