From 4f2d7949f03e1c198bc888f2d05f421d35c57e21 Mon Sep 17 00:00:00 2001 From: V3n3RiX Date: Mon, 9 Oct 2017 18:53:29 +0100 Subject: reinit the tree, so we can have metadata --- sci-chemistry/procheck/Manifest | 9 +++ .../procheck/files/procheck-3.5.4-close.patch | 35 +++++++++ .../procheck/files/procheck-3.5.4-ldflags.patch | 49 ++++++++++++ sci-chemistry/procheck/metadata.xml | 8 ++ sci-chemistry/procheck/procheck-3.5.4-r3.ebuild | 86 ++++++++++++++++++++++ 5 files changed, 187 insertions(+) create mode 100644 sci-chemistry/procheck/Manifest create mode 100644 sci-chemistry/procheck/files/procheck-3.5.4-close.patch create mode 100644 sci-chemistry/procheck/files/procheck-3.5.4-ldflags.patch create mode 100644 sci-chemistry/procheck/metadata.xml create mode 100644 sci-chemistry/procheck/procheck-3.5.4-r3.ebuild (limited to 'sci-chemistry/procheck') diff --git a/sci-chemistry/procheck/Manifest b/sci-chemistry/procheck/Manifest new file mode 100644 index 000000000000..ac9339e2d620 --- /dev/null +++ b/sci-chemistry/procheck/Manifest @@ -0,0 +1,9 @@ +AUX procheck-3.5.4-close.patch 1073 SHA256 8819ed952ac6361f19141dc589e2ce81310729c4308ec010dae187cc8308f340 SHA512 3d18df23858acc46a12f884d4904ca3f60e05e663746e768f5f08d0370b2e335cfde09c08566c4869adfa0f9c0d75ae527fe0ed2666f603818b11f91a3349307 WHIRLPOOL dc76f7d4cc062e8aa7a8bcee738c06a11b28670ee989aaf0290e5e57442f3627c9287361c073d9fb077ca8280c8c76217217142e53cc6f0a7fc345c355e067f3 +AUX procheck-3.5.4-ldflags.patch 1649 SHA256 d46c5f8fbb6d7f6f1fedc522f311ae4c5baa12b9ff47e6d3970312e1b2b34e57 SHA512 f7f2e06a77058f7e743a1c1367d40c2683a2aefbf2910a807d1b0a77d19024446f978ec34a8e5187338a7e98b6651592a37c024e8a2ea955d9bd736d47bfeb4f WHIRLPOOL 1b4c6b1563251d2b37edfcdaeb49c8c963559c1823a3cf724e78c6f8a2ba4e53fd79b0da4a40339a55a608f470c3db38c5869cc4c058cf5bc9cc21cf8ee77b52 +DIST procheck-3.5.4-README 6585 SHA256 202d5b4d9ffaebdad19c368e6e6fd8ab54744c511609b1c609ef46c21fa0ffa0 SHA512 c6eff94cef9b67fd61884e88fa77ec381553d4dba53f477023738e1e44a6191c4241b14543ee7ecb93b049f16f262db2a09cf5d1a63248057633aab290f1f82a WHIRLPOOL 53a618978a9285e8a8f09c7ebd3e34951a8c1056c0894c1f4e4c11f73ad3127829322c9c7597fc6dea98f1fa4c40552e6caf383eed15aaeef0594cf93887d196 +DIST procheck-3.5.4-manual.tar.gz 517840 SHA256 3c2faa505be05102ccbe23473abdddc1cd4dc87c6b5e74222b7ea5c27b18db5a SHA512 0fa9c7d50b7ca43c626d5261c524166938d3a92be1d02221721bc7ce7e91ac4919e7200b946ce563f9bb696d7dab9588c1d1b31a4d551cafa2f2bce4931a212c WHIRLPOOL 591afad0a534762d654779722b229e3dcb9cc1ed0f9216c443d4872dd7379257638e5cf3ee5844adf15b2ec55d5c5b15ab585ae52ae993678311985642aa8eaf +DIST procheck-3.5.4.tar.gz 522013 SHA256 4923fe5a7b86d5369fd639d0c77cfb866e574f076ec8c52424d746e843a404f4 SHA512 1dd78b53070484fbcdca51001fd147ab13fd5e51b3d1da54fd529531917c31012393751ee514f0c79d579b17a1701dde04f81b1c9ac27b2b835a43fa96785ecc WHIRLPOOL 2732981bdbb5269567019a645b401009bd48d782ab20b4f68bd213a90f7248a9fa3f46ab3a026aa0515a677a99826040d4c3f5464816ed4390b5091a6a98b375 +EBUILD procheck-3.5.4-r3.ebuild 1687 SHA256 53450ba0e302dd1f7a4930235e114d3212851f8725969aabeaaa1323905aa688 SHA512 abc659dbe5947b16259e05128c5e0607fdbe3c251595b7c5589502c8d6465264bfec243820abec345980d66cfe0b3eaa8183a41aeb2e2a8a81a929b0128364e7 WHIRLPOOL 3ee37116675c8133ab0047a301364921bc78573f1bd0d4925ab49e19405e93f01677c0d0d632cf201f2505d658fbedc897c8fd1d9622d17a359fdae933ffe617 +MISC ChangeLog 2706 SHA256 59b2234decdf7f54d1f1eb4490cd94211d6a1ced3f7b535764178cfe7b6914f0 SHA512 f536b799232fd119c8531c4300b48761a41678cd85cb0270410d9a44aee0ac74c1955b40adb5bdbb8c259699fd327134c66bb13d27210e30aa2cf19ac62a72bd WHIRLPOOL 57331e6b198004b3c635f77983ae2c36f2fb2ba2fc83358b8f8571f643b41fb87465ebfc898b384fd543b8c69d594230b2a9f99cf735402ac80a754721dfc3a3 +MISC ChangeLog-2015 1737 SHA256 32c08c17c06bea867f3d413a81040737bd92aba7c5e0e0b738f739ce808d7ccc SHA512 b1a1c456069655bdebbc15db326ab7efcacef6d56a0cac67858676831529f41730fc2060e150623a571f9bcbde38d893231960a042f0e1aa4561a8e00048bae7 WHIRLPOOL 325a3d995cb55fefc26ff4dff076cd2f3bab9cfb0540521bd187c6c4e6af9cc35e03447fc6675da1dcd7f2478b0ab1e0e12f07b718d9fcae2b25ba3dc5b68bd1 +MISC metadata.xml 271 SHA256 70036ea85140f86ed670bc2791c9de861c4b6164755ee36a2560d1c812ec13f6 SHA512 3e6e6047a29e07123b81279cae1de17bc4bd4c3d7d8a8d26560114a18185f473d038fc220fa81c7213fa203ce197bad8b1c272d9b7e41cd770a953fa6308ff92 WHIRLPOOL 1ccb964819c99258af550a41c6712ba8ebdecbec1c821106de2f22c37b1c981cd4f324856a8014b08bd186bcd2a7fa45a7e772cc15705d1a39016b5229e77269 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 index 000000000000..16a0658e654d --- /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/files/procheck-3.5.4-ldflags.patch b/sci-chemistry/procheck/files/procheck-3.5.4-ldflags.patch new file mode 100644 index 000000000000..453aebe3211f --- /dev/null +++ b/sci-chemistry/procheck/files/procheck-3.5.4-ldflags.patch @@ -0,0 +1,49 @@ +diff --git a/Makefile b/Makefile +index c5bb58f..0394b0a 100644 +--- a/Makefile ++++ b/Makefile +@@ -35,31 +35,31 @@ distrib : + # Individual executables + # ---------------------- + anglen : anglen.o +- $(F77) $(FOPTS) -o $@ anglen.o ++ $(F77) $(FOPTS) $(LDFLAGS) -o $@ anglen.o + clean : clean.o +- $(F77) $(FOPTS) -o $@ clean.o ++ $(F77) $(FOPTS) $(LDFLAGS) -o $@ clean.o + rmsdev : rmsdev.o +- $(F77) $(FOPTS) -o $@ rmsdev.o ++ $(F77) $(FOPTS) $(LDFLAGS) -o $@ rmsdev.o + secstr : secstr.o +- $(F77) $(FOPTS) -o $@ secstr.o ++ $(F77) $(FOPTS) $(LDFLAGS) -o $@ secstr.o + gfac2pdb : gfac2pdb.o ps.o +- $(F77) $(FOPTS) -o $@ gfac2pdb.o ps.o ++ $(F77) $(FOPTS) $(LDFLAGS) -o $@ gfac2pdb.o ps.o + pplot : pplot.o ps.o +- $(F77) $(FOPTS) -o $@ pplot.o ps.o ++ $(F77) $(FOPTS) $(LDFLAGS) -o $@ pplot.o ps.o + bplot : bplot.o ps.o +- $(F77) $(FOPTS) -o $@ bplot.o ps.o ++ $(F77) $(FOPTS) $(LDFLAGS) -o $@ bplot.o ps.o + tplot : tplot.o ps.o +- $(F77) $(FOPTS) -o $@ tplot.o ps.o ++ $(F77) $(FOPTS) $(LDFLAGS) -o $@ tplot.o ps.o + mplot : mplot.o ps.o +- $(F77) $(FOPTS) -o $@ mplot.o ps.o ++ $(F77) $(FOPTS) $(LDFLAGS) -o $@ mplot.o ps.o + vplot : vplot.o ps.o +- $(F77) $(FOPTS) -o $@ vplot.o ps.o ++ $(F77) $(FOPTS) $(LDFLAGS) -o $@ vplot.o ps.o + viol2pdb : viol2pdb.o ps.o +- $(F77) $(FOPTS) -o $@ viol2pdb.o ps.o ++ $(F77) $(FOPTS) $(LDFLAGS) -o $@ viol2pdb.o ps.o + wirplot : wirplot.o ps.o +- $(F77) $(FOPTS) -o $@ wirplot.o ps.o ++ $(F77) $(FOPTS) $(LDFLAGS) -o $@ wirplot.o ps.o + nb : nb.c +- $(CC) $(COPTS) -o nb nb.c $(CLIBS) ++ $(CC) $(COPTS) $(LDFLAGS) -o nb nb.c $(CLIBS) + + # Individual rules for FORTRAN files with .inc files + # -------------------------------------------------- diff --git a/sci-chemistry/procheck/metadata.xml b/sci-chemistry/procheck/metadata.xml new file mode 100644 index 000000000000..8937bad0b175 --- /dev/null +++ b/sci-chemistry/procheck/metadata.xml @@ -0,0 +1,8 @@ + + + + + sci-chemistry@gentoo.org + Gentoo Chemistry Project + + diff --git a/sci-chemistry/procheck/procheck-3.5.4-r3.ebuild b/sci-chemistry/procheck/procheck-3.5.4-r3.ebuild new file mode 100644 index 000000000000..4b188e5a9824 --- /dev/null +++ b/sci-chemistry/procheck/procheck-3.5.4-r3.ebuild @@ -0,0 +1,86 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit 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" +} + +PATCHES=( + "${FILESDIR}"/${P}-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 +} -- cgit v1.2.3