From 90c88731bd036e5698b281fbc0a5f3aa4c9983ac Mon Sep 17 00:00:00 2001 From: V3n3RiX Date: Mon, 29 Jun 2020 11:38:31 +0100 Subject: gentoo resync : 29.06.2020 --- sci-biology/poa/Manifest | 5 ++-- sci-biology/poa/files/2-respect-flags.patch | 26 ----------------- sci-biology/poa/files/poa-2-fno-common.patch | 13 +++++++++ sci-biology/poa/files/poa-2-respect-flags.patch | 38 +++++++++++++++++++++++++ sci-biology/poa/poa-2-r1.ebuild | 28 +++++++++--------- 5 files changed, 68 insertions(+), 42 deletions(-) delete mode 100644 sci-biology/poa/files/2-respect-flags.patch create mode 100644 sci-biology/poa/files/poa-2-fno-common.patch create mode 100644 sci-biology/poa/files/poa-2-respect-flags.patch (limited to 'sci-biology/poa') 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/2-respect-flags.patch b/sci-biology/poa/files/2-respect-flags.patch deleted file mode 100644 index bdd638cf64b7..000000000000 --- a/sci-biology/poa/files/2-respect-flags.patch +++ /dev/null @@ -1,26 +0,0 @@ -diff --git a/Makefile b/Makefile -index a65bed0..713a7ab 100644 ---- a/Makefile -+++ b/Makefile -@@ -26,9 +26,10 @@ LIBOBJECTS= \ - 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= $(OPT_CFLAGS) -DUSE_WEIGHTED_LINKS -DUSE_PROJECT_HEADER -I. - # -I$(HOME)/lib/include - # -DREPORT_MAX_ALLOC - -@@ -44,7 +45,7 @@ liblpo.a: $(LIBOBJECTS) - - # NB: LIBRARY MUST FOLLOW OBJECTS OR LINK FAILS WITH UNRESOLVED REFERENCES!! - poa: $(OBJECTS) liblpo.a -- $(CC) -o $@ $(OBJECTS) -lm liblpo.a -+ $(CC) $(LDFLAGS) -o $@ $(OBJECTS) -lm liblpo.a - - what: - @echo poa: partial-order based sequence alignment program diff --git a/sci-biology/poa/files/poa-2-fno-common.patch b/sci-biology/poa/files/poa-2-fno-common.patch new file mode 100644 index 000000000000..ddd738a5524c --- /dev/null +++ b/sci-biology/poa/files/poa-2-fno-common.patch @@ -0,0 +1,13 @@ +--- a/black_flag.h ++++ b/black_flag.h +@@ -236,8 +236,8 @@ + int sourceline, + char sourcefile_revision[]); + +-char *Program_name; +-char *Program_version; ++extern char *Program_name; ++extern char *Program_version; + + void black_flag_init(char progname[],char progversion[]); + void black_flag_init_args(int narg,char *arg[],char progversion[]); diff --git a/sci-biology/poa/files/poa-2-respect-flags.patch b/sci-biology/poa/files/poa-2-respect-flags.patch new file mode 100644 index 000000000000..fb01f0b5f934 --- /dev/null +++ b/sci-biology/poa/files/poa-2-respect-flags.patch @@ -0,0 +1,38 @@ +--- a/Makefile ++++ b/Makefile +@@ -1,6 +1,3 @@ +- +-AR=ar rc +- + TARGETS=poa liblpo.a poa_doc libbflag.a + + # align_score.c CAN BE USED TO ADD CUSTOMIZED SCORING FUNCTIONS +@@ -26,9 +23,8 @@ + stringptr.o + + +-CC = gcc + #CFLAGS= -g -ansi-strict -W -Wall -DUSE_WEIGHTED_LINKS -DUSE_PROJECT_HEADER -I. +-CFLAGS= -g -DUSE_WEIGHTED_LINKS -DUSE_PROJECT_HEADER -I. ++CPPFLAGS+= -DUSE_WEIGHTED_LINKS -DUSE_PROJECT_HEADER -I. + # -I$(HOME)/lib/include + # -DREPORT_MAX_ALLOC + +@@ -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) $(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/." } -- cgit v1.2.3