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:[log in to unmask]]
Sent: 30 November 2012 09:18
To: Amadeus Stevenson
Cc: [log in to unmask]
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:[log in to unmask]] On Behalf Of
> Amadeus Stevenson Sent: 29 November 2012 18:42 To:
> [log in to unmask] 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:[log in to unmask]] 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
>>
>> $AUTOBUILD_BUILD /include/python2.7/
>>
>> Amadeus
>>
>>
>> -----Original Message----- From: Jeffrey Van Voorst
>> [mailto:[log in to unmask]] Sent: 29 November 2012 17:36 To:
>> Amadeus Stevenson Subject: Re: Autobuilding coot 0.7 fails on coot
>> (Ubuntu 12.04 x64)
>>
>> Hi Amadeus,
>>
>> The -lpython flag is for linking to the python library. In this
>> command you need to specify the location of the directory that
>> contains the python header file.
>>
>> Is the Python development package included in your Ubuntu
>> installation? If so, do you know the path to where Ubuntu installed
>> the Python header files?
>>
>> --Jeff
>>
>> On 11/29/12 11:09 AM, Amadeus Stevenson wrote:
>>> Hello,
>>>
>>> I'm trying to autobuild coot 0.7 on Ubuntu 12.04 x64.
>>>
>>> Running :
>>>
>>> wget http://coot.googlecode.com/svn/trunk/build-it-gtk2-simple
>>>
>>> export AUTOBUILD_INSTALLED=/data/software/coot export
>>> AUTOBUILD_BUILD=/tmp/autobuild export LOGS=$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
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