[BioLib-dev] GSL

[Xin Shuai]

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