From: Justin Lecher Date: Mon, 5 Jan 2015 20:20:12 +0000 (+0000) Subject: sci-chemistry/procheck: Add patch to fix problems with newer gfortran, thanks xarthis... X-Git-Url: http://git.tremily.us/?a=commitdiff_plain;h=8ac1067946500a651b2ed2403ff19242b0ec611b;p=gentoo.git sci-chemistry/procheck: Add patch to fix problems with newer gfortran, thanks xarthisius for the patch 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 52c3b2303a61..63a58f7b7b93 100644 --- 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 +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 metadata.xml: Changed herd to sci-chemistry diff --git a/sci-chemistry/procheck/Manifest b/sci-chemistry/procheck/Manifest index a2faee5b6fa4..f0ffcf205c19 100644 --- 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 +AUX 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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 95180e10e21c..b3618ba38c1c 100644 --- a/sci-chemistry/procheck/metadata.xml +++ b/sci-chemistry/procheck/metadata.xml @@ -1,9 +1,9 @@ - sci-chemistry - - jlec@gentoo.org - Justin Lecher - + sci-chemistry + + jlec@gentoo.org + Justin Lecher + 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 index 000000000000..e27265bd436a --- /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 +}