Version Bump, removed old

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

4 files changed, 179 insertions, 5 deletions

diff --git a/sci-chemistry/refmac/ChangeLog b/sci-chemistry/refmac/ChangeLog
index 7cdbf97c470f..3a4af17923a4 100644
--- a/sci-chemistry/refmac/ChangeLog
+++ b/sci-chemistry/refmac/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-chemistry/refmac
 # Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/refmac/ChangeLog,v 1.12 2010/07/02 06:36:10 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/refmac/ChangeLog,v 1.13 2010/07/03 08:33:57 jlec Exp $
+
+*refmac-5.6.0080 (03 Jul 2010)
+
+  03 Jul 2010; Justin Lecher <jlec@gentoo.org>
+  +files/5.6.0080-allow-dynamic-linking.patch, +refmac-5.6.0080.ebuild:
+  Version Bump, removed old
 
 *refmac-5.6.0079 (02 Jul 2010)
 
diff --git a/sci-chemistry/refmac/Manifest b/sci-chemistry/refmac/Manifest
index 0371018228cc..3b93838cda68 100644
--- a/sci-chemistry/refmac/Manifest
+++ b/sci-chemistry/refmac/Manifest
@@ -6,9 +6,11 @@ AUX 5.5-test.log.patch 1146 RMD160 0ea6293e8ecde3b9ae12658a523e3c30a5c9f01b SHA1
 AUX 5.5.0110-allow-dynamic-linking.patch 2265 RMD160 191b90c619a3a0a6cd71b819b4517d639f9912e0 SHA1 23df6c19a6fa9a41ed19d4ec36bd3130ffdb40b7 SHA256 ed10babfa6f9521b1b8e0dd574aa5fa4207d64bcd57332e97f0b35039b66942b
 AUX 5.6.0075-allow-dynamic-linking.patch 1447 RMD160 5b4eca9f5e03aa0dea24fe4e391c363b3600eb4a SHA1 a3e4989d6b68c77e69e1bfcb76ddbc98c6e7a157 SHA256 0e54d70ac56326422158d19268432772813d34b653b041554ac6e08981ff0140
 AUX 5.6.0078-allow-dynamic-linking.patch 3254 RMD160 0136fa28503c10c07ae3e7b653c04cd1e03e3641 SHA1 8b896a003dad2ab840bd7310871fab8191930de6 SHA256 ad4c0feaefcdac5b834549f99ae69aa0b0b33c37332e7e385ee04258b4c51326
+AUX 5.6.0080-allow-dynamic-linking.patch 3680 RMD160 656b50c14ae3b8b886967c39bb73c22d5e8c9ea1 SHA1 bab840c675e4628ee2220c87859fd08f0e88b95b SHA256 1aa6c02ec0aa04e044c5627d649b09402d7d95c44752f9137f62e5d513b171d9
 DIST refmac5.6_source_v5.6.0077.tar.gz 1281296 RMD160 3af10c692dcca23bce735b6b45c129c4a1c029e6 SHA1 881d3e456436e15073be495a340504770884e06f SHA256 9f5df52e5b42d5c4e83388f9acd900461c66b76b25248fb539432d4dacb38d50
 DIST refmac5.6_source_v5.6.0078.tar.gz 1285576 RMD160 9d5a56a6ae5f5cd03b081607a9916ba543d258a1 SHA1 cc5543cddfbd9f4dfb9105c6472f091cffca7e38 SHA256 a23d657098d890c2ce2c20de35865f512b841c1357611ae3aca31897df1ab832
 DIST refmac5.6_source_v5.6.0079.tar.gz 1285637 RMD160 462ba6f5814d724f678ca39f00b52dc4b0ac0649 SHA1 386d48b905e1297983d84f35d0ab276583494153 SHA256 47a943344962e0559ba1d3c57d0c6562cee03013a62b9c1b66dce4e574a409d7
+DIST refmac5.6_source_v5.6.0080.tar.gz 1317431 RMD160 13f306092428bf87a29fa456c03f33c318183110 SHA1 17796be16dbbf4d442fed8814edbf6bb175a4aaf SHA256 cae4017c5a75b185c99a5460c96386978f7959c28c870b80ec9df272f9b3da53
 DIST refmac_5.5.0109.tar.gz 1326779 RMD160 3b603c13638407cceb907bd43ac0a971b587c116 SHA1 3cc35a55df71bac4de3eec9cf0e690e221ae3c86 SHA256 38d416c94e1f86a0676d48d7ddaeb4af272970b8cd6b084e70aa38481327c59e
 DIST refmac_5.5.0110.tar.gz 1326832 RMD160 6613ca8b70e54e7827f8ff02b7d497560cb83e39 SHA1 ba2e38db6c88550bd901b474de881d6514b4d74e SHA256 1353fb1042586ec8fa37d0a90f274890d0ccc02377af5216200662338dfe08ca
 DIST test-framework.tar.gz 130933173 RMD160 7122539dc713615dca2ddaddfd8d152cd22624d0 SHA1 1d3e3019a67afb9b2346e919c859d402d3250fea SHA256 df050a2a29da80518cb0616a0bbeb82298ea0721549348d15353bf0f66240605
@@ -18,12 +20,13 @@ EBUILD refmac-5.5.0110.ebuild 1805 RMD160 80e546666e72290365c99c542abcef90a3394b
 EBUILD refmac-5.6.0077.ebuild 1789 RMD160 e5433f715ae0693c4ccbf65cb44f64b988199ea2 SHA1 dfaa458bfa184ffc2118bcc13e0a3b30caa472e8 SHA256 f23cc970ed7fc6766fddd8ceef788c58fd254bbe2be53f9df14561a06c13b1be
 EBUILD refmac-5.6.0078.ebuild 1786 RMD160 3a75889780b1118f2481991a56b95e62ab8363c4 SHA1 537ab12d16126fff356781f66b1d3aa2edb49117 SHA256 e43fce8f9a0fd05c6a02edb534c09a31017b2bf9274886ee0755993078e23520
 EBUILD refmac-5.6.0079.ebuild 1792 RMD160 e013a579d25f02149d1a990f8169ed612a072cde SHA1 f203e1bf374ec9af4ed37f6cbeea33ce15cfd998 SHA256 987d7ab0ab86168df29edc608d02d1dddea421bac0ee8e93541eee035894b112
-MISC ChangeLog 2118 RMD160 9d29943905e4c531444d90704cf5c08a3de7c093 SHA1 c6fb45ebe54ca76d0812d9d3053a1616c0d8ce52 SHA256 18ac25d0a5833d72d2e395471e971fba2cb83a91c4298b282cd11262c4c09126
+EBUILD refmac-5.6.0080.ebuild 1786 RMD160 5851ff9ac4b5fbb60bbc76baca5a2cf060ed5d69 SHA1 5eeaef1b03d2bda2be97fe43defd5e0602661750 SHA256 c891536606c9ad16198d181a6938012b2c1c6b0fde35bfedb96d44a6e1ec8eb5
+MISC ChangeLog 2298 RMD160 b65adc697a377c370b2275e83ff3c4cc44ad32d8 SHA1 cf3fa1dfbeac6429243ab89ec7d4f83879ab8d69 SHA256 c3e010266bfa745733f40683fa9ab453ed30fdae14f9059e711f8a9d3a39a8c6
 MISC metadata.xml 311 RMD160 df83b13d491a71b729455b664088d89ddbde1c8c SHA1 fffd2a5645181aa12ac9b6f74da9a011cdcf1b97 SHA256 782521c7e16d7eec82d7b7e7c43102806e7f72bc7366401808b1e1ac6e26045a
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+iEYEARECAAYFAkwu9fsACgkQgAnW8HDreRZogACgkbhbQUMLMAGX71l1JRLhx6P8
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diff --git a/sci-chemistry/refmac/files/5.6.0080-allow-dynamic-linking.patch b/sci-chemistry/refmac/files/5.6.0080-allow-dynamic-linking.patch
new file mode 100644
index 000000000000..6f5d1c6efe98
--- /dev/null
+++ b/sci-chemistry/refmac/files/5.6.0080-allow-dynamic-linking.patch
@@ -0,0 +1,94 @@
+diff --git a/makefile_refmac.inc1 b/makefile_refmac.inc1
+index 3f858c8..04e6790 100644
+--- a/makefile_refmac.inc1
++++ b/makefile_refmac.inc1
+@@ -89,9 +89,7 @@ messy_pdb.o                 \
+ bridge.o                    \
+ i0.o                        \
+ i1.o                        \
+-chbevl.o                    \
+-$(LLIBCIF)                  \
+-$(LLIBLAPACK)
++chbevl.o
+ 
+ 
+ SUBL =                      \
+@@ -124,9 +122,7 @@ cell_symm_subrs.o           \
+ iheap_sort.o                \
+ linalgebra.o                \
+ math_refmac.o               \
+-subnumrec.o                 \
+-$(LLIBLAPACK)               \
+-$(LLIBCCP)
++subnumrec.o
+ 
+ #--------------------------------------------------------------------------------
+ 
+@@ -150,7 +146,7 @@ twin77mod.o:  twin77mod.f
+ 	$(FC) $(FFLAGS) -c twin77mod.f
+ 
+ 
+-optimise_solvent_all.o: optimise_solvent_all.f90
++optimise_solvent_all.o: optimise_solvent_all.f90 atomf77mod.o
+ 	$(FC) $(FFLAGS) -c optimise_solvent_all.f90
+ 
+ ncs_rest.o: ncs_ncs_generate.f90 ncs_rest.f
+@@ -178,7 +174,7 @@ align_refmac.o: align_refmac.f90
+ 	$(FC) $(FFLAGS) -c align_refmac.f90
+ 
+ 
+-hkon_secder_tch.o: hkon_secder_tch.f local_tls.f90 ncs_simil.f90 optimise_solvent_all.f90
++hkon_secder_tch.o: hkon_secder_tch.f local_tls.f90 ncs_simil.f90 optimise_solvent_all.f90 optimise_solvent_all.o
+ 	$(FC) $(FFLAGS) -c optimise_solvent_all.f90 ncs_simil.f90 local_tls.f90 hkon_secder_tch.f
+ 
+ oppro_allocate.o: oppro_allocate.f filter_params.f90 optimise_solvent_all.f90
+@@ -220,8 +216,8 @@ refall_twin.o: refall_twin.f optimise_solvent_all.f90
+ rharvest.o: rharvest.f optimise_solvent_all.f90
+ 	$(FC) $(FFLAGS) -c optimise_solvent_all.f90 rharvest.f
+ 
+-solvent_contr_mask.o: solvent_contr_mask.f optimise_solvent_all.f90
+-	$(FC) $(FFLAGS) -c optimise_solvent_all.f90 solvent_contr_mask.f
++solvent_contr_mask.o: solvent_contr_mask.f optimise_solvent_all.f90 atomf77mod.o
++	$(FC) $(FFLAGS) -c  atomf77mod.f optimise_solvent_all.f90 solvent_contr_mask.f
+ 
+ subag_scale_hessian.o: subag_scale_hessian.f optimise_solvent_all.f90
+ 	$(FC) $(FFLAGS) -c optimise_solvent_all.f90 subag_scale_hessian.f
+@@ -229,7 +225,7 @@ subag_scale_hessian.o: subag_scale_hessian.f optimise_solvent_all.f90
+ subcf_scale1.o: subcf_scale1.f optimise_solvent_all.f90
+ 	$(FC) $(FFLAGS) -c optimise_solvent_all.f90 subcf_scale1.f
+ 
+-refmac_xml.o: refmac_xml.f optimise_solvent_all.f90
++refmac_xml.o: refmac_xml.f optimise_solvent_all.f90 optimise_solvent_all.o
+ 	$(FC) $(FFLAGS) -c optimise_solvent_all.f90 refmac_xml.f
+ 
+ hkl_pack.o:  hkl_pack.f90
+@@ -239,9 +235,9 @@ subvag.o: subvag.f hkl_pack.f90
+ 	$(FC) $(FFLAGS) -c hkl_pack.f90 subvag.f
+ 
+ refmac:	$(SUBR)
+-	$(FC) $(FFLAGS) -o refmac${VERSION}   ${SUBR} $(LLIBOTHERS) $(LLIBCCP)
++	$(FC) $(FFLAGS) $(LDFLAGS) -o refmac${VERSION}   ${SUBR} $(LLIBOTHERS) $(LLIBCCP) $(LLIBCIF) $(LLIBLAPACK)
+ 
+-mol2_file.o:	mol2_file.f odb_files.f90
++mol2_file.o:	mol2_file.f odb_files.o
+ 	$(FC) $(FFLAGS) -c odb_files.f90 mol2_file.f
+ 
+ odb_files.o:	odb_files.f90 elements_module.f90 enerf77mod.f
+@@ -250,7 +246,7 @@ odb_files.o:	odb_files.f90 elements_module.f90 enerf77mod.f
+ elements_module.o:	elements_module.f90
+ 	$(FC) $(FFLAGS) -c elements_module.f90
+ 
+-make_lib2.o:	make_lib2.f odb_files.f90 
++make_lib2.o:	make_lib2.f odb_files.o
+ 	$(FC) $(FFLAGS) -c odb_files.f90 make_lib2.f
+ 
+ pdb2libcheck.o:	pdb2libcheck.f90
+@@ -260,7 +256,7 @@ libcheck.o:	libcheck.f elements_module.f90 pdb2libcheck.f90
+ 	$(FC) $(FFLAGS) -c elements_module.f90 pdb2libcheck.f90 libcheck.f
+ 
+ libcheck:	$(SUBL)
+-	$(FC) $(FFLAGS) -o libcheck${VERSION} $(SUBL)
++	$(FC) $(FFLAGS) $(LDFLAGS) -o libcheck${VERSION} $(SUBL) $(LLIBCCP) $(LLIBCIF) $(LLIBLAPACK)
+ 
+ clean:
+ 	/bin/rm *.o
diff --git a/sci-chemistry/refmac/refmac-5.6.0080.ebuild b/sci-chemistry/refmac/refmac-5.6.0080.ebuild
new file mode 100644
index 000000000000..8f6bdbfaa1ce
--- /dev/null
+++ b/sci-chemistry/refmac/refmac-5.6.0080.ebuild
@@ -0,0 +1,71 @@
+# Copyright 1999-2010 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/refmac/refmac-5.6.0080.ebuild,v 1.1 2010/07/03 08:33:57 jlec Exp $
+
+EAPI="2"
+
+inherit fortran base toolchain-funcs versionator
+
+MY_PV="$(get_version_component_range 1-2)_source_v${PV}"
+
+DESCRIPTION="Macromolecular crystallographic refinement program"
+HOMEPAGE="http://www.ysbl.york.ac.uk/~garib/refmac/"
+SRC_URI="${HOMEPAGE}data/refmac_experimental/${PN}${MY_PV}.tar.gz
+	test? ( http://dev.gentooexperimental.org/~jlec/distfiles/test-framework.tar.gz )"
+
+SLOT="0"
+LICENSE="ccp4"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="test"
+
+RDEPEND="
+	sci-libs/ccp4-libs
+	sci-libs/mmdb
+	>sci-libs/monomer-db-1
+	virtual/blas
+	virtual/lapack"
+DEPEND="${RDEPEND}"
+
+S="${WORKDIR}"
+
+PATCHES=(
+	"${FILESDIR}"/${PV}-allow-dynamic-linking.patch
+	)
+
+src_prepare() {
+	base_src_prepare
+	use test && epatch "${FILESDIR}"/5.5-test.log.patch
+}
+
+src_compile() {
+	emake \
+		FC=$(tc-getFC) \
+		CC=$(tc-getCC) \
+		CXX=$(tc-getCXX) \
+		COPTIM="${CFLAGS}" \
+		FOPTIM="${FFLAGS:- -O2}" \
+		VERSION="" \
+		XFFLAGS="-fno-second-underscore" \
+		LLIBCCP="-lccp4f -lccp4c -lccif -lmmdb -lstdc++" \
+		LLIBLAPACK="$(pkg-config --libs lapack blas)" \
+		|| die
+}
+
+src_test() {
+	einfo "Starting tests ..."
+	export PATH="${WORKDIR}/test-framework/scripts:${S}:${PATH}"
+	export CCP4_TEST="${WORKDIR}"/test-framework
+	export CCP4_SCR="${T}"
+	ln -sf refmac "${S}"/refmac5
+	sed '/^ANISOU/d' -i ${CCP4_TEST}/data/pdb/1vr7.pdb
+	ccp4-run-thorough-tests -v test_refmac5 || die
+}
+
+src_install() {
+	for i in refmac libcheck; do
+		exeinto /usr/libexec/ccp4/bin/
+		doexe ${i} || die
+		dosym ../libexec/ccp4/bin/${i} /usr/bin/${i}
+	done
+	dosym refmac /usr/bin/refmac5 || die
+}