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<title>[145130] trunk/dports/science/eo</title>
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<dl class="meta">
<dt>Revision</dt> <dd><a href="https://trac.macports.org/changeset/145130">145130</a></dd>
<dt>Author</dt> <dd>dstrubbe@macports.org</dd>
<dt>Date</dt> <dd>2016-01-26 07:00:10 -0800 (Tue, 26 Jan 2016)</dd>
</dl>
<h3>Log Message</h3>
<pre>eo: Update to 1.3.1. Now uses cmake, has somewhat different archive and directory names. Most patches not required, can now use clang with a patch. gnuplot is now required, no options to install applications.</pre>
<h3>Modified Paths</h3>
<ul>
<li><a href="#trunkdportsscienceeoPortfile">trunk/dports/science/eo/Portfile</a></li>
</ul>
<h3>Added Paths</h3>
<ul>
<li><a href="#trunkdportsscienceeofilespatchrenamestringhdiff">trunk/dports/science/eo/files/patch-rename-string.h.diff</a></li>
</ul>
<h3>Removed Paths</h3>
<ul>
<li><a href="#trunkdportsscienceeofilespatcheoBithdiff">trunk/dports/science/eo/files/patch-eoBit.h.diff</a></li>
<li><a href="#trunkdportsscienceeofilespatcheoFileSnapshothdiff">trunk/dports/science/eo/files/patch-eoFileSnapshot.h.diff</a></li>
<li><a href="#trunkdportsscienceeofilespatcheoGnuplotcppdiff">trunk/dports/science/eo/files/patch-eoGnuplot.cpp.diff</a></li>
<li><a href="#trunkdportsscienceeofilespatchmake_checkpointhdiff">trunk/dports/science/eo/files/patch-make_checkpoint.h.diff</a></li>
<li><a href="#trunkdportsscienceeofilespatchmake_checkpoint_FDChdiff">trunk/dports/science/eo/files/patch-make_checkpoint_FDC.h.diff</a></li>
<li><a href="#trunkdportsscienceeofilespatchmake_checkpoint_assembledhdiff">trunk/dports/science/eo/files/patch-make_checkpoint_assembled.h.diff</a></li>
<li><a href="#trunkdportsscienceeofilespatchmake_checkpoint_paretohdiff">trunk/dports/science/eo/files/patch-make_checkpoint_pareto.h.diff</a></li>
<li><a href="#trunkdportsscienceeofilespatchmake_helpcppdiff">trunk/dports/science/eo/files/patch-make_help.cpp.diff</a></li>
<li><a href="#trunkdportsscienceeofilespatchtestteoSelectcppdiff">trunk/dports/science/eo/files/patch-test-t-eoSelect.cpp.diff</a></li>
</ul>
</div>
<div id="patch">
<h3>Diff</h3>
<a id="trunkdportsscienceeoPortfile"></a>
<div class="modfile"><h4>Modified: trunk/dports/science/eo/Portfile (145129 => 145130)</h4>
<pre class="diff"><span>
<span class="info">--- trunk/dports/science/eo/Portfile 2016-01-26 14:58:33 UTC (rev 145129)
+++ trunk/dports/science/eo/Portfile 2016-01-26 15:00:10 UTC (rev 145130)
</span><span class="lines">@@ -2,13 +2,14 @@
</span><span class="cx"> # $Id$
</span><span class="cx">
</span><span class="cx"> PortSystem 1.0
</span><ins>+PortGroup cmake 1.0
</ins><span class="cx"> PortGroup compilers 1.0
</span><span class="cx">
</span><span class="cx"> name eo
</span><span class="cx"> categories science
</span><span class="cx"> license LGPL-2.1+
</span><del>-version 1.0.1
-revision 2
</del><ins>+version 1.3.1
+revision 0
</ins><span class="cx"> categories science math
</span><span class="cx"> platforms darwin
</span><span class="cx"> maintainers openmaintainer jochen
</span><span class="lines">@@ -25,53 +26,34 @@
</span><span class="cx">
</span><span class="cx"> homepage http://eodev.sourceforge.net/
</span><span class="cx"> master_sites sourceforge:eodev
</span><del>-use_bzip2 yes
-checksums rmd160 33721e4a700f72a34cd69be1b488068bc54c5b79 \
- sha256 a8539dd9b48ddca153fa7f833da3e10fc923b0af51efae195b19b3613f617d89
</del><ins>+distname EO-${version}
+use_zip yes
+worksrcdir eo
+checksums rmd160 d0882988b4e6debbe059bfd4183ced54bf0f2d1d \
+ sha256 230886e0c857a8497b2e1c892ff2bfa1d9d4115199d9267b3bdb89ff0f846850
</ins><span class="cx">
</span><del>-default_variants +gnuplot
</del><ins>+depends_lib port:gnuplot
+#TODO: Add support for mpi, openmp, boost
</ins><span class="cx">
</span><del>-patchfiles patch-eoBit.h.diff \
- patch-eoFileSnapshot.h.diff \
- patch-eoGnuplot.cpp.diff \
- patch-make_checkpoint.h.diff \
- patch-make_checkpoint_assembled.h.diff \
- patch-make_checkpoint_FDC.h.diff \
- patch-make_checkpoint_pareto.h.diff \
- patch-make_help.cpp.diff \
- patch-test-t-eoSelect.cpp.diff \
- patch-src-utils-eoGnuplot1DSnapshot.h.diff
-# last is required for 'port test' with a GCC compiler.
</del><ins>+patchfiles patch-src-utils-eoGnuplot1DSnapshot.h.diff \
+ patch-rename-string.h.diff
</ins><span class="cx">
</span><del>-configure.args-append --disable-applications --disable-gnuplot --disable-tutorial
</del><ins>+# see https://github.com/torognes/vsearch/issues/91
+post-patch {
+ file rename ${worksrcpath}/src/serial/String.h ${worksrcpath}/src/serial/serial_String.h
+}
</ins><span class="cx">
</span><ins>+configure.args-append -DENABLE_CMAKE_TESTING:BOOL=ON
+
</ins><span class="cx"> test.run yes
</span><del>-test.target check
</del><span class="cx">
</span><span class="cx"> compilers.choose cc cxx
</span><del>-# TODO: Fix this project's buggy C++ code or file a bug upstream
-compilers.setup -clang -dragonegg -gcc gcc45
-compiler.blacklist *clang*
</del><ins>+compilers.setup -gcc44 -gcc45 -gcc46 -dragonegg
</ins><span class="cx">
</span><del>-# clang++ gives: "error: use of undeclared identifier 'value'"
</del><ins>+#gcc44 gcc45 gcc46 dragonegg: cc1: error: unrecognized command line option "-arch"
</ins><span class="cx">
</span><del>-# gcc5:
-#../../src/utils/eoStat.h:382:34: error: type 'eoDistanceStat<EOT>' is not a base type for type 'eoDistanceStat<EOT>'
-# using eoDistanceStat< EOT >::value;
</del><ins>+# gcc, clang: fails test 40 - t-eoIQRStat (Failed)
</ins><span class="cx">
</span><del>-# gcc46, gcc47, dragonegg33, dragonegg34:
-# eoFunctorStore.cpp: In destructor 'virtual eoFunctorStore::~eoFunctorStore()':
-# eoFunctorStore.cpp:13:9: error: 'size_t' was not declared in this scope
-# eoFunctorStore.cpp:13:9: note: suggested alternatives:
-# In file included from /opt/local/include/gcc47/c++/bits/stl_algobase.h:60:0,
-# from /opt/local/include/gcc47/c++/vector:61,
-# from ./eoFunctorStore.h:30,
-# from eoFunctorStore.cpp:6:
-# /opt/local/include/gcc47/c++//x86_64-apple-darwin14/bits/c++config.h:173:26: note: 'std::size_t'
-# /opt/local/include/gcc47/c++//x86_64-apple-darwin14/bits/c++config.h:173:26: note: 'std::size_t'
-# eoFunctorStore.cpp:13:16: error: expected ';' before 'i'
-# eoFunctorStore.cpp:13:23: error: 'i' was not declared in this scope
-
</del><span class="cx"> # caused by gcc use of -ftree-vectorize -march=native -O3
</span><span class="cx"> # if /opt/local/bin/g++-mp-4.4 -DHAVE_CONFIG_H -I. -I. -I../.. -I/opt/local/include -I../../src -pipe -Os -fpermissive -ftree-vectorize -march=native -O3 -MT make_genotype_real.o -MD -MP -MF ".deps/make_genotype_real.Tpo" -c -o make_genotype_real.o make_genotype_real.cpp; \
</span><span class="cx"> # then mv -f ".deps/make_genotype_real.Tpo" ".deps/make_genotype_real.Po"; else rm -f ".deps/make_genotype_real.Tpo"; exit 1; fi
</span><span class="lines">@@ -82,45 +64,12 @@
</span><span class="cx"> # {standard input}:813:no such instruction: `vandpd %xmm2, %xmm0,%xmm0'
</span><span class="cx"> # {standard input}:814:no such instruction: `vandnpd %xmm1, %xmm2,%xmm1'
</span><span class="cx">
</span><del>-# gcc44 test: FAIL: t-eoRandom
-
-#platform darwin {
-# if {${os.major} >= 13} {
-# depends_lib
-# depends_run
-# pre-fetch {
-# ui_error "$name does not build on Mavericks or later."
-# error "unsupported platform"
-# }
-# }
</del><ins>+# There is no longer an option (as there was in 1.0.1) to install applications
+#variant applications {
+# license-append GPL-2+
+# configure.args-append --enable-applications
+# configure.args-delete --disable-applications
</ins><span class="cx"> #}
</span><ins>+#
</ins><span class="cx">
</span><del>-variant applications {
- license-append GPL-2+
- configure.args-append --enable-applications
- configure.args-delete --disable-applications
-}
-
-variant gnuplot {
- depends_lib port:gnuplot
- configure.args-append --enable-gnuplot
- configure.args-delete --disable-gnuplot
-}
-
-variant tutorial {
- configure.args-append --enable-tutorial
- configure.args-delete --disable-tutorial
-}
-
-pre-configure {
- configure.args-append CC=${configure.cc} CFLAGS="${configure.cflags}" \
- CXX=${configure.cxx}
-
- if {[gcc_variant_isset]} {
- configure.cxxflags-append "-fpermissive"
-# configure.cflags-append "-ftree-vectorize -march=native -O3"
-# configure.cxxflags-append "-ftree-vectorize -march=native -O3"
- }
-}
-
</del><span class="cx"> livecheck.distname eo
</span></span></pre></div>
<a id="trunkdportsscienceeofilespatcheoBithdiff"></a>
<div class="delfile"><h4>Deleted: trunk/dports/science/eo/files/patch-eoBit.h.diff (145129 => 145130)</h4>
<pre class="diff"><span>
<span class="info">--- trunk/dports/science/eo/files/patch-eoBit.h.diff 2016-01-26 14:58:33 UTC (rev 145129)
+++ trunk/dports/science/eo/files/patch-eoBit.h.diff 2016-01-26 15:00:10 UTC (rev 145130)
</span><span class="lines">@@ -1,10 +0,0 @@
</span><del>---- src/ga/eoBit.h 2008-03-31 21:18:37.000000000 +0200
-+++ src/ga/eoBit.h 2008-03-31 21:08:17.000000000 +0200
-@@ -35,6 +35,7 @@
-
- //-----------------------------------------------------------------------------
-
-+#include <algorithm>
- #include <iostream> // std::ostream, std::istream
- #include <functional> // bind2nd
- #include <string> // std::string
</del></span></pre></div>
<a id="trunkdportsscienceeofilespatcheoFileSnapshothdiff"></a>
<div class="delfile"><h4>Deleted: trunk/dports/science/eo/files/patch-eoFileSnapshot.h.diff (145129 => 145130)</h4>
<pre class="diff"><span>
<span class="info">--- trunk/dports/science/eo/files/patch-eoFileSnapshot.h.diff 2016-01-26 14:58:33 UTC (rev 145129)
+++ trunk/dports/science/eo/files/patch-eoFileSnapshot.h.diff 2016-01-26 15:00:10 UTC (rev 145130)
</span><span class="lines">@@ -1,10 +0,0 @@
</span><del>---- src/utils/eoFileSnapshot.h 2008-03-31 21:21:34.000000000 +0200
-+++ src/utils/eoFileSnapshot.h 2008-03-31 21:08:17.000000000 +0200
-@@ -27,6 +27,7 @@
- #ifndef _eoFileSnapshot_h
- #define _eoFileSnapshot_h
-
-+#include <cstdlib>
- #include <string>
- #include <fstream>
- #include <utils/eoParam.h>
</del></span></pre></div>
<a id="trunkdportsscienceeofilespatcheoGnuplotcppdiff"></a>
<div class="delfile"><h4>Deleted: trunk/dports/science/eo/files/patch-eoGnuplot.cpp.diff (145129 => 145130)</h4>
<pre class="diff"><span>
<span class="info">--- trunk/dports/science/eo/files/patch-eoGnuplot.cpp.diff 2016-01-26 14:58:33 UTC (rev 145129)
+++ trunk/dports/science/eo/files/patch-eoGnuplot.cpp.diff 2016-01-26 15:00:10 UTC (rev 145130)
</span><span class="lines">@@ -1,10 +0,0 @@
</span><del>---- src/utils/eoGnuplot.cpp 2008-03-31 21:25:16.000000000 +0200
-+++ src/utils/eoGnuplot.cpp 2008-03-31 21:08:17.000000000 +0200
-@@ -24,6 +24,7 @@
- #include <config.h>
- #endif
-
-+#include <cstring>
- #include <sstream>
- #include <stdexcept>
-
</del></span></pre></div>
<a id="trunkdportsscienceeofilespatchmake_checkpointhdiff"></a>
<div class="delfile"><h4>Deleted: trunk/dports/science/eo/files/patch-make_checkpoint.h.diff (145129 => 145130)</h4>
<pre class="diff"><span>
<span class="info">--- trunk/dports/science/eo/files/patch-make_checkpoint.h.diff 2016-01-26 14:58:33 UTC (rev 145129)
+++ trunk/dports/science/eo/files/patch-make_checkpoint.h.diff 2016-01-26 15:00:10 UTC (rev 145130)
</span><span class="lines">@@ -1,11 +0,0 @@
</span><del>---- src/do/make_checkpoint.h.orig 2008-03-31 15:37:21.000000000 +0200
-+++ src/do/make_checkpoint.h 2008-03-31 15:37:46.000000000 +0200
-@@ -27,6 +27,8 @@
- #ifndef _make_checkpoint_h
- #define _make_checkpoint_h
-
-+#include<climits>
-+
- #include <eoScalarFitness.h>
- #include <utils/selectors.h> // for minimizing_fitness()
- #include <EO.h>
</del></span></pre></div>
<a id="trunkdportsscienceeofilespatchmake_checkpoint_FDChdiff"></a>
<div class="delfile"><h4>Deleted: trunk/dports/science/eo/files/patch-make_checkpoint_FDC.h.diff (145129 => 145130)</h4>
<pre class="diff"><span>
<span class="info">--- trunk/dports/science/eo/files/patch-make_checkpoint_FDC.h.diff 2016-01-26 14:58:33 UTC (rev 145129)
+++ trunk/dports/science/eo/files/patch-make_checkpoint_FDC.h.diff 2016-01-26 15:00:10 UTC (rev 145130)
</span><span class="lines">@@ -1,34 +0,0 @@
</span><del>-Index: src/do/make_checkpoint_FDC.h
-===================================================================
-RCS file: /cvsroot/eodev/eo/src/do/make_checkpoint_FDC.h,v
-retrieving revision 1.3
-diff -u -r1.3 make_checkpoint_FDC.h
---- src/do/make_checkpoint_FDC.h 27 Feb 2003 19:25:25 -0000 1.3
-+++ src/do/make_checkpoint_FDC.h 31 Mar 2008 13:21:10 -0000
-@@ -3,7 +3,7 @@
- //-----------------------------------------------------------------------------
- // make_checkpoint.h
- // (c) Maarten Keijzer, Marc Schoenauer and GeNeura Team, 2000
--/*
-+/*
- This library is free software; you can redistribute it and/or
- modify it under the terms of the GNU Lesser General Public
- License as published by the Free Software Foundation; either
-@@ -27,6 +27,8 @@
- #ifndef _make_checkpoint_h
- #define _make_checkpoint_h
-
-+#include <climits>
-+
- #include <eoScalarFitness.h>
- #include <utils/selectors.h> // for minimizing_fitness()
- #include <EO.h>
-@@ -56,7 +58,7 @@
- eoValueParam<unsigned> *generationCounter = new eoValueParam<unsigned>(0, "Gen.");
- // Create an incrementor (sub-class of eoUpdater).
- eoIncrementor<unsigned>* increment = new eoIncrementor<unsigned>(generationCounter->value());
-- // Add it to the checkpoint,
-+ // Add it to the checkpoint,
- checkpoint->add(*increment);
- // and store it in the state
- _state.storeFunctor(increment);
</del></span></pre></div>
<a id="trunkdportsscienceeofilespatchmake_checkpoint_assembledhdiff"></a>
<div class="delfile"><h4>Deleted: trunk/dports/science/eo/files/patch-make_checkpoint_assembled.h.diff (145129 => 145130)</h4>
<pre class="diff"><span>
<span class="info">--- trunk/dports/science/eo/files/patch-make_checkpoint_assembled.h.diff 2016-01-26 14:58:33 UTC (rev 145129)
+++ trunk/dports/science/eo/files/patch-make_checkpoint_assembled.h.diff 2016-01-26 15:00:10 UTC (rev 145130)
</span><span class="lines">@@ -1,15 +0,0 @@
</span><del>-Index: src/do/make_checkpoint_assembled.h
-===================================================================
-RCS file: /cvsroot/eodev/eo/src/do/make_checkpoint_assembled.h,v
-retrieving revision 1.5
-diff -u -r1.5 make_checkpoint_assembled.h
---- src/do/make_checkpoint_assembled.h 19 Sep 2007 11:42:24 -0000 1.5
-+++ src/do/make_checkpoint_assembled.h 31 Mar 2008 13:21:24 -0000
-@@ -34,6 +34,7 @@
- #include <config.h>
- #endif
-
-+#include <climits>
- #include <vector>
- #include <string>
-
</del></span></pre></div>
<a id="trunkdportsscienceeofilespatchmake_checkpoint_paretohdiff"></a>
<div class="delfile"><h4>Deleted: trunk/dports/science/eo/files/patch-make_checkpoint_pareto.h.diff (145129 => 145130)</h4>
<pre class="diff"><span>
<span class="info">--- trunk/dports/science/eo/files/patch-make_checkpoint_pareto.h.diff 2016-01-26 14:58:33 UTC (rev 145129)
+++ trunk/dports/science/eo/files/patch-make_checkpoint_pareto.h.diff 2016-01-26 15:00:10 UTC (rev 145130)
</span><span class="lines">@@ -1,17 +0,0 @@
</span><del>-Index: src/do/make_checkpoint_pareto.h
-===================================================================
-RCS file: /cvsroot/eodev/eo/src/do/make_checkpoint_pareto.h,v
-retrieving revision 1.10
-diff -u -r1.10 make_checkpoint_pareto.h
---- src/do/make_checkpoint_pareto.h 10 Oct 2005 13:34:21 -0000 1.10
-+++ src/do/make_checkpoint_pareto.h 31 Mar 2008 13:22:07 -0000
-@@ -27,7 +27,8 @@
- #ifndef _make_checkpoint_pareto_h
- #define _make_checkpoint_pareto_h
-
--#include <stdlib.h>
-+#include <climits>
-+#include <cstdlib>
- #include <sstream>
-
- #include "EO.h"
</del></span></pre></div>
<a id="trunkdportsscienceeofilespatchmake_helpcppdiff"></a>
<div class="delfile"><h4>Deleted: trunk/dports/science/eo/files/patch-make_help.cpp.diff (145129 => 145130)</h4>
<pre class="diff"><span>
<span class="info">--- trunk/dports/science/eo/files/patch-make_help.cpp.diff 2016-01-26 14:58:33 UTC (rev 145129)
+++ trunk/dports/science/eo/files/patch-make_help.cpp.diff 2016-01-26 15:00:10 UTC (rev 145130)
</span><span class="lines">@@ -1,16 +0,0 @@
</span><del>---- src/utils/make_help.cpp 2008-03-31 21:26:37.000000000 +0200
-+++ src/utils/make_help.cpp 2008-03-31 21:08:17.000000000 +0200
-@@ -28,10 +28,12 @@
- #pragma warning(disable:4786)
- #endif
-
-+#include <cstdlib>
--#include <utils/eoParser.h>
- #include <fstream>
- #include <stdexcept>
-
-+#include <utils/eoParser.h>
-+
- using namespace std;
-
- /** Generation of the status file, and output of the help message if needed
</del></span></pre></div>
<a id="trunkdportsscienceeofilespatchrenamestringhdiff"></a>
<div class="addfile"><h4>Added: trunk/dports/science/eo/files/patch-rename-string.h.diff (0 => 145130)</h4>
<pre class="diff"><span>
<span class="info">--- trunk/dports/science/eo/files/patch-rename-string.h.diff (rev 0)
+++ trunk/dports/science/eo/files/patch-rename-string.h.diff 2016-01-26 15:00:10 UTC (rev 145130)
</span><span class="lines">@@ -0,0 +1,55 @@
</span><ins>+--- src/serial/eoSerial.h.orig 2016-01-26 15:26:43.000000000 +0100
++++ src/serial/eoSerial.h 2016-01-26 15:24:02.000000000 +0100
+@@ -26,7 +26,7 @@
+ # include "Serializable.h"
+ # include "Array.h"
+ # include "Object.h"
+-# include "String.h"
++# include "serial_String.h"
+ # include "Parser.h"
+ # include "Utils.h"
+
+--- src/serial/Parser.h.orig 2016-01-26 15:26:49.000000000 +0100
++++ src/serial/Parser.h 2016-01-26 15:24:11.000000000 +0100
+@@ -23,7 +23,7 @@
+ # define __EOSERIAL_PARSER_H__
+
+ # include "Entity.h"
+-# include "String.h"
++# include "serial_String.h"
+ # include "Object.h"
+
+ /**
+--- src/serial/Parser.cpp.orig 2016-01-26 15:26:50.000000000 +0100
++++ src/serial/Parser.cpp 2016-01-26 15:24:17.000000000 +0100
+@@ -25,7 +25,7 @@
+
+ # include "Array.h"
+ # include "Object.h"
+-# include "String.h"
++# include "serial_String.h"
+
+ // in debug mode only
+ // # define DEBUG(x) std::cout << x << std::endl;
+--- src/serial/String.cpp.orig 2016-01-26 15:26:57.000000000 +0100
++++ src/serial/String.cpp 2016-01-26 15:24:28.000000000 +0100
+@@ -19,7 +19,7 @@
+ Authors:
+ Benjamin Bouvier <benjamin.bouvier@gmail.com>
+ */
+-# include "String.h"
++# include "serial_String.h"
+
+ namespace eoserial
+ {
+--- src/serial/Utils.h.orig 2016-01-26 15:26:59.000000000 +0100
++++ src/serial/Utils.h 2016-01-26 15:24:37.000000000 +0100
+@@ -24,7 +24,7 @@
+
+ # include "Array.h"
+ # include "Object.h"
+-# include "String.h"
++# include "serial_String.h"
+
+ namespace eoserial
+ {
</ins></span></pre></div>
<a id="trunkdportsscienceeofilespatchtestteoSelectcppdiff"></a>
<div class="delfile"><h4>Deleted: trunk/dports/science/eo/files/patch-test-t-eoSelect.cpp.diff (145129 => 145130)</h4>
<pre class="diff"><span>
<span class="info">--- trunk/dports/science/eo/files/patch-test-t-eoSelect.cpp.diff 2016-01-26 14:58:33 UTC (rev 145129)
+++ trunk/dports/science/eo/files/patch-test-t-eoSelect.cpp.diff 2016-01-26 15:00:10 UTC (rev 145130)
</span><span class="lines">@@ -1,10 +0,0 @@
</span><del>---- test/t-eoSelect.cpp.orig 2016-01-26 11:34:44.000000000 +0100
-+++ test/t-eoSelect.cpp 2016-01-26 11:34:35.000000000 +0100
-@@ -6,6 +6,7 @@
- #endif
-
- #include <stdexcept> // runtime_error
-+#include <cstring>
-
- // general
- #include <eo>
</del></span></pre>
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