gentoo resync : 29.06.2020

4 files changed, 50 insertions, 24 deletions

diff --git a/sci-biology/poa/Manifest b/sci-biology/poa/Manifest
index c7e6e27a6c45..7b85951ec539 100644
--- a/sci-biology/poa/Manifest
+++ b/sci-biology/poa/Manifest
@@ -1,4 +1,5 @@
-AUX 2-respect-flags.patch 743 BLAKE2B f4da40ae90b7304520232cc9c2d61a3eecaac6ba1b9b886b29e473b1df8766286e3fd89874e2e836b9ddcd91f4bffe276ad74c1b6d073af3c1ca91e540f96c30 SHA512 496415d501040057155ba2ba261564fc00dc764626c8d41081f5463b0b40f9eae978bb8a81db15cf90f193c4ca9fe8725a2876ed175e15d37a983196b70e192f
+AUX poa-2-fno-common.patch 357 BLAKE2B 5d239201e987f1fc45e82019a27b2c8e81015cd2b6b5b35f90838a8fff16bb08b51da5e6e9e1ac163bd6591341ba96a870fce4949a79e9ca558ce8c765d15ba4 SHA512 9d8f6552fd43a0f40da9cb7a5316e0e434df793fb9f7522b60e067061d14a7b27299feb02a8603cb4f6039b205723f562ea5c54c15ab3bd6582f2e6e7c223c43
+AUX poa-2-respect-flags.patch 874 BLAKE2B ee278cdbc6ec0603bc28087bd008caa70fe39668360a1473891ed997bde93f31ef7586acc9137a23a4d3123047ce5b600c3d6418a89e1e62ca70545b99a3112b SHA512 95e2e7c43ba18f9238b379ea13d3a6004cf580c75d484dbe43f01c823484f84eb93c3d2fe1ae3c98583c51c660ab24e6dc580d132649adedbf30d8675d8107b0
 DIST poaV2.tar.gz 62612 BLAKE2B 92f7b2926dd7fc93745411fc04c8dd3380c32e3e87cf89afa81aefe787a1aa0e7a416d08809cce531a21d5118398a9474a751a742ee1fca47e83bd907444e9c0 SHA512 2a54b025f0a74ff4c01828f3e4b9e8e135bffe26d08f651f981bc95a64196173b5d887ef988a25c1f5fbf89333b4771622d5dc93946d66e7ec9abacb6167595c
-EBUILD poa-2-r1.ebuild 945 BLAKE2B 73d50cff0c550fe82490c93ca07db3661a71a0a2d6f67ad2d69fe658f156734aba5702137adae5cf091ff9e1e6f153894259ecfaabed05be92858038c7042668 SHA512 2c76bd5587239e7f260aeb82c362008610904dda01907a224577af9e0ef06cad8012ff21788edc24d7d3ae360867748b5e245fc73b6e1480f890787cea727c66
+EBUILD poa-2-r1.ebuild 857 BLAKE2B 436c6a4db2fa826ebb3f0a3d59df5d88f746a6c025f227be6b4916f7b6b34dde51013ae48355ea080dc19ba763972e62d3b1a87b17c19349ba0f3ed2df50409c SHA512 7fadf68dd86ac01c83eb65ef6e8512428b7c5fa84b1071f538458e46ff3116d02ff4f18a7d8e2bc32c360caee2bac2ca998a3a824442f662613a8808e893e7b7
 MISC metadata.xml 347 BLAKE2B f003b9e0541ffd38d84b2daf8b4df59bfbec1510ae162ac42af1cb1cb110f19297074d61b9b84d71441a0ceba9acbd38123db467e8500c482165fcd6c7e7b90b SHA512 8610e747bbc86428757f77ed688520cdd9efeabc08e08f99ce74d98e7763f3f8cb7648b1eea01bc4db79ae16a650cb119b82022d1ac41e8fcbd6a6b40385e580
diff --git a/sci-biology/poa/files/poa-2-fno-common.patch b/sci-biology/poa/files/poa-2-fno-common.patch
new file mode 100644
index 000000000000..ddd738a5524c
--- /dev/null
+++ b/sci-biology/poa/files/poa-2-fno-common.patch
@@ -0,0 +1,13 @@
+--- a/black_flag.h
++++ b/black_flag.h
+@@ -236,8 +236,8 @@
+ 	       int sourceline,
+ 	       char sourcefile_revision[]);
+ 
+-char *Program_name;
+-char *Program_version;
++extern char *Program_name;
++extern char *Program_version;
+ 
+ void black_flag_init(char progname[],char progversion[]);
+ void black_flag_init_args(int narg,char *arg[],char progversion[]);
diff --git a/sci-biology/poa/files/2-respect-flags.patch b/sci-biology/poa/files/poa-2-respect-flags.patch
index bdd638cf64b7..fb01f0b5f934 100644
--- a/sci-biology/poa/files/2-respect-flags.patch
+++ b/sci-biology/poa/files/poa-2-respect-flags.patch
@@ -1,26 +1,38 @@
-diff --git a/Makefile b/Makefile
-index a65bed0..713a7ab 100644
 --- a/Makefile
 +++ b/Makefile
-@@ -26,9 +26,10 @@ LIBOBJECTS= \
+@@ -1,6 +1,3 @@
+-
+-AR=ar rc
+-
+ TARGETS=poa liblpo.a poa_doc libbflag.a
+ 
+ # align_score.c CAN BE USED TO ADD CUSTOMIZED SCORING FUNCTIONS
+@@ -26,9 +23,8 @@
  	stringptr.o
  
  
 -CC = gcc
-+CC ?= gcc
  #CFLAGS= -g -ansi-strict -W -Wall -DUSE_WEIGHTED_LINKS -DUSE_PROJECT_HEADER -I.
 -CFLAGS= -g -DUSE_WEIGHTED_LINKS -DUSE_PROJECT_HEADER -I.
-+OPT_CFLAGS = -g
-+CFLAGS= $(OPT_CFLAGS) -DUSE_WEIGHTED_LINKS -DUSE_PROJECT_HEADER -I.
++CPPFLAGS+= -DUSE_WEIGHTED_LINKS -DUSE_PROJECT_HEADER -I.
  # -I$(HOME)/lib/include
  # -DREPORT_MAX_ALLOC
  
-@@ -44,7 +45,7 @@ liblpo.a: $(LIBOBJECTS)
+@@ -37,14 +33,14 @@
+ 
+ liblpo.a: $(LIBOBJECTS)
+ 	rm -f $@
+-	$(AR) $@ $(LIBOBJECTS)
+-	ranlib $@
++	$(AR) rc $@ $(LIBOBJECTS)
++	$(RANLIB) $@
+ 
+ 
  
  # NB: LIBRARY MUST FOLLOW OBJECTS OR LINK FAILS WITH UNRESOLVED REFERENCES!!
  poa: $(OBJECTS) liblpo.a
 -	$(CC) -o $@ $(OBJECTS) -lm liblpo.a
-+	$(CC) $(LDFLAGS) -o $@ $(OBJECTS) -lm liblpo.a
++	$(CC) $(CFLAGS) $(LDFLAGS) -o $@ $(OBJECTS) -lm liblpo.a
  
  what:
  	@echo poa: partial-order based sequence alignment program
diff --git a/sci-biology/poa/poa-2-r1.ebuild b/sci-biology/poa/poa-2-r1.ebuild
index fc472ce96007..d87f2a638117 100644
--- a/sci-biology/poa/poa-2-r1.ebuild
+++ b/sci-biology/poa/poa-2-r1.ebuild
@@ -1,9 +1,9 @@
 # Copyright 1999-2020 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
+EAPI=7
 
-inherit eutils toolchain-funcs
+inherit toolchain-funcs
 
 MY_P="${PN}V${PV}"
 
@@ -15,30 +15,30 @@ SRC_URI="mirror://sourceforge/poamsa/${MY_P}.tar.gz"
 LICENSE="GPL-2"
 SLOT="0"
 KEYWORDS="~amd64 ~x86"
-IUSE="static-libs"
 
 S="${WORKDIR}/${MY_P}"
 
-src_prepare() {
-	epatch "${FILESDIR}"/${PV}-respect-flags.patch
+PATCHES=(
+	"${FILESDIR}"/${P}-respect-flags.patch
+	"${FILESDIR}"/${P}-fno-common.patch
+)
+
+src_configure() {
+	tc-export AR CC RANLIB
 }
 
 src_compile() {
-	emake \
-		CC="$(tc-getCC)" \
-		OPT_CFLAGS="${CFLAGS}" \
-		poa
+	emake poa
 }
 
 src_install() {
-	dobin "${S}"/poa "${S}"/make_pscores.pl
-	use static-libs && dolib.a "${S}"/liblpo.a
-	dodoc "${S}"/README "${S}"/multidom.*
+	dobin poa make_pscores.pl
+	dodoc README multidom.*
 	insinto /usr/share/poa
-	doins "${S}"/*.mat
+	doins *.mat
 }
 
 pkg_postinst() {
 	elog "poa requires a score matrix as the first argument."
-	elog "This package installs two examples to ${EROOT}usr/share/poa/."
+	elog "This package installs two examples to ${EROOT}/usr/share/poa/."
 }