[SciPy-User] lnpymath cannot find error during scipy installation
Gökhan Sever
gokhansever at gmail.com
Fri Aug 14 17:03:09 EDT 2009
Hello,
A solution form the self :)
I fixed this compilation error by putting a symbolic to the npy_math.o file
(/home/gsever/Desktop/python-repo/numpy/build/temp.linux-i686-2.6/numpy/core/src/npymath)
under /usr/lib as libnpymath.so (the library files like having "so" postfix
in lib so I just follow the convention.)
When I issued python setupegg.py develop as a root user it was finally been
able to compiled and working properly.
Wondering it is something related to the new code in the SVN-bases since I
remember I successfully built scipy (on top of SVN-numpy) from the SVN
without encountering this missing library (or not properly placed) issue.
The way I do the check-outs is as a regular user and then invoke the python
setupegg.py develop commands (where available) as root to place the links or
files properly under /usr directories. Before I had given full read-write
access to all /usr directories and files, but had observed weird issues due
to this change.
On Thu, Aug 13, 2009 at 2:56 PM, Gökhan Sever <gokhansever at gmail.com> wrote:
> /usr/bin/ld: cannot find -lnpymath
> collect2: ld returned 1 exit status
> error: Command "/usr/bin/g77 -g -Wall -g -Wall -shared
> build/temp.linux-i686-2.6/scipy/special/_cephesmodule.o
> build/temp.linux-i686-2.6/scipy/special/amos_wrappers.o
> build/temp.linux-i686-2.6/scipy/special/specfun_wrappers.o
> build/temp.linux-i686-2.6/scipy/special/toms_wrappers.o
> build/temp.linux-i686-2.6/scipy/special/cdf_wrappers.o
> build/temp.linux-i686-2.6/scipy/special/ufunc_extras.o
> -L/usr/lib/python2.6/site-packages/numpy/core/lib -L/usr/lib
> -Lbuild/temp.linux-i686-2.6 -lsc_amos -lsc_toms -lsc_c_misc -lsc_cephes
> -lsc_mach -lsc_cdf -lsc_specfun -lnpymath -lm -lpython2.6 -lg2c -o
> scipy/special/_cephes.so" failed with exit status 1
>
> Did a python setupegg.py develop install for numpy and when I tried to do
> the same for scipy I stuck at that error. I know there is a libnpymath file
> under one of the numpy build dirs, however not sure how to show that path
> for the linker.
>
> Any ideas?
>
> Thank you
>
>
> ##############################################
> python -c 'from numpy.f2py.diagnose import run; run()'
> ##############################################
> ------
> os.name='posix'
> ------
> sys.platform='linux2'
> ------
> sys.version:
> 2.6 (r26:66714, Jun 8 2009, 16:07:26)
> [GCC 4.4.0 20090506 (Red Hat 4.4.0-4)]
> ------
> sys.prefix:
> /usr
> ------
>
> sys.path=':/usr/lib/python2.6/site-packages/foolscap-0.4.2-py2.6.egg:/usr/lib/python2.6/site-packages/Twisted-8.2.0-py2.6-linux-i686.egg:/home/gsever/Desktop/python-repo/ipython:/home/gsever/Desktop/python-repo/numpy:/home/gsever/Desktop/python-repo/matplotlib/lib:/usr/lib/python2.6/site-packages/Sphinx-0.6.2-py2.6.egg:/usr/lib/python2.6/site-packages/docutils-0.5-py2.6.egg:/usr/lib/python2.6/site-packages/Jinja2-2.1.1-py2.6-linux-i686.egg:/usr/lib/python2.6/site-packages/Pygments-1.0-py2.6.egg:/usr/lib/python2.6/site-packages/xlwt-0.7.2-py2.6.egg:/usr/lib/python2.6/site-packages/spyder-1.0.0beta1-py2.6.egg:/usr/lib/python26.zip:/usr/lib/python2.6:/usr/lib/python2.6/plat-linux2:/usr/lib/python2.6/lib-tk:/usr/lib/python2.6/lib-old:/usr/lib/python2.6/lib-dynload:/usr/lib/python2.6/site-packages:/usr/lib/python2.6/site-packages/Numeric:/usr/lib/python2.6/site-packages/PIL:/usr/lib/python2.6/site-packages/gst-0.10:/usr/lib/python2.6/site-packages/gtk-2.0:/usr/lib/python2.6/site-packages:/usr/lib/python2.6/site-packages/wx-2.8-gtk2-unicode'
> ------
> Failed to import numarray: No module named numarray
> Found Numeric version '24.2' in
> /usr/lib/python2.6/site-packages/Numeric/Numeric.pyc
> Found new numpy version '1.4.0.dev' in
> /home/gsever/Desktop/python-repo/numpy/numpy/__init__.pyc
> Found f2py2e version '2' in
> /home/gsever/Desktop/python-repo/numpy/numpy/f2py/f2py2e.pyc
> Found numpy.distutils version '0.4.0' in
> '/home/gsever/Desktop/python-repo/numpy/numpy/distutils/__init__.pyc'
> ------
> Importing numpy.distutils.fcompiler ... ok
> ------
> Checking availability of supported Fortran compilers:
> GnuFCompiler instance properties:
> archiver = ['/usr/bin/g77', '-cr']
> compile_switch = '-c'
> compiler_f77 = ['/usr/bin/g77', '-g', '-Wall', '-fno-second-
> underscore', '-fPIC', '-O3', '-funroll-loops']
> compiler_f90 = None
> compiler_fix = None
> libraries = ['g2c']
> library_dirs = []
> linker_exe = ['/usr/bin/g77', '-g', '-Wall', '-g', '-Wall']
> linker_so = ['/usr/bin/g77', '-g', '-Wall', '-g', '-Wall', '-
> shared']
> object_switch = '-o '
> ranlib = ['/usr/bin/g77']
> version = LooseVersion ('3.4.6')
> version_cmd = ['/usr/bin/g77', '--version']
> Gnu95FCompiler instance properties:
> archiver = ['/usr/bin/gfortran', '-cr']
> compile_switch = '-c'
> compiler_f77 = ['/usr/bin/gfortran', '-Wall', '-ffixed-form', '-fno-
> second-underscore', '-fPIC', '-O3', '-funroll-loops']
> compiler_f90 = ['/usr/bin/gfortran', '-Wall',
> '-fno-second-underscore',
> '-fPIC', '-O3', '-funroll-loops']
> compiler_fix = ['/usr/bin/gfortran', '-Wall', '-ffixed-form', '-fno-
> second-underscore', '-Wall', '-fno-second-underscore',
> '-
> fPIC', '-O3', '-funroll-loops']
> libraries = ['gfortran']
> library_dirs = []
> linker_exe = ['/usr/bin/gfortran', '-Wall', '-Wall']
> linker_so = ['/usr/bin/gfortran', '-Wall', '-Wall', '-shared']
> object_switch = '-o '
> ranlib = ['/usr/bin/gfortran']
> version = LooseVersion ('4.4.0')
> version_cmd = ['/usr/bin/gfortran', '--version']
> Fortran compilers found:
> --fcompiler=gnu GNU Fortran 77 compiler (3.4.6)
> --fcompiler=gnu95 GNU Fortran 95 compiler (4.4.0)
> Compilers available for this platform, but not found:
> --fcompiler=absoft Absoft Corp Fortran Compiler
> --fcompiler=compaq Compaq Fortran Compiler
> --fcompiler=g95 G95 Fortran Compiler
> --fcompiler=intel Intel Fortran Compiler for 32-bit apps
> --fcompiler=intele Intel Fortran Compiler for Itanium apps
> --fcompiler=intelem Intel Fortran Compiler for EM64T-based apps
> --fcompiler=lahey Lahey/Fujitsu Fortran 95 Compiler
> --fcompiler=nag NAGWare Fortran 95 Compiler
> --fcompiler=pg Portland Group Fortran Compiler
> --fcompiler=vast Pacific-Sierra Research Fortran 90 Compiler
> Compilers not available on this platform:
> --fcompiler=hpux HP Fortran 90 Compiler
> --fcompiler=ibm IBM XL Fortran Compiler
> --fcompiler=intelev Intel Visual Fortran Compiler for Itanium apps
> --fcompiler=intelv Intel Visual Fortran Compiler for 32-bit apps
> --fcompiler=mips MIPSpro Fortran Compiler
> --fcompiler=none Fake Fortran compiler
> --fcompiler=sun Sun or Forte Fortran 95 Compiler
> For compiler details, run 'config_fc --verbose' setup command.
> ------
> Importing numpy.distutils.cpuinfo ... ok
> ------
> CPU information: CPUInfoBase__get_nbits getNCPUs has_mmx has_sse has_sse2
> has_sse3 has_ssse3 is_32bit is_Intel is_i686 ------
>
>
>
> --
> Gökhan
>
--
Gökhan
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.scipy.org/pipermail/scipy-user/attachments/20090814/07fb960b/attachment.html>
More information about the SciPy-User
mailing list