respect LDFLAGS and declarations

Package-Manager: portage-2.2_rc67/cvs/Linux x86_64

6 files changed, 198 insertions, 9 deletions

diff --git a/sci-chemistry/namd/ChangeLog b/sci-chemistry/namd/ChangeLog
index 019ea0af2f00..4c3f229cbdb3 100644
--- a/sci-chemistry/namd/ChangeLog
+++ b/sci-chemistry/namd/ChangeLog
@@ -1,6 +1,13 @@
 # ChangeLog for sci-chemistry/namd
 # Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/namd/ChangeLog,v 1.12 2010/06/24 20:06:06 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/namd/ChangeLog,v 1.13 2010/06/24 20:37:03 jlec Exp $
+
+*namd-2.7_beta2-r1 (24 Jun 2010)
+
+  24 Jun 2010; Justin Lecher <jlec@gentoo.org> namd-2.7_beta2.ebuild,
+  +namd-2.7_beta2-r1.ebuild, +files/namd-2.7-iml-dec.patch,
+  +files/namd-2.7-ldflags.patch:
+  respect LDFLAGS and declarations
 
   24 Jun 2010; Justin Lecher <jlec@gentoo.org> -namd-2.7_beta1.ebuild:
   Removed unneeded
diff --git a/sci-chemistry/namd/Manifest b/sci-chemistry/namd/Manifest
index 72825510f0dc..f8be35206820 100644
--- a/sci-chemistry/namd/Manifest
+++ b/sci-chemistry/namd/Manifest
@@ -3,6 +3,8 @@ Hash: SHA1
 
 AUX namd-2.6-gentoo.patch 3650 RMD160 e7cc7fa0e20b01295d6f7c83211f961720e8beaa SHA1 f5525811cc092c5125be93cdce0e8c4e22fbee38 SHA256 55fad22d757d83d786b279a50a724499fb915767ade827895d686df16fa829d9
 AUX namd-2.7-gentoo.patch 4046 RMD160 a7d087c47088d9a8df8f804e023d1a882e281e74 SHA1 333fe98dcfb54736f192f3baa82280dcab1fbd21 SHA256 9416859fa9f065f3f269441cbbb44d4f627b71c8cba29ba9e6765c08dae3611f
+AUX namd-2.7-iml-dec.patch 520 RMD160 f8f33d8e10a7c6933369c3a6b857d44243bb1c74 SHA1 2edd740e3b6cb5514bde0c4742d0ca4bf6b98126 SHA256 6be7d0a3b4dff7fa39246e7ce49afb82ff508456ebbe3983e2def1202ebb3024
+AUX namd-2.7-ldflags.patch 1547 RMD160 bfaf2ca893168e1a652e75a186817d8149af94d8 SHA1 a0ce28bcc65e1cb7ff5c61723e602c26f5eef16b SHA256 ce2fd68cf2bf0c459c65caef4e71010b2ae5bf3c2c16770d44ca461291b9b924
 AUX namd-2.7_beta2-gentoo.patch 4409 RMD160 301bc17156f10a552eae4c2b3ed91ed2ea9fae6a SHA1 3cb0deb35e690156cf1a41e35482fab42480e3af SHA256 c56728dbf426540f9558db31f7e45cacc654112022f42917e715dbaa6c05373d
 AUX namd-barrier-fix-gentoo.patch 2362 RMD160 c6b045a0f2ec9f29bf7f98db7a71c1533f2a20d3 SHA1 5d42ef58f08914ecdf4afe735345ff1264389544 SHA256 f0186fada88b387c0681095174be336d61b2968197d223c15c840c1ca96e4992
 AUX namd-fftw-lib-gentoo.patch 528 RMD160 bb776e58497f0ec672bf5fc9ef22d0717d8c27ad SHA1 b8ca7a0521900bd9dbf725d9ce7ed809ff2d1aa0 SHA256 04528fd52f70cccbba1ccf844b97b256a35f9b1b85ca3ef8a56b4c9308b22696
@@ -11,13 +13,14 @@ AUX namd-tcl-lib-gentoo.patch 576 RMD160 0992dd4103b97baed85e66a8d4fc04c3991bedd
 DIST NAMD_2.6_Source.tar.gz 8963319 RMD160 186f79322226a20398031618011104a666237298 SHA1 3b3d83fdc54a520cb6c59b34cde03c9f74d2f443 SHA256 bf353ff13eae18b5a8dc33d79d295e9fe73fb87482858309b7695ce3e24f0d0b
 DIST NAMD_2.7b2_Source.tar.gz 9094631 RMD160 ec2c46f6cdb582dca73ebdbd894a9827f2e276d9 SHA1 0acab2a3bb6fca67b767f02bf7d2d2045ce6c3b9 SHA256 5675eb08534a6e4ea7a59e52e949991b3ba42abd78b45a46976ac3d7ed3b8d67
 EBUILD namd-2.6.ebuild 2263 RMD160 f846abf600169a6542e7a577724a8827b91fc515 SHA1 504275ea6effca39d3381409f4a9da52d907db31 SHA256 dc4868ffea8c831981080d501efd4dc18f03304cc5971cd4f1ece76a4f4b876e
-EBUILD namd-2.7_beta2.ebuild 2830 RMD160 e477f73c4687e6f7b034b696eb55116fa7179a71 SHA1 80ec984ef5e69af7de7ebd47380e51b4a82791df SHA256 31306db2ebf653bbbaa3bf1efd6d5d11ab6c80e2dcdfef8a469623ca6e2d2f1c
-MISC ChangeLog 2564 RMD160 b9a051e565aa174040b34b13af21c0704fba8c05 SHA1 5bda2952debd007c0da71afc87dda21971035457 SHA256 8744689ca0d602a59f9554b51cfc9f8d6ec65456043c92c62e0daf7b0154770f
+EBUILD namd-2.7_beta2-r1.ebuild 2895 RMD160 cdaef224fd40f6bd38e69b8c80518579fbb1a731 SHA1 673fec92ba21e82dc438819cf035ba3988d0c8fa SHA256 303bbac24eab8d3f1ed149436cde75530f51a396b63f1b343f4c94b714eaf61a
+EBUILD namd-2.7_beta2.ebuild 2892 RMD160 26696e2d4dfdefa900831ffbaa85e85af144fc46 SHA1 b6f7dba07ce941d7e0ef0c4c9dbea64bf941e70c SHA256 4f4d18836aaee2cb6bb988199962bacb33c4bc6c158c366a4e423a6a7f26d3ed
+MISC ChangeLog 2797 RMD160 050da7ba2120061612df6321b0ffd2e49c1ae9e6 SHA1 06d5dc422168a91e935ebd7d5596f4a474ce0c53 SHA256 05c0e8e730d8ba7cebcd8bb0435aa8980e686b908713cc340c222d0455ad8421
 MISC metadata.xml 282 RMD160 539a53475b01291eadb86c8c53a0fbc02b4a34d4 SHA1 7f42dcea44641b8a77ab9644791344ec6ed6c327 SHA256 3c1785eb4ab63774ed3a6b1bddd602ef24cd6795f690bb3289d5a980bca06349
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diff --git a/sci-chemistry/namd/files/namd-2.7-iml-dec.patch b/sci-chemistry/namd/files/namd-2.7-iml-dec.patch
new file mode 100644
index 000000000000..e5ee3bd6c818
--- /dev/null
+++ b/sci-chemistry/namd/files/namd-2.7-iml-dec.patch
@@ -0,0 +1,24 @@
+diff --git a/src/flipbinpdb.c b/src/flipbinpdb.c
+index 94b71ba..01a2529 100644
+--- a/src/flipbinpdb.c
++++ b/src/flipbinpdb.c
+@@ -9,6 +9,7 @@
+ #include <sys/mman.h>
+ #include <fcntl.h>
+ #include <stdio.h>
++#include <stdlib.h>
+ 
+ #ifndef MAP_FILE
+ #define MAP_FILE 0
+diff --git a/src/flipdcd.c b/src/flipdcd.c
+index 8ec85b7..1c23433 100644
+--- a/src/flipdcd.c
++++ b/src/flipdcd.c
+@@ -13,6 +13,7 @@
+ #include <sys/mman.h>
+ #include <fcntl.h>
+ #include <stdio.h>
++#include <stdlib.h>
+ 
+ #ifndef MAP_FILE
+ #define MAP_FILE 0
diff --git a/sci-chemistry/namd/files/namd-2.7-ldflags.patch b/sci-chemistry/namd/files/namd-2.7-ldflags.patch
new file mode 100644
index 000000000000..686eba83a2de
--- /dev/null
+++ b/sci-chemistry/namd/files/namd-2.7-ldflags.patch
@@ -0,0 +1,41 @@
+diff --git a/Makefile b/Makefile
+index fd20f12..0821bed 100644
+--- a/Makefile
++++ b/Makefile
+@@ -339,7 +339,7 @@ all:	$(BINARIES) $(LIBCUDARTSO)
+ 
+ namd2:	$(INCDIR) $(DSTDIR) $(OBJS) $(LIBS)
+ 	$(MAKEBUILDINFO)
+-	$(CHARMC) -verbose -ld++-option \
++	$(CHARMC) $(LDFLAGS) -verbose -ld++-option \
+ 	"$(COPTI)$(CHARMINC) $(COPTI)$(INCDIR) $(COPTI)$(SRCDIR) $(CXXOPTS)" \
+ 	-module NeighborLB -module commlib -language charm++ \
+ 	$(BUILDINFO).o \
+@@ -394,23 +394,23 @@ charmrun.exe:
+ 	$(COPY) $(CHARM)/bin/charmrun.exe charmrun.exe
+ 
+ psfgen:	$(DSTDIR) $(SBOBJS) $(PLUGINOBJS)
+-	$(CC) $(SBCFLAGS) -o psfgen $(SBOBJS) $(PLUGINOBJS) $(TCLLIB) $(TCLAPPLIB) -lm
++	$(CC) $(SBCFLAGS) $(LDFLAGS) -o psfgen $(SBOBJS) $(PLUGINOBJS) $(TCLLIB) $(TCLAPPLIB) -lm
+ 
+ psfgen.exe:	$(DSTDIR) $(SBOBJS) $(PLUGINOBJS) $(TCLDLL)
+ 	$(CC) $(SBCFLAGS) -o psfgen $(SBOBJS) $(PLUGINOBJS) $(TCLLIB) $(TCLAPPLIB) -lm
+ 
+ flipdcd:	$(SRCDIR)/flipdcd.c
+-	$(CC) $(CFLAGS) -o $@ $(SRCDIR)/flipdcd.c || \
++	$(CC) $(CFLAGS) $(LDFLAGS) -o $@ $(SRCDIR)/flipdcd.c || \
+ 	echo "#!/bin/sh\necho unavailable on this platform" > $@; \
+ 	chmod +x $@
+ 
+ flipbinpdb:	$(SRCDIR)/flipbinpdb.c
+-	$(CC) $(CFLAGS) -o $@ $(SRCDIR)/flipbinpdb.c || \
++	$(CC) $(CFLAGS) $(LDFLAGS) -o $@ $(SRCDIR)/flipbinpdb.c || \
+ 	echo "#!/bin/sh\necho unavailable on this platform" > $@; \
+ 	chmod +x $@
+ 
+ fixdcd:	$(SRCDIR)/fixdcd.c
+-	$(CC) $(CFLAGS) -o fixdcd $(SRCDIR)/fixdcd.c
++	$(CC) $(CFLAGS) $(LDFLAGS) -o fixdcd $(SRCDIR)/fixdcd.c
+ 
+ dumpdcd:	$(SRCDIR)/dumpdcd.c
+ 	$(CC) $(CFLAGS) -o dumpdcd $(SRCDIR)/dumpdcd.c
diff --git a/sci-chemistry/namd/namd-2.7_beta2-r1.ebuild b/sci-chemistry/namd/namd-2.7_beta2-r1.ebuild
new file mode 100644
index 000000000000..3d0115b67590
--- /dev/null
+++ b/sci-chemistry/namd/namd-2.7_beta2-r1.ebuild
@@ -0,0 +1,112 @@
+# Copyright 1999-2010 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/namd/namd-2.7_beta2-r1.ebuild,v 1.1 2010/06/24 20:37:03 jlec Exp $
+
+inherit eutils toolchain-funcs flag-o-matic
+
+DESCRIPTION="A powerful and highly parallelized molecular dynamics code"
+LICENSE="namd"
+HOMEPAGE="http://www.ks.uiuc.edu/Research/namd/"
+
+MY_PN="NAMD"
+MY_PV="2.7b2"
+
+SRC_URI="${MY_PN}_${MY_PV}_Source.tar.gz"
+
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE=""
+
+RESTRICT="fetch"
+
+DEPEND="
+	app-shells/tcsh
+	sys-cluster/charm
+	=sci-libs/fftw-2*
+	dev-lang/tcl"
+
+RDEPEND=${DEPEND}
+
+NAMD_ARCH="Linux-x86_64-g++"
+
+NAMD_DOWNLOAD="http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=NAMD"
+
+S="${WORKDIR}/${MY_PN}_${MY_PV}_Source"
+
+pkg_nofetch() {
+	echo
+	einfo "Please download ${MY_PN}_${MY_PV}_Source.tar.gz from"
+	einfo "${NAMD_DOWNLOAD}"
+	einfo "after agreeing to the license and then move it to"
+	einfo "${DISTDIR}"
+	einfo "Be sure to select the ${MY_PV} version!"
+	echo
+}
+
+src_unpack() {
+	unpack ${A}
+	cd "${S}"
+
+	CHARM_VERSION=$(best_version sys-cluster/charm | cut -d- -f3)
+
+	# apply a few small fixes to make NAMD compile and
+	# link to the proper libraries
+	epatch "${FILESDIR}"/namd-2.7_beta2-gentoo.patch
+	epatch "${FILESDIR}"/namd-2.7-ldflags.patch
+	epatch "${FILESDIR}"/namd-2.7-iml-dec.patch
+	sed -e "s:charm-6.1.3:charm-${CHARM_VERSION}:" \
+		Make.charm || \
+		die
+
+	rm -f charm-6.1.3.tar || die
+
+	# proper compiler and cflags
+	sed -e "s/g++/$(tc-getCXX)/" \
+		-e "s/gcc/$(tc-getCC)/" \
+		-e "s/CXXOPTS = -O3 -m64 -fexpensive-optimizations -ffast-math/CXXOPTS = ${CXXFLAGS}/" \
+		-e "s/COPTS = -O3 -m64 -fexpensive-optimizations -ffast-math/COPTS = ${CFLAGS}/" \
+		-i arch/${NAMD_ARCH}.arch || \
+		die "Failed to setup ${NAMD_ARCH}.arch"
+
+	sed -e "s/gentoo-libdir/$(get_libdir)/g" \
+		-e "s/gentoo-charm/charm-${CHARM_VERSION}/g" \
+		-i Makefile || die "Failed gentooizing Makefile."
+	sed -e "s/gentoo-libdir/$(get_libdir)/g" -i arch/Linux-x86_64.fftw || \
+		die "Failed gentooizing Linux-x86_64.fftw."
+	sed -e "s/gentoo-libdir/$(get_libdir)/g" -i arch/Linux-x86_64.tcl || \
+		die "Failed gentooizing Linux-x86_64.tcl."
+
+	# configure
+	./config ${NAMD_ARCH}
+}
+
+src_compile() {
+	# build namd
+	cd "${S}/${NAMD_ARCH}"
+	emake || die "Failed to build namd"
+}
+
+src_install() {
+	cd "${S}/${NAMD_ARCH}"
+
+	# the binaries
+	dobin ${PN}2 psfgen flipbinpdb flipdcd || \
+		die "Failed to install binaries"
+
+	cd "${S}"
+
+	# some docs
+	dodoc announce.txt license.txt notes.txt || \
+		die "Failed to install docs"
+}
+
+pkg_postinst() {
+	echo
+	einfo "For detailed instructions on how to run and configure"
+	einfo "NAMD please consults the extensive documentation at"
+	einfo "http://www.ks.uiuc.edu/Research/namd/"
+	einfo "and the NAMD tutorials available at"
+	einfo "http://www.ks.uiuc.edu/Training/Tutorials/"
+	einfo "Have fun :)"
+	echo
+}
diff --git a/sci-chemistry/namd/namd-2.7_beta2.ebuild b/sci-chemistry/namd/namd-2.7_beta2.ebuild
index b63de6f52789..bc90354b4c61 100644
--- a/sci-chemistry/namd/namd-2.7_beta2.ebuild
+++ b/sci-chemistry/namd/namd-2.7_beta2.ebuild
@@ -1,6 +1,6 @@
 # Copyright 1999-2010 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/namd/namd-2.7_beta2.ebuild,v 1.1 2010/04/24 00:02:02 dberkholz Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/namd/namd-2.7_beta2.ebuild,v 1.2 2010/06/24 20:37:03 jlec Exp $
 
 inherit eutils toolchain-funcs flag-o-matic
 
@@ -19,8 +19,8 @@ IUSE=""
 
 RESTRICT="fetch"
 
-DEPEND="|| ( app-shells/csh
-			app-shells/tcsh )
+DEPEND="
+	app-shells/tcsh
 	sys-cluster/charm
 	=sci-libs/fftw-2*
 	dev-lang/tcl"
@@ -52,6 +52,8 @@ src_unpack() {
 	# apply a few small fixes to make NAMD compile and
 	# link to the proper libraries
 	epatch "${FILESDIR}"/namd-2.7_beta2-gentoo.patch
+	epatch "${FILESDIR}"/namd-2.7-ldflags.patch
+	epatch "${FILESDIR}"/namd-2.7-iml-dec.patch
 	sed -e "s:charm-6.1.3:charm-${CHARM_VERSION}:" \
 		Make.charm || \
 		die