gentoo resync : 09.07.2022

5 files changed, 55 insertions, 24 deletions

diff --git a/sci-biology/clustalw/Manifest b/sci-biology/clustalw/Manifest
index f642140dff2e..d26b15faea9f 100644
--- a/sci-biology/clustalw/Manifest
+++ b/sci-biology/clustalw/Manifest
@@ -1,6 +1,7 @@
-AUX 1.83-as-needed.patch 388 BLAKE2B 8da98e05dcdc74ee41ff7a3d75b11590507bc769df0adb181f7c2d0a656f80d15b7363723bd760c359efb666cf962f5cf8c055abc1b7181d37203b0bfe659717 SHA512 1f66a0b539f9101a52b4117d0369294f706a048464d1908ae457def27d33ace0e5c5f9ba507f82a1406bb78ff51896ac6bb76cb03dfe8ff6bbb8ed182dc0f5ea
+AUX 1.83-as-needed.patch 800 BLAKE2B 37db9a8c0f7b5db47065f5c6e01cefc095363e30a5f07a95bc7b71af80f12c59b8f70bc898b77ab40ab13120c7d2a851eb177543c5a1d58f24cb2d9b8921993c SHA512 42d4982cb1f2070c9c09312ec9ffadfa274740e2dcaa688f7d1314aa47b88f9e59a6a452cb3481a64f57816786523352a10deb498c7235e2bc1b5999858e0201
+AUX 1.83-clang.patch 162 BLAKE2B b4ed2add1aaf33ef3d3138124377ed88bbe030b2e50f24e7dc87717fd06e3f76c6660c518d60083520f13b2349a1051a3981605e6130e0632e112212af345f51 SHA512 0e9aa3e61194f6d35449544c31693ee9f23ced8460b6ef4eca45b7f969867a6de04b898531e2749e65ee353547bd6fd3f19b7ee29d202ca30b5043567bf045bd
 DIST clustalw-2.1.tar.gz 350761 BLAKE2B 479acb42ec0b0adee8e04e99132a782c947a1261f48e674c6a11e4f38e44e5709d03f0c864f0cd3cf7eb4faf76a36b6121c3e3d3573c86ee3895971df07f1a58 SHA512 659cfe0121015dd2b84578b1a0a7f016fc944de155686b9bdef31122200a21e792203f3a6ab93a31676a50ffb70858b506ceb7ac27d921189a8381dbe0887921
 DIST clustalw1.83.UNIX.tar.gz 166863 BLAKE2B a3b1eabad8bc736cde4655f13fa8544759b7b5c50ea97fd45ee0be45ac6c361db5ced8ad21622ac2530b57c37c77dfd67657afd2c411acbfb7ff2a3ba014637e SHA512 c0cc9ebf4c8869be819065546b499b547990342c87425fae8f921a141704343f2a518ecfc2b8bfd527061902825fc5befcb2cd080c83ba887390e48338c9dc1a
-EBUILD clustalw-1.83-r4.ebuild 816 BLAKE2B 216e179d5da96bb16b46b64366c54f0482863ebcbb983c19cedadb7d898ed512b9ac679d696f8f74966fc3b24560951674b8eb09c97010c8300785cec01bc887 SHA512 3c013eaabd1f1f951067d6494c03b70913263d71f62fea4669f30dad3d18d52c02b9e8614854350ac8da2b033a7257d708e637e4ac89247a37be492b5d79e87d
-EBUILD clustalw-2.1-r1.ebuild 489 BLAKE2B af8ab15dcb6e2fb20199c7054940eaf53bbbcc72ec1fd7c37fc0aa3f3c28e7a23c640e70eb33956367a12ecc04990a3d6b63ad2b3d8bdf35396debff35dc6da6 SHA512 ad9b200b16d55df114440a44f8d771a406e518a49ca140de106ee38b4e8afc7f0acc7ccb18d81ea90f541637013915c6e793832d26a8b4465925fa101747498c
+EBUILD clustalw-1.83-r4.ebuild 824 BLAKE2B fbe940a15f3649f3e89bec7fdeed8b2a51b16441c449cfda705a43a632e4125f8ca2aec47efd3dc6c191c9ed4053a82026b3ec6c4a4ef43289ef357bdd9ec277 SHA512 0a5dd3fef90b72aa869104686af477297cbd9dc8c32bd13b2a8f330f161679d41add9ff94198189f32188b82bd9efad74456f0a1b472b323eded33985785f216
+EBUILD clustalw-2.1-r2.ebuild 479 BLAKE2B 2b8cdab7e004824ca9e515d114e49f21abed58bed18229a407e861f4756377771345c9971e5945c258a5d7891f052245443b1f731fc231cc7fe7154f38ab1422 SHA512 16d6478b5ed34f0aa7ac3441cf8b49820ef74e46315363078f82227c865067d950c24c41d309192520adae15b72916fbc3a3e5a12e439d4437effcb9f0d43b7d
 MISC metadata.xml 268 BLAKE2B a4d67334cdad8626d60e46b677ee1c83f569e5e20b3739a7664bb33be1829f8478af35e135bf734a6ff151b8543ea6c4ecafbf822cee8189f7e7096bd9698711 SHA512 59d3d8213b1a219396b74b6f4188c01e1cb4eb1c63e6792ce1e7fdb8000d1a4625919337ff77288ca7f7e07d9753f481d2381a06f554012633cd678194c980de
diff --git a/sci-biology/clustalw/clustalw-1.83-r4.ebuild b/sci-biology/clustalw/clustalw-1.83-r4.ebuild
index 076f16300b3a..62c59747adf3 100644
--- a/sci-biology/clustalw/clustalw-1.83-r4.ebuild
+++ b/sci-biology/clustalw/clustalw-1.83-r4.ebuild
@@ -1,34 +1,35 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=6
+EAPI=8
 
 inherit toolchain-funcs
 
 DESCRIPTION="General purpose multiple alignment program for DNA and proteins"
 HOMEPAGE="http://www.embl-heidelberg.de/~seqanal/"
 SRC_URI="ftp://ftp.ebi.ac.uk/pub/software/unix/clustalw/${PN}${PV}.UNIX.tar.gz"
+S="${WORKDIR}/${PN}${PV}"
 
 LICENSE="clustalw"
 SLOT="1"
 KEYWORDS="amd64 ~ppc ppc64 sparc x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris"
-IUSE=""
 
-S="${WORKDIR}"/${PN}${PV}
-
-PATCHES=( "${FILESDIR}"/${PV}-as-needed.patch )
+PATCHES=(
+	"${FILESDIR}"/${PV}-as-needed.patch
+	"${FILESDIR}"/${PV}-clang.patch
+)
 
 src_prepare() {
 	default
-
-	sed \
-		-e "/^CC/s:cc:$(tc-getCC):g" \
-		-i makefile || die
 	sed \
-		-e "s%clustalw_help%/usr/share/doc/${PF}/clustalw_help%" \
+		-e "s|clustalw_help|${EPREFIX}/usr/share/doc/${PF}/clustalw_help|" \
 		-i clustalw.c || die
 }
 
+src_configure() {
+	tc-export CC
+}
+
 src_install() {
 	dobin clustalw
 	dodoc README clustalv.doc clustalw{.doc,.ms,_help}
diff --git a/sci-biology/clustalw/clustalw-2.1-r1.ebuild b/sci-biology/clustalw/clustalw-2.1-r2.ebuild
index f42f1ed031b0..58a28e3ef7a5 100644
--- a/sci-biology/clustalw/clustalw-2.1-r1.ebuild
+++ b/sci-biology/clustalw/clustalw-2.1-r2.ebuild
@@ -1,7 +1,7 @@
-# Copyright 1999-2020 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=6
+EAPI=8
 
 DESCRIPTION="General purpose multiple alignment program for DNA and proteins"
 HOMEPAGE="http://www.clustal.org/"
@@ -10,9 +10,8 @@ SRC_URI="http://www.clustal.org/download/current/${P}.tar.gz"
 LICENSE="GPL-3 LGPL-3"
 SLOT="2"
 KEYWORDS="amd64 ~ppc ~ppc64 ~sparc x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris"
-IUSE=""
 
 src_install() {
 	default
-	rmdir "${ED%/}"/usr/share/aclocal || die
+	rmdir "${ED}"/usr/share/aclocal || die
 }
diff --git a/sci-biology/clustalw/files/1.83-as-needed.patch b/sci-biology/clustalw/files/1.83-as-needed.patch
index 9bb35b43f24a..54b78b0811e0 100644
--- a/sci-biology/clustalw/files/1.83-as-needed.patch
+++ b/sci-biology/clustalw/files/1.83-as-needed.patch
@@ -1,17 +1,36 @@
 --- a/makefile
 +++ b/makefile
-@@ -11,11 +11,11 @@
+@@ -10,25 +10,22 @@
+ 
  HEADERS = general.h clustalw.h
  
- CC	= cc
+-CC	= cc
 -CFLAGS  = -c -O
 -LFLAGS	= -O -lm 
-+CFLAGS  += -c
-+LIBS	= -lm 
++# C99 for gets()
++CFLAGS	+= -std=gnu99
++LIBS	+= -lm
  
  clustalw : $(OBJECTS) amenu.o clustalw.o
 -	$(CC) -o $@ $(OBJECTS) amenu.o clustalw.o $(LFLAGS)
-+	$(CC) $(LDFLAGS) -o $@ $(OBJECTS) amenu.o clustalw.o $(LIBS)
++	$(CC) $(LDFLAGS) $(CFLAGS) -o $@ $(OBJECTS) amenu.o clustalw.o $(LIBS)
  
  interface.o : interface.c $(HEADERS) param.h
- 	$(CC) $(CFLAGS) $*.c
+-	$(CC) $(CFLAGS) $*.c
++	$(CC) $(CFLAGS) $(CPPFLAGS) -c $<
+ 
+ amenu.o : amenu.c $(HEADERS) param.h
+-	$(CC) $(CFLAGS) $*.c
++	$(CC) $(CFLAGS) $(CPPFLAGS) -c $<
+ 
+ readmat.o : readmat.c $(HEADERS) matrices.h
+-	$(CC) $(CFLAGS) $*.c
++	$(CC) $(CFLAGS) $(CPPFLAGS) -c $<
+ 
+ trees.o : trees.c $(HEADERS) dayhoff.h
+-	$(CC) $(CFLAGS) $*.c
+-
+-.c.o :
+-	$(CC) $(CFLAGS) $?
++	$(CC) $(CFLAGS) $(CPPFLAGS) -c $<
+ 
diff --git a/sci-biology/clustalw/files/1.83-clang.patch b/sci-biology/clustalw/files/1.83-clang.patch
new file mode 100644
index 000000000000..ea1202079d9e
--- /dev/null
+++ b/sci-biology/clustalw/files/1.83-clang.patch
@@ -0,0 +1,11 @@
+--- a/interface.c
++++ b/interface.c
+@@ -210,7 +210,7 @@
+ 		Boolean 	name1 = FALSE;
+ 		sint ajb;
+ 
+-	if(args[0]==NULL) return;
++	if(args[0]==NULL) return 0;
+ 
+ 
+