Thanks Clemens. I tried removing all references to CCP from the environment variables, doing a fresh autobuild, and I return to the python initialise error (error #1).
With CCP environment variables included, I get linking errors (error #2). Is there any way you could tar up your binaries for me to try (via ftp, http or dropbox)? I could then see if I can get your binaries running or which linked libraries are missing. Many thanks, Amadeus -----Original Message----- From: Clemens Vonrhein [mailto:[email protected]] Sent: 30 November 2012 17:15 To: Amadeus Stevenson Subject: Re: Autobuilding coot 0.7 fails on coot (Ubuntu 12.04 x64) Hi Amadeus, That might not be directly useful, but running the script #!/bin/bash [ ! -f build-it-gtk2-simple ] && wget http://coot.googlecode.com/svn/trunk/build-it-gtk2-simple OS=`uname` HOST=`hostname` AUTOBUILD_BUILD=`pwd`/autobuild/building AUTOBUILD_INSTALL=`pwd`/autobuild/${OS}-${HOST} AUTOBUILD_INSTALLED=`pwd`/autobuild/${OS}-${HOST} LOGS=`pwd`/build-logs/${OS}-${HOST} NIGHTLY_DEST_DIR=`pwd`/binaries/nightlies/pre-release STABLE_DEST_DIR=`pwd`/binaries/stable . ./build-it-gtk2-simple python on my "12.04.1 LTS x86_64" system runs through and creates a working binary (as far as I can tell). Cheers Clemens On Fri, Nov 30, 2012 at 04:00:37PM +0000, Amadeus Stevenson wrote: > 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/li > > bc > > 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/li > > bc > > oot-ligand.a > > /tmp/autobuild/cmlx21_2012-11-29__T19_45_09/coot-0.7/ideal/.libs/lib > > co > > ot-ideal.a > > /tmp/autobuild/cmlx21_2012-11-29__T19_45_09/coot-0.7/db-main/.libs/l > > ib > > coot-db-main.a > > /tmp/autobuild/cmlx21_2012-11-29__T19_45_09/coot-0.7/ccp4mg-utils/.l > > ib > > s/libccp4mg-utils.a > > ../ideal/.libs/libcoot-ideal.a > > /tmp/autobuild/cmlx21_2012-11-29__T19_45_09/coot-0.7/coot-utils/.lib > > s/ > > libcoot-map-heavy.a > > /tmp/autobuild/cmlx21_2012-11-29__T19_45_09/coot-0.7/coords/.libs/li > > bc > > oot-coords.a > > /tmp/autobuild/cmlx21_2012-11-29__T19_45_09/coot-0.7/coot-utils/.lib > > s/ > > 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/.lib > > s/ > > libcoot-shelx.a > > /tmp/autobuild/cmlx21_2012-11-29__T19_45_09/coot-0.7/lidia-core/.lib > > s/ 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/l > > ib > > 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/.lib > > s/ 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/.lib > > s/ > > 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/lib > > co 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----- -- *************************************************************** * Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com * * Global Phasing Ltd. * Sheraton House, Castle Park * Cambridge CB3 0AX, UK *-------------------------------------------------------------- * BUSTER Development Group (http://www.globalphasing.com) ***************************************************************
