Bump to 2.7_beta2. The previous 2.7 ebuild was actually 2.7 beta 1 but was not named as such, so rename it to allow people to upgrade to beta 2.

Package-Manager: portage-2.1.8.3/cvs/Linux x86_64

5 files changed, 255 insertions, 7 deletions

diff --git a/sci-chemistry/namd/ChangeLog b/sci-chemistry/namd/ChangeLog
index 5b1fd4f51222..321c3119f5a5 100644
--- a/sci-chemistry/namd/ChangeLog
+++ b/sci-chemistry/namd/ChangeLog
@@ -1,6 +1,15 @@
 # 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 1.10 2010/04/23 19:38:39 dberkholz Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/namd/ChangeLog,v 1.11 2010/04/24 00:02:02 dberkholz Exp $
+
+*namd-2.7_beta2 (24 Apr 2010)
+*namd-2.7_beta1 (24 Apr 2010)
+
+  24 Apr 2010; Donnie Berkholz <dberkholz@gentoo.org>;
+  +namd-2.7_beta1.ebuild, +namd-2.7_beta2.ebuild, -namd-2.7.ebuild,
+  +files/namd-2.7_beta2-gentoo.patch:
+  Bump to 2.7_beta2. The previous 2.7 ebuild was actually 2.7 beta 1 but was
+  not named as such, so rename it to allow people to upgrade to beta 2.
 
   23 Apr 2010; Donnie Berkholz <dberkholz@gentoo.org>; namd-2.7.ebuild:
   All tc-get* sed replacements must happen before C*FLAGS-related ones,
diff --git a/sci-chemistry/namd/Manifest b/sci-chemistry/namd/Manifest
index 3b19ec645fb2..94c2e56e0c24 100644
--- a/sci-chemistry/namd/Manifest
+++ b/sci-chemistry/namd/Manifest
@@ -3,20 +3,23 @@ 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_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
 AUX namd-makefile-gentoo.patch 2804 RMD160 e52934e5a1aa7ed34e270dc11e780b1bdef3011d SHA1 22d5bd779a280c1287c936dd855f8359fa7b1b4e SHA256 f3945ae8fff113286847d61a00d5a749b1c3a00b65394085e56ff47a0a209250
 AUX namd-tcl-lib-gentoo.patch 576 RMD160 0992dd4103b97baed85e66a8d4fc04c3991bedd1 SHA1 f1cc944b14f7f77785f1a914d3d50f44d9929aec SHA256 7a57497410f5791b1b9fa0535e66137bd1b4c5008e0253c7467bc40af7b6ac01
 DIST NAMD_2.6_Source.tar.gz 8963319 RMD160 186f79322226a20398031618011104a666237298 SHA1 3b3d83fdc54a520cb6c59b34cde03c9f74d2f443 SHA256 bf353ff13eae18b5a8dc33d79d295e9fe73fb87482858309b7695ce3e24f0d0b
 DIST NAMD_2.7b1_Source.tar.gz 26302404 RMD160 ccb73606d3f0724c55ce022aa130656444825f5e SHA1 955e096a6c70e1e7786d10334bec3cae1eb4fff6 SHA256 cf48b659667fe9e03af27c8d434567525e924ebd08c801321c71361a8f166b2e
+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.ebuild 2652 RMD160 4daba1e26065307c20828d3c58abc65d0d469038 SHA1 03fb05e99de39329ae4a2daf97c7dc9ab83ba41d SHA256 01c8390e328ee39fd1647fbb0dd253b41d98b2a0db250640faf124440c98a713
-MISC ChangeLog 2106 RMD160 a982f8a885675f6f9ff4e2087a38ad19628e55ec SHA1 8e0d1b07f086b953c7e6001f7a542dae723b0c39 SHA256 04f6a2058e3960cc5627c6a0ecf0869c45bde0abb82954268589dd56996f6389
+EBUILD namd-2.7_beta1.ebuild 2658 RMD160 c928b75a108e1e3b590c840e4f5afb8a791df147 SHA1 d37b46c9100b1e0dec2c03ecfab9cbfce0883f13 SHA256 34a7a205c621fad15d0c97099128386fa29cc96e40a928d38df35f82df2d8751
+EBUILD namd-2.7_beta2.ebuild 2830 RMD160 e477f73c4687e6f7b034b696eb55116fa7179a71 SHA1 80ec984ef5e69af7de7ebd47380e51b4a82791df SHA256 31306db2ebf653bbbaa3bf1efd6d5d11ab6c80e2dcdfef8a469623ca6e2d2f1c
+MISC ChangeLog 2478 RMD160 31bbe13dc16f9205d6279ab419daf610cb7493aa SHA1 e9d8d08529c52e9fed85bb450c755f615df7bfc6 SHA256 211fc82e963551e1956b8e47b9146f290592d699090a1938f193c1d3e9535b36
 MISC metadata.xml 282 RMD160 539a53475b01291eadb86c8c53a0fbc02b4a34d4 SHA1 7f42dcea44641b8a77ab9644791344ec6ed6c327 SHA256 3c1785eb4ab63774ed3a6b1bddd602ef24cd6795f690bb3289d5a980bca06349
 -----BEGIN PGP SIGNATURE-----
 Version: GnuPG v2.0.14 (GNU/Linux)
 
-iEYEARECAAYFAkvR90YACgkQXVaO67S1rtta2QCg9AjgQbnSK61979RIMQU43Jtb
-+9QAoI8jFococeVUgfjFsb93R98lqnw+
-=zCrw
+iEYEARECAAYFAkvSNQEACgkQXVaO67S1rtv1cwCcCG9dfnl8ede13FlljiEcLnRs
+4FwAoNbxzWTVBnHCgCiLtWWc2bSfALkl
+=rqhe
 -----END PGP SIGNATURE-----
diff --git a/sci-chemistry/namd/files/namd-2.7_beta2-gentoo.patch b/sci-chemistry/namd/files/namd-2.7_beta2-gentoo.patch
new file mode 100644
index 000000000000..898d6b5d0980
--- /dev/null
+++ b/sci-chemistry/namd/files/namd-2.7_beta2-gentoo.patch
@@ -0,0 +1,126 @@
+diff -ur NAMD_2.7b2_Source.orig//arch/Linux-x86_64.fftw NAMD_2.7b2_Source//arch/Linux-x86_64.fftw
+--- NAMD_2.7b2_Source.orig//arch/Linux-x86_64.fftw	2010-04-23 14:40:54.566510874 -0500
++++ NAMD_2.7b2_Source//arch/Linux-x86_64.fftw	2010-04-23 14:41:08.106528893 -0500
+@@ -1,7 +1,7 @@
+ 
+-FFTDIR=/Projects/namd2/fftw/linux-x86_64
++FFTDIR=/usr
+ FFTINCL=-I$(FFTDIR)/include
+-FFTLIB=-L$(FFTDIR)/lib -lsrfftw -lsfftw
++FFTLIB=-L$(FFTDIR)/gentoo-libdir -lsrfftw -lsfftw
+ FFTFLAGS=-DNAMD_FFTW
+ FFT=$(FFTINCL) $(FFTFLAGS)
+ 
+diff -ur NAMD_2.7b2_Source.orig//arch/Linux-x86_64.tcl NAMD_2.7b2_Source//arch/Linux-x86_64.tcl
+--- NAMD_2.7b2_Source.orig//arch/Linux-x86_64.tcl	2010-04-23 14:40:54.566510874 -0500
++++ NAMD_2.7b2_Source//arch/Linux-x86_64.tcl	2010-04-23 14:41:08.106528893 -0500
+@@ -1,7 +1,7 @@
+ 
+-TCLDIR=/Projects/namd2/tcl/linux-x86_64
++TCLDIR=/usr
+ TCLINCL=-I$(TCLDIR)/include
+-TCLLIB=-L$(TCLDIR)/lib -ltcl8.3 -ldl
++TCLLIB=-L$(TCLDIR)/gentoo-libdir -ltcl8.5 -ldl
+ TCLFLAGS=-DNAMD_TCL
+ TCL=$(TCLINCL) $(TCLFLAGS)
+ 
+diff -ur NAMD_2.7b2_Source.orig//Make.charm NAMD_2.7b2_Source//Make.charm
+--- NAMD_2.7b2_Source.orig//Make.charm	2010-04-23 14:40:54.556517020 -0500
++++ NAMD_2.7b2_Source//Make.charm	2010-04-23 14:42:16.026530011 -0500
+@@ -2,5 +2,5 @@
+ # The config script will override this setting if there is a directory
+ # called charm-6.1 or charm in the NAMD base directory.
+ 
+-CHARMBASE = /Projects/namd2/charm-6.1.3
++CHARMBASE = /usr/include/charm-6.1.3
+ 
+Only in NAMD_2.7b2_Source/: Make.charm.~1~
+Only in NAMD_2.7b2_Source/: Make.charm.porig
+diff -ur NAMD_2.7b2_Source.orig//Makefile NAMD_2.7b2_Source//Makefile
+--- NAMD_2.7b2_Source.orig//Makefile	2010-04-23 14:40:54.556517020 -0500
++++ NAMD_2.7b2_Source//Makefile	2010-04-23 14:42:59.446523306 -0500
+@@ -300,10 +300,10 @@
+ 	$(DSTDIR)/stringhash.o
+ 
+ # definitions for Charm routines
+-CHARMC = $(CHARM)/bin/charmc
+-CHARMXI = $(CHARM)/bin/charmc
+-CHARMINC = $(CHARM)/include $(COPTD)CMK_OPTIMIZE=1
+-CHARMLIB = $(CHARM)/lib
++CHARMC = /usr/bin/charmc
++CHARMXI = /usr/bin/charmc
++CHARMINC = /usr/include/gentoo-charm $(COPTD)CMK_OPTIMIZE=1
++CHARMLIB = /usr/gentoo-libdir
+ 
+ # Libraries we may have changed
+ LIBS = $(CUDAOBJS) $(PLUGINLIB) $(DPMTALIBS) $(DPMELIBS) $(TCLDLL)
+@@ -323,7 +323,7 @@
+ 
+ # Add new executables here.
+ 
+-BINARIES = namd2 psfgen charmrun flipdcd flipbinpdb
++BINARIES = namd2 psfgen flipdcd flipbinpdb
+ 
+ # This should be rebuilt at every compile, but not on Win32.
+ BUILDINFO = $(DSTDIR)/buildinfo
+@@ -354,9 +354,6 @@
+ 	$(CHARMOPTS) \
+ 	-lm -o namd2
+ 
+-charmrun: $(CHARM)/bin/charmrun # XXX
+-	$(COPY) $(CHARM)/bin/charmrun $@
+-
+ $(LIBCUDARTSO):
+ 	if [ -r $(CUDADIR)/lib64/$(LIBCUDARTSO) ]; then \
+ 	  $(COPY) $(CUDADIR)/lib64/$(LIBCUDARTSO) $@; \
+@@ -364,10 +361,6 @@
+ 	  $(COPY) $(CUDADIR)/lib/$(LIBCUDARTSO) $@; \
+ 	fi
+ 
+-WINDOWSBINARIES = namd2.exe psfgen.exe
+-# WINDOWSBINARIES = namd2.exe psfgen.exe charmd.exe charmd_faceless.exe charmrun.exe
+-windowsbinaries: $(WINDOWSBINARIES)
+-
+ namd2.exe:  $(INCDIR) $(DSTDIR) $(OBJS) $(LIBS) $(TCLDLL)
+ 	$(MAKEBUILDINFO)
+ 	$(CHARMC) -verbose \
+@@ -390,9 +383,6 @@
+ charmd_faceless.exe:
+ 	$(COPY) $(CHARM)/bin/charmd_faceless.exe charmd_faceless.exe
+ 
+-charmrun.exe:
+-	$(COPY) $(CHARM)/bin/charmrun.exe charmrun.exe
+-
+ psfgen:	$(DSTDIR) $(SBOBJS) $(PLUGINOBJS)
+ 	$(CC) $(SBCFLAGS) -o psfgen $(SBOBJS) $(PLUGINOBJS) $(TCLLIB) $(TCLAPPLIB) -lm
+ 
+@@ -716,9 +706,7 @@
+ 
+ DOC_FILES = README.txt announce.txt license.txt notes.txt
+ 
+-RELEASE_FILES = $(LIBCUDARTSO) flipdcd flipbinpdb psfgen charmrun namd2
+-
+-WINDOWS_RELEASE_FILES = $(WINDOWSBINARIES) $(TCLDLL)
++RELEASE_FILES = $(LIBCUDARTSO) flipdcd flipbinpdb psfgen namd2
+ 
+ release: all
+ 	$(ECHO) Creating release $(RELEASE_DIR_NAME)
+@@ -727,17 +715,9 @@
+ 	for f in $(DOC_FILES); do cp .rootdir/$$f $(RELEASE_DIR_NAME); done
+ 	cp -r .rootdir/lib $(RELEASE_DIR_NAME)
+ 	/bin/rm -rf $(RELEASE_DIR_NAME)/lib/CVS $(RELEASE_DIR_NAME)/lib/*/CVS
+-	if [ -r $(CHARM)/bin/charmd ]; then \
+-	  $(COPY) $(CHARM)/bin/charmd $(RELEASE_DIR_NAME); \
+-	fi
+-	if [ -r $(CHARM)/bin/charmd_faceless ]; then \
+-	  $(COPY) $(CHARM)/bin/charmd_faceless $(RELEASE_DIR_NAME); \
+-	fi
+ 	chmod -R a+rX $(RELEASE_DIR_NAME)
+ 	tar cf $(RELEASE_DIR_NAME).tar $(RELEASE_DIR_NAME)
+ 	gzip $(RELEASE_DIR_NAME).tar
+-	echo $(CHARM)
+-	ls -l $(CHARM)/lib
+ 	-for f in $(RELEASE_FILES); do echo $$f; $(LDD) $$f; done
+ 
+ winrelease: winall
+Only in NAMD_2.7b2_Source/: Makefile.porig
diff --git a/sci-chemistry/namd/namd-2.7.ebuild b/sci-chemistry/namd/namd-2.7_beta1.ebuild
index 327d7440a8c8..997bef370e3b 100644
--- a/sci-chemistry/namd/namd-2.7.ebuild
+++ b/sci-chemistry/namd/namd-2.7_beta1.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.ebuild,v 1.3 2010/04/23 19:38:39 dberkholz Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/namd/namd-2.7_beta1.ebuild,v 1.1 2010/04/24 00:02:02 dberkholz Exp $
 
 inherit eutils toolchain-funcs flag-o-matic
 
diff --git a/sci-chemistry/namd/namd-2.7_beta2.ebuild b/sci-chemistry/namd/namd-2.7_beta2.ebuild
new file mode 100644
index 000000000000..b63de6f52789
--- /dev/null
+++ b/sci-chemistry/namd/namd-2.7_beta2.ebuild
@@ -0,0 +1,110 @@
+# 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 $
+
+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/csh
+			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
+	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
+}