Attachment #81996 for bug #117336

View | Details | Raw Unified | Return to bug 117336
Collapse All | Expand All

Lines 6-12 Link Here

(-)biology/lamarc/Makefile (-1 / +1 lines)
6	#	6	#
7		7
8	PORTNAME= lamarc	8	PORTNAME= lamarc
9	PORTVERSION= 2.1	9	PORTVERSION= 2.1.2b
10	PORTEPOCH= 1	10	PORTEPOCH= 1
11	CATEGORIES= biology	11	CATEGORIES= biology
12	MASTER_SITES= http://evolution.gs.washington.edu/lamarc/download/	12	MASTER_SITES= http://evolution.gs.washington.edu/lamarc/download/

Lines 1-3 Link Here

(-)biology/lamarc/distinfo (-3 / +3 lines)
1	MD5 (lamarc-2.1.src.tar.gz) = ed98383ed97acb99330d080a3b457ab0	1	MD5 (lamarc-2.1.2b.src.tar.gz) = 5aafde30e46856636170cabaef522083
2	SHA256 (lamarc-2.1.src.tar.gz) = 3a17b6dec3c313193b48b94d0b4f8b3bbd01badb7f0c6f179aabbf3dfba625e2	2	SHA256 (lamarc-2.1.2b.src.tar.gz) = 0ceb1ac3cd441a7a197d0cb7a8d45829dfec61d96eaf471a9e6a847ba14386be
3	SIZE (lamarc-2.1.src.tar.gz) = 23427309	3	SIZE (lamarc-2.1.2b.src.tar.gz) = 23522591




--- Makefile.in.orig	Fri Oct  5 06:17:37 2007
+++ Makefile.in	Sat Oct 13 00:44:22 2007
@@ -2011,7 +2011,7 @@
 @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 = 

 html_DATA = \
 			doc/html/bayes.html \
 			doc/html/bayes_howto.html \
@@ -2054,7 +2054,7 @@
 			doc/html/viral_data.html \
 			doc/html/xmlinput.html
 

 htmlimg_DATA = \
 			doc/html/images/browser-gtk.gif \
 			doc/html/images/correlated1.gif \
@@ -2072,7 +2072,7 @@
 			doc/html/images/uncorrelated.gif \
 			doc/html/images/variably_correlated.gif
 

 htmlbconv_DATA = \
 			doc/html/batch_converter/README.txt \
 			doc/html/batch_converter/chrom1_lamarc.xml \
@@ -2086,7 +2086,7 @@
 			doc/html/batch_converter/exported-lamarc-input.xml \
 			doc/html/batch_converter/sample-conv-cmd.xml
 

 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 \
@@ -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
 

Lines 1-11 Link Here

(-)biology/lamarc/files/patch-configure (-8 / +8 lines)
1	--- configure.orig Wed May 2 05:59:05 2007	1	--- configure.orig Thu Oct 4 01:33:34 2007
2	+++ configure Thu Aug 30 18:26:42 2007	2	+++ configure Sat Oct 13 00:47:54 2007
3	@@ -1494,7 +1494,7 @@	3	@@ -2029,7 +2029,7 @@
4	OSTYPE=MACOSX	4	LAMARC_CODE_OSTYPE=LAMARC_COMPILE_MACOSX
5	GUI_PKG=mac	5	fi
6	;;	6	;;
7	- linux*)	7	- linux*)
8	+ freebsd\|linux)	8	+ freebsd\|linux)
9	OSTYPE=LINUX	9	if test "X${lamCONV}" = "Xyes" ; then
10	GUI_PKG=gtk2	10	if test "X${lamGUI}" = "Xyes" ; then
11	;;	11	if test "X${GUI_TOOLKIT}" = "X" ; then

Lines 51-56 Link Here

(-)biology/lamarc/pkg-plist (+1 lines)
51	%%PORTDOCS%%%%DOCSDIR%%/images/partitions2-gtk.png	51	%%PORTDOCS%%%%DOCSDIR%%/images/partitions2-gtk.png
52	%%PORTDOCS%%%%DOCSDIR%%/images/populations-gtk.png	52	%%PORTDOCS%%%%DOCSDIR%%/images/populations-gtk.png
53	%%PORTDOCS%%%%DOCSDIR%%/images/startup-gtk.png	53	%%PORTDOCS%%%%DOCSDIR%%/images/startup-gtk.png
		54	%%PORTDOCS%%%%DOCSDIR%%/images/tracer_trend.png
54	%%PORTDOCS%%%%DOCSDIR%%/images/uncorrelated.gif	55	%%PORTDOCS%%%%DOCSDIR%%/images/uncorrelated.gif
55	%%PORTDOCS%%%%DOCSDIR%%/images/variably_correlated.gif	56	%%PORTDOCS%%%%DOCSDIR%%/images/variably_correlated.gif
56	%%PORTDOCS%%%%DOCSDIR%%/index.html	57	%%PORTDOCS%%%%DOCSDIR%%/index.html

Return to bug 117336

Lines 1-24 Link Here

(-)biology/lamarc/files/patch-Makefile.in (-25 / +7 lines)
1	--- Makefile.in.orig Mon May 7 06:58:52 2007	1	--- Makefile.in.orig Fri Oct 5 06:17:37 2007
2	+++ Makefile.in Fri Aug 31 01:11:04 2007	2	+++ Makefile.in Sat Oct 13 00:44:22 2007
3	@@ -51,7 +51,7 @@	3	@@ -2011,7 +2011,7 @@
4	@OSX_APP_FALSE@am__append_8 = -ggdb
5	@NODATA_TRUE@am__append_9 = -DSTATIONARIES -DNOPROGRESSBAR
6	@DEBUG_TRUE@am__append_10 = $(debugflags)
7	-@DEBUG_FALSE@am__append_11 = -O3 -funroll-loops -DNDEBUG
8	+@DEBUG_FALSE@am__append_11 = -DNDEBUG
9	@DMALLOC_TRUE@am__append_12 = -ldmallocxx
10	@DMALLOC_TRUE@am__append_13 = -DDMALLOC_FUNC_CHECK
11	@EFENCE_TRUE@am__append_14 = -lefence
12	@@ -1155,7 +1155,7 @@
13	CPPFLAGS = @CPPFLAGS@
14	CXX = @CXX@
15	CXXDEPMODE = @CXXDEPMODE@
16	-CXXFLAGS =
17	+CXXFLAGS = @CXXFLAGS@
18	CYGPATH_W = @CYGPATH_W@
19	DEBUG_FALSE = @DEBUG_FALSE@
20	DEBUG_TRUE = @DEBUG_TRUE@
21	@@ -1994,7 +1994,7 @@
22	EXTRA_batch_lam_conv_SOURCES = $(tinyxml_suite)	4	EXTRA_batch_lam_conv_SOURCES = $(tinyxml_suite)
23	lam_conv_app_SOURCES =	5	lam_conv_app_SOURCES =
24	lamarc_app_SOURCES =	6	lamarc_app_SOURCES =
Lines 27-33 Link Here
27	html_DATA = \	9	html_DATA = \
28	doc/html/bayes.html \	10	doc/html/bayes.html \
29	doc/html/bayes_howto.html \	11	doc/html/bayes_howto.html \
30	@@ -2037,7 +2037,7 @@	12	@@ -2054,7 +2054,7 @@
31	doc/html/viral_data.html \	13	doc/html/viral_data.html \
32	doc/html/xmlinput.html	14	doc/html/xmlinput.html
33		15
Lines 36-42 Link Here
36	htmlimg_DATA = \	18	htmlimg_DATA = \
37	doc/html/images/browser-gtk.gif \	19	doc/html/images/browser-gtk.gif \
38	doc/html/images/correlated1.gif \	20	doc/html/images/correlated1.gif \
39	@@ -2054,7 +2054,7 @@	21	@@ -2072,7 +2072,7 @@
40	doc/html/images/uncorrelated.gif \	22	doc/html/images/uncorrelated.gif \
41	doc/html/images/variably_correlated.gif	23	doc/html/images/variably_correlated.gif
42		24
Lines 45-51 Link Here
45	htmlbconv_DATA = \	27	htmlbconv_DATA = \
46	doc/html/batch_converter/README.txt \	28	doc/html/batch_converter/README.txt \
47	doc/html/batch_converter/chrom1_lamarc.xml \	29	doc/html/batch_converter/chrom1_lamarc.xml \
48	@@ -2068,7 +2068,7 @@	30	@@ -2086,7 +2086,7 @@
49	doc/html/batch_converter/exported-lamarc-input.xml \	31	doc/html/batch_converter/exported-lamarc-input.xml \
50	doc/html/batch_converter/sample-conv-cmd.xml	32	doc/html/batch_converter/sample-conv-cmd.xml
51		33
Lines 54-60 Link Here
54	htmlbconvimg_DATA = \	36	htmlbconvimg_DATA = \
55	doc/html/batch_converter/images/lam_conv_chrom1_export_file_selection.png \	37	doc/html/batch_converter/images/lam_conv_chrom1_export_file_selection.png \
56	doc/html/batch_converter/images/lam_conv_chrom1_export_warn_1.png \	38	doc/html/batch_converter/images/lam_conv_chrom1_export_warn_1.png \
57	@@ -2082,7 +2082,7 @@	39	@@ -2100,7 +2100,7 @@
58	doc/html/batch_converter/images/lam_conv_chrom3_region_table.png \	40	doc/html/batch_converter/images/lam_conv_chrom3_region_table.png \
59	doc/html/batch_converter/images/lam_conv_chrom3_segment_snp.png	41	doc/html/batch_converter/images/lam_conv_chrom3_segment_snp.png
60		42