Installation can't find locally installed Numeric

John_Hunter · October 6, 2005, 5:12pm

One never ceases to learn I discovered ldd, and

    > when I run it on the offending file _nc_image.so, I see
    > that libpng isn't linked into it at all. So there's
    > probably an linking option set wrong in setupext.py
    > responsable for linking libpng. I'll try and find it,
    > but if anyone here can save me some time and tell me,
    > I'd greatly appreciate it.

The place to start poking around is in setupext.py's build_image

This function does a numerix switch to add flags for Numeric and
numarray if it finds them. Both paths (Numeric and numarray) call

add_agg_flags(module)

and add_agg_flags calls

module.libraries.append('png')

so libpng should be in your link chain. Since you have a nonstandard
Numeric install, make sure the numerix logic is working as it should
(eg what is the value of "numerix" in build_image?)

I suggest rm -rf ing your build subdir and starting cleanly.

Let us know what you find....

JDH

_Alexander_Borghgrae · October 10, 2005, 9:38am

The value of numerix is “Numeric”, as it should be. Also, add_agg_flags is called four times,

of which once inside build_image, so libpng should be linked in. I tried linking libpng into a simple

c++ program, no problem there.

···

On 10/6/05, John Hunter <jdhunter@…4…> wrote:

The place to start poking around is in setupext.py’s build_image

This function does a numerix switch to add flags for Numeric and
numarray if it finds them. Both paths (Numeric and numarray) call
add_agg_flags(module)
and add_agg_flags calls
module.libraries.append('png')
so libpng should be in your link chain. Since you have a nonstandard
Numeric install, make sure the numerix logic is working as it should

(eg what is the value of “numerix” in build_image?)

–
Alex Borghgraef

Nadezhda_Dencheva1 · October 10, 2005, 6:15pm

Alex,

It would be helpful if you post your basedir (from the beginning of setupext.py),
the output of the build command (maybe just the lines for nc_image) and the operating
system you are using. This will show whether python is looking for libpng in
the correct directory.

Nadia

···

On Oct 10, 2005, at 5:38 AM, Alexander Borghgraef wrote:

On 10/6/05, John Hunter <jdhunter@...4...> wrote:
The place to start poking around is in setupext.py's build_image

This function does a numerix switch to add flags for Numeric and
numarray if it finds them. Both paths (Numeric and numarray) call
add\_agg\_flags\(module\)
and add_agg_flags calls
module\.libraries\.append\(&#39;png&#39;\)
so libpng should be in your link chain. Since you have a nonstandard
Numeric install, make sure the numerix logic is working as it should
(eg what is the value of "numerix" in build_image?)
The value of numerix is "Numeric", as it should be. Also, add_agg_flags is called four times,
of which once inside build_image, so libpng should be linked in. I tried linking libpng into a simple
c++ program, no problem there.

--
Alex Borghgraef

_Alexander_Borghgrae · October 11, 2005, 8:12am

Alex,

It would be helpful if you post your basedir (from the beginning of
setupext.py),

basedir = {

'win32'  : ['win32_static',],

'linux2' : ['/usr/local', '/usr',],

'linux'  : ['/usr/local', '/usr',],

# Charles Moad recommends not putting in /usr/X11R6 for darwin

# because freetype in this dir is too old for mpl

'darwin' : ['/sw/lib/freetype2', '/sw/lib/freetype219', '/usr/local',

            '/usr', '/sw'],

'freebsd4' : ['/usr/local', '/usr'],

'freebsd5' : ['/usr/local', '/usr'],

'freebsd6' : ['/usr/local', '/usr'],   

'sunos5' : [os.getenv('MPLIB_BASE') or '/usr/local',],

}

the output of the build command (maybe just the lines for nc_image)

The lines containing -lpng:
c++ -pthread -shared
build/temp.linux-i686-2.3/src/_gtkagg.o
build/temp.linux-i686-2.3/src/mplutils.o
build/temp.linux-i686-2.3/src/_transforms.o
build/temp.linux-i686-2.3/CXX/cxx_extensions.o
build/temp.linux-i686-2.3/CXX/IndirectPythonInterface.o
build/temp.linux-i686-2.3/CXX/cxxsupport.o
build/temp.linux-i686-2.3/CXX/cxxextensions.o -L/usr/local/lib
-L/usr/lib -L/usr/local/lib -L/usr/lib -L/usr/local/lib -L/usr/lib
-lpng -lz -lstdc++ -lm -lfreetype -lz -lstdc++ -lm -lgobject-2.0
-lglib-2.0 -lgtk-x11-2.0 -lgdk-x11-2.0 -latk-1.0 -lgdk_pixbuf-2.0 -lm
-lpangoxft-1.0 -lpangox-1.0 -lpango-1.0 -lgobject-2.0 -lgmodule-2.0
-ldl -lglib-2.0 -o
build/lib.linux-i686-2.3/matplotlib/backends/_gtkagg.so
-Wl,–export-dynamic

building ‘matplotlib.backends._tkagg’ extension

…

c++ -pthread -shared build/temp.linux-i686-2.3/src/_tkagg.o
build/temp.linux-i686-2.3/CXX/cxx_extensions.o
build/temp.linux-i686-2.3/CXX/IndirectPythonInterface.o
build/temp.linux-i686-2.3/CXX/cxxsupport.o
build/temp.linux-i686-2.3/CXX/cxxextensions.o -L/usr/share/tcl8.4/…/
-L/usr/share/tk8.4/…/ -L/usr/local/lib -L/usr/lib -L/usr/local/lib
-L/usr/lib -ltk8.4 -ltcl8.4 -lpng -lz -lstdc++ -lm -lfreetype -lz
-lstdc++ -lm -o build/lib.linux-i686-2.3/matplotlib/backends/_tkagg.so

building ‘matplotlib.backends._nc_backend_agg’ extension

…

c++ -pthread -shared
build/temp.linux-i686-2.3/agg23/src/agg_trans_affine.o
build/temp.linux-i686-2.3/agg23/src/agg_path_storage.o
build/temp.linux-i686-2.3/agg23/src/agg_bezier_arc.o
build/temp.linux-i686-2.3/agg23/src/agg_curves.o
build/temp.linux-i686-2.3/agg23/src/agg_vcgen_dash.o
build/temp.linux-i686-2.3/agg23/src/agg_vcgen_stroke.o
build/temp.linux-i686-2.3/agg23/src/agg_rasterizer_scanline_aa.o
build/temp.linux-i686-2.3/agg23/src/agg_image_filters.o
build/temp.linux-i686-2.3/src/_image.o
build/temp.linux-i686-2.3/src/ft2font.o
build/temp.linux-i686-2.3/src/mplutils.o
build/temp.linux-i686-2.3/CXX/cxx_extensions.o
build/temp.linux-i686-2.3/CXX/IndirectPythonInterface.o
build/temp.linux-i686-2.3/CXX/cxxsupport.o
build/temp.linux-i686-2.3/CXX/cxxextensions.o
build/temp.linux-i686-2.3/src/_nc_backend_agg.o -L/usr/local/lib
-L/usr/lib -L/usr/local/lib -L/usr/lib -lpng -lz -lstdc++ -lm
-lfreetype -lz -lstdc++ -lm -o
build/lib.linux-i686-2.3/matplotlib/backends/_nc_backend_agg.so

building ‘matplotlib.ft2font’ extension

…

c++ -pthread -shared build/temp.linux-i686-2.3/src/_nc_image.o
build/temp.linux-i686-2.3/src/mplutils.o
build/temp.linux-i686-2.3/agg23/src/agg_trans_affine.o
build/temp.linux-i686-2.3/agg23/src/agg_path_storage.o
build/temp.linux-i686-2.3/agg23/src/agg_rasterizer_scanline_aa.o
build/temp.linux-i686-2.3/agg23/src/agg_image_filters.o
build/temp.linux-i686-2.3/agg23/src/agg_bezier_arc.o
build/temp.linux-i686-2.3/CXX/cxx_extensions.o
build/temp.linux-i686-2.3/CXX/IndirectPythonInterface.o
build/temp.linux-i686-2.3/CXX/cxxsupport.o
build/temp.linux-i686-2.3/CXX/cxxextensions.o -L/usr/local/lib
-L/usr/lib -lpng -lz -lstdc++ -lm -o
build/lib.linux-i686-2.3/matplotlib/_nc_image.so

building ‘matplotlib._nc_cntr’ extension

None of these .so files have libpng linked in. I’ll include the output of ldd for the last one:

~/incoming/matplotlib-0.84 |10> ldd build/lib.linux-i686-2.3/matplotlib/_nc_image.so

    libz.so.1 => /usr/lib/libz.so.1 (0x0017b000)

    libstdc++.so.6 => /usr/lib/libstdc++.so.6 (0x0075e000)

    libm.so.6 => /lib/tls/libm.so.6 (0x005fd000)

    libgcc_s.so.1 => /lib/libgcc_s.so.1 (0x00111000)

    libpthread.so.0 => /lib/tls/libpthread.so.0 (0x006f9000)

    libc.so.6 => /lib/tls/libc.so.6 (0x00e29000)

    /lib/ld-linux.so.2 (0x00139000)

and
the operating
system you are using. This will show whether python is looking for

libpng in
the correct directory.

I’m using Fedora core 3 as user (meaning I have installed Numeric locally). The libpng.so file is where you’d

expect it to be, in /usr/lib. This is seriously strange, I didn’t get any errors either, just a bunch of warnings.

I’ll include them as well, though I doubt they’ll be useful:

~/incoming/matplotlib-0.84 |6> python setup.py build > buildlog

In file included from /usr/include/python2.3/Python.h:8,

             from ./CXX/Objects.hxx:9,

             from ./CXX/Extensions.hxx:19,

             from src/_transforms.h:12,

             from src/_nc_transforms.cpp:2:

/usr/include/python2.3/pyconfig.h:850:1: warning: “_POSIX_C_SOURCE” redefined

In file included from /usr/lib/gcc/i386-redhat-linux/3.4.4/…/…/…/…/include/c++/3.4.4/i386-redhat-linux/bits/os_defines.h:39,

from
/usr/lib/gcc/i386-redhat-linux/3.4.4/…/…/…/…/include/c++/3.4.4/i386-redhat-linux/bits/c++config.h:35,

from
/usr/lib/gcc/i386-redhat-linux/3.4.4/…/…/…/…/include/c++/3.4.4/functional:54,

             from src/_nc_transforms.cpp:1:

/usr/include/features.h:150:1: warning: this is the location of the previous definition

In file included from /usr/include/python2.3/Python.h:8,

from /usr/include/pygtk-2.0/pygobject.h:5,

             from src/_gtkagg.cpp:10:

/usr/include/python2.3/pyconfig.h:850:1: warning: “_POSIX_C_SOURCE” redefined

In file included from /usr/include/string.h:26,

from
/usr/lib/gcc/i386-redhat-linux/3.4.4/…/…/…/…/include/c++/3.4.4/cstring:51,

             from src/_gtkagg.cpp:1:

/usr/include/features.h:150:1: warning: this is the location of the previous definition

In file included from /usr/include/python2.3/Python.h:8,

             from ./CXX/Objects.hxx:9,

             from ./CXX/Extensions.hxx:19,

             from src/_transforms.h:12,

             from src/_transforms.cpp:2:

/usr/include/python2.3/pyconfig.h:850:1: warning: “_POSIX_C_SOURCE” redefined

In file included from /usr/lib/gcc/i386-redhat-linux/3.4.4/…/…/…/…/include/c++/3.4.4/i386-redhat-linux/bits/os_defines.h:39,

from
/usr/lib/gcc/i386-redhat-linux/3.4.4/…/…/…/…/include/c++/3.4.4/i386-redhat-linux/bits/c++config.h:35,

from
/usr/lib/gcc/i386-redhat-linux/3.4.4/…/…/…/…/include/c++/3.4.4/functional:54,

             from src/_transforms.cpp:1:

/usr/include/features.h:150:1: warning: this is the location of the previous definition

In file included from /usr/include/python2.3/Python.h:8,

             from src/_image.cpp:7:

/usr/include/python2.3/pyconfig.h:850:1: warning: “_POSIX_C_SOURCE” redefined

In file included from /usr/lib/gcc/i386-redhat-linux/3.4.4/…/…/…/…/include/c++/3.4.4/i386-redhat-linux/bits/os_defines.h:39,

from
/usr/lib/gcc/i386-redhat-linux/3.4.4/…/…/…/…/include/c++/3.4.4/i386-redhat-linux/bits/c++config.h:35,

from
/usr/lib/gcc/i386-redhat-linux/3.4.4/…/…/…/…/include/c++/3.4.4/iostream:44,

             from src/_image.cpp:1:

/usr/include/features.h:150:1: warning: this is the location of the previous definition

In file included from /usr/include/python2.3/Python.h:8,

             from ./CXX/Objects.hxx:9,

             from ./CXX/Extensions.hxx:19,

             from src/ft2font.h:18,

from src/_nc_backend_agg.cpp:18:

/usr/include/python2.3/pyconfig.h:850:1: warning: “_POSIX_C_SOURCE” redefined

In file included from /usr/lib/gcc/i386-redhat-linux/3.4.4/…/…/…/…/include/c++/3.4.4/i386-redhat-linux/bits/os_defines.h:39,

from
/usr/lib/gcc/i386-redhat-linux/3.4.4/…/…/…/…/include/c++/3.4.4/i386-redhat-linux/bits/c++config.h:35,

from
/usr/lib/gcc/i386-redhat-linux/3.4.4/…/…/…/…/include/c++/3.4.4/iostream:44,

             from src/_nc_backend_agg.cpp:4:

/usr/include/features.h:150:1: warning: this is the location of the previous definition

In file included from /usr/include/python2.3/Python.h:8,

             from ./CXX/Objects.hxx:9,

             from ./CXX/Extensions.hxx:19,

             from src/ft2font.h:18,

             from src/ft2font.cpp:2:

/usr/include/python2.3/pyconfig.h:850:1: warning: “_POSIX_C_SOURCE” redefined

In file included from /usr/lib/gcc/i386-redhat-linux/3.4.4/…/…/…/…/include/c++/3.4.4/i386-redhat-linux/bits/os_defines.h:39,

from
/usr/lib/gcc/i386-redhat-linux/3.4.4/…/…/…/…/include/c++/3.4.4/i386-redhat-linux/bits/c++config.h:35,

from
/usr/lib/gcc/i386-redhat-linux/3.4.4/…/…/…/…/include/c++/3.4.4/iosfwd:45,

from
/usr/lib/gcc/i386-redhat-linux/3.4.4/…/…/…/…/include/c++/3.4.4/ios:44,

from
/usr/lib/gcc/i386-redhat-linux/3.4.4/…/…/…/…/include/c++/3.4.4/istream:45,

from
/usr/lib/gcc/i386-redhat-linux/3.4.4/…/…/…/…/include/c++/3.4.4/sstream:45,

             from src/ft2font.cpp:1:

/usr/include/features.h:150:1: warning: this is the location of the previous definition

In file included from /usr/include/python2.3/Python.h:8,

             from src/_nc_image.cpp:7:

/usr/include/python2.3/pyconfig.h:850:1: warning: “_POSIX_C_SOURCE” redefined

In file included from /usr/lib/gcc/i386-redhat-linux/3.4.4/…/…/…/…/include/c++/3.4.4/i386-redhat-linux/bits/os_defines.h:39,

from
/usr/lib/gcc/i386-redhat-linux/3.4.4/…/…/…/…/include/c++/3.4.4/i386-redhat-linux/bits/c++config.h:35,

from
/usr/lib/gcc/i386-redhat-linux/3.4.4/…/…/…/…/include/c++/3.4.4/iostream:44,

             from src/_nc_image.cpp:1:

/usr/include/features.h:150:1: warning: this is the location of the previous definition

74.056u 3.357s 1:17.71 99.6% 0+0k 0+0io 75pf+0w

···

On 10/10/05, Nadia Dencheva <dencheva@…86…> wrote:

–
Alex Borghgraef

_Alexander_Borghgrae · October 13, 2005, 12:27pm

Nobody has any ideas? I’m really clueless on this one. The logs clearly show the .so files being compiled with
-L/usr/lib -lpng as flags, yet ldd shows libpng is not linked in. Could it be that libpng needs to be linked in the
.o files? Any other sane explanations?

···

–
Alex Borghgraef