From 63b15e9dd17c41d7c4b6827e794854ca58169d56 Mon Sep 17 00:00:00 2001 From: David Seifert Date: Thu, 7 Jul 2022 21:56:54 +0200 Subject: sci-biology/exonerate: update EAPI 6 -> 8 Closes: https://bugs.gentoo.org/600766 Signed-off-by: David Seifert --- sci-biology/exonerate/exonerate-2.2.0-r2.ebuild | 48 ---------------------- sci-biology/exonerate/exonerate-2.2.0-r3.ebuild | 45 ++++++++++++++++++++ .../exonerate/files/exonerate-2.2.0-asneeded.patch | 15 ------- .../files/exonerate-2.2.0-autotools.patch | 43 +++++++++++++++++++ sci-biology/exonerate/metadata.xml | 2 +- 5 files changed, 89 insertions(+), 64 deletions(-) delete mode 100644 sci-biology/exonerate/exonerate-2.2.0-r2.ebuild create mode 100644 sci-biology/exonerate/exonerate-2.2.0-r3.ebuild delete mode 100644 sci-biology/exonerate/files/exonerate-2.2.0-asneeded.patch create mode 100644 sci-biology/exonerate/files/exonerate-2.2.0-autotools.patch (limited to 'sci-biology') diff --git a/sci-biology/exonerate/exonerate-2.2.0-r2.ebuild b/sci-biology/exonerate/exonerate-2.2.0-r2.ebuild deleted file mode 100644 index 53ae5a97c6ae..000000000000 --- a/sci-biology/exonerate/exonerate-2.2.0-r2.ebuild +++ /dev/null @@ -1,48 +0,0 @@ -# Copyright 1999-2019 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -inherit autotools toolchain-funcs - -DESCRIPTION="Generic tool for pairwise sequence comparison" -HOMEPAGE="https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate" -SRC_URI="http://ftp.ebi.ac.uk/pub/software/vertebrategenomics/exonerate/${P}.tar.gz" - -LICENSE="GPL-3" -SLOT="0" -KEYWORDS="~amd64 ~x86 ~ppc-macos ~x64-macos" -IUSE="test threads utils" -RESTRICT="!test? ( test )" -REQUIRED_USE="test? ( utils )" - -DEPEND="dev-libs/glib:2" -RDEPEND="${DEPEND}" - -PATCHES=( "${FILESDIR}"/${P}-asneeded.patch ) - -src_prepare() { - default - sed \ - -e 's: -O3 -finline-functions::g' \ - -i configure.in || die - mv configure.{in,ac} || die - - eautoreconf -} - -src_configure() { - tc-export CC - - econf \ - --enable-glib2 \ - --enable-largefile \ - $(use_enable utils utilities) \ - $(use_enable threads pthreads) -} - -src_install() { - default - - doman doc/man/man1/*.1 -} diff --git a/sci-biology/exonerate/exonerate-2.2.0-r3.ebuild b/sci-biology/exonerate/exonerate-2.2.0-r3.ebuild new file mode 100644 index 000000000000..73fa9eca83e5 --- /dev/null +++ b/sci-biology/exonerate/exonerate-2.2.0-r3.ebuild @@ -0,0 +1,45 @@ +# Copyright 1999-2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +inherit autotools toolchain-funcs + +DESCRIPTION="Generic tool for pairwise sequence comparison" +HOMEPAGE="https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate" +SRC_URI="http://ftp.ebi.ac.uk/pub/software/vertebrategenomics/exonerate/${P}.tar.gz" + +LICENSE="GPL-3" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~ppc-macos ~x64-macos" +IUSE="test utils" +REQUIRED_USE="test? ( utils )" +RESTRICT="!test? ( test )" + +DEPEND="dev-libs/glib:2" +RDEPEND="${DEPEND}" + +PATCHES=( "${FILESDIR}"/${P}-autotools.patch ) + +src_prepare() { + default + eautoreconf +} + +src_configure() { + # the bootstrapping code loads AR and CC from the environment + tc-export CC RANLIB + export C4_AR="$(tc-getAR)" + + econf \ + --enable-glib2 \ + --enable-largefile \ + --enable-pthreads \ + $(use_enable utils utilities) +} + +src_install() { + default + + doman doc/man/man1/*.1 +} diff --git a/sci-biology/exonerate/files/exonerate-2.2.0-asneeded.patch b/sci-biology/exonerate/files/exonerate-2.2.0-asneeded.patch deleted file mode 100644 index 5c428979a1af..000000000000 --- a/sci-biology/exonerate/files/exonerate-2.2.0-asneeded.patch +++ /dev/null @@ -1,15 +0,0 @@ -Fix build with --as-needed - -https://bugs.gentoo.org/268094 - ---- a/configure.in -+++ b/configure.in -@@ -289,7 +289,7 @@ - if test "$enable_pthreads" = yes; then - echo "Using PTHREADS" - CFLAGS="$CFLAGS -DUSE_PTHREADS" -- LDFLAGS="$LDFLAGS -lpthread" -+ LIBS="$LIBS -lpthread" - elif test "$enable_pthreads" = no; then - echo "Not using pthreads" - else diff --git a/sci-biology/exonerate/files/exonerate-2.2.0-autotools.patch b/sci-biology/exonerate/files/exonerate-2.2.0-autotools.patch new file mode 100644 index 000000000000..af95b5c8f77a --- /dev/null +++ b/sci-biology/exonerate/files/exonerate-2.2.0-autotools.patch @@ -0,0 +1,43 @@ +Fix build with --as-needed + +https://bugs.gentoo.org/268094 + +--- a/configure.in ++++ b/configure.in +@@ -144,11 +145,6 @@ + elif test "$enable_assert" = no; then + CFLAGS="$CFLAGS -DG_DISABLE_ASSERT" + echo "Turning assertions off" +- if test "$GCC" = "yes"; then +- # Not currently using -fomit-frame-pointer as clashes with -pg +- # CFLAGS="$CFLAGS -O3 -fomit-frame-pointer -finline-functions" +- CFLAGS="$CFLAGS -O3 -finline-functions" +- fi + else + echo "error: must be yes or no: --enable-assert:[$enable_assert]" + exit 1 +@@ -289,7 +285,7 @@ + if test "$enable_pthreads" = yes; then + echo "Using PTHREADS" + CFLAGS="$CFLAGS -DUSE_PTHREADS" +- LDFLAGS="$LDFLAGS -lpthread" ++ LIBS="$LIBS -lpthread" + elif test "$enable_pthreads" = no; then + echo "Not using pthreads" + else +--- a/src/model/bootstrapper.c ++++ b/src/model/bootstrapper.c +@@ -146,8 +146,12 @@ + + static void Bootstrapper_index_archive(Bootstrapper *bs){ + register gchar *command; ++ register gchar *ranlib = "ranlib"; ++ register gchar *tmp = (gchar*)g_getenv("RANLIB"); ++ if(tmp) ++ ranlib = tmp; + register gint ret_val; +- command = g_strdup_printf("ranlib %s", bs->archive_path); ++ command = g_strdup_printf("%s %s", ranlib, bs->archive_path); + g_message("Indexing archive [%s]", bs->archive_path); + g_print("%s\n", command); + ret_val = system(command); diff --git a/sci-biology/exonerate/metadata.xml b/sci-biology/exonerate/metadata.xml index 110611751dc3..421b8ef55beb 100644 --- a/sci-biology/exonerate/metadata.xml +++ b/sci-biology/exonerate/metadata.xml @@ -6,6 +6,6 @@ Gentoo Biology Project - Install all utilities + Install the follow binaries: esd2esi, fasta2esd, fastaannotatecdna, fastachecksum, fastaclean, fastaclip, fastacomposition, fastadiff, fastaexplode, fastafetch, fastahardmask, fastaindex, fastalength, fastanrdb, fastaoverlap, fastareformat, fastaremove, fastarevcomp, fastasoftmask, fastasort, fastasplit, fastasubseq, fastatranslate, fastavalidcds -- cgit v1.2.3-65-gdbad