sci-biology/exonerate: update EAPI 6 -> 8

Closes: https://bugs.gentoo.org/600766
Signed-off-by: David Seifert <soap@gentoo.org>

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
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>