From 4919e107f95d762348df57ca9a8e75307d9222bc Mon Sep 17 00:00:00 2001 From: NHOrus Date: Wed, 8 May 2024 13:30:27 +0400 Subject: sci-biology/hmmer: Add missing include into configure There are no autotools source files, so we can't just autoreconf the problem out of existence [sam: Revbump.] Closes: https://bugs.gentoo.org/900551 Signed-off-by: NHOrus Closes: https://github.com/gentoo/gentoo/pull/36599 Signed-off-by: Sam James --- ...er-2.3.2-fix-missing-include-in-configure.patch | 18 +++++ sci-biology/hmmer/hmmer-2.3.2-r5.ebuild | 83 --------------------- sci-biology/hmmer/hmmer-2.3.2-r6.ebuild | 84 ++++++++++++++++++++++ 3 files changed, 102 insertions(+), 83 deletions(-) create mode 100644 sci-biology/hmmer/files/hmmer-2.3.2-fix-missing-include-in-configure.patch delete mode 100644 sci-biology/hmmer/hmmer-2.3.2-r5.ebuild create mode 100644 sci-biology/hmmer/hmmer-2.3.2-r6.ebuild (limited to 'sci-biology') diff --git a/sci-biology/hmmer/files/hmmer-2.3.2-fix-missing-include-in-configure.patch b/sci-biology/hmmer/files/hmmer-2.3.2-fix-missing-include-in-configure.patch new file mode 100644 index 000000000000..37683d425edb --- /dev/null +++ b/sci-biology/hmmer/files/hmmer-2.3.2-fix-missing-include-in-configure.patch @@ -0,0 +1,18 @@ +--- a/squid/configure 2024-05-08 09:21:15.751063495 -0000 ++++ b/squid/configure 2024-05-08 09:22:50.491502934 -0000 +@@ -2493,6 +2493,7 @@ + cat confdefs.h >>conftest.$ac_ext + cat >>conftest.$ac_ext <<_ACEOF + /* end confdefs.h. */ ++#include + int + main () + { +@@ -3500,6 +3501,7 @@ + cat >>conftest.$ac_ext <<_ACEOF + /* end confdefs.h. */ + #include ++#include + #if ((' ' & 0x0FF) == 0x020) + # define ISLOWER(c) ('a' <= (c) && (c) <= 'z') + # define TOUPPER(c) (ISLOWER(c) ? 'A' + ((c) - 'a') : (c)) diff --git a/sci-biology/hmmer/hmmer-2.3.2-r5.ebuild b/sci-biology/hmmer/hmmer-2.3.2-r5.ebuild deleted file mode 100644 index b305820faff3..000000000000 --- a/sci-biology/hmmer/hmmer-2.3.2-r5.ebuild +++ /dev/null @@ -1,83 +0,0 @@ -# Copyright 1999-2022 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -inherit flag-o-matic toolchain-funcs - -DESCRIPTION="Sequence analysis using profile hidden Markov models" -HOMEPAGE="http://hmmer.org/" -SRC_URI="http://eddylab.org/software/${PN}/${PV}/${P}.tar.gz" - -LICENSE="GPL-2" -SLOT="2" -KEYWORDS="~amd64 ~x86" -IUSE="cpu_flags_ppc_altivec test" -RESTRICT="!test? ( test )" - -BDEPEND="test? ( dev-lang/perl )" - -PATCHES=( - "${FILESDIR}/${P}-fix-perl-shebangs.patch" - "${FILESDIR}/${P}-fix-build-system-destdir.patch" -) - -src_configure() { - # required to expose pthread_setconcurrency(), #882279 - append-cppflags -D_XOPEN_SOURCE=500 - - # prevent stray environmental variable - # from causing issues in the test phase - unset TMPDIR - - econf \ - --enable-lfs \ - --enable-threads \ - $(use_enable cpu_flags_ppc_altivec altivec) -} - -src_compile() { - emake AR="$(tc-getAR) rcs" -} - -src_install() { - default - - newlib.a src/libhmmer.a libhmmer2.a - insinto /usr/include/hmmer2 - doins src/*.h - - dobin squid/{afetch,alistat,compalign,compstruct,revcomp,seqstat,seqsplit,sfetch,shuffle,sreformat,sindex,weight,translate} - dolib.a squid/libsquid.a - insinto /usr/include/hmmer2 - doins squid/*.h - - dodoc NOTES Userguide.pdf - newdoc 00README README - - # rename files due to collisions with hmmer-3 - # in order to make SLOTing possible - local i - - # first rename man pages... - pushd "${ED}"/usr/share/man/man1/ >/dev/null || die - for i in hmm*.1; do - mv ${i%.1}{,2}.1 || die - done - popd >/dev/null || die - - # ... then rename binaries - pushd "${ED}"/usr/bin/ >/dev/null || die - for i in hmm*; do - mv ${i}{,2} || die - done - popd >/dev/null || die -} - -pkg_postinst() { - elog "All ${P} binaries have been renamed, in order" - elog "to avoid collisions with hmmer-3. For instance" - elog - elog " hmmalign -> hmmalign2" - elog -} diff --git a/sci-biology/hmmer/hmmer-2.3.2-r6.ebuild b/sci-biology/hmmer/hmmer-2.3.2-r6.ebuild new file mode 100644 index 000000000000..74a8a151b0c4 --- /dev/null +++ b/sci-biology/hmmer/hmmer-2.3.2-r6.ebuild @@ -0,0 +1,84 @@ +# Copyright 1999-2024 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +inherit flag-o-matic toolchain-funcs + +DESCRIPTION="Sequence analysis using profile hidden Markov models" +HOMEPAGE="http://hmmer.org/" +SRC_URI="http://eddylab.org/software/${PN}/${PV}/${P}.tar.gz" + +LICENSE="GPL-2" +SLOT="2" +KEYWORDS="~amd64 ~x86" +IUSE="cpu_flags_ppc_altivec test" +RESTRICT="!test? ( test )" + +BDEPEND="test? ( dev-lang/perl )" + +PATCHES=( + "${FILESDIR}/${P}-fix-perl-shebangs.patch" + "${FILESDIR}/${P}-fix-build-system-destdir.patch" + "${FILESDIR}/${P}-fix-missing-include-in-configure.patch" +) + +src_configure() { + # required to expose pthread_setconcurrency(), #882279 + append-cppflags -D_XOPEN_SOURCE=500 + + # prevent stray environmental variable + # from causing issues in the test phase + unset TMPDIR + + econf \ + --enable-lfs \ + --enable-threads \ + $(use_enable cpu_flags_ppc_altivec altivec) +} + +src_compile() { + emake AR="$(tc-getAR) rcs" +} + +src_install() { + default + + newlib.a src/libhmmer.a libhmmer2.a + insinto /usr/include/hmmer2 + doins src/*.h + + dobin squid/{afetch,alistat,compalign,compstruct,revcomp,seqstat,seqsplit,sfetch,shuffle,sreformat,sindex,weight,translate} + dolib.a squid/libsquid.a + insinto /usr/include/hmmer2 + doins squid/*.h + + dodoc NOTES Userguide.pdf + newdoc 00README README + + # rename files due to collisions with hmmer-3 + # in order to make SLOTing possible + local i + + # first rename man pages... + pushd "${ED}"/usr/share/man/man1/ >/dev/null || die + for i in hmm*.1; do + mv ${i%.1}{,2}.1 || die + done + popd >/dev/null || die + + # ... then rename binaries + pushd "${ED}"/usr/bin/ >/dev/null || die + for i in hmm*; do + mv ${i}{,2} || die + done + popd >/dev/null || die +} + +pkg_postinst() { + elog "All ${P} binaries have been renamed, in order" + elog "to avoid collisions with hmmer-3. For instance" + elog + elog " hmmalign -> hmmalign2" + elog +} -- cgit v1.2.3-65-gdbad