commit: 63b15e9dd17c41d7c4b6827e794854ca58169d56 Author: David Seifert <soap <AT> gentoo <DOT> org> AuthorDate: Thu Jul 7 19:56:54 2022 +0000 Commit: David Seifert <soap <AT> gentoo <DOT> org> CommitDate: Thu Jul 7 19:56:54 2022 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=63b15e9d
sci-biology/exonerate: update EAPI 6 -> 8 Closes: https://bugs.gentoo.org/600766 Signed-off-by: David Seifert <soap <AT> gentoo.org> ...e-2.2.0-r2.ebuild => exonerate-2.2.0-r3.ebuild} | 23 +++++------- .../exonerate/files/exonerate-2.2.0-asneeded.patch | 15 -------- .../files/exonerate-2.2.0-autotools.patch | 43 ++++++++++++++++++++++ sci-biology/exonerate/metadata.xml | 2 +- 4 files changed, 54 insertions(+), 29 deletions(-) diff --git a/sci-biology/exonerate/exonerate-2.2.0-r2.ebuild b/sci-biology/exonerate/exonerate-2.2.0-r3.ebuild similarity index 69% rename from sci-biology/exonerate/exonerate-2.2.0-r2.ebuild rename to sci-biology/exonerate/exonerate-2.2.0-r3.ebuild index 53ae5a97c6ae..73fa9eca83e5 100644 --- a/sci-biology/exonerate/exonerate-2.2.0-r2.ebuild +++ b/sci-biology/exonerate/exonerate-2.2.0-r3.ebuild @@ -1,7 +1,7 @@ -# Copyright 1999-2019 Gentoo Authors +# Copyright 1999-2022 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=8 inherit autotools toolchain-funcs @@ -12,33 +12,30 @@ SRC_URI="http://ftp.ebi.ac.uk/pub/software/vertebrategenomics/exonerate/${P}.tar LICENSE="GPL-3" SLOT="0" KEYWORDS="~amd64 ~x86 ~ppc-macos ~x64-macos" -IUSE="test threads utils" -RESTRICT="!test? ( test )" +IUSE="test utils" REQUIRED_USE="test? ( utils )" +RESTRICT="!test? ( test )" DEPEND="dev-libs/glib:2" RDEPEND="${DEPEND}" -PATCHES=( "${FILESDIR}"/${P}-asneeded.patch ) +PATCHES=( "${FILESDIR}"/${P}-autotools.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 + # the bootstrapping code loads AR and CC from the environment + tc-export CC RANLIB + export C4_AR="$(tc-getAR)" econf \ --enable-glib2 \ --enable-largefile \ - $(use_enable utils utilities) \ - $(use_enable threads pthreads) + --enable-pthreads \ + $(use_enable utils utilities) } src_install() { diff --git a/sci-biology/exonerate/files/exonerate-2.2.0-asneeded.patch b/sci-biology/exonerate/files/exonerate-2.2.0-asneeded.patch deleted file mode 100644 index 5c428979a1af..000000000000 --- a/sci-biology/exonerate/files/exonerate-2.2.0-asneeded.patch +++ /dev/null @@ -1,15 +0,0 @@ -Fix build with --as-needed - -https://bugs.gentoo.org/268094 - ---- a/configure.in -+++ b/configure.in -@@ -289,7 +289,7 @@ - if test "$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 @@ <name>Gentoo Biology Project</name> </maintainer> <use> - <flag name="utils">Install all utilities</flag> + <flag name="utils">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</flag> </use> </pkgmetadata>
