* [gentoo-commits] repo/gentoo:master commit in: sci-biology/primer3/, sci-biology/primer3/files/
@ 2017-12-24 19:46 David Seifert
0 siblings, 0 replies; 2+ messages in thread
From: David Seifert @ 2017-12-24 19:46 UTC (permalink / raw
To: gentoo-commits
commit: 7b52bc0205bc66c7e130b7794a76b5c455395232
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Sun Dec 24 18:24:32 2017 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Sun Dec 24 19:46:02 2017 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=7b52bc02
sci-biology/primer3: Fix building with GCC 7
Closes: https://bugs.gentoo.org/638604
Package-Manager: Portage-2.3.19, Repoman-2.3.6
sci-biology/primer3/files/primer3-2.3.7-gcc7.patch | 17 +++++++++++++++
sci-biology/primer3/primer3-2.3.7.ebuild | 24 ++++++++++++++--------
2 files changed, 32 insertions(+), 9 deletions(-)
diff --git a/sci-biology/primer3/files/primer3-2.3.7-gcc7.patch b/sci-biology/primer3/files/primer3-2.3.7-gcc7.patch
new file mode 100644
index 00000000000..a04ee1ac3b1
--- /dev/null
+++ b/sci-biology/primer3/files/primer3-2.3.7-gcc7.patch
@@ -0,0 +1,17 @@
+--- a/src/thal.c
++++ b/src/thal.c
+@@ -426,12 +426,12 @@
+ "Illegal type");
+ o->align_end_1 = -1;
+ o->align_end_2 = -1;
+- if ('\0' == oligo_f) {
++ if ('\0' == oligo_f[0]) {
+ strcpy(o->msg, "Empty first sequence");
+ o->temp = 0.0;
+ return;
+ }
+- if ('\0' == oligo_r) {
++ if ('\0' == oligo_r[0]) {
+ strcpy(o->msg, "Empty second sequence");
+ o->temp = 0.0;
+ return;
diff --git a/sci-biology/primer3/primer3-2.3.7.ebuild b/sci-biology/primer3/primer3-2.3.7.ebuild
index d0dbc736368..4c6c9ce7bf4 100644
--- a/sci-biology/primer3/primer3-2.3.7.ebuild
+++ b/sci-biology/primer3/primer3-2.3.7.ebuild
@@ -1,30 +1,34 @@
-# Copyright 1999-2016 Gentoo Foundation
+# Copyright 1999-2017 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
EAPI=6
-inherit eutils toolchain-funcs
+inherit toolchain-funcs
DESCRIPTION="Primer Design for PCR reactions"
HOMEPAGE="http://primer3.sourceforge.net/"
SRC_URI="mirror://sourceforge/project/${PN}/${PN}/${PV}/${P}.tar.gz"
-SLOT="0"
LICENSE="GPL-2"
-IUSE=""
+SLOT="0"
KEYWORDS="~amd64 ~ppc ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris"
DEPEND="dev-lang/perl"
RDEPEND=""
-PATCHES=( "${FILESDIR}"/${PN}-2.3.4-buildsystem.patch )
+PATCHES=(
+ "${FILESDIR}"/${PN}-2.3.4-buildsystem.patch
+ "${FILESDIR}"/${PN}-2.3.7-gcc7.patch
+)
src_prepare() {
default
if [[ ${CHOST} == *-darwin* ]]; then
sed -e "s:LIBOPTS ='-static':LIBOPTS =:" -i Makefile || die
fi
+}
+src_configure() {
tc-export CC CXX AR RANLIB
}
@@ -32,16 +36,18 @@ src_compile() {
emake -C src
}
-src_test () {
+src_test() {
emake -C test | tee "${T}"/test.log
grep -q "\[FAILED\]" && die "test failed. See "${T}"/test.log"
}
-src_install () {
+src_install() {
dobin src/{long_seq_tm_test,ntdpal,oligotm,primer3_core}
- dodoc src/release_notes.txt example
+
insinto /opt/primer3_config
- doins -r src/primer3_config/* primer3*settings.txt
+ doins -r src/primer3_config/. primer3*settings.txt
+
+ dodoc src/release_notes.txt example
docinto html
dodoc primer3_manual.htm
}
^ permalink raw reply related [flat|nested] 2+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/primer3/, sci-biology/primer3/files/
@ 2022-06-19 18:04 David Seifert
0 siblings, 0 replies; 2+ messages in thread
From: David Seifert @ 2022-06-19 18:04 UTC (permalink / raw
To: gentoo-commits
commit: a6ac5b96c3fb9bd7f096d432522a77ab24d7f30a
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Sun Jun 19 18:04:30 2022 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Sun Jun 19 18:04:30 2022 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=a6ac5b96
sci-biology/primer3: update EAPI 6 -> 8
Signed-off-by: David Seifert <soap <AT> gentoo.org>
...ystem.patch => primer3-2.3.7-buildsystem.patch} | 69 +++++++++++++++-------
...rimer3-2.3.7.ebuild => primer3-2.3.7-r1.ebuild} | 15 +++--
2 files changed, 54 insertions(+), 30 deletions(-)
diff --git a/sci-biology/primer3/files/primer3-2.3.4-buildsystem.patch b/sci-biology/primer3/files/primer3-2.3.7-buildsystem.patch
similarity index 83%
rename from sci-biology/primer3/files/primer3-2.3.4-buildsystem.patch
rename to 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 && $(MAKE)
+ endif
+
+ clean:
diff --git a/sci-biology/primer3/primer3-2.3.7.ebuild b/sci-biology/primer3/primer3-2.3.7-r1.ebuild
similarity index 77%
rename from sci-biology/primer3/primer3-2.3.7.ebuild
rename to sci-biology/primer3/primer3-2.3.7-r1.ebuild
index 4c6c9ce7bf44..b36e9291db94 100644
--- a/sci-biology/primer3/primer3-2.3.7.ebuild
+++ b/sci-biology/primer3/primer3-2.3.7-r1.ebuild
@@ -1,7 +1,7 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=6
+EAPI=8
inherit toolchain-funcs
@@ -13,12 +13,11 @@ LICENSE="GPL-2"
SLOT="0"
KEYWORDS="~amd64 ~ppc ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris"
-DEPEND="dev-lang/perl"
-RDEPEND=""
+BDEPEND="dev-lang/perl"
PATCHES=(
- "${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() {
^ permalink raw reply related [flat|nested] 2+ messages in thread
end of thread, other threads:[~2022-06-19 18:04 UTC | newest]
Thread overview: 2+ messages (download: mbox.gz follow: Atom feed
-- links below jump to the message on this page --
2022-06-19 18:04 [gentoo-commits] repo/gentoo:master commit in: sci-biology/primer3/, sci-biology/primer3/files/ David Seifert
-- strict thread matches above, loose matches on Subject: below --
2017-12-24 19:46 David Seifert
This is a public inbox, see mirroring instructions
for how to clone and mirror all data and code used for this inbox