<thomas.e.kel...@gmail.com> wrote:
> Hello all! I've been using Cython now for a couple years and it has been a
> great help. I recently, however, ran into a bit of a snag when I tried
> compiling some bindings I had used in the past on a new server. It works
> fine on my home laptop and on our cluster, just not this partilcular server,
> which leads me to believe something is missing or configured incorrectly.

> The error I get is "/usr/bin/ld: cannot find -lRNA" . In the setup_pyfold.py
> file, the ext_module line is:

>  ext_modules=[
>     Extension("pyfold",
> ["pyfold.pyx"],library_dirs=['/home/thomas/ViennaRNA-1.7/lib'],libraries=[' RNA'],include_dirs=['/home/thomas/ViennaRNA-1.7/H',numpy.get_include()]),

> ]

> Now, I had thought that the libraries option didn't really matter unless you
> were linking to a system library (obviously I was wrong), but having
> "libraries=['RNA']" in that bit of code has never mattered before.

> Any thoughts as to what might be going on?

> Cheers,
> Thomas

> Here is the full output when I try compiling the cython module.

> [2003] lja485@Anu $ python setup_pyfold.py build_ext -i
> running build_ext
> cythoning pyfold.pyx to pyfold.c
> building 'pyfold' extension
> creating build
> creating build/temp.linux-x86_64-2.7
> gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall
> -Wstrict-prototypes -fPIC -I/home/lja485/ViennaRNA-1.8.
> 5/H
> -I/usr/lib/pymodules/python2.7/numpy/core/include
> -I/usr/include/python2.7 -c pyfold.c -o
> build/temp.linux-x86_64-2.7/pyfold.o
> /usr/lib/pymodules/python2.7/numpy/core/include/numpy/__multiarray_api.h:11 87:
> warning: ‘_import_array’ defined but not used
> /usr/lib/pymodules/python2.7/numpy/core/include/numpy/__ufunc_api.h:196:
> warning: ‘_import_umath’ defined but not used
> gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions
> -Wl,-Bsymbolic-functions build/temp.linux-x86_64-2.7/pyfold.o
> -L/home/lja485/ViennaRNA-1.8.5/lib -lRNA -o /home/lja485/dir/pyfold.so
> /usr/bin/ld: cannot find -lRNA
> collect2: ld returned 1 exit status
> error: command 'gcc' failed with exit status 1

On Saturday, June 16, 2012 1:14:30 PM UTC-5, Robert Bradshaw wrote:

> On Fri, Jun 15, 2012 at 10:54 AM, Thomas Keller
> <thomas.e.kel...@gmail.com> wrote:
> > Hello all! I've been using Cython now for a couple years and it has been
> a
> > great help. I recently, however, ran into a bit of a snag when I tried ,
> > compiling some bindings I had used in the past on a new server. It works
> > fine on my home laptop and on our cluster, just not this partilcular
> server,
> > which leads me to believe something is missing or configured
> incorrectly.

> > The error I get is "/usr/bin/ld: cannot find -lRNA" . In the
> setup_pyfold.py
> > file, the ext_module line is:

> >  ext_modules=[
> >     Extension("pyfold",

> ["pyfold.pyx"],library_dirs=['/home/thomas/ViennaRNA-1.7/lib'],libraries=[' RNA'],include_dirs=['/home/thomas/ViennaRNA-1.7/H',numpy.get_include()]),

> > ]

> > Now, I had thought that the libraries option didn't really matter unless
> you
> > were linking to a system library (obviously I was wrong), but having
> > "libraries=['RNA']" in that bit of code has never mattered before.

> > Any thoughts as to what might be going on?

> > Cheers,
> > Thomas

> > Here is the full output when I try compiling the cython module.

> > [2003] lja485@Anu $ python setup_pyfold.py build_ext -i
> > running build_ext
> > cythoning pyfold.pyx to pyfold.c
> > building 'pyfold' extension
> > creating build
> > creating build/temp.linux-x86_64-2.7
> > gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall
> > -Wstrict-prototypes -fPIC -I/home/lja485/ViennaRNA-1.8.
> > 5/H
> > -I/usr/lib/pymodules/python2.7/numpy/core/include
> > -I/usr/include/python2.7 -c pyfold.c -o
> > build/temp.linux-x86_64-2.7/pyfold.o

> /usr/lib/pymodules/python2.7/numpy/core/include/numpy/__multiarray_api.h:11 87:

> > warning: ‘_import_array’ defined but not used
> > /usr/lib/pymodules/python2.7/numpy/core/include/numpy/__ufunc_api.h:196:
> > warning: ‘_import_umath’ defined but not used
> > gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions
> > -Wl,-Bsymbolic-functions build/temp.linux-x86_64-2.7/pyfold.o
> > -L/home/lja485/ViennaRNA-1.8.5/lib -lRNA -o /home/lja485/dir/pyfold.so
> > /usr/bin/ld: cannot find -lRNA
> > collect2: ld returned 1 exit status
> > error: command 'gcc' failed with exit status 1

> It can't find your library. What is the contents of
> /home/thomas/ViennaRNA-1.7/lib? Are you sure your library is in there
> and named appropriately and the right architecture?

> - Robert

> On Saturday, June 16, 2012 1:14:30 PM UTC-5, Robert Bradshaw wrote:
>> On Fri, Jun 15, 2012 at 10:54 AM, Thomas Keller wrote:
>>> Hello all! I've been using Cython now for a couple years and it has been
>>> a great help. I recently, however, ran into a bit of a snag when I tried,
>>> compiling some bindings I had used in the past on a new server. It works
>>> fine on my home laptop and on our cluster, just not this partilcular
>>> server, which leads me to believe something is missing or configured
>>> incorrectly.

>>> The error I get is "/usr/bin/ld: cannot find -lRNA" . In the
>>> setup_pyfold.py file, the ext_module line is:

>>>  ext_modules=[
>>>     Extension("pyfold",
>>> ["pyfold.pyx"],library_dirs=['/home/thomas/ViennaRNA-1.7/lib'],libraries=[' RNA'],include_dirs=['/home/thomas/ViennaRNA-1.7/H',numpy.get_include()]),
>>> ]

>>> Now, I had thought that the libraries option didn't really matter unless
>>> you were linking to a system library (obviously I was wrong), but having
>>> "libraries=['RNA']" in that bit of code has never mattered before.

>>> Any thoughts as to what might be going on?

>> It can't find your library. What is the contents of
>> /home/thomas/ViennaRNA-1.7/lib? Are you sure your library is in there
>> and named appropriately and the right architecture?

> Ah, I think I see what the problem is. So I should be using the libraries
> option to specify the exact libraries that the .pyx files uses, correct?

> For instance, it uses functions/etc from the stdlib, libRNA_a-fold,
> libRNA_a-cofold, libRNA_a-fold_vars, libRNA_a-part_func, and
> libRNA_a-inverse libraries. Thus, the libraries option should be
> "libraries=['stdlib','libRNA_a-fold',..etc]", correct?

> I still have no idea why it worked fine on the other computers, as there's
> not even a library called RNA in that directory. Anyway, thanks!