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authorJustin Lecher <jlec@gentoo.org>2013-09-21 11:23:14 +0200
committerJustin Lecher <jlec@gentoo.org>2013-09-28 11:06:59 +0200
commit4e20152045ceb0f0a851b14fe5e867c844e97b73 (patch)
treecc09cea6a39b8bbd0e5d5b185d05e6ebe87ad4fb
parentsci-chemistry/freeon-1.0.5: Version bump. (diff)
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sci-chemistry/coot: Adjust pc patch for latest head
Package-Manager: portage-2.2.6
-rw-r--r--sci-chemistry/coot/ChangeLog3
-rw-r--r--sci-chemistry/coot/files/9999-pc.patch42
2 files changed, 21 insertions, 24 deletions
diff --git a/sci-chemistry/coot/ChangeLog b/sci-chemistry/coot/ChangeLog
index 43da81892..2d2b7c315 100644
--- a/sci-chemistry/coot/ChangeLog
+++ b/sci-chemistry/coot/ChangeLog
@@ -2,6 +2,9 @@
# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 21 Sep 2013; Justin Lecher <jlec@gentoo.org> files/9999-pc.patch:
+ Adjust pc patch for latest head
+
19 Sep 2013; Justin Lecher <jlec@gentoo.org> coot-9999.ebuild:
Clean for latest HEAD
diff --git a/sci-chemistry/coot/files/9999-pc.patch b/sci-chemistry/coot/files/9999-pc.patch
index 16e899fb5..2f97194e2 100644
--- a/sci-chemistry/coot/files/9999-pc.patch
+++ b/sci-chemistry/coot/files/9999-pc.patch
@@ -313,7 +313,7 @@ index 399f453..3d2ff55 100755
# $(WITH_SCRIPT_CFLAGS)
diff --git a/configure.in b/configure.in
-index 5928c3c..9e235b5 100644
+index cc549a5..d56f856 100644
--- a/configure.in
+++ b/configure.in
@@ -108,14 +108,18 @@ esac
@@ -357,15 +357,15 @@ index 5928c3c..9e235b5 100644
+ fi
+ ])
- AC_ARG_WITH(enterprise-tools, [ --with-enterprise-tools with optional complicated/experimental ligand-related dependencies ],
- coot_enterprise_additions="true",
+ AC_ARG_WITH(enhanced-ligand-tools, [ --with-enhanced-ligand-tools with optional complicated/experimental ligand-related dependencies ],
+ coot_enhanced_ligand_additions="true",
diff --git a/coords/Makefile.am b/coords/Makefile.am
-index 009841e..7687d56 100644
+index 05fdf70..1e1c5d2 100644
--- a/coords/Makefile.am
+++ b/coords/Makefile.am
@@ -29,7 +29,7 @@ INCLUDES = \
-I$(top_srcdir) \
- $(ENTERPRISE_TOOLS_CFLAGS) \
+ $(ENHANCED_LIGAND_TOOLS_CFLAGS) \
$(RDKIT_CXXFLAGS) \
- $(CLIPPER_CXXFLAGS) $(MMDB_CXXFLAGS)
+ $(CLIPPER_CFLAGS) $(MMDB_CFLAGS)
@@ -443,7 +443,7 @@ index 3a85b9e..1a11cdf 100644
pkginclude_HEADERS = db-main.hh db-strands.hh
pkgincludedir = $(includedir)/coot/db-main
diff --git a/db-main/Makefile.simple b/db-main/Makefile.simple
-index cec561d..31d35a0 100644
+index cec561d..c207a43 100644
--- a/db-main/Makefile.simple
+++ b/db-main/Makefile.simple
@@ -19,7 +19,7 @@ CLIPPER = $(HOME)/crystal
@@ -463,7 +463,7 @@ index cec561d..31d35a0 100644
+CLIPPER_CFLAGS = -I$(CLIPPER)/include -I$(MCCP4)/include
-INCLUDES = $(CLIPPER_CXXFLAGS) $(MCCP4_CFLAGS) $(MMDB_CXXFLAGS) -I../mini-mol
-+INCLUDES = $(CLIPPER_CFLAGS) $(MCCP4_CFLAGS) $(MMDB_CFLAGS) -I$(top_srcdir)/mini-mol
++INCLUDES = $(CLIPPER_CFLAGS) $(MCCP4_CFLAGS) $(MMDB_CFLAGS) -I../mini-mol
CXXFLAGS = -g $(INCLUDES)
LDFLAGS = -static -L../mini-mol -lcoot-mini-mol $(CLIPPER_LIBS) $(MMDB_LIBS)
@@ -584,7 +584,7 @@ index 3c32c3c..0abd514 100644
-I$(top_srcdir)/geometry
diff --git a/lbg/Makefile.am b/lbg/Makefile.am
-index 12d4ca6..5367e39 100644
+index df74b90..7f54567 100644
--- a/lbg/Makefile.am
+++ b/lbg/Makefile.am
@@ -6,7 +6,7 @@ INCLUDES = \
@@ -594,7 +594,7 @@ index 12d4ca6..5367e39 100644
- $(CLIPPER_CXXFLAGS) $(CCP4SRS_CXXFLAGS) $(MMDB_CXXFLAGS) \
+ $(CLIPPER_CFLAGS) $(CCP4SRS_CXXFLAGS) $(MMDB_CFLAGS) \
$(COOT_WINDOWS_CFLAGS) \
- $(ENTERPRISE_TOOLS_CFLAGS) \
+ $(ENHANCED_LIGAND_TOOLS_CFLAGS) \
$(RDKIT_CXXFLAGS) \
diff --git a/lbg/Makefile.simple b/lbg/Makefile.simple
index 48d091b..5b148b4 100644
@@ -624,7 +624,7 @@ index 48d091b..5b148b4 100644
lbg: lbg.o wmolecule.o lbg-callbacks.o lbg-search.o some-coot-utils.o residue-circles.o
diff --git a/lidia-core/Makefile.am b/lidia-core/Makefile.am
-index 2fcb96b..201ceb0 100644
+index 72b28ca..2a184b4 100644
--- a/lidia-core/Makefile.am
+++ b/lidia-core/Makefile.am
@@ -24,13 +24,13 @@ pkgincludedir = $(includedir)/coot/lidia-core
@@ -636,7 +636,7 @@ index 2fcb96b..201ceb0 100644
#
INCLUDES = \
-I$(top_srcdir) \
- $(ENTERPRISE_TOOLS_CFLAGS) \
+ $(ENHANCED_LIGAND_TOOLS_CFLAGS) \
$(RDKIT_CXXFLAGS) \
- $(CLIPPER_CXXFLAGS) $(MMDB_CXXFLAGS)
+ $(CLIPPER_CFLAGS) $(MMDB_CFLAGS)
@@ -848,18 +848,15 @@ index 30fdcb9..3e4c0c6 100644
ifelse([$1], , :, [$1])
diff --git a/macros/mmdb-ssm.m4 b/macros/mmdb-ssm.m4
-index 25dc502..fcfde1d 100644
+index 25dc502..21646a5 100644
--- a/macros/mmdb-ssm.m4
+++ b/macros/mmdb-ssm.m4
-@@ -31,14 +31,13 @@ AC_ARG_WITH(ssmlib-prefix,
- AC_MSG_CHECKING([for ssm library])
+@@ -34,11 +34,11 @@ if test x$with_ssmlib_prefix != x; then
- if test x$with_ssmlib_prefix != x; then
--
if test -r "$with_ssmlib_prefix/include/ssm/ssm_superpose.h"; then
- MMDBSSM_CXXFLAGS="-DHAVE_SSMLIB"
-+ MMDBSSM_CFLAGS="-DHAVE_SSMLIB"
++ MMDBSSM_CFLAGS="-DHAVE_SSMLIB"
# AFAICS, ssm does not put its libs in $acl_libdirstem
# MMDBSSM_LIBS="-L$with_ssmlib_prefix/$acl_libdirstem -lssm"
MMDBSSM_LIBS="-L$with_ssmlib_prefix/lib -lssm"
@@ -868,15 +865,12 @@ index 25dc502..fcfde1d 100644
# saved_LIBS="$LIBS"
# saved_CPPFLAGS="$CPPFLAGS"
-@@ -49,12 +48,13 @@ if test x$with_ssmlib_prefix != x; then
-
+@@ -50,11 +50,11 @@ if test x$with_ssmlib_prefix != x; then
else
AC_MSG_FAILURE([ --with-ssmlib-prefix specified but include files not found])
-- fi
+ fi
- MMDBSSM_CXXFLAGS="$MMDBSSM_CXXFLAGS $ac_MMDBSSM_CXXFLAGS"
-+ fi
-+
-+ MMDBSSM_CFLAGS="$MMDBSSM_CFLAGS $ac_MMDBSSM_CFLAGS"
++ MMDBSSM_CFLAGS="$MMDBSSM_CFLAGS $ac_MMDBSSM_CFLAGS"
else
@@ -1015,7 +1009,7 @@ index 54872fe..bef7d0e 100644
AM_CXXFLAGS = $(COOT_WINDOWS_CFLAGS)
diff --git a/src/Makefile.am b/src/Makefile.am
-index fe9656f..384991b 100644
+index af5276b..d0ab482 100644
--- a/src/Makefile.am
+++ b/src/Makefile.am
@@ -195,11 +195,11 @@ INCLUDES = \