Fix for Molrep: input fixed model mode failure

Package-Manager: portage-2.2.0_alpha60/cvs/Linux x86_64

4 files changed, 89 insertions, 5 deletions

diff --git a/sci-chemistry/molrep/ChangeLog b/sci-chemistry/molrep/ChangeLog
index 59cc4096e09b..56390e985234 100644
--- a/sci-chemistry/molrep/ChangeLog
+++ b/sci-chemistry/molrep/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-chemistry/molrep
 # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/molrep/ChangeLog,v 1.19 2011/09/07 16:40:39 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/molrep/ChangeLog,v 1.20 2011/10/04 15:21:19 jlec Exp $
+
+*molrep-11.0.03-r1 (04 Oct 2011)
+
+  04 Oct 2011; Justin Lecher <jlec@gentoo.org> +files/11.0.03-EOR.patch,
+  +molrep-11.0.03-r1.ebuild:
+  Fix for Molrep: input fixed model mode failure
 
 *molrep-11.0.03 (07 Sep 2011)
 
diff --git a/sci-chemistry/molrep/Manifest b/sci-chemistry/molrep/Manifest
index d98cb45f06d7..79e105609d53 100644
--- a/sci-chemistry/molrep/Manifest
+++ b/sci-chemistry/molrep/Manifest
@@ -4,16 +4,18 @@ Hash: SHA512
 AUX 10.2.35-respect-FLAGS.patch 2368 RMD160 4f24b345f0c78de0c0222abfef987d61fe1356d0 SHA1 bc445d646208de7e879a5989b66296fd89b2fc96 SHA256 809d9f290a1eb59b8fc5904328e72c30b65d3be821a61a1bff050bc446bdc991
 AUX 11.0.00-respect-FLAGS.patch 364 RMD160 b364dfd896cd954740960eb32c15f47e9c2cdffd SHA1 50e945f5f6f8b0785547c2bebeea26f93421bb39 SHA256 04a8fbd74b3f9280fbb7d5abe701cee5f59901c258afdfc16b4d37809200c461
 AUX 11.0.00-test.patch 5153 RMD160 70dabd2f772cbcad4c8cd1ea617838a6a1b61f55 SHA1 b3b66bcb1661a1fcd3c7700310dda4a1642293c3 SHA256 f057baee3a42a3a517199c039018d8042d4da098976636950871d650e6d5acd1
+AUX 11.0.03-EOR.patch 513 RMD160 1a81d602555b623d9a521fc2826577e483bd2aa6 SHA1 76569a0846677cb2482098bf8d24196607071d07 SHA256 e413668dbe47d072ce7deb5b19584f45edf148e69522f6afa50eb39ec1c88bda
 DIST molrep-11.0.02.tar.gz 3594084 RMD160 d4238e39a21aa6c7b3373a8db243c54f817e4408 SHA1 f54becab42f5a484a33e11e3c8515d8bed37a880 SHA256 6acb00bc91ad76027461ce6055eda72c8de34e5243449a31d5ede9e537e9adce
 DIST molrep-11.0.03.tar.gz 3643087 RMD160 fce47895d194db79c2b5b32ccc7b6f87779dc0c8 SHA1 a6af659714a9df2b658811f853880602df85bae6 SHA256 f4c317713b0dddf0ca883734f0bfe27600b50f8d4dd354ea8ae8245e21ce4392
 EBUILD molrep-11.0.02.ebuild 1321 RMD160 57658320e01c25d541111e696673ac53cb15b3f9 SHA1 dd02dccd6159e89fcbb62947de7254a2fbe28239 SHA256 37b5a21b9933ac19b5fc4c2f2b9551d84c2cd3359ef9f300b5c93d505f582a8d
+EBUILD molrep-11.0.03-r1.ebuild 1433 RMD160 3b3624641c63181ae57a2746b935ae130cfb7614 SHA1 20b1cde02c44a9c8dc9eac380b98e5845ef2aa89 SHA256 1f1ede97bf18198007b5ce45c1fa8b207ab07708b3d6f011ef4608a39d0f2bee
 EBUILD molrep-11.0.03.ebuild 1396 RMD160 4732300b9e46d5ec710751712d037d5e732c26bd SHA1 a358cfe0404f87a0ecefdcaecaf9efa20315f1d3 SHA256 7ade7d97df43efbbf799a5b5fd09d5e372d089c83a79a862595c4f3f17ca7e9a
-MISC ChangeLog 2606 RMD160 858a9b0ef0fb53135074aed8046241437d100204 SHA1 5176a02f19053d37dc29d3fa73682e171f835291 SHA256 0be96595d02d9f8c92e22eda339f6f7eaf4a9c56130a7a28b54b3e264065df15
+MISC ChangeLog 2792 RMD160 64d9d84193fe4d3e744cc7b1f2a27e03e74477a2 SHA1 f4571ac1212cfbfe13f33fec195ba8f632bae037 SHA256 83b879b959dfc98255112310fab676d86c8c4a99eda2358edc8440e8af488ea5
 MISC metadata.xml 229 RMD160 e5d681054ef371ecfe4d6828e8b722b716968b37 SHA1 e91b223d4c687993ccca1be424e4feedad208570 SHA256 0f110645272f37341c3729c03cf88dbb871ed82db98c8b0dbda8734343b88567
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diff --git a/sci-chemistry/molrep/files/11.0.03-EOR.patch b/sci-chemistry/molrep/files/11.0.03-EOR.patch
new file mode 100644
index 000000000000..430629e8dcc1
--- /dev/null
+++ b/sci-chemistry/molrep/files/11.0.03-EOR.patch
@@ -0,0 +1,16 @@
+ src/molrep.f |    2 +-
+ 1 files changed, 1 insertions(+), 1 deletions(-)
+
+diff --git a/src/molrep.f b/src/molrep.f
+index eac0cfc..94f74c6 100755
+--- a/src/molrep.f
++++ b/src/molrep.f
+@@ -1257,7 +1257,7 @@ C         CHECK_DENS_FILE( 2 )
+         LEN1 = 1
+         IF(LEN.GT.60) LEN1 = LEN - 59
+         WRITE(LINE,'(''Input MODEL_2(fixed)_file:'',A)') 
+-     *                                 NAME2(LEN11:LEN)
++     *                                 NAME2(LEN1:LEN)
+         CALL MSGDOC(MDoc,LINE)
+ 
+       ENDIF
diff --git a/sci-chemistry/molrep/molrep-11.0.03-r1.ebuild b/sci-chemistry/molrep/molrep-11.0.03-r1.ebuild
new file mode 100644
index 000000000000..57a2b3bc4513
--- /dev/null
+++ b/sci-chemistry/molrep/molrep-11.0.03-r1.ebuild
@@ -0,0 +1,60 @@
+# Copyright 1999-2011 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/molrep/molrep-11.0.03-r1.ebuild,v 1.1 2011/10/04 15:21:19 jlec Exp $
+
+EAPI=4
+
+inherit eutils flag-o-matic fortran-2 multilib toolchain-funcs
+
+DESCRIPTION="molecular replacement program"
+HOMEPAGE="http://www.ysbl.york.ac.uk/~alexei/molrep.html"
+SRC_URI="http://dev.gentoo.org/~jlec/distfiles/${P}.tar.gz"
+
+LICENSE="ccp4"
+SLOT="0"
+KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux"
+IUSE=""
+
+RDEPEND="
+	virtual/fortran
+
+	>=sci-libs/ccp4-libs-6.1.3
+	sci-libs/mmdb
+	virtual/lapack"
+DEPEND="${RDEPEND}"
+
+S="${WORKDIR}/${PN}"
+
+src_prepare() {
+	epatch \
+		"${FILESDIR}"/11.0.00-respect-FLAGS.patch \
+		"${FILESDIR}"/11.0.00-test.patch \
+		"${FILESDIR}"/${PV}-EOR.patch
+	[[ $(tc-getFC) =~ gfortran ]] && append-fflags -fno-second-underscore
+}
+
+src_compile() {
+	cd "${S}"/src
+	emake clean
+	emake \
+		MR_FORT="$(tc-getFC) ${FFLAGS}" \
+		FFLAGS="${FFLAGS}" \
+		LDFLAGS="${LDFLAGS}" \
+		MR_LIBRARY="-L${EPREFIX}/usr/$(get_libdir) -lccp4f -lccp4c $(pkg-config --libs mmdb lapack) -lccif -lstdc++ -lm"
+}
+
+src_test() {
+	export MR_TEST="${S}/bin/"
+	cd "${S}"/molrep_check/work
+	mkdir out scr
+	cp ../*.bat .
+	bash em.bat || die
+	bash mr.bat || die
+}
+
+src_install() {
+	exeinto /usr/libexec/ccp4/bin/
+	doexe bin/${PN}
+	dosym ../libexec/ccp4/bin/${PN} /usr/bin/${PN}
+	dodoc readme doc/${PN}.rtf
+}