* [gentoo-commits] proj/sci:ccp4 commit in: sci-libs/clipper/, sci-libs/clipper/files/
@ 2013-06-01 17:24 Justin Lecher
0 siblings, 0 replies; 2+ messages in thread
From: Justin Lecher @ 2013-06-01 17:24 UTC (permalink / raw
To: gentoo-commits
commit: aec5808d5af9a23dc710abc3e7477d0395b91648
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sat Jun 1 15:01:58 2013 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sat Jun 1 15:01:58 2013 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=aec5808d
sci-libs/clipper: Version Bump
Package-Manager: portage-2.2.0_alpha177
---
sci-libs/clipper/ChangeLog | 7 +++++
sci-libs/clipper/clipper-2.1_p20130528.ebuild | 6 ++++
...0130528.ebuild => clipper-2.1_p20130601.ebuild} | 0
.../clipper/files/clipper-2.1_p20130528-pc-2.patch | 36 ++++++++++++++++++++++
.../clipper/files/clipper-2.1_p20130528-pc.patch | 16 ++++++++++
5 files changed, 65 insertions(+)
diff --git a/sci-libs/clipper/ChangeLog b/sci-libs/clipper/ChangeLog
index 0e970e6..d767bf3 100644
--- a/sci-libs/clipper/ChangeLog
+++ b/sci-libs/clipper/ChangeLog
@@ -2,6 +2,13 @@
# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
# $Header: /var/cvsroot/gentoo-x86/sci-libs/clipper/ChangeLog,v 1.22 2013/05/28 18:15:50 jlec Exp $
+*clipper-2.1_p20130601 (01 Jun 2013)
+
+ 01 Jun 2013; Justin Lecher <jlec@gentoo.org> clipper-2.1_p20130528.ebuild,
+ +clipper-2.1_p20130601.ebuild, +files/clipper-2.1_p20130528-pc.patch,
+ +files/clipper-2.1_p20130528-pc-2.patch:
+ Version Bump
+
30 May 2013; Justin Lecher <jlec@gentoo.org> clipper-2.1_p20130528.ebuild:
Bump EAPI to 5, clean unused code, fix slot of fftw dep
diff --git a/sci-libs/clipper/clipper-2.1_p20130528.ebuild b/sci-libs/clipper/clipper-2.1_p20130528.ebuild
index 5e486bc..bbe1011 100644
--- a/sci-libs/clipper/clipper-2.1_p20130528.ebuild
+++ b/sci-libs/clipper/clipper-2.1_p20130528.ebuild
@@ -4,6 +4,8 @@
EAPI=5
+AUTOTOOLS_AUTORECONF=true
+
inherit autotools-utils flag-o-matic
MY_PV=${PV/_p/.}
@@ -26,6 +28,10 @@ DEPEND="${RDEPEND}"
S="${WORKDIR}"/${MY_P}
+PATCHES=(
+ "${FILESDIR}"/${P}-pc.patch
+ "${FILESDIR}"/${P}-pc-2.patch )
+
src_configure() {
# Recommended on ccp4bb/coot ML to fix crashes when calculating maps
# on 64-bit systems
diff --git a/sci-libs/clipper/clipper-2.1_p20130528.ebuild b/sci-libs/clipper/clipper-2.1_p20130601.ebuild
similarity index 100%
copy from sci-libs/clipper/clipper-2.1_p20130528.ebuild
copy to sci-libs/clipper/clipper-2.1_p20130601.ebuild
diff --git a/sci-libs/clipper/files/clipper-2.1_p20130528-pc-2.patch b/sci-libs/clipper/files/clipper-2.1_p20130528-pc-2.patch
new file mode 100644
index 0000000..ac832d1
--- /dev/null
+++ b/sci-libs/clipper/files/clipper-2.1_p20130528-pc-2.patch
@@ -0,0 +1,36 @@
+ configure.ac | 22 +++++++++++-----------
+ 1 file changed, 11 insertions(+), 11 deletions(-)
+
+diff --git a/configure.ac b/configure.ac
+index 7a56297..8173052 100644
+--- a/configure.ac
++++ b/configure.ac
+@@ -67,17 +67,17 @@ case $host_os in
+ ;;
+ esac
+
+-CLIPPER_LIBS="clipper-core"
+-test "x$enable_contrib" != xno && CLIPPER_LIBS="clipper-contrib $CLIPPER_LIBS"
+-test "x$enable_phs" != xno && CLIPPER_LIBS="clipper-phs $CLIPPER_LIBS"
+-test "x$enable_cns" != xno && CLIPPER_LIBS="clipper-cns $CLIPPER_LIBS"
+-test "x$enable_mmdb" = xyes && CLIPPER_LIBS="clipper-mmdb $CLIPPER_LIBS"
+-test "x$enable_mmdbold" = xyes && CLIPPER_LIBS="clipper-mmdbold $CLIPPER_LIBS"
+-test "x$enable_minimol" = xyes && CLIPPER_LIBS="clipper-minimol $CLIPPER_LIBS"
+-test "x$enable_cif" = xyes && CLIPPER_LIBS="clipper-cif $CLIPPER_LIBS"
+-test "x$enable_ccp4" = xyes && CLIPPER_LIBS="clipper-ccp4 $CLIPPER_LIBS"
+-#test "x$enable_cctbx" = xyes && CLIPPER_LIBS="clipper-cctbx $CLIPPER_LIBS"
+-test "x$enable_fortran" = xyes && CLIPPER_LIBS="clipper-fortran $CLIPPER_LIBS"
++CLIPPER_LIBS="-lclipper-core"
++test "x$enable_contrib" != xno && CLIPPER_LIBS="-lclipper-contrib $CLIPPER_LIBS"
++test "x$enable_phs" != xno && CLIPPER_LIBS="-lclipper-phs $CLIPPER_LIBS"
++test "x$enable_cns" != xno && CLIPPER_LIBS="-lclipper-cns $CLIPPER_LIBS"
++test "x$enable_mmdb" = xyes && CLIPPER_LIBS="-lclipper-mmdb $CLIPPER_LIBS"
++test "x$enable_mmdbold" = xyes && CLIPPER_LIBS="-lclipper-mmdbold $CLIPPER_LIBS"
++test "x$enable_minimol" = xyes && CLIPPER_LIBS="-lclipper-minimol $CLIPPER_LIBS"
++test "x$enable_cif" = xyes && CLIPPER_LIBS="-lclipper-cif $CLIPPER_LIBS"
++test "x$enable_ccp4" = xyes && CLIPPER_LIBS="-lclipper-ccp4 $CLIPPER_LIBS"
++#test "x$enable_cctbx" = xyes && CLIPPER_LIBS="-lclipper-cctbx $CLIPPER_LIBS"
++test "x$enable_fortran" = xyes && CLIPPER_LIBS="-lclipper-fortran $CLIPPER_LIBS"
+
+ if test "x$enable_mmdb" = "xyes" -o "x$enable_mmdbold" = "xyes" -o \
+ "x$enable_minimol" = "xyes" -o "x$enable_cif" = "xyes"; then
diff --git a/sci-libs/clipper/files/clipper-2.1_p20130528-pc.patch b/sci-libs/clipper/files/clipper-2.1_p20130528-pc.patch
new file mode 100644
index 0000000..086451f
--- /dev/null
+++ b/sci-libs/clipper/files/clipper-2.1_p20130528-pc.patch
@@ -0,0 +1,16 @@
+ configure.ac | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/configure.ac b/configure.ac
+index 3f9096d..7a56297 100644
+--- a/configure.ac
++++ b/configure.ac
+@@ -93,7 +93,7 @@ if test "x$enable_ccp4" = "xyes"; then
+ AC_CHECK_LIB(ccp4c, ccp4_banner, :, AC_MSG_WARN(ccp4c library not found))
+ AC_CHECK_HEADER(ccp4/ccp4_general.h, :,
+ AC_MSG_ERROR(libccp4 headers not found))
+- CLIPPER_REQUIRES="ccp4c $CLIPPER_REQUIRES"
++ CLIPPER_REQUIRES="libccp4c $CLIPPER_REQUIRES"
+ fi
+
+ if test "x$enable_cctbx" = "xyes"; then
^ permalink raw reply related [flat|nested] 2+ messages in thread
* [gentoo-commits] proj/sci:ccp4 commit in: sci-libs/clipper/, sci-libs/clipper/files/
@ 2013-06-10 11:25 Justin Lecher
0 siblings, 0 replies; 2+ messages in thread
From: Justin Lecher @ 2013-06-10 11:25 UTC (permalink / raw
To: gentoo-commits
commit: 4aeeca7e79dc3487ab6366485f9f7c490a71c705
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Wed Jun 5 09:05:55 2013 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Thu Jun 6 08:28:20 2013 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=4aeeca7e
sci-libs/clipper: Add patch for detection of dependencies using pkg-config
Package-Manager: portage-2.2.0_alpha177
---
sci-libs/clipper/ChangeLog | 4 +
sci-libs/clipper/clipper-2.1_p20130601.ebuild | 4 +
.../files/clipper-2.1_p20130601-pkgconfig.patch | 164 +++++++++++++++++++++
3 files changed, 172 insertions(+)
diff --git a/sci-libs/clipper/ChangeLog b/sci-libs/clipper/ChangeLog
index d767bf3..2c3b745 100644
--- a/sci-libs/clipper/ChangeLog
+++ b/sci-libs/clipper/ChangeLog
@@ -2,6 +2,10 @@
# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
# $Header: /var/cvsroot/gentoo-x86/sci-libs/clipper/ChangeLog,v 1.22 2013/05/28 18:15:50 jlec Exp $
+ 05 Jun 2013; Justin Lecher <jlec@gentoo.org> clipper-2.1_p20130601.ebuild,
+ +files/clipper-2.1_p20130601-pkgconfig.patch:
+ Add patch for detection of dependencies using pkg-config
+
*clipper-2.1_p20130601 (01 Jun 2013)
01 Jun 2013; Justin Lecher <jlec@gentoo.org> clipper-2.1_p20130528.ebuild,
diff --git a/sci-libs/clipper/clipper-2.1_p20130601.ebuild b/sci-libs/clipper/clipper-2.1_p20130601.ebuild
index 5e486bc..3e51f98 100644
--- a/sci-libs/clipper/clipper-2.1_p20130601.ebuild
+++ b/sci-libs/clipper/clipper-2.1_p20130601.ebuild
@@ -4,6 +4,8 @@
EAPI=5
+AUTOTOOLS_AUTORECONF=true
+
inherit autotools-utils flag-o-matic
MY_PV=${PV/_p/.}
@@ -26,6 +28,8 @@ DEPEND="${RDEPEND}"
S="${WORKDIR}"/${MY_P}
+PATCHES=( "${FILESDIR}"/${P}-pkgconfig.patch )
+
src_configure() {
# Recommended on ccp4bb/coot ML to fix crashes when calculating maps
# on 64-bit systems
diff --git a/sci-libs/clipper/files/clipper-2.1_p20130601-pkgconfig.patch b/sci-libs/clipper/files/clipper-2.1_p20130601-pkgconfig.patch
new file mode 100644
index 0000000..a64e45f
--- /dev/null
+++ b/sci-libs/clipper/files/clipper-2.1_p20130601-pkgconfig.patch
@@ -0,0 +1,164 @@
+ clipper/Makefile.am | 12 ++++-----
+ configure.ac | 78 +++++++++++++++++++++++++++++++----------------------
+ 2 files changed, 52 insertions(+), 38 deletions(-)
+
+diff --git a/clipper/Makefile.am b/clipper/Makefile.am
+index d5d0197..f16e39b 100644
+--- a/clipper/Makefile.am
++++ b/clipper/Makefile.am
+@@ -18,7 +18,7 @@ lib_LTLIBRARIES =
+ if BUILD_MMDB
+ lib_LTLIBRARIES += mmdb/libclipper-mmdb.la
+ mmdb_libclipper_mmdb_la_LDFLAGS = @VERSION_INFO@
+-mmdb_libclipper_mmdb_la_LIBADD = core/libclipper-core.la -lmmdb
++mmdb_libclipper_mmdb_la_LIBADD = core/libclipper-core.la @MMDB_LIBS@
+ mmdb_libclipper_mmdb_la_SOURCES = mmdb/clipper_mmdb.cpp
+ mmdb_includedir=$(pkgincludedir)/mmdb
+ mmdb_include_HEADERS = mmdb/clipper_mmdb.h
+@@ -30,7 +30,7 @@ minimol_libclipper_minimol_la_LDFLAGS = @VERSION_INFO@
+ # minimol uses libmmdb directly (although <mmdb/mmdb_manager.h> is included
+ # indirectly, via clipper/clipper-mmdb.h)
+ minimol_libclipper_minimol_la_LIBADD = core/libclipper-core.la \
+- mmdb/libclipper-mmdb.la -lmmdb
++ mmdb/libclipper-mmdb.la @MMDB_LIBS@
+ minimol_libclipper_minimol_la_SOURCES = \
+ minimol/minimol.cpp minimol/container_minimol.cpp minimol/minimol_data.cpp \
+ minimol/minimol_io.cpp minimol/minimol_seq.cpp minimol/minimol_utils.cpp
+@@ -52,7 +52,7 @@ endif
+ if BUILD_CIF
+ lib_LTLIBRARIES += cif/libclipper-cif.la
+ cif_libclipper_cif_la_LDFLAGS = @VERSION_INFO@
+-cif_libclipper_cif_la_LIBADD = core/libclipper-core.la -lmmdb
++cif_libclipper_cif_la_LIBADD = core/libclipper-core.la @MMDB_LIBS@
+ cif_libclipper_cif_la_SOURCES = cif/cif_data_io.cpp
+ cif_includedir=$(pkgincludedir)/cif
+ cif_include_HEADERS = cif/cif_data_io.h
+@@ -61,7 +61,7 @@ endif
+ if BUILD_MMDBOLD
+ lib_LTLIBRARIES += mmdbold/libclipper-mmdbold.la
+ mmdbold_libclipper_mmdbold_la_LDFLAGS = @VERSION_INFO@
+-mmdbold_libclipper_mmdbold_la_LIBADD = core/libclipper-core.la -lmmdb
++mmdbold_libclipper_mmdbold_la_LIBADD = core/libclipper-core.la @MMDB_LIBS@
+ mmdbold_libclipper_mmdbold_la_SOURCES = \
+ mmdbold/clipper_mmdb.cpp mmdbold/clipper_mmdb_wrapper.cpp \
+ mmdbold/clipper_mmdb_types.cpp mmdbold/container_mmdb.cpp
+@@ -75,7 +75,7 @@ endif
+ if BUILD_CCP4
+ lib_LTLIBRARIES += ccp4/libclipper-ccp4.la
+ ccp4_libclipper_ccp4_la_LDFLAGS = @VERSION_INFO@
+-ccp4_libclipper_ccp4_la_LIBADD = core/libclipper-core.la -lccp4c
++ccp4_libclipper_ccp4_la_LIBADD = core/libclipper-core.la @CCP4_LIBS@
+ ccp4_libclipper_ccp4_la_SOURCES = \
+ ccp4/ccp4_mtz_types.cpp ccp4/ccp4_mtz_io.cpp \
+ ccp4/ccp4_map_io.cpp ccp4/ccp4_utils.cpp
+@@ -88,7 +88,7 @@ endif
+ if BUILD_CCTBX
+ lib_LTLIBRARIES += cctbx/libclipper-cctbx.la
+ cctbx_libclipper_cctbx_la_LDFLAGS = @VERSION_INFO@
+-cctbx_libclipper_cctbx_la_LIBADD = core/libclipper-core.la -lsgtbx -luctbx
++cctbx_libclipper_cctbx_la_LIBADD = core/libclipper-core.la @CCTBX_LIBS@
+ cctbx_libclipper_cctbx_la_SOURCES = cctbx/clipper_cctbx.cpp
+ cctbx_includedir=$(pkgincludedir)/cctbx
+ cctbx_include_HEADERS = cctbx/clipper_cctbx.h
+diff --git a/configure.ac b/configure.ac
+index 73131bc..cdee003 100644
+--- a/configure.ac
++++ b/configure.ac
+@@ -1,4 +1,4 @@
+-
++<
+ AC_INIT(clipper, 2.1.20130601)
+
+ AC_CONFIG_AUX_DIR(build-aux)
+@@ -50,10 +50,53 @@ AM_CONDITIONAL([BUILD_CCP4], [test "x$enable_ccp4" = xyes])
+ AM_CONDITIONAL([BUILD_CCTBX], [test "x$enable_cctbx" = xyes])
+ AM_CONDITIONAL([BUILD_FORTRAN], [test "x$enable_fortran" = xyes])
+
+-if test "x$enable_fortran" = "xyes"; then
++if test "x$enable_mmdb" = "xyes" -o "x$enable_mmdbold" = "xyes" -o \
++ "x$enable_minimol" = "xyes" -o "x$enable_cif" = "xyes"; then
++ PKG_CHECK_MODULES([MMDB], [mmdb],,[
++ AC_LANG_PUSH(C++)
++ AC_CHECK_LIB(mmdb, MMDB_CCIF_Init, :,
++ AC_MSG_WARN(mmdb library not found))
++ AC_CHECK_HEADER(mmdb/mmdb_manager.h, :,
++ AC_MSG_ERROR(mmdb headers not found))
++ AC_LANG_POP(C++)
++ CLIPPER_REQUIRES="mmdb"
++ MMDB_LIBS="-lmmdb"
++ AC_SUBST([MMDB_LIBS])
++ ])
++fi
++
++AM_COND_IF([BUILD_CCP4],[
++ PKG_CHECK_MODULES([CCP4], [libccp4c],,[
++ AC_CHECK_LIB(ccp4c, ccp4_banner, :,
++ AC_MSG_WARN(ccp4c library not found))
++ AC_CHECK_HEADER(ccp4/ccp4_general.h, :,
++ AC_MSG_ERROR(libccp4 headers not found))
++ CLIPPER_REQUIRES="libccp4c $CLIPPER_REQUIRES"
++ CCP4_LIBS="-lccp4c"
++ AC_SUBST([CCP4_LIBS])
++ ])
++])
++
++AM_COND_IF([BUILD_CCTBX],[
++ PKG_CHECK_MODULES([CCTBX], [cctbx cctbx_sgtbx_asu],,[
++ AC_LANG_PUSH(C++)
++ AC_CHECK_HEADER(cctbx/miller.h, :, AC_MSG_ERROR(cctbx headers not found))
++ AC_MSG_CHECKING(for cctbx)
++ AC_LINK_IFELSE([AC_LANG_PROGRAM([#include <cctbx/miller.h>],
++ [cctbx::Miller::Index a])],
++ AC_MSG_RESULT(yes),
++ [AC_MSG_RESULT(no)
++ AC_MSG_WARN(cctbx library not found)])
++ AC_LANG_POP(C++)
++ CCTBX_LIBS="-lsgtbx -luctbx"
++ AC_SUBST([CCTBX_LIBS])
++ ])
++])
++
++AM_COND_IF([BUILD_FORTRAN],[
+ AC_PROG_F77
+ AC_F77_WRAPPERS
+-fi
++ ])
+
+ AC_SEARCH_LIBS(cos, m, , AC_MSG_ERROR([math library not found.]))
+ SINGLE_FFTW
+@@ -79,35 +122,6 @@ test "x$enable_ccp4" = xyes && CLIPPER_LIBS="-lclipper-ccp4 $CLIPPER_LIBS"
+ #test "x$enable_cctbx" = xyes && CLIPPER_LIBS="-lclipper-cctbx $CLIPPER_LIBS"
+ test "x$enable_fortran" = xyes && CLIPPER_LIBS="-lclipper-fortran $CLIPPER_LIBS"
+
+-if test "x$enable_mmdb" = "xyes" -o "x$enable_mmdbold" = "xyes" -o \
+- "x$enable_minimol" = "xyes" -o "x$enable_cif" = "xyes"; then
+- AC_LANG_PUSH(C++)
+- AC_CHECK_LIB(mmdb, MMDB_CCIF_Init, :, AC_MSG_WARN(mmdb library not found))
+- AC_CHECK_HEADER(mmdb/mmdb_manager.h, :,
+- AC_MSG_ERROR(mmdb headers not found))
+- AC_LANG_POP(C++)
+- CLIPPER_REQUIRES="mmdb"
+-fi
+-
+-if test "x$enable_ccp4" = "xyes"; then
+- AC_CHECK_LIB(ccp4c, ccp4_banner, :, AC_MSG_WARN(ccp4c library not found))
+- AC_CHECK_HEADER(ccp4/ccp4_general.h, :,
+- AC_MSG_ERROR(libccp4 headers not found))
+- CLIPPER_REQUIRES="libccp4c $CLIPPER_REQUIRES"
+-fi
+-
+-if test "x$enable_cctbx" = "xyes"; then
+- AC_LANG_PUSH(C++)
+- AC_CHECK_HEADER(cctbx/miller.h, :, AC_MSG_ERROR(cctbx headers not found))
+- AC_MSG_CHECKING(for cctbx)
+- AC_LINK_IFELSE([AC_LANG_PROGRAM([#include <cctbx/miller.h>],
+- [cctbx::Miller::Index a])],
+- AC_MSG_RESULT(yes),
+- [AC_MSG_RESULT(no)
+- AC_MSG_WARN(cctbx library not found)])
+- AC_LANG_POP(C++)
+-fi
+-
+ VERSION_INFO="-version-info 2:1"
+ AC_SUBST(VERSION_INFO)
+ AC_SUBST(CLIPPER_LIBS)
^ permalink raw reply related [flat|nested] 2+ messages in thread
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