Just my two cents: I would always send this as an attachment, because some (all?) email clients will mess with line breaks.
-jens On Mon, 2014-10-27 at 16:43 -0700, Cyrus Harmon wrote: > Following up on my on email... > > The following patch fixes the build for me from the latest SVN > coot-read-only sources. Is the list preference to paste these sorts of > things inline to the email, or to send the patch as an attachment? > > If anyone has any comments/suggestions on the patches, I would > appreciate hearing them. > > thanks, > > Cyrus > > > > diff --git a/coot-utils/Makefile.am b/coot-utils/Makefile.am > index 6612f82..c19a66d 100644 > --- a/coot-utils/Makefile.am > +++ b/coot-utils/Makefile.am > @@ -62,7 +62,8 @@ libcoot_coord_utils_la_SOURCES = coot-coord-utils.cc \ > # clean > libcoot_coord_utils_la_LIBADD = \ > $(top_builddir)/geometry/libcoot-geometry.la \ > - $(GSL_LIBS) > + $(GSL_LIBS) \ > + $(CLIPPER_LIBS) > > libcoot_coord_utils_la_LDFLAGS = -no-undefined > > @@ -96,7 +97,8 @@ libcoot_map_utils_la_SOURCES = coot-map-utils.cc > peak-search.cc peak-search-from > # clean > libcoot_map_utils_la_LIBADD = \ > libcoot-coord-utils.la \ > - $(GSL_LIBS) > + $(GSL_LIBS) \ > + $(CLIPPER_LIBS) > > libcoot_map_utils_la_LDFLAGS = -no-undefined > > @@ -109,7 +111,8 @@ libcoot_map_heavy_la_SOURCES = coot-map-heavy.cc > coot-fffear.cc > libcoot_map_heavy_la_LIBADD = \ > libcoot-map-utils.la \ > libcoot-coord-utils.la \ > - $(GSL_LIBS) > + $(GSL_LIBS) \ > + $(CLIPPER_LIBS) > > libcoot_map_heavy_la_LDFLAGS = -no-undefined > > @@ -145,6 +148,7 @@ testcootutils_LDADD = \ > ./libcoot-coord-extras.la\ > ./libcoot-coord-utils.la \ > $(GSL_LIBS) \ > + $(CLIPPER_LIBS) \ > $(GLOB_LIBS) > > # $(top_builddir)/geometry/libcoot-geometry.la > @@ -172,7 +176,7 @@ test_elastic_SOURCES = test-elastic.cc > test_elastic_LDADD = ./libcoot-coord-utils.la $(GLOB_LIBS) > > test_spherical_SOURCES = test-spherical.cc > -test_spherical_LDADD = ./libcoot-coord-utils.la $(GSL_LIBS) > +test_spherical_LDADD = ./libcoot-coord-utils.la $(GSL_LIBS) > $(CLIPPER_LIBS) > > glyco_torsions_SOURCES = test-glyco-torsions.cc > glyco_torsions_LDADD = ./libcoot-coord-utils.la > diff --git a/geometry/Makefile.am b/geometry/Makefile.am > index 266eb04..89f6bb5 100644 > --- a/geometry/Makefile.am > +++ b/geometry/Makefile.am > @@ -85,5 +85,5 @@ make_shelx_restraints_SOURCES = make-shelx-restraints.cc > > # why is coot-utils.la needed? I don't understand. > make_shelx_restraints_LDADD = ./libcoot-geometry.la \ > - $(top_builddir)/utils/libcoot-utils.la > + $(top_builddir)/utils/libcoot-utils.la $(CLIPPER_LIBS) > > diff --git a/src/c-interface-mogul.cc b/src/c-interface-mogul.cc > index cad0b32..08a0d05 100644 > --- a/src/c-interface-mogul.cc > +++ b/src/c-interface-mogul.cc > @@ -1,4 +1,6 @@ > > +#include <string.h> > + > #ifdef USE_PYTHON > #include <Python.h> // before system includes to stop > "POSIX_C_SOURCE" redefined problems > #endif > diff --git a/src/generic-objects.cc b/src/generic-objects.cc > index ba5c394..8c93401 100644 > --- a/src/generic-objects.cc > +++ b/src/generic-objects.cc > @@ -30,6 +30,8 @@ > #include <vector> > #include <string> > > +#include <string.h> > + > #include <gtk/gtk.h> > #include <math.h> > > > > > On 10/27/2014 01:55 PM, Cyrus Harmon wrote: > > In what I gather is a rite of passage for folks wishing to build/use > > coot, I'm running into some troubles trying to build coot from source. > > I think I've got the right prerequisites built and installed: > > > > mmdb2 > > libccp4 > > clipper-2.1 > > ssm-1.4 > > and of course the various prerequisites (python, gtk, etc...) > > > > When I try to build I coot, I get the following error message: > > > > make[1]: Entering directory > > '/home/sly/projects/structure/coot/coot-read-only/analysis' > > /bin/bash ../libtool --tag=CXX --mode=link g++ -o bfactan > > bfactan.o libcoot-analysis.la ../coot-utils/libcoot-coord-utils.la > > ../geometry/libcoot-geometry.la ../mini-mol/libcoot-mini-mol.la > > ../utils/libcoot-utils.la -L/usr/local/lib -lclipper-ccp4 > > -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns > > -lclipper-phs -lclipper-contrib -lclipper-core -lccp4c -lmmdb2 > > -L/usr/local/lib -lmmdb2 > > libtool: link: g++ -o .libs/bfactan bfactan.o > > ./.libs/libcoot-analysis.so ../coot-utils/.libs/libcoot-coord-utils.so > > ../geometry/.libs/libcoot-geometry.so > > ../mini-mol/.libs/libcoot-mini-mol.so ../utils/.libs/libcoot-utils.so > > -L/usr/local/lib /usr/local/lib/libclipper-ccp4.so > > /usr/local/lib/libclipper-cif.so /usr/local/lib/libclipper-minimol.so > > /usr/local/lib/libclipper-mmdb.so /usr/local/lib/libclipper-cns.so > > /usr/local/lib/libclipper-phs.so /usr/local/lib/libclipper-contrib.so > > /usr/local/lib/libclipper-core.so /usr/local/lib/libccp4c.so > > /usr/local/lib/libmmdb2.so > > ../coot-utils/.libs/libcoot-coord-utils.so: undefined reference to > > `clipper::SFweight_spline<float>::operator()(clipper::HKL_data<clipper::datatypes::F_phi<float> > > > > >&, clipper::HKL_data<clipper::datatypes::F_phi<float> >&, > > clipper::HKL_data<clipper::datatypes::Phi_fom<float> >&, > > clipper::HKL_data<clipper::datatypes::F_sigF<float> > const&, > > clipper::HKL_data<clipper::datatypes::F_phi<float> > const&, > > clipper::HKL_data<clipper::datatypes::Flag> const&)' > > ../coot-utils/.libs/libcoot-coord-utils.so: undefined reference to > > `clipper::MMDBManager::cell() const' > > ../coot-utils/.libs/libcoot-coord-utils.so: undefined reference to > > `clipper::MMDBManager::spacegroup() const' > > ../coot-utils/.libs/libcoot-coord-utils.so: undefined reference to > > `clipper::SFweight_spline<float>::init(int, int, int)' > > collect2: error: ld returned 1 exit status > > Makefile:647: recipe for target 'bfactan' failed > > make[1]: *** [bfactan] Error 1 > > > > I'm a bit at a loss trying to figure out the templated classes, etc... > > in sfweight.cpp so I thought I'd check to see if anyone else is having > > (or has run into) this problem. Also the clipper::MMDBxxx stuff make > > me wonder if this isn't the result of some stuff not yet being > > converted over to mmdb2. Pointers appreciated. > > > > thanks, > > > > Cyrus
