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[PyMOL] errors compiling fink pymol 0.98
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From: Jean-Christophe A. <am...@es...> - 2005-11-22 13:23:37
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Hello,
I tried to compile pymol 0.98 from fink distribution but I got the =20
following error (see bellow) during gmp-4.1.4-2 which seems to be =20
required for pymol compilation. I got the same result on both =20
MacOSX10.3.9 and 10.4.3. How can I overcome this problem? Did anybody =20=
got the same error?
Thank a lot for any responses.
Jean-Christophe
Making check in misc
make t-printf t-scanf t-locale
gcc-3.3 -DHAVE_CONFIG_H -I. -I. -I../.. -I../.. -I../../tests -I/sw/=20
include -g -O2 -mpowerpc -no-cpp-precomp -c `test -f t-printf.c || =20
echo './'`t-printf.c
/bin/sh ../../libtool --mode=3Dlink gcc-3.3 -g -O2 -mpowerpc -no-cpp-=20=
precomp -L/sw/lib -o t-printf t-printf.o ../../tests/=20
libtests.la ../../libgmp.la
mkdir .libs
gcc-3.3 -g -O2 -mpowerpc -no-cpp-precomp -o .libs/t-printf t-=20
printf.o -L/sw/lib ../../tests/.libs/libtests.a -L/sw/src/fink.build/=20=
gmp-4.1.4-2/gmp-4.1.4/.libs -L../../.libs -lgmp
ld: warning prebinding disabled because dependent library: /sw/lib/=20
libgmp.3.dylib is not prebound
creating t-printf
gcc-3.3 -DHAVE_CONFIG_H -I. -I. -I../.. -I../.. -I../../tests -I/sw/=20
include -g -O2 -mpowerpc -no-cpp-precomp -c `test -f t-scanf.c || =20
echo './'`t-scanf.c
/bin/sh ../../libtool --mode=3Dlink gcc-3.3 -g -O2 -mpowerpc -no-cpp-=20=
precomp -L/sw/lib -o t-scanf t-scanf.o ../../tests/=20
libtests.la ../../libgmp.la
gcc-3.3 -g -O2 -mpowerpc -no-cpp-precomp -o .libs/t-scanf t-scanf.o -=20=
L/sw/lib ../../tests/.libs/libtests.a -L/sw/src/fink.build/=20
gmp-4.1.4-2/gmp-4.1.4/.libs -L../../.libs -lgmp
ld: warning prebinding disabled because dependent library: /sw/lib/=20
libgmp.3.dylib is not prebound
creating t-scanf
gcc-3.3 -DHAVE_CONFIG_H -I. -I. -I../.. -I../.. -I../../tests -I/sw/=20
include -g -O2 -mpowerpc -no-cpp-precomp -c `test -f t-locale.c || =20
echo './'`t-locale.c
/bin/sh ../../libtool --mode=3Dlink gcc-3.3 -g -O2 -mpowerpc -no-cpp-=20=
precomp -L/sw/lib -o t-locale t-locale.o ../../tests/=20
libtests.la ../../libgmp.la
gcc-3.3 -g -O2 -mpowerpc -no-cpp-precomp -o .libs/t-locale t-=20
locale.o -L/sw/lib ../../tests/.libs/libtests.a -L/sw/src/fink.build/=20=
gmp-4.1.4-2/gmp-4.1.4/.libs -L../../.libs -lgmp
ld: warning prebinding disabled because dependent library: /sw/lib/=20
libgmp.3.dylib is not prebound
ld: warning multiple definitions of symbol _localeconv
t-locale.o definition of _localeconv in section (__TEXT,__text)
/usr/lib/libSystem.dylib(localeconv.So) definition of _localeconv
creating t-locale
make check-TESTS
PASS: t-printf
Warning, sscanf("","%d",&x) doesn't return EOF.
This affects gmp_sscanf, tests involving it will be suppressed.
You should try to get a fix for your libc.
PASS: t-scanf
PASS: t-locale
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
All 3 tests passed
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
Making check in cxx
make t-cast t-headers t-ostream t-constr t-expr
g++-3.3 -DHAVE_CONFIG_H -I. -I. -I../.. -I../.. -I../../tests -I/sw/=20
include -g -O2 -mpowerpc -no-cpp-precomp -c -o t-cast.o `test -f t-=20
cast.cc || echo './'`t-cast.cc
In file included from t-cast.cc:23:
../../gmpxx.h:2379: warning: use of `long double' type; its size may =20
change in
a future release
../../gmpxx.h:2379: warning: (Long double usage is reported only once =20=
for each
file.
../../gmpxx.h:2379: warning: To disable this warning, use -Wno-long-=20
double.)
/bin/sh ../../libtool --mode=3Dlink g++-3.3 -g -O2 -mpowerpc -no-cpp-=20=
precomp -L/sw/lib -o t-cast t-cast.o ../../tests/libtests.la ../../=20
libgmpxx.la ../../libgmp.la
mkdir .libs
g++-3.3 -g -O2 -mpowerpc -no-cpp-precomp -o .libs/t-cast t-cast.o -L/=20=
sw/lib ../../tests/.libs/libtests.a ../../.libs/libgmpxx.dylib /sw/=20
src/fink.build/gmp-4.1.4-2/gmp-4.1.4/.libs/libgmp.dylib -L/usr/lib/=20
gcc/darwin/3.3 -L/usr/lib/gcc/darwin -L/usr/libexec/gcc/darwin/ppc/=20
3.3/../../.. /usr/local/lib/libstdc++.a -L/Users/logan/Development/=20
CVS/1008/powerpc-apple-darwin6.1/libstdc++-v3/src -L/Users/logan/=20
Development/CVS/1008/powerpc-apple-darwin6.1/libstdc++-v3/src/.libs -=20
lm -lm -lm -L/Users/logan/Development/CVS/1008/gcc -L/usr/local/lib/=20
gcc-lib/powerpc-apple-darwin6.1/3.3 -L/usr/local/lib/gcc-lib/powerpc-=20
apple-darwin6.1/3.3/../../.. -lgcc -lSystem -L: -lm -lgcc -lSystem -=20
lgcc -lSystem ../../.libs/libgmp.dylib
ld: warning -L: directory name (/Users/logan/Development/CVS/1008/=20
powerpc-apple-darwin6.1/libstdc++-v3/src) does not exist
ld: warning -L: directory name (/Users/logan/Development/CVS/1008/=20
powerpc-apple-darwin6.1/libstdc++-v3/src/.libs) does not exist
ld: warning -L: directory name (/Users/logan/Development/CVS/1008/=20
gcc) does not exist
ld: warning -L: directory name (:) does not exist
ld: warning prebinding disabled because dependent library: /sw/lib/=20
libgmpxx.3.dylib is not prebound
creating t-cast
g++-3.3 -DHAVE_CONFIG_H -I. -I. -I../.. -I../.. -I../../tests -I/sw/=20
include -g -O2 -mpowerpc -no-cpp-precomp -c -o t-headers.o `test -f =20
t-headers.cc || echo './'`t-headers.cc
In file included from t-headers.cc:22:
../../gmpxx.h:2379: warning: use of `long double' type; its size may =20
change in
a future release
../../gmpxx.h:2379: warning: (Long double usage is reported only once =20=
for each
file.
../../gmpxx.h:2379: warning: To disable this warning, use -Wno-long-=20
double.)
/bin/sh ../../libtool --mode=3Dlink g++-3.3 -g -O2 -mpowerpc -no-cpp-=20=
precomp -L/sw/lib -o t-headers t-headers.o ../../tests/=20
libtests.la ../../libgmpxx.la ../../libgmp.la
g++-3.3 -g -O2 -mpowerpc -no-cpp-precomp -o .libs/t-headers t-=20
headers.o -L/sw/lib ../../tests/.libs/libtests.a ../../.libs/=20
libgmpxx.dylib /sw/src/fink.build/gmp-4.1.4-2/gmp-4.1.4/.libs/=20
libgmp.dylib -L/usr/lib/gcc/darwin/3.3 -L/usr/lib/gcc/darwin -L/usr/=20
libexec/gcc/darwin/ppc/3.3/../../.. /usr/local/lib/libstdc++.a -L/=20
Users/logan/Development/CVS/1008/powerpc-apple-darwin6.1/libstdc++-v3/=20=
src -L/Users/logan/Development/CVS/1008/powerpc-apple-darwin6.1/=20
libstdc++-v3/src/.libs -lm -lm -lm -L/Users/logan/Development/CVS/=20
1008/gcc -L/usr/local/lib/gcc-lib/powerpc-apple-darwin6.1/3.3 -L/usr/=20
local/lib/gcc-lib/powerpc-apple-darwin6.1/3.3/../../.. -lgcc -lSystem =20=
-L: -lm -lgcc -lSystem -lgcc -lSystem ../../.libs/libgmp.dylib
ld: warning -L: directory name (/Users/logan/Development/CVS/1008/=20
powerpc-apple-darwin6.1/libstdc++-v3/src) does not exist
ld: warning -L: directory name (/Users/logan/Development/CVS/1008/=20
powerpc-apple-darwin6.1/libstdc++-v3/src/.libs) does not exist
ld: warning -L: directory name (/Users/logan/Development/CVS/1008/=20
gcc) does not exist
ld: warning -L: directory name (:) does not exist
ld: warning prebinding disabled because dependent library: /sw/lib/=20
libgmpxx.3.dylib is not prebound
creating t-headers
g++-3.3 -DHAVE_CONFIG_H -I. -I. -I../.. -I../.. -I../../tests -I/sw/=20
include -g -O2 -mpowerpc -no-cpp-precomp -c -o t-ostream.o `test -f =20
t-ostream.cc || echo './'`t-ostream.cc
/bin/sh ../../libtool --mode=3Dlink g++-3.3 -g -O2 -mpowerpc -no-cpp-=20=
precomp -L/sw/lib -o t-ostream t-ostream.o ../../tests/=20
libtests.la ../../libgmpxx.la ../../libgmp.la
g++-3.3 -g -O2 -mpowerpc -no-cpp-precomp -o .libs/t-ostream t-=20
ostream.o -L/sw/lib ../../tests/.libs/libtests.a ../../.libs/=20
libgmpxx.dylib /sw/src/fink.build/gmp-4.1.4-2/gmp-4.1.4/.libs/=20
libgmp.dylib -L/usr/lib/gcc/darwin/3.3 -L/usr/lib/gcc/darwin -L/usr/=20
libexec/gcc/darwin/ppc/3.3/../../.. /usr/local/lib/libstdc++.a -L/=20
Users/logan/Development/CVS/1008/powerpc-apple-darwin6.1/libstdc++-v3/=20=
src -L/Users/logan/Development/CVS/1008/powerpc-apple-darwin6.1/=20
libstdc++-v3/src/.libs -lm -lm -lm -L/Users/logan/Development/CVS/=20
1008/gcc -L/usr/local/lib/gcc-lib/powerpc-apple-darwin6.1/3.3 -L/usr/=20
local/lib/gcc-lib/powerpc-apple-darwin6.1/3.3/../../.. -lgcc -lSystem =20=
-L: -lm -lgcc -lSystem -lgcc -lSystem ../../.libs/libgmp.dylib
ld: warning -L: directory name (/Users/logan/Development/CVS/1008/=20
powerpc-apple-darwin6.1/libstdc++-v3/src) does not exist
ld: warning -L: directory name (/Users/logan/Development/CVS/1008/=20
powerpc-apple-darwin6.1/libstdc++-v3/src/.libs) does not exist
ld: warning -L: directory name (/Users/logan/Development/CVS/1008/=20
gcc) does not exist
ld: warning -L: directory name (:) does not exist
ld: warning prebinding disabled because dependent library: /sw/lib/=20
libgmpxx.3.dylib is not prebound
ld: Undefined symbols:
virtual thunk to std::basic_istream<char, std::char_traits<char> =20
>::~basic_istream()
virtual thunk to std::basic_istream<char, std::char_traits<char> =20
>::~basic_istream()
virtual thunk to std::basic_ostream<char, std::char_traits<char> =20
>::~basic_ostream()
virtual thunk to std::basic_ostream<char, std::char_traits<char> =20
>::~basic_ostream()
make[3]: *** [t-ostream] Error 1
make[2]: *** [check-am] Error 2
make[1]: *** [check-recursive] Error 1
make: *** [check-recursive] Error 1
### execution of /var/tmp/tmp.5.gja4ng failed, exit code 2
Removing build lock...
/sw/bin/dpkg-lockwait -r fink-buildlock-gmp-4.1.4-2
(Reading database ... 22053 files and directories currently installed.)
Removing fink-buildlock-gmp-4.1.4-2 ...
Failed: phase compiling: gmp-4.1.4-2 failed
Before reporting any errors, please run "fink selfupdate" and
try again. If you continue to have issues, please check to see if the
FAQ on fink's website solves the problem. If not, ask on the fink-users
or fink-beginners mailing lists. As a last resort, you can try e-=20
mailing
the maintainer directly:
Dave Morrison <dm...@us...>
________________________
Jean-Christophe Am=E9, PhD
D=E9partement Int=E9grit=E9 du G=E9nome, UMR 7175-LC1 du CNRS
=C9cole Sup=E9rieure de Biotechnologie de Strasbourg
P=F4le API
Parc d'innovation, Boulevard S=E9bastien Brant
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67412 ILLKIRCH CEDEX
France
tel.: +33 (0)3 90 24 47 05
Fax.: +33 (0)3 90 24 46 86
http://parplink.u-strasbg.fr
http://www-esbs.u-strasbg.fr/centrerech/upr9003/upr9003.html
=AB Science sans conscience n'est que ruine de l'=E2me ...=BB (Fran=E7ois =
=20
Rabelais, 1483-1553)
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