gentoo resync : 29.12.2022

3 files changed, 56 insertions, 32 deletions

diff --git a/sci-biology/primer3/Manifest b/sci-biology/primer3/Manifest
index a8ab456f2e41..f6611ee55622 100644
--- a/sci-biology/primer3/Manifest
+++ b/sci-biology/primer3/Manifest
@@ -1,5 +1,5 @@
-AUX primer3-2.3.4-buildsystem.patch 5460 BLAKE2B 1e7680501e9c4a74c599f52caa787751f74f6a4fd028d8273d00364c7d2e59c0a641d343386e6ff7598d7d0bbfa66ce80412d300646cd54d0112ce118ff8422d SHA512 52f539f52c92e5e21c3166da62813c6fa9f90fd9e0ca87d9ab67658496e13f4b5ce5c53770802cb1cdd21044244e21f09b0de2ce3c6d3db0182b3d9cbf64a037
+AUX primer3-2.3.7-buildsystem.patch 5855 BLAKE2B 74395e3ecaf16e10bce493337681f2ab7b2b6016bb784854777c2a00cb09f9ab1275d9955d622bdd2d887bb7763a5d2addd7064fafb00b4d2102463491a112d1 SHA512 4cc3492b1c93e2d736493fe04e18b544dc9487ded5e6ebb4bc64e19b38ca125aafa4732e80cfab83d6467ba4d8e11ca7c59342188c7e4464e9a674e7ac26c59f
 AUX primer3-2.3.7-gcc7.patch 421 BLAKE2B 3f861ecb493ce9673cdebac9ea224a0588bd3b758d72a7ef4e41d4efb929db444a8c2808a55ead42dcb174265a926c021a89dd83dc8a1e5ba4eb5ed26280be43 SHA512 c818cd80e4762ef46e4e52acd27f4eb966d676995154b3503c98d8defb545c3dd7ea307c8946b5b5c462dd7f5dee6abc254cea59e21e2229cb779a7178dec04d
 DIST primer3-2.3.7.tar.gz 1658090 BLAKE2B 0bc9a0faa19c4ac3b48680d65b0d91a13d8bdd651ad3a0d344b4f50ce8dc510fe7a22665192751fb2c8ff6282b560daf4540a02cc70482dba0fcc344f7727e37 SHA512 f227f80d395cb682a9d65e0ac3afdcacb8385d66e721b9163fda939a9c788a7c6907273f6223782702b48d7df66ea2331114f6303fcd29e3b3c50a2717da2fa7
-EBUILD primer3-2.3.7.ebuild 1116 BLAKE2B 1aff6985a9ad3ad0ee523f18061c7f31bd26d3cc6c72f440a15c0ae2bc21f84ad360f51b021079efde09ef386f1c92f4dec7d155b970247e9ee87c376e0b36ee SHA512 56b127a7282b1c9dcc514758899d46e23ad79178f402beee270a03959eb01ae28e03720fba1c4dfbfc050e2932a15f5e2254705a048acf8ef8f7db0998327e61
+EBUILD primer3-2.3.7-r1.ebuild 1080 BLAKE2B 89a48de004236190b5708cf8e1ce256af3b6f6a5cbd1ed03b2f54bba5ff162cb88dd81117cce9737714b53ea2ad247f3d07da02b2d912006f903aabdb4d3d6af SHA512 a879dc2c2cc5b8799e05334226f1aa612c2534bb94404d3ce4d4649e6b7322890a549c56f961c869cfe3cdd2d0e613345dd70dbc11ee3e42af34fb8955c936b6
 MISC metadata.xml 798 BLAKE2B b57850f7ea949d9e026fba81ffb483b542f725aa96477b013ac635ef058c42fa925cc104ccac89e07cb655939364effc5193c9665264145b6d892593c133856a SHA512 1f1541c1a632b9ad37359bb60cb7e4fa4e583d9eafa10f9ec43450c30ade6ae88289ca62c793ec63da376306ab383b399ff4ab89483bcc43588aab78249100f8
diff --git a/sci-biology/primer3/files/primer3-2.3.4-buildsystem.patch b/sci-biology/primer3/files/primer3-2.3.7-buildsystem.patch
index cf47b35af502..8f9bf4042758 100644
--- a/sci-biology/primer3/files/primer3-2.3.4-buildsystem.patch
+++ b/sci-biology/primer3/files/primer3-2.3.7-buildsystem.patch
@@ -1,11 +1,6 @@
- src/Makefile | 61 ++++++++++++++++++++++++++++++------------------------------
- 1 file changed, 31 insertions(+), 30 deletions(-)
-
-diff --git a/src/Makefile b/src/Makefile
-index 607ab45..a88adf4 100644
 --- a/src/Makefile
 +++ b/src/Makefile
-@@ -52,15 +52,16 @@ TESTOPTS=
+@@ -52,15 +52,13 @@
  WINMAKE=mingw32-make
  
  LDLIBS     = -lm
@@ -15,56 +10,66 @@ index 607ab45..a88adf4 100644
 -O_OPTS     = -O2
 -CC_OPTS    = -g -Wall -D__USE_FIXED_PROTOTYPES__
 -P_DEFINES  =
-+AR         ?= ar
-+CC         ?= gcc
-+CXX        ?= g++
+-
+-CFLAGS  = $(CC_OPTS) $(O_OPTS)
+-LDFLAGS = -g
 +O_OPTS     ?= 
 +CC_OPTS    ?= -Wall -D__USE_FIXED_PROTOTYPES__
 +P_DEFINES  ?=
- 
--CFLAGS  = $(CC_OPTS) $(O_OPTS)
--LDFLAGS = -g
++
 +CFLAGS    += $(CC_OPTS) $(O_OPTS)
 +CXXFLAGS  += $(CC_OPTS) $(O_OPTS)
 +LDFLAGS   +=
  # Note, for profiling, use
  # make O_OPTS='-pg -O0' LDFLAGS='-g -pg'
  
-@@ -92,7 +93,7 @@ LIBPRIMER3      = libprimer3.a
+@@ -92,7 +90,6 @@
  LIBPRIMER3_DYN  = libprimer3.so.1.0.0
  LIBRARIES       = $(LIBPRIMER3) $(LIBDPAL) $(LIBTHAL) $(LIBOLIGOTM) 
  DYNLIBS         = $(LIBPRIMER3_DYN) $(LIBDPAL_DYN) $(LIBTHAL_DYN) $(LIBOLIGOTM_DYN)
 -RANLIB          = ranlib
-+RANLIB          ?= ranlib
  
  PRIMER_OBJECTS1=primer3_boulder_main.o\
                  format_output.o\
-@@ -127,85 +128,85 @@ $(LIBOLIGOTM): oligotm.o
- 	$(RANLIB) $@
+@@ -119,93 +116,89 @@
+ ifeq ($(TESTOPTS),--windows)
+ 	cd ..\test & $(WINMAKE) clean TESTOPTS=$(TESTOPTS)
+ else
+-	cd ../test/; make clean
++	cd ../test/ && $(MAKE) clean
+ endif
+ 
+ $(LIBOLIGOTM): oligotm.o
+-	$(AR) rv $@ oligotm.o
+-	$(RANLIB) $@
++	$(AR) rcs $@ oligotm.o
  
  $(LIBOLIGOTM_LIB): oligotm.o
 -	$(CC) -shared -W1,-soname,liboligotm.so.1 -o $(LIBOLIGOTM_DYN) oligotm.o
 +	$(CC) $(LDFLAGS) -shared -W1,-soname,liboligotm.so.1 -o $(LIBOLIGOTM_DYN) oligotm.o
  
  $(LIBDPAL): dpal_primer.o
- 	$(AR) rv $@ dpal_primer.o
- 	$(RANLIB) $@
+-	$(AR) rv $@ dpal_primer.o
+-	$(RANLIB) $@
++	$(AR) rcs $@ dpal_primer.o
  
  $(LIBDPAL_DYN): dpal_primer.o
 -	$(CC) -shared -W1,-soname,libdpal.so.1 -o $(LIBDPAL_DYN_LIB) dpal_primer.o
 +	$(CC) $(LDFLAGS) -shared -W1,-soname,libdpal.so.1 -o $(LIBDPAL_DYN_LIB) dpal_primer.o
  
  $(LIBTHAL): thal_primer.o
- 	$(AR) rv $@ thal_primer.o
- 	$(RANLIB) $@
+-	$(AR) rv $@ thal_primer.o
+-	$(RANLIB) $@
++	$(AR) rcs $@ thal_primer.o
  
  $(LIBTHAL_DYN): thal_primer.o
 -	$(CC) -shared -W1,-soname,libthal.so.1 -o $(LIBTHAL_DYN_LIB) thal_primer.o
 +	$(CC) $(LDFLAGS) -shared -W1,-soname,libthal.so.1 -o $(LIBTHAL_DYN_LIB) thal_primer.o
  
  $(LIBPRIMER3): libprimer3.o p3_seq_lib.o
- 	$(AR) rv $@ libprimer3.o p3_seq_lib.o
- 	$(RANLIB) $@
+-	$(AR) rv $@ libprimer3.o p3_seq_lib.o
+-	$(RANLIB) $@
++	$(AR) rcs $@ libprimer3.o p3_seq_lib.o
  
  $(LIBPRIMER3_DYN): libprimer3.o p3_seq_lib.o
 -	$(CC) -shared -W1,-soname,liprimer3.so.1 -o $(LIBPRIMER3_DYN) libprimer3.o p3_seq_lib.o
@@ -146,3 +151,23 @@ index 607ab45..a88adf4 100644
  
  primer_test: test
  
+@@ -213,7 +206,7 @@
+ ifeq ($(TESTOPTS),--windows)
+ 	cd ..\test & $(WINMAKE) TESTOPTS=$(TESTOPTS)
+ else
+-	cd ../test; make test
++	cd ../test && $(MAKE) test
+ endif
+ 
+ # ======================================================================
+--- a/test/Makefile
++++ b/test/Makefile
+@@ -86,7 +86,7 @@
+ ifeq ($(TESTOPTS),--windows)
+ 	cd ..\src & $(WINMAKE)
+ else
+-	cd ../src; make
++	cd ../src && $(MAKE)
+ endif
+ 
+ clean:
diff --git a/sci-biology/primer3/primer3-2.3.7.ebuild b/sci-biology/primer3/primer3-2.3.7-r1.ebuild
index 4c6c9ce7bf44..b36e9291db94 100644
--- a/sci-biology/primer3/primer3-2.3.7.ebuild
+++ b/sci-biology/primer3/primer3-2.3.7-r1.ebuild
@@ -1,7 +1,7 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2022 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=6
+EAPI=8
 
 inherit toolchain-funcs
 
@@ -13,12 +13,11 @@ LICENSE="GPL-2"
 SLOT="0"
 KEYWORDS="~amd64 ~ppc ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris"
 
-DEPEND="dev-lang/perl"
-RDEPEND=""
+BDEPEND="dev-lang/perl"
 
 PATCHES=(
-	"${FILESDIR}"/${PN}-2.3.4-buildsystem.patch
-	"${FILESDIR}"/${PN}-2.3.7-gcc7.patch
+	"${FILESDIR}"/${P}-buildsystem.patch
+	"${FILESDIR}"/${P}-gcc7.patch
 )
 
 src_prepare() {
@@ -29,7 +28,7 @@ src_prepare() {
 }
 
 src_configure() {
-	tc-export CC CXX AR RANLIB
+	tc-export AR CC CXX
 }
 
 src_compile() {
@@ -38,7 +37,7 @@ src_compile() {
 
 src_test() {
 	emake -C test | tee "${T}"/test.log
-	grep -q "\[FAILED\]" && die "test failed. See "${T}"/test.log"
+	grep -q "\[FAILED\]" && die "test failed. See ${T}/test.log"
 }
 
 src_install() {