Sorry Paul .. Didnt understand your suggestion. In which makefile do I have to move the -ldl after -lpython2.7
I checked out tag 4546 and not I get a different error "Py_Initialize" , "PySys_SetArgv" not declared in scope. ( see bottom of his email) I guess these also have to do with python libs. How do I get around this new error. I know you are moving the source tree over to Cambridge from Oxford and the build script looks for the prerelease server at the URL below..but that returns a 404. I commented it out to get it built till the error below. Also reverting to 4454 I cannot reproduce the error message from yesterday. Sorry for trying to build it while it is still in mid-migration. Thanks for your help Paul and Tim Hari Commented this URL out #pre_release_server_dir= http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/coot/source/pre-releases/ Error I am getting with 4456 g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.7.1-pre\" -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/home/ubuntu/autobuild/coot-pre-release-gtk2-python/include -DHAVE_GOOCANVAS -I/home/ubuntu/autobuild/coot-pre-release-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/home/ubuntu/autobuild/coot-pre-release-gtk2-python/include -I/home/ubuntu/autobuild/coot-pre-release-gtk2-python/include -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -DPKGDATADIR='"/home/ubuntu/autobuild/coot-pre-release-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 make[1]: *** [lidia-main.o] Error 1 make[1]: *** Waiting for unfinished jobs.... mv -f .deps/lbg-drag-and-drop.Tpo .deps/lbg-drag-and-drop.Plo mv -f .deps/lbg-callbacks-outer.Tpo .deps/lbg-callbacks-outer.Po mv -f .deps/lbg.Tpo .deps/lbg.Plo make[1]: Leaving directory `/home/ubuntu/autobuild/ubuntu_2013-01-24__T19_00_19/coot-0.7.1-pre/lbg' make: *** [all-recursive] Error 1 make failed. On Thu, Jan 24, 2013 at 6:55 AM, Paul Emsley <pems...@mrc-lmb.cam.ac.uk>wrote: > On Thu, 2013-01-24 at 11:35 +0000, Paul Emsley wrote: > > On Wed, 2013-01-23 at 19:17 -0500, hari jayaram wrote: > > > Hi I am trying to build the subversion coot on a Ubuntu machine > > > running 12.10 using the build-it-gtk2-simple python script. > > > > > > > > > I get all the way to compiling the final coot and get an error in the > > > final linking part. > > > > > > > > > (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/4.7/../../../x86_64-linux-gnu/libdl.so so try > adding it to the linker command line > > > /usr/lib/gcc/x86_64-linux-gnu/4.7/../../../x86_64-linux-gnu/libdl.so: > > > could not read symbols: Invalid operation > > > collect2: error: ld returned 1 exit status > > > make[1]: *** [coot-real] Error 1 > > > make[1]: Leaving directory > > > > `/home/ubuntu/autobuild/ubuntu_2013-01-23__T22_55_56/coot-0.7.1-pre/src' > > > make: *** [all-recursive] Error 1 > > > make failed. > > > > > > > > > The detailed error is at http://dpaste.com/889587/ > > > > > > > > > I had buidling using a script that Clemens had shared ( which also > > > calls build-it-gtk2-simple) but that too failed at an earlier step. > > > > At a guess I'd suggest putting -ldl after -lpython2.7. That seems a > > sane way of doing things - I don't know why it's not arranged like that > > already. I'll dig... > > > > > $ python-config --ld-flags > -lpthread -ldl -lutil -lm -lpython2.6 > > Urgh! >
