FreeBSD Bugzilla – Attachment 81996 Details for
Bug 117336
Update port: biology/lamarc to 2.1.2b
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[patch]
file.diff
file.diff (text/plain), 4.60 KB, created by
tkato432
on 2007-10-19 19:20:04 UTC
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Description:
file.diff
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tkato432
Created:
2007-10-19 19:20:04 UTC
Size:
4.60 KB
patch
obsolete
>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@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 @@ >+--- 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
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bug 117336
: 81996