[gentoo-commits] repo/gentoo:master commit in: sci-biology/poa/files/, sci-biology/poa/

[gentoo-commits] repo/gentoo:master commit in: sci-biology/poa/files/, sci-biology/poa/

[David Seifert]

commit:     162385507f481aee99dcb578b64138b10e261d22
Author:     David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Sun Jun 21 17:40:52 2020 +0000
Commit:     David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Sun Jun 21 17:40:52 2020 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=16238550

sci-biology/poa: [QA] Pass AR/RANLIB to build system

Closes: https://bugs.gentoo.org/725324
Package-Manager: Portage-2.3.101, Repoman-2.3.22
Signed-off-by: David Seifert <soap <AT> gentoo.org>

 ...spect-flags.patch => poa-2-respect-flags.patch} | 28 +++++++++++++++------
 sci-biology/poa/poa-2-r1.ebuild                    | 29 +++++++++++-----------
 2 files changed, 34 insertions(+), 23 deletions(-)

diff --git a/sci-biology/poa/files/2-respect-flags.patch b/sci-biology/poa/files/poa-2-respect-flags.patch
similarity index 52%
rename from sci-biology/poa/files/2-respect-flags.patch
rename to sci-biology/poa/files/poa-2-respect-flags.patch
index bdd638cf64b..fb01f0b5f93 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 126272f06c6..d87f2a63811 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}"
 
@@ -15,31 +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
-	epatch "${FILESDIR}"/${P}-fno-common.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/."
 }

[gentoo-commits] repo/gentoo:master commit in: sci-biology/poa/files/, sci-biology/poa/

[David Seifert]

commit:     8674063d381e616d093806be74b00c64fe5b5c81
Author:     David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Sun Jun 21 17:40:49 2020 +0000
Commit:     David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Sun Jun 21 17:40:49 2020 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=8674063d

sci-biology/poa: Fix building against GCC 10

Closes: https://bugs.gentoo.org/707028
Package-Manager: Portage-2.3.101, Repoman-2.3.22
Signed-off-by: David Seifert <soap <AT> gentoo.org>

 sci-biology/poa/files/poa-2-fno-common.patch | 13 +++++++++++++
 sci-biology/poa/poa-2-r1.ebuild              |  1 +
 2 files changed, 14 insertions(+)

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 00000000000..ddd738a5524
--- /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/poa-2-r1.ebuild b/sci-biology/poa/poa-2-r1.ebuild
index fc472ce9600..126272f06c6 100644
--- a/sci-biology/poa/poa-2-r1.ebuild
+++ b/sci-biology/poa/poa-2-r1.ebuild
@@ -21,6 +21,7 @@ S="${WORKDIR}/${MY_P}"
 
 src_prepare() {
 	epatch "${FILESDIR}"/${PV}-respect-flags.patch
+	epatch "${FILESDIR}"/${P}-fno-common.patch
 }
 
 src_compile() {