[ghemical-devel] Ghemical Crash
Jason Rigby
sirjasonr at gmail.com
Wed May 17 08:08:19 EDT 2006
Thanks for the reply Tommi,
I tried to compile Ghemical 2.01 but, as always, I ran into some issues.....
Below is the output from ./configure (further down is output from make)
jdrig2-wired-self:/home/jason/Desktop/ghemical-2.01# ./configure
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for gawk... no
checking for mawk... mawk
checking whether make sets $(MAKE)... yes
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ANSI C... none needed
checking for style of include used by make... GNU
checking dependency style of gcc... gcc3
checking for g++... g++
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking dependency style of g++... gcc3
checking how to run the C preprocessor... gcc -E
checking how to run the C++ preprocessor... g++ -E
checking for a BSD-compatible install... /usr/bin/install -c
checking for a sed that does not truncate output... /bin/sed
checking for egrep... grep -E
checking for ld used by gcc... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for /usr/bin/ld option to reload object files... -r
checking for BSD-compatible nm... /usr/bin/nm -B
checking whether ln -s works... yes
checking how to recognise dependent libraries... pass_all
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking dlfcn.h usability... yes
checking dlfcn.h presence... yes
checking for dlfcn.h... yes
checking how to run the C++ preprocessor... g++ -E
checking for g77... no
checking for f77... no
checking for xlf... no
checking for frt... no
checking for pgf77... no
checking for fort77... no
checking for fl32... no
checking for af77... no
checking for f90... no
checking for xlf90... no
checking for pgf90... no
checking for epcf90... no
checking for f95... no
checking for fort... no
checking for xlf95... no
checking for ifc... no
checking for efc... no
checking for pgf95... no
checking for lf95... no
checking for gfortran... no
checking whether we are using the GNU Fortran 77 compiler... no
checking whether accepts -g... no
checking the maximum length of command line arguments... 32768
checking command to parse /usr/bin/nm -B output from gcc object... ok
checking for objdir... .libs
checking for ar... ar
checking for ranlib... ranlib
checking for strip... strip
checking for correct ltmain.sh version... yes
checking if gcc supports -fno-rtti -fno-exceptions... no
checking for gcc option to produce PIC... -fPIC
checking if gcc PIC flag -fPIC works... yes
checking if gcc static flag -static works... yes
checking if gcc supports -c -o file.o... yes
checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports
shared libraries... yes
checking whether -lc should be explicitly linked in... no
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... yes
configure: creating libtool
appending configuration tag "CXX" to libtool
checking for ld used by g++... /usr/bin/ld -m elf_x86_64
checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes
checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports
shared libraries... yes
checking for g++ option to produce PIC... -fPIC
checking if g++ PIC flag -fPIC works... yes
checking if g++ static flag -static works... yes
checking if g++ supports -c -o file.o... yes
checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports
shared libraries... yes
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
appending configuration tag "F77" to libtool
checking for ar... /usr/bin/ar
checking for sh... /bin/sh
checking whether make sets $(MAKE)... (cached) yes
checking whether build environment is sane... yes
checking for acos in -lm... yes
checking for pkg-config... /usr/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for GTK... yes
checking for GTKGLEXT... yes
checking for LIBGLADE... yes
checking for GTHREAD... yes
checking for LIBGHEMICAL... yes
checking for glMatrixMode in -lGL... no
checking for main in -lGLU... no
checking for glutInit in -lglut... no
checking for main in -lX11... no
checking for main in -lXmu... no
checking for main in -lXext... no
checking for main in -lXi... no
checking GL/glut.h usability... yes
checking GL/glut.h presence... yes
checking for GL/glut.h... yes
checking for an ANSI C-conforming const... yes
checking for inline... inline
checking for ANSI C header files... (cached) yes
configure: creating ./config.status
config.status: creating Makefile
config.status: creating docs/Makefile
config.status: creating docs/user-docs/Makefile
config.status: creating docs/user-docs/images/Makefile
config.status: creating examples/Makefile
config.status: creating examples/TSS/Makefile
config.status: creating
examples/TSS/carbocation_rearrangement_hydride_shift/Makefile
config.status: creating
examples/TSS/carbocation_rearrangement_methide_shift/Makefile
config.status: creating examples/TSS/cycloaddition_Diels-Alder/Makefile
config.status: creating examples/TSS/E2-reaction/Makefile
config.status: creating examples/TSS/sigmatropic_rearrangement_Cope/Makefile
config.status: creating examples/TSS/SN2-reaction/Makefile
config.status: creating examples/TSS/tautomeric_shift_keto_enol/Makefile
config.status: creating src/Makefile
config.status: creating src/ghemicalconfig.h
config.status: src/ghemicalconfig.h is unchanged
config.status: executing src/ghemicalconfig2.h commands
config.status: executing depfiles commands
build options:
^^^^^^^^^^^^^^
enable threads : yes
enable bonobo : no
enable OpenBabel : no
enable GAMESS : no
enable shortcuts : no
And here is the output from make.....
Making all in docs
make[1]: Entering directory `/home/jason/Desktop/ghemical-2.01/docs'
Making all in user-docs
make[2]: Entering directory `/home/jason/Desktop/ghemical-2.01/docs/user-docs'
Making all in images
make[3]: Entering directory
`/home/jason/Desktop/ghemical-2.01/docs/user-docs/images'
make[3]: Nothing to be done for `all'.
make[3]: Leaving directory
`/home/jason/Desktop/ghemical-2.01/docs/user-docs/images'
make[3]: Entering directory `/home/jason/Desktop/ghemical-2.01/docs/user-docs'
make[3]: Nothing to be done for `all-am'.
make[3]: Leaving directory `/home/jason/Desktop/ghemical-2.01/docs/user-docs'
make[2]: Leaving directory `/home/jason/Desktop/ghemical-2.01/docs/user-docs'
make[2]: Entering directory `/home/jason/Desktop/ghemical-2.01/docs'
make[2]: Nothing to be done for `all-am'.
make[2]: Leaving directory `/home/jason/Desktop/ghemical-2.01/docs'
make[1]: Leaving directory `/home/jason/Desktop/ghemical-2.01/docs'
Making all in examples
make[1]: Entering directory `/home/jason/Desktop/ghemical-2.01/examples'
Making all in TSS
make[2]: Entering directory `/home/jason/Desktop/ghemical-2.01/examples/TSS'
Making all in carbocation_rearrangement_hydride_shift
make[3]: Entering directory
`/home/jason/Desktop/ghemical-2.01/examples/TSS/carbocation_rearrangement_hydride_shift'
make[3]: Nothing to be done for `all'.
make[3]: Leaving directory
`/home/jason/Desktop/ghemical-2.01/examples/TSS/carbocation_rearrangement_hydride_shift'
Making all in carbocation_rearrangement_methide_shift
make[3]: Entering directory
`/home/jason/Desktop/ghemical-2.01/examples/TSS/carbocation_rearrangement_methide_shift'
make[3]: Nothing to be done for `all'.
make[3]: Leaving directory
`/home/jason/Desktop/ghemical-2.01/examples/TSS/carbocation_rearrangement_methide_shift'
Making all in cycloaddition_Diels-Alder
make[3]: Entering directory
`/home/jason/Desktop/ghemical-2.01/examples/TSS/cycloaddition_Diels-Alder'
make[3]: Nothing to be done for `all'.
make[3]: Leaving directory
`/home/jason/Desktop/ghemical-2.01/examples/TSS/cycloaddition_Diels-Alder'
Making all in E2-reaction
make[3]: Entering directory
`/home/jason/Desktop/ghemical-2.01/examples/TSS/E2-reaction'
make[3]: Nothing to be done for `all'.
make[3]: Leaving directory
`/home/jason/Desktop/ghemical-2.01/examples/TSS/E2-reaction'
Making all in sigmatropic_rearrangement_Cope
make[3]: Entering directory
`/home/jason/Desktop/ghemical-2.01/examples/TSS/sigmatropic_rearrangement_Cope'
make[3]: Nothing to be done for `all'.
make[3]: Leaving directory
`/home/jason/Desktop/ghemical-2.01/examples/TSS/sigmatropic_rearrangement_Cope'
Making all in SN2-reaction
make[3]: Entering directory
`/home/jason/Desktop/ghemical-2.01/examples/TSS/SN2-reaction'
make[3]: Nothing to be done for `all'.
make[3]: Leaving directory
`/home/jason/Desktop/ghemical-2.01/examples/TSS/SN2-reaction'
Making all in tautomeric_shift_keto_enol
make[3]: Entering directory
`/home/jason/Desktop/ghemical-2.01/examples/TSS/tautomeric_shift_keto_enol'
make[3]: Nothing to be done for `all'.
make[3]: Leaving directory
`/home/jason/Desktop/ghemical-2.01/examples/TSS/tautomeric_shift_keto_enol'
make[3]: Entering directory `/home/jason/Desktop/ghemical-2.01/examples/TSS'
make[3]: Nothing to be done for `all-am'.
make[3]: Leaving directory `/home/jason/Desktop/ghemical-2.01/examples/TSS'
make[2]: Leaving directory `/home/jason/Desktop/ghemical-2.01/examples/TSS'
make[2]: Entering directory `/home/jason/Desktop/ghemical-2.01/examples'
make[2]: Nothing to be done for `all-am'.
make[2]: Leaving directory `/home/jason/Desktop/ghemical-2.01/examples'
make[1]: Leaving directory `/home/jason/Desktop/ghemical-2.01/examples'
Making all in src
make[1]: Entering directory `/home/jason/Desktop/ghemical-2.01/src'
make all-am
make[2]: Entering directory `/home/jason/Desktop/ghemical-2.01/src'
if g++ -DHAVE_CONFIG_H -I. -I. -I. -I/usr/include/gtk-2.0
-I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo
-I/usr/include/pango-1.0 -I/usr/include/glib-2.0
-I/usr/lib/glib-2.0/include -I/usr/include/gtkglext-1.0
-I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0
-I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0
-I/usr/include/cairo -I/usr/include/glib-2.0
-I/usr/lib/glib-2.0/include -I/usr/include/atk-1.0
-I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0
-I/usr/include/libxml2 -I/usr/lib/gtk-2.0/include
-I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0
-I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -pthread
-I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include
-I/usr/include/ghemical -I/usr/include/sc -g -O2 -MT fileio.o -MD
-MP -MF ".deps/fileio.Tpo" -c -o fileio.o fileio.cpp; \
then mv -f ".deps/fileio.Tpo" ".deps/fileio.Po"; else rm -f
".deps/fileio.Tpo"; exit 1; fi
In file included from filetrans.h:14,
from project.h:51,
from fileio.cpp:10:
ghemicalconfig2.h:103:1: warning: "VERSION" redefined
In file included from filetrans.h:13,
from project.h:51,
from fileio.cpp:10:
/usr/include/ghemical/libghemicalconfig2.h:88:1: warning: this is the
location of the previous definition
if g++ -DHAVE_CONFIG_H -I. -I. -I. -I/usr/include/gtk-2.0
-I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo
-I/usr/include/pango-1.0 -I/usr/include/glib-2.0
-I/usr/lib/glib-2.0/include -I/usr/include/gtkglext-1.0
-I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0
-I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0
-I/usr/include/cairo -I/usr/include/glib-2.0
-I/usr/lib/glib-2.0/include -I/usr/include/atk-1.0
-I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0
-I/usr/include/libxml2 -I/usr/lib/gtk-2.0/include
-I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0
-I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -pthread
-I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include
-I/usr/include/ghemical -I/usr/include/sc -g -O2 -MT filetrans.o
-MD -MP -MF ".deps/filetrans.Tpo" -c -o filetrans.o filetrans.cpp; \
then mv -f ".deps/filetrans.Tpo" ".deps/filetrans.Po"; else rm
-f ".deps/filetrans.Tpo"; exit 1; fi
In file included from filetrans.h:14,
from filetrans.cpp:10:
ghemicalconfig2.h:103:1: warning: "VERSION" redefined
In file included from filetrans.h:13,
from filetrans.cpp:10:
/usr/include/ghemical/libghemicalconfig2.h:88:1: warning: this is the
location of the previous definition
if g++ -DHAVE_CONFIG_H -I. -I. -I. -I/usr/include/gtk-2.0
-I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo
-I/usr/include/pango-1.0 -I/usr/include/glib-2.0
-I/usr/lib/glib-2.0/include -I/usr/include/gtkglext-1.0
-I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0
-I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0
-I/usr/include/cairo -I/usr/include/glib-2.0
-I/usr/lib/glib-2.0/include -I/usr/include/atk-1.0
-I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0
-I/usr/include/libxml2 -I/usr/lib/gtk-2.0/include
-I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0
-I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -pthread
-I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include
-I/usr/include/ghemical -I/usr/include/sc -g -O2 -MT project.o -MD
-MP -MF ".deps/project.Tpo" -c -o project.o project.cpp; \
then mv -f ".deps/project.Tpo" ".deps/project.Po"; else rm -f
".deps/project.Tpo"; exit 1; fi
In file included from filetrans.h:14,
from project.h:51,
from project.cpp:10:
ghemicalconfig2.h:103:1: warning: "VERSION" redefined
In file included from filetrans.h:13,
from project.h:51,
from project.cpp:10:
/usr/include/ghemical/libghemicalconfig2.h:88:1: warning: this is the
location of the previous definition
if g++ -DHAVE_CONFIG_H -I. -I. -I. -I/usr/include/gtk-2.0
-I/usr/lib/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo
-I/usr/include/pango-1.0 -I/usr/include/glib-2.0
-I/usr/lib/glib-2.0/include -I/usr/include/gtkglext-1.0
-I/usr/lib/gtkglext-1.0/include -I/usr/include/gtk-2.0
-I/usr/lib/gtk-2.0/include -I/usr/include/pango-1.0
-I/usr/include/cairo -I/usr/include/glib-2.0
-I/usr/lib/glib-2.0/include -I/usr/include/atk-1.0
-I/usr/include/libglade-2.0 -I/usr/include/gtk-2.0
-I/usr/include/libxml2 -I/usr/lib/gtk-2.0/include
-I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/pango-1.0
-I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -pthread
-I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include
-I/usr/include/ghemical -I/usr/include/sc -g -O2 -MT views.o -MD
-MP -MF ".deps/views.Tpo" -c -o views.o views.cpp; \
then mv -f ".deps/views.Tpo" ".deps/views.Po"; else rm -f
".deps/views.Tpo"; exit 1; fi
In file included from filetrans.h:14,
from project.h:51,
from views.h:41,
from views.cpp:10:
ghemicalconfig2.h:103:1: warning: "VERSION" redefined
In file included from filetrans.h:13,
from project.h:51,
from views.h:41,
from views.cpp:10:
/usr/include/ghemical/libghemicalconfig2.h:88:1: warning: this is the
location of the previous definition
views.cpp: In function 'void* convert_cset_to_plotting_udata(project*, i32s)':
views.cpp:260: error: cast from 'void*' to 'i32u' loses precision
views.cpp: In function 'void apply_udata_as_cset(project*, void*)':
views.cpp:281: error: cast from 'void*' to 'i32u' loses precision
make[2]: *** [views.o] Error 1
make[2]: Leaving directory `/home/jason/Desktop/ghemical-2.01/src'
make[1]: *** [all] Error 2
make[1]: Leaving directory `/home/jason/Desktop/ghemical-2.01/src'
make: *** [all-recursive] Error 1
Again, any help would be appreciated!
Thanks,
Jason
On 17/05/06, Tommi Hassinen <thassine at messi.uku.fi> wrote:
> On Wed, 17 May 2006, Jason Rigby wrote:
>
> > This error occurs if I click the black area where you draw the
> > molecule straight after opening the application - it crashes straight
> > away. If I select the draw tool and attempt to place an atom, this
> > error is generated:
>
> > The version of Ghemical is 1.91.
>
> Hello, the above is a known problem of 1.9x versions on 64 bit systems.
> The only fix is upgrading to v2.0x versions.
>
> > Also, is there a precompiled deb available for AMD64 of the new 2.01
> > version of ghemical?
>
> Sorry, can't help with this one.
>
> Regards,
>
> Tommi
>
>
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