commit: fc53999cdafb11f8611f825c5f280478338313d7 Author: Brahmajit Das <listout <AT> listout <DOT> xyz> AuthorDate: Sun Apr 6 16:45:40 2025 +0000 Commit: Nowa Ammerlaan <nowa <AT> gentoo <DOT> org> CommitDate: Thu Apr 17 10:02:23 2025 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=fc53999c
sci-biology/fasta: implicit declaration of function ftello Closes: https://bugs.gentoo.org/938324 Signed-off-by: Brahmajit Das <listout <AT> listout.xyz> Closes: https://github.com/gentoo/gentoo/pull/38344 Signed-off-by: Nowa Ammerlaan <nowa <AT> gentoo.org> sci-biology/fasta/fasta-36.3.8i-r1.ebuild | 85 ++++++++++++++++++++++ .../fasta/files/fasta-36.3.8i-musl-build-fix.patch | 15 ++++ 2 files changed, 100 insertions(+) diff --git a/sci-biology/fasta/fasta-36.3.8i-r1.ebuild b/sci-biology/fasta/fasta-36.3.8i-r1.ebuild new file mode 100644 index 000000000000..6fa29e9baed1 --- /dev/null +++ b/sci-biology/fasta/fasta-36.3.8i-r1.ebuild @@ -0,0 +1,85 @@ +# Copyright 1999-2025 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +inherit flag-o-matic toolchain-funcs + +MY_PV="${PV}_14-Nov-2020" + +DESCRIPTION="FASTA is a DNA and Protein sequence alignment software package" +HOMEPAGE="https://fasta.bioch.virginia.edu/fasta_www2/fasta_down.shtml"; +SRC_URI="https://github.com/wrpearson/fasta36/archive/refs/tags/v${MY_PV}.tar.gz -> ${P}.tar.gz" +S="${WORKDIR}/${PN}36-${MY_PV}" + +LICENSE="fasta" +SLOT="0" +KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~x64-macos" +IUSE="debug cpu_flags_x86_sse2" + +PATCHES=( + "${FILESDIR}/${PN}-36.3.8i-musl-build-fix.patch" +) + +src_prepare() { + CC_ALT= + CFLAGS_ALT= + ALT= + + use debug && append-flags -DDEBUG + + if [[ "$(tc-getCC)" == *icc* ]]; then + CC_ALT=icc + ALT="${ALT}_icc" + else + CC_ALT="$(tc-getCC)" + use x86 && ALT="32" + use amd64 && ALT="64" + fi + + if use cpu_flags_x86_sse2 ; then + ALT="${ALT}_sse2" + append-flags -msse2 + [[ "$(tc-getCC)" == *icc* ]] || append-flags -ffast-math + fi + + export CC_ALT="${CC_ALT}" + export ALT="${ALT}" + + # -Werror=lto-type-mismatch + # https://bugs.gentoo.org/862267 + # https://github.com/wrpearson/fasta36/issues/63 + filter-lto + + sed \ + -e 's:-ffast-math::g' \ + -i make/Makefile* || die + + default +} + +src_compile() { + emake -C src -f ../make/Makefile.linux${ALT} CC="${CC_ALT} ${CFLAGS}" HFLAGS="${LDFLAGS}" all +} + +src_test() { + cd test || die + FASTLIBS="../conf" bash test.sh || die +} + +src_install() { + dobin bin/* + + pushd bin >/dev/null || die + local i + for i in *36; do + dosym ${i} /usr/bin/${i%36} + done + popd >/dev/null || die + + insinto /usr/share/${PN} + doins -r conf/. data seq + + doman doc/{prss3.1,fasta36.1,fasts3.1,fastf3.1,ps_lav.1,map_db.1} + dodoc FASTA_LIST README* doc/{README*,readme*,fasta*,changes*} +} diff --git a/sci-biology/fasta/files/fasta-36.3.8i-musl-build-fix.patch b/sci-biology/fasta/files/fasta-36.3.8i-musl-build-fix.patch new file mode 100644 index 000000000000..1ce5e0089611 --- /dev/null +++ b/sci-biology/fasta/files/fasta-36.3.8i-musl-build-fix.patch @@ -0,0 +1,15 @@ +https://patch-diff.githubusercontent.com/raw/wrpearson/fasta36/pull/64.patch +--- a/make/Makefile.linux64_sse2 ++++ b/make/Makefile.linux64_sse2 +@@ -28,7 +28,7 @@ LIB_DB= + + # standard options + +-CFLAGS += -DPOSIX_C_SOURCE=2 -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 ++CFLAGS += -DPOSIX_C_SOURCE=2 -D_GNU_SOURCE -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 + + # -I/usr/include/mysql -DMYSQL_DB + # -DSUPERFAMNUM -DSFCHAR="'|'" +-- +2.46.0 +
