commit: d054c7afa64ca9d73a37ae32a8ada66c87152ea8 Author: Arthur Zamarin <arthurzam <AT> gentoo <DOT> org> AuthorDate: Fri Jul 19 11:33:27 2024 +0000 Commit: Arthur Zamarin <arthurzam <AT> gentoo <DOT> org> CommitDate: Fri Jul 19 11:34:43 2024 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=d054c7af
sci-chemistry/procheck: treeclean Bug: https://bugs.gentoo.org/928067 Signed-off-by: Arthur Zamarin <arthurzam <AT> gentoo.org> profiles/package.mask | 7 -- sci-chemistry/procheck/Manifest | 3 - .../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 | 87 ---------------------- 6 files changed, 189 deletions(-) diff --git a/profiles/package.mask b/profiles/package.mask index 609909201453..7aa95ad21c0c 100644 --- a/profiles/package.mask +++ b/profiles/package.mask @@ -279,13 +279,6 @@ sci-astronomy/predict ~dev-vcs/mercurial-6.7.2 ~dev-vcs/mercurial-6.7.3 -# Arthur Zamarin <arthur...@gentoo.org> (2024-06-14) -# EAPI=6, not maintained in Gentoo for a long time. procheck is -# fetch restricted, and the file you download from upstream -# doesn't match size and manifests. aqua depends on procheck. -# Removal on 2024-07-14. Bugs #928067, #928068. -sci-chemistry/procheck - # Viorel Munteanu <cea...@gentoo.org> (2024-06-11) # dev-php/pear, dev-php/PEAR-* and their reverse dependencies: mask for removal # in 30 days. diff --git a/sci-chemistry/procheck/Manifest b/sci-chemistry/procheck/Manifest deleted file mode 100644 index 48f2a0e21fda..000000000000 --- a/sci-chemistry/procheck/Manifest +++ /dev/null @@ -1,3 +0,0 @@ -DIST procheck-3.5.4-README 6585 BLAKE2B c61606848f30728b67d2ab51e0beadec1c30aaa0ca65a68834bff3ed3e3f466e34a0e4b64323e80cce9cee83854650ebe0805abf0509c0a9154bf08e3e0a2d6b SHA512 c6eff94cef9b67fd61884e88fa77ec381553d4dba53f477023738e1e44a6191c4241b14543ee7ecb93b049f16f262db2a09cf5d1a63248057633aab290f1f82a -DIST procheck-3.5.4-manual.tar.gz 517840 BLAKE2B 33c5da5888bcd263e900cf2839f9287373e032fdde234e0375af061ec1c588d1ea5d2718da2a050da8060ba4003748a8fef3ff35b22f424c1cf6a1892aec0fe6 SHA512 0fa9c7d50b7ca43c626d5261c524166938d3a92be1d02221721bc7ce7e91ac4919e7200b946ce563f9bb696d7dab9588c1d1b31a4d551cafa2f2bce4931a212c -DIST procheck-3.5.4.tar.gz 522013 BLAKE2B be6764bc741ec3f868aee349fc7e23608c612758029d0b745c421f40b47c896dd48de84ee7df6d09a64a20695bd5a1ed0a96464e6dcaf44de03da1ae231787f8 SHA512 1dd78b53070484fbcdca51001fd147ab13fd5e51b3d1da54fd529531917c31012393751ee514f0c79d579b17a1701dde04f81b1c9ac27b2b835a43fa96785ecc diff --git a/sci-chemistry/procheck/files/procheck-3.5.4-close.patch b/sci-chemistry/procheck/files/procheck-3.5.4-close.patch deleted file mode 100644 index 16a0658e654d..000000000000 --- a/sci-chemistry/procheck/files/procheck-3.5.4-close.patch +++ /dev/null @@ -1,35 +0,0 @@ -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 deleted file mode 100644 index 453aebe3211f..000000000000 --- a/sci-chemistry/procheck/files/procheck-3.5.4-ldflags.patch +++ /dev/null @@ -1,49 +0,0 @@ -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 deleted file mode 100644 index e490bcb8aa87..000000000000 --- a/sci-chemistry/procheck/metadata.xml +++ /dev/null @@ -1,8 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd";> -<pkgmetadata> - <maintainer type="project"> - <email>sci-chemis...@gentoo.org</email> - <name>Gentoo Chemistry Project</name> - </maintainer> -</pkgmetadata> diff --git a/sci-chemistry/procheck/procheck-3.5.4-r3.ebuild b/sci-chemistry/procheck/procheck-3.5.4-r3.ebuild deleted file mode 100644 index 3db0e3f24244..000000000000 --- a/sci-chemistry/procheck/procheck-3.5.4-r3.ebuild +++ /dev/null @@ -1,87 +0,0 @@ -# Copyright 1999-2023 Gentoo Authors -# 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="https://www.ebi.ac.uk/thornton-srv/software/PROCHECK"; -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 https://www.ebi.ac.uk/thornton-srv/software/PROCHECK/download.html"; - elog "and follow the instruction for downloading." - elog "Files should be renamed in the following way before being copied to your" - elog "DISTDIR directory:" - elog " ${PN}.tar.gz -> ${P}.tar.gz" - elog " README -> ${P}-README" - use doc && elog " manual.tar.gz -> ${P}-manual.tar.gz" -} - -PATCHES=( - "${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 -}
