- Update to 2.1

PR:		116017
Submitted by:	KATO Tsuguru <tkato432@yahoo.com>

7 files changed, 196 insertions, 18 deletions

diff --git a/biology/lamarc/Makefile b/biology/lamarc/Makefile
index cffd1d7a1f55..491e6b1cbfe3 100644
--- a/biology/lamarc/Makefile
+++ b/biology/lamarc/Makefile
@@ -6,22 +6,29 @@
 #
 
 PORTNAME=	lamarc
-PORTVERSION=	2001.08.06
-PORTREVISION=	1
+PORTVERSION=	2.1
+PORTEPOCH=	1
 CATEGORIES=	biology
-MASTER_SITES=	# empty
-DISTFILES=	# none
-EXTRACT_ONLY=	# empty
+MASTER_SITES=	http://evolution.gs.washington.edu/lamarc/download/
+EXTRACT_SUFX=	.src.tar.gz
 
 MAINTAINER=	ports@FreeBSD.org
 COMMENT=	A package of programs for computing population parameters
 
-RUN_DEPENDS=	fluctuate:${PORTSDIR}/biology/fluctuate \
-		migrate:${PORTSDIR}/biology/migrate \
-		recombine:${PORTSDIR}/biology/recombine
+USE_GNOME=	gnometarget
+GNU_CONFIGURE=	yes
 
-NO_BUILD=	yes
+.if defined(WITH_WXGTK2)
+USE_WX=		2.8
+CONFIGURE_ARGS+=	--with-wx-config=${WX_CONFIG}
+PLIST_SUB+=	WXGTK2=""
+.else
+CONFIGURE_ARGS+=	--disable-converter
+PLIST_SUB+=	WXGTK2="@comment "
+.endif
 
-do-install:	# empty
+.if defined(NOPORTDOCS)
+INSTALL_TARGET=	install-exec-am
+.endif
 
 .include <bsd.port.mk>
diff --git a/biology/lamarc/distinfo b/biology/lamarc/distinfo
new file mode 100644
index 000000000000..84334a8ec506
--- /dev/null
+++ b/biology/lamarc/distinfo
@@ -0,0 +1,3 @@
+MD5 (lamarc-2.1.src.tar.gz) = ed98383ed97acb99330d080a3b457ab0
+SHA256 (lamarc-2.1.src.tar.gz) = 3a17b6dec3c313193b48b94d0b4f8b3bbd01badb7f0c6f179aabbf3dfba625e2
+SIZE (lamarc-2.1.src.tar.gz) = 23427309
diff --git a/biology/lamarc/files/patch-Makefile.in b/biology/lamarc/files/patch-Makefile.in
new file mode 100644
index 000000000000..dd417d23d7db
--- /dev/null
+++ b/biology/lamarc/files/patch-Makefile.in
@@ -0,0 +1,65 @@
+--- Makefile.in.orig	Mon May  7 06:58:52 2007
++++ Makefile.in	Fri Aug 31 01:11:04 2007
+@@ -51,7 +51,7 @@
+ @OSX_APP_FALSE@am__append_8 = -ggdb
+ @NODATA_TRUE@am__append_9 = -DSTATIONARIES -DNOPROGRESSBAR
+ @DEBUG_TRUE@am__append_10 = $(debugflags)
+-@DEBUG_FALSE@am__append_11 = -O3 -funroll-loops -DNDEBUG
++@DEBUG_FALSE@am__append_11 = -DNDEBUG
+ @DMALLOC_TRUE@am__append_12 = -ldmallocxx
+ @DMALLOC_TRUE@am__append_13 = -DDMALLOC_FUNC_CHECK
+ @EFENCE_TRUE@am__append_14 = -lefence 
+@@ -1155,7 +1155,7 @@
+ CPPFLAGS = @CPPFLAGS@
+ CXX = @CXX@
+ CXXDEPMODE = @CXXDEPMODE@
+-CXXFLAGS = 
++CXXFLAGS = @CXXFLAGS@
+ CYGPATH_W = @CYGPATH_W@
+ DEBUG_FALSE = @DEBUG_FALSE@
+ DEBUG_TRUE = @DEBUG_TRUE@
+@@ -1994,7 +1994,7 @@
+ EXTRA_batch_lam_conv_SOURCES = $(tinyxml_suite)
+ lam_conv_app_SOURCES = 
+ lamarc_app_SOURCES = 
+-htmldir = $(prefix)/html/lamarc
++htmldir = $(prefix)/share/doc/lamarc
+ html_DATA = \
+ 			doc/html/bayes.html \
+ 			doc/html/bayes_howto.html \
+@@ -2037,7 +2037,7 @@
+ 			doc/html/viral_data.html \
+ 			doc/html/xmlinput.html
+ 
+-htmlimgdir = $(prefix)/html/lamarc/images
++htmlimgdir = $(prefix)/share/doc/lamarc/images
+ htmlimg_DATA = \
+ 			doc/html/images/browser-gtk.gif \
+ 			doc/html/images/correlated1.gif \
+@@ -2054,7 +2054,7 @@
+ 			doc/html/images/uncorrelated.gif \
+ 			doc/html/images/variably_correlated.gif
+ 
+-htmlbconvdir = $(prefix)/html/lamarc/batch_converter
++htmlbconvdir = $(prefix)/share/doc/lamarc/batch_converter
+ htmlbconv_DATA = \
+ 			doc/html/batch_converter/README.txt \
+ 			doc/html/batch_converter/chrom1_lamarc.xml \
+@@ -2068,7 +2068,7 @@
+ 			doc/html/batch_converter/exported-lamarc-input.xml \
+ 			doc/html/batch_converter/sample-conv-cmd.xml
+ 
+-htmlbconvimgdir = $(prefix)/html/lamarc/batch_converter/images
++htmlbconvimgdir = $(prefix)/share/doc/lamarc/batch_converter/images
+ htmlbconvimg_DATA = \
+ 			doc/html/batch_converter/images/lam_conv_chrom1_export_file_selection.png \
+ 			doc/html/batch_converter/images/lam_conv_chrom1_export_warn_1.png \
+@@ -2082,7 +2082,7 @@
+ 			doc/html/batch_converter/images/lam_conv_chrom3_region_table.png \
+ 			doc/html/batch_converter/images/lam_conv_chrom3_segment_snp.png
+ 
+-htmltraitdir = $(prefix)/html/lamarc/trait_mapping
++htmltraitdir = $(prefix)/share/doc/lamarc/trait_mapping
+ htmltrait_DATA = \
+ 			doc/html/trait_mapping/README.txt \
+ 			doc/html/trait_mapping/lamarc-trait-input.xml \
diff --git a/biology/lamarc/files/patch-configure b/biology/lamarc/files/patch-configure
new file mode 100644
index 000000000000..54c5317ec075
--- /dev/null
+++ b/biology/lamarc/files/patch-configure
@@ -0,0 +1,11 @@
+--- configure.orig	Wed May  2 05:59:05 2007
++++ configure	Thu Aug 30 18:26:42 2007
+@@ -1494,7 +1494,7 @@
+         OSTYPE=MACOSX
+         GUI_PKG=mac
+         ;;
+-    linux*)
++    freebsd*|linux*)
+         OSTYPE=LINUX
+         GUI_PKG=gtk2
+         ;;
diff --git a/biology/lamarc/files/patch-src__control__defaults.h b/biology/lamarc/files/patch-src__control__defaults.h
new file mode 100644
index 000000000000..6c28dc27649e
--- /dev/null
+++ b/biology/lamarc/files/patch-src__control__defaults.h
@@ -0,0 +1,11 @@
+--- src/control/defaults.h.orig	Sat Apr 28 04:56:55 2007
++++ src/control/defaults.h	Thu Aug 30 17:31:51 2007
+@@ -243,7 +243,7 @@
+   static const verbosity_type verbosity;
+   static const verbosity_type progress;
+ 
+-  static const long programstarttime;
++  static const time_t programstarttime;
+   static const long randomseed;
+ 
+   static const bool plotpost;
diff --git a/biology/lamarc/pkg-descr b/biology/lamarc/pkg-descr
index 27742c70aa62..c7f535b33e3e 100644
--- a/biology/lamarc/pkg-descr
+++ b/biology/lamarc/pkg-descr
@@ -4,10 +4,4 @@ such as population size, population growth rate and migration rates.  It does
 this by using likelihoods for samples of data (sequences, microsatellites,
 and electrophoretic polymorphisms) from populations.
 
-This port does not contain anything by itself; it is a "meta-port" which
-installs the four packages that make up LAMARC:  Coalesce, Fluctuate, Migrate
-and Recombine.
-
-WWW: http://evolution.genetics.washington.edu/lamarc.html
-
--- Johann Visagie <wjv@FreeBSD.org>
+WWW: http://evolution.genetics.washington.edu/lamarc/
diff --git a/biology/lamarc/pkg-plist b/biology/lamarc/pkg-plist
index 549a621fec0c..2408f836a7be 100644
--- a/biology/lamarc/pkg-plist
+++ b/biology/lamarc/pkg-plist
@@ -1 +1,88 @@
-@comment this plist intentionally left empty
+bin/lamarc
+%%WXGTK2%%bin/lam_conv
+%%PORTDOCS%%%%DOCSDIR%%/batch_converter/README.txt
+%%PORTDOCS%%%%DOCSDIR%%/batch_converter/chrom1.mig
+%%PORTDOCS%%%%DOCSDIR%%/batch_converter/chrom1_lamarc.xml
+%%PORTDOCS%%%%DOCSDIR%%/batch_converter/chrom2.mig
+%%PORTDOCS%%%%DOCSDIR%%/batch_converter/chrom2_lamarc.xml
+%%PORTDOCS%%%%DOCSDIR%%/batch_converter/chrom3_lamarc.xml
+%%PORTDOCS%%%%DOCSDIR%%/batch_converter/chrom3_phase_cmd.xml
+%%PORTDOCS%%%%DOCSDIR%%/batch_converter/chrom3microsat.mig
+%%PORTDOCS%%%%DOCSDIR%%/batch_converter/chrom3snp.mig
+%%PORTDOCS%%%%DOCSDIR%%/batch_converter/exported-lamarc-input.xml
+%%PORTDOCS%%%%DOCSDIR%%/batch_converter/images/lam_conv_chrom1_export_file_selection.png
+%%PORTDOCS%%%%DOCSDIR%%/batch_converter/images/lam_conv_chrom1_export_warn_1.png
+%%PORTDOCS%%%%DOCSDIR%%/batch_converter/images/lam_conv_chrom1_input.png
+%%PORTDOCS%%%%DOCSDIR%%/batch_converter/images/lam_conv_chrom1_segment_panel.png
+%%PORTDOCS%%%%DOCSDIR%%/batch_converter/images/lam_conv_chrom2_segment1.png
+%%PORTDOCS%%%%DOCSDIR%%/batch_converter/images/lam_conv_chrom3_error_map_position.png
+%%PORTDOCS%%%%DOCSDIR%%/batch_converter/images/lam_conv_chrom3_error_phase_file_needed.png
+%%PORTDOCS%%%%DOCSDIR%%/batch_converter/images/lam_conv_chrom3_input.png
+%%PORTDOCS%%%%DOCSDIR%%/batch_converter/images/lam_conv_chrom3_region_panel.png
+%%PORTDOCS%%%%DOCSDIR%%/batch_converter/images/lam_conv_chrom3_region_table.png
+%%PORTDOCS%%%%DOCSDIR%%/batch_converter/images/lam_conv_chrom3_segment_snp.png
+%%PORTDOCS%%%%DOCSDIR%%/batch_converter/sample-conv-cmd.xml
+%%PORTDOCS%%%%DOCSDIR%%/bayes.html
+%%PORTDOCS%%%%DOCSDIR%%/bayes_howto.html
+%%PORTDOCS%%%%DOCSDIR%%/changes.html
+%%PORTDOCS%%%%DOCSDIR%%/comparing_curvefiles.sxc
+%%PORTDOCS%%%%DOCSDIR%%/comparing_curvefiles.xls
+%%PORTDOCS%%%%DOCSDIR%%/compiling.html
+%%PORTDOCS%%%%DOCSDIR%%/converter.html
+%%PORTDOCS%%%%DOCSDIR%%/converter_cmd.html
+%%PORTDOCS%%%%DOCSDIR%%/curve-smoothing.html
+%%PORTDOCS%%%%DOCSDIR%%/data_models.html
+%%PORTDOCS%%%%DOCSDIR%%/data_required.html
+%%PORTDOCS%%%%DOCSDIR%%/forces.html
+%%PORTDOCS%%%%DOCSDIR%%/gamma.html
+%%PORTDOCS%%%%DOCSDIR%%/genetic_map.html
+%%PORTDOCS%%%%DOCSDIR%%/genotype.html
+%%PORTDOCS%%%%DOCSDIR%%/glossary.html
+%%PORTDOCS%%%%DOCSDIR%%/growthmenu.html
+%%PORTDOCS%%%%DOCSDIR%%/images/browser-gtk.gif
+%%PORTDOCS%%%%DOCSDIR%%/images/correlated1.gif
+%%PORTDOCS%%%%DOCSDIR%%/images/correlated2.gif
+%%PORTDOCS%%%%DOCSDIR%%/images/gui_lam_conv.gif
+%%PORTDOCS%%%%DOCSDIR%%/images/lam_conv.gif
+%%PORTDOCS%%%%DOCSDIR%%/images/lamarc.gif
+%%PORTDOCS%%%%DOCSDIR%%/images/loci-gtk.png
+%%PORTDOCS%%%%DOCSDIR%%/images/loci2-gtk.png
+%%PORTDOCS%%%%DOCSDIR%%/images/partitions-gtk.png
+%%PORTDOCS%%%%DOCSDIR%%/images/partitions2-gtk.png
+%%PORTDOCS%%%%DOCSDIR%%/images/populations-gtk.png
+%%PORTDOCS%%%%DOCSDIR%%/images/startup-gtk.png
+%%PORTDOCS%%%%DOCSDIR%%/images/uncorrelated.gif
+%%PORTDOCS%%%%DOCSDIR%%/images/variably_correlated.gif
+%%PORTDOCS%%%%DOCSDIR%%/index.html
+%%PORTDOCS%%%%DOCSDIR%%/insumfile.2reg3rep.xml
+%%PORTDOCS%%%%DOCSDIR%%/insumfile.3rep.xml
+%%PORTDOCS%%%%DOCSDIR%%/limitations.html
+%%PORTDOCS%%%%DOCSDIR%%/mapping.html
+%%PORTDOCS%%%%DOCSDIR%%/menu.html
+%%PORTDOCS%%%%DOCSDIR%%/messages.html
+%%PORTDOCS%%%%DOCSDIR%%/output.html
+%%PORTDOCS%%%%DOCSDIR%%/outsumfile.2reg3rep.xml
+%%PORTDOCS%%%%DOCSDIR%%/outsumfile.3rep.xml
+%%PORTDOCS%%%%DOCSDIR%%/overview.html
+%%PORTDOCS%%%%DOCSDIR%%/parallel.html
+%%PORTDOCS%%%%DOCSDIR%%/parameters.html
+%%PORTDOCS%%%%DOCSDIR%%/regions.html
+%%PORTDOCS%%%%DOCSDIR%%/search.html
+%%PORTDOCS%%%%DOCSDIR%%/tracer.html
+%%PORTDOCS%%%%DOCSDIR%%/trait_mapping/README.txt
+%%PORTDOCS%%%%DOCSDIR%%/trait_mapping/lamarc-trait-input.xml
+%%PORTDOCS%%%%DOCSDIR%%/trait_mapping/outfile.txt
+%%PORTDOCS%%%%DOCSDIR%%/trait_mapping/traitCmd.xml
+%%PORTDOCS%%%%DOCSDIR%%/trait_mapping/traitCmd.xml.txt
+%%PORTDOCS%%%%DOCSDIR%%/trait_mapping/traitData.mig
+%%PORTDOCS%%%%DOCSDIR%%/troubleshooting.html
+%%PORTDOCS%%%%DOCSDIR%%/tutorial.html
+%%PORTDOCS%%%%DOCSDIR%%/tutorial2.html
+%%PORTDOCS%%%%DOCSDIR%%/upcoming.html
+%%PORTDOCS%%%%DOCSDIR%%/viral_data.html
+%%PORTDOCS%%%%DOCSDIR%%/xmlinput.html
+%%PORTDOCS%%@dirrm %%DOCSDIR%%/trait_mapping
+%%PORTDOCS%%@dirrm %%DOCSDIR%%/images
+%%PORTDOCS%%@dirrm %%DOCSDIR%%/batch_converter/images
+%%PORTDOCS%%@dirrm %%DOCSDIR%%/batch_converter
+%%PORTDOCS%%@dirrm %%DOCSDIR%%