gentoo resync : 25.11.2020

5 files changed, 36 insertions, 21 deletions

diff --git a/sci-biology/clustalw-mpi/Manifest b/sci-biology/clustalw-mpi/Manifest
index 3088142ea209..23d86f7036f9 100644
--- a/sci-biology/clustalw-mpi/Manifest
+++ b/sci-biology/clustalw-mpi/Manifest
@@ -1,4 +1,5 @@
-AUX 0.13-gentoo.patch 596 BLAKE2B 3d302656dfd4a4ecae645753643a9bf93c9643818e61f8ebda910eeea668bf5c5458f670e84243cb044cdad1add35a26b365f3478eb6f7ef7f98b8bc6bbf6f55 SHA512 4b0350f9ca8ce0d6e098faae5749bdc120b853dec745a07899e81bb195623affe46560d28a3c79db7af57551c9c873d91e693ee30a5c185ac4d2adb26a9d27c8
+AUX clustalw-mpi-0.13-fno-common.patch 449 BLAKE2B e1d8e7cd34e5fea17fb883861e2cb32874c34340b37f6d2983688930706b41cf1a7653b73d3860b8b5adcdca353b7a9ec94d9bda5090048d040dc6eb2b1a3d6b SHA512 71ea0f57c7235bc99f3e0d364476c268a27d2eeaba8e9bbcc01eceb0c84b1aabd0d9ce66dd738e6b0e75919f6cc18890e4dde7be6097e0e3051a9907bee56b4f
+AUX clustalw-mpi-0.13-makefile.patch 596 BLAKE2B 3d302656dfd4a4ecae645753643a9bf93c9643818e61f8ebda910eeea668bf5c5458f670e84243cb044cdad1add35a26b365f3478eb6f7ef7f98b8bc6bbf6f55 SHA512 4b0350f9ca8ce0d6e098faae5749bdc120b853dec745a07899e81bb195623affe46560d28a3c79db7af57551c9c873d91e693ee30a5c185ac4d2adb26a9d27c8
 DIST clustalw-mpi-0.13.tar.gz 154911 BLAKE2B 705f62263340b0ac13895657c97e185f395910f25653bdcc20cf867732c270c65eebebe5b914367a534a5d058909d0baf307c0a3727a2095d4f21c313e83b94d SHA512 e0008accb6c07584dc5ad1b953e0c668fad43ca3a86d88dbcf50fbfa858870131e4db005cc87b46f5268cd0795e9a2ce01326d8318d66b694a92b85e6f9635df
-EBUILD clustalw-mpi-0.13-r2.ebuild 962 BLAKE2B bcc71a3c09ae2d9e3c4f41b6a4e0771dd778c3cbdcf650cb9319124834a02d40b129757675ea060b6d39c699d3b123b757129f08b8d98c65b619b74467d8bd4b SHA512 48cd3c0ff42cf9c5185e70d0fbdb1b21020a7ad75156adba06346b7cd6847dfbb2752164edd93238890ef55d38565cdcc196355094ca3e8e253f3d508b409ef3
-MISC metadata.xml 491 BLAKE2B b65663a63fa098ac80bc0226163188776cb7805688651ea22724ed457924a3d970e5e368210a994f536f9152b3af2766d07c1eefb8b620299c3e1efffda840c3 SHA512 d242bee2ea381f992deb30b406b89ec2da08e1d513da5d9a94016ea07247670744d25bac8175607291c39d80090d3d1746154d3c60ba95bdd720d57c0212b3d0
+EBUILD clustalw-mpi-0.13-r3.ebuild 1012 BLAKE2B e1ae0c2237433f8826bcc66b6c3b11e8313a41ddb8201a6ffbb1300b7f9bfbb45c568e9903f9296ca97f54a9aec98199c2c9e4f942b43e89cfaff4fe982d7472 SHA512 9b5af106fa5daed7ff7c6ab49037ca82b42ce781138fa076efaf43f70b09ebfdcd45dc5e63d53a95a9414ca273260ebe5971664559001499cba8eefb80e26694
+MISC metadata.xml 487 BLAKE2B 7ca9b9cccd9bf7468703e755d4090e077a975c6463d97c612be7508ec38497d391e10fa5a50d5e76fc1f94f735b4062a4ea894d588706092166339c2046410f3 SHA512 4b7038b53d689f5a2e0f6a0b121235efb6d5c6fa9b8586107071f7820b0c2d9274a3b8b533afc84709df408751addf2b2408850542ed0083f47c7220d4bc61f5
diff --git a/sci-biology/clustalw-mpi/clustalw-mpi-0.13-r2.ebuild b/sci-biology/clustalw-mpi/clustalw-mpi-0.13-r3.ebuild
index 76d3b80cde32..334c34e78ce6 100644
--- a/sci-biology/clustalw-mpi/clustalw-mpi-0.13-r2.ebuild
+++ b/sci-biology/clustalw-mpi/clustalw-mpi-0.13-r3.ebuild
@@ -1,7 +1,7 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2020 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=6
+EAPI=7
 
 inherit toolchain-funcs
 
@@ -12,28 +12,31 @@ SRC_URI="http://web.bii.a-star.edu.sg/~kuobin/${PN}/${P}.tar.gz"
 LICENSE="public-domain"
 SLOT="0"
 KEYWORDS="~amd64 ~x86"
-IUSE="mpi_njtree static_pairalign"
+IUSE="mpi-njtree static-pairalign"
 
 DEPEND="virtual/mpi"
 RDEPEND="${DEPEND}"
 
-PATCHES=( "${FILESDIR}"/${PV}-gentoo.patch )
+PATCHES=(
+	"${FILESDIR}"/${P}-makefile.patch
+	"${FILESDIR}"/${P}-fno-common.patch
+)
 
 src_prepare() {
 	default
 
-	if use mpi_njtree; then
+	if use mpi-njtree; then
 		sed -e "s/TREES_FLAG/#TREES_FLAG/" -i Makefile || \
 			die "Failed to configure MPI code for NJ trees"
 	fi
 
-	if use static_pairalign; then
+	if use static-pairalign; then
 		sed -e "s/DDYNAMIC_SCHEDULING/DSTATIC_SCHEDULING/" -i Makefile || \
 			die "Failed to configure static scheduling for pair alignments"
 	fi
 }
 
 src_install() {
-	dobin ${PN}
-	newdoc README.${PN} README
+	dobin clustalw-mpi
+	newdoc README.clustalw-mpi README
 }
diff --git a/sci-biology/clustalw-mpi/files/clustalw-mpi-0.13-fno-common.patch b/sci-biology/clustalw-mpi/files/clustalw-mpi-0.13-fno-common.patch
new file mode 100644
index 000000000000..da74f0ba172d
--- /dev/null
+++ b/sci-biology/clustalw-mpi/files/clustalw-mpi-0.13-fno-common.patch
@@ -0,0 +1,13 @@
+--- a/parallel_compare.c
++++ b/parallel_compare.c
+@@ -74,8 +74,8 @@
+ static sint 	**accum;
+ static sint 	*diag_index;
+ static char 	*slopes;
+-sint ktup,window,wind_gap,signif; 
+-sint *zza, *zzb, *zzc, *zzd;
++extern sint ktup,window,wind_gap,signif;
++extern sint *zza, *zzb, *zzc, *zzd;
+ extern Boolean percent;
+ static void make_p_ptrs(sint *tptr, sint *pl, sint naseq, sint l);
+ static void make_n_ptrs(sint *tptr, sint *pl, sint naseq, sint len);
diff --git a/sci-biology/clustalw-mpi/files/0.13-gentoo.patch b/sci-biology/clustalw-mpi/files/clustalw-mpi-0.13-makefile.patch
index 6e36061cbb39..6e36061cbb39 100644
--- a/sci-biology/clustalw-mpi/files/0.13-gentoo.patch
+++ b/sci-biology/clustalw-mpi/files/clustalw-mpi-0.13-makefile.patch
diff --git a/sci-biology/clustalw-mpi/metadata.xml b/sci-biology/clustalw-mpi/metadata.xml
index 8ab4494152c8..ffe2c4efec87 100644
--- a/sci-biology/clustalw-mpi/metadata.xml
+++ b/sci-biology/clustalw-mpi/metadata.xml
@@ -1,14 +1,12 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
-<maintainer type="project">
-  <email>sci-biology@gentoo.org</email>
-  <name>Gentoo Biology Project</name>
-</maintainer>
-<use>
-  <flag name="mpi_njtree">Use MPI (as opposed to serial) code for computing
-    neighbor-joining trees</flag>
-  <flag name="static_pairalign">Use static (as opposed to dynamic) scheduling
-    for pair alignments</flag>
-</use>
+	<maintainer type="project">
+		<email>sci-biology@gentoo.org</email>
+		<name>Gentoo Biology Project</name>
+	</maintainer>
+	<use>
+		<flag name="mpi-njtree">Use MPI (as opposed to serial) code for computing neighbor-joining trees</flag>
+		<flag name="static-pairalign">Use static (as opposed to dynamic) scheduling for pair alignments</flag>
+	</use>
 </pkgmetadata>