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 <[email protected]> (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 <[email protected]> (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>[email protected]</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"; -}
