[gentoo-commits] repo/gentoo:master commit in: sci-biology/mira/, profiles/, sci-biology/mira/files/

[Jakov Smolić]

commit:     35d98adecae341f50c42caf4cea4bb264a57fd67
Author:     Jakov Smolić <jsmolic <AT> gentoo <DOT> org>
AuthorDate: Tue Sep 28 14:31:19 2021 +0000
Commit:     Jakov Smolić <jsmolic <AT> gentoo <DOT> org>
CommitDate: Tue Sep 28 14:31:19 2021 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=35d98ade

sci-biology/mira: Remove last-rited package

Closes: https://bugs.gentoo.org/808667
Closes: https://bugs.gentoo.org/585942
Closes: https://bugs.gentoo.org/731880
Signed-off-by: Jakov Smolić <jsmolic <AT> gentoo.org>

 profiles/package.mask                              |  7 --
 sci-biology/mira/Manifest                          |  2 -
 sci-biology/mira/files/mira-4.0.2-boost-1.50.patch | 22 -----
 sci-biology/mira/files/mira-4.0.2-cmath.patch      | 14 ----
 sci-biology/mira/files/mira-4.0.2-cout.patch       | 27 ------
 sci-biology/mira/metadata.xml                      | 11 ---
 sci-biology/mira/mira-4.0.2-r1.ebuild              | 97 ----------------------
 7 files changed, 180 deletions(-)

diff --git a/profiles/package.mask b/profiles/package.mask
index ce047751e24..3479a66b74a 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -240,13 +240,6 @@ dev-util/trinity
 # Should be safe to unmask if you are using x11-wm/mutter instead.
 >=gui-libs/egl-wayland-1.1.8
 
-# David Seifert <soap@g.o> (2021-08-29)
-# Broken for the past 5 years (#585942), no new upstream release in over
-# 5 years. Same issues as sci-biology/wgs-assembler, use a modern
-# assembler like sci-biology/abyss or canu.
-# Bug #585942, #731880, #808667, removal in 30 days.
-sci-biology/mira
-
 # Alexey Sokolov <alexey+gentoo@××××××××.org> (2021-08-30)
 # Homepage dead, uses gtk2, fails to build, https://bugs.gentoo.org/711344
 games-puzzle/gnudoku

diff --git a/sci-biology/mira/Manifest b/sci-biology/mira/Manifest
deleted file mode 100644
index 48fa9af279d..00000000000
--- a/sci-biology/mira/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST mira-4.0.2.tar.bz2 10368046 BLAKE2B cc84c6c13c8024409634ccafd103be8a4f2a9e27fa7f19d2ef401393db9e8063a6fac2f21cd25dfe58e90aee8cf38983369d928241f9bc65e78da0e95fa41d3b SHA512 a7f9845de207cefb87ffa652f4f6b9b85735ef22eeb29b456e4d946ba1675e7dd2c78abb2da56f11fddcb699f5c0700a08ce298196ce1a8e586a758a8d3bdc7e
-DIST mira_3rdparty_06-07-2012.tar.bz2 31656 BLAKE2B 7e952d96e9073acd8ab1d1fc7c51c37f6526287d31698c5090500d421147285b535e8cab7e49f4e51a5634c901d1cd969206b1727e683d3fcebdc195399e3589 SHA512 4d4dbdf7ab5126f9d47160bee8bc127b6a225de8087f6b9914c754324a74d966333207c86a3f38cf0ea9f91408707e2a24086dbe1318fdfa2870b0c39bc5033b

diff --git a/sci-biology/mira/files/mira-4.0.2-boost-1.50.patch b/sci-biology/mira/files/mira-4.0.2-boost-1.50.patch
deleted file mode 100644
index 50f83c9021d..00000000000
--- a/sci-biology/mira/files/mira-4.0.2-boost-1.50.patch
+++ /dev/null
@@ -1,22 +0,0 @@
-ax_boost_regex.m4 |    4 ++--
-1 file changed, 2 insertions(+), 2 deletions(-)
-
---- mira-4.0.2/m4/ax_boost_regex.m4
-+++ mira-4.0.2/m4/ax_boost_regex.m4
-@@ -78,14 +78,14 @@
-                 for libextension in `ls $BOOSTLIBDIR/libboost_regex*.so* $BOOSTLIBDIR/libboost_regex*.a* 2>/dev/null | sed 's,.*/,,' | sed -e 's;^lib\(boost_regex.*\)\.so.*$;\1;' -e 's;^lib\(boost_regex.*\)\.a*$;\1;'` ; do
-                      ax_lib=${libextension}
- 				    AC_CHECK_LIB($ax_lib, exit,
--                                 [BOOST_REGEX_LIB="-l$ax_lib"; AC_SUBST(BOOST_REGEX_LIB) link_regex="yes"; break],
-+                                 [BOOST_REGEX_LIB="-l$ax_lib -lboost_system"; AC_SUBST(BOOST_REGEX_LIB) link_regex="yes"; break],
-                                  [link_regex="no"])
- 				done
-                 if test "x$link_regex" != "xyes"; then
-                 for libextension in `ls $BOOSTLIBDIR/boost_regex*.{dll,a}* 2>/dev/null | sed 's,.*/,,' | sed -e 's;^\(boost_regex.*\)\.dll.*$;\1;' -e 's;^\(boost_regex.*\)\.a*$;\1;'` ; do
-                      ax_lib=${libextension}
- 				    AC_CHECK_LIB($ax_lib, exit,
--                                 [BOOST_REGEX_LIB="-l$ax_lib"; AC_SUBST(BOOST_REGEX_LIB) link_regex="yes"; break],
-+                                 [BOOST_REGEX_LIB="-l$ax_lib -lboost_system"; AC_SUBST(BOOST_REGEX_LIB) link_regex="yes"; break],
-                                  [link_regex="no"])
- 				done
-                 fi

diff --git a/sci-biology/mira/files/mira-4.0.2-cmath.patch b/sci-biology/mira/files/mira-4.0.2-cmath.patch
deleted file mode 100644
index a4a020177af..00000000000
--- a/sci-biology/mira/files/mira-4.0.2-cmath.patch
+++ /dev/null
@@ -1,14 +0,0 @@
---- mira-4.0.2/src/mira/ads.C
-+++ mira-4.0.2/src/mira/ads.C
-@@ -31,10 +31,11 @@
-  * Routines for computing scores and some other classification number are
-  *  provided, too.
-  *
-  */
- 
-+#include <cmath>
- 
- #include "ads.H"
- 
- #include "errorhandling/errorhandling.H"
- #include "util/dptools.H"

diff --git a/sci-biology/mira/files/mira-4.0.2-cout.patch b/sci-biology/mira/files/mira-4.0.2-cout.patch
deleted file mode 100644
index 78e7168cb49..00000000000
--- a/sci-biology/mira/files/mira-4.0.2-cout.patch
+++ /dev/null
@@ -1,27 +0,0 @@
- src/progs/quirks.C | 2 ++
- 1 file changed, 2 insertions(+)
-
-diff --git a/src/progs/quirks.C b/src/progs/quirks.C
-index 47e5ee8..060b6f3 100644
---- a/src/progs/quirks.C
-+++ b/src/progs/quirks.C
-@@ -25,6 +25,8 @@
- 
- #include <boost/filesystem.hpp>
- 
-+#include <iostream>
-+
- // make the "tcmalloc: large alloc" messages from TCMallom disappear
- // by setting the reporting environment variable to a very large value
- // see: http://groups.google.com/group/google-perftools/browse_thread/thread/24a003fc35f3d470?pli=1
---- a/src/mira/parameters.C
-+++ b/src/mira/parameters.C
-@@ -2222,7 +2222,7 @@
-     MIRANOTIFY(Notify::FATAL, "File not found: " << pfile);
-   }
- 
--  parse(fin, Pv, nullptr);
-+  parse(fin, Pv, false);
- 
-   fin.close();
- 

diff --git a/sci-biology/mira/metadata.xml b/sci-biology/mira/metadata.xml
deleted file mode 100644
index 5ef527dc14c..00000000000
--- a/sci-biology/mira/metadata.xml
+++ /dev/null
@@ -1,11 +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-biology@g.o</email>
-    <name>Gentoo Biology Project</name>
-  </maintainer>
-  <upstream>
-    <remote-id type="sourceforge">mira-assembler</remote-id>
-  </upstream>
-</pkgmetadata>

diff --git a/sci-biology/mira/mira-4.0.2-r1.ebuild b/sci-biology/mira/mira-4.0.2-r1.ebuild
deleted file mode 100644
index cbd1309c474..00000000000
--- a/sci-biology/mira/mira-4.0.2-r1.ebuild
+++ /dev/null
@@ -1,97 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-MIRA_3RDPARTY_PV="06-07-2012"
-MY_PV="${PV/_}" # convert from mira-4.0_rc2 (Gentoo ebuild filename derived) to mira-4.0rc2 (upstream fromat)
-
-inherit autotools multilib
-
-DESCRIPTION="Whole Genome Shotgun and EST Sequence Assembler for Sanger, 454 and Illumina"
-HOMEPAGE="http://www.chevreux.org/projects_mira.html"
-SRC_URI="
-	https://sourceforge.net/projects/mira-assembler/files/MIRA/stable/"${PN}"-"${MY_PV}".tar.bz2
-	mirror://sourceforge/mira-assembler/mira_3rdparty_${MIRA_3RDPARTY_PV}.tar.bz2"
-#	https://sourceforge.net/projects/mira-assembler/files/MIRA/development/${P}.tar.bz2
-#	mirror://sourceforge/mira-assembler/mira_3rdparty_${MIRA_3RDPARTY_PV}.tar.bz2"
-
-S="${WORKDIR}"/"${PN}"-"${MY_PV}"
-
-SLOT="0"
-LICENSE="GPL-2"
-KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux"
-IUSE="doc"
-
-CDEPEND="
-	dev-libs/boost:=[threads(+)]
-	dev-util/google-perftools"
-DEPEND="${CDEPEND}
-	sys-devel/flex
-	app-editors/vim-core
-	dev-libs/expat"
-RDEPEND="${CDEPEND}"
-
-#DOCS=( AUTHORS GETTING_STARTED NEWS README HELP_WANTED
-#	THANKS doc/3rdparty/scaffolding_MIRA_BAMBUS.pdf )
-DOCS=( AUTHORS GETTING_STARTED NEWS README HELP_WANTED THANKS )
-
-PATCHES=(
-	"${FILESDIR}/${PN}-4.0.2-boost-1.50.patch"
-	"${FILESDIR}/${PN}-4.0.2-cout.patch"
-	"${FILESDIR}/${PN}-4.0.2-cmath.patch"
-)
-
-src_prepare() {
-	find -name 'configure*' -or -name 'Makefile*' | xargs sed -i 's/flex++/flex -+/' || die
-
-	default
-
-	sed \
-		-e "s:-O[23]::g" \
-		-e "s:-funroll-loops::g" \
-		-i configure.ac || die
-
-	eautoreconf
-
-	# Remove C++ source files that upstream built with flex.
-	local f
-	local PREBUILT_CXX_LEXER_FILES=(
-		"${S}"/src/caf/caf_flexer.cc
-		"${S}"/src/io/exp_flexer.cc
-		"${S}"/src/mira/parameters_flexer.cc
-	)
-
-	for f in "${PREBUILT_CXX_LEXER_FILES[@]}"; do
-		if [[ -f ${f} ]] ; then
-			rm "${f}" || die "Failed to remove ${f}"
-		else
-			die "${f} not found"
-		fi
-	done
-}
-
-src_configure() {
-	econf \
-		--with-boost="${EPREFIX}/usr/$(get_libdir)" \
-		--with-boost-libdir="${EPREFIX}/usr/$(get_libdir)" \
-		--with-boost-thread=boost_thread-mt
-}
-
-#src_compile() {
-#	base_src_compile
-#	# TODO: resolve docbook incompatibility for building docs
-#	use doc && emake -C doc clean docs
-#}
-
-src_install() {
-	default
-
-	dobin "${WORKDIR}"/3rdparty/{sff_extract,qual2ball,*.pl}
-	dodoc "${WORKDIR}"/3rdparty/{README.txt,midi_screen.fasta}
-}
-
-pkg_postinst() {
-	einfo "Documentation is no longer built, you can find it at:"
-	einfo "http://mira-assembler.sourceforge.net/docs/DefinitiveGuideToMIRA.html"
-}