ports/116017: Update port: biology/lamarc to 2.1
KATO Tsuguru
tkato432 at yahoo.com
Sun Sep 2 17:10:05 UTC 2007
>Number: 116017
>Category: ports
>Synopsis: Update port: biology/lamarc to 2.1
>Confidential: no
>Severity: non-critical
>Priority: low
>Responsible: freebsd-ports-bugs
>State: open
>Quarter:
>Keywords:
>Date-Required:
>Class: change-request
>Submitter-Id: current-users
>Arrival-Date: Sun Sep 02 17:10:04 GMT 2007
>Closed-Date:
>Last-Modified:
>Originator: KATO Tsuguru
>Release: FreeBSD 6.2-RELEASE-p7 i386
>Organization:
>Environment:
>Description:
- Update to version 2.1
New file:
distinfo
files/patch-Makefile.in
files/patch-configure
files/patch-src__control__defaults.h
>How-To-Repeat:
>Fix:
diff -urN /usr/ports/biology/lamarc/Makefile biology/lamarc/Makefile
--- /usr/ports/biology/lamarc/Makefile Thu Jan 25 20:10:43 2007
+++ biology/lamarc/Makefile Fri Aug 31 02:58:06 2007
@@ -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 at 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 -urN /usr/ports/biology/lamarc/distinfo biology/lamarc/distinfo
--- /usr/ports/biology/lamarc/distinfo Thu Jan 1 09:00:00 1970
+++ biology/lamarc/distinfo Thu Aug 30 13:26:41 2007
@@ -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 -urN /usr/ports/biology/lamarc/files/patch-Makefile.in biology/lamarc/files/patch-Makefile.in
--- /usr/ports/biology/lamarc/files/patch-Makefile.in Thu Jan 1 09:00:00 1970
+++ biology/lamarc/files/patch-Makefile.in Fri Aug 31 01:11:13 2007
@@ -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 at am__append_8 = -ggdb
+ @NODATA_TRUE at am__append_9 = -DSTATIONARIES -DNOPROGRESSBAR
+ @DEBUG_TRUE at am__append_10 = $(debugflags)
+- at DEBUG_FALSE@am__append_11 = -O3 -funroll-loops -DNDEBUG
++ at DEBUG_FALSE@am__append_11 = -DNDEBUG
+ @DMALLOC_TRUE at am__append_12 = -ldmallocxx
+ @DMALLOC_TRUE at am__append_13 = -DDMALLOC_FUNC_CHECK
+ @EFENCE_TRUE at 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 -urN /usr/ports/biology/lamarc/files/patch-configure biology/lamarc/files/patch-configure
--- /usr/ports/biology/lamarc/files/patch-configure Thu Jan 1 09:00:00 1970
+++ biology/lamarc/files/patch-configure Thu Aug 30 18:26:53 2007
@@ -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 -urN /usr/ports/biology/lamarc/files/patch-src__control__defaults.h biology/lamarc/files/patch-src__control__defaults.h
--- /usr/ports/biology/lamarc/files/patch-src__control__defaults.h Thu Jan 1 09:00:00 1970
+++ biology/lamarc/files/patch-src__control__defaults.h Thu Aug 30 18:27:59 2007
@@ -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 -urN /usr/ports/biology/lamarc/pkg-descr biology/lamarc/pkg-descr
--- /usr/ports/biology/lamarc/pkg-descr Tue Aug 7 17:17:58 2001
+++ biology/lamarc/pkg-descr Thu Aug 30 01:14:15 2007
@@ -4,10 +4,4 @@
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 at FreeBSD.org>
+WWW: http://evolution.genetics.washington.edu/lamarc/
diff -urN /usr/ports/biology/lamarc/pkg-plist biology/lamarc/pkg-plist
--- /usr/ports/biology/lamarc/pkg-plist Tue Aug 7 17:17:58 2001
+++ biology/lamarc/pkg-plist Fri Aug 31 02:57:31 2007
@@ -1 +1,88 @@
- at 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%%
>Release-Note:
>Audit-Trail:
>Unformatted:
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