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a738cfecfe... to avoid installing broken static libraries w/ LTO. Closes: https://bugs.gentoo.org/958379 Signed-off-by: Eli Schwartz <eschwartz@gentoo.org>
88 lines
1.9 KiB
Bash
88 lines
1.9 KiB
Bash
# Copyright 1999-2025 Gentoo Authors
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# Distributed under the terms of the GNU General Public License v2
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EAPI=8
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inherit dot-a flag-o-matic toolchain-funcs
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DESCRIPTION="Sequence analysis using profile hidden Markov models"
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HOMEPAGE="http://hmmer.org/"
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SRC_URI="http://eddylab.org/software/${PN}/${PV}/${P}.tar.gz"
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LICENSE="GPL-2"
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SLOT="2"
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KEYWORDS="~amd64 ~x86"
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IUSE="cpu_flags_ppc_altivec test"
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RESTRICT="!test? ( test )"
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BDEPEND="test? ( dev-lang/perl )"
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PATCHES=(
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"${FILESDIR}/${P}-fix-perl-shebangs.patch"
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"${FILESDIR}/${P}-fix-build-system-destdir.patch"
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"${FILESDIR}/${P}-fix-missing-include-in-configure.patch"
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)
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src_configure() {
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# required to expose pthread_setconcurrency(), #882279
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append-cppflags -D_XOPEN_SOURCE=500
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lto-guarantee-fat
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# prevent stray environmental variable
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# from causing issues in the test phase
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unset TMPDIR
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econf \
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--enable-lfs \
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--enable-threads \
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$(use_enable cpu_flags_ppc_altivec altivec)
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}
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src_compile() {
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emake AR="$(tc-getAR) rcs"
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}
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src_install() {
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default
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newlib.a src/libhmmer.a libhmmer2.a
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insinto /usr/include/hmmer2
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doins src/*.h
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dobin squid/{afetch,alistat,compalign,compstruct,revcomp,seqstat,seqsplit,sfetch,shuffle,sreformat,sindex,weight,translate}
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dolib.a squid/libsquid.a
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insinto /usr/include/hmmer2
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doins squid/*.h
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strip-lto-bytecode
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dodoc NOTES Userguide.pdf
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newdoc 00README README
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# rename files due to collisions with hmmer-3
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# in order to make SLOTing possible
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local i
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# first rename man pages...
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pushd "${ED}"/usr/share/man/man1/ >/dev/null || die
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for i in hmm*.1; do
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mv ${i%.1}{,2}.1 || die
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done
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popd >/dev/null || die
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# ... then rename binaries
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pushd "${ED}"/usr/bin/ >/dev/null || die
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for i in hmm*; do
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mv ${i}{,2} || die
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done
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popd >/dev/null || die
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}
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pkg_postinst() {
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elog "All ${P} binaries have been renamed, in order"
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elog "to avoid collisions with hmmer-3. For instance"
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elog
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elog " hmmalign -> hmmalign2"
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elog
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}
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