Hi Tim, Thanks for your help.
I am wiping all signs of the previous autobuild when I attempt a new autobuild, and doing so again yields the same error. Perhaps someone else on this platform could have a go at compiling it? http://lmb.bioch.ox.ac.uk/coot/devel/build-info.html shows the same system failing, though in the log files the build seems to complete satisfactorily. Amadeus -----Original Message----- From: Tim Gruene [mailto:[email protected]] Sent: 30 November 2012 09:18 To: Amadeus Stevenson Cc: [email protected] Subject: Re: Autobuilding coot 0.7 fails on coot (Ubuntu 12.04 x64) -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hi Amadeus, I see such errors when I did not do a proper "make clean" or "make distclean", i.e. when compiling parts of the system with one build setup and another part with a new one. I would suggest to install the python developers packages - with Debian it is called python2.7-dev, and I guess with Ubuntu it would be similar. In your previous mail you did not mention "Python.h", and once you have the header it's a good sign your system is ready to compile python-related code. Best, Tim On 11/29/2012 09:10 PM, Amadeus Stevenson wrote: > Apologies for another message, but a modification of the autobuild > command to run > > export AUTOBUILD_INSTALLED=/data/software/coot export > AUTOBUILD_BUILD=/tmp/autobuild export LOGS=$AUTOBUILD_BUILD/logs > export build_coot_prerelease=0 bash build-it-gtk2-simple python > > build.log > > gets me a little further. > > Coot is now failing to compile with: > > /bin/bash ../libtool --tag=CXX --mode=link g++ > -DPKGDATADIR='"/data/software/coot-gtk2-python/share/coot"' > -DPACKAGE_LOCALE_DIR='"/data/software/coot-gtk2-python/share/coot/locale"' > -DDATADIR='"/data/software/coot-gtk2-python/share"' > -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-ubuntu-12.04.1-python-gtk2"' > -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK > -I/data/software/coot-gtk2-python/include -P -pthread -DUSE_PYTHON > -I/data/software/coot-gtk2-python/include/python2.7 > -I/data/software/coot-gtk2-python/include/python2.7 -DUSE_PYGTK > -DHAVE_GSL -fopenmp -g -O -o coot-real main.o svn-revision.o > c-inner-main.o c-interface-analysis.o c-interface-build.o > c-interface-build-gui.o c-interface-database.o c-interface-gui.o > c-interface-gtk2.o c-interface-info.o c-interface-kk.o > c-interface-ligands.o c-interface-ligands-gui.o c-interface-maps.o > c-interface-mmdb.o c-interface-mogul.o c-interface-mutate.o > c-interface-ncs.o c-interface-network.o c-interface-nucleotides.o > c-interface-python.o c-interface-pisa.o c-interface-pisa-gui.o > c-interface-preferences.o c-interface-refine.o c-interface-residues.o > c-interface-scm.o c-interface-sfs.o c-interface-superpose.o > c-interface-validate.o c-interface-view.o c-interface-widgets.o > c-interface-waters.o c-interface-waters-gui.o c-interface.o > c-interface-test.o callbacks.o cmtz-interface.o command-line.o > coot-colour.o coot-align.o coot-nomenclature.o coot-glue.o > coot-glue-gtk2.o coot-glue-gtk2-python.o coot-hydrogens.o > coot_pythonmodule.o coot_wrap_guile_gtk1.o coot_wrap_guile_gtk2.o > drag-and-drop.o geometry-graphs.o get-residue.o flev.o > generic-objects.o globjects.o graphics-info.o graphics-info-defines.o > graphics-info-graphs.o graphics-info-gui.o graphics-info-modelling.o > graphics-info-navigation.o graphics-info-navigation-gtk1.o > graphics-info-navigation-gtk2.o graphics-info-preferences.o > graphics-info-network.o graphics-info-mutate.o graphics-info-lsq.o > graphics-info-pick.o graphics-info-refmac.o graphics-info-render.o > graphics-info-residues.o graphics-info-scripting.o > graphics-info-state.o graphics-info-superpose.o graphics-ligand-view.o > gl-matrix.o gtk-manual.o gtk-widget-conversion-utils.o > gtk2-interface.o interface.o lbg-callbacks-outer.o lbg-interface.o > molecule-class-info.o molecule-class-info-maps.o > molecule-class-info-kdc.o molecule-class-info-dots.o > molecule-class-info-other.o molecule-class-info-build.o > molecule-class-info-mutate.o molecule-class-info-residues.o > molecule-class-info-refine.o molecule-class-info-kk.o > molecule-class-info-surface.o molecule-class-info-ncs.o > molecule-class-info-widget-work.o nsv.o pick.o protein_db-interface.o > read-phs.o read-cif.o rama_mousey.o rama_plot.o restraints-editor.o > sdf-interface.o support.o support-gtk2-extras.o testing.o trackball.o > sequence-view.o seq-view-interface.o user-mods.o xmap-utils.o > coot_wrap_python_gtk2.o -fopenmp ../lbg/libcoot-lidia.la > ../ligand/libcoot-ligand.la ../lidia-core/libcoot-lidia-core.la > ../goograph/libcoot-goograph.la ../libgtkgraph/libcoot-gtkgraph.la > ../density-contour/libcoot-isosurface.la > ../build/libcoot-cabuild.la ../skeleton/libcoot-skeleton.la > ../angles/libcoot-AngleInfo.la ../db-main/libcoot-db-main.la > ../high-res/libcoot-high-res.la ../ideal/libcoot-ideal.la > ../geometry/libcoot-geometry.la ../coords/libcoot-coords.la > ../coot-surface/libcoot-surface.la ../surface/libccp4mg-surface.la > ../ccp4mg-utils/libccp4mg-utils.la > ../coot-utils/libcoot-map-heavy.la > ../coot-utils/libcoot-map-utils.la > ../coot-utils/libcoot-coord-extras.la > ../coot-utils/libcoot-coord-utils.la ../coot-utils/libcoot-shelx.la > ../utils/libcoot-utils.la ../mini-mol/libcoot-mini-mol.la > ../analysis/libcoot-analysis.la ../protein_db/libcoot-protein-db.la > ../cootilus/libcootilus.la ../cootaneer/libcootaneer.la > ../compat/libcoot-compat.la > /data/software/coot-gtk2-python/lib/libguilegtk-2.0.la -P -pthread > -L/data/software/coot-gtk2-python/lib -lguile -lltdl > -L/data/software/coot-gtk2-python/lib -lgmp -lcrypt -lm -lltdl > -L/data/software/coot-gtk2-python/lib -lclipper-ccp4 -lclipper-cif > -lclipper-phs -lclipper-contrib -lclipper-minimol -lclipper-cns > -lclipper-mmdb -lclipper-core -lccp4c > -L/data/software/coot-gtk2-python/lib > -L/data/software/coot-gtk2-python -lmmdb -lm -lrfftw -lfftw -lz -lm > -lpthread -L/data/software/coot-gtk2-python/lib -lssm > -L/data/software/coot-gtk2-python/lib > -L/data/software/coot-gtk2-python -lmmdb -lm > -L/data/software/coot-gtk2-python/lib/python2.7/config -lpthread -ldl > -lutil -lm -lpython2.7 -Xlinker -export-dynamic -lutil > -Wl,--export-dynamic -pthread -L/data/software/coot-gtk2-python/lib > -lgtkglext-x11-1.0 -lgdkglext-x11-1.0 -lGLU -lGL -lXmu -lXt -lSM -lICE > -lgtk-x11-2.0 -lpangox-1.0 -lX11 -lgmodule-2.0 -lrt > -lgdk-x11-2.0 -latk-1.0 -lgio-2.0 -lpangoft2-1.0 -lpangocairo-1.0 > -lgdk_pixbuf-2.0 -lcairo -lpango-1.0 -lfreetype -lfontconfig > -lgobject-2.0 -lglib-2.0 -L/data/software/coot-gtk2-python/lib > -lglut -L/usr/X11R6/lib -lgnomecanvas-2 -lart_lgpl_2 > -lgtk-x11-2.0 -lgdk-x11-2.0 -latk-1.0 -lgio-2.0 -lpangoft2-1.0 > -lpangocairo-1.0 -lgdk_pixbuf-2.0 -lcairo -lpango-1.0 -lfreetype > -lfontconfig -lgobject-2.0 -lglib-2.0 > -L/data/software/coot-gtk2-python/lib -lgsl -lgslcblas -lm > -L/data/software/coot-gtk2-python/lib -lcurl > /data/software/coot-gtk2-python/lib/libgoocanvas.la -lgtk-x11-2.0 > -lgdk-x11-2.0 -latk-1.0 -lgio-2.0 -lpangoft2-1.0 -lpangocairo-1.0 > -lgdk_pixbuf-2.0 -lcairo -lpango-1.0 -lfreetype -lfontconfig > -lgobject-2.0 -lglib-2.0 libtool: link: g++ > -DPKGDATADIR=\"/data/software/coot-gtk2-python/share/coot\" > -DPACKAGE_LOCALE_DIR=\"/data/software/coot-gtk2-python/share/coot/locale\" > -DDATADIR=\"/data/software/coot-gtk2-python/share\" > -DCOOT_SYS_BUILD_TYPE=\"Linux-x86_64-ubuntu-12.04.1-python-gtk2\" > -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK > -I/data/software/coot-gtk2-python/include -P -pthread -DUSE_PYTHON > -I/data/software/coot-gtk2-python/include/python2.7 > -I/data/software/coot-gtk2-python/include/python2.7 -DUSE_PYGTK > -DHAVE_GSL -fopenmp -g -O -o coot-real main.o svn-revision.o > c-inner-main.o c-interface-analysis.o c-interface-build.o > c-interface-build-gui.o c-interface-database.o c-interface-gui.o > c-interface-gtk2.o c-interface-info.o c-interface-kk.o > c-interface-ligands.o c-interface-ligands-gui.o c-interface-maps.o > c-interface-mmdb.o c-interface-mogul.o c-interface-mutate.o > c-interface-ncs.o c-interface-network.o c-interface-nucleotides.o > c-interface-python.o c-interface-pisa.o c-interface-pisa-gui.o > c-interface-preferences.o c-interface-refine.o c-interface-residues.o > c-interface-scm.o c-interface-sfs.o c-interface-superpose.o > c-interface-validate.o c-interface-view.o c-interface-widgets.o > c-interface-waters.o c-interface-waters-gui.o c-interface.o > c-interface-test.o callbacks.o cmtz-interface.o command-line.o > coot-colour.o coot-align.o coot-nomenclature.o coot-glue.o > coot-glue-gtk2.o coot-glue-gtk2-python.o coot-hydrogens.o > coot_pythonmodule.o coot_wrap_guile_gtk1.o coot_wrap_guile_gtk2.o > drag-and-drop.o geometry-graphs.o get-residue.o flev.o > generic-objects.o globjects.o graphics-info.o graphics-info-defines.o > graphics-info-graphs.o graphics-info-gui.o graphics-info-modelling.o > graphics-info-navigation.o graphics-info-navigation-gtk1.o > graphics-info-navigation-gtk2.o graphics-info-preferences.o > graphics-info-network.o graphics-info-mutate.o graphics-info-lsq.o > graphics-info-pick.o graphics-info-refmac.o graphics-info-render.o > graphics-info-residues.o graphics-info-scripting.o > graphics-info-state.o graphics-info-superpose.o graphics-ligand-view.o > gl-matrix.o gtk-manual.o gtk-widget-conversion-utils.o > gtk2-interface.o interface.o lbg-callbacks-outer.o lbg-interface.o > molecule-class-info.o molecule-class-info-maps.o > molecule-class-info-kdc.o molecule-class-info-dots.o > molecule-class-info-other.o molecule-class-info-build.o > molecule-class-info-mutate.o molecule-class-info-residues.o > molecule-class-info-refine.o molecule-class-info-kk.o > molecule-class-info-surface.o molecule-class-info-ncs.o > molecule-class-info-widget-work.o nsv.o pick.o protein_db-interface.o > read-phs.o read-cif.o rama_mousey.o rama_plot.o restraints-editor.o > sdf-interface.o support.o support-gtk2-extras.o testing.o trackball.o > sequence-view.o seq-view-interface.o user-mods.o xmap-utils.o > coot_wrap_python_gtk2.o -fopenmp -P -pthread -Wl,-export-dynamic > -Wl,--export-dynamic -pthread ../lbg/.libs/libcoot-lidia.a > -L/data/software/coot-gtk2-python/lib > -L/data/software/coot-gtk2-python ../ligand/.libs/libcoot-ligand.a > ../lidia-core/.libs/libcoot-lidia-core.a > ../goograph/.libs/libcoot-goograph.a > ../libgtkgraph/.libs/libcoot-gtkgraph.a > ../density-contour/.libs/libcoot-isosurface.a > ../build/.libs/libcoot-cabuild.a > ../skeleton/.libs/libcoot-skeleton.a > /tmp/autobuild/cmlx21_2012-11-29__T19_45_09/coot-0.7/angles/.libs/libc > oot-AngleInfo.a > ../angles/.libs/libcoot-AngleInfo.a > ../db-main/.libs/libcoot-db-main.a > ../high-res/.libs/libcoot-high-res.a > /tmp/autobuild/cmlx21_2012-11-29__T19_45_09/coot-0.7/ligand/.libs/libc > oot-ligand.a > /tmp/autobuild/cmlx21_2012-11-29__T19_45_09/coot-0.7/ideal/.libs/libco > ot-ideal.a > /tmp/autobuild/cmlx21_2012-11-29__T19_45_09/coot-0.7/db-main/.libs/lib > coot-db-main.a > /tmp/autobuild/cmlx21_2012-11-29__T19_45_09/coot-0.7/ccp4mg-utils/.lib > s/libccp4mg-utils.a > ../ideal/.libs/libcoot-ideal.a > /tmp/autobuild/cmlx21_2012-11-29__T19_45_09/coot-0.7/coot-utils/.libs/ > libcoot-map-heavy.a > /tmp/autobuild/cmlx21_2012-11-29__T19_45_09/coot-0.7/coords/.libs/libc > oot-coords.a > /tmp/autobuild/cmlx21_2012-11-29__T19_45_09/coot-0.7/coot-utils/.libs/ > libcoot-coord-extras.a > ../geometry/.libs/libcoot-geometry.a > ../coords/.libs/libcoot-coords.a > /tmp/autobuild/cmlx21_2012-11-29__T19_45_09/coot-0.7/coot-utils/.libs/ > libcoot-shelx.a > /tmp/autobuild/cmlx21_2012-11-29__T19_45_09/coot-0.7/lidia-core/.libs/ > libcoot-lidia-core.a ../coot-surface/.libs/libcoot-surface.a > -L/usr/X11R6/lib > /tmp/autobuild/cmlx21_2012-11-29__T19_45_09/coot-0.7/surface/.libs/lib > ccp4mg-surface.a > ../surface/.libs/libccp4mg-surface.a > ../ccp4mg-utils/.libs/libccp4mg-utils.a -lpng > ../coot-utils/.libs/libcoot-map-heavy.a > /tmp/autobuild/cmlx21_2012-11-29__T19_45_09/coot-0.7/coot-utils/.libs/ > libcoot-map-utils.a ../coot-utils/.libs/libcoot-map-utils.a > ../coot-utils/.libs/libcoot-coord-extras.a > ../coot-utils/.libs/libcoot-coord-utils.a > ../coot-utils/.libs/libcoot-shelx.a ../utils/.libs/libcoot-utils.a > ../mini-mol/.libs/libcoot-mini-mol.a > ../analysis/.libs/libcoot-analysis.a > /tmp/autobuild/cmlx21_2012-11-29__T19_45_09/coot-0.7/coot-utils/.libs/ > libcoot-coord-utils.a > /tmp/autobuild/cmlx21_2012-11-29__T19_45_09/coot-0.7/geometry/.libs/li > bcoot-geometry.a > /tmp/autobuild/cmlx21_2012-11-29__T19_45_09/coot-0.7/mini-mol/.libs/li > bcoot-mini-mol.a > /tmp/autobuild/cmlx21_2012-11-29__T19_45_09/coot-0.7/utils/.libs/libco > ot-utils.a ../protein_db/.libs/libcoot-protein-db.a > ../cootilus/.libs/libcootilus.a ../cootaneer/.libs/libcootaneer.a > ../compat/.libs/libcoot-compat.a > /data/software/coot-gtk2-python/lib/libguilegtk-2.0.so > -lgthread-2.0 /data/software/coot-gtk2-python/lib/libguile.so > /data/software/coot-gtk2-python/lib/libgmp.so -lcrypt > /data/software/coot-gtk2-python/lib/libltdl.so > /data/software/coot-gtk2-python/lib/libclipper-ccp4.so > /data/software/coot-gtk2-python/lib/libclipper-cif.so > /data/software/coot-gtk2-python/lib/libclipper-phs.so > /data/software/coot-gtk2-python/lib/libclipper-contrib.so > /data/software/coot-gtk2-python/lib/libclipper-minimol.so > /data/software/coot-gtk2-python/lib/libclipper-cns.so > /data/software/coot-gtk2-python/lib/libclipper-mmdb.so > /data/software/coot-gtk2-python/lib/libclipper-core.so > /data/software/coot-gtk2-python/lib/libccp4c.so > /data/software/coot-gtk2-python/lib/librfftw.so > /data/software/coot-gtk2-python/lib/libfftw.so > /data/software/coot-gtk2-python/lib/libssm.so > /data/software/coot-gtk2-python/lib/libmmdb.so > -L/data/software/coot-gtk2-python/lib/python2.7/config -lpthread -ldl > -lpython2.7 -lutil > /data/software/coot-gtk2-python/lib/libgtkglext-x11-1.0.so > /data/software/coot-gtk2-python/lib/libgdkglext-x11-1.0.so -lXmu -lXt > -lSM -lICE -lpangox-1.0 -lgmodule-2.0 > /data/software/coot-gtk2-python/lib/libglut.so -lGL -lGLU -lXext > -lX11 -lXxf86vm -lgnomecanvas-2 > /usr/lib/x86_64-linux-gnu/libart_lgpl_2.so > /data/software/coot-gtk2-python/lib/libgsl.so > /data/software/coot-gtk2-python/lib/libgslcblas.so -lm > /data/software/coot-gtk2-python/lib/libcurl.so > /data/software/coot-gtk2-python/lib/libidn.so -lrt -lssl -lcrypto -lz > /data/software/coot-gtk2-python/lib/libgoocanvas.so > -lgtk-x11-2.0 -lgdk-x11-2.0 -latk-1.0 -lgio-2.0 -lpangoft2-1.0 > -lpangocairo-1.0 -lgdk_pixbuf-2.0 > /usr/lib/x86_64-linux-gnu/libcairo.so -lpango-1.0 > /usr/lib/x86_64-linux-gnu/libfreetype.so -lfontconfig -lgobject-2.0 > -lglib-2.0 -pthread -Wl,-rpath > -Wl,/data/software/coot-gtk2-python/lib -Wl,-rpath > -Wl,/data/software/coot-gtk2-python/lib /usr/bin/ld: > /data/software/coot-gtk2-python/lib/libpython2.7.a(dynload_shlib.o): > undefined reference to symbol 'dlsym@@GLIBC_2.2.5' /usr/bin/ld: > note: 'dlsym@@GLIBC_2.2.5' is defined in DSO > /usr/lib/gcc/x86_64-linux-gnu/4.6/../../../x86_64-linux-gnu/libdl.so > so try adding it to the linker command line > /usr/lib/gcc/x86_64-linux-gnu/4.6/../../../x86_64-linux-gnu/libdl.so: > could not read symbols: Invalid operation collect2: ld returned 1 exit > status make[1]: *** [coot-real] Error 1 make[1]: Leaving directory > `/tmp/autobuild/cmlx21_2012-11-29__T19_45_09/coot-0.7/src' make: > *** [all-recursive] Error 1 make failed. > > Pretty stumped here, will give it a break for tonight, > > Amadeus > > > -----Original Message----- From: Mailing list for users of COOT > Crystallographic Software [mailto:[email protected]] On Behalf Of > Amadeus Stevenson Sent: 29 November 2012 18:42 To: > [email protected] Subject: Re: Autobuilding coot 0.7 fails on coot > (Ubuntu 12.04 x64) > > Thanks Jeff, Pete. Digging around in the system for the python headers > gives me: > > /usr/include/python2.7/pythonrun.h > /data/software/coot-gtk2-python/include/python2.7/pythonrun.h > > I've done some more digging, this time from the coot config.log: > > configure:19879: result: yes configure:19907: checking for Python > configure:20020: checking Python.h usability configure:20037: gcc -c > -g -O2 -DUSE_PYTHON conftest.c >&5 conftest.c:55:20: fatal > error: Python.h: No such file or directory compilation terminated. > configure:20044: $? = 1 > > and then some more from 16-coot.txt > > checking for Python... ImportError: No module named site python not > found. error ImportError: No module named site ImportError: No module > named site ImportError: No module named site checking Python.h > usability... no checking Python.h presence... no checking for > Python.h... no > > So it looks like the Python libraries are not being passed. I'm not > sure which script to modify to include them? I will keep digging. > > Amadeus > > > -----Original Message----- From: Jeffrey Van Voorst > [mailto:[email protected]] Sent: 29 November 2012 17:56 To: Amadeus > Stevenson Subject: Re: Autobuilding coot 0.7 fails on coot (Ubuntu > 12.04 x64) > > I am not familiar with building coot, but you will need to get the > build system to include the headers for the Python that Autobuild > compiled. Supposing that directory is ../include/python2.7, you will > need to add -I../include/python2.7 to the build command. > > For example on debian, the system header file that contains the > prototype for Py_Initialize is /usr/include/python2.6/pythonrun.h. > If you need to find this header file, you could try 'find > /path/to/coot/build/dir -name "*.h" | xargs grep Py_Initialize' > (without the quotes -- ' ' ). > > I am assuming that the autobuild process would have taken care of > providing the correct C flags and C library to build coot (if it does > build its own Python). In other words, maybe this particular way of > building coot is unsupported or has fallen out of use. > > On 11/29/12 11:41 AM, Amadeus Stevenson wrote: >> Hi Jeff, >> >> Thanks for the quick reply. >> >> I have installed the Ubuntu python-dev package: >> >> $ dpkg --listfiles python-dev /. /usr /usr/bin /usr/share >> /usr/share/man /usr/share/man/man1 /usr/share/doc /usr/lib >> /usr/lib/pkgconfig /usr/bin/python-config /usr/bin/python2-config >> /usr/share/man/man1/python-config.1.gz >> /usr/share/man/man1/python2-config.1.gz >> /usr/share/doc/python-dev /usr/lib/pkgconfig/python.pc >> >> Autobuild has compiled its own version of python >> >> $AUTOBUILD_BUILD /include/python2.7/ >> >> Amadeus >> >> >> -----Original Message----- From: Jeffrey Van Voorst >> [mailto:[email protected]] Sent: 29 November 2012 17:36 To: >> Amadeus Stevenson Subject: Re: Autobuilding coot 0.7 fails on coot >> (Ubuntu 12.04 x64) >> >> Hi Amadeus, >> >> The -lpython flag is for linking to the python library. In this >> command you need to specify the location of the directory that >> contains the python header file. >> >> Is the Python development package included in your Ubuntu >> installation? If so, do you know the path to where Ubuntu installed >> the Python header files? >> >> --Jeff >> >> On 11/29/12 11:09 AM, Amadeus Stevenson wrote: >>> Hello, >>> >>> I'm trying to autobuild coot 0.7 on Ubuntu 12.04 x64. >>> >>> Running : >>> >>> wget http://coot.googlecode.com/svn/trunk/build-it-gtk2-simple >>> >>> export AUTOBUILD_INSTALLED=/data/software/coot export >>> AUTOBUILD_BUILD=/tmp/autobuild export LOGS=$AUTOBUILD_BUILD/logs >>> export NIGHTLY_DEST_DIR=$AUTOBUILD_BUILD export >>> STABLE_DEST_DIR=$AUTOBUILD_BUILD export build_coot_prerelease=0 >>> export do_nightlies=0 export >>> check_dependencies_in_install_only=0 >>> >>> ./build-it-gtk2-simple python >>> >>> makes it as far as 16-coot.txt: >>> >>> g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" >>> -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" >>> -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7\" >>> -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 >>> -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 >>> -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 >>> -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. >>> -I../lidia-core -I../coot-utils -I../mini-mol -I../geometry >>> -I../coot-utils -I../utils -I/data/software/coot-gtk2-python/include >>> -DHAVE_GOOCANVAS >>> -I/data/software/coot-gtk2-python/include/goocanvas-1.0 >>> -pthread -I/usr/include/gtk-2.0 >>> -I/usr/lib/x86_64-linux-gnu/gtk-2.0/include >>> -I/usr/include/atk-1.0 -I/usr/include/cairo >>> -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 >>> -I/usr/include/gio-unix-2.0/ -I/usr/include/glib-2.0 >>> -I/usr/lib/x86_64-linux-gnu/glib-2.0/include >>> -I/usr/include/pixman-1 -I/usr/include/freetype2 >>> -I/usr/include/libpng12 >>> -I/data/software/coot-gtk2-python/include >>> -I/data/software/coot-gtk2-python/include >>> -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP >>> -DPKGDATADIR='"/data/software/coot-gtk2-python/share/coot"' -g -O >>> -MT lbg-callbacks-outer.o -MD -MP -MF .deps/lbg-callbacks-outer.Tpo >>> -c -o lbg-callbacks-outer.o lbg-callbacks-outer.cc lidia-main.cc: In >>> function 'int main(int, char**)': lidia-main.cc:61:18: error: >>> 'Py_Initialize' >>> was not declared in this scope lidia-main.cc:62:28: error: >>> 'PySys_SetArgv' was not declared in this scope mv -f >>> .deps/lbg-drag-and-drop.Tpo .deps/lbg-drag-and-drop.Plo >>> make[1]: *** [lidia-main.o] Error 1 make[1]: *** Waiting for >>> unfinished jobs.... mv -f .deps/lbg-callbacks-outer.Tpo >>> .deps/lbg-callbacks-outer.Po mv -f .deps/lbg.Tpo .deps/lbg.Plo >>> make[1]: Leaving directory >>> `/tmp/autobuild/cmlx21_2012-11-29__T15_04_26/coot-0.7/lbg' >>> make: *** [all-recursive] Error 1 make failed. >>> >>> Googling the compiler error leads to suggestions that -lpython needs >>> to be included, but I can't figure out where to insert it into the >>> Makefile, or if it indeed will help. >>> >>> Also, I noticed that despite python being installed system-wide, >>> autobuild compiles its own version. Not a big deal, but was >>> wondering if there's a way to use the system-wide version to reduce >>> duplication. >>> >>> Any help much appreciated, >>> >>> Amadeus >> > - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFQuHnfUxlJ7aRr7hoRAv4XAKCJGMQ88wvyCtZT2CvYdmG5XCd1XACg4koQ bCyPnfrkI9DTioxQArQs8TI= =cFQ+ -----END PGP SIGNATURE-----
