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Mon, 10 Nov 2014 15:14:23 +0000 (UTC) From: "Justin Lecher" To: gentoo-commits@lists.gentoo.org Content-Transfer-Encoding: 8bit Content-type: text/plain; charset=UTF-8 Reply-To: gentoo-dev@lists.gentoo.org, "Justin Lecher" Message-ID: <1415629263.45e9860a0fc44c1194202dc3c0a45db80187f338.jlec@gentoo> Subject: [gentoo-commits] proj/sci:master commit in: sci-biology/proda/, sci-biology/proda/files/ X-VCS-Repository: proj/sci X-VCS-Files: sci-biology/proda/ChangeLog sci-biology/proda/files/proda-1.0-buildsystem.patch sci-biology/proda/files/proda-1.0-newgcc.patch sci-biology/proda/proda-1.0.ebuild X-VCS-Directories: sci-biology/proda/ sci-biology/proda/files/ X-VCS-Committer: jlec X-VCS-Committer-Name: Justin Lecher X-VCS-Revision: 45e9860a0fc44c1194202dc3c0a45db80187f338 X-VCS-Branch: master Date: Mon, 10 Nov 2014 15:14:23 +0000 (UTC) Precedence: bulk List-Post: List-Help: List-Unsubscribe: List-Subscribe: List-Id: Gentoo Linux mail X-BeenThere: gentoo-commits@lists.gentoo.org X-Archives-Salt: 0b540995-9e3c-4964-a8d4-70976c5bff43 X-Archives-Hash: 07cce986ff374abbc03a424a6a5bcf0c commit: 45e9860a0fc44c1194202dc3c0a45db80187f338 Author: Justin Lecher gentoo org> AuthorDate: Mon Nov 10 14:21:03 2014 +0000 Commit: Justin Lecher gentoo org> CommitDate: Mon Nov 10 14:21:03 2014 +0000 URL: http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=45e9860a sci-biology/proda: Bump EAPI; Update for newer compiler Package-Manager: portage-2.2.14 --- sci-biology/proda/ChangeLog | 6 +- .../proda/files/proda-1.0-buildsystem.patch | 35 ++++++ sci-biology/proda/files/proda-1.0-newgcc.patch | 136 +++++++++++++++++++++ sci-biology/proda/proda-1.0.ebuild | 27 ++-- 4 files changed, 191 insertions(+), 13 deletions(-) diff --git a/sci-biology/proda/ChangeLog b/sci-biology/proda/ChangeLog index 46cc65f..cedee64 100644 --- a/sci-biology/proda/ChangeLog +++ b/sci-biology/proda/ChangeLog @@ -1,7 +1,11 @@ # ChangeLog for sci-biology/proda -# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 10 Nov 2014; Justin Lecher proda-1.0.ebuild, + +files/proda-1.0-buildsystem.patch, +files/proda-1.0-newgcc.patch: + Bump EAPI; Update for newer compiler + 25 Jun 2011; Justin Lecher metadata.xml: Fixed herd entry in metadata.xml diff --git a/sci-biology/proda/files/proda-1.0-buildsystem.patch b/sci-biology/proda/files/proda-1.0-buildsystem.patch new file mode 100644 index 0000000..71836c4 --- /dev/null +++ b/sci-biology/proda/files/proda-1.0-buildsystem.patch @@ -0,0 +1,35 @@ + Makefile | 7 ++++--- + 1 file changed, 4 insertions(+), 3 deletions(-) + +diff --git a/Makefile b/Makefile +index 76824c4..746b925 100644 +--- a/Makefile ++++ b/Makefile +@@ -6,7 +6,7 @@ + # 1) Choose C++ compiler. + ################################################################################ + +-CXX = g++ ++CXX ?= g++ + + ################################################################################ + # 2) Set C++ flags. +@@ -18,7 +18,8 @@ CXX = g++ + OTHERFLAGS = -DVERSION="\"1.00\"" + + # debug mode +-CXXFLAGS = -g -W -Wall -pedantic $(OTHERFLAGS) ++CXXFLAGS ?= -g -W -Wall -pedantic ++CXXFLAGS += $(OTHERFLAGS) + + # profile mode + #CXXFLAGS = -pg -W -Wall -pedantic $(OTHERFLAGS) +@@ -38,7 +39,7 @@ OBJECTS = AlignedFragment.o Assert.o Block.o Consistency.o GlobalAlign.o LocalAl + all : $(TARGETS) + + proda : $(OBJECTS) +- $(CXX) $(CXXFLAGS) -lm $(OBJECTS) -o proda ++ $(CXX) $(CXXFLAGS) $(OBJECTS) -lm -o proda + + Assert.o: Assert.h + AlignedFragment.o: AlignedFragment.h Utilities.h diff --git a/sci-biology/proda/files/proda-1.0-newgcc.patch b/sci-biology/proda/files/proda-1.0-newgcc.patch new file mode 100644 index 0000000..3ac199a --- /dev/null +++ b/sci-biology/proda/files/proda-1.0-newgcc.patch @@ -0,0 +1,136 @@ + AlignedFragment.cc | 1 + + AlignedFragment.h | 2 ++ + Assert.cc | 2 +- + Assert.h | 4 ++-- + Block.cc | 1 + + Main.cc | 1 + + MultiSequence.cc | 2 +- + PairAligner.cc | 2 ++ + ProbModel.cc | 3 ++- + 9 files changed, 13 insertions(+), 5 deletions(-) + +diff --git a/AlignedFragment.cc b/AlignedFragment.cc +index b553862..9c734b9 100644 +--- a/AlignedFragment.cc ++++ b/AlignedFragment.cc +@@ -2,6 +2,7 @@ + // + ////////////////////////////////////////////////////////////////////// + ++#include + #include "AlignedFragment.h" + #include "Assert.h" + #include "Utilities.h" +diff --git a/AlignedFragment.h b/AlignedFragment.h +index ffc4642..17ae615 100644 +--- a/AlignedFragment.h ++++ b/AlignedFragment.h +@@ -8,6 +8,8 @@ + #define ALIGNFRAGMENT_H + + #include ++#include ++#include + + class Fragment; + class AlignedFragment; +diff --git a/Assert.cc b/Assert.cc +index ac9a7df..449e00a 100644 +--- a/Assert.cc ++++ b/Assert.cc +@@ -10,7 +10,7 @@ + // Write out assertion error message + ////////////////////////////////////////////////////////////////////// + +-int _ASSERT_FAILED (char *filename, int line_number, const char *error_msg){ ++int _ASSERT_FAILED (const char *filename, int line_number, const char *error_msg){ + fprintf (stderr, "Assertion failed in file \"%s\", line %d: %s\n", + filename, line_number, error_msg); + abort(); +diff --git a/Assert.h b/Assert.h +index 0222d17..069705b 100644 +--- a/Assert.h ++++ b/Assert.h +@@ -10,9 +10,9 @@ + int _ASSERT_FAILED (char *filename, int line_number, const char *error_msg); + + #ifdef NDEBUG +-#define ASSERT(test,error_msg) ++#define ASSERT(test, error_msg) + #else +-#define ASSERT(test,error_msg) (test ? 0 : _ASSERT_FAILED(__FILE__, __LINE__, error_msg)) ++#define ASSERT(test, error_msg) (test ? 0 : _ASSERT_FAILED(__FILE__, __LINE__, error_msg)) + #endif + + #endif +diff --git a/Block.cc b/Block.cc +index 35b050d..a24ad0e 100644 +--- a/Block.cc ++++ b/Block.cc +@@ -2,6 +2,7 @@ + // + ////////////////////////////////////////////////////////////////////// + ++#include + #include "Block.h" + #include "AlignedFragment.h" + #include "Sequence.h" +diff --git a/Main.cc b/Main.cc +index 8ceded3..7cf1b75 100644 +--- a/Main.cc ++++ b/Main.cc +@@ -5,6 +5,7 @@ + #include + #include + #include ++#include + #include + #include "Assert.h" + #include "MultiSequence.h" +diff --git a/MultiSequence.cc b/MultiSequence.cc +index 86e493f..2b70723 100644 +--- a/MultiSequence.cc ++++ b/MultiSequence.cc +@@ -386,7 +386,7 @@ void MultiSequence::WriteMFA (FILE *file) const { + ////////////////////////////////////////////////////////////////////// + + const char MultiSequence::ComputeAnnotation (const char *data, const int size) const { +- static char *groups[47] = { ++ static const char *groups[47] = { + + // Identities + "A", "B", "C", "D", "E", "F", "G", "H", "I", "J", "K", "L", "M", +diff --git a/PairAligner.cc b/PairAligner.cc +index 7fdc21f..8bbc4a5 100644 +--- a/PairAligner.cc ++++ b/PairAligner.cc +@@ -4,6 +4,8 @@ + // Implementation of PairAligner class + //////////////////////////////////////////////////////////////////// + ++#include ++#include + #include "PairAligner.h" + #include "Utilities.h" + #include "LocalAlign.h" +diff --git a/ProbModel.cc b/ProbModel.cc +index 6d74e3d..5d5a838 100644 +--- a/ProbModel.cc ++++ b/ProbModel.cc +@@ -4,6 +4,7 @@ + + #include + #include ++#include + #include "ProbModel.h" + #include "Utilities.h" + +@@ -30,7 +31,7 @@ const int TRANSITIONS[NUM_STATES][NUM_STATES] = { + { 0, 0, 0, 0, 0, 0, 1 } + }; + +-char *ALPHABET = "ARNDCQEGHILKMFPSTWYV"; ++const char *ALPHABET = "ARNDCQEGHILKMFPSTWYV"; + + + float INIT_A = 0.9860202074; diff --git a/sci-biology/proda/proda-1.0.ebuild b/sci-biology/proda/proda-1.0.ebuild index 7365765..5a35693 100644 --- a/sci-biology/proda/proda-1.0.ebuild +++ b/sci-biology/proda/proda-1.0.ebuild @@ -2,7 +2,9 @@ # Distributed under the terms of the GNU General Public License v2 # $Header: $ -inherit versionator +EAPI=5 + +inherit eutils flag-o-matic toolchain-funcs versionator MY_PV=$(replace_all_version_separators '_') @@ -12,21 +14,22 @@ SRC_URI="http://proda.stanford.edu/proda_${MY_PV}.tar.gz" LICENSE="public-domain" SLOT="0" -IUSE="" -KEYWORDS="~x86" +IUSE="debug " +KEYWORDS="~amd64 ~x86" -DEPEND="" -RDEPEND="" +S="${WORKDIR}"/${PN} -S="${WORKDIR}/${PN}" +PATCHES=( + "${FILESDIR}"/${P}-newgcc.patch + "${FILESDIR}"/${P}-buildsystem.patch + ) -src_unpack() { - unpack ${A} - sed -i -e 's/^\(CXXFLAGS =\)/#\1/' \ - -e 's/#CXXFLAGS = \(-O3.*$(OTHERFLAGS) -funroll-loops\)/CXXFLAGS := ${CXXFLAGS} \1/' \ - "${S}/Makefile" || die "sed failed" +src_prepare() { + epatch ${PATCHES[@]} + use debug || append-flags -DNDEBUG + tc-export CXX } src_install() { - dobin proda + dobin ${PN} }