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sci-chemistry/procheck: treeclean
Bug: https://bugs.gentoo.org/928067 Signed-off-by: Arthur Zamarin <arthurzam@gentoo.org>
This commit is contained in:
Arthur Zamarin
@@ -279,13 +279,6 @@ sci-astronomy/predict
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~dev-vcs/mercurial-6.7.2
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~dev-vcs/mercurial-6.7.3
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# Arthur Zamarin <arthurzam@gentoo.org> (2024-06-14)
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# EAPI=6, not maintained in Gentoo for a long time. procheck is
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# fetch restricted, and the file you download from upstream
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# doesn't match size and manifests. aqua depends on procheck.
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# Removal on 2024-07-14. Bugs #928067, #928068.
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sci-chemistry/procheck
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# Viorel Munteanu <ceamac@gentoo.org> (2024-06-11)
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# dev-php/pear, dev-php/PEAR-* and their reverse dependencies: mask for removal
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# in 30 days.
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@@ -1,3 +0,0 @@
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DIST procheck-3.5.4-README 6585 BLAKE2B c61606848f30728b67d2ab51e0beadec1c30aaa0ca65a68834bff3ed3e3f466e34a0e4b64323e80cce9cee83854650ebe0805abf0509c0a9154bf08e3e0a2d6b SHA512 c6eff94cef9b67fd61884e88fa77ec381553d4dba53f477023738e1e44a6191c4241b14543ee7ecb93b049f16f262db2a09cf5d1a63248057633aab290f1f82a
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DIST procheck-3.5.4-manual.tar.gz 517840 BLAKE2B 33c5da5888bcd263e900cf2839f9287373e032fdde234e0375af061ec1c588d1ea5d2718da2a050da8060ba4003748a8fef3ff35b22f424c1cf6a1892aec0fe6 SHA512 0fa9c7d50b7ca43c626d5261c524166938d3a92be1d02221721bc7ce7e91ac4919e7200b946ce563f9bb696d7dab9588c1d1b31a4d551cafa2f2bce4931a212c
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DIST procheck-3.5.4.tar.gz 522013 BLAKE2B be6764bc741ec3f868aee349fc7e23608c612758029d0b745c421f40b47c896dd48de84ee7df6d09a64a20695bd5a1ed0a96464e6dcaf44de03da1ae231787f8 SHA512 1dd78b53070484fbcdca51001fd147ab13fd5e51b3d1da54fd529531917c31012393751ee514f0c79d579b17a1701dde04f81b1c9ac27b2b835a43fa96785ecc
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@@ -1,35 +0,0 @@
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diff --git a/pplot.f b/pplot.f
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index 7e06e68..c86b2b2 100644
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--- a/pplot.f
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+++ b/pplot.f
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@@ -4720,6 +4720,7 @@ C---- Initialise variables
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SCORE(IDIST) = 0.0
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50 CONTINUE
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+ REWIND(3)
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C---- If the required residue is of a greater number than that required,
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C read through the file until come to it
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IF (IRESID.GT.INRES) THEN
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diff --git a/ps.f b/ps.f
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index b652a7d..858b8e5 100644
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--- a/ps.f
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+++ b/ps.f
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@@ -1705,12 +1705,14 @@ CVAX - CARRIAGECONTROL='LIST',
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C---- If this is an existing file, then read through all its records until
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C get to the end of file
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IF (.NOT.NEWFIL) THEN
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+ CLOSE(14)
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+ OPEN(14, file=fname, status='old', position='append', err=900)
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C---- Loop through the file until reach the end
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- 100 CONTINUE
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- READ(14,110,END=500) IREC
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- 110 FORMAT(A)
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- GO TO 100
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+C 100 CONTINUE
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+C READ(14,110,END=500) IREC
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+C 110 FORMAT(A)
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+C GO TO 100
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C---- If this is a new file, then write the header records to it
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ELSE
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@@ -1,49 +0,0 @@
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diff --git a/Makefile b/Makefile
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index c5bb58f..0394b0a 100644
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--- a/Makefile
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+++ b/Makefile
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@@ -35,31 +35,31 @@ distrib :
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# Individual executables
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# ----------------------
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anglen : anglen.o
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- $(F77) $(FOPTS) -o $@ anglen.o
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+ $(F77) $(FOPTS) $(LDFLAGS) -o $@ anglen.o
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clean : clean.o
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- $(F77) $(FOPTS) -o $@ clean.o
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+ $(F77) $(FOPTS) $(LDFLAGS) -o $@ clean.o
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rmsdev : rmsdev.o
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- $(F77) $(FOPTS) -o $@ rmsdev.o
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+ $(F77) $(FOPTS) $(LDFLAGS) -o $@ rmsdev.o
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secstr : secstr.o
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- $(F77) $(FOPTS) -o $@ secstr.o
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+ $(F77) $(FOPTS) $(LDFLAGS) -o $@ secstr.o
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gfac2pdb : gfac2pdb.o ps.o
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- $(F77) $(FOPTS) -o $@ gfac2pdb.o ps.o
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+ $(F77) $(FOPTS) $(LDFLAGS) -o $@ gfac2pdb.o ps.o
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pplot : pplot.o ps.o
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- $(F77) $(FOPTS) -o $@ pplot.o ps.o
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+ $(F77) $(FOPTS) $(LDFLAGS) -o $@ pplot.o ps.o
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bplot : bplot.o ps.o
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- $(F77) $(FOPTS) -o $@ bplot.o ps.o
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+ $(F77) $(FOPTS) $(LDFLAGS) -o $@ bplot.o ps.o
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tplot : tplot.o ps.o
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- $(F77) $(FOPTS) -o $@ tplot.o ps.o
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+ $(F77) $(FOPTS) $(LDFLAGS) -o $@ tplot.o ps.o
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mplot : mplot.o ps.o
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- $(F77) $(FOPTS) -o $@ mplot.o ps.o
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+ $(F77) $(FOPTS) $(LDFLAGS) -o $@ mplot.o ps.o
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vplot : vplot.o ps.o
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- $(F77) $(FOPTS) -o $@ vplot.o ps.o
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+ $(F77) $(FOPTS) $(LDFLAGS) -o $@ vplot.o ps.o
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viol2pdb : viol2pdb.o ps.o
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- $(F77) $(FOPTS) -o $@ viol2pdb.o ps.o
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+ $(F77) $(FOPTS) $(LDFLAGS) -o $@ viol2pdb.o ps.o
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wirplot : wirplot.o ps.o
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- $(F77) $(FOPTS) -o $@ wirplot.o ps.o
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+ $(F77) $(FOPTS) $(LDFLAGS) -o $@ wirplot.o ps.o
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nb : nb.c
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- $(CC) $(COPTS) -o nb nb.c $(CLIBS)
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+ $(CC) $(COPTS) $(LDFLAGS) -o nb nb.c $(CLIBS)
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# Individual rules for FORTRAN files with .inc files
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# --------------------------------------------------
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@@ -1,8 +0,0 @@
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<?xml version="1.0" encoding="UTF-8"?>
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<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
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<pkgmetadata>
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<maintainer type="project">
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<email>sci-chemistry@gentoo.org</email>
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<name>Gentoo Chemistry Project</name>
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</maintainer>
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</pkgmetadata>
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@@ -1,87 +0,0 @@
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# Copyright 1999-2023 Gentoo Authors
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# Distributed under the terms of the GNU General Public License v2
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EAPI=6
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inherit fortran-2 multilib toolchain-funcs versionator
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DESCRIPTION="Checks the stereochemical quality of a protein structure"
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HOMEPAGE="https://www.ebi.ac.uk/thornton-srv/software/PROCHECK"
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SRC_URI="
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${P}.tar.gz ${P}-README
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doc? ( ${P}-manual.tar.gz )"
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LICENSE="procheck"
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SLOT="0"
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KEYWORDS="amd64 ~x86 ~amd64-linux ~x86-linux"
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IUSE="doc"
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RDEPEND="app-shells/tcsh"
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DEPEND="${RDEPEND}"
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RESTRICT="fetch"
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S="${WORKDIR}/${PN}"
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pkg_nofetch() {
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elog "Please visit https://www.ebi.ac.uk/thornton-srv/software/PROCHECK/download.html"
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elog "and follow the instruction for downloading."
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elog "Files should be renamed in the following way before being copied to your"
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elog "DISTDIR directory:"
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elog " ${PN}.tar.gz -> ${P}.tar.gz"
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elog " README -> ${P}-README"
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use doc && elog " manual.tar.gz -> ${P}-manual.tar.gz"
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}
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PATCHES=(
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"${FILESDIR}"/${P}-ldflags.patch
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"${FILESDIR}"/${P}-close.patch
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)
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src_compile() {
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emake \
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F77="$(tc-getFC)" \
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CC="$(tc-getCC)" \
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COPTS="${CFLAGS}" \
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FOPTS="${FFLAGS} -std=legacy"
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}
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src_install() {
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for i in *.scr; do
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newbin ${i} ${i%.scr}
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done
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exeinto /usr/libexec/${PN}/
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doexe \
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anglen \
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clean \
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rmsdev \
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secstr \
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gfac2pdb \
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pplot \
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bplot \
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tplot \
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mplot \
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vplot \
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viol2pdb \
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wirplot \
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nb
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dodoc "${DISTDIR}"/${P}-README
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insinto /usr/libexec/${PN}/
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doins *.dat *.prm
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newins resdefs.dat resdefs.data
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cat >> "${T}"/30${PN} <<- EOF
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prodir="${EPREFIX}/usr/libexec/${PN}/"
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EOF
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doenvd "${T}"/30${PN}
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if use doc; then
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pushd "${WORKDIR}" > /dev/null
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docinto html
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dodoc -r manual
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popd > /dev/null
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fi
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}
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