* [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/procheck/, profiles/, sci-chemistry/procheck/files/
@ 2024-07-19 11:34 Arthur Zamarin
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From: Arthur Zamarin @ 2024-07-19 11:34 UTC (permalink / raw
To: gentoo-commits
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 <arthurzam@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 <ceamac@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-chemistry@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
-}
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