gentoo resync : 09.07.2022

5 files changed, 57 insertions, 32 deletions

diff --git a/sci-biology/exonerate/Manifest b/sci-biology/exonerate/Manifest
index a265c7bd94a4..5474f7a87784 100644
--- a/sci-biology/exonerate/Manifest
+++ b/sci-biology/exonerate/Manifest
@@ -1,4 +1,4 @@
-AUX exonerate-2.2.0-asneeded.patch 362 BLAKE2B 57bb7d7d57bf2347fc0cb20f650cd0a452bd70ed8ed46a87d132cf8d68e152438ec2c4e877129feb91748f5ca43021cc0010cf2f50b3bdb8eed60218d904eb27 SHA512 7c08fe7ee520ab7198557f5ac7f99f0bae53da77d46949d6bac78a3330fc9023a4aece085e060ad6a40303475999654dcfe5311d3a78f1d1be0d461cefbfcfb0
+AUX exonerate-2.2.0-autotools.patch 1407 BLAKE2B b34e8c4d8301d4f416b44f4516154917943e17d30b548c7710e097706ce2c9123770d97d3ae962a268c6253a83ab60159f9285fadab1328be4ad5dc48249ee3f SHA512 f34c35228d23a8fd9402c514312c58bd877a7844487ade7f9f8d545d66c5d350f3f82f1aab1862a7b647b7f7aaaa0dbd8100d34bc0ef7d79969063c30a8558d0
 DIST exonerate-2.2.0.tar.gz 509870 BLAKE2B 58b12338ef7d819a8e33ab87d72afe807ca219581a8f35ae38951860915a676bb9ba34a481f685e970948d9272be3e5f28d6b63c14f4d5facf35c4be52530d3b SHA512 c0aec4df83fbf6bcd1b27242397349769211ab88d71e2d081e20cb5453a03acd805807535a69841e991cf543d99fcd458cbd22d60b21f0fc6ce813eac45b838c
-EBUILD exonerate-2.2.0-r2.ebuild 967 BLAKE2B 27a48f5dc4e1040f4296152ae445ba6bb2dc29132605b6cce240c40d2719d16c0c7d80103d2b9f8440fb7d5bb8fec3e8ba0385f6f87b9196b443dd14ae1a6310 SHA512 1d5be70396afabf08489501cba460bb47a7bfe9efead75226b07707ed00813f0dcd69611b75e3135444ee100ceeaf2cd492cd79ffc5f3d01e6f5d808ce84f2e1
-MISC metadata.xml 327 BLAKE2B 6aaa3e563d3d8f980c3f42b7e5aa1f8cd5e67e5dcea0f467e6698731480ae7cb587b75516931c351f0e562ddebc4811f359f9ec9fb9c16cb93bc0842bd24d2d7 SHA512 82cd2f3b95540ef6132985b835bf482498f60495c7e4718aaae3bfb500a017bc367cd844992b6b3a3f68be276183f62c91ee517f6a72a19d058775f40a95eb0f
+EBUILD exonerate-2.2.0-r3.ebuild 945 BLAKE2B 5df41a4c19730cb7b342dcae7875fba40b7c7404ceb85f4568f55f0eaf9d8446195e922c709ae09a62f4a5c0a35b581ef86f03c3a58ead41b0d70313ec7da76f SHA512 f928328f1cb14719343df4c4d7df4fc834b59a3909c6f47ca9d1358d4d2d1d6d31c404074e45e747b3e5736040897861c00bb9e0974582f3472639638cc4c80d
+MISC metadata.xml 654 BLAKE2B c84cf7eb3eed086e51e990906b2ea2645160683ba9314d2d15790e03d077714c1592bd4f305a8f3ed9109e376292118b44a1d10ea9ad1118139874a4e451bf6b SHA512 820b824d3d2a05feee023573580135fa2895832dd1b602c35253c1b8ee46aafdd0e010b5e8a77ce1805058264e3110821d27533a1dfe9d30799a5e63ea1551f1
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>