gentoo resync : 09.07.2022

4 files changed, 56 insertions, 34 deletions

diff --git a/sci-biology/kalign/Manifest b/sci-biology/kalign/Manifest
index 62fab70bdcdb..ca16027a136e 100644
--- a/sci-biology/kalign/Manifest
+++ b/sci-biology/kalign/Manifest
@@ -1,3 +1,4 @@
+AUX kalign-2.03-makefile.patch 1115 BLAKE2B 12fb13e6644a81ce4977a134d594b1bc5fa1c4da90a78e905c8aa607d490a1968daf65e5f59c4d8adbb42a5cac1854610c88f8036448f456659505d1c191dbea SHA512 4d41f4c18864b697ef6e54f176ded2a74c44e943d4956617c273655121df70dd1cc8d9a723dda3aa92428a6a9356863f5bd8558411d86827c2fcd2386212938e
 DIST kalign_2.03.orig.tar.gz 114022 BLAKE2B 3637bde4e9b900def668043e75b2a52ed17a8aed6f894e323b1b76f216ad50784fb2ee352389f8888b5365efd5681361af3818ba0ca593721b19c497ffb83930 SHA512 d60152bd7124f77ea972ea7dac19f47eb731646a12ecafbee8a99335c20a36fb3ce2bdc633b346e4da1016d8e56a0f297f9b33c9b6285197946f404dbc390b0a
-EBUILD kalign-2.03-r2.ebuild 601 BLAKE2B 4d988368b81b04012c426de46f87d8287a685617eee1c727a899a9c1a5165130970d08efb5f48b1afadb947ec4a6a0effabf56de00c9eeeb08ec40cc482e58a2 SHA512 f19df61247a35a5a03164ad1a01968a078be043e53f53ff62ea35ba20787d84067fb4cd9212a9294a26270f95c7702ffdf571691df0311856f1de1973d6012ff
+EBUILD kalign-2.03-r3.ebuild 397 BLAKE2B ca5aa8d8d0e4ed29ce2480373e7155da54a41377e773e93f0a48cfb53cb489d916e98feceac74d1cc728da634aea81005fbf71ec2ff91b61c7bf4b2bc7aff0fe SHA512 8bd596122b0fb5ba2c4b9664b5e99984f9e52e3ea457bc39d0f3aff4e97d26e56c32e32f228292d4e25422eca59186c46525c84d9a6a1488deaa1114cee4129a
 MISC metadata.xml 268 BLAKE2B a4d67334cdad8626d60e46b677ee1c83f569e5e20b3739a7664bb33be1829f8478af35e135bf734a6ff151b8543ea6c4ecafbf822cee8189f7e7096bd9698711 SHA512 59d3d8213b1a219396b74b6f4188c01e1cb4eb1c63e6792ce1e7fdb8000d1a4625919337ff77288ca7f7e07d9753f481d2381a06f554012633cd678194c980de
diff --git a/sci-biology/kalign/files/kalign-2.03-makefile.patch b/sci-biology/kalign/files/kalign-2.03-makefile.patch
new file mode 100644
index 000000000000..61e65c0b73ce
--- /dev/null
+++ b/sci-biology/kalign/files/kalign-2.03-makefile.patch
@@ -0,0 +1,39 @@
+--- a/Makefile.in
++++ b/Makefile.in
+@@ -1,7 +1,11 @@
+-PREFIX			= /usr/local/bin
++prefix			= @prefix@
++exec_prefix		= @exec_prefix@
++bindir			= @bindir@
+ TEST				= test/
+-CC					= gcc  
+-CFLAGS			= -O9  -Wall 
++CC				= @CC@  
++CFLAGS			= @CFLAGS@
++CPPFLAGS		= @CPPFLAGS@
++LDFLAGS			= @LDFLAGS@
+ DEBUGFLAGS		= -ggdb -Wall 
+ 
+ SOURCES			= kalign2_distance_calculation.c kalign2_dp.c kalign2_input.c kalign2_main.c kalign2_mem.c kalign2_inferface.c kalign2_misc.c kalign2_tree.c  kalign2_profile.c kalign2_alignment_types.c kalign2_feature.c kalign2_hirschberg.c  kalign2_advanced_gaps.c kalign2_hirschberg_dna.c  kalign2_output.c kalign2_string_matching.c kalign2_profile_alignment.c 
+@@ -16,10 +20,7 @@
+ .PHONY: clean
+ 
+ all: $(OBJECTS)
+-	$(CC) $(CFLAGS) $(OBJECTS) -o $(PROGS)
+-	
+-%.o:	%.c
+-	$(CC) $(CFLAGS) -c $<
++	$(CC) $(LDFLAGS) $(CFLAGS) $(OBJECTS) -o $(PROGS)
+ 	
+ debug: $(DEBUGOBJECTS)
+ 	$(CC) $(DEBUGFLAGS) $(DEBUGOBJECTS) -o $(DEBUGPROGS)	
+@@ -29,7 +30,8 @@
+ 
+ 
+ install:
+-	cp $(PROGS) /usr/local/bin/
++	mkdir -p $(DESTDIR)$(bindir)
++	cp $(PROGS) $(DESTDIR)$(bindir)
+ 	
+ clean: 
+ 	rm -f $(PROGS) $(OBJECTS)
diff --git a/sci-biology/kalign/kalign-2.03-r2.ebuild b/sci-biology/kalign/kalign-2.03-r2.ebuild
deleted file mode 100644
index 53b4490bef71..000000000000
--- a/sci-biology/kalign/kalign-2.03-r2.ebuild
+++ /dev/null
@@ -1,33 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit toolchain-funcs
-
-DESCRIPTION="Global and progressive multiple sequence alignment"
-HOMEPAGE="http://msa.cgb.ki.se/"
-SRC_URI="mirror://debian/pool/main/k/kalign/${PN}_${PV}.orig.tar.gz"
-
-LICENSE="GPL-2"
-SLOT="0"
-IUSE=""
-KEYWORDS="~amd64 ~x86"
-
-S=${WORKDIR}/${PN}
-
-src_prepare() {
-	default
-	sed \
-		-e "s/\$(CFLAGS) \$(OBJECTS)/\$(LDFLAGS) &/" \
-		-i Makefile.in || die
-}
-
-src_compile() {
-	emake CC="$(tc-getCC)" CFLAGS="${CFLAGS}"
-}
-
-src_install() {
-	dobin ${PN}
-	einstalldocs
-}
diff --git a/sci-biology/kalign/kalign-2.03-r3.ebuild b/sci-biology/kalign/kalign-2.03-r3.ebuild
new file mode 100644
index 000000000000..22d92963a0ea
--- /dev/null
+++ b/sci-biology/kalign/kalign-2.03-r3.ebuild
@@ -0,0 +1,15 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DESCRIPTION="Global and progressive multiple sequence alignment"
+HOMEPAGE="http://msa.cgb.ki.se/"
+SRC_URI="mirror://debian/pool/main/k/kalign/${PN}_${PV}.orig.tar.gz"
+S="${WORKDIR}/${PN}"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+PATCHES=( "${FILESDIR}"/${P}-makefile.patch )