Revision: 145130 https://trac.macports.org/changeset/145130 Author: dstrubbe@macports.org Date: 2016-01-26 07:00:10 -0800 (Tue, 26 Jan 2016) Log Message: ----------- 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. Modified Paths: -------------- trunk/dports/science/eo/Portfile Added Paths: ----------- trunk/dports/science/eo/files/patch-rename-string.h.diff Removed Paths: ------------- trunk/dports/science/eo/files/patch-eoBit.h.diff trunk/dports/science/eo/files/patch-eoFileSnapshot.h.diff trunk/dports/science/eo/files/patch-eoGnuplot.cpp.diff trunk/dports/science/eo/files/patch-make_checkpoint.h.diff trunk/dports/science/eo/files/patch-make_checkpoint_FDC.h.diff trunk/dports/science/eo/files/patch-make_checkpoint_assembled.h.diff trunk/dports/science/eo/files/patch-make_checkpoint_pareto.h.diff trunk/dports/science/eo/files/patch-make_help.cpp.diff trunk/dports/science/eo/files/patch-test-t-eoSelect.cpp.diff Modified: trunk/dports/science/eo/Portfile =================================================================== --- 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) @@ -2,13 +2,14 @@ # $Id$ PortSystem 1.0 +PortGroup cmake 1.0 PortGroup compilers 1.0 name eo categories science license LGPL-2.1+ -version 1.0.1 -revision 2 +version 1.3.1 +revision 0 categories science math platforms darwin maintainers openmaintainer jochen @@ -25,53 +26,34 @@ homepage http://eodev.sourceforge.net/ master_sites sourceforge:eodev -use_bzip2 yes -checksums rmd160 33721e4a700f72a34cd69be1b488068bc54c5b79 \ - sha256 a8539dd9b48ddca153fa7f833da3e10fc923b0af51efae195b19b3613f617d89 +distname EO-${version} +use_zip yes +worksrcdir eo +checksums rmd160 d0882988b4e6debbe059bfd4183ced54bf0f2d1d \ + sha256 230886e0c857a8497b2e1c892ff2bfa1d9d4115199d9267b3bdb89ff0f846850 -default_variants +gnuplot +depends_lib port:gnuplot +#TODO: Add support for mpi, openmp, boost -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. +patchfiles patch-src-utils-eoGnuplot1DSnapshot.h.diff \ + patch-rename-string.h.diff -configure.args-append --disable-applications --disable-gnuplot --disable-tutorial +# see https://github.com/torognes/vsearch/issues/91 +post-patch { + file rename ${worksrcpath}/src/serial/String.h ${worksrcpath}/src/serial/serial_String.h +} +configure.args-append -DENABLE_CMAKE_TESTING:BOOL=ON + test.run yes -test.target check compilers.choose cc cxx -# TODO: Fix this project's buggy C++ code or file a bug upstream -compilers.setup -clang -dragonegg -gcc gcc45 -compiler.blacklist *clang* +compilers.setup -gcc44 -gcc45 -gcc46 -dragonegg -# clang++ gives: "error: use of undeclared identifier 'value'" +#gcc44 gcc45 gcc46 dragonegg: cc1: error: unrecognized command line option "-arch" -# gcc5: -#../../src/utils/eoStat.h:382:34: error: type 'eoDistanceStat<EOT>' is not a base type for type 'eoDistanceStat<EOT>' -# using eoDistanceStat< EOT >::value; +# gcc, clang: fails test 40 - t-eoIQRStat (Failed) -# 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 - # caused by gcc use of -ftree-vectorize -march=native -O3 # 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; \ # then mv -f ".deps/make_genotype_real.Tpo" ".deps/make_genotype_real.Po"; else rm -f ".deps/make_genotype_real.Tpo"; exit 1; fi @@ -82,45 +64,12 @@ # {standard input}:813:no such instruction: `vandpd %xmm2, %xmm0,%xmm0' # {standard input}:814:no such instruction: `vandnpd %xmm1, %xmm2,%xmm1' -# gcc44 test: FAIL: t-eoRandom - -#platform darwin { -# if {${os.major} >= 13} { -# depends_lib -# depends_run -# pre-fetch { -# ui_error "$name does not build on Mavericks or later." -# error "unsupported platform" -# } -# } +# There is no longer an option (as there was in 1.0.1) to install applications +#variant applications { +# license-append GPL-2+ +# configure.args-append --enable-applications +# configure.args-delete --disable-applications #} +# -variant applications { - license-append GPL-2+ - configure.args-append --enable-applications - configure.args-delete --disable-applications -} - -variant gnuplot { - depends_lib port:gnuplot - configure.args-append --enable-gnuplot - configure.args-delete --disable-gnuplot -} - -variant tutorial { - configure.args-append --enable-tutorial - configure.args-delete --disable-tutorial -} - -pre-configure { - configure.args-append CC=${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" - } -} - livecheck.distname eo Deleted: trunk/dports/science/eo/files/patch-eoBit.h.diff =================================================================== --- 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) @@ -1,10 +0,0 @@ ---- 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 Deleted: trunk/dports/science/eo/files/patch-eoFileSnapshot.h.diff =================================================================== --- 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) @@ -1,10 +0,0 @@ ---- 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> Deleted: trunk/dports/science/eo/files/patch-eoGnuplot.cpp.diff =================================================================== --- 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) @@ -1,10 +0,0 @@ ---- 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> - Deleted: trunk/dports/science/eo/files/patch-make_checkpoint.h.diff =================================================================== --- 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) @@ -1,11 +0,0 @@ ---- 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> Deleted: trunk/dports/science/eo/files/patch-make_checkpoint_FDC.h.diff =================================================================== --- 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) @@ -1,34 +0,0 @@ -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); Deleted: trunk/dports/science/eo/files/patch-make_checkpoint_assembled.h.diff =================================================================== --- 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) @@ -1,15 +0,0 @@ -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> - Deleted: trunk/dports/science/eo/files/patch-make_checkpoint_pareto.h.diff =================================================================== --- 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) @@ -1,17 +0,0 @@ -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" Deleted: trunk/dports/science/eo/files/patch-make_help.cpp.diff =================================================================== --- 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) @@ -1,16 +0,0 @@ ---- 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 Added: trunk/dports/science/eo/files/patch-rename-string.h.diff =================================================================== --- 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) @@ -0,0 +1,55 @@ +--- 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 + { Deleted: trunk/dports/science/eo/files/patch-test-t-eoSelect.cpp.diff =================================================================== --- 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) @@ -1,10 +0,0 @@ ---- 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>