ghemical build.log

ghemical_build.log (text/plain), 18.45 KB, created by Myckel Habets on 2010-08-12 19:31:05 UTC

 [32;01m*[0m CPV:  sci-chemistry/ghemical-2.01
 [32;01m*[0m REPO: gentoo
 [32;01m*[0m USE:  elibc_glibc kernel_linux test threads userland_GNU x86
Switching to xorg-x11 OpenGL interface... done
>>> Unpacking source...
>>> Unpacking ghemical-2.01.tar.gz to /var/tmp/portage/sci-chemistry/ghemical-2.01/work
>>> Source unpacked in /var/tmp/portage/sci-chemistry/ghemical-2.01/work
>>> Compiling source in /var/tmp/portage/sci-chemistry/ghemical-2.01/work/ghemical-2.01 ...
 * econf: updating ghemical-2.01/config.guess with /usr/share/gnuconfig/config.guess
 * econf: updating ghemical-2.01/config.sub with /usr/share/gnuconfig/config.sub
./configure --prefix=/usr --build=i686-pc-linux-gnu --host=i686-pc-linux-gnu --mandir=/usr/share/man --infodir=/usr/share/info --datadir=/usr/share --sysconfdir=/etc --localstatedir=/var/lib --disable-shortcuts --disable-openbabel --enable-threads --enable-gamess
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking build system type... i686-pc-linux-gnu
checking host system type... i686-pc-linux-gnu
checking for i686-pc-linux-gnu-gcc... i686-pc-linux-gnu-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 i686-pc-linux-gnu-gcc accepts -g... yes
checking for i686-pc-linux-gnu-gcc option to accept ANSI C... none needed
checking for style of include used by make... GNU
checking dependency style of i686-pc-linux-gnu-gcc... gcc3
checking for i686-pc-linux-gnu-g++... i686-pc-linux-gnu-g++
checking whether we are using the GNU C++ compiler... yes
checking whether i686-pc-linux-gnu-g++ accepts -g... yes
checking dependency style of i686-pc-linux-gnu-g++... gcc3
checking how to run the C preprocessor... i686-pc-linux-gnu-gcc -E
checking how to run the C++ preprocessor... i686-pc-linux-gnu-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 i686-pc-linux-gnu-gcc... /usr/i686-pc-linux-gnu/bin/ld
checking if the linker (/usr/i686-pc-linux-gnu/bin/ld) is GNU ld... yes
checking for /usr/i686-pc-linux-gnu/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... i686-pc-linux-gnu-g++ -E
checking for i686-pc-linux-gnu-g77... no
checking for i686-pc-linux-gnu-f77... no
checking for i686-pc-linux-gnu-xlf... no
checking for i686-pc-linux-gnu-frt... no
checking for i686-pc-linux-gnu-pgf77... no
checking for i686-pc-linux-gnu-fort77... no
checking for i686-pc-linux-gnu-fl32... no
checking for i686-pc-linux-gnu-af77... no
checking for i686-pc-linux-gnu-f90... no
checking for i686-pc-linux-gnu-xlf90... no
checking for i686-pc-linux-gnu-pgf90... no
checking for i686-pc-linux-gnu-epcf90... no
checking for i686-pc-linux-gnu-f95... no
checking for i686-pc-linux-gnu-fort... no
checking for i686-pc-linux-gnu-xlf95... no
checking for i686-pc-linux-gnu-ifc... no
checking for i686-pc-linux-gnu-efc... no
checking for i686-pc-linux-gnu-pgf95... no
checking for i686-pc-linux-gnu-lf95... no
checking for i686-pc-linux-gnu-gfortran... i686-pc-linux-gnu-gfortran
checking whether we are using the GNU Fortran 77 compiler... yes
checking whether i686-pc-linux-gnu-gfortran accepts -g... yes
checking the maximum length of command line arguments... 32768
checking command to parse /usr/bin/nm -B output from i686-pc-linux-gnu-gcc object... ok
checking for objdir... .libs
checking for i686-pc-linux-gnu-ar... i686-pc-linux-gnu-ar
checking for i686-pc-linux-gnu-ranlib... i686-pc-linux-gnu-ranlib
checking for i686-pc-linux-gnu-strip... i686-pc-linux-gnu-strip
checking for correct ltmain.sh version... yes
checking if i686-pc-linux-gnu-gcc supports -fno-rtti -fno-exceptions... no
checking for i686-pc-linux-gnu-gcc option to produce PIC... -fPIC
checking if i686-pc-linux-gnu-gcc PIC flag -fPIC works... yes
checking if i686-pc-linux-gnu-gcc static flag -static works... yes
checking if i686-pc-linux-gnu-gcc supports -c -o file.o... yes
checking whether the i686-pc-linux-gnu-gcc linker (/usr/i686-pc-linux-gnu/bin/ld) supports shared libraries... yes
checking whether -lc should be explicitly linked in... no
checking dynamic linker characteristics... cat: ld.so.conf.d/*.conf: No such file or directory
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 i686-pc-linux-gnu-g++... /usr/i686-pc-linux-gnu/bin/ld
checking if the linker (/usr/i686-pc-linux-gnu/bin/ld) is GNU ld... yes
checking whether the i686-pc-linux-gnu-g++ linker (/usr/i686-pc-linux-gnu/bin/ld) supports shared libraries... yes
checking for i686-pc-linux-gnu-g++ option to produce PIC... -fPIC
checking if i686-pc-linux-gnu-g++ PIC flag -fPIC works... yes
checking if i686-pc-linux-gnu-g++ static flag -static works... yes
checking if i686-pc-linux-gnu-g++ supports -c -o file.o... yes
checking whether the i686-pc-linux-gnu-g++ linker (/usr/i686-pc-linux-gnu/bin/ld) supports shared libraries... yes
checking dynamic linker characteristics... cat: ld.so.conf.d/*.conf: No such file or directory
GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
appending configuration tag "F77" to libtool
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... yes
checking for i686-pc-linux-gnu-gfortran option to produce PIC... -fPIC
checking if i686-pc-linux-gnu-gfortran PIC flag -fPIC works... yes
checking if i686-pc-linux-gnu-gfortran static flag -static works... yes
checking if i686-pc-linux-gnu-gfortran supports -c -o file.o... yes
checking whether the i686-pc-linux-gnu-gfortran linker (/usr/i686-pc-linux-gnu/bin/ld) supports shared libraries... yes
checking dynamic linker characteristics... cat: ld.so.conf.d/*.conf: No such file or directory
GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
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 i686-pc-linux-gnu-pkg-config... no
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... yes
checking for main in -lGLU... yes
checking for glutInit in -lglut... yes
checking for main in -lX11... yes
checking for main in -lXmu... yes
checking for main in -lXext... yes
checking for main in -lXi... yes
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: executing src/ghemicalconfig2.h commands
config.status: executing depfiles commands

build options:
^^^^^^^^^^^^^^
enable threads : yes
enable bonobo : no
enable OpenBabel : no
enable GAMESS : yes
enable shortcuts : no

make -j2 
Making all in docs
make[1]: Entering directory `/var/tmp/portage/sci-chemistry/ghemical-2.01/work/ghemical-2.01/docs'
Making all in user-docs
make[2]: Entering directory `/var/tmp/portage/sci-chemistry/ghemical-2.01/work/ghemical-2.01/docs/user-docs'
Making all in images
make[3]: Entering directory `/var/tmp/portage/sci-chemistry/ghemical-2.01/work/ghemical-2.01/docs/user-docs/images'
make[3]: Nothing to be done for `all'.
make[3]: Leaving directory `/var/tmp/portage/sci-chemistry/ghemical-2.01/work/ghemical-2.01/docs/user-docs/images'
make[3]: Entering directory `/var/tmp/portage/sci-chemistry/ghemical-2.01/work/ghemical-2.01/docs/user-docs'
make[3]: Nothing to be done for `all-am'.
make[3]: Leaving directory `/var/tmp/portage/sci-chemistry/ghemical-2.01/work/ghemical-2.01/docs/user-docs'
make[2]: Leaving directory `/var/tmp/portage/sci-chemistry/ghemical-2.01/work/ghemical-2.01/docs/user-docs'
make[2]: Entering directory `/var/tmp/portage/sci-chemistry/ghemical-2.01/work/ghemical-2.01/docs'
make[2]: Nothing to be done for `all-am'.
make[2]: Leaving directory `/var/tmp/portage/sci-chemistry/ghemical-2.01/work/ghemical-2.01/docs'
make[1]: Leaving directory `/var/tmp/portage/sci-chemistry/ghemical-2.01/work/ghemical-2.01/docs'
Making all in examples
make[1]: Entering directory `/var/tmp/portage/sci-chemistry/ghemical-2.01/work/ghemical-2.01/examples'
Making all in TSS
make[2]: Entering directory `/var/tmp/portage/sci-chemistry/ghemical-2.01/work/ghemical-2.01/examples/TSS'
Making all in carbocation_rearrangement_hydride_shift
make[3]: Entering directory `/var/tmp/portage/sci-chemistry/ghemical-2.01/work/ghemical-2.01/examples/TSS/carbocation_rearrangement_hydride_shift'
make[3]: Nothing to be done for `all'.
make[3]: Leaving directory `/var/tmp/portage/sci-chemistry/ghemical-2.01/work/ghemical-2.01/examples/TSS/carbocation_rearrangement_hydride_shift'
Making all in carbocation_rearrangement_methide_shift
make[3]: Entering directory `/var/tmp/portage/sci-chemistry/ghemical-2.01/work/ghemical-2.01/examples/TSS/carbocation_rearrangement_methide_shift'
make[3]: Nothing to be done for `all'.
make[3]: Leaving directory `/var/tmp/portage/sci-chemistry/ghemical-2.01/work/ghemical-2.01/examples/TSS/carbocation_rearrangement_methide_shift'
Making all in cycloaddition_Diels-Alder
make[3]: Entering directory `/var/tmp/portage/sci-chemistry/ghemical-2.01/work/ghemical-2.01/examples/TSS/cycloaddition_Diels-Alder'
make[3]: Nothing to be done for `all'.
make[3]: Leaving directory `/var/tmp/portage/sci-chemistry/ghemical-2.01/work/ghemical-2.01/examples/TSS/cycloaddition_Diels-Alder'
Making all in E2-reaction
make[3]: Entering directory `/var/tmp/portage/sci-chemistry/ghemical-2.01/work/ghemical-2.01/examples/TSS/E2-reaction'
make[3]: Nothing to be done for `all'.
make[3]: Leaving directory `/var/tmp/portage/sci-chemistry/ghemical-2.01/work/ghemical-2.01/examples/TSS/E2-reaction'
Making all in sigmatropic_rearrangement_Cope
make[3]: Entering directory `/var/tmp/portage/sci-chemistry/ghemical-2.01/work/ghemical-2.01/examples/TSS/sigmatropic_rearrangement_Cope'
make[3]: Nothing to be done for `all'.
make[3]: Leaving directory `/var/tmp/portage/sci-chemistry/ghemical-2.01/work/ghemical-2.01/examples/TSS/sigmatropic_rearrangement_Cope'
Making all in SN2-reaction
make[3]: Entering directory `/var/tmp/portage/sci-chemistry/ghemical-2.01/work/ghemical-2.01/examples/TSS/SN2-reaction'
make[3]: Nothing to be done for `all'.
make[3]: Leaving directory `/var/tmp/portage/sci-chemistry/ghemical-2.01/work/ghemical-2.01/examples/TSS/SN2-reaction'
Making all in tautomeric_shift_keto_enol
make[3]: Entering directory `/var/tmp/portage/sci-chemistry/ghemical-2.01/work/ghemical-2.01/examples/TSS/tautomeric_shift_keto_enol'
make[3]: Nothing to be done for `all'.
make[3]: Leaving directory `/var/tmp/portage/sci-chemistry/ghemical-2.01/work/ghemical-2.01/examples/TSS/tautomeric_shift_keto_enol'
make[3]: Entering directory `/var/tmp/portage/sci-chemistry/ghemical-2.01/work/ghemical-2.01/examples/TSS'
make[3]: Nothing to be done for `all-am'.
make[3]: Leaving directory `/var/tmp/portage/sci-chemistry/ghemical-2.01/work/ghemical-2.01/examples/TSS'
make[2]: Leaving directory `/var/tmp/portage/sci-chemistry/ghemical-2.01/work/ghemical-2.01/examples/TSS'
make[2]: Entering directory `/var/tmp/portage/sci-chemistry/ghemical-2.01/work/ghemical-2.01/examples'
make[2]: Nothing to be done for `all-am'.
make[2]: Leaving directory `/var/tmp/portage/sci-chemistry/ghemical-2.01/work/ghemical-2.01/examples'
make[1]: Leaving directory `/var/tmp/portage/sci-chemistry/ghemical-2.01/work/ghemical-2.01/examples'
Making all in src
make[1]: Entering directory `/var/tmp/portage/sci-chemistry/ghemical-2.01/work/ghemical-2.01/src'
make  all-am
make[2]: Entering directory `/var/tmp/portage/sci-chemistry/ghemical-2.01/work/ghemical-2.01/src'
if i686-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I. -I.   -pthread -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/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng14   -pthread -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/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng14 -I/usr/include/atk-1.0   -pthread -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 -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng14   -pthread -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include   -I/usr/include/ghemical    -march=athlon-xp -O2 -pipe -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
if i686-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I. -I.   -pthread -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/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng14   -pthread -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/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng14 -I/usr/include/atk-1.0   -pthread -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 -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng14   -pthread -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include   -I/usr/include/ghemical    -march=athlon-xp -O2 -pipe -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 fileio.cpp:10:
project.h:14:61: error: ghemical/libghemicalconfig2.h: No such file or directory
In file included from filetrans.cpp:10:
filetrans.h:13:61: error: ghemical/libghemicalconfig2.h: No such file or directory
make[2]: *** [filetrans.o] Error 1
make[2]: *** Waiting for unfinished jobs....
fileio.cpp: In function 'bool ReadGPR_v110(project&, std::istream&, bool, bool)':
fileio.cpp:468: error: no matching function for call to 'setup1_sf::setup1_sf(project*, bool)'
/usr/include/ghemical/eng1_sf.h:389: note: candidates are: setup1_sf::setup1_sf(model*, setup1_sf::SFmode, bool)
/usr/include/ghemical/eng1_sf.h:362: note:                 setup1_sf::setup1_sf(const setup1_sf&)
fileio.cpp: In function 'bool ReadGPR(project&, std::istream&, bool, bool)':
fileio.cpp:760: error: no matching function for call to 'setup1_sf::setup1_sf(project*, bool)'
/usr/include/ghemical/eng1_sf.h:389: note: candidates are: setup1_sf::setup1_sf(model*, setup1_sf::SFmode, bool)
/usr/include/ghemical/eng1_sf.h:362: note:                 setup1_sf::setup1_sf(const setup1_sf&)
fileio.cpp: In function 'void WriteGPR(project&, std::ostream&)':
fileio.cpp:944: error: 'class setup' has no member named 'GetClassName'
make[2]: *** [fileio.o] Error 1
make[2]: Leaving directory `/var/tmp/portage/sci-chemistry/ghemical-2.01/work/ghemical-2.01/src'
make[1]: *** [all] Error 2
make[1]: Leaving directory `/var/tmp/portage/sci-chemistry/ghemical-2.01/work/ghemical-2.01/src'
make: *** [all-recursive] Error 1
 [31;01m*[0m ERROR: sci-chemistry/ghemical-2.01 failed:
 [31;01m*[0m   make failed
 [31;01m*[0m 
 [31;01m*[0m Call stack:
 [31;01m*[0m     ebuild.sh, line  54:  Called src_compile
 [31;01m*[0m   environment, line 2299:  Called die
 [31;01m*[0m The specific snippet of code:
 [31;01m*[0m       emake || die "make failed"
 [31;01m*[0m 
 [31;01m*[0m If you need support, post the output of 'emerge --info =sci-chemistry/ghemical-2.01',
 [31;01m*[0m the complete build log and the output of 'emerge -pqv =sci-chemistry/ghemical-2.01'.
 [31;01m*[0m The complete build log is located at '/var/tmp/portage/sci-chemistry/ghemical-2.01/temp/build.log'.
 [31;01m*[0m The ebuild environment file is located at '/var/tmp/portage/sci-chemistry/ghemical-2.01/temp/environment'.
 [31;01m*[0m S: '/var/tmp/portage/sci-chemistry/ghemical-2.01/work/ghemical-2.01'