Package manager version: 0.24.23
Distribution version: 0.8.1.rsync powerpc
Upgrading from 10.4 transitional (unstable tree) to 10.4
(unstable tree) was without any problem except for coot and
xdrawchem.
coot:
end of compilation:
w.a /sw/share/xtal/ccp4-onlylibs-dev-6.0/lib/libfftw.a -lz -lmmdb
-L/sw/lib /sw/lib/libgsl.dylib /sw/lib/libgslcblas.dylib -lm
/usr/bin/ld: Undefined symbols:
typeinfo for CMMDBManager
collect2: ld returned 1 exit status
make[1]: *** [with-geometry] Error 1
make: *** [all-recursive] Error 1
### execution of /var/tmp/tmp.2.59mZHO failed, exit code 2
Removing build lock...
/sw/bin/dpkg-lockwait -r fink-buildlock-coot-0.1.1-1002
(Lecture de la base de donn'ees... 120978 fichiers et r'epertoires d'ej`a install'es.)
Suppression de fink-buildlock-coot-0.1.1-1002 ...
Failed: phase compiling: coot-0.1.1-1002 failed
/usr/bin/ld: Undefined symbols:
typeinfo for CMMDBManager
collect2: ld returned 1 exit status
make[1]: *** [with-geometry] Error 1
make: *** [all-recursive] Error 1
### execution of /var/tmp/tmp.2.59mZHO failed, exit code 2
Removing build lock...
/sw/bin/dpkg-lockwait -r fink-buildlock-coot-0.1.1-1002
(Lecture de la base de donn'ees... 120978 fichiers et r'epertoires d'ej`a install'es.)
Suppression de fink-buildlock-coot-0.1.1-1002 ...
Failed: phase compiling: coot-0.1.1-1002 failed
......
and also relevant (?) part of config.log
...
configure:2840: $? = 1
configure: failed program was:
| #ifndef __cplusplus
| choke me
| #endif
configure:2975: checking dependency style of gcc
configure: failed program was:
| #ifndef __cplusplus
| choke me
| #endif
configure:2975: checking dependency style of gcc
configure:3065: result: gcc3
......
configure: failed program was:
| /* confdefs.h. */
|
| #define PACKAGE_NAME ""
| #define PACKAGE_TARNAME ""
| #define PACKAGE_VERSION ""
| #define PACKAGE_STRING ""
| #define PACKAGE_BUGREPORT ""
| #define PACKAGE "coot"
| #define VERSION "0.1.1"
| /* end confdefs.h. */
| #include <ac_nonexistent.h>
configure:5011: result: gcc -E
configure:5035: gcc -E -I/sw/share/xtal/c
| /* confdefs.h. */
|
| #define PACKAGE_NAME ""
| #define PACKAGE_TARNAME ""
| #define PACKAGE_VERSION ""
| #define PACKAGE_STRING ""
| #define PACKAGE_BUGREPORT ""
| #define PACKAGE "coot"
| #define VERSION "0.1.1"
| /* end confdefs.h. */
| #include <ac_nonexistent.h>
configure:5011: result: gcc -E
configure:5035: gcc -E -I/sw/share/xtal/c
.....
configure: failed program was:
| /* confdefs.h. */
|
| #define PACKAGE_NAME ""
| #define PACKAGE_TARNAME ""
| #define PACKAGE_VERSION ""
| #define PACKAGE_STRING ""
| #define PACKAGE_BUGREPORT ""
| #define PACKAGE "coot"
| #define VERSION "0.1.1"
| #define STDC_HEADERS 1
| /* end confdefs.h. */
|
| int
| main ()
| {
| exit (42);
| ;
| return 0;
| }
configure:5570: g++ -c -g -O2 -I/sw/share/xtal/ccp4-onlylibs-dev-6.0/lib/clipper/clipper/mmdbold conftest.cc >&5
/usr/include/stdlib.h:158: error: declaration of 'void std::exit(int)' throws different exceptions
conftest.cc:12: error: than previous declaration 'void std::exit(int) throw ()'
configure:5576: $? = 1
| /* confdefs.h. */
|
| #define PACKAGE_NAME ""
| #define PACKAGE_TARNAME ""
| #define PACKAGE_VERSION ""
| #define PACKAGE_STRING ""
| #define PACKAGE_BUGREPORT ""
| #define PACKAGE "coot"
| #define VERSION "0.1.1"
| #define STDC_HEADERS 1
| /* end confdefs.h. */
|
| int
| main ()
| {
| exit (42);
| ;
| return 0;
| }
configure:5570: g++ -c -g -O2 -I/sw/share/xtal/ccp4-onlylibs-dev-6.0/lib/clipper/clipper/mmdbold conftest.cc >&5
/usr/include/stdlib.h:158: error: declaration of 'void std::exit(int)' throws different exceptions
conftest.cc:12: error: than previous declaration 'void std::exit(int) throw ()'
configure:5576: $? = 1
...........
and for xdrawchem:
end of compilation:
......
de/qt -D_REENTRANT -DQT_THREAD_SUPPORT -g -O2 -c -o
application_ring.o `test -f 'application_ring.cpp' || echo
'./'`application_ring.cpp
application_ring.cpp: In member function 'QPopupMenu* ApplicationWindow::BuildCustomRingMenu()':
application_ring.cpp:357: warning: comparison between signed and unsigned integer expressions
g++ -DHAVE_CONFIG_H -I. -I. -I.. -Wall -I/usr/X11R6/include -DUNIX -DRINGHOME="\"/sw/share/xdrawchem/\"" -DXDC_SERVER=\"www.xdrawchem.org\" -I/sw/include/openbabel -I/sw/include -g -I/sw/include/qt -D_REENTRANT -DQT_THREAD_SUPPORT -g -O2 -c -o arrow.o `test -f 'arrow.cpp' || echo './'`arrow.cpp
g++ -DHAVE_CONFIG_H -I. -I. -I.. -Wall -I/usr/X11R6/include -DUNIX -DRINGHOME="\"/sw/share/xdrawchem/\"" -DXDC_SERVER=\"www.xdrawchem.org\" -I/sw/include/openbabel -I/sw/include -g -I/sw/include/qt -D_REENTRANT -DQT_THREAD_SUPPORT -g -O2 -c -o bond.o `test -f 'bond.cpp' || echo './'`bond.cpp
g++ -DHAVE_CONFIG_H -I. -I. -I.. -Wall -I/usr/X11R6/include -DUNIX -DRINGHOME="\"/sw/share/xdrawchem/\"" -DXDC_SERVER=\"www.xdrawchem.org\" -I/sw/include/openbabel -I/sw/include -g -I/sw/include/qt -D_REENTRANT -DQT_THREAD_SUPPORT -g -O2 -c -o bondedit.o `test -f 'bondedit.cpp' || echo './'`bondedit.cpp
application_ring.cpp: In member function 'QPopupMenu* ApplicationWindow::BuildCustomRingMenu()':
application_ring.cpp:357: warning: comparison between signed and unsigned integer expressions
g++ -DHAVE_CONFIG_H -I. -I. -I.. -Wall -I/usr/X11R6/include -DUNIX -DRINGHOME="\"/sw/share/xdrawchem/\"" -DXDC_SERVER=\"www.xdrawchem.org\" -I/sw/include/openbabel -I/sw/include -g -I/sw/include/qt -D_REENTRANT -DQT_THREAD_SUPPORT -g -O2 -c -o arrow.o `test -f 'arrow.cpp' || echo './'`arrow.cpp
g++ -DHAVE_CONFIG_H -I. -I. -I.. -Wall -I/usr/X11R6/include -DUNIX -DRINGHOME="\"/sw/share/xdrawchem/\"" -DXDC_SERVER=\"www.xdrawchem.org\" -I/sw/include/openbabel -I/sw/include -g -I/sw/include/qt -D_REENTRANT -DQT_THREAD_SUPPORT -g -O2 -c -o bond.o `test -f 'bond.cpp' || echo './'`bond.cpp
g++ -DHAVE_CONFIG_H -I. -I. -I.. -Wall -I/usr/X11R6/include -DUNIX -DRINGHOME="\"/sw/share/xdrawchem/\"" -DXDC_SERVER=\"www.xdrawchem.org\" -I/sw/include/openbabel -I/sw/include -g -I/sw/include/qt -D_REENTRANT -DQT_THREAD_SUPPORT -g -O2 -c -o bondedit.o `test -f 'bondedit.cpp' || echo './'`bondedit.cpp
g++ -DHAVE_CONFIG_H -I. -I. -I.. -Wall -I/usr/X11R6/include
-DUNIX -DRINGHOME="\"/sw/share/xdrawchem/\""
-DXDC_SERVER=\"www.xdrawchem.org\"
-I/sw/include/openbabel -I/sw/include -g -I/sw/include/qt
-D_REENTRANT -DQT_THREAD_SUPPORT -g -O2 -c -o boshcp.o `test -f
'boshcp.cpp' || echo './'`boshcp.cpp
compilation hanged up there and I had to interrupt it with
^C .
......
and relevant (?) part of config.log
......
configure:2471: g++ -c -g -O2 -I/sw/include conftest.cc
>&5
configure: In function 'int main()':
configure: In function 'int main()':
configure:2468: error: 'exit' was not declared in this scope
configure:2474: $? = 1
configure: failed program was:
| #line 2454 "configure"
| /* confdefs.h. */
|
| #define PACKAGE_NAME "xdrawchem"
| #define PACKAGE_TARNAME "xdrawchem"
| #define PACKAGE_VERSION "1.9.4"
| #define PACKAGE_STRING "xdrawchem 1.9.4"
| #define PACKAGE_BUGREPORT "[EMAIL PROTECTED]"
| #define PACKAGE "xdrawchem"
| #define VERSION "1.9.4"
| /* end confdefs.h. */
|
| int
| main ()
| {
| exit (42);
| ;
| return 0;
| }
configure:2435: g++ -c -g -O2 -I/sw/include conftest.cc >&5
configure:2474: $? = 1
configure: failed program was:
| #line 2454 "configure"
| /* confdefs.h. */
|
| #define PACKAGE_NAME "xdrawchem"
| #define PACKAGE_TARNAME "xdrawchem"
| #define PACKAGE_VERSION "1.9.4"
| #define PACKAGE_STRING "xdrawchem 1.9.4"
| #define PACKAGE_BUGREPORT "[EMAIL PROTECTED]"
| #define PACKAGE "xdrawchem"
| #define VERSION "1.9.4"
| /* end confdefs.h. */
|
| int
| main ()
| {
| exit (42);
| ;
| return 0;
| }
configure:2435: g++ -c -g -O2 -I/sw/include conftest.cc >&5
configure:2438: $? = 0
.....
and also
.....
target_alias=''
top_builddir='/sw/src/fink.build/xdrawchem-1.9.5-1010/xdrawchem-1.9.5'
## ----------- ##
## confdefs.h. ##
## ----------- ##
#define HAVE_DLFCN_H 1
#define HAVE_ERRNO_H 1
#define HAVE_FLOOR 1
#define HAVE_INTTYPES_H 1
#define HAVE_MALLOC 1
#define HAVE_MEMORY_H 1
#define HAVE_POW 1
#define HAVE_SQRT 1
#define HAVE_STDINT_H 1
#define HAVE_STDLIB_H 1
#define HAVE_STDLIB_H 1
#define HAVE_STDLIB_H 1
#define HAVE_STRINGS_H 1
#define HAVE_STRING_H 1
#define HAVE_SYS_STAT_H 1
#define HAVE_SYS_TYPES_H 1
#define HAVE_UNISTD_H 1
#define HAVE_UNISTD_H 1
#define PACKAGE "xdrawchem"
#define PACKAGE_BUGREPORT "[EMAIL PROTECTED]"
#define PACKAGE_NAME "xdrawchem"
#define PACKAGE_STRING "xdrawchem 1.9.4"
#define PACKAGE_TARNAME "xdrawchem"
#define PACKAGE_VERSION "1.9.4"
#define STDC_HEADERS 1
#define STDC_HEADERS 1
#define VERSION "1.9.4"
#endif
#ifdef __cplusplus
#include <stdlib.h>
configure: exit 0
## ---------------------- ##
## Running config.status. ##
## ---------------------- ##
This file was extended by xdrawchem config.status 1.9.4, which was
generated by GNU Autoconf 2.57. Invocation command line was
CONFIG_FILES =
CONFIG_HEADERS =
CONFIG_LINKS =
CONFIG_COMMANDS =
$ ./config.status config.h
on chamaerops.ibgc.u-bordeaux2.fr
config.status:792: creating config.h
top_builddir='/sw/src/fink.build/xdrawchem-1.9.5-1010/xdrawchem-1.9.5'
## ----------- ##
## confdefs.h. ##
## ----------- ##
#define HAVE_DLFCN_H 1
#define HAVE_ERRNO_H 1
#define HAVE_FLOOR 1
#define HAVE_INTTYPES_H 1
#define HAVE_MALLOC 1
#define HAVE_MEMORY_H 1
#define HAVE_POW 1
#define HAVE_SQRT 1
#define HAVE_STDINT_H 1
#define HAVE_STDLIB_H 1
#define HAVE_STDLIB_H 1
#define HAVE_STDLIB_H 1
#define HAVE_STRINGS_H 1
#define HAVE_STRING_H 1
#define HAVE_SYS_STAT_H 1
#define HAVE_SYS_TYPES_H 1
#define HAVE_UNISTD_H 1
#define HAVE_UNISTD_H 1
#define PACKAGE "xdrawchem"
#define PACKAGE_BUGREPORT "[EMAIL PROTECTED]"
#define PACKAGE_NAME "xdrawchem"
#define PACKAGE_STRING "xdrawchem 1.9.4"
#define PACKAGE_TARNAME "xdrawchem"
#define PACKAGE_VERSION "1.9.4"
#define STDC_HEADERS 1
#define STDC_HEADERS 1
#define VERSION "1.9.4"
#endif
#ifdef __cplusplus
#include <stdlib.h>
configure: exit 0
## ---------------------- ##
## Running config.status. ##
## ---------------------- ##
This file was extended by xdrawchem config.status 1.9.4, which was
generated by GNU Autoconf 2.57. Invocation command line was
CONFIG_FILES =
CONFIG_HEADERS =
CONFIG_LINKS =
CONFIG_COMMANDS =
$ ./config.status config.h
on chamaerops.ibgc.u-bordeaux2.fr
config.status:792: creating config.h
Any idea?
--
**********************************************************
Guy Lauquin.
IBGC/CNRS 1 rue C. St. Saens, 33077 Bordeaux-cedex France
tel.(33) 556 99 90 37 fax: (33) 556 99 90 63
e-mail: [EMAIL PROTECTED]
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