From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from lists.gentoo.org (pigeon.gentoo.org [208.92.234.80]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (No client certificate requested) by finch.gentoo.org (Postfix) with ESMTPS id EC3C1138359 for ; Tue, 22 Sep 2020 11:12:30 +0000 (UTC) Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id 447FCE0887; Tue, 22 Sep 2020 11:12:28 +0000 (UTC) Received: from smtp.gentoo.org (smtp.gentoo.org [140.211.166.183]) (using TLSv1.2 with cipher ECDHE-RSA-AES128-GCM-SHA256 (128/128 bits)) (No client certificate requested) by pigeon.gentoo.org (Postfix) with ESMTPS id 1845FE0887 for ; Tue, 22 Sep 2020 11:12:28 +0000 (UTC) Received: from oystercatcher.gentoo.org (oystercatcher.gentoo.org [148.251.78.52]) (using TLSv1.2 with cipher ECDHE-RSA-AES128-GCM-SHA256 (128/128 bits)) (No client certificate requested) by smtp.gentoo.org (Postfix) with ESMTPS id 4DDC3340DD5 for ; Tue, 22 Sep 2020 11:12:26 +0000 (UTC) Received: from localhost.localdomain (localhost [IPv6:::1]) by oystercatcher.gentoo.org (Postfix) with ESMTP id D84A5380 for ; Tue, 22 Sep 2020 11:12:22 +0000 (UTC) From: "Aisha Tammy" To: gentoo-commits@lists.gentoo.org Content-Transfer-Encoding: 8bit Content-type: text/plain; charset=UTF-8 Reply-To: gentoo-dev@lists.gentoo.org, "Aisha Tammy" Message-ID: <1600772856.0406b0d1d4a8a775323fed57801dedf70517cc5b.epsilon-0@gentoo> Subject: [gentoo-commits] proj/sci:master commit in: sci-biology/mira/, sci-biology/mira/files/ X-VCS-Repository: proj/sci X-VCS-Files: sci-biology/mira/files/mira-3.4.0.2-boost-1.50.patch sci-biology/mira/files/mira-4.9.5-cout.patch sci-biology/mira/files/mira-4.9.5-fix-miramer-symlink-error.patch sci-biology/mira/metadata.xml sci-biology/mira/mira-4.9.5.ebuild X-VCS-Directories: sci-biology/mira/files/ sci-biology/mira/ X-VCS-Committer: epsilon-0 X-VCS-Committer-Name: Aisha Tammy X-VCS-Revision: 0406b0d1d4a8a775323fed57801dedf70517cc5b X-VCS-Branch: master Date: Tue, 22 Sep 2020 11:12:22 +0000 (UTC) Precedence: bulk List-Post: List-Help: List-Unsubscribe: List-Subscribe: List-Id: Gentoo Linux mail X-BeenThere: gentoo-commits@lists.gentoo.org X-Auto-Response-Suppress: DR, RN, NRN, OOF, AutoReply X-Archives-Salt: b5382d92-50a3-498e-8d45-56434a6abeb6 X-Archives-Hash: e2be46ad26da3f8445825f4103a35665 commit: 0406b0d1d4a8a775323fed57801dedf70517cc5b Author: Aisha Tammy aisha cc> AuthorDate: Tue Sep 22 11:07:36 2020 +0000 Commit: Aisha Tammy aisha cc> CommitDate: Tue Sep 22 11:07:36 2020 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=0406b0d1 sci-biology/mira: drop package present in ::gentoo Package-Manager: Portage-3.0.7, Repoman-3.0.1 Signed-off-by: Aisha Tammy aisha.cc> .../mira/files/mira-3.4.0.2-boost-1.50.patch | 24 ------ sci-biology/mira/files/mira-4.9.5-cout.patch | 16 ---- .../mira-4.9.5-fix-miramer-symlink-error.patch | 22 ------ sci-biology/mira/metadata.xml | 11 --- sci-biology/mira/mira-4.9.5.ebuild | 92 ---------------------- 5 files changed, 165 deletions(-) diff --git a/sci-biology/mira/files/mira-3.4.0.2-boost-1.50.patch b/sci-biology/mira/files/mira-3.4.0.2-boost-1.50.patch deleted file mode 100644 index 427192294..000000000 --- a/sci-biology/mira/files/mira-3.4.0.2-boost-1.50.patch +++ /dev/null @@ -1,24 +0,0 @@ - config/m4/ax_boost_regex.m4 | 4 ++-- - 1 file changed, 2 insertions(+), 2 deletions(-) - -diff --git a/config/m4/ax_boost_regex.m4 b/config/m4/ax_boost_regex.m4 -index 1ac06af..5b7be93 100644 ---- a/config/m4/ax_boost_regex.m4 -+++ b/config/m4/ax_boost_regex.m4 -@@ -78,14 +78,14 @@ AC_DEFUN([AX_BOOST_REGEX], - 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$ax_lib -lboost_system"; AC_SUBST(BOOST_REGEX_LIB) link_regex="yes"; break], - [link_regex="no"]) - done - fi diff --git a/sci-biology/mira/files/mira-4.9.5-cout.patch b/sci-biology/mira/files/mira-4.9.5-cout.patch deleted file mode 100644 index 14feb0284..000000000 --- a/sci-biology/mira/files/mira-4.9.5-cout.patch +++ /dev/null @@ -1,16 +0,0 @@ - src/progs/quirks.C | 2 ++ - 1 file changed, 2 insertions(+) - -diff --git a/src/progs/quirks.C b/src/progs/quirks.C -index 47e5ee8..060b6f3 100644 ---- a/src/progs/quirks.C -+++ b/src/progs/quirks.C -@@ -25,6 +25,8 @@ - - #include - -+#include -+ - // make the "tcmalloc: large alloc" messages from TCMallom disappear - // by setting the reporting environment variable to a very large value - // see: http://groups.google.com/group/google-perftools/browse_thread/thread/24a003fc35f3d470?pli=1 diff --git a/sci-biology/mira/files/mira-4.9.5-fix-miramer-symlink-error.patch b/sci-biology/mira/files/mira-4.9.5-fix-miramer-symlink-error.patch deleted file mode 100644 index 6bdda946a..000000000 --- a/sci-biology/mira/files/mira-4.9.5-fix-miramer-symlink-error.patch +++ /dev/null @@ -1,22 +0,0 @@ ---- mira-4.9.5/src/progs/Makefile.in.ori 2015-07-21 00:55:09.860884698 +0200 -+++ mira-4.9.5/src/progs/Makefile.in 2015-07-21 00:55:29.660884750 +0200 -@@ -717,7 +717,7 @@ - rm -f mirabait$(EXEEXT) && \ - $(LN_S) mira$(EXEEXT) mirabait$(EXEEXT) &&\ - rm -f miraconvert$(EXEEXT) && \ -- $(LN_S) mira$(EXEEXT) miraconvert$(EXEEXT) \ -+ $(LN_S) mira$(EXEEXT) miraconvert$(EXEEXT) && \ - rm -f miramer$(EXEEXT) && \ - $(LN_S) mira$(EXEEXT) miramer$(EXEEXT) - ---- mira-4.9.5/src/progs/Makefile.am.ori 2015-07-21 01:30:09.580890184 +0200 -+++ mira-4.9.5/src/progs/Makefile.am 2015-07-21 01:30:24.590890223 +0200 -@@ -51,7 +51,7 @@ - rm -f mirabait$(EXEEXT) && \ - $(LN_S) mira$(EXEEXT) mirabait$(EXEEXT) &&\ - rm -f miraconvert$(EXEEXT) && \ -- $(LN_S) mira$(EXEEXT) miraconvert$(EXEEXT) \ -+ $(LN_S) mira$(EXEEXT) miraconvert$(EXEEXT) && \ - rm -f miramer$(EXEEXT) && \ - $(LN_S) mira$(EXEEXT) miramer$(EXEEXT) - diff --git a/sci-biology/mira/metadata.xml b/sci-biology/mira/metadata.xml deleted file mode 100644 index 65cad0432..000000000 --- a/sci-biology/mira/metadata.xml +++ /dev/null @@ -1,11 +0,0 @@ - - - - - sci-biology@gentoo.org - Gentoo Biology Project - - - mira-assembler - - diff --git a/sci-biology/mira/mira-4.9.5.ebuild b/sci-biology/mira/mira-4.9.5.ebuild deleted file mode 100644 index 7c888a5e7..000000000 --- a/sci-biology/mira/mira-4.9.5.ebuild +++ /dev/null @@ -1,92 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -MIRA_3RDPARTY_PV="06-07-2012" -MY_PV="${PV/_}" # convert from mira-4.0_rc2 (Gentoo ebuild filename derived) to mira-4.0rc2 (upstream fromat) - -inherit autotools eutils multilib - -DESCRIPTION="Whole Genome Shotgun and EST Sequence Assembler" -HOMEPAGE="http://www.chevreux.org/projects_mira.html" -SRC_URI=" - http://sourceforge.net/projects/mira-assembler/files/MIRA/development/"${PN}"-"${MY_PV}".tar.bz2 - mirror://sourceforge/mira-assembler/mira_3rdparty_${MIRA_3RDPARTY_PV}.tar.bz2" -# http://sourceforge.net/projects/mira-assembler/files/MIRA/stable/"${PN}"-"${MY_PV}".tar.bz2 -# http://sourceforge.net/projects/mira-assembler/files/MIRA/development/${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 ~x86-macos" -IUSE="doc" - -CDEPEND=" - dev-libs/boost - dev-util/google-perftools" -DEPEND="${CDEPEND} - app-editors/vim-core - dev-libs/expat" -RDEPEND="${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 ) - -# mira 4.9.x requires C++14 standard compliant compiler, so >=gcc-4.9.1 -src_prepare() { - find -name 'configure*' -or -name 'Makefile*' | xargs sed -i 's/flex++/flex -+/' || die - epatch \ - "${FILESDIR}"/${PN}-3.4.0.2-boost-1.50.patch \ - "${FILESDIR}"/${P}-cout.patch \ - "${FILESDIR}"/${P}-fix-miramer-symlink-error.patch - - sed \ - -e "s:-O[23]::g" \ - -e "s:-funroll-loops::g" \ - -i configure.ac || die - - eautoreconf -} - -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 -# if use doc; then emake -C doc clean docs || die; fi -#} - -src_install() { - default - dodoc ${DOCS[@]} - - dobin "${WORKDIR}"/3rdparty/{sff_extract,qual2ball,*.pl} - dodoc "${WORKDIR}"/3rdparty/{README.txt,midi_screen.fasta} - - # if sci-biology/staden is installed, ideally use configprotect? - if [ -e "${ED}"/usr/share/staden/etc/GTAGDB ]; then - if [ `grep -c HAF "${ED}"/usr/share/staden/etc/GTAGDB` -eq 0 ]; then - cat "${ED}"/usr/share/staden/etc/GTAGDB "${S}"/src/support/GTAGDB > "${WORKDIR}"/GTAGDB || die - insinto /usr/share/staden/etc/ - doins "${WORKDIR}"/GTAGDB - fi - fi - if [ -e "/etc/consedrc/" ]; then - insinto /etc/consedrc - doins "${S}"/src/support/consedtaglib.txt - fi -} - -pkg_postinst() { - einfo "Documentation is no longer built, you can find it at:" - einfo "http://mira-assembler.sourceforge.net/docs/DefinitiveGuideToMIRA.html" -}