commit: eb36afed0ebdb0323da077573076f795b2038741
Author: Andreas Sturmlechner <asturm <AT> gentoo <DOT> org>
AuthorDate: Sun Feb 22 14:05:45 2026 +0000
Commit: Andreas Sturmlechner <asturm <AT> gentoo <DOT> org>
CommitDate: Sun Feb 22 15:56:48 2026 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=eb36afed
sci-biology/muscle: drop 3.8.31
Signed-off-by: Andreas Sturmlechner <asturm <AT> gentoo.org>
sci-biology/muscle/Manifest | 1 -
sci-biology/muscle/files/3.8.31-make.patch | 24 ------------------
sci-biology/muscle/muscle-3.8.31.ebuild | 39 ------------------------------
3 files changed, 64 deletions(-)
diff --git a/sci-biology/muscle/Manifest b/sci-biology/muscle/Manifest
index 0741cc695e2f..47000518089c 100644
--- a/sci-biology/muscle/Manifest
+++ b/sci-biology/muscle/Manifest
@@ -1,2 +1 @@
DIST muscle-5.1.0.tar.gz 185437 BLAKE2B
b3742c37179fc8c36fb6160be4c3a8b4afa2f686bc018ec8e97a10834c1f1901b54b489faa9c365aa65c8514f378b7b5518d91a4e2fb067492e32202a06c4f64
SHA512
0cafc7ce07e5d0c261811e085e0fec8e44318a3d2604ad530ad95b370d6386143a4eeb59012e17cfc703f54bde5ee0752c3ce7fc8bb489748dbe89b2229dd6eb
-DIST muscle3.8.31_src.tar.gz 515267 BLAKE2B
79a8517f7a14d8ee907104e9035e1284fcabec556544508fd9b712789759448969ce39ecbefcedac62c435dc91e109b3b5b7027120691310ffebda80ca80dd9e
SHA512
2baf2aae354ae1e3f529e627be2ace86e89dd15567e1f642a625b63f08ebe3d4bd7315080c7d786d95e3eda8703545ec74af9fe83ad1523d55d00137fb7274ce
diff --git a/sci-biology/muscle/files/3.8.31-make.patch
b/sci-biology/muscle/files/3.8.31-make.patch
deleted file mode 100644
index fa3f5c3a014b..000000000000
--- a/sci-biology/muscle/files/3.8.31-make.patch
+++ /dev/null
@@ -1,24 +0,0 @@
---- a/mk
-+++ b/mk
-@@ -5,17 +5,14 @@ ObjNames='aligngivenpath.o aligngivenpathsw.o aligntwomsas.o
aligntwoprofs.o aln
- rm -f *.o muscle.make.stdout.txt muscle.make.stderr.txt
- for CPPName in $CPPNames
- do
-- echo $CPPName >> /dev/tty
-- g++ $ENV_GCC_OPTS -c -O3 -msse2 -mfpmath=sse -D_FILE_OFFSET_BITS=64
-DNDEBUG=1 $CPPName.cpp -o $CPPName.o >> muscle.make.stdout.txt 2>>
muscle.make.stderr.txt
-+ echo "${CXX} ${CXXFLAGS} -c -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 $CPPName.cpp
-o $CPPName.o"
-+ ${CXX} ${CXXFLAGS} -c -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 $CPPName.cpp -o
$CPPName.o
- done
-
- LINK_OPTS=
- if [ `uname -s` == Linux ] ; then
- LINK_OPTS=-static
- fi
--g++ $LINK_OPTS $ENV_LINK_OPTS -g -o muscle $ObjNames >>
muscle.make.stdout.txt 2>> muscle.make.stderr.txt
--tail muscle.make.stderr.txt
-
--strip muscle
--ls -lh muscle
--sum muscle
-+echo "${CXX} ${LDFLAGS} -o muscle $ObjNames"
-+${CXX} ${LDFLAGS} -o muscle $ObjNames
diff --git a/sci-biology/muscle/muscle-3.8.31.ebuild
b/sci-biology/muscle/muscle-3.8.31.ebuild
deleted file mode 100644
index faefc5b1a280..000000000000
--- a/sci-biology/muscle/muscle-3.8.31.ebuild
+++ /dev/null
@@ -1,39 +0,0 @@
-# Copyright 1999-2024 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit flag-o-matic toolchain-funcs
-
-MY_P="${PN}${PV}_src"
-
-DESCRIPTION="Multiple sequence comparison by log-expectation"
-HOMEPAGE="https://www.drive5.com/muscle/";
-SRC_URI="https://www.drive5.com/muscle/downloads${PV}/${MY_P}.tar.gz";
-
-LICENSE="public-domain"
-SLOT="0"
-KEYWORDS="amd64 ~ppc ~x86"
-
-RDEPEND="!sci-libs/libmuscle"
-
-S="${WORKDIR}"/${PN}${PV}/src
-
-PATCHES=( "${FILESDIR}"/${PV}-make.patch )
-
-src_configure() {
- # -Werror=strict-aliasing
- # https://bugs.gentoo.org/862276
- # Fixed upstream in later releases
- #
- # Do not trust with LTO either.
- append-flags -fno-strict-aliasing
- filter-lto
-
- tc-export CXX
-}
-
-src_install() {
- dobin muscle
- dodoc *.txt
-}
