Hi all,
Clemens kindly sent me a binary compile of coot from the same Linux (12.04.1
LTS x86_64).
I was missing the following libraries: libguilegtk-2.0.so.0 libssm.so.0
libgtkglext-x11-1.0.so.0 libgdkglext-x11-1.0.so.0 libgoocanvas.so.3, but had
compiled these from the previous autobuild which failed on coot.
Bit messy, but by combining his binaries and mine, and tweaking the environment
coot is now running on the system:
export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:/data/software/coot-gtk2-python/lib
export PATH=${PATH}:/data/software/coot-gtk2-python/bin
Thanks to everyone for your help. Still no clue why this wasn't compiling
cleanly in the first place but it is working now.
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)
***************************************************************
