[gentoo-commits] proj/sci:master commit in: sci-biology/proda/, sci-biology/proda/files/

[gentoo-commits] proj/sci:master commit in: sci-biology/proda/, sci-biology/proda/files/

[Justin Lecher]

commit:     45e9860a0fc44c1194202dc3c0a45db80187f338
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Nov 10 14:21:03 2014 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> 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 <jlec@gentoo.org> 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 <jlec@gentoo.org> 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 <stdlib.h>
+ #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 <vector>
++#include <string.h>
++#include <stdio.h>
+ 
+ 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 <stdlib.h>
+ #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 <stdio.h>
+ #include <stdlib.h>
+ #include <string.h>
++#include <limits.h>
+ #include <vector>
+ #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 <string.h>
++#include <stdlib.h>
+ #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 <stdio.h>
+ #include <ctype.h>
++#include <string.h>
+ #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}
 }