ports/117336: Update port: biology/lamarc to 2.1.2b

[KATO Tsuguru]

>Number:         117336
>Category:       ports
>Synopsis:       Update port: biology/lamarc to 2.1.2b
>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:   Fri Oct 19 18:20:04 UTC 2007
>Closed-Date:
>Last-Modified:
>Originator:     KATO Tsuguru
>Release:        FreeBSD 6.2-RELEASE-p8 i386
>Organization:
>Environment:
>Description:
- Update to version 2.1.2b

>How-To-Repeat:
>Fix:

diff -urN /usr/ports/biology/lamarc/Makefile biology/lamarc/Makefile
--- /usr/ports/biology/lamarc/Makefile	Tue Oct  9 00:39:11 2007
+++ biology/lamarc/Makefile	Fri Oct 19 01:31:36 2007
@@ -6,7 +6,7 @@
 #
 
 PORTNAME=	lamarc
-PORTVERSION=	2.1
+PORTVERSION=	2.1.2b
 PORTEPOCH=	1
 CATEGORIES=	biology
 MASTER_SITES=	http://evolution.gs.washington.edu/lamarc/download/
diff -urN /usr/ports/biology/lamarc/distinfo biology/lamarc/distinfo
--- /usr/ports/biology/lamarc/distinfo	Mon Oct  8 22:04:50 2007
+++ biology/lamarc/distinfo	Fri Oct 19 02:35:11 2007
@@ -1,3 +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
+MD5 (lamarc-2.1.2b.src.tar.gz) = 5aafde30e46856636170cabaef522083
+SHA256 (lamarc-2.1.2b.src.tar.gz) = 0ceb1ac3cd441a7a197d0cb7a8d45829dfec61d96eaf471a9e6a847ba14386be
+SIZE (lamarc-2.1.2b.src.tar.gz) = 23522591
diff -urN /usr/ports/biology/lamarc/files/patch-Makefile.in biology/lamarc/files/patch-Makefile.in
--- /usr/ports/biology/lamarc/files/patch-Makefile.in	Mon Oct  8 22:04:51 2007
+++ biology/lamarc/files/patch-Makefile.in	Sat Oct 13 01:07:37 2007
@@ -1,24 +1,6 @@
---- 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 @@
+--- Makefile.in.orig	Fri Oct  5 06:17:37 2007
++++ Makefile.in	Sat Oct 13 00:44:22 2007
+@@ -2011,7 +2011,7 @@
  EXTRA_batch_lam_conv_SOURCES = $(tinyxml_suite)
  lam_conv_app_SOURCES = 
  lamarc_app_SOURCES = 
@@ -27,7 +9,7 @@
  html_DATA = \
  			doc/html/bayes.html \
  			doc/html/bayes_howto.html \
-@@ -2037,7 +2037,7 @@
+@@ -2054,7 +2054,7 @@
  			doc/html/viral_data.html \
  			doc/html/xmlinput.html
  
@@ -36,7 +18,7 @@
  htmlimg_DATA = \
  			doc/html/images/browser-gtk.gif \
  			doc/html/images/correlated1.gif \
-@@ -2054,7 +2054,7 @@
+@@ -2072,7 +2072,7 @@
  			doc/html/images/uncorrelated.gif \
  			doc/html/images/variably_correlated.gif
  
@@ -45,7 +27,7 @@
  htmlbconv_DATA = \
  			doc/html/batch_converter/README.txt \
  			doc/html/batch_converter/chrom1_lamarc.xml \
-@@ -2068,7 +2068,7 @@
+@@ -2086,7 +2086,7 @@
  			doc/html/batch_converter/exported-lamarc-input.xml \
  			doc/html/batch_converter/sample-conv-cmd.xml
  
@@ -54,7 +36,7 @@
  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 @@
+@@ -2100,7 +2100,7 @@
  			doc/html/batch_converter/images/lam_conv_chrom3_region_table.png \
  			doc/html/batch_converter/images/lam_conv_chrom3_segment_snp.png
  
diff -urN /usr/ports/biology/lamarc/files/patch-configure biology/lamarc/files/patch-configure
--- /usr/ports/biology/lamarc/files/patch-configure	Mon Oct  8 22:04:51 2007
+++ biology/lamarc/files/patch-configure	Sat Oct 13 01:07:37 2007
@@ -1,11 +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
+--- configure.orig	Thu Oct  4 01:33:34 2007
++++ configure	Sat Oct 13 00:47:54 2007
+@@ -2029,7 +2029,7 @@
+             LAMARC_CODE_OSTYPE=LAMARC_COMPILE_MACOSX
+         fi
          ;;
 -    linux*)
 +    freebsd*|linux*)
-         OSTYPE=LINUX
-         GUI_PKG=gtk2
-         ;;
+         if test "X${lamCONV}" = "Xyes" ; then
+             if test "X${lamGUI}" = "Xyes" ; then
+                 if test "X${GUI_TOOLKIT}" = "X" ; then
diff -urN /usr/ports/biology/lamarc/pkg-plist biology/lamarc/pkg-plist
--- /usr/ports/biology/lamarc/pkg-plist	Tue Oct  9 00:39:12 2007
+++ biology/lamarc/pkg-plist	Sat Oct 13 01:07:37 2007
@@ -51,6 +51,7 @@
 %%PORTDOCS%%%%DOCSDIR%%/images/partitions2-gtk.png
 %%PORTDOCS%%%%DOCSDIR%%/images/populations-gtk.png
 %%PORTDOCS%%%%DOCSDIR%%/images/startup-gtk.png
+%%PORTDOCS%%%%DOCSDIR%%/images/tracer_trend.png
 %%PORTDOCS%%%%DOCSDIR%%/images/uncorrelated.gif
 %%PORTDOCS%%%%DOCSDIR%%/images/variably_correlated.gif
 %%PORTDOCS%%%%DOCSDIR%%/index.html
>Release-Note:
>Audit-Trail:
>Unformatted: