sci-chemistry/procheck: Add patch to fix problems with newer gfortran, thanks xarthis...

Package-Manager: portage-2.2.15/cvs/Linux x86_64
Manifest-Sign-Key: 0xB9D4F231BD1558AB!

diff --git a/sci-chemistry/procheck/ChangeLog b/sci-chemistry/procheck/ChangeLog
index 52c3b2303a6150917fe6f610fe74f4cd8ed1fe19..63a58f7b7b93c9d8372b7884e0f32071ee5868db 100644 (file)
--- a/sci-chemistry/procheck/ChangeLog
+++ b/sci-chemistry/procheck/ChangeLog
@@ -1,6 +1,13 @@
 # ChangeLog for sci-chemistry/procheck
-# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/procheck/ChangeLog,v 1.10 2013/06/19 04:17:56 bicatali Exp $
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/procheck/ChangeLog,v 1.11 2015/01/05 20:20:04 jlec Exp $
+
+*procheck-3.5.4-r2 (05 Jan 2015)
+
+  05 Jan 2015; Justin Lecher <jlec@gentoo.org> +procheck-3.5.4-r2.ebuild,
+  +files/procheck-3.5.4-close.patch, metadata.xml:
+  Add patch to fix problems with newer gfortran, thanks xarthisius for the
+  patch
 
   19 Jun 2013; Sébastien Fabbro <bicatali@gentoo.org> metadata.xml:
   Changed herd to sci-chemistry

diff --git a/sci-chemistry/procheck/Manifest b/sci-chemistry/procheck/Manifest
index a2faee5b6fa413e715462417ffbca48898241910..f0ffcf205c19fb3312921e37e334b61bbf27f9b5 100644 (file)
--- a/sci-chemistry/procheck/Manifest
+++ b/sci-chemistry/procheck/Manifest
@@ -1,17 +1,31 @@
 -----BEGIN PGP SIGNED MESSAGE-----
-Hash: SHA256
+Hash: SHA512
 
 AUX 3.5.4-ldflags.patch 1649 SHA256 d46c5f8fbb6d7f6f1fedc522f311ae4c5baa12b9ff47e6d3970312e1b2b34e57 SHA512 f7f2e06a77058f7e743a1c1367d40c2683a2aefbf2910a807d1b0a77d19024446f978ec34a8e5187338a7e98b6651592a37c024e8a2ea955d9bd736d47bfeb4f WHIRLPOOL 1b4c6b1563251d2b37edfcdaeb49c8c963559c1823a3cf724e78c6f8a2ba4e53fd79b0da4a40339a55a608f470c3db38c5869cc4c058cf5bc9cc21cf8ee77b52
-DIST procheck-3.5.4-README 6585 SHA256 202d5b4d9ffaebdad19c368e6e6fd8ab54744c511609b1c609ef46c21fa0ffa0
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 DIST procheck-3.5.4-manual.tar.gz 517840 SHA256 3c2faa505be05102ccbe23473abdddc1cd4dc87c6b5e74222b7ea5c27b18db5a
-DIST procheck-3.5.4.tar.gz 522013 SHA256 4923fe5a7b86d5369fd639d0c77cfb866e574f076ec8c52424d746e843a404f4
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 EBUILD procheck-3.5.4-r1.ebuild 1773 SHA256 e2bfae5fb806fd7647c071a7180ff38b7001187e713612b1b66091e9c2c5fbd4 SHA512 90ebec3223a575f7010e27015fac8c3f0aef013d56fe470aea95f4869902195e334a394ab2b81b6d2629ddd2b08fb7d216449ef96db4b5f9aa70cf15437f254a WHIRLPOOL 7b8a4adb8ce68645fcc269ed7a09287ee29a9e0bff4d9a4abbbd8e85573a1ea4bf0fd22dafb15fc8a09b4a0764225ba2efb033bf2565a6e48a994a4139b9604a
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diff --git a/sci-chemistry/procheck/files/procheck-3.5.4-close.patch b/sci-chemistry/procheck/files/procheck-3.5.4-close.patch
new file mode 100644 (file)
index 0000000..16a0658
--- /dev/null
+++ b/sci-chemistry/procheck/files/procheck-3.5.4-close.patch
@@ -0,0 +1,35 @@
+diff --git a/pplot.f b/pplot.f
+index 7e06e68..c86b2b2 100644
+--- a/pplot.f
++++ b/pplot.f
+@@ -4720,6 +4720,7 @@ C---- Initialise variables
+           SCORE(IDIST) = 0.0
+  50   CONTINUE
+ 
++      REWIND(3)
+ C---- If the required residue is of a greater number than that required,
+ C     read through the file until come to it
+       IF (IRESID.GT.INRES) THEN
+diff --git a/ps.f b/ps.f
+index b652a7d..858b8e5 100644
+--- a/ps.f
++++ b/ps.f
+@@ -1705,12 +1705,14 @@ CVAX     -    CARRIAGECONTROL='LIST',
+ C---- If this is an existing file, then read through all its records until
+ C     get to the end of file
+       IF (.NOT.NEWFIL) THEN
++          CLOSE(14)
++          OPEN(14, file=fname, status='old', position='append', err=900)
+ 
+ C----     Loop through the file until reach the end
+- 100      CONTINUE
+-             READ(14,110,END=500) IREC
+- 110         FORMAT(A)
+-          GO TO 100
++C 100      CONTINUE
++C             READ(14,110,END=500) IREC
++C 110         FORMAT(A)
++C          GO TO 100
+ 
+ C---- If this is a new file, then write the header records to it
+       ELSE
\ No newline at end of file

diff --git a/sci-chemistry/procheck/metadata.xml b/sci-chemistry/procheck/metadata.xml
index 95180e10e21c0376eb69938e01a13c09d6befb92..b3618ba38c1c03ac4697a473c9fac66fa0012198 100644 (file)
--- a/sci-chemistry/procheck/metadata.xml
+++ b/sci-chemistry/procheck/metadata.xml
@@ -1,9 +1,9 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
-       <herd>sci-chemistry</herd>
-       <maintainer>
-               <email>jlec@gentoo.org</email>
-               <name>Justin Lecher</name>
-       </maintainer>
+  <herd>sci-chemistry</herd>
+  <maintainer>
+    <email>jlec@gentoo.org</email>
+    <name>Justin Lecher</name>
+  </maintainer>
 </pkgmetadata>

diff --git a/sci-chemistry/procheck/procheck-3.5.4-r2.ebuild b/sci-chemistry/procheck/procheck-3.5.4-r2.ebuild
new file mode 100644 (file)
index 0000000..e27265b
--- /dev/null
+++ b/sci-chemistry/procheck/procheck-3.5.4-r2.ebuild
@@ -0,0 +1,88 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/procheck/procheck-3.5.4-r2.ebuild,v 1.1 2015/01/05 20:20:04 jlec Exp $
+
+EAPI=5
+
+inherit eutils fortran-2 multilib toolchain-funcs versionator
+
+DESCRIPTION="Checks the stereochemical quality of a protein structure"
+HOMEPAGE="http://www.biochem.ucl.ac.uk/~roman/procheck/procheck.html"
+SRC_URI="
+       ${P}.tar.gz ${P}-README
+       doc? ( ${P}-manual.tar.gz )"
+
+LICENSE="procheck"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="doc"
+
+RDEPEND="app-shells/tcsh"
+DEPEND="${RDEPEND}"
+
+RESTRICT="fetch"
+
+S="${WORKDIR}/${PN}"
+
+pkg_nofetch() {
+       elog "Please visit http://www.ebi.ac.uk/thornton-srv/software/PROCHECK/download.html"
+       elog "And follow the instruction for downloading."
+       elog "Files should be stored in following way"
+       elog "${PN}.tar.gz  ->  ${DISTDIR}/${P}.tar.gz"
+       elog "README  ->  ${DISTDIR}/${P}-README"
+       use doc && elog "manual.tar.gz  ->  ${DISTDIR}/${P}-manual.tar.gz"
+}
+
+src_prepare() {
+       epatch \
+               "${FILESDIR}"/${PV}-ldflags.patch \
+               "${FILESDIR}"/${P}-close.patch
+}
+
+src_compile() {
+       emake \
+               F77=$(tc-getFC) \
+               CC=$(tc-getCC) \
+               COPTS="${CFLAGS}" \
+               FOPTS="${FFLAGS} -std=legacy"
+}
+
+src_install() {
+       for i in *.scr; do
+               newbin ${i} ${i%.scr}
+       done
+
+       exeinto /usr/libexec/${PN}/
+       doexe \
+               anglen \
+               clean \
+               rmsdev \
+               secstr \
+               gfac2pdb \
+               pplot \
+               bplot \
+               tplot \
+               mplot \
+               vplot \
+               viol2pdb \
+               wirplot \
+               nb
+       dodoc "${DISTDIR}"/${P}-README
+
+       insinto /usr/libexec/${PN}/
+       doins *.dat *.prm
+       newins resdefs.dat resdefs.data
+
+       cat >> "${T}"/30${PN} <<- EOF
+       prodir="${EPREFIX}/usr/libexec/${PN}/"
+       EOF
+
+       doenvd "${T}"/30${PN}
+
+       if use doc; then
+               pushd "${WORKDIR}" > /dev/null
+                       docinto html
+                       dodoc -r manual
+               popd > /dev/null
+       fi
+}