diff options
| author |   Justin Lecher (jlec) <jlec@j-schmitz.net> | 2009-12-14 22:13:29 +0100 |
|---|---|---|
| committer | Justin Lecher (jlec) <jlec@j-schmitz.net> | 2009-12-14 22:13:45 +0100 |
| commit | 8336fc0f8950bb0653352f0c7d95f2ba6a74daa1 (patch) | |
| tree | 825a793003b4645e0b2895ae629d0062e3090e80 /sci-chemistry/coot/files | |
| parent | sci-mathematics/octave-forge-meta -- dep of sci-mathematics/octave-forge-quat... (diff) | |
| download | sci-8336fc0f8950bb0653352f0c7d95f2ba6a74daa1.tar.gz sci-8336fc0f8950bb0653352f0c7d95f2ba6a74daa1.tar.bz2 sci-8336fc0f8950bb0653352f0c7d95f2ba6a74daa1.zip | |
sci-chemistry/coot -- clean up
(Portage version: 2.2_rc58/git/Linux x86_64)
(Signed Manifest commit)
Diffstat (limited to 'sci-chemistry/coot/files')
| -rw-r--r-- | sci-chemistry/coot/files/0.5.2-as-needed.patch | 477 | ||||
| -rw-r--r-- | sci-chemistry/coot/files/0.5.2-gcc-4.3.patch | 10 | ||||
| -rw-r--r-- | sci-chemistry/coot/files/0.5.2-gcc-4.4.patch | 11 | ||||
| -rw-r--r-- | sci-chemistry/coot/files/0.6_pre1-as-needed.patch | 481 | ||||
| -rw-r--r-- | sci-chemistry/coot/files/0.6_pre1-gcc4.4.patch | 10 | ||||
| -rw-r--r-- | sci-chemistry/coot/files/0.6_pre1-test-rama.patch | 15 | ||||
| -rw-r--r-- | sci-chemistry/coot/files/9999-as-needed.patch | 481 | ||||
| -rw-r--r-- | sci-chemistry/coot/files/9999-as-needed2.patch | 481 | ||||
| -rw-r--r-- | sci-chemistry/coot/files/9999-check-include.patch | 23 | ||||
| -rw-r--r-- | sci-chemistry/coot/files/9999-gcc4.4.patch | 10 | ||||
| -rw-r--r-- | sci-chemistry/coot/files/9999-test-rama.patch | 15 | ||||
| -rw-r--r-- | sci-chemistry/coot/files/fix-namespace-error.patch | 52 | ||||
| -rw-r--r-- | sci-chemistry/coot/files/glib.m4 | 196 | ||||
| -rw-r--r-- | sci-chemistry/coot/files/gtk.m4 | 199 | ||||
| -rw-r--r-- | sci-chemistry/coot/files/gtkgl.m4 | 47 | ||||
| -rw-r--r-- | sci-chemistry/coot/files/imlib.m4 | 301 | ||||
| -rw-r--r-- | sci-chemistry/coot/files/link-against-guile-gtk-properly.patch | 15 |
17 files changed, 0 insertions, 2824 deletions
diff --git a/sci-chemistry/coot/files/0.5.2-as-needed.patch b/sci-chemistry/coot/files/0.5.2-as-needed.patch deleted file mode 100644 index 2db2ecf84..000000000 --- a/sci-chemistry/coot/files/0.5.2-as-needed.patch +++ /dev/null @@ -1,477 +0,0 @@ ---- coot-0.5-pre-1.orig/analysis/Makefile.am 2008-07-13 16:40:27.000000000 -0700 -+++ coot-0.5-pre-1/analysis/Makefile.am 2008-07-13 16:40:40.000000000 -0700 -@@ -9,6 +9,7 @@ - $(MMDB_CXXFLAGS) - - libcoot_analysis_la_SOURCES = bfkurt.cc -+libcoot_analysis_la_LIBADD = $(top_builddir)/coot-utils/libcoot-coord-utils.la - - bin_PROGRAMS = bfactan - -@@ -16,7 +17,6 @@ - - bfactan_LDADD = \ - libcoot-analysis.la \ -- $(top_builddir)/coot-utils/libcoot-coord-utils.la \ - $(top_builddir)/coot-utils/libcoot-utils.la \ - $(top_builddir)/geometry/libcoot-geometry.la \ - $(CLIPPER_LIBS) \ ---- coot-0.5-pre-1.orig/coords/Makefile.am 2008-07-13 16:40:27.000000000 -0700 -+++ coot-0.5-pre-1/coords/Makefile.am 2008-07-13 16:40:40.000000000 -0700 -@@ -37,4 +37,6 @@ - libcoot_coords_la_SOURCES = Bond_lines.cc Cartesian.cc cos-sin.cc \ - mmdb-extras.cc utils.cc mmdb.cc mmdb-crystal.cc \ - Bond_lines_ext.cc coot-close.cc -- -+libcoot_coords_la_LIBADD = \ -+ $(top_builddir)/coot-utils/libcoot-shelx.la \ -+ $(top_builddir)/mini-mol/libcoot-mini-mol.la ---- coot-0.5-pre-1.orig/cootaneer/Makefile.am 2008-07-13 16:40:27.000000000 -0700 -+++ coot-0.5-pre-1/cootaneer/Makefile.am 2008-07-13 16:40:40.000000000 -0700 -@@ -34,6 +34,7 @@ - buccaneer-sequence.cpp cootaneer-sequence.cpp \ - buccaneer-lib.h buccaneer-prot.h \ - buccaneer-sequence.h cootaneer-sequence.h -+libcootaneer_la_LIBADD = $(CLIPPER_LIBS) - - subpkgdatadir = $(pkgdatadir) - subpkgdata_DATA = cootaneer-llk-2.40.dat ---- coot-0.5-pre-1.orig/coot-surface/Makefile.am 2008-07-13 16:40:27.000000000 -0700 -+++ coot-0.5-pre-1/coot-surface/Makefile.am 2008-07-13 16:40:40.000000000 -0700 -@@ -25,3 +25,4 @@ - - libcoot_surface_la_SOURCES = \ - coot-surface.cc coot-surface.hh rgbreps.cc rgbreps.h -+libcoot_surface_la_LIBADD = $(top_builddir)/surface/libccp4mg-surface.la ---- coot-0.5-pre-1.orig/coot-utils/Makefile.am 2008-07-13 16:40:27.000000000 -0700 -+++ coot-0.5-pre-1/coot-utils/Makefile.am 2008-07-13 16:40:40.000000000 -0700 -@@ -51,9 +51,11 @@ - # for pure coordinates (mmdb) things - libcoot_coord_utils_la_SOURCES = coot-coord-utils.cc \ - coot-coord-utils-nucleotides.cc coot-rama.cc -+libcoot_coord_utils_la_LIBADD = $(CLIPPER_LIBS) libcoot-utils.la - - # shelx - libcoot_shelx_la_SOURCES = coot-shelx-ins.cc -+libcoot_shelx_la_LIBADD = $(MMDB_LIBS) libcoot-coord-utils.la - - # for non-simple coordinates things - libcoot_coord_extras_la_SOURCES = coot-coord-extras.cc coot-coord-lsq.cc -@@ -63,21 +65,20 @@ - - # for map things that need mmdb, clipper, gsl and other things - libcoot_map_heavy_la_SOURCES = coot-map-heavy.cc coot-fffear.cc -+libcoot_map_heavy_la_LIBADD = $(GSL_LIBS) - - noinst_PROGRAMS = testshelxreader testcootutils - - testshelxreader_SOURCES = test-shelx-reader.cc - testshelxreader_LDADD = \ - ./libcoot-shelx.la \ -- ./libcoot-coord-utils.la \ -- ./libcoot-utils.la \ -- $(CLIPPER_LIBS) $(MMDB_LIBS) -+ ./libcoot-utils.la - - testcootutils_SOURCES = test-utils.cc - testcootutils_LDADD = \ - ./libcoot-shelx.la \ - ./libcoot-coord-utils.la \ - ./libcoot-utils.la \ -- $(CLIPPER_LIBS) $(MMDB_LIBS) -+ $(MMDB_LIBS) - - ---- coot-0.5/geometry/Makefile.am 2008-09-08 15:22:01.000000000 +0200 -+++ coot-0.5/geometry/Makefile.am.new 2008-11-20 12:01:08.000000000 +0100 -@@ -35,6 +35,10 @@ - - libcoot_geometry_la_SOURCES = protein-geometry.cc protein-geometry-mmdb.cc - -+libcoot_geometry_la_LIBADD = \ -+ $(top_builddir)/coot-utils/libcoot-utils.la \ -+ $(CLIPPER_LIBS) $(MMDB_LIBS) -+ - # libcoot_geometry_la_CXXFLAGS = -g -O1 - - noinst_PROGRAMS = test-geometry test-read-components -@@ -43,12 +47,6 @@ - - test_read_components_SOURCES = test-read-components.cc test-read-components.hh - --test_geometry_LDADD = ./libcoot-geometry.la \ -- $(top_builddir)/coot-utils/libcoot-utils.la \ -- $(CLIPPER_LIBS) $(MMDB_LIBS) -- --test_read_components_LDADD = \ -- ./libcoot-geometry.la \ -- $(top_builddir)/coot-utils/libcoot-utils.la \ -- $(CLIPPER_LIBS) $(MMDB_LIBS) -+test_geometry_LDADD = ./libcoot-geometry.la - -+test_read_components_LDADD = ./libcoot-geometry.la - ---- coot-0.5-pre-1.orig/high-res/Makefile.am 2008-07-13 16:40:27.000000000 -0700 -+++ coot-0.5-pre-1/high-res/Makefile.am 2008-07-13 16:40:40.000000000 -0700 -@@ -39,13 +39,16 @@ - - libcoot_high_res_la_SOURCES = high-res.cc coot-atom-graph.cc residue-distortions.cc \ - sequence-assignment.cc -+libcoot_high_res_la_LIBADD = \ -+ $(top_builddir)/ligand/libcoot-ligand.la \ -+ $(top_builddir)/coot-utils/libcoot-map-utils.la \ -+ $(CLIPPER_LIBS) $(MMDB_LIBS) - - noinst_PROGRAMS = testatomgraph tracehighres testseqalign testseqassignment globularize_protein - - testatomgraph_SOURCES = test-atom-graph.cc - - testatomgraph_LDADD = libcoot-high-res.la \ -- $(top_builddir)/ligand/libcoot-ligand.la \ - $(top_builddir)/db-main/libcoot-db-main.la \ - $(top_builddir)/ideal/libcoot-ideal.la \ - $(top_builddir)/geometry/libcoot-geometry.la \ -@@ -53,90 +56,73 @@ - $(top_builddir)/mini-mol/libcoot-mini-mol.la \ - $(top_builddir)/coot-utils/libcoot-coord-extras.la \ - $(top_builddir)/coot-utils/libcoot-coord-utils.la \ -- $(top_builddir)/coot-utils/libcoot-map-utils.la \ - $(top_builddir)/coot-utils/libcoot-shelx.la \ - $(top_builddir)/coot-utils/libcoot-utils.la \ - $(top_builddir)/ccp4mg-utils/libccp4mg-utils.la \ - $(top_builddir)/compat/libcoot-compat.la \ -- $(GSL_LIBS) \ -- $(CLIPPER_LIBS) -+ $(GSL_LIBS) - - testseqassignment_SOURCES = testseqassignment.cc - testseqassignment_LDADD = libcoot-high-res.la \ -- $(top_builddir)/ligand/libcoot-ligand.la \ - $(top_builddir)/db-main/libcoot-db-main.la \ - $(top_builddir)/ideal/libcoot-ideal.la \ - $(top_builddir)/geometry/libcoot-geometry.la \ - $(top_builddir)/coords/libcoot-coords.la \ - $(top_builddir)/mini-mol/libcoot-mini-mol.la \ - $(top_builddir)/coot-utils/libcoot-coord-extras.la \ -- $(top_builddir)/coot-utils/libcoot-map-utils.la \ - $(top_builddir)/coot-utils/libcoot-coord-utils.la \ - $(top_builddir)/coot-utils/libcoot-shelx.la \ - $(top_builddir)/coot-utils/libcoot-utils.la \ - $(top_builddir)/compat/libcoot-compat.la \ - $(top_builddir)/ccp4mg-utils/libccp4mg-utils.la \ -- $(GSL_LIBS) \ -- $(CLIPPER_LIBS) -+ $(GSL_LIBS) - - # tracehighres_LDFLAGS = -static - tracehighres_SOURCES = trace-high-res.cc - tracehighres_LDADD = libcoot-high-res.la \ -- $(top_builddir)/ligand/libcoot-ligand.la \ - $(top_builddir)/ideal/libcoot-ideal.la \ - $(top_builddir)/db-main/libcoot-db-main.la \ - $(top_builddir)/geometry/libcoot-geometry.la \ - $(top_builddir)/coords/libcoot-coords.la \ - $(top_builddir)/mini-mol/libcoot-mini-mol.la \ - $(top_builddir)/coot-utils/libcoot-coord-extras.la \ -- $(top_builddir)/coot-utils/libcoot-map-utils.la \ - $(top_builddir)/coot-utils/libcoot-coord-utils.la \ - $(top_builddir)/coot-utils/libcoot-shelx.la \ - $(top_builddir)/coot-utils/libcoot-utils.la \ - $(top_builddir)/compat/libcoot-compat.la \ - $(top_builddir)/ccp4mg-utils/libccp4mg-utils.la \ -- $(GSL_LIBS) \ -- $(CLIPPER_LIBS) -- -+ $(GSL_LIBS) - - testseqalign_SOURCES = testseqalign.cc - - # why do we need to link with all this (junk)? - testseqalign_LDADD = libcoot-high-res.la \ -- $(top_builddir)/ligand/libcoot-ligand.la \ - $(top_builddir)/ideal/libcoot-ideal.la \ - $(top_builddir)/db-main/libcoot-db-main.la \ - $(top_builddir)/geometry/libcoot-geometry.la \ - $(top_builddir)/coords/libcoot-coords.la \ - $(top_builddir)/mini-mol/libcoot-mini-mol.la \ - $(top_builddir)/coot-utils/libcoot-coord-extras.la \ -- $(top_builddir)/coot-utils/libcoot-map-utils.la \ - $(top_builddir)/coot-utils/libcoot-coord-utils.la \ - $(top_builddir)/coot-utils/libcoot-shelx.la \ - $(top_builddir)/coot-utils/libcoot-utils.la \ - $(top_builddir)/ccp4mg-utils/libccp4mg-utils.la \ - $(top_builddir)/compat/libcoot-compat.la \ -- $(GSL_LIBS) \ -- $(CLIPPER_LIBS) -- -+ $(GSL_LIBS) - - globularize_protein_SOURCES = globularize.cc - - globularize_protein_LDADD = libcoot-high-res.la \ -- $(top_builddir)/ligand/libcoot-ligand.la \ - $(top_builddir)/db-main/libcoot-db-main.la \ - $(top_builddir)/ideal/libcoot-ideal.la \ - $(top_builddir)/geometry/libcoot-geometry.la \ - $(top_builddir)/coords/libcoot-coords.la \ - $(top_builddir)/mini-mol/libcoot-mini-mol.la \ - $(top_builddir)/coot-utils/libcoot-coord-extras.la \ -- $(top_builddir)/coot-utils/libcoot-map-utils.la \ - $(top_builddir)/coot-utils/libcoot-coord-utils.la \ - $(top_builddir)/coot-utils/libcoot-shelx.la \ - $(top_builddir)/coot-utils/libcoot-utils.la \ - $(top_builddir)/ccp4mg-utils/libccp4mg-utils.la \ - $(top_builddir)/compat/libcoot-compat.la \ -- $(GSL_LIBS) \ -- $(CLIPPER_LIBS) -- -+ $(GSL_LIBS) - ---- coot-0.5-pre-1.orig/ideal/Makefile.am 2008-07-13 16:40:27.000000000 -0700 -+++ coot-0.5-pre-1/ideal/Makefile.am 2008-07-13 16:41:14.000000000 -0700 -@@ -44,6 +44,12 @@ - AM_CXXFLAGS = $(COOT_GSL_FLAGS) $(GSL_CFLAGS) - - libcoot_ideal_la_SOURCES = simple-restraint.cc pepflip.cc regularize-minimol.cc lograma.cpp -+libcoot_ideal_la_LIBADD = \ -+ $(top_builddir)/coot-utils/libcoot-utils.la \ -+ $(top_builddir)/mini-mol/libcoot-mini-mol.la \ -+ $(top_builddir)/coot-utils/libcoot-shelx.la \ -+ $(top_builddir)/coot-utils/libcoot-coord-extras.la \ -+ $(GSL_LIBS) - - noinst_PROGRAMS = test-indexing with-geometry with-map logramatest - # bin_PROGRAMS = -@@ -63,36 +69,25 @@ - with_geometry_LDADD = \ - ./libcoot-ideal.la \ - $(top_builddir)/geometry/libcoot-geometry.la \ -- $(top_builddir)/mini-mol/libcoot-mini-mol.la \ - $(top_builddir)/coords/libcoot-coords.la \ -- $(top_builddir)/coot-utils/libcoot-shelx.la \ -- $(top_builddir)/coot-utils/libcoot-coord-extras.la \ - $(top_builddir)/coot-utils/libcoot-coord-utils.la \ -- $(top_builddir)/coot-utils/libcoot-utils.la \ -- $(CLIPPER_LIBS) $(MMDB_LIBS) $(GSL_LIBS) -+ $(CLIPPER_LIBS) $(MMDB_LIBS) - - # add libcoot-map-utils for the debugging density_around_point function - with_map_LDADD = \ - ./libcoot-ideal.la \ - $(top_builddir)/geometry/libcoot-geometry.la \ -- $(top_builddir)/mini-mol/libcoot-mini-mol.la \ - $(top_builddir)/coords/libcoot-coords.la \ - $(top_builddir)/coot-utils/libcoot-map-utils.la \ -- $(top_builddir)/coot-utils/libcoot-shelx.la \ -- $(top_builddir)/coot-utils/libcoot-coord-extras.la \ -- $(top_builddir)/coot-utils/libcoot-coord-utils.la \ -- $(top_builddir)/coot-utils/libcoot-utils.la \ -- $(top_builddir)/compat/libcoot-compat.la \ -- $(CLIPPER_LIBS) $(MMDB_LIBS) $(GSL_LIBS) -+ $(top_builddir)/coot-utils/libcoot-coord-utils.la \ -+ $(top_builddir)/compat/libcoot-compat.la \ -+ $(CLIPPER_LIBS) $(MMDB_LIBS) - - test_indexing_LDADD = \ - ./libcoot-ideal.la \ - $(top_builddir)/geometry/libcoot-geometry.la \ -- $(top_builddir)/mini-mol/libcoot-mini-mol.la \ -- $(top_builddir)/coot-utils/libcoot-coord-extras.la \ - $(top_builddir)/coot-utils/libcoot-coord-utils.la \ -- $(top_builddir)/coot-utils/libcoot-utils.la \ -- $(CLIPPER_LIBS) $(MMDB_LIBS) $(GSL_LIBS) -+ $(CLIPPER_LIBS) $(MMDB_LIBS) - - # Why do I need all these libraries to simply link a trivial test program? - # Badness.... ---- coot-0.5-pre-1.orig/ligand/Makefile.am 2008-07-13 16:40:27.000000000 -0700 -+++ coot-0.5-pre-1/ligand/Makefile.am 2008-07-13 16:40:40.000000000 -0700 -@@ -46,6 +46,16 @@ - chi-angles.cc helix-placement.cc rigid-body.cc ideal-rna.cc \ - richardson-rotamers.cc richardson-rotamer.cc rotamer.cc \ - torsion-general.cc rotamer-tables.cc primitive-chi-angles.cc -+libcoot_ligand_la_LIBADD = \ -+ $(top_builddir)/ideal/libcoot-ideal.la \ -+ $(top_builddir)/coords/libcoot-coords.la \ -+ $(top_builddir)/coot-utils/libcoot-coord-extras.la \ -+ $(top_builddir)/coot-utils/libcoot-map-utils.la \ -+ $(top_builddir)/db-main/libcoot-db-main.la \ -+ $(top_builddir)/coot-utils/libcoot-shelx.la \ -+ $(top_builddir)/geometry/libcoot-geometry.la \ -+ $(top_builddir)/coot-utils/libcoot-coord-utils.la \ -+ $(top_builddir)/ccp4mg-utils/libccp4mg-utils.la - - AM_CXXFLAGS = \ - -DPKGDATADIR='"$(pkgdatadir)"' \ -@@ -83,35 +93,17 @@ - - test_ligand_LDADD = \ - ./libcoot-ligand.la \ -- $(top_builddir)/ideal/libcoot-ideal.la \ - $(top_builddir)/mini-mol/libcoot-mini-mol.la \ -- $(top_builddir)/coords/libcoot-coords.la \ -- $(top_builddir)/coot-utils/libcoot-coord-extras.la \ -- $(top_builddir)/coot-utils/libcoot-map-utils.la \ -- $(top_builddir)/db-main/libcoot-db-main.la \ -- $(top_builddir)/coot-utils/libcoot-shelx.la \ -- $(top_builddir)/geometry/libcoot-geometry.la \ - $(top_builddir)/mini-mol/libcoot-mini-mol.la \ -- $(top_builddir)/coot-utils/libcoot-coord-utils.la \ - $(top_builddir)/coot-utils/libcoot-utils.la \ -- $(top_builddir)/ccp4mg-utils/libccp4mg-utils.la \ - $(top_builddir)/compat/libcoot-compat.la \ - $(CLIPPER_LIBS) $(MMDB_LIBS) $(GSL_LIBS) - - test_helix_placement_LDADD = \ - ./libcoot-ligand.la \ -- $(top_builddir)/ideal/libcoot-ideal.la \ - $(top_builddir)/mini-mol/libcoot-mini-mol.la \ -- $(top_builddir)/coords/libcoot-coords.la \ -- $(top_builddir)/coot-utils/libcoot-coord-extras.la \ -- $(top_builddir)/coot-utils/libcoot-map-utils.la \ -- $(top_builddir)/coot-utils/libcoot-shelx.la \ -- $(top_builddir)/geometry/libcoot-geometry.la \ -- $(top_builddir)/db-main/libcoot-db-main.la \ - $(top_builddir)/mini-mol/libcoot-mini-mol.la \ -- $(top_builddir)/coot-utils/libcoot-coord-utils.la \ - $(top_builddir)/coot-utils/libcoot-utils.la \ -- $(top_builddir)/ccp4mg-utils/libccp4mg-utils.la \ - $(top_builddir)/compat/libcoot-compat.la \ - $(CLIPPER_LIBS) $(MMDB_LIBS) $(GSL_LIBS) - -@@ -119,19 +111,10 @@ - - test_fffear_in_coot_LDADD = \ - ./libcoot-ligand.la \ -- $(top_builddir)/ideal/libcoot-ideal.la \ - $(top_builddir)/mini-mol/libcoot-mini-mol.la \ -- $(top_builddir)/coot-utils/libcoot-coord-extras.la \ -- $(top_builddir)/coords/libcoot-coords.la \ -- $(top_builddir)/coot-utils/libcoot-shelx.la \ -- $(top_builddir)/geometry/libcoot-geometry.la \ - $(top_builddir)/mini-mol/libcoot-mini-mol.la \ - $(top_builddir)/coot-utils/libcoot-map-heavy.la \ -- $(top_builddir)/db-main/libcoot-db-main.la \ -- $(top_builddir)/coot-utils/libcoot-map-utils.la \ -- $(top_builddir)/coot-utils/libcoot-coord-utils.la \ - $(top_builddir)/coot-utils/libcoot-utils.la \ -- $(top_builddir)/ccp4mg-utils/libccp4mg-utils.la \ - $(top_builddir)/compat/libcoot-compat.la \ - $(CLIPPER_LIBS) $(MMDB_LIBS) $(GSL_LIBS) - -@@ -143,33 +126,15 @@ - - findligand_real_LDADD = \ - ./libcoot-ligand.la \ -- $(top_builddir)/ideal/libcoot-ideal.la \ -- $(top_builddir)/geometry/libcoot-geometry.la \ - $(top_builddir)/mini-mol/libcoot-mini-mol.la \ -- $(top_builddir)/coords/libcoot-coords.la \ -- $(top_builddir)/db-main/libcoot-db-main.la \ -- $(top_builddir)/ccp4mg-utils/libccp4mg-utils.la \ -- $(top_builddir)/coot-utils/libcoot-map-utils.la \ -- $(top_builddir)/coot-utils/libcoot-coord-extras.la \ -- $(top_builddir)/coot-utils/libcoot-coord-utils.la \ - $(top_builddir)/coot-utils/libcoot-utils.la \ -- $(top_builddir)/coot-utils/libcoot-shelx.la \ - $(top_builddir)/compat/libcoot-compat.la \ - $(CLIPPER_LIBS) $(MMDB_LIBS) $(GSL_LIBS) - - findwaters_real_LDADD = \ - ./libcoot-ligand.la \ -- $(top_builddir)/ideal/libcoot-ideal.la \ -- $(top_builddir)/geometry/libcoot-geometry.la \ -- $(top_builddir)/coords/libcoot-coords.la \ - $(top_builddir)/mini-mol/libcoot-mini-mol.la \ -- $(top_builddir)/ccp4mg-utils/libccp4mg-utils.la \ -- $(top_builddir)/db-main/libcoot-db-main.la \ -- $(top_builddir)/coot-utils/libcoot-coord-extras.la \ -- $(top_builddir)/coot-utils/libcoot-map-utils.la \ -- $(top_builddir)/coot-utils/libcoot-coord-utils.la \ - $(top_builddir)/coot-utils/libcoot-utils.la \ -- $(top_builddir)/coot-utils/libcoot-shelx.la \ - $(top_builddir)/compat/libcoot-compat.la \ - $(CLIPPER_LIBS) $(MMDB_LIBS) $(GSL_LIBS) - -@@ -190,17 +155,8 @@ - testdunbrack_SOURCES = testdunbrack.cc - - testdunbrack_LDADD = ./libcoot-ligand.la \ -- $(top_builddir)/ideal/libcoot-ideal.la \ - $(top_builddir)/mini-mol/libcoot-mini-mol.la \ -- $(top_builddir)/geometry/libcoot-geometry.la \ -- $(top_builddir)/coords/libcoot-coords.la \ -- $(top_builddir)/ccp4mg-utils/libccp4mg-utils.la \ -- $(top_builddir)/coot-utils/libcoot-map-utils.la \ -- $(top_builddir)/db-main/libcoot-db-main.la \ -- $(top_builddir)/coot-utils/libcoot-coord-extras.la \ -- $(top_builddir)/coot-utils/libcoot-coord-utils.la \ - $(top_builddir)/coot-utils/libcoot-utils.la \ -- $(top_builddir)/coot-utils/libcoot-shelx.la \ - $(CLIPPER_LIBS) $(MMDB_LIBS) $(GSL_LIBS) - - # lib coot-coords depends on mmdb, even though Cartesian doesn't ---- coot-0.5-pre-1.orig/Makefile.am 2008-07-13 16:40:27.000000000 -0700 -+++ coot-0.5-pre-1/Makefile.am 2008-07-13 16:40:40.000000000 -0700 -@@ -25,10 +25,10 @@ - - # see configure.in for po intl - SUBDIRS = auxil scheme python macros compat coot-utils surface coot-surface \ -- skeleton ccp4mg-utils density-contour coords angles \ -- mini-mol db-main geometry \ -+ atom-utils skeleton ccp4mg-utils density-contour mini-mol coords angles \ -+ db-main geometry \ - ideal ligand high-res build greg-tests python-tests \ -- analysis sequence-view tw atom-utils cootaneer src rama-data doc -+ analysis sequence-view tw cootaneer src rama-data doc - - # po, no po today. - ---- coot-0.5-pre-1.orig/mini-mol/Makefile.am 2008-07-13 16:40:27.000000000 -0700 -+++ coot-0.5-pre-1/mini-mol/Makefile.am 2008-07-13 16:40:40.000000000 -0700 -@@ -32,8 +32,9 @@ - testminimol_SOURCES = testminimol.cc - - libcoot_mini_mol_la_SOURCES = mini-mol.cc mini-mol-utils.cc -+libcoot_mini_mol_la_LIBADD = \ -+ $(top_builddir)/coot-utils/libcoot-coord-utils.la \ -+ $(CLIPPER_LIBS) - - testminimol_LDADD = libcoot-mini-mol.la \ -- $(top_builddir)/coot-utils/libcoot-coord-utils.la \ -- $(top_builddir)/coot-utils/libcoot-utils.la \ -- $(CLIPPER_LIBS) $(MMDB_LIBS) -+ $(MMDB_LIBS) ---- coot-0.5-pre-1.orig/skeleton/Makefile.am 2008-07-13 16:40:27.000000000 -0700 -+++ coot-0.5-pre-1/skeleton/Makefile.am 2008-07-13 16:40:40.000000000 -0700 -@@ -36,7 +36,7 @@ - - - libcoot_skeleton_la_SOURCES = $(libskeleton_a_sources) -- -+libcoot_skeleton_la_LIBADD = ../atom-utils/libcoot-atomutils.la - - # bin_PROGRAMS = ncssearch test_various test_torsion test_theta_2 - ---- coot-0.5-pre-1.orig/tw/Makefile.am 2008-07-13 16:40:27.000000000 -0700 -+++ coot-0.5-pre-1/tw/Makefile.am 2008-07-13 16:40:40.000000000 -0700 -@@ -39,15 +39,15 @@ - include_HEADERS = coot-tw.hh - - libcoot_tw_la_SOURCES = tw.cc -+libcoot_tw_la_LIBADD = \ -+ $(GTKCANVAS_LIBS) \ -+ @GTK_LIBS@ - - noinst_PROGRAMS = coot-tiddly - - coot_tiddly_SOURCES = tiddly.cc - --coot_tiddly_LDADD = libcoot-tw.la \ -- $(GTKCANVAS_LIBS) \ -- @GTK_LIBS@ -- -+coot_tiddly_LDADD = libcoot-tw.la - - # cootsound_LDADD = -L/sw/lib -lvorbisfile -logg -lao - diff --git a/sci-chemistry/coot/files/0.5.2-gcc-4.3.patch b/sci-chemistry/coot/files/0.5.2-gcc-4.3.patch deleted file mode 100644 index 26377ed9d..000000000 --- a/sci-chemistry/coot/files/0.5.2-gcc-4.3.patch +++ /dev/null @@ -1,10 +0,0 @@ ---- coot-0.5-pre-1.orig/ligand/rotamer.cc 2008-07-01 18:14:54.000000000 -0700 -+++ coot-0.5-pre-1/ligand/rotamer.cc 2008-07-01 18:15:10.000000000 -0700 -@@ -21,6 +21,7 @@ - * 02110-1301, USA - */ - -+#include <cstring> - #include <fstream> - #include <stdexcept> - diff --git a/sci-chemistry/coot/files/0.5.2-gcc-4.4.patch b/sci-chemistry/coot/files/0.5.2-gcc-4.4.patch deleted file mode 100644 index d754a519c..000000000 --- a/sci-chemistry/coot/files/0.5.2-gcc-4.4.patch +++ /dev/null @@ -1,11 +0,0 @@ ---- coot-utils/coot-utils.cc 2008-12-10 01:22:01.000000000 +0100 -+++ coot-utils/coot-utils.cc.new 2009-08-06 00:31:18.000000000 +0200 -@@ -47,7 +47,7 @@ - - #include "clipper/core/hkl_compute.h" - #include "coot-utils.hh" -- -+#include <cstdio> - - - std::string diff --git a/sci-chemistry/coot/files/0.6_pre1-as-needed.patch b/sci-chemistry/coot/files/0.6_pre1-as-needed.patch deleted file mode 100644 index 0cfce54dd..000000000 --- a/sci-chemistry/coot/files/0.6_pre1-as-needed.patch +++ /dev/null @@ -1,481 +0,0 @@ -Index: mini-mol/Makefile.am -=================================================================== ---- mini-mol/Makefile.am (revision 2293) -+++ mini-mol/Makefile.am (working copy) -@@ -35,8 +35,9 @@ - testminimol_SOURCES = testminimol.cc - - libcoot_mini_mol_la_SOURCES = mini-mol.cc mini-mol-utils.cc atom-quads.cc -+libcoot_mini_mol_la_LIBADD = \ -+ $(top_builddir)/coot-utils/libcoot-coord-utils.la \ -+ $(CLIPPER_LIBS) - - testminimol_LDADD = libcoot-mini-mol.la \ -- $(top_builddir)/coot-utils/libcoot-coord-utils.la \ -- $(top_builddir)/coot-utils/libcoot-utils.la \ -- $(CLIPPER_LIBS) $(MMDB_LIBS) -+ $(MMDB_LIBS) -Index: coords/Makefile.am -=================================================================== ---- coords/Makefile.am (revision 2293) -+++ coords/Makefile.am (working copy) -@@ -40,3 +40,7 @@ - mmdb-extras.cc utils.cc mmdb.cc mmdb-crystal.cc \ - Bond_lines_ext.cc coot-close.cc - -+libcoot_coords_la_LIBADD = \ -+ $(top_builddir)/coot-utils/libcoot-shelx.la \ -+ $(top_builddir)/mini-mol/libcoot-mini-mol.la -+ -Index: ligand/Makefile.am -=================================================================== ---- ligand/Makefile.am (revision 2293) -+++ ligand/Makefile.am (working copy) -@@ -49,6 +49,17 @@ - torsion-general.cc rotamer-tables.cc primitive-chi-angles.cc dipole.cc\ - base-pairing.cc backrub-rotamer.cc - -+libcoot_ligand_la_LIBADD = \ -+ $(top_builddir)/ideal/libcoot-ideal.la \ -+ $(top_builddir)/coords/libcoot-coords.la \ -+ $(top_builddir)/coot-utils/libcoot-coord-extras.la \ -+ $(top_builddir)/coot-utils/libcoot-map-utils.la \ -+ $(top_builddir)/db-main/libcoot-db-main.la \ -+ $(top_builddir)/coot-utils/libcoot-shelx.la \ -+ $(top_builddir)/geometry/libcoot-geometry.la \ -+ $(top_builddir)/coot-utils/libcoot-coord-utils.la \ -+ $(top_builddir)/ccp4mg-utils/libccp4mg-utils.la -+ - AM_CXXFLAGS = \ - -DPKGDATADIR='"$(pkgdatadir)"' \ - $(COOT_WINDOWS_CFLAGS) -@@ -68,7 +79,6 @@ - - test_random_LDADD = \ - ./libcoot-ligand.la \ -- $(top_builddir)/ideal/libcoot-ideal.la \ - $(top_builddir)/coords/libcoot-coords.la \ - $(top_builddir)/coot-utils/libcoot-coord-extras.la \ - $(top_builddir)/coot-utils/libcoot-map-utils.la \ -@@ -85,31 +95,14 @@ - - test_ligand_LDADD = \ - ./libcoot-ligand.la \ -- $(top_builddir)/ideal/libcoot-ideal.la \ - $(top_builddir)/mini-mol/libcoot-mini-mol.la \ -- $(top_builddir)/coords/libcoot-coords.la \ -- $(top_builddir)/coot-utils/libcoot-coord-extras.la \ -- $(top_builddir)/coot-utils/libcoot-map-utils.la \ -- $(top_builddir)/db-main/libcoot-db-main.la \ -- $(top_builddir)/coot-utils/libcoot-shelx.la \ -- $(top_builddir)/geometry/libcoot-geometry.la \ -- $(top_builddir)/coot-utils/libcoot-coord-utils.la \ - $(top_builddir)/coot-utils/libcoot-utils.la \ - $(top_builddir)/mini-mol/libcoot-mini-mol.la \ -- $(top_builddir)/ccp4mg-utils/libccp4mg-utils.la \ - $(top_builddir)/compat/libcoot-compat.la \ - $(CLIPPER_LIBS) $(MMDB_LIBS) $(GSL_LIBS) - - test_helix_placement_LDADD = \ - ./libcoot-ligand.la \ -- $(top_builddir)/ideal/libcoot-ideal.la \ -- $(top_builddir)/coords/libcoot-coords.la \ -- $(top_builddir)/coot-utils/libcoot-coord-extras.la \ -- $(top_builddir)/coot-utils/libcoot-map-utils.la \ -- $(top_builddir)/coot-utils/libcoot-shelx.la \ -- $(top_builddir)/geometry/libcoot-geometry.la \ -- $(top_builddir)/db-main/libcoot-db-main.la \ -- $(top_builddir)/coot-utils/libcoot-coord-utils.la \ - $(top_builddir)/coot-utils/libcoot-utils.la \ - $(top_builddir)/mini-mol/libcoot-mini-mol.la \ - $(top_builddir)/ccp4mg-utils/libccp4mg-utils.la \ -@@ -120,18 +113,9 @@ - - test_fffear_in_coot_LDADD = \ - ./libcoot-ligand.la \ -- $(top_builddir)/ideal/libcoot-ideal.la \ -- $(top_builddir)/coot-utils/libcoot-coord-extras.la \ -- $(top_builddir)/coords/libcoot-coords.la \ -- $(top_builddir)/coot-utils/libcoot-shelx.la \ -- $(top_builddir)/geometry/libcoot-geometry.la \ - $(top_builddir)/coot-utils/libcoot-map-heavy.la \ -- $(top_builddir)/db-main/libcoot-db-main.la \ -- $(top_builddir)/coot-utils/libcoot-map-utils.la \ -- $(top_builddir)/coot-utils/libcoot-coord-utils.la \ - $(top_builddir)/coot-utils/libcoot-utils.la \ - $(top_builddir)/mini-mol/libcoot-mini-mol.la \ -- $(top_builddir)/ccp4mg-utils/libccp4mg-utils.la \ - $(top_builddir)/compat/libcoot-compat.la \ - $(CLIPPER_LIBS) $(MMDB_LIBS) $(GSL_LIBS) - -@@ -143,23 +127,13 @@ - - findligand_real_LDADD = \ - ./libcoot-ligand.la \ -- $(top_builddir)/ideal/libcoot-ideal.la \ -- $(top_builddir)/geometry/libcoot-geometry.la \ -- $(top_builddir)/coords/libcoot-coords.la \ -- $(top_builddir)/db-main/libcoot-db-main.la \ -- $(top_builddir)/ccp4mg-utils/libccp4mg-utils.la \ -- $(top_builddir)/coot-utils/libcoot-map-utils.la \ -- $(top_builddir)/coot-utils/libcoot-coord-extras.la \ -- $(top_builddir)/coot-utils/libcoot-coord-utils.la \ - $(top_builddir)/coot-utils/libcoot-utils.la \ -- $(top_builddir)/coot-utils/libcoot-shelx.la \ - $(top_builddir)/mini-mol/libcoot-mini-mol.la \ - $(top_builddir)/compat/libcoot-compat.la \ - $(CLIPPER_LIBS) $(MMDB_LIBS) $(GSL_LIBS) - - findwaters_real_LDADD = \ - ./libcoot-ligand.la \ -- $(top_builddir)/ideal/libcoot-ideal.la \ - $(top_builddir)/geometry/libcoot-geometry.la \ - $(top_builddir)/coords/libcoot-coords.la \ - $(top_builddir)/ccp4mg-utils/libccp4mg-utils.la \ -@@ -190,16 +164,7 @@ - testdunbrack_SOURCES = testdunbrack.cc - - testdunbrack_LDADD = ./libcoot-ligand.la \ -- $(top_builddir)/ideal/libcoot-ideal.la \ -- $(top_builddir)/geometry/libcoot-geometry.la \ -- $(top_builddir)/coords/libcoot-coords.la \ -- $(top_builddir)/ccp4mg-utils/libccp4mg-utils.la \ -- $(top_builddir)/coot-utils/libcoot-map-utils.la \ -- $(top_builddir)/db-main/libcoot-db-main.la \ -- $(top_builddir)/coot-utils/libcoot-coord-extras.la \ -- $(top_builddir)/coot-utils/libcoot-coord-utils.la \ - $(top_builddir)/coot-utils/libcoot-utils.la \ -- $(top_builddir)/coot-utils/libcoot-shelx.la \ - $(top_builddir)/mini-mol/libcoot-mini-mol.la \ - $(CLIPPER_LIBS) $(MMDB_LIBS) $(GSL_LIBS) - -Index: analysis/Makefile.am -=================================================================== ---- analysis/Makefile.am (revision 2293) -+++ analysis/Makefile.am (working copy) -@@ -9,6 +9,7 @@ - $(MMDB_CXXFLAGS) - - libcoot_analysis_la_SOURCES = bfkurt.cc -+libcoot_analysis_la_LIBADD = $(top_builddir)/coot-utils/libcoot-coord-utils.la - - bin_PROGRAMS = bfactan - -@@ -16,7 +17,6 @@ - - bfactan_LDADD = \ - libcoot-analysis.la \ -- $(top_builddir)/coot-utils/libcoot-coord-utils.la \ - $(top_builddir)/coot-utils/libcoot-utils.la \ - $(top_builddir)/geometry/libcoot-geometry.la \ - $(CLIPPER_LIBS) \ -Index: skeleton/Makefile.am -=================================================================== ---- skeleton/Makefile.am (revision 2293) -+++ skeleton/Makefile.am (working copy) -@@ -39,8 +39,8 @@ - - - libcoot_skeleton_la_SOURCES = $(libskeleton_a_sources) -+libcoot_skeleton_la_LIBADD = ../atom-utils/libcoot-atomutils.la - -- - # bin_PROGRAMS = ncssearch test_various test_torsion test_theta_2 - - # ncssearch_SOURCES = ncs-search.cc ncs-search.h -Index: coot-surface/Makefile.am -=================================================================== ---- coot-surface/Makefile.am (revision 2293) -+++ coot-surface/Makefile.am (working copy) -@@ -25,3 +25,4 @@ - - libcoot_surface_la_SOURCES = \ - coot-surface.cc coot-surface.hh rgbreps.cc rgbreps.h -+libcoot_surface_la_LIBADD = $(top_builddir)/surface/libccp4mg-surface.la -Index: high-res/Makefile.am -=================================================================== ---- high-res/Makefile.am (revision 2293) -+++ high-res/Makefile.am (working copy) -@@ -39,13 +39,16 @@ - - libcoot_high_res_la_SOURCES = high-res.cc coot-atom-graph.cc residue-distortions.cc \ - sequence-assignment.cc -+libcoot_high_res_la_LIBADD = \ -+ $(top_builddir)/ligand/libcoot-ligand.la \ -+ $(top_builddir)/coot-utils/libcoot-map-utils.la \ -+ $(CLIPPER_LIBS) $(MMDB_LIBS) - - check_PROGRAMS = testatomgraph tracehighres testseqalign testseqassignment globularize_protein - - testatomgraph_SOURCES = test-atom-graph.cc - - testatomgraph_LDADD = libcoot-high-res.la \ -- $(top_builddir)/ligand/libcoot-ligand.la \ - $(top_builddir)/db-main/libcoot-db-main.la \ - $(top_builddir)/ideal/libcoot-ideal.la \ - $(top_builddir)/geometry/libcoot-geometry.la \ -@@ -53,71 +56,60 @@ - $(top_builddir)/mini-mol/libcoot-mini-mol.la \ - $(top_builddir)/coot-utils/libcoot-coord-extras.la \ - $(top_builddir)/coot-utils/libcoot-coord-utils.la \ -- $(top_builddir)/coot-utils/libcoot-map-utils.la \ - $(top_builddir)/coot-utils/libcoot-shelx.la \ - $(top_builddir)/coot-utils/libcoot-utils.la \ - $(top_builddir)/ccp4mg-utils/libccp4mg-utils.la \ - $(top_builddir)/compat/libcoot-compat.la \ -- $(GSL_LIBS) \ -- $(CLIPPER_LIBS) -+ $(GSL_LIBS) - - testseqassignment_SOURCES = testseqassignment.cc - testseqassignment_LDADD = libcoot-high-res.la \ -- $(top_builddir)/ligand/libcoot-ligand.la \ - $(top_builddir)/db-main/libcoot-db-main.la \ - $(top_builddir)/ideal/libcoot-ideal.la \ - $(top_builddir)/geometry/libcoot-geometry.la \ - $(top_builddir)/coords/libcoot-coords.la \ - $(top_builddir)/mini-mol/libcoot-mini-mol.la \ - $(top_builddir)/coot-utils/libcoot-coord-extras.la \ -- $(top_builddir)/coot-utils/libcoot-map-utils.la \ - $(top_builddir)/coot-utils/libcoot-coord-utils.la \ - $(top_builddir)/coot-utils/libcoot-shelx.la \ - $(top_builddir)/coot-utils/libcoot-utils.la \ - $(top_builddir)/compat/libcoot-compat.la \ - $(top_builddir)/ccp4mg-utils/libccp4mg-utils.la \ -- $(GSL_LIBS) \ -- $(CLIPPER_LIBS) -+ $(GSL_LIBS) - - # tracehighres_LDFLAGS = -static - tracehighres_SOURCES = trace-high-res.cc - tracehighres_LDADD = libcoot-high-res.la \ -- $(top_builddir)/ligand/libcoot-ligand.la \ - $(top_builddir)/ideal/libcoot-ideal.la \ - $(top_builddir)/db-main/libcoot-db-main.la \ - $(top_builddir)/geometry/libcoot-geometry.la \ - $(top_builddir)/coords/libcoot-coords.la \ - $(top_builddir)/mini-mol/libcoot-mini-mol.la \ - $(top_builddir)/coot-utils/libcoot-coord-extras.la \ -- $(top_builddir)/coot-utils/libcoot-map-utils.la \ - $(top_builddir)/coot-utils/libcoot-coord-utils.la \ - $(top_builddir)/coot-utils/libcoot-shelx.la \ - $(top_builddir)/coot-utils/libcoot-utils.la \ - $(top_builddir)/compat/libcoot-compat.la \ - $(top_builddir)/ccp4mg-utils/libccp4mg-utils.la \ -- $(GSL_LIBS) \ -- $(CLIPPER_LIBS) -+ $(GSL_LIBS) - - - testseqalign_SOURCES = testseqalign.cc - - # why do we need to link with all this (junk)? - testseqalign_LDADD = libcoot-high-res.la \ -- $(top_builddir)/ligand/libcoot-ligand.la \ - $(top_builddir)/ideal/libcoot-ideal.la \ - $(top_builddir)/db-main/libcoot-db-main.la \ - $(top_builddir)/geometry/libcoot-geometry.la \ - $(top_builddir)/coords/libcoot-coords.la \ - $(top_builddir)/mini-mol/libcoot-mini-mol.la \ - $(top_builddir)/coot-utils/libcoot-coord-extras.la \ -- $(top_builddir)/coot-utils/libcoot-map-utils.la \ - $(top_builddir)/coot-utils/libcoot-coord-utils.la \ - $(top_builddir)/coot-utils/libcoot-shelx.la \ - $(top_builddir)/coot-utils/libcoot-utils.la \ - $(top_builddir)/ccp4mg-utils/libccp4mg-utils.la \ - $(top_builddir)/compat/libcoot-compat.la \ -- $(GSL_LIBS) \ -- $(CLIPPER_LIBS) -+ $(GSL_LIBS) - - - globularize_protein_SOURCES = globularize.cc -Index: cootaneer/Makefile.am -=================================================================== ---- cootaneer/Makefile.am (revision 2293) -+++ cootaneer/Makefile.am (working copy) -@@ -34,6 +34,7 @@ - buccaneer-sequence.cpp cootaneer-sequence.cpp \ - buccaneer-lib.h buccaneer-prot.h \ - buccaneer-sequence.h cootaneer-sequence.h -+libcootaneer_la_LIBADD = $(CLIPPER_LIBS) - - subpkgdatadir = $(pkgdatadir) - subpkgdata_DATA = cootaneer-llk-2.40.dat -Index: geometry/Makefile.am -=================================================================== ---- geometry/Makefile.am (revision 2293) -+++ geometry/Makefile.am (working copy) -@@ -35,6 +35,9 @@ - # -DHAVE_SYS_STDTYPES_H - - libcoot_geometry_la_SOURCES = protein-geometry.cc protein-geometry-mmdb.cc -+libcoot_geometry_la_LIBADD = \ -+ $(top_builddir)/coot-utils/libcoot-utils.la \ -+ $(CLIPPER_LIBS) $(MMDB_LIBS) - - # libcoot_geometry_la_CXXFLAGS = -g -O1 - -@@ -44,12 +47,7 @@ - - test_read_components_SOURCES = test-read-components.cc test-read-components.hh - --test_geometry_LDADD = ./libcoot-geometry.la \ -- $(top_builddir)/coot-utils/libcoot-utils.la \ -- $(CLIPPER_LIBS) $(MMDB_LIBS) -+test_geometry_LDADD = ./libcoot-geometry.la -+ -+test_read_components_LDADD = ./libcoot-geometry.la - --test_read_components_LDADD = \ -- ./libcoot-geometry.la \ -- $(top_builddir)/coot-utils/libcoot-utils.la \ -- $(CLIPPER_LIBS) $(MMDB_LIBS) -- -Index: ideal/Makefile.am -=================================================================== ---- ideal/Makefile.am (revision 2293) -+++ ideal/Makefile.am (working copy) -@@ -54,6 +54,12 @@ - - - libcoot_ideal_la_SOURCES = simple-restraint.cc pepflip.cc regularize-minimol.cc lograma.cpp -+libcoot_ideal_la_LIBADD = \ -+ $(top_builddir)/coot-utils/libcoot-utils.la \ -+ $(top_builddir)/mini-mol/libcoot-mini-mol.la \ -+ $(top_builddir)/coot-utils/libcoot-shelx.la \ -+ $(top_builddir)/coot-utils/libcoot-coord-extras.la \ -+ $(GSL_LIBS) - - - noinst_PROGRAMS = test-indexing with-geometry with-map logramatest -@@ -75,12 +81,8 @@ - ./libcoot-ideal.la \ - $(top_builddir)/geometry/libcoot-geometry.la \ - $(top_builddir)/coords/libcoot-coords.la \ -- $(top_builddir)/coot-utils/libcoot-shelx.la \ -- $(top_builddir)/coot-utils/libcoot-coord-extras.la \ - $(top_builddir)/coot-utils/libcoot-coord-utils.la \ -- $(top_builddir)/coot-utils/libcoot-utils.la \ -- $(top_builddir)/mini-mol/libcoot-mini-mol.la \ -- $(CLIPPER_LIBS) $(MMDB_LIBS) $(GSL_LIBS) -+ $(CLIPPER_LIBS) $(MMDB_LIBS) - - # add libcoot-map-utils for the debugging density_around_point function - with_map_LDADD = \ -@@ -88,22 +90,16 @@ - $(top_builddir)/geometry/libcoot-geometry.la \ - $(top_builddir)/coords/libcoot-coords.la \ - $(top_builddir)/coot-utils/libcoot-map-utils.la \ -- $(top_builddir)/coot-utils/libcoot-shelx.la \ -- $(top_builddir)/coot-utils/libcoot-coord-extras.la \ - $(top_builddir)/coot-utils/libcoot-coord-utils.la \ - $(top_builddir)/coot-utils/libcoot-utils.la \ -- $(top_builddir)/compat/libcoot-compat.la \ -- $(top_builddir)/mini-mol/libcoot-mini-mol.la \ -- $(CLIPPER_LIBS) $(MMDB_LIBS) $(GSL_LIBS) -+ $(top_builddir)/compat/libcoot-compat.la \ -+ $(CLIPPER_LIBS) $(MMDB_LIBS) - - test_indexing_LDADD = \ - ./libcoot-ideal.la \ - $(top_builddir)/geometry/libcoot-geometry.la \ -- $(top_builddir)/mini-mol/libcoot-mini-mol.la \ -- $(top_builddir)/coot-utils/libcoot-coord-extras.la \ - $(top_builddir)/coot-utils/libcoot-coord-utils.la \ -- $(top_builddir)/coot-utils/libcoot-utils.la \ -- $(CLIPPER_LIBS) $(MMDB_LIBS) $(GSL_LIBS) -+ $(CLIPPER_LIBS) $(MMDB_LIBS) - - # Why do I need all these libraries to simply link a trivial test program? - # Badness.... -Index: tw/Makefile.am -=================================================================== ---- tw/Makefile.am (revision 2293) -+++ tw/Makefile.am (working copy) -@@ -39,14 +39,15 @@ - include_HEADERS = coot-tw.hh - - libcoot_tw_la_SOURCES = tw.cc -+libcoot_tw_la_LIBADD = \ -+ $(GTKCANVAS_LIBS) \ -+ @GTK_LIBS@ - - noinst_PROGRAMS = coot-tiddly - - coot_tiddly_SOURCES = tiddly.cc - --coot_tiddly_LDADD = libcoot-tw.la \ -- $(GTKCANVAS_LIBS) \ -- @GTK_LIBS@ -+coot_tiddly_LDADD = libcoot-tw.la - - - # cootsound_LDADD = -L/sw/lib -lvorbisfile -logg -lao -Index: coot-utils/Makefile.am -=================================================================== ---- coot-utils/Makefile.am (revision 2293) -+++ coot-utils/Makefile.am (working copy) -@@ -49,6 +49,7 @@ - # for simple things: - libcoot_utils_la_SOURCES = coot-utils.cc coot-fasta.cc atomic-numbers.cc \ - gdk-keysyms.cc -+libcoot_coord_utils_la_LIBADD = $(CLIPPER_LIBS) libcoot-utils.la - - # for pure coordinates (mmdb) things - libcoot_coord_utils_la_SOURCES = coot-coord-utils.cc \ -@@ -56,6 +57,7 @@ - - # shelx - libcoot_shelx_la_SOURCES = coot-shelx-ins.cc -+libcoot_shelx_la_LIBADD = $(MMDB_LIBS) libcoot-coord-utils.la - - # for non-simple coordinates things - libcoot_coord_extras_la_SOURCES = coot-coord-extras.cc coot-coord-lsq.cc \ -@@ -63,24 +65,23 @@ - - # for (map) things that need to link mmdb and clipper: - libcoot_map_utils_la_SOURCES = coot-map-utils.cc peak-search.cc trim.cc xmap-stats.cc -+libcoot_map_utils_la_LIBADD = $(CLIPPER_LIBS) - - # for map things that need mmdb, clipper, gsl and other things - libcoot_map_heavy_la_SOURCES = coot-map-heavy.cc coot-fffear.cc -+libcoot_map_heavy_la_LIBADD = $(GSL_LIBS) - - noinst_PROGRAMS = testshelxreader testcootutils - - testshelxreader_SOURCES = test-shelx-reader.cc - testshelxreader_LDADD = \ - ./libcoot-shelx.la \ -- ./libcoot-coord-utils.la \ - ./libcoot-utils.la \ -- $(CLIPPER_LIBS) $(MMDB_LIBS) -+ $(MMDB_LIBS) - - testcootutils_SOURCES = test-utils.cc - testcootutils_LDADD = \ - ./libcoot-shelx.la \ -- ./libcoot-coord-utils.la \ - ./libcoot-utils.la \ -- $(CLIPPER_LIBS) $(MMDB_LIBS) -+ $(MMDB_LIBS) - -- -Index: Makefile.am -=================================================================== ---- Makefile.am (revision 2293) -+++ Makefile.am (working copy) -@@ -25,10 +25,10 @@ - - # see configure.in for po intl - SUBDIRS = auxil scheme python macros compat coot-utils surface coot-surface \ -- skeleton ccp4mg-utils density-contour coords angles \ -- mini-mol db-main geometry \ -+ atom-utils skeleton ccp4mg-utils density-contour mini-mol coords angles \ -+ db-main geometry \ - ideal ligand high-res build greg-tests python-tests \ -- analysis sequence-view tw atom-utils cootaneer src rama-data doc -+ analysis sequence-view tw cootaneer src rama-data doc - - # po, no po today. - diff --git a/sci-chemistry/coot/files/0.6_pre1-gcc4.4.patch b/sci-chemistry/coot/files/0.6_pre1-gcc4.4.patch deleted file mode 100644 index b7cd75662..000000000 --- a/sci-chemistry/coot/files/0.6_pre1-gcc4.4.patch +++ /dev/null @@ -1,10 +0,0 @@ ---- coot-utils/coot-utils.cc 2009-08-06 00:02:51.000000000 +0200 -+++ coot-utils/coot-utils.cc.new 2009-08-06 00:06:13.000000000 +0200 -@@ -25,6 +25,7 @@ - - #include <stdexcept> // for string_to_int. - #include <sstream> // ditto. -+#include <cstdio> - - #include "coot-sysdep.h" - #if defined _MSC_VER diff --git a/sci-chemistry/coot/files/0.6_pre1-test-rama.patch b/sci-chemistry/coot/files/0.6_pre1-test-rama.patch deleted file mode 100644 index 96bfbf60c..000000000 --- a/sci-chemistry/coot/files/0.6_pre1-test-rama.patch +++ /dev/null @@ -1,15 +0,0 @@ ---- src/graphics-info.h (revision 2296) -+++ src/graphics-info.h (working copy) -@@ -798,12 +798,10 @@ - // guess we shall rather use COOT_DATA_DIR and only as fallback PKGDATADIR?! - // maybe only for windows!? - std::string tables_dir = PKGDATADIR; --#ifdef WINDOWS_MINGW - char *data_dir = getenv("COOT_DATA_DIR"); - if (data_dir) { - tables_dir = data_dir; - } --#endif // MINGW - tables_dir += "/rama-data"; - rot_prob_tables.set_tables_dir(tables_dir); - diff --git a/sci-chemistry/coot/files/9999-as-needed.patch b/sci-chemistry/coot/files/9999-as-needed.patch deleted file mode 100644 index 0cfce54dd..000000000 --- a/sci-chemistry/coot/files/9999-as-needed.patch +++ /dev/null @@ -1,481 +0,0 @@ -Index: mini-mol/Makefile.am -=================================================================== ---- mini-mol/Makefile.am (revision 2293) -+++ mini-mol/Makefile.am (working copy) -@@ -35,8 +35,9 @@ - testminimol_SOURCES = testminimol.cc - - libcoot_mini_mol_la_SOURCES = mini-mol.cc mini-mol-utils.cc atom-quads.cc -+libcoot_mini_mol_la_LIBADD = \ -+ $(top_builddir)/coot-utils/libcoot-coord-utils.la \ -+ $(CLIPPER_LIBS) - - testminimol_LDADD = libcoot-mini-mol.la \ -- $(top_builddir)/coot-utils/libcoot-coord-utils.la \ -- $(top_builddir)/coot-utils/libcoot-utils.la \ -- $(CLIPPER_LIBS) $(MMDB_LIBS) -+ $(MMDB_LIBS) -Index: coords/Makefile.am -=================================================================== ---- coords/Makefile.am (revision 2293) -+++ coords/Makefile.am (working copy) -@@ -40,3 +40,7 @@ - mmdb-extras.cc utils.cc mmdb.cc mmdb-crystal.cc \ - Bond_lines_ext.cc coot-close.cc - -+libcoot_coords_la_LIBADD = \ -+ $(top_builddir)/coot-utils/libcoot-shelx.la \ -+ $(top_builddir)/mini-mol/libcoot-mini-mol.la -+ -Index: ligand/Makefile.am -=================================================================== ---- ligand/Makefile.am (revision 2293) -+++ ligand/Makefile.am (working copy) -@@ -49,6 +49,17 @@ - torsion-general.cc rotamer-tables.cc primitive-chi-angles.cc dipole.cc\ - base-pairing.cc backrub-rotamer.cc - -+libcoot_ligand_la_LIBADD = \ -+ $(top_builddir)/ideal/libcoot-ideal.la \ -+ $(top_builddir)/coords/libcoot-coords.la \ -+ $(top_builddir)/coot-utils/libcoot-coord-extras.la \ -+ $(top_builddir)/coot-utils/libcoot-map-utils.la \ -+ $(top_builddir)/db-main/libcoot-db-main.la \ -+ $(top_builddir)/coot-utils/libcoot-shelx.la \ -+ $(top_builddir)/geometry/libcoot-geometry.la \ -+ $(top_builddir)/coot-utils/libcoot-coord-utils.la \ -+ $(top_builddir)/ccp4mg-utils/libccp4mg-utils.la -+ - AM_CXXFLAGS = \ - -DPKGDATADIR='"$(pkgdatadir)"' \ - $(COOT_WINDOWS_CFLAGS) -@@ -68,7 +79,6 @@ - - test_random_LDADD = \ - ./libcoot-ligand.la \ -- $(top_builddir)/ideal/libcoot-ideal.la \ - $(top_builddir)/coords/libcoot-coords.la \ - $(top_builddir)/coot-utils/libcoot-coord-extras.la \ - $(top_builddir)/coot-utils/libcoot-map-utils.la \ -@@ -85,31 +95,14 @@ - - test_ligand_LDADD = \ - ./libcoot-ligand.la \ -- $(top_builddir)/ideal/libcoot-ideal.la \ - $(top_builddir)/mini-mol/libcoot-mini-mol.la \ -- $(top_builddir)/coords/libcoot-coords.la \ -- $(top_builddir)/coot-utils/libcoot-coord-extras.la \ -- $(top_builddir)/coot-utils/libcoot-map-utils.la \ -- $(top_builddir)/db-main/libcoot-db-main.la \ -- $(top_builddir)/coot-utils/libcoot-shelx.la \ -- $(top_builddir)/geometry/libcoot-geometry.la \ -- $(top_builddir)/coot-utils/libcoot-coord-utils.la \ - $(top_builddir)/coot-utils/libcoot-utils.la \ - $(top_builddir)/mini-mol/libcoot-mini-mol.la \ -- $(top_builddir)/ccp4mg-utils/libccp4mg-utils.la \ - $(top_builddir)/compat/libcoot-compat.la \ - $(CLIPPER_LIBS) $(MMDB_LIBS) $(GSL_LIBS) - - test_helix_placement_LDADD = \ - ./libcoot-ligand.la \ -- $(top_builddir)/ideal/libcoot-ideal.la \ -- $(top_builddir)/coords/libcoot-coords.la \ -- $(top_builddir)/coot-utils/libcoot-coord-extras.la \ -- $(top_builddir)/coot-utils/libcoot-map-utils.la \ -- $(top_builddir)/coot-utils/libcoot-shelx.la \ -- $(top_builddir)/geometry/libcoot-geometry.la \ -- $(top_builddir)/db-main/libcoot-db-main.la \ -- $(top_builddir)/coot-utils/libcoot-coord-utils.la \ - $(top_builddir)/coot-utils/libcoot-utils.la \ - $(top_builddir)/mini-mol/libcoot-mini-mol.la \ - $(top_builddir)/ccp4mg-utils/libccp4mg-utils.la \ -@@ -120,18 +113,9 @@ - - test_fffear_in_coot_LDADD = \ - ./libcoot-ligand.la \ -- $(top_builddir)/ideal/libcoot-ideal.la \ -- $(top_builddir)/coot-utils/libcoot-coord-extras.la \ -- $(top_builddir)/coords/libcoot-coords.la \ -- $(top_builddir)/coot-utils/libcoot-shelx.la \ -- $(top_builddir)/geometry/libcoot-geometry.la \ - $(top_builddir)/coot-utils/libcoot-map-heavy.la \ -- $(top_builddir)/db-main/libcoot-db-main.la \ -- $(top_builddir)/coot-utils/libcoot-map-utils.la \ -- $(top_builddir)/coot-utils/libcoot-coord-utils.la \ - $(top_builddir)/coot-utils/libcoot-utils.la \ - $(top_builddir)/mini-mol/libcoot-mini-mol.la \ -- $(top_builddir)/ccp4mg-utils/libccp4mg-utils.la \ - $(top_builddir)/compat/libcoot-compat.la \ - $(CLIPPER_LIBS) $(MMDB_LIBS) $(GSL_LIBS) - -@@ -143,23 +127,13 @@ - - findligand_real_LDADD = \ - ./libcoot-ligand.la \ -- $(top_builddir)/ideal/libcoot-ideal.la \ -- $(top_builddir)/geometry/libcoot-geometry.la \ -- $(top_builddir)/coords/libcoot-coords.la \ -- $(top_builddir)/db-main/libcoot-db-main.la \ -- $(top_builddir)/ccp4mg-utils/libccp4mg-utils.la \ -- $(top_builddir)/coot-utils/libcoot-map-utils.la \ -- $(top_builddir)/coot-utils/libcoot-coord-extras.la \ -- $(top_builddir)/coot-utils/libcoot-coord-utils.la \ - $(top_builddir)/coot-utils/libcoot-utils.la \ -- $(top_builddir)/coot-utils/libcoot-shelx.la \ - $(top_builddir)/mini-mol/libcoot-mini-mol.la \ - $(top_builddir)/compat/libcoot-compat.la \ - $(CLIPPER_LIBS) $(MMDB_LIBS) $(GSL_LIBS) - - findwaters_real_LDADD = \ - ./libcoot-ligand.la \ -- $(top_builddir)/ideal/libcoot-ideal.la \ - $(top_builddir)/geometry/libcoot-geometry.la \ - $(top_builddir)/coords/libcoot-coords.la \ - $(top_builddir)/ccp4mg-utils/libccp4mg-utils.la \ -@@ -190,16 +164,7 @@ - testdunbrack_SOURCES = testdunbrack.cc - - testdunbrack_LDADD = ./libcoot-ligand.la \ -- $(top_builddir)/ideal/libcoot-ideal.la \ -- $(top_builddir)/geometry/libcoot-geometry.la \ -- $(top_builddir)/coords/libcoot-coords.la \ -- $(top_builddir)/ccp4mg-utils/libccp4mg-utils.la \ -- $(top_builddir)/coot-utils/libcoot-map-utils.la \ -- $(top_builddir)/db-main/libcoot-db-main.la \ -- $(top_builddir)/coot-utils/libcoot-coord-extras.la \ -- $(top_builddir)/coot-utils/libcoot-coord-utils.la \ - $(top_builddir)/coot-utils/libcoot-utils.la \ -- $(top_builddir)/coot-utils/libcoot-shelx.la \ - $(top_builddir)/mini-mol/libcoot-mini-mol.la \ - $(CLIPPER_LIBS) $(MMDB_LIBS) $(GSL_LIBS) - -Index: analysis/Makefile.am -=================================================================== ---- analysis/Makefile.am (revision 2293) -+++ analysis/Makefile.am (working copy) -@@ -9,6 +9,7 @@ - $(MMDB_CXXFLAGS) - - libcoot_analysis_la_SOURCES = bfkurt.cc -+libcoot_analysis_la_LIBADD = $(top_builddir)/coot-utils/libcoot-coord-utils.la - - bin_PROGRAMS = bfactan - -@@ -16,7 +17,6 @@ - - bfactan_LDADD = \ - libcoot-analysis.la \ -- $(top_builddir)/coot-utils/libcoot-coord-utils.la \ - $(top_builddir)/coot-utils/libcoot-utils.la \ - $(top_builddir)/geometry/libcoot-geometry.la \ - $(CLIPPER_LIBS) \ -Index: skeleton/Makefile.am -=================================================================== ---- skeleton/Makefile.am (revision 2293) -+++ skeleton/Makefile.am (working copy) -@@ -39,8 +39,8 @@ - - - libcoot_skeleton_la_SOURCES = $(libskeleton_a_sources) -+libcoot_skeleton_la_LIBADD = ../atom-utils/libcoot-atomutils.la - -- - # bin_PROGRAMS = ncssearch test_various test_torsion test_theta_2 - - # ncssearch_SOURCES = ncs-search.cc ncs-search.h -Index: coot-surface/Makefile.am -=================================================================== ---- coot-surface/Makefile.am (revision 2293) -+++ coot-surface/Makefile.am (working copy) -@@ -25,3 +25,4 @@ - - libcoot_surface_la_SOURCES = \ - coot-surface.cc coot-surface.hh rgbreps.cc rgbreps.h -+libcoot_surface_la_LIBADD = $(top_builddir)/surface/libccp4mg-surface.la -Index: high-res/Makefile.am -=================================================================== ---- high-res/Makefile.am (revision 2293) -+++ high-res/Makefile.am (working copy) -@@ -39,13 +39,16 @@ - - libcoot_high_res_la_SOURCES = high-res.cc coot-atom-graph.cc residue-distortions.cc \ - sequence-assignment.cc -+libcoot_high_res_la_LIBADD = \ -+ $(top_builddir)/ligand/libcoot-ligand.la \ -+ $(top_builddir)/coot-utils/libcoot-map-utils.la \ -+ $(CLIPPER_LIBS) $(MMDB_LIBS) - - check_PROGRAMS = testatomgraph tracehighres testseqalign testseqassignment globularize_protein - - testatomgraph_SOURCES = test-atom-graph.cc - - testatomgraph_LDADD = libcoot-high-res.la \ -- $(top_builddir)/ligand/libcoot-ligand.la \ - $(top_builddir)/db-main/libcoot-db-main.la \ - $(top_builddir)/ideal/libcoot-ideal.la \ - $(top_builddir)/geometry/libcoot-geometry.la \ -@@ -53,71 +56,60 @@ - $(top_builddir)/mini-mol/libcoot-mini-mol.la \ - $(top_builddir)/coot-utils/libcoot-coord-extras.la \ - $(top_builddir)/coot-utils/libcoot-coord-utils.la \ -- $(top_builddir)/coot-utils/libcoot-map-utils.la \ - $(top_builddir)/coot-utils/libcoot-shelx.la \ - $(top_builddir)/coot-utils/libcoot-utils.la \ - $(top_builddir)/ccp4mg-utils/libccp4mg-utils.la \ - $(top_builddir)/compat/libcoot-compat.la \ -- $(GSL_LIBS) \ -- $(CLIPPER_LIBS) -+ $(GSL_LIBS) - - testseqassignment_SOURCES = testseqassignment.cc - testseqassignment_LDADD = libcoot-high-res.la \ -- $(top_builddir)/ligand/libcoot-ligand.la \ - $(top_builddir)/db-main/libcoot-db-main.la \ - $(top_builddir)/ideal/libcoot-ideal.la \ - $(top_builddir)/geometry/libcoot-geometry.la \ - $(top_builddir)/coords/libcoot-coords.la \ - $(top_builddir)/mini-mol/libcoot-mini-mol.la \ - $(top_builddir)/coot-utils/libcoot-coord-extras.la \ -- $(top_builddir)/coot-utils/libcoot-map-utils.la \ - $(top_builddir)/coot-utils/libcoot-coord-utils.la \ - $(top_builddir)/coot-utils/libcoot-shelx.la \ - $(top_builddir)/coot-utils/libcoot-utils.la \ - $(top_builddir)/compat/libcoot-compat.la \ - $(top_builddir)/ccp4mg-utils/libccp4mg-utils.la \ -- $(GSL_LIBS) \ -- $(CLIPPER_LIBS) -+ $(GSL_LIBS) - - # tracehighres_LDFLAGS = -static - tracehighres_SOURCES = trace-high-res.cc - tracehighres_LDADD = libcoot-high-res.la \ -- $(top_builddir)/ligand/libcoot-ligand.la \ - $(top_builddir)/ideal/libcoot-ideal.la \ - $(top_builddir)/db-main/libcoot-db-main.la \ - $(top_builddir)/geometry/libcoot-geometry.la \ - $(top_builddir)/coords/libcoot-coords.la \ - $(top_builddir)/mini-mol/libcoot-mini-mol.la \ - $(top_builddir)/coot-utils/libcoot-coord-extras.la \ -- $(top_builddir)/coot-utils/libcoot-map-utils.la \ - $(top_builddir)/coot-utils/libcoot-coord-utils.la \ - $(top_builddir)/coot-utils/libcoot-shelx.la \ - $(top_builddir)/coot-utils/libcoot-utils.la \ - $(top_builddir)/compat/libcoot-compat.la \ - $(top_builddir)/ccp4mg-utils/libccp4mg-utils.la \ -- $(GSL_LIBS) \ -- $(CLIPPER_LIBS) -+ $(GSL_LIBS) - - - testseqalign_SOURCES = testseqalign.cc - - # why do we need to link with all this (junk)? - testseqalign_LDADD = libcoot-high-res.la \ -- $(top_builddir)/ligand/libcoot-ligand.la \ - $(top_builddir)/ideal/libcoot-ideal.la \ - $(top_builddir)/db-main/libcoot-db-main.la \ - $(top_builddir)/geometry/libcoot-geometry.la \ - $(top_builddir)/coords/libcoot-coords.la \ - $(top_builddir)/mini-mol/libcoot-mini-mol.la \ - $(top_builddir)/coot-utils/libcoot-coord-extras.la \ -- $(top_builddir)/coot-utils/libcoot-map-utils.la \ - $(top_builddir)/coot-utils/libcoot-coord-utils.la \ - $(top_builddir)/coot-utils/libcoot-shelx.la \ - $(top_builddir)/coot-utils/libcoot-utils.la \ - $(top_builddir)/ccp4mg-utils/libccp4mg-utils.la \ - $(top_builddir)/compat/libcoot-compat.la \ -- $(GSL_LIBS) \ -- $(CLIPPER_LIBS) -+ $(GSL_LIBS) - - - globularize_protein_SOURCES = globularize.cc -Index: cootaneer/Makefile.am -=================================================================== ---- cootaneer/Makefile.am (revision 2293) -+++ cootaneer/Makefile.am (working copy) -@@ -34,6 +34,7 @@ - buccaneer-sequence.cpp cootaneer-sequence.cpp \ - buccaneer-lib.h buccaneer-prot.h \ - buccaneer-sequence.h cootaneer-sequence.h -+libcootaneer_la_LIBADD = $(CLIPPER_LIBS) - - subpkgdatadir = $(pkgdatadir) - subpkgdata_DATA = cootaneer-llk-2.40.dat -Index: geometry/Makefile.am -=================================================================== ---- geometry/Makefile.am (revision 2293) -+++ geometry/Makefile.am (working copy) -@@ -35,6 +35,9 @@ - # -DHAVE_SYS_STDTYPES_H - - libcoot_geometry_la_SOURCES = protein-geometry.cc protein-geometry-mmdb.cc -+libcoot_geometry_la_LIBADD = \ -+ $(top_builddir)/coot-utils/libcoot-utils.la \ -+ $(CLIPPER_LIBS) $(MMDB_LIBS) - - # libcoot_geometry_la_CXXFLAGS = -g -O1 - -@@ -44,12 +47,7 @@ - - test_read_components_SOURCES = test-read-components.cc test-read-components.hh - --test_geometry_LDADD = ./libcoot-geometry.la \ -- $(top_builddir)/coot-utils/libcoot-utils.la \ -- $(CLIPPER_LIBS) $(MMDB_LIBS) -+test_geometry_LDADD = ./libcoot-geometry.la -+ -+test_read_components_LDADD = ./libcoot-geometry.la - --test_read_components_LDADD = \ -- ./libcoot-geometry.la \ -- $(top_builddir)/coot-utils/libcoot-utils.la \ -- $(CLIPPER_LIBS) $(MMDB_LIBS) -- -Index: ideal/Makefile.am -=================================================================== ---- ideal/Makefile.am (revision 2293) -+++ ideal/Makefile.am (working copy) -@@ -54,6 +54,12 @@ - - - libcoot_ideal_la_SOURCES = simple-restraint.cc pepflip.cc regularize-minimol.cc lograma.cpp -+libcoot_ideal_la_LIBADD = \ -+ $(top_builddir)/coot-utils/libcoot-utils.la \ -+ $(top_builddir)/mini-mol/libcoot-mini-mol.la \ -+ $(top_builddir)/coot-utils/libcoot-shelx.la \ -+ $(top_builddir)/coot-utils/libcoot-coord-extras.la \ -+ $(GSL_LIBS) - - - noinst_PROGRAMS = test-indexing with-geometry with-map logramatest -@@ -75,12 +81,8 @@ - ./libcoot-ideal.la \ - $(top_builddir)/geometry/libcoot-geometry.la \ - $(top_builddir)/coords/libcoot-coords.la \ -- $(top_builddir)/coot-utils/libcoot-shelx.la \ -- $(top_builddir)/coot-utils/libcoot-coord-extras.la \ - $(top_builddir)/coot-utils/libcoot-coord-utils.la \ -- $(top_builddir)/coot-utils/libcoot-utils.la \ -- $(top_builddir)/mini-mol/libcoot-mini-mol.la \ -- $(CLIPPER_LIBS) $(MMDB_LIBS) $(GSL_LIBS) -+ $(CLIPPER_LIBS) $(MMDB_LIBS) - - # add libcoot-map-utils for the debugging density_around_point function - with_map_LDADD = \ -@@ -88,22 +90,16 @@ - $(top_builddir)/geometry/libcoot-geometry.la \ - $(top_builddir)/coords/libcoot-coords.la \ - $(top_builddir)/coot-utils/libcoot-map-utils.la \ -- $(top_builddir)/coot-utils/libcoot-shelx.la \ -- $(top_builddir)/coot-utils/libcoot-coord-extras.la \ - $(top_builddir)/coot-utils/libcoot-coord-utils.la \ - $(top_builddir)/coot-utils/libcoot-utils.la \ -- $(top_builddir)/compat/libcoot-compat.la \ -- $(top_builddir)/mini-mol/libcoot-mini-mol.la \ -- $(CLIPPER_LIBS) $(MMDB_LIBS) $(GSL_LIBS) -+ $(top_builddir)/compat/libcoot-compat.la \ -+ $(CLIPPER_LIBS) $(MMDB_LIBS) - - test_indexing_LDADD = \ - ./libcoot-ideal.la \ - $(top_builddir)/geometry/libcoot-geometry.la \ -- $(top_builddir)/mini-mol/libcoot-mini-mol.la \ -- $(top_builddir)/coot-utils/libcoot-coord-extras.la \ - $(top_builddir)/coot-utils/libcoot-coord-utils.la \ -- $(top_builddir)/coot-utils/libcoot-utils.la \ -- $(CLIPPER_LIBS) $(MMDB_LIBS) $(GSL_LIBS) -+ $(CLIPPER_LIBS) $(MMDB_LIBS) - - # Why do I need all these libraries to simply link a trivial test program? - # Badness.... -Index: tw/Makefile.am -=================================================================== ---- tw/Makefile.am (revision 2293) -+++ tw/Makefile.am (working copy) -@@ -39,14 +39,15 @@ - include_HEADERS = coot-tw.hh - - libcoot_tw_la_SOURCES = tw.cc -+libcoot_tw_la_LIBADD = \ -+ $(GTKCANVAS_LIBS) \ -+ @GTK_LIBS@ - - noinst_PROGRAMS = coot-tiddly - - coot_tiddly_SOURCES = tiddly.cc - --coot_tiddly_LDADD = libcoot-tw.la \ -- $(GTKCANVAS_LIBS) \ -- @GTK_LIBS@ -+coot_tiddly_LDADD = libcoot-tw.la - - - # cootsound_LDADD = -L/sw/lib -lvorbisfile -logg -lao -Index: coot-utils/Makefile.am -=================================================================== ---- coot-utils/Makefile.am (revision 2293) -+++ coot-utils/Makefile.am (working copy) -@@ -49,6 +49,7 @@ - # for simple things: - libcoot_utils_la_SOURCES = coot-utils.cc coot-fasta.cc atomic-numbers.cc \ - gdk-keysyms.cc -+libcoot_coord_utils_la_LIBADD = $(CLIPPER_LIBS) libcoot-utils.la - - # for pure coordinates (mmdb) things - libcoot_coord_utils_la_SOURCES = coot-coord-utils.cc \ -@@ -56,6 +57,7 @@ - - # shelx - libcoot_shelx_la_SOURCES = coot-shelx-ins.cc -+libcoot_shelx_la_LIBADD = $(MMDB_LIBS) libcoot-coord-utils.la - - # for non-simple coordinates things - libcoot_coord_extras_la_SOURCES = coot-coord-extras.cc coot-coord-lsq.cc \ -@@ -63,24 +65,23 @@ - - # for (map) things that need to link mmdb and clipper: - libcoot_map_utils_la_SOURCES = coot-map-utils.cc peak-search.cc trim.cc xmap-stats.cc -+libcoot_map_utils_la_LIBADD = $(CLIPPER_LIBS) - - # for map things that need mmdb, clipper, gsl and other things - libcoot_map_heavy_la_SOURCES = coot-map-heavy.cc coot-fffear.cc -+libcoot_map_heavy_la_LIBADD = $(GSL_LIBS) - - noinst_PROGRAMS = testshelxreader testcootutils - - testshelxreader_SOURCES = test-shelx-reader.cc - testshelxreader_LDADD = \ - ./libcoot-shelx.la \ -- ./libcoot-coord-utils.la \ - ./libcoot-utils.la \ -- $(CLIPPER_LIBS) $(MMDB_LIBS) -+ $(MMDB_LIBS) - - testcootutils_SOURCES = test-utils.cc - testcootutils_LDADD = \ - ./libcoot-shelx.la \ -- ./libcoot-coord-utils.la \ - ./libcoot-utils.la \ -- $(CLIPPER_LIBS) $(MMDB_LIBS) -+ $(MMDB_LIBS) - -- -Index: Makefile.am -=================================================================== ---- Makefile.am (revision 2293) -+++ Makefile.am (working copy) -@@ -25,10 +25,10 @@ - - # see configure.in for po intl - SUBDIRS = auxil scheme python macros compat coot-utils surface coot-surface \ -- skeleton ccp4mg-utils density-contour coords angles \ -- mini-mol db-main geometry \ -+ atom-utils skeleton ccp4mg-utils density-contour mini-mol coords angles \ -+ db-main geometry \ - ideal ligand high-res build greg-tests python-tests \ -- analysis sequence-view tw atom-utils cootaneer src rama-data doc -+ analysis sequence-view tw cootaneer src rama-data doc - - # po, no po today. - diff --git a/sci-chemistry/coot/files/9999-as-needed2.patch b/sci-chemistry/coot/files/9999-as-needed2.patch deleted file mode 100644 index 0cfce54dd..000000000 --- a/sci-chemistry/coot/files/9999-as-needed2.patch +++ /dev/null @@ -1,481 +0,0 @@ -Index: mini-mol/Makefile.am -=================================================================== ---- mini-mol/Makefile.am (revision 2293) -+++ mini-mol/Makefile.am (working copy) -@@ -35,8 +35,9 @@ - testminimol_SOURCES = testminimol.cc - - libcoot_mini_mol_la_SOURCES = mini-mol.cc mini-mol-utils.cc atom-quads.cc -+libcoot_mini_mol_la_LIBADD = \ -+ $(top_builddir)/coot-utils/libcoot-coord-utils.la \ -+ $(CLIPPER_LIBS) - - testminimol_LDADD = libcoot-mini-mol.la \ -- $(top_builddir)/coot-utils/libcoot-coord-utils.la \ -- $(top_builddir)/coot-utils/libcoot-utils.la \ -- $(CLIPPER_LIBS) $(MMDB_LIBS) -+ $(MMDB_LIBS) -Index: coords/Makefile.am -=================================================================== ---- coords/Makefile.am (revision 2293) -+++ coords/Makefile.am (working copy) -@@ -40,3 +40,7 @@ - mmdb-extras.cc utils.cc mmdb.cc mmdb-crystal.cc \ - Bond_lines_ext.cc coot-close.cc - -+libcoot_coords_la_LIBADD = \ -+ $(top_builddir)/coot-utils/libcoot-shelx.la \ -+ $(top_builddir)/mini-mol/libcoot-mini-mol.la -+ -Index: ligand/Makefile.am -=================================================================== ---- ligand/Makefile.am (revision 2293) -+++ ligand/Makefile.am (working copy) -@@ -49,6 +49,17 @@ - torsion-general.cc rotamer-tables.cc primitive-chi-angles.cc dipole.cc\ - base-pairing.cc backrub-rotamer.cc - -+libcoot_ligand_la_LIBADD = \ -+ $(top_builddir)/ideal/libcoot-ideal.la \ -+ $(top_builddir)/coords/libcoot-coords.la \ -+ $(top_builddir)/coot-utils/libcoot-coord-extras.la \ -+ $(top_builddir)/coot-utils/libcoot-map-utils.la \ -+ $(top_builddir)/db-main/libcoot-db-main.la \ -+ $(top_builddir)/coot-utils/libcoot-shelx.la \ -+ $(top_builddir)/geometry/libcoot-geometry.la \ -+ $(top_builddir)/coot-utils/libcoot-coord-utils.la \ -+ $(top_builddir)/ccp4mg-utils/libccp4mg-utils.la -+ - AM_CXXFLAGS = \ - -DPKGDATADIR='"$(pkgdatadir)"' \ - $(COOT_WINDOWS_CFLAGS) -@@ -68,7 +79,6 @@ - - test_random_LDADD = \ - ./libcoot-ligand.la \ -- $(top_builddir)/ideal/libcoot-ideal.la \ - $(top_builddir)/coords/libcoot-coords.la \ - $(top_builddir)/coot-utils/libcoot-coord-extras.la \ - $(top_builddir)/coot-utils/libcoot-map-utils.la \ -@@ -85,31 +95,14 @@ - - test_ligand_LDADD = \ - ./libcoot-ligand.la \ -- $(top_builddir)/ideal/libcoot-ideal.la \ - $(top_builddir)/mini-mol/libcoot-mini-mol.la \ -- $(top_builddir)/coords/libcoot-coords.la \ -- $(top_builddir)/coot-utils/libcoot-coord-extras.la \ -- $(top_builddir)/coot-utils/libcoot-map-utils.la \ -- $(top_builddir)/db-main/libcoot-db-main.la \ -- $(top_builddir)/coot-utils/libcoot-shelx.la \ -- $(top_builddir)/geometry/libcoot-geometry.la \ -- $(top_builddir)/coot-utils/libcoot-coord-utils.la \ - $(top_builddir)/coot-utils/libcoot-utils.la \ - $(top_builddir)/mini-mol/libcoot-mini-mol.la \ -- $(top_builddir)/ccp4mg-utils/libccp4mg-utils.la \ - $(top_builddir)/compat/libcoot-compat.la \ - $(CLIPPER_LIBS) $(MMDB_LIBS) $(GSL_LIBS) - - test_helix_placement_LDADD = \ - ./libcoot-ligand.la \ -- $(top_builddir)/ideal/libcoot-ideal.la \ -- $(top_builddir)/coords/libcoot-coords.la \ -- $(top_builddir)/coot-utils/libcoot-coord-extras.la \ -- $(top_builddir)/coot-utils/libcoot-map-utils.la \ -- $(top_builddir)/coot-utils/libcoot-shelx.la \ -- $(top_builddir)/geometry/libcoot-geometry.la \ -- $(top_builddir)/db-main/libcoot-db-main.la \ -- $(top_builddir)/coot-utils/libcoot-coord-utils.la \ - $(top_builddir)/coot-utils/libcoot-utils.la \ - $(top_builddir)/mini-mol/libcoot-mini-mol.la \ - $(top_builddir)/ccp4mg-utils/libccp4mg-utils.la \ -@@ -120,18 +113,9 @@ - - test_fffear_in_coot_LDADD = \ - ./libcoot-ligand.la \ -- $(top_builddir)/ideal/libcoot-ideal.la \ -- $(top_builddir)/coot-utils/libcoot-coord-extras.la \ -- $(top_builddir)/coords/libcoot-coords.la \ -- $(top_builddir)/coot-utils/libcoot-shelx.la \ -- $(top_builddir)/geometry/libcoot-geometry.la \ - $(top_builddir)/coot-utils/libcoot-map-heavy.la \ -- $(top_builddir)/db-main/libcoot-db-main.la \ -- $(top_builddir)/coot-utils/libcoot-map-utils.la \ -- $(top_builddir)/coot-utils/libcoot-coord-utils.la \ - $(top_builddir)/coot-utils/libcoot-utils.la \ - $(top_builddir)/mini-mol/libcoot-mini-mol.la \ -- $(top_builddir)/ccp4mg-utils/libccp4mg-utils.la \ - $(top_builddir)/compat/libcoot-compat.la \ - $(CLIPPER_LIBS) $(MMDB_LIBS) $(GSL_LIBS) - -@@ -143,23 +127,13 @@ - - findligand_real_LDADD = \ - ./libcoot-ligand.la \ -- $(top_builddir)/ideal/libcoot-ideal.la \ -- $(top_builddir)/geometry/libcoot-geometry.la \ -- $(top_builddir)/coords/libcoot-coords.la \ -- $(top_builddir)/db-main/libcoot-db-main.la \ -- $(top_builddir)/ccp4mg-utils/libccp4mg-utils.la \ -- $(top_builddir)/coot-utils/libcoot-map-utils.la \ -- $(top_builddir)/coot-utils/libcoot-coord-extras.la \ -- $(top_builddir)/coot-utils/libcoot-coord-utils.la \ - $(top_builddir)/coot-utils/libcoot-utils.la \ -- $(top_builddir)/coot-utils/libcoot-shelx.la \ - $(top_builddir)/mini-mol/libcoot-mini-mol.la \ - $(top_builddir)/compat/libcoot-compat.la \ - $(CLIPPER_LIBS) $(MMDB_LIBS) $(GSL_LIBS) - - findwaters_real_LDADD = \ - ./libcoot-ligand.la \ -- $(top_builddir)/ideal/libcoot-ideal.la \ - $(top_builddir)/geometry/libcoot-geometry.la \ - $(top_builddir)/coords/libcoot-coords.la \ - $(top_builddir)/ccp4mg-utils/libccp4mg-utils.la \ -@@ -190,16 +164,7 @@ - testdunbrack_SOURCES = testdunbrack.cc - - testdunbrack_LDADD = ./libcoot-ligand.la \ -- $(top_builddir)/ideal/libcoot-ideal.la \ -- $(top_builddir)/geometry/libcoot-geometry.la \ -- $(top_builddir)/coords/libcoot-coords.la \ -- $(top_builddir)/ccp4mg-utils/libccp4mg-utils.la \ -- $(top_builddir)/coot-utils/libcoot-map-utils.la \ -- $(top_builddir)/db-main/libcoot-db-main.la \ -- $(top_builddir)/coot-utils/libcoot-coord-extras.la \ -- $(top_builddir)/coot-utils/libcoot-coord-utils.la \ - $(top_builddir)/coot-utils/libcoot-utils.la \ -- $(top_builddir)/coot-utils/libcoot-shelx.la \ - $(top_builddir)/mini-mol/libcoot-mini-mol.la \ - $(CLIPPER_LIBS) $(MMDB_LIBS) $(GSL_LIBS) - -Index: analysis/Makefile.am -=================================================================== ---- analysis/Makefile.am (revision 2293) -+++ analysis/Makefile.am (working copy) -@@ -9,6 +9,7 @@ - $(MMDB_CXXFLAGS) - - libcoot_analysis_la_SOURCES = bfkurt.cc -+libcoot_analysis_la_LIBADD = $(top_builddir)/coot-utils/libcoot-coord-utils.la - - bin_PROGRAMS = bfactan - -@@ -16,7 +17,6 @@ - - bfactan_LDADD = \ - libcoot-analysis.la \ -- $(top_builddir)/coot-utils/libcoot-coord-utils.la \ - $(top_builddir)/coot-utils/libcoot-utils.la \ - $(top_builddir)/geometry/libcoot-geometry.la \ - $(CLIPPER_LIBS) \ -Index: skeleton/Makefile.am -=================================================================== ---- skeleton/Makefile.am (revision 2293) -+++ skeleton/Makefile.am (working copy) -@@ -39,8 +39,8 @@ - - - libcoot_skeleton_la_SOURCES = $(libskeleton_a_sources) -+libcoot_skeleton_la_LIBADD = ../atom-utils/libcoot-atomutils.la - -- - # bin_PROGRAMS = ncssearch test_various test_torsion test_theta_2 - - # ncssearch_SOURCES = ncs-search.cc ncs-search.h -Index: coot-surface/Makefile.am -=================================================================== ---- coot-surface/Makefile.am (revision 2293) -+++ coot-surface/Makefile.am (working copy) -@@ -25,3 +25,4 @@ - - libcoot_surface_la_SOURCES = \ - coot-surface.cc coot-surface.hh rgbreps.cc rgbreps.h -+libcoot_surface_la_LIBADD = $(top_builddir)/surface/libccp4mg-surface.la -Index: high-res/Makefile.am -=================================================================== ---- high-res/Makefile.am (revision 2293) -+++ high-res/Makefile.am (working copy) -@@ -39,13 +39,16 @@ - - libcoot_high_res_la_SOURCES = high-res.cc coot-atom-graph.cc residue-distortions.cc \ - sequence-assignment.cc -+libcoot_high_res_la_LIBADD = \ -+ $(top_builddir)/ligand/libcoot-ligand.la \ -+ $(top_builddir)/coot-utils/libcoot-map-utils.la \ -+ $(CLIPPER_LIBS) $(MMDB_LIBS) - - check_PROGRAMS = testatomgraph tracehighres testseqalign testseqassignment globularize_protein - - testatomgraph_SOURCES = test-atom-graph.cc - - testatomgraph_LDADD = libcoot-high-res.la \ -- $(top_builddir)/ligand/libcoot-ligand.la \ - $(top_builddir)/db-main/libcoot-db-main.la \ - $(top_builddir)/ideal/libcoot-ideal.la \ - $(top_builddir)/geometry/libcoot-geometry.la \ -@@ -53,71 +56,60 @@ - $(top_builddir)/mini-mol/libcoot-mini-mol.la \ - $(top_builddir)/coot-utils/libcoot-coord-extras.la \ - $(top_builddir)/coot-utils/libcoot-coord-utils.la \ -- $(top_builddir)/coot-utils/libcoot-map-utils.la \ - $(top_builddir)/coot-utils/libcoot-shelx.la \ - $(top_builddir)/coot-utils/libcoot-utils.la \ - $(top_builddir)/ccp4mg-utils/libccp4mg-utils.la \ - $(top_builddir)/compat/libcoot-compat.la \ -- $(GSL_LIBS) \ -- $(CLIPPER_LIBS) -+ $(GSL_LIBS) - - testseqassignment_SOURCES = testseqassignment.cc - testseqassignment_LDADD = libcoot-high-res.la \ -- $(top_builddir)/ligand/libcoot-ligand.la \ - $(top_builddir)/db-main/libcoot-db-main.la \ - $(top_builddir)/ideal/libcoot-ideal.la \ - $(top_builddir)/geometry/libcoot-geometry.la \ - $(top_builddir)/coords/libcoot-coords.la \ - $(top_builddir)/mini-mol/libcoot-mini-mol.la \ - $(top_builddir)/coot-utils/libcoot-coord-extras.la \ -- $(top_builddir)/coot-utils/libcoot-map-utils.la \ - $(top_builddir)/coot-utils/libcoot-coord-utils.la \ - $(top_builddir)/coot-utils/libcoot-shelx.la \ - $(top_builddir)/coot-utils/libcoot-utils.la \ - $(top_builddir)/compat/libcoot-compat.la \ - $(top_builddir)/ccp4mg-utils/libccp4mg-utils.la \ -- $(GSL_LIBS) \ -- $(CLIPPER_LIBS) -+ $(GSL_LIBS) - - # tracehighres_LDFLAGS = -static - tracehighres_SOURCES = trace-high-res.cc - tracehighres_LDADD = libcoot-high-res.la \ -- $(top_builddir)/ligand/libcoot-ligand.la \ - $(top_builddir)/ideal/libcoot-ideal.la \ - $(top_builddir)/db-main/libcoot-db-main.la \ - $(top_builddir)/geometry/libcoot-geometry.la \ - $(top_builddir)/coords/libcoot-coords.la \ - $(top_builddir)/mini-mol/libcoot-mini-mol.la \ - $(top_builddir)/coot-utils/libcoot-coord-extras.la \ -- $(top_builddir)/coot-utils/libcoot-map-utils.la \ - $(top_builddir)/coot-utils/libcoot-coord-utils.la \ - $(top_builddir)/coot-utils/libcoot-shelx.la \ - $(top_builddir)/coot-utils/libcoot-utils.la \ - $(top_builddir)/compat/libcoot-compat.la \ - $(top_builddir)/ccp4mg-utils/libccp4mg-utils.la \ -- $(GSL_LIBS) \ -- $(CLIPPER_LIBS) -+ $(GSL_LIBS) - - - testseqalign_SOURCES = testseqalign.cc - - # why do we need to link with all this (junk)? - testseqalign_LDADD = libcoot-high-res.la \ -- $(top_builddir)/ligand/libcoot-ligand.la \ - $(top_builddir)/ideal/libcoot-ideal.la \ - $(top_builddir)/db-main/libcoot-db-main.la \ - $(top_builddir)/geometry/libcoot-geometry.la \ - $(top_builddir)/coords/libcoot-coords.la \ - $(top_builddir)/mini-mol/libcoot-mini-mol.la \ - $(top_builddir)/coot-utils/libcoot-coord-extras.la \ -- $(top_builddir)/coot-utils/libcoot-map-utils.la \ - $(top_builddir)/coot-utils/libcoot-coord-utils.la \ - $(top_builddir)/coot-utils/libcoot-shelx.la \ - $(top_builddir)/coot-utils/libcoot-utils.la \ - $(top_builddir)/ccp4mg-utils/libccp4mg-utils.la \ - $(top_builddir)/compat/libcoot-compat.la \ -- $(GSL_LIBS) \ -- $(CLIPPER_LIBS) -+ $(GSL_LIBS) - - - globularize_protein_SOURCES = globularize.cc -Index: cootaneer/Makefile.am -=================================================================== ---- cootaneer/Makefile.am (revision 2293) -+++ cootaneer/Makefile.am (working copy) -@@ -34,6 +34,7 @@ - buccaneer-sequence.cpp cootaneer-sequence.cpp \ - buccaneer-lib.h buccaneer-prot.h \ - buccaneer-sequence.h cootaneer-sequence.h -+libcootaneer_la_LIBADD = $(CLIPPER_LIBS) - - subpkgdatadir = $(pkgdatadir) - subpkgdata_DATA = cootaneer-llk-2.40.dat -Index: geometry/Makefile.am -=================================================================== ---- geometry/Makefile.am (revision 2293) -+++ geometry/Makefile.am (working copy) -@@ -35,6 +35,9 @@ - # -DHAVE_SYS_STDTYPES_H - - libcoot_geometry_la_SOURCES = protein-geometry.cc protein-geometry-mmdb.cc -+libcoot_geometry_la_LIBADD = \ -+ $(top_builddir)/coot-utils/libcoot-utils.la \ -+ $(CLIPPER_LIBS) $(MMDB_LIBS) - - # libcoot_geometry_la_CXXFLAGS = -g -O1 - -@@ -44,12 +47,7 @@ - - test_read_components_SOURCES = test-read-components.cc test-read-components.hh - --test_geometry_LDADD = ./libcoot-geometry.la \ -- $(top_builddir)/coot-utils/libcoot-utils.la \ -- $(CLIPPER_LIBS) $(MMDB_LIBS) -+test_geometry_LDADD = ./libcoot-geometry.la -+ -+test_read_components_LDADD = ./libcoot-geometry.la - --test_read_components_LDADD = \ -- ./libcoot-geometry.la \ -- $(top_builddir)/coot-utils/libcoot-utils.la \ -- $(CLIPPER_LIBS) $(MMDB_LIBS) -- -Index: ideal/Makefile.am -=================================================================== ---- ideal/Makefile.am (revision 2293) -+++ ideal/Makefile.am (working copy) -@@ -54,6 +54,12 @@ - - - libcoot_ideal_la_SOURCES = simple-restraint.cc pepflip.cc regularize-minimol.cc lograma.cpp -+libcoot_ideal_la_LIBADD = \ -+ $(top_builddir)/coot-utils/libcoot-utils.la \ -+ $(top_builddir)/mini-mol/libcoot-mini-mol.la \ -+ $(top_builddir)/coot-utils/libcoot-shelx.la \ -+ $(top_builddir)/coot-utils/libcoot-coord-extras.la \ -+ $(GSL_LIBS) - - - noinst_PROGRAMS = test-indexing with-geometry with-map logramatest -@@ -75,12 +81,8 @@ - ./libcoot-ideal.la \ - $(top_builddir)/geometry/libcoot-geometry.la \ - $(top_builddir)/coords/libcoot-coords.la \ -- $(top_builddir)/coot-utils/libcoot-shelx.la \ -- $(top_builddir)/coot-utils/libcoot-coord-extras.la \ - $(top_builddir)/coot-utils/libcoot-coord-utils.la \ -- $(top_builddir)/coot-utils/libcoot-utils.la \ -- $(top_builddir)/mini-mol/libcoot-mini-mol.la \ -- $(CLIPPER_LIBS) $(MMDB_LIBS) $(GSL_LIBS) -+ $(CLIPPER_LIBS) $(MMDB_LIBS) - - # add libcoot-map-utils for the debugging density_around_point function - with_map_LDADD = \ -@@ -88,22 +90,16 @@ - $(top_builddir)/geometry/libcoot-geometry.la \ - $(top_builddir)/coords/libcoot-coords.la \ - $(top_builddir)/coot-utils/libcoot-map-utils.la \ -- $(top_builddir)/coot-utils/libcoot-shelx.la \ -- $(top_builddir)/coot-utils/libcoot-coord-extras.la \ - $(top_builddir)/coot-utils/libcoot-coord-utils.la \ - $(top_builddir)/coot-utils/libcoot-utils.la \ -- $(top_builddir)/compat/libcoot-compat.la \ -- $(top_builddir)/mini-mol/libcoot-mini-mol.la \ -- $(CLIPPER_LIBS) $(MMDB_LIBS) $(GSL_LIBS) -+ $(top_builddir)/compat/libcoot-compat.la \ -+ $(CLIPPER_LIBS) $(MMDB_LIBS) - - test_indexing_LDADD = \ - ./libcoot-ideal.la \ - $(top_builddir)/geometry/libcoot-geometry.la \ -- $(top_builddir)/mini-mol/libcoot-mini-mol.la \ -- $(top_builddir)/coot-utils/libcoot-coord-extras.la \ - $(top_builddir)/coot-utils/libcoot-coord-utils.la \ -- $(top_builddir)/coot-utils/libcoot-utils.la \ -- $(CLIPPER_LIBS) $(MMDB_LIBS) $(GSL_LIBS) -+ $(CLIPPER_LIBS) $(MMDB_LIBS) - - # Why do I need all these libraries to simply link a trivial test program? - # Badness.... -Index: tw/Makefile.am -=================================================================== ---- tw/Makefile.am (revision 2293) -+++ tw/Makefile.am (working copy) -@@ -39,14 +39,15 @@ - include_HEADERS = coot-tw.hh - - libcoot_tw_la_SOURCES = tw.cc -+libcoot_tw_la_LIBADD = \ -+ $(GTKCANVAS_LIBS) \ -+ @GTK_LIBS@ - - noinst_PROGRAMS = coot-tiddly - - coot_tiddly_SOURCES = tiddly.cc - --coot_tiddly_LDADD = libcoot-tw.la \ -- $(GTKCANVAS_LIBS) \ -- @GTK_LIBS@ -+coot_tiddly_LDADD = libcoot-tw.la - - - # cootsound_LDADD = -L/sw/lib -lvorbisfile -logg -lao -Index: coot-utils/Makefile.am -=================================================================== ---- coot-utils/Makefile.am (revision 2293) -+++ coot-utils/Makefile.am (working copy) -@@ -49,6 +49,7 @@ - # for simple things: - libcoot_utils_la_SOURCES = coot-utils.cc coot-fasta.cc atomic-numbers.cc \ - gdk-keysyms.cc -+libcoot_coord_utils_la_LIBADD = $(CLIPPER_LIBS) libcoot-utils.la - - # for pure coordinates (mmdb) things - libcoot_coord_utils_la_SOURCES = coot-coord-utils.cc \ -@@ -56,6 +57,7 @@ - - # shelx - libcoot_shelx_la_SOURCES = coot-shelx-ins.cc -+libcoot_shelx_la_LIBADD = $(MMDB_LIBS) libcoot-coord-utils.la - - # for non-simple coordinates things - libcoot_coord_extras_la_SOURCES = coot-coord-extras.cc coot-coord-lsq.cc \ -@@ -63,24 +65,23 @@ - - # for (map) things that need to link mmdb and clipper: - libcoot_map_utils_la_SOURCES = coot-map-utils.cc peak-search.cc trim.cc xmap-stats.cc -+libcoot_map_utils_la_LIBADD = $(CLIPPER_LIBS) - - # for map things that need mmdb, clipper, gsl and other things - libcoot_map_heavy_la_SOURCES = coot-map-heavy.cc coot-fffear.cc -+libcoot_map_heavy_la_LIBADD = $(GSL_LIBS) - - noinst_PROGRAMS = testshelxreader testcootutils - - testshelxreader_SOURCES = test-shelx-reader.cc - testshelxreader_LDADD = \ - ./libcoot-shelx.la \ -- ./libcoot-coord-utils.la \ - ./libcoot-utils.la \ -- $(CLIPPER_LIBS) $(MMDB_LIBS) -+ $(MMDB_LIBS) - - testcootutils_SOURCES = test-utils.cc - testcootutils_LDADD = \ - ./libcoot-shelx.la \ -- ./libcoot-coord-utils.la \ - ./libcoot-utils.la \ -- $(CLIPPER_LIBS) $(MMDB_LIBS) -+ $(MMDB_LIBS) - -- -Index: Makefile.am -=================================================================== ---- Makefile.am (revision 2293) -+++ Makefile.am (working copy) -@@ -25,10 +25,10 @@ - - # see configure.in for po intl - SUBDIRS = auxil scheme python macros compat coot-utils surface coot-surface \ -- skeleton ccp4mg-utils density-contour coords angles \ -- mini-mol db-main geometry \ -+ atom-utils skeleton ccp4mg-utils density-contour mini-mol coords angles \ -+ db-main geometry \ - ideal ligand high-res build greg-tests python-tests \ -- analysis sequence-view tw atom-utils cootaneer src rama-data doc -+ analysis sequence-view tw cootaneer src rama-data doc - - # po, no po today. - diff --git a/sci-chemistry/coot/files/9999-check-include.patch b/sci-chemistry/coot/files/9999-check-include.patch deleted file mode 100644 index feb5d86ca..000000000 --- a/sci-chemistry/coot/files/9999-check-include.patch +++ /dev/null @@ -1,23 +0,0 @@ -diff -arNu -uarN work/auxil/catcheck/catcheck.cc work.new/auxil/catcheck/catcheck.cc ---- work/auxil/catcheck/catcheck.cc 2009-08-31 23:07:25.000000000 +0200 -+++ work.new/auxil/catcheck/catcheck.cc 2009-08-31 23:08:22.000000000 +0200 -@@ -1,6 +1,7 @@ - - #include <unistd.h> - #include <iostream> -+#include <algorithm> - #include "catcheck.hh" - - int main(int argc, char **argv) { -diff -arNu -uarN work/auxil/strand-analysis/strand-analysis.cc work.new/auxil/strand-analysis/strand-analysis.cc ---- work/auxil/strand-analysis/strand-analysis.cc 2009-08-31 23:07:25.000000000 +0200 -+++ work.new/auxil/strand-analysis/strand-analysis.cc 2009-08-31 23:08:40.000000000 +0200 -@@ -4,6 +4,8 @@ - - #include <unistd.h> - #include <iostream> -+#include <cstdlib> -+#include <cstring> - #include "strand-analysis.hh" - - int main(int argc, char **argv) { diff --git a/sci-chemistry/coot/files/9999-gcc4.4.patch b/sci-chemistry/coot/files/9999-gcc4.4.patch deleted file mode 100644 index b7cd75662..000000000 --- a/sci-chemistry/coot/files/9999-gcc4.4.patch +++ /dev/null @@ -1,10 +0,0 @@ ---- coot-utils/coot-utils.cc 2009-08-06 00:02:51.000000000 +0200 -+++ coot-utils/coot-utils.cc.new 2009-08-06 00:06:13.000000000 +0200 -@@ -25,6 +25,7 @@ - - #include <stdexcept> // for string_to_int. - #include <sstream> // ditto. -+#include <cstdio> - - #include "coot-sysdep.h" - #if defined _MSC_VER diff --git a/sci-chemistry/coot/files/9999-test-rama.patch b/sci-chemistry/coot/files/9999-test-rama.patch deleted file mode 100644 index 96bfbf60c..000000000 --- a/sci-chemistry/coot/files/9999-test-rama.patch +++ /dev/null @@ -1,15 +0,0 @@ ---- src/graphics-info.h (revision 2296) -+++ src/graphics-info.h (working copy) -@@ -798,12 +798,10 @@ - // guess we shall rather use COOT_DATA_DIR and only as fallback PKGDATADIR?! - // maybe only for windows!? - std::string tables_dir = PKGDATADIR; --#ifdef WINDOWS_MINGW - char *data_dir = getenv("COOT_DATA_DIR"); - if (data_dir) { - tables_dir = data_dir; - } --#endif // MINGW - tables_dir += "/rama-data"; - rot_prob_tables.set_tables_dir(tables_dir); - diff --git a/sci-chemistry/coot/files/fix-namespace-error.patch b/sci-chemistry/coot/files/fix-namespace-error.patch deleted file mode 100644 index 5bf8a2d4b..000000000 --- a/sci-chemistry/coot/files/fix-namespace-error.patch +++ /dev/null @@ -1,52 +0,0 @@ ---- coot-utils/coot-coord-utils.cc.orig 2007-11-14 09:38:31.000000000 -0800 -+++ coot-utils/coot-coord-utils.cc 2007-11-14 09:44:50.000000000 -0800 -@@ -395,28 +395,30 @@ - return SelHnd; - } - --std::ostream& coot::operator<< (std::ostream& s, const coot::atom_spec_t &spec) { -+namespace coot { -+ std::ostream& operator<< (std::ostream& s, const atom_spec_t &spec) { - -- s << "[spec: "; -- s << "\""; -- s << spec.chain; -- s << "\" "; -- s << spec.resno; -- s << " "; -- s << "\""; -- s << spec.insertion_code; -- s << "\""; -- s << " "; -- s << "\""; -- s << spec.atom_name; -- s << "\""; -- s << " "; -- s << "\""; -- s << spec.alt_conf; -- s << "\"]"; -+ s << "[spec: "; -+ s << "\""; -+ s << spec.chain; -+ s << "\" "; -+ s << spec.resno; -+ s << " "; -+ s << "\""; -+ s << spec.insertion_code; -+ s << "\""; -+ s << " "; -+ s << "\""; -+ s << spec.atom_name; -+ s << "\""; -+ s << " "; -+ s << "\""; -+ s << spec.alt_conf; -+ s << "\"]"; - -- return s; -+ return s; - -+ } - } - - diff --git a/sci-chemistry/coot/files/glib.m4 b/sci-chemistry/coot/files/glib.m4 deleted file mode 100644 index b3c632b0e..000000000 --- a/sci-chemistry/coot/files/glib.m4 +++ /dev/null @@ -1,196 +0,0 @@ -# Configure paths for GLIB -# Owen Taylor 97-11-3 - -dnl AM_PATH_GLIB([MINIMUM-VERSION, [ACTION-IF-FOUND [, ACTION-IF-NOT-FOUND [, MODULES]]]]) -dnl Test for GLIB, and define GLIB_CFLAGS and GLIB_LIBS, if "gmodule" or -dnl gthread is specified in MODULES, pass to glib-config -dnl -AC_DEFUN([AM_PATH_GLIB], -[dnl -dnl Get the cflags and libraries from the glib-config script -dnl -AC_ARG_WITH(glib-prefix,[ --with-glib-prefix=PFX Prefix where GLIB is installed (optional)], - glib_config_prefix="$withval", glib_config_prefix="") -AC_ARG_WITH(glib-exec-prefix,[ --with-glib-exec-prefix=PFX Exec prefix where GLIB is installed (optional)], - glib_config_exec_prefix="$withval", glib_config_exec_prefix="") -AC_ARG_ENABLE(glibtest, [ --disable-glibtest Do not try to compile and run a test GLIB program], - , enable_glibtest=yes) - - if test x$glib_config_exec_prefix != x ; then - glib_config_args="$glib_config_args --exec-prefix=$glib_config_exec_prefix" - if test x${GLIB_CONFIG+set} != xset ; then - GLIB_CONFIG=$glib_config_exec_prefix/bin/glib-config - fi - fi - if test x$glib_config_prefix != x ; then - glib_config_args="$glib_config_args --prefix=$glib_config_prefix" - if test x${GLIB_CONFIG+set} != xset ; then - GLIB_CONFIG=$glib_config_prefix/bin/glib-config - fi - fi - - for module in . $4 - do - case "$module" in - gmodule) - glib_config_args="$glib_config_args gmodule" - ;; - gthread) - glib_config_args="$glib_config_args gthread" - ;; - esac - done - - AC_PATH_PROG(GLIB_CONFIG, glib-config, no) - min_glib_version=ifelse([$1], ,0.99.7,$1) - AC_MSG_CHECKING(for GLIB - version >= $min_glib_version) - no_glib="" - if test "$GLIB_CONFIG" = "no" ; then - no_glib=yes - else - GLIB_CFLAGS=`$GLIB_CONFIG $glib_config_args --cflags` - GLIB_LIBS=`$GLIB_CONFIG $glib_config_args --libs` - glib_config_major_version=`$GLIB_CONFIG $glib_config_args --version | \ - sed 's/\([[0-9]]*\).\([[0-9]]*\).\([[0-9]]*\)/\1/'` - glib_config_minor_version=`$GLIB_CONFIG $glib_config_args --version | \ - sed 's/\([[0-9]]*\).\([[0-9]]*\).\([[0-9]]*\)/\2/'` - glib_config_micro_version=`$GLIB_CONFIG $glib_config_args --version | \ - sed 's/\([[0-9]]*\).\([[0-9]]*\).\([[0-9]]*\)/\3/'` - if test "x$enable_glibtest" = "xyes" ; then - ac_save_CFLAGS="$CFLAGS" - ac_save_LIBS="$LIBS" - CFLAGS="$CFLAGS $GLIB_CFLAGS" - LIBS="$GLIB_LIBS $LIBS" -dnl -dnl Now check if the installed GLIB is sufficiently new. (Also sanity -dnl checks the results of glib-config to some extent -dnl - rm -f conf.glibtest - AC_TRY_RUN([ -#include <glib.h> -#include <stdio.h> -#include <stdlib.h> - -int -main () -{ - int major, minor, micro; - char *tmp_version; - - system ("touch conf.glibtest"); - - /* HP/UX 9 (%@#!) writes to sscanf strings */ - tmp_version = g_strdup("$min_glib_version"); - if (sscanf(tmp_version, "%d.%d.%d", &major, &minor, µ) != 3) { - printf("%s, bad version string\n", "$min_glib_version"); - exit(1); - } - - if ((glib_major_version != $glib_config_major_version) || - (glib_minor_version != $glib_config_minor_version) || - (glib_micro_version != $glib_config_micro_version)) - { - printf("\n*** 'glib-config --version' returned %d.%d.%d, but GLIB (%d.%d.%d)\n", - $glib_config_major_version, $glib_config_minor_version, $glib_config_micro_version, - glib_major_version, glib_minor_version, glib_micro_version); - printf ("*** was found! If glib-config was correct, then it is best\n"); - printf ("*** to remove the old version of GLIB. You may also be able to fix the error\n"); - printf("*** by modifying your LD_LIBRARY_PATH enviroment variable, or by editing\n"); - printf("*** /etc/ld.so.conf. Make sure you have run ldconfig if that is\n"); - printf("*** required on your system.\n"); - printf("*** If glib-config was wrong, set the environment variable GLIB_CONFIG\n"); - printf("*** to point to the correct copy of glib-config, and remove the file config.cache\n"); - printf("*** before re-running configure\n"); - } - else if ((glib_major_version != GLIB_MAJOR_VERSION) || - (glib_minor_version != GLIB_MINOR_VERSION) || - (glib_micro_version != GLIB_MICRO_VERSION)) - { - printf("*** GLIB header files (version %d.%d.%d) do not match\n", - GLIB_MAJOR_VERSION, GLIB_MINOR_VERSION, GLIB_MICRO_VERSION); - printf("*** library (version %d.%d.%d)\n", - glib_major_version, glib_minor_version, glib_micro_version); - } - else - { - if ((glib_major_version > major) || - ((glib_major_version == major) && (glib_minor_version > minor)) || - ((glib_major_version == major) && (glib_minor_version == minor) && (glib_micro_version >= micro))) - { - return 0; - } - else - { - printf("\n*** An old version of GLIB (%d.%d.%d) was found.\n", - glib_major_version, glib_minor_version, glib_micro_version); - printf("*** You need a version of GLIB newer than %d.%d.%d. The latest version of\n", - major, minor, micro); - printf("*** GLIB is always available from ftp://ftp.gtk.org.\n"); - printf("***\n"); - printf("*** If you have already installed a sufficiently new version, this error\n"); - printf("*** probably means that the wrong copy of the glib-config shell script is\n"); - printf("*** being found. The easiest way to fix this is to remove the old version\n"); - printf("*** of GLIB, but you can also set the GLIB_CONFIG environment to point to the\n"); - printf("*** correct copy of glib-config. (In this case, you will have to\n"); - printf("*** modify your LD_LIBRARY_PATH enviroment variable, or edit /etc/ld.so.conf\n"); - printf("*** so that the correct libraries are found at run-time))\n"); - } - } - return 1; -} -],, no_glib=yes,[echo $ac_n "cross compiling; assumed OK... $ac_c"]) - CFLAGS="$ac_save_CFLAGS" - LIBS="$ac_save_LIBS" - fi - fi - if test "x$no_glib" = x ; then - AC_MSG_RESULT(yes) - ifelse([$2], , :, [$2]) - else - AC_MSG_RESULT(no) - if test "$GLIB_CONFIG" = "no" ; then - echo "*** The glib-config script installed by GLIB could not be found" - echo "*** If GLIB was installed in PREFIX, make sure PREFIX/bin is in" - echo "*** your path, or set the GLIB_CONFIG environment variable to the" - echo "*** full path to glib-config." - else - if test -f conf.glibtest ; then - : - else - echo "*** Could not run GLIB test program, checking why..." - CFLAGS="$CFLAGS $GLIB_CFLAGS" - LIBS="$LIBS $GLIB_LIBS" - AC_TRY_LINK([ -#include <glib.h> -#include <stdio.h> -], [ return ((glib_major_version) || (glib_minor_version) || (glib_micro_version)); ], - [ echo "*** The test program compiled, but did not run. This usually means" - echo "*** that the run-time linker is not finding GLIB or finding the wrong" - echo "*** version of GLIB. If it is not finding GLIB, you'll need to set your" - echo "*** LD_LIBRARY_PATH environment variable, or edit /etc/ld.so.conf to point" - echo "*** to the installed location Also, make sure you have run ldconfig if that" - echo "*** is required on your system" - echo "***" - echo "*** If you have an old version installed, it is best to remove it, although" - echo "*** you may also be able to get things to work by modifying LD_LIBRARY_PATH" - echo "***" - echo "*** If you have a RedHat 5.0 system, you should remove the GTK package that" - echo "*** came with the system with the command" - echo "***" - echo "*** rpm --erase --nodeps gtk gtk-devel" ], - [ echo "*** The test program failed to compile or link. See the file config.log for the" - echo "*** exact error that occured. This usually means GLIB was incorrectly installed" - echo "*** or that you have moved GLIB since it was installed. In the latter case, you" - echo "*** may want to edit the glib-config script: $GLIB_CONFIG" ]) - CFLAGS="$ac_save_CFLAGS" - LIBS="$ac_save_LIBS" - fi - fi - GLIB_CFLAGS="" - GLIB_LIBS="" - ifelse([$3], , :, [$3]) - fi - AC_SUBST(GLIB_CFLAGS) - AC_SUBST(GLIB_LIBS) - rm -f conf.glibtest -]) diff --git a/sci-chemistry/coot/files/gtk.m4 b/sci-chemistry/coot/files/gtk.m4 deleted file mode 100644 index beb1859e3..000000000 --- a/sci-chemistry/coot/files/gtk.m4 +++ /dev/null @@ -1,199 +0,0 @@ -# Configure paths for GTK+ -# Owen Taylor 97-11-3 -AC_DEFUN([GTK_AC_DIVERT_BEFORE_HELP], -[ifdef([m4_divert_text], [m4_divert_text([NOTICE],[$1])], - [ifdef([AC_DIVERT], [AC_DIVERT([NOTICE],[$1])], - [AC_DIVERT_PUSH(AC_DIVERSION_NOTICE)dnl -$1 -AC_DIVERT_POP()])])]) -dnl AM_PATH_GTK([MINIMUM-VERSION, [ACTION-IF-FOUND [, ACTION-IF-NOT-FOUND [, MODULES]]]]) -dnl Test for GTK, and define GTK_CFLAGS and GTK_LIBS -dnl -AC_DEFUN([AM_PATH_GTK], -[dnl -dnl Get the cflags and libraries from the gtk-config script -dnl -AC_ARG_WITH(gtk-prefix,[ --with-gtk-prefix=PFX Prefix where GTK is installed (optional)], - gtk_config_prefix="$withval", gtk_config_prefix="") -AC_ARG_WITH(gtk-exec-prefix,[ --with-gtk-exec-prefix=PFX Exec prefix where GTK is installed (optional)], - gtk_config_exec_prefix="$withval", gtk_config_exec_prefix="") -AC_ARG_ENABLE(gtktest, [ --disable-gtktest Do not try to compile and run a test GTK program], - , enable_gtktest=yes) - - for module in . $4 - do - case "$module" in - gthread) - gtk_config_args="$gtk_config_args gthread" - ;; - esac - done - - if test x$gtk_config_exec_prefix != x ; then - gtk_config_args="$gtk_config_args --exec-prefix=$gtk_config_exec_prefix" - if test x${GTK_CONFIG+set} != xset ; then - GTK_CONFIG=$gtk_config_exec_prefix/bin/gtk-config - fi - fi - if test x$gtk_config_prefix != x ; then - gtk_config_args="$gtk_config_args --prefix=$gtk_config_prefix" - if test x${GTK_CONFIG+set} != xset ; then - GTK_CONFIG=$gtk_config_prefix/bin/gtk-config - fi - fi - - AC_PATH_PROG(GTK_CONFIG, gtk-config, no) - min_gtk_version=ifelse([$1], ,0.99.7,$1) - AC_MSG_CHECKING(for GTK - version >= $min_gtk_version) - no_gtk="" - if test "$GTK_CONFIG" = "no" ; then - no_gtk=yes - else - GTK_CFLAGS=`$GTK_CONFIG $gtk_config_args --cflags` - GTK_LIBS=`$GTK_CONFIG $gtk_config_args --libs` - gtk_config_major_version=`$GTK_CONFIG $gtk_config_args --version | \ - sed 's/\([[0-9]]*\).\([[0-9]]*\).\([[0-9]]*\)/\1/'` - gtk_config_minor_version=`$GTK_CONFIG $gtk_config_args --version | \ - sed 's/\([[0-9]]*\).\([[0-9]]*\).\([[0-9]]*\)/\2/'` - gtk_config_micro_version=`$GTK_CONFIG $gtk_config_args --version | \ - sed 's/\([[0-9]]*\).\([[0-9]]*\).\([[0-9]]*\)/\3/'` - if test "x$enable_gtktest" = "xyes" ; then - ac_save_CFLAGS="$CFLAGS" - ac_save_LIBS="$LIBS" - CFLAGS="$CFLAGS $GTK_CFLAGS" - LIBS="$GTK_LIBS $LIBS" -dnl -dnl Now check if the installed GTK is sufficiently new. (Also sanity -dnl checks the results of gtk-config to some extent -dnl - rm -f conf.gtktest - AC_TRY_RUN([ -#include <gtk/gtk.h> -#include <stdio.h> -#include <stdlib.h> - -int -main () -{ - int major, minor, micro; - char *tmp_version; - - system ("touch conf.gtktest"); - - /* HP/UX 9 (%@#!) writes to sscanf strings */ - tmp_version = g_strdup("$min_gtk_version"); - if (sscanf(tmp_version, "%d.%d.%d", &major, &minor, µ) != 3) { - printf("%s, bad version string\n", "$min_gtk_version"); - exit(1); - } - - if ((gtk_major_version != $gtk_config_major_version) || - (gtk_minor_version != $gtk_config_minor_version) || - (gtk_micro_version != $gtk_config_micro_version)) - { - printf("\n*** 'gtk-config --version' returned %d.%d.%d, but GTK+ (%d.%d.%d)\n", - $gtk_config_major_version, $gtk_config_minor_version, $gtk_config_micro_version, - gtk_major_version, gtk_minor_version, gtk_micro_version); - printf ("*** was found! If gtk-config was correct, then it is best\n"); - printf ("*** to remove the old version of GTK+. You may also be able to fix the error\n"); - printf("*** by modifying your LD_LIBRARY_PATH enviroment variable, or by editing\n"); - printf("*** /etc/ld.so.conf. Make sure you have run ldconfig if that is\n"); - printf("*** required on your system.\n"); - printf("*** If gtk-config was wrong, set the environment variable GTK_CONFIG\n"); - printf("*** to point to the correct copy of gtk-config, and remove the file config.cache\n"); - printf("*** before re-running configure\n"); - } -#if defined (GTK_MAJOR_VERSION) && defined (GTK_MINOR_VERSION) && defined (GTK_MICRO_VERSION) - else if ((gtk_major_version != GTK_MAJOR_VERSION) || - (gtk_minor_version != GTK_MINOR_VERSION) || - (gtk_micro_version != GTK_MICRO_VERSION)) - { - printf("*** GTK+ header files (version %d.%d.%d) do not match\n", - GTK_MAJOR_VERSION, GTK_MINOR_VERSION, GTK_MICRO_VERSION); - printf("*** library (version %d.%d.%d)\n", - gtk_major_version, gtk_minor_version, gtk_micro_version); - } -#endif /* defined (GTK_MAJOR_VERSION) ... */ - else - { - if ((gtk_major_version > major) || - ((gtk_major_version == major) && (gtk_minor_version > minor)) || - ((gtk_major_version == major) && (gtk_minor_version == minor) && (gtk_micro_version >= micro))) - { - return 0; - } - else - { - printf("\n*** An old version of GTK+ (%d.%d.%d) was found.\n", - gtk_major_version, gtk_minor_version, gtk_micro_version); - printf("*** You need a version of GTK+ newer than %d.%d.%d. The latest version of\n", - major, minor, micro); - printf("*** GTK+ is always available from ftp://ftp.gtk.org.\n"); - printf("***\n"); - printf("*** If you have already installed a sufficiently new version, this error\n"); - printf("*** probably means that the wrong copy of the gtk-config shell script is\n"); - printf("*** being found. The easiest way to fix this is to remove the old version\n"); - printf("*** of GTK+, but you can also set the GTK_CONFIG environment to point to the\n"); - printf("*** correct copy of gtk-config. (In this case, you will have to\n"); - printf("*** modify your LD_LIBRARY_PATH enviroment variable, or edit /etc/ld.so.conf\n"); - printf("*** so that the correct libraries are found at run-time))\n"); - } - } - return 1; -} -],, no_gtk=yes,[echo $ac_n "cross compiling; assumed OK... $ac_c"]) - CFLAGS="$ac_save_CFLAGS" - LIBS="$ac_save_LIBS" - fi - fi - if test "x$no_gtk" = x ; then - AC_MSG_RESULT(yes) - ifelse([$2], , :, [$2]) - else - AC_MSG_RESULT(no) - if test "$GTK_CONFIG" = "no" ; then - echo "*** The gtk-config script installed by GTK could not be found" - echo "*** If GTK was installed in PREFIX, make sure PREFIX/bin is in" - echo "*** your path, or set the GTK_CONFIG environment variable to the" - echo "*** full path to gtk-config." - else - if test -f conf.gtktest ; then - : - else - echo "*** Could not run GTK test program, checking why..." - CFLAGS="$CFLAGS $GTK_CFLAGS" - LIBS="$LIBS $GTK_LIBS" - AC_TRY_LINK([ -#include <gtk/gtk.h> -#include <stdio.h> -], [ return ((gtk_major_version) || (gtk_minor_version) || (gtk_micro_version)); ], - [ echo "*** The test program compiled, but did not run. This usually means" - echo "*** that the run-time linker is not finding GTK or finding the wrong" - echo "*** version of GTK. If it is not finding GTK, you'll need to set your" - echo "*** LD_LIBRARY_PATH environment variable, or edit /etc/ld.so.conf to point" - echo "*** to the installed location Also, make sure you have run ldconfig if that" - echo "*** is required on your system" - echo "***" - echo "*** If you have an old version installed, it is best to remove it, although" - echo "*** you may also be able to get things to work by modifying LD_LIBRARY_PATH" - echo "***" - echo "*** If you have a RedHat 5.0 system, you should remove the GTK package that" - echo "*** came with the system with the command" - echo "***" - echo "*** rpm --erase --nodeps gtk gtk-devel" ], - [ echo "*** The test program failed to compile or link. See the file config.log for the" - echo "*** exact error that occured. This usually means GTK was incorrectly installed" - echo "*** or that you have moved GTK since it was installed. In the latter case, you" - echo "*** may want to edit the gtk-config script: $GTK_CONFIG" ]) - CFLAGS="$ac_save_CFLAGS" - LIBS="$ac_save_LIBS" - fi - fi - GTK_CFLAGS="" - GTK_LIBS="" - ifelse([$3], , :, [$3]) - fi - AC_SUBST(GTK_CFLAGS) - AC_SUBST(GTK_LIBS) - rm -f conf.gtktest -]) diff --git a/sci-chemistry/coot/files/gtkgl.m4 b/sci-chemistry/coot/files/gtkgl.m4 deleted file mode 100644 index 5de62525e..000000000 --- a/sci-chemistry/coot/files/gtkgl.m4 +++ /dev/null @@ -1,47 +0,0 @@ -dnl -dnl AM_PATH_GTKGL([ACTION-IF-FOUND [, ACTION-IF-NOT-FOUND]]) -dnl -AC_DEFUN([AM_PATH_GTKGL], - [ - AC_REQUIRE([AM_PATH_GTK]) - - AC_ARG_WITH(gtkgl-prefix, [ --with-gtkgl-prefix=DIR prefix where GtkGLArea is installed ]) - if test -n "${with_gtkgl_pefix}"; then - gtkgl__Idir="-I${with_gtkgl_prefix}/include" - gtkgl__Ldir="-L${with_gtkgl_prefix}/lib" - fi - - GTKGL_CFLAGS="" - GTKGL_LIBS="" - - AC_LANG_SAVE - AC_LANG_C - AC_CHECK_LIB(gtkgl, gdk_gl_query, - [ - ac_save_CPPFLAGS="${CPPFLAGS}" - CPPFLAGS="${CPPFLAGS} ${GTK_CFLAGS} ${gtkgl__Idir}" - AC_CHECK_HEADER(gtkgl/gtkglarea.h, - [ - have_gtkgl=yes - GTKGL_CFLAGS="${GTK_CFLAGS} ${gtkgl__Idir}" - GTKGL_LIBS="${gtkgl__Ldir} -lgtkgl" - ], - have_gtkgl=no - ) - CPPGLAGS="${ac_save_CPPFLAGS}" - ], - have_gtkgl=no, - ${gtkgl__Ldir} - ) - AC_LANG_RESTORE - - if test "X${have_gtkgl}" = Xyes; then - ifelse([$1], , :, [$1]) - else - ifelse([$2], , :, [$2]) - fi - - AC_SUBST(GTKGL_CFLAGS) - AC_SUBST(GTKGL_LIBS) - ] -) diff --git a/sci-chemistry/coot/files/imlib.m4 b/sci-chemistry/coot/files/imlib.m4 deleted file mode 100644 index cbff0c932..000000000 --- a/sci-chemistry/coot/files/imlib.m4 +++ /dev/null @@ -1,301 +0,0 @@ -# Configure paths for IMLIB -# Frank Belew 98-8-31 -# stolen from Manish Singh -# Shamelessly stolen from Owen Taylor - -dnl AM_PATH_IMLIB([MINIMUM-VERSION, [ACTION-IF-FOUND [, ACTION-IF-NOT-FOUND]]]) -dnl Test for IMLIB, and define IMLIB_CFLAGS and IMLIB_LIBS -dnl -AC_DEFUN(AM_PATH_IMLIB, -[dnl -dnl Get the cflags and libraries from the imlib-config script -dnl -AC_ARG_WITH(imlib-prefix,[ --with-imlib-prefix=PFX Prefix where IMLIB is installed (optional)], - imlib_prefix="$withval", imlib_prefix="") -AC_ARG_WITH(imlib-exec-prefix,[ --with-imlib-exec-prefix=PFX Exec prefix where IMLIB is installed (optional)], - imlib_exec_prefix="$withval", imlib_exec_prefix="") -AC_ARG_ENABLE(imlibtest, [ --disable-imlibtest Do not try to compile and run a test IMLIB program], - , enable_imlibtest=yes) - - if test x$imlib_exec_prefix != x ; then - imlib_args="$imlib_args --exec-prefix=$imlib_exec_prefix" - if test x${IMLIB_CONFIG+set} != xset ; then - IMLIB_CONFIG=$imlib_exec_prefix/bin/imlib-config - fi - fi - if test x$imlib_prefix != x ; then - imlib_args="$imlib_args --prefix=$imlib_prefix" - if test x${IMLIB_CONFIG+set} != xset ; then - IMLIB_CONFIG=$imlib_prefix/bin/imlib-config - fi - fi - - AC_PATH_PROG(IMLIB_CONFIG, imlib-config, no) - min_imlib_version=ifelse([$1], ,1.8.2,$1) - AC_MSG_CHECKING(for IMLIB - version >= $min_imlib_version) - no_imlib="" - if test "$IMLIB_CONFIG" = "no" ; then - no_imlib=yes - else - IMLIB_CFLAGS=`$IMLIB_CONFIG $imlibconf_args --cflags` - IMLIB_LIBS=`$IMLIB_CONFIG $imlibconf_args --libs` - - imlib_major_version=`$IMLIB_CONFIG $imlib_args --version | \ - sed 's/\([[0-9]]*\).\([[0-9]]*\).\([[0-9]]*\)/\1/'` - imlib_minor_version=`$IMLIB_CONFIG $imlib_args --version | \ - sed 's/\([[0-9]]*\).\([[0-9]]*\).\([[0-9]]*\)/\2/'` - imlib_micro_version=`$IMLIB_CONFIG $imlib_args --version | \ - sed 's/\([[0-9]]*\).\([[0-9]]*\).\([[0-9]]*\)/\3/'` - if test "x$enable_imlibtest" = "xyes" ; then - ac_save_CFLAGS="$CFLAGS" - ac_save_LIBS="$LIBS" - CFLAGS="$CFLAGS $IMLIB_CFLAGS" - LIBS="$LIBS $IMLIB_LIBS" -dnl -dnl Now check if the installed IMLIB is sufficiently new. (Also sanity -dnl checks the results of imlib-config to some extent -dnl - rm -f conf.imlibtest - AC_TRY_RUN([ -#include <stdio.h> -#include <stdlib.h> -#include <string.h> -#include <Imlib.h> - -char* -my_strdup (char *str) -{ - char *new_str; - - if (str) - { - new_str = malloc ((strlen (str) + 1) * sizeof(char)); - strcpy (new_str, str); - } - else - new_str = NULL; - - return new_str; -} - -int main () -{ - int major, minor, micro; - char *tmp_version; - - system ("touch conf.imlibtest"); - - /* HP/UX 9 (%@#!) writes to sscanf strings */ - tmp_version = my_strdup("$min_imlib_version"); - if (sscanf(tmp_version, "%d.%d.%d", &major, &minor, µ) != 3) { - printf("%s, bad version string\n", "$min_imlib_version"); - exit(1); - } - - if (($imlib_major_version > major) || - (($imlib_major_version == major) && ($imlib_minor_version > minor)) || - (($imlib_major_version == major) && ($imlib_minor_version == minor) && - ($imlib_micro_version >= micro))) - { - return 0; - } - else - { - printf("\n*** 'imlib-config --version' returned %d.%d, but the minimum version\n", $imlib_major_version, $imlib_minor_version); - printf("*** of IMLIB required is %d.%d. If imlib-config is correct, then it is\n", major, minor); - printf("*** best to upgrade to the required version.\n"); - printf("*** If imlib-config was wrong, set the environment variable IMLIB_CONFIG\n"); - printf("*** to point to the correct copy of imlib-config, and remove the file\n"); - printf("*** config.cache before re-running configure\n"); - return 1; - } -} - -],, no_imlib=yes,[echo $ac_n "cross compiling; assumed OK... $ac_c"]) - CFLAGS="$ac_save_CFLAGS" - LIBS="$ac_save_LIBS" - fi - fi - if test "x$no_imlib" = x ; then - AC_MSG_RESULT(yes) - ifelse([$2], , :, [$2]) - else - AC_MSG_RESULT(no) - if test "$IMLIB_CONFIG" = "no" ; then - echo "*** The imlib-config script installed by IMLIB could not be found" - echo "*** If IMLIB was installed in PREFIX, make sure PREFIX/bin is in" - echo "*** your path, or set the IMLIB_CONFIG environment variable to the" - echo "*** full path to imlib-config." - else - if test -f conf.imlibtest ; then - : - else - echo "*** Could not run IMLIB test program, checking why..." - CFLAGS="$CFLAGS $IMLIB_CFLAGS" - LIBS="$LIBS $IMLIB_LIBS" - AC_TRY_LINK([ -#include <stdio.h> -#include <Imlib.h> -], [ return 0; ], - [ echo "*** The test program compiled, but did not run. This usually means" - echo "*** that the run-time linker is not finding IMLIB or finding the wrong" - echo "*** version of IMLIB. If it is not finding IMLIB, you'll need to set your" - echo "*** LD_LIBRARY_PATH environment variable, or edit /etc/ld.so.conf to point" - echo "*** to the installed location Also, make sure you have run ldconfig if that" - echo "*** is required on your system" - echo "***" - echo "*** If you have an old version installed, it is best to remove it, although" - echo "*** you may also be able to get things to work by modifying LD_LIBRARY_PATH"], - [ echo "*** The test program failed to compile or link. See the file config.log for the" - echo "*** exact error that occured. This usually means IMLIB was incorrectly installed" - echo "*** or that you have moved IMLIB since it was installed. In the latter case, you" - echo "*** may want to edit the imlib-config script: $IMLIB_CONFIG" ]) - CFLAGS="$ac_save_CFLAGS" - LIBS="$ac_save_LIBS" - fi - fi - IMLIB_CFLAGS="" - IMLIB_LIBS="" - ifelse([$3], , :, [$3]) - fi - AC_SUBST(IMLIB_CFLAGS) - AC_SUBST(IMLIB_LIBS) - rm -f conf.imlibtest -]) - -# Check for gdk-imlib -AC_DEFUN(AM_PATH_GDK_IMLIB, -[dnl -dnl Get the cflags and libraries from the imlib-config script -dnl -AC_ARG_WITH(imlib-prefix,[ --with-imlib-prefix=PFX Prefix where IMLIB is installed (optional)], - imlib_prefix="$withval", imlib_prefix="") -AC_ARG_WITH(imlib-exec-prefix,[ --with-imlib-exec-prefix=PFX Exec prefix where IMLIB is installed (optional)], - imlib_exec_prefix="$withval", imlib_exec_prefix="") -AC_ARG_ENABLE(imlibtest, [ --disable-imlibtest Do not try to compile and run a test IMLIB program], - , enable_imlibtest=yes) - - if test x$imlib_exec_prefix != x ; then - imlib_args="$imlib_args --exec-prefix=$imlib_exec_prefix" - if test x${IMLIB_CONFIG+set} != xset ; then - IMLIB_CONFIG=$imlib_exec_prefix/bin/imlib-config - fi - fi - if test x$imlib_prefix != x ; then - imlib_args="$imlib_args --prefix=$imlib_prefix" - if test x${IMLIB_CONFIG+set} != xset ; then - IMLIB_CONFIG=$imlib_prefix/bin/imlib-config - fi - fi - - AC_PATH_PROG(IMLIB_CONFIG, imlib-config, no) - min_imlib_version=ifelse([$1], ,1.8.2,$1) - AC_MSG_CHECKING(for IMLIB - version >= $min_imlib_version) - no_imlib="" - if test "$IMLIB_CONFIG" = "no" ; then - no_imlib=yes - else - GDK_IMLIB_CFLAGS=`$IMLIB_CONFIG $imlibconf_args --cflags-gdk` - GDK_IMLIB_LIBS=`$IMLIB_CONFIG $imlibconf_args --libs-gdk` - - imlib_major_version=`$IMLIB_CONFIG $imlib_args --version | \ - sed 's/\([[0-9]]*\).\([[0-9]]*\).\([[0-9]]*\)/\1/'` - imlib_minor_version=`$IMLIB_CONFIG $imlib_args --version | \ - sed 's/\([[0-9]]*\).\([[0-9]]*\).\([[0-9]]*\)/\2/'` - if test "x$enable_imlibtest" = "xyes" ; then - ac_save_CFLAGS="$CFLAGS" - ac_save_LIBS="$LIBS" - CFLAGS="$CFLAGS $GDK_IMLIB_CFLAGS" - LIBS="$LIBS $GDK_IMLIB_LIBS" -dnl -dnl Now check if the installed IMLIB is sufficiently new. (Also sanity -dnl checks the results of imlib-config to some extent -dnl - rm -f conf.imlibtest - AC_TRY_RUN([ -#include <stdio.h> -#include <stdlib.h> -#include <gdk_imlib.h> - -int main () -{ - int major, minor; - char *tmp_version; - - system ("touch conf.gdkimlibtest"); - - /* HP/UX 9 (%@#!) writes to sscanf strings */ - tmp_version = g_strdup("$min_imlib_version"); - if (sscanf(tmp_version, "%d.%d", &major, &minor) != 2) { - printf("%s, bad version string\n", "$min_imlib_version"); - exit(1); - } - - if (($imlib_major_version > major) || - (($imlib_major_version == major) && ($imlib_minor_version >= minor))) - { - return 0; - } - else - { - printf("\n*** 'imlib-config --version' returned %d.%d, but the minimum version\n", $imlib_major_version, $imlib_minor_version); - printf("*** of IMLIB required is %d.%d. If imlib-config is correct, then it is\n", major, minor); - printf("*** best to upgrade to the required version.\n"); - printf("*** If imlib-config was wrong, set the environment variable IMLIB_CONFIG\n"); - printf("*** to point to the correct copy of imlib-config, and remove the file\n"); - printf("*** config.cache before re-running configure\n"); - return 1; - } -} - -],, no_imlib=yes,[echo $ac_n "cross compiling; assumed OK... $ac_c"]) - CFLAGS="$ac_save_CFLAGS" - LIBS="$ac_save_LIBS" - fi - fi - if test "x$no_imlib" = x ; then - AC_MSG_RESULT(yes) - ifelse([$2], , :, [$2]) - else - AC_MSG_RESULT(no) - if test "$IMLIB_CONFIG" = "no" ; then - echo "*** The imlib-config script installed by IMLIB could not be found" - echo "*** If IMLIB was installed in PREFIX, make sure PREFIX/bin is in" - echo "*** your path, or set the IMLIB_CONFIG environment variable to the" - echo "*** full path to imlib-config." - else - if test -f conf.gdkimlibtest ; then - : - else - echo "*** Could not run IMLIB test program, checking why..." - CFLAGS="$CFLAGS $GDK_IMLIB_CFLAGS" - LIBS="$LIBS $GDK_IMLIB_LIBS" - AC_TRY_LINK([ -#include <stdio.h> -#include <gdk_imlib.h> -], [ return 0; ], - [ echo "*** The test program compiled, but did not run. This usually means" - echo "*** that the run-time linker is not finding IMLIB or finding the wrong" - echo "*** version of IMLIB. If it is not finding IMLIB, you'll need to set your" - echo "*** LD_LIBRARY_PATH environment variable, or edit /etc/ld.so.conf to point" - echo "*** to the installed location Also, make sure you have run ldconfig if that" - echo "*** is required on your system" - echo "***" - echo "*** If you have an old version installed, it is best to remove it, although" - echo "*** you may also be able to get things to work by modifying LD_LIBRARY_PATH"], - [ echo "*** The test program failed to compile or link. See the file config.log for the" - echo "*** exact error that occured. This usually means IMLIB was incorrectly installed" - echo "*** or that you have moved IMLIB since it was installed. In the latter case, you" - echo "*** may want to edit the imlib-config script: $IMLIB_CONFIG" ]) - CFLAGS="$ac_save_CFLAGS" - LIBS="$ac_save_LIBS" - fi - fi - IMLIB_CFLAGS="" - IMLIB_LIBS="" - ifelse([$3], , :, [$3]) - fi - AC_SUBST(GDK_IMLIB_CFLAGS) - AC_SUBST(GDK_IMLIB_LIBS) - rm -f conf.gdkimlibtest -]) diff --git a/sci-chemistry/coot/files/link-against-guile-gtk-properly.patch b/sci-chemistry/coot/files/link-against-guile-gtk-properly.patch deleted file mode 100644 index e30a0d4c9..000000000 --- a/sci-chemistry/coot/files/link-against-guile-gtk-properly.patch +++ /dev/null @@ -1,15 +0,0 @@ -diff -ur coot-0.4-pre-1.orig/macros/guile-gtk.m4 coot-0.4-pre-1/macros/guile-gtk.m4 ---- coot-0.4-pre-1.orig/macros/guile-gtk.m4 2007-11-07 18:25:15.000000000 -0800 -+++ coot-0.4-pre-1/macros/guile-gtk.m4 2007-11-07 18:25:20.000000000 -0800 -@@ -66,9 +66,9 @@ - # we have the variable coot_gtk2 in configure.in, which is either TRUE or FALSE - # Let's use that here. Perhaps there is a better (set by gtk macro?) variable? - if test $coot_gtk2 = TRUE ; then -- GUILE_GTK_LIBS=$guile_gtk_prefix/lib/libguilegtk-2.0.la -+ GUILE_GTK_LIBS="-L$guile_gtk_prefix/lib -lguilegtk-2.1" - else -- GUILE_GTK_LIBS=$guile_gtk_prefix/lib/libguilegtk-1.2.la -+ GUILE_GTK_LIBS="-L$guile_gtk_prefix/lib -lguilegtk-1.2" - fi - # do we need to set this in fact? - GUILE_GTK_CFLAGS="-I$guile_gtk_prefix/include" |