4 files changed, 53 insertions, 23 deletions
diff --git a/sci-biology/clustalw/clustalw-1.83-r4.ebuild b/sci-biology/clustalw/clustalw-1.83-r4.ebuild
index 076f16300b3a..23c4ba9a3229 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 1999-2023 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=""
+KEYWORDS="amd64 ~ppc ppc64 sparc ~x86 ~amd64-linux ~x86-linux ~ppc-macos"
 
-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..16a957f6c636 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 1999-2023 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/"
@@ -9,10 +9,9 @@ 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=""
+KEYWORDS="amd64 ~ppc ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~ppc-macos"
 
 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;
+ 
+ 
+