[87941] trunk/dports/science/arb
macsforever2000 at macports.org
macsforever2000 at macports.org
Tue Dec 13 10:02:03 PST 2011
Revision: 87941
http://trac.macports.org/changeset/87941
Author: macsforever2000 at macports.org
Date: 2011-12-13 10:02:01 -0800 (Tue, 13 Dec 2011)
Log Message:
-----------
arb: maintainer update to version 5.3. Removed and added some patchfiles. (#32054)
Modified Paths:
--------------
trunk/dports/science/arb/Portfile
trunk/dports/science/arb/files/patch-ARB-makefile.diff
Added Paths:
-----------
trunk/dports/science/arb/files/patch-ARB-intro.fig.diff
trunk/dports/science/arb/files/patch-ARB_GDEmenus.source.diff
trunk/dports/science/arb/files/patch-GDEHELP-Makefile.diff
Removed Paths:
-------------
trunk/dports/science/arb/files/arb_intro.fig.diff
trunk/dports/science/arb/files/patch-ARB-Flatio.diff
trunk/dports/science/arb/files/patch-ARB-Zuk_to_gen.c.diff
trunk/dports/science/arb/files/patch-ARB-count.c.diff
trunk/dports/science/arb/files/patch-ARB-glpng.diff
trunk/dports/science/arb/files/patch-ARB-interface.c.diff
trunk/dports/science/arb/files/patch-ARB-lsadt.c.diff
Modified: trunk/dports/science/arb/Portfile
===================================================================
--- trunk/dports/science/arb/Portfile 2011-12-13 17:52:05 UTC (rev 87940)
+++ trunk/dports/science/arb/Portfile 2011-12-13 18:02:01 UTC (rev 87941)
@@ -5,8 +5,7 @@
name arb
epoch 1
-version 5.2
-revision 3
+version 5.3
categories science
maintainers me.com:matt.cottrell
platforms darwin
@@ -28,10 +27,10 @@
distname arbsrc
extract.suffix .tgz
dist_subdir ${name}/${version}
-worksrcdir arbsrc_6779
+worksrcdir arbsrc_8210
-checksums sha1 4ee493a16ece5231d46ed1071407c06e733d67c8 \
- rmd160 d9d99d0ebadaa293091ff93f6ca588b2321bd8b0
+checksums sha1 535b72bfbf99f498deee17824c1f167228ad2088 \
+ rmd160 d4b240da693f903d0e8bd59f4b1f1043b6935508
depends_build port:imake \
port:makedepend
@@ -53,13 +52,9 @@
patch-ARB-makefile.diff \
patch-ARB-RNA3D_GlobalHeader.hxx.diff \
patch-ARB-DARWIN.pl.diff \
- patch-ARB-glpng.diff \
- arb_intro.fig.diff \
- patch-ARB-Flatio.diff \
- patch-ARB-Zuk_to_gen.c.diff \
- patch-ARB-count.c.diff \
- patch-ARB-lsadt.c.diff \
- patch-ARB-interface.c.diff
+ patch-ARB-intro.fig.diff \
+ patch-GDEHELP-Makefile.diff \
+ patch-ARB_GDEmenus.source.diff
configure {
reinplace "s| sed | gsed |g" ${worksrcpath}/GDEHELP/MENUS/align.menu \
@@ -98,8 +93,7 @@
}
build.args GCC=${configure.cc} \
- GPP=${configure.cxx} \
- CPPreal=${configure.cpp}
+ GPP=${configure.cxx}
destroot.keepdirs ${destroot}${prefix}/share/arb/lib/pts
destroot {
@@ -187,9 +181,10 @@
D)
type arb to start ARB
+***********************************************************
+
A demo data base is located at ${prefix}/share/arb/demo.arb
-************************************************************************
User generated macros, arb_tcp.dat and pt_servers have been preserved,
but you should keep backups of these just in case. They are located at:
@@ -202,6 +197,12 @@
${prefix}/share/arb/lib/macros.default/
${prefix}/share/arb/lib/arb_tcp.dat.default
+Use keys Control+Command Arrow Key to jump over bases
+Use Keys Option Arrow Key to pull in bases across alignment gaps
+Use the right Command Key plus a letter key to activate a menu item
+
+These notes can be viewed at any time by typing 'port notes arb'
+
Please cite: Wolfgang Ludwig, et al. (2004) ARB: a software environment for sequence data. Nucleic Acids Research. 32:1363-1371
"
Deleted: trunk/dports/science/arb/files/arb_intro.fig.diff
===================================================================
--- trunk/dports/science/arb/files/arb_intro.fig.diff 2011-12-13 17:52:05 UTC (rev 87940)
+++ trunk/dports/science/arb/files/arb_intro.fig.diff 2011-12-13 18:02:01 UTC (rev 87941)
@@ -1,88 +0,0 @@
---- arb_intro.fig.orig 2011-02-04 01:01:34.000000000 -0300
-+++ lib/pictures/arb_intro.fig 2010-10-24 18:34:25.000000000 -0300
-@@ -1,4 +1,4 @@
--#FIG 3.2
-+#FIG 3.2 Produced by xfig version 3.2.5
- Landscape
- Center
- Metric
-@@ -8,18 +8,18 @@
- -2
- 1200 2
- 6 8010 5175 9315 5445
--4 0 -1 0 0 18 12 0.0000 4 135 495 8025 5340 Suffix\001
--4 0 -1 0 0 18 12 0.0000 4 180 495 8550 5415 $filter\001
--4 2 -1 0 0 18 12 0.0000 4 180 720 9300 5415 $to:filter\001
-+4 0 -1 0 0 18 12 0.0000 4 165 570 8025 5340 Suffix\001
-+4 0 -1 0 0 18 12 0.0000 4 210 585 8550 5415 $filter\001
-+4 2 -1 0 0 18 12 0.0000 4 210 870 9300 5415 $to:filter\001
- -6
- 6 2655 2025 8235 2295
- 2 1 0 2 -1 -1 0 0 -1 0.000 0 0 -1 0 0 2
- 2700 2250 8190 2250
--4 1 -1 0 0 18 14 0.0000 4 210 5070 5400 2175 ARB - A Software Environment for Sequence Data\001
-+4 1 -1 0 0 18 14 0.0000 4 240 5925 5400 2175 ARB - A Software Environment for Sequence Data\001
- -6
- 6 1800 10890 9090 11250
--4 0 -1 0 0 18 10 0.0000 4 135 7095 1800 11025 Y:Wolfgang Ludwig, Oliver Strunk, Ralf Westram, Lothar Richter, Harald Meier, Yadhukumar et al.\001
--4 0 -1 0 0 18 10 0.0000 4 135 7260 1800 11205 Y:ARB: a software environment for sequence data. Nucleic Acids Research. 2004. 32(4):1363-1371.\001
-+4 0 -1 0 0 18 10 0.0000 4 150 7335 1800 11025 Y:Wolfgang Ludwig, Oliver Strunk, Ralf Westram, Lothar Richter, Harald Meier, Yadhukumar et al.\001
-+4 0 -1 0 0 18 10 0.0000 4 150 7395 1800 11205 Y:ARB: a software environment for sequence data. Nucleic Acids Research. 2004. 32(4):1363-1371.\001
- -6
- 2 1 0 1 0 7 100 0 -1 0.000 0 0 -1 0 0 1
- 1170 540
-@@ -29,28 +29,29 @@
- 1350 4950 1350 4230 9090 4230
- 2 1 0 1 0 7 100 0 -1 0.000 0 0 -1 0 0 1
- 9630 11340
--4 0 -1 0 0 18 12 0.0000 4 180 570 1425 1050 $close\001
--4 2 -1 0 0 18 12 0.0000 4 195 465 9450 1050 $help\001
--4 2 -1 0 0 18 12 0.0000 4 180 945 9375 9990 $to:XY:box\001
--4 0 -1 0 0 18 12 0.0000 4 195 840 9150 10440 $Y:expert\001
--4 0 -1 0 0 18 12 0.0000 4 180 420 1500 5865 $box\001
--4 0 -1 0 0 18 12 0.0000 4 195 2970 1500 5340 Existing Files (f) and Directories (D)\001
--4 0 -1 0 0 18 12 0.0000 4 180 540 1620 10395 $Y:old\001
--4 0 -1 0 0 18 12 0.0000 4 180 540 4725 10388 $Y:del\001
--4 0 -1 0 0 18 12 0.0000 4 195 1290 1620 4725 $new_complex\001
--4 0 -1 0 0 18 12 0.0000 4 195 660 4455 4725 $merge\001
--4 1 -1 0 0 18 12 0.0000 4 150 750 7140 2865 Authors:\001
--4 1 -1 0 0 18 12 0.0000 4 195 465 5265 945 $logo\001
--4 1 -1 0 0 18 12 0.0000 4 195 2055 2745 3870 http://www.arb-home.de/\001
--4 1 -1 0 0 18 12 0.0000 4 195 915 2745 2970 $copyright\001
--4 1 -1 0 0 18 12 0.0000 4 195 2370 2745 3150 Department of Microbiology\001
--4 1 -1 0 0 18 10 0.0000 4 135 2265 2745 3375 Technical University of Munich\001
--4 1 -1 0 0 18 10 0.0000 4 135 675 2745 3555 Germany\001
--4 1 -1 0 0 18 11 0.0000 4 150 2070 7140 3345 Harald Meier, Yadhukumar\001
--4 1 -1 0 0 18 12 0.0000 4 195 3915 7140 3135 Ralf Westram, Oliver Strunk, Wolfgang Ludwig\001
--4 1 -1 0 0 18 10 0.0000 4 105 2070 7140 3960 Lead tester: F. O. Gloeckner\001
--4 1 -1 0 0 18 10 0.0000 4 135 3615 7140 3780 L. Richter, T.Ginhart, S.Gerbers, J. Huber, R.Jost,\001
--4 1 -1 0 0 18 10 0.0000 4 135 3285 7140 3555 K. Bader, E. Pruesse, C. Hodges, J. Boehnel,\001
--4 1 -1 0 0 18 12 0.0000 4 180 750 5265 2610 $version\001
--4 0 -1 0 0 18 12 0.0000 4 195 1890 7350 10365 Y:Enable Expert Mode\001
--4 0 -1 0 0 18 10 0.0000 4 135 2130 1440 10800 Y:If you use ARB, please cite\001
-+4 0 -1 0 0 18 12 0.0000 4 210 675 1425 1050 $close\001
-+4 2 -1 0 0 18 12 0.0000 4 225 570 9450 1050 $help\001
-+4 2 -1 0 0 18 12 0.0000 4 210 1140 9375 9990 $to:XY:box\001
-+4 0 -1 0 0 18 12 0.0000 4 225 990 9150 10440 $Y:expert\001
-+4 0 -1 0 0 18 12 0.0000 4 210 495 1500 5865 $box\001
-+4 0 -1 0 0 18 12 0.0000 4 210 3690 1500 5340 Existing Files (f) and Directories (D)\001
-+4 0 -1 0 0 18 12 0.0000 4 210 675 1620 10395 $Y:old\001
-+4 0 -1 0 0 18 12 0.0000 4 210 660 4725 10388 $Y:del\001
-+4 0 -1 0 0 18 12 0.0000 4 225 1500 1620 4725 $new_complex\001
-+4 0 -1 0 0 18 12 0.0000 4 225 765 4455 4725 $merge\001
-+4 1 -1 0 0 18 12 0.0000 4 165 915 7140 2865 Authors:\001
-+4 1 -1 0 0 18 12 0.0000 4 225 585 5265 945 $logo\001
-+4 1 -1 0 0 18 12 0.0000 4 210 2475 2745 3870 http://www.arb-home.de/\001
-+4 1 -1 0 0 18 12 0.0000 4 210 2910 2745 3150 Department of Microbiology\001
-+4 1 -1 0 0 18 10 0.0000 4 150 2295 2745 3375 Technical University of Munich\001
-+4 1 -1 0 0 18 10 0.0000 4 150 675 2745 3555 Germany\001
-+4 1 -1 0 0 18 11 0.0000 4 165 2340 7140 3345 Harald Meier, Yadhukumar\001
-+4 1 -1 0 0 18 12 0.0000 4 210 4800 7140 3135 Ralf Westram, Oliver Strunk, Wolfgang Ludwig\001
-+4 1 -1 0 0 18 10 0.0000 4 150 3660 7140 3780 L. Richter, T.Ginhart, S.Gerbers, J. Huber, R.Jost,\001
-+4 1 -1 0 0 18 10 0.0000 4 150 3285 7140 3555 K. Bader, E. Pruesse, C. Hodges, J. Boehnel,\001
-+4 1 -1 0 0 18 12 0.0000 4 210 900 5265 2610 $version\001
-+4 0 -1 0 0 18 12 0.0000 4 210 2295 7350 10365 Y:Enable Expert Mode\001
-+4 0 -1 0 0 18 10 0.0000 4 150 2190 1440 10800 Y:If you use ARB, please cite\001
-+4 1 -1 0 0 18 10 0.0000 4 120 2085 7110 3960 Lead tester: F. O. Gloeckner\001
-+4 1 -1 0 0 18 12 0.0000 4 225 1125 2745 2970 $copyright\001
-+4 1 -1 0 0 18 12 0.0000 4 210 3600 7155 4185 Mac OS X port: Matthew T. Cottrell\001
Deleted: trunk/dports/science/arb/files/patch-ARB-Flatio.diff
===================================================================
--- trunk/dports/science/arb/files/patch-ARB-Flatio.diff 2011-12-13 17:52:05 UTC (rev 87940)
+++ trunk/dports/science/arb/files/patch-ARB-Flatio.diff 2011-12-13 18:02:01 UTC (rev 87941)
@@ -1,20 +0,0 @@
---- GDE/SUPPORT/Flatio.c.orig 2008-07-22 05:11:25.000000000 -0400
-+++ GDE/SUPPORT/Flatio.c 2011-07-25 22:52:15.000000000 -0400
-@@ -24,7 +24,7 @@
- fprintf(stderr,"Error:%s\n",string);
- exit(1);
- }
-- return;
-+ return 0;
- }
-
- char *Calloc2(count,size)
-@@ -163,7 +163,7 @@
- fputc(data[j].nuc[i],file);
- }
- }
-- return;
-+ return 0;
- }
-
-
Deleted: trunk/dports/science/arb/files/patch-ARB-Zuk_to_gen.c.diff
===================================================================
--- trunk/dports/science/arb/files/patch-ARB-Zuk_to_gen.c.diff 2011-12-13 17:52:05 UTC (rev 87940)
+++ trunk/dports/science/arb/files/patch-ARB-Zuk_to_gen.c.diff 2011-12-13 18:02:01 UTC (rev 87941)
@@ -1,10 +0,0 @@
---- GDE/SUPPORT/Zuk_to_gen.c.orig 2008-07-22 05:11:25.000000000 -0400
-+++ GDE/SUPPORT/Zuk_to_gen.c 2011-07-25 23:14:06.000000000 -0400
-@@ -99,6 +99,6 @@
- }
- fprintf(file,"\n//\n");
- }
-- return;
-+ return 0;
- }
-
Deleted: trunk/dports/science/arb/files/patch-ARB-count.c.diff
===================================================================
--- trunk/dports/science/arb/files/patch-ARB-count.c.diff 2011-12-13 17:52:05 UTC (rev 87940)
+++ trunk/dports/science/arb/files/patch-ARB-count.c.diff 2011-12-13 18:02:01 UTC (rev 87941)
@@ -1,38 +0,0 @@
---- GDE/SUPPORT/count.c.orig 2008-07-22 05:11:25.000000000 -0400
-+++ GDE/SUPPORT/count.c 2011-07-25 23:24:50.000000000 -0400
-@@ -255,7 +255,7 @@
- }
- if(special)
- (*num) = *denom - (int)fnum;
-- return;
-+ return 0;
- }
-
-
-@@ -317,7 +317,7 @@
- aval[i] = c;
- aval[i] = '\0';
- }
-- return;
-+ return 0;
- }
-
- SetPart()
-@@ -369,7 +369,7 @@
- partg[j] = (float)g / (float)tot;
- partu[j] = (float)u / (float)tot;
- }
-- return;
-+ return 0;
- }
-
-
-@@ -394,7 +394,7 @@
- printf("\n");
- jj++;
- }
-- return;
-+ return 0;
- }
-
-
Deleted: trunk/dports/science/arb/files/patch-ARB-glpng.diff
===================================================================
--- trunk/dports/science/arb/files/patch-ARB-glpng.diff 2011-12-13 17:52:05 UTC (rev 87940)
+++ trunk/dports/science/arb/files/patch-ARB-glpng.diff 2011-12-13 18:02:01 UTC (rev 87941)
@@ -1,33 +0,0 @@
---- GL/glpng/glpng.c 2008-07-22 05:11:32.000000000 -0400
-+++ GL/glpng/glpng.c 2011-02-02 03:49:05.000000000 -0500
-@@ -37,6 +37,12 @@
- #include <math.h>
- #include <png.h>
-
-+#if 0
-+#define PNG_CHECK_SIG(header,size) png_check_sig(header,size) // old libpng
-+#else
-+#define PNG_CHECK_SIG(header,size) (png_sig_cmp(header,0,size)==0)
-+#endif
-+
- /* Used to decide if GL/gl.h supports the paletted extension */
- #ifdef GL_COLOR_INDEX1_EXT
- #define SUPPORTS_PALETTE_EXT
-@@ -278,7 +284,7 @@
- if (pinfo == NULL) return 0;
-
- fread(header, 1, 8, fp);
-- if (!png_check_sig(header, 8)) return 0;
-+ if (!PNG_CHECK_SIG(header, 8)) return 0;
-
- png = png_create_read_struct(PNG_LIBPNG_VER_STRING, NULL, NULL, NULL);
- info = png_create_info_struct(png);
-@@ -383,7 +389,7 @@
- png_uint_32 i;
-
- fread(header, 1, 8, fp);
-- if (!png_check_sig(header, 8)) return 0;
-+ if (!PNG_CHECK_SIG(header, 8)) return 0;
-
- png = png_create_read_struct(PNG_LIBPNG_VER_STRING, NULL, NULL, NULL);
- info = png_create_info_struct(png);
Deleted: trunk/dports/science/arb/files/patch-ARB-interface.c.diff
===================================================================
--- trunk/dports/science/arb/files/patch-ARB-interface.c.diff 2011-12-13 17:52:05 UTC (rev 87940)
+++ trunk/dports/science/arb/files/patch-ARB-interface.c.diff 2011-12-13 18:02:01 UTC (rev 87941)
@@ -1,11 +0,0 @@
---- GDE/CLUSTALW/interface.c.orig 2008-07-22 05:11:26.000000000 -0400
-+++ GDE/CLUSTALW/interface.c 2011-07-25 23:48:32.000000000 -0400
-@@ -210,7 +210,7 @@
- Boolean name1 = FALSE;
- sint ajb;
-
-- if(args[0]==NULL) return;
-+ if(args[0]==NULL) return 0;
-
-
-
Added: trunk/dports/science/arb/files/patch-ARB-intro.fig.diff
===================================================================
--- trunk/dports/science/arb/files/patch-ARB-intro.fig.diff (rev 0)
+++ trunk/dports/science/arb/files/patch-ARB-intro.fig.diff 2011-12-13 18:02:01 UTC (rev 87941)
@@ -0,0 +1,88 @@
+--- arb_intro.fig.orig 2011-02-04 01:01:34.000000000 -0300
++++ lib/pictures/arb_intro.fig 2010-10-24 18:34:25.000000000 -0300
+@@ -1,4 +1,4 @@
+-#FIG 3.2
++#FIG 3.2 Produced by xfig version 3.2.5
+ Landscape
+ Center
+ Metric
+@@ -8,18 +8,18 @@
+ -2
+ 1200 2
+ 6 8010 5175 9315 5445
+-4 0 -1 0 0 18 12 0.0000 4 135 495 8025 5340 Suffix\001
+-4 0 -1 0 0 18 12 0.0000 4 180 495 8550 5415 $filter\001
+-4 2 -1 0 0 18 12 0.0000 4 180 720 9300 5415 $to:filter\001
++4 0 -1 0 0 18 12 0.0000 4 165 570 8025 5340 Suffix\001
++4 0 -1 0 0 18 12 0.0000 4 210 585 8550 5415 $filter\001
++4 2 -1 0 0 18 12 0.0000 4 210 870 9300 5415 $to:filter\001
+ -6
+ 6 2655 2025 8235 2295
+ 2 1 0 2 -1 -1 0 0 -1 0.000 0 0 -1 0 0 2
+ 2700 2250 8190 2250
+-4 1 -1 0 0 18 14 0.0000 4 210 5070 5400 2175 ARB - A Software Environment for Sequence Data\001
++4 1 -1 0 0 18 14 0.0000 4 240 5925 5400 2175 ARB - A Software Environment for Sequence Data\001
+ -6
+ 6 1800 10890 9090 11250
+-4 0 -1 0 0 18 10 0.0000 4 135 7095 1800 11025 Y:Wolfgang Ludwig, Oliver Strunk, Ralf Westram, Lothar Richter, Harald Meier, Yadhukumar et al.\001
+-4 0 -1 0 0 18 10 0.0000 4 135 7260 1800 11205 Y:ARB: a software environment for sequence data. Nucleic Acids Research. 2004. 32(4):1363-1371.\001
++4 0 -1 0 0 18 10 0.0000 4 150 7335 1800 11025 Y:Wolfgang Ludwig, Oliver Strunk, Ralf Westram, Lothar Richter, Harald Meier, Yadhukumar et al.\001
++4 0 -1 0 0 18 10 0.0000 4 150 7395 1800 11205 Y:ARB: a software environment for sequence data. Nucleic Acids Research. 2004. 32(4):1363-1371.\001
+ -6
+ 2 1 0 1 0 7 100 0 -1 0.000 0 0 -1 0 0 1
+ 1170 540
+@@ -29,28 +29,29 @@
+ 1350 4950 1350 4230 9090 4230
+ 2 1 0 1 0 7 100 0 -1 0.000 0 0 -1 0 0 1
+ 9630 11340
+-4 0 -1 0 0 18 12 0.0000 4 180 570 1425 1050 $close\001
+-4 2 -1 0 0 18 12 0.0000 4 195 465 9450 1050 $help\001
+-4 2 -1 0 0 18 12 0.0000 4 180 945 9375 9990 $to:XY:box\001
+-4 0 -1 0 0 18 12 0.0000 4 195 840 9150 10440 $Y:expert\001
+-4 0 -1 0 0 18 12 0.0000 4 180 420 1500 5865 $box\001
+-4 0 -1 0 0 18 12 0.0000 4 195 2970 1500 5340 Existing Files (f) and Directories (D)\001
+-4 0 -1 0 0 18 12 0.0000 4 180 540 1620 10395 $Y:old\001
+-4 0 -1 0 0 18 12 0.0000 4 180 540 4725 10388 $Y:del\001
+-4 0 -1 0 0 18 12 0.0000 4 195 1290 1620 4725 $new_complex\001
+-4 0 -1 0 0 18 12 0.0000 4 195 660 4455 4725 $merge\001
+-4 1 -1 0 0 18 12 0.0000 4 150 750 7140 2865 Authors:\001
+-4 1 -1 0 0 18 12 0.0000 4 195 465 5265 945 $logo\001
+-4 1 -1 0 0 18 12 0.0000 4 195 2055 2745 3870 http://www.arb-home.de/\001
+-4 1 -1 0 0 18 12 0.0000 4 195 915 2745 2970 $copyright\001
+-4 1 -1 0 0 18 12 0.0000 4 195 2370 2745 3150 Department of Microbiology\001
+-4 1 -1 0 0 18 10 0.0000 4 135 2265 2745 3375 Technical University of Munich\001
+-4 1 -1 0 0 18 10 0.0000 4 135 675 2745 3555 Germany\001
+-4 1 -1 0 0 18 11 0.0000 4 150 2070 7140 3345 Harald Meier, Yadhukumar\001
+-4 1 -1 0 0 18 12 0.0000 4 195 3915 7140 3135 Ralf Westram, Oliver Strunk, Wolfgang Ludwig\001
+-4 1 -1 0 0 18 10 0.0000 4 105 2070 7140 3960 Lead tester: F. O. Gloeckner\001
+-4 1 -1 0 0 18 10 0.0000 4 135 3615 7140 3780 L. Richter, T.Ginhart, S.Gerbers, J. Huber, R.Jost,\001
+-4 1 -1 0 0 18 10 0.0000 4 135 3285 7140 3555 K. Bader, E. Pruesse, C. Hodges, J. Boehnel,\001
+-4 1 -1 0 0 18 12 0.0000 4 180 750 5265 2610 $version\001
+-4 0 -1 0 0 18 12 0.0000 4 195 1890 7350 10365 Y:Enable Expert Mode\001
+-4 0 -1 0 0 18 10 0.0000 4 135 2130 1440 10800 Y:If you use ARB, please cite\001
++4 0 -1 0 0 18 12 0.0000 4 210 675 1425 1050 $close\001
++4 2 -1 0 0 18 12 0.0000 4 225 570 9450 1050 $help\001
++4 2 -1 0 0 18 12 0.0000 4 210 1140 9375 9990 $to:XY:box\001
++4 0 -1 0 0 18 12 0.0000 4 225 990 9150 10440 $Y:expert\001
++4 0 -1 0 0 18 12 0.0000 4 210 495 1500 5865 $box\001
++4 0 -1 0 0 18 12 0.0000 4 210 3690 1500 5340 Existing Files (f) and Directories (D)\001
++4 0 -1 0 0 18 12 0.0000 4 210 675 1620 10395 $Y:old\001
++4 0 -1 0 0 18 12 0.0000 4 210 660 4725 10388 $Y:del\001
++4 0 -1 0 0 18 12 0.0000 4 225 1500 1620 4725 $new_complex\001
++4 0 -1 0 0 18 12 0.0000 4 225 765 4455 4725 $merge\001
++4 1 -1 0 0 18 12 0.0000 4 165 915 7140 2865 Authors:\001
++4 1 -1 0 0 18 12 0.0000 4 225 585 5265 945 $logo\001
++4 1 -1 0 0 18 12 0.0000 4 210 2475 2745 3870 http://www.arb-home.de/\001
++4 1 -1 0 0 18 12 0.0000 4 210 2910 2745 3150 Department of Microbiology\001
++4 1 -1 0 0 18 10 0.0000 4 150 2295 2745 3375 Technical University of Munich\001
++4 1 -1 0 0 18 10 0.0000 4 150 675 2745 3555 Germany\001
++4 1 -1 0 0 18 11 0.0000 4 165 2340 7140 3345 Harald Meier, Yadhukumar\001
++4 1 -1 0 0 18 12 0.0000 4 210 4800 7140 3135 Ralf Westram, Oliver Strunk, Wolfgang Ludwig\001
++4 1 -1 0 0 18 10 0.0000 4 150 3660 7140 3780 L. Richter, T.Ginhart, S.Gerbers, J. Huber, R.Jost,\001
++4 1 -1 0 0 18 10 0.0000 4 150 3285 7140 3555 K. Bader, E. Pruesse, C. Hodges, J. Boehnel,\001
++4 1 -1 0 0 18 12 0.0000 4 210 900 5265 2610 $version\001
++4 0 -1 0 0 18 12 0.0000 4 210 2295 7350 10365 Y:Enable Expert Mode\001
++4 0 -1 0 0 18 10 0.0000 4 150 2190 1440 10800 Y:If you use ARB, please cite\001
++4 1 -1 0 0 18 10 0.0000 4 120 2085 7110 3960 Lead tester: F. O. Gloeckner\001
++4 1 -1 0 0 18 12 0.0000 4 225 1125 2745 2970 $copyright\001
++4 1 -1 0 0 18 12 0.0000 4 210 3600 7155 4185 Mac OS X port: Matthew T. Cottrell\001
Deleted: trunk/dports/science/arb/files/patch-ARB-lsadt.c.diff
===================================================================
--- trunk/dports/science/arb/files/patch-ARB-lsadt.c.diff 2011-12-13 17:52:05 UTC (rev 87940)
+++ trunk/dports/science/arb/files/patch-ARB-lsadt.c.diff 2011-12-13 18:02:01 UTC (rev 87941)
@@ -1,53 +0,0 @@
---- GDE/SUPPORT/lsadt.c.orig 2008-07-22 05:11:25.000000000 -0400
-+++ GDE/SUPPORT/lsadt.c 2011-07-25 23:34:23.000000000 -0400
-@@ -522,7 +522,7 @@
- for(i=2; i<=n; i++)
- for(j=1; j<i; j++)
- d[i][j] = runif();
-- return;
-+ return 0;
- }
- if(nempty == 0 && start == 2)
- {
-@@ -530,12 +530,12 @@
- for(i=2; i<=n; i++)
- for(j=1; j<i; j++)
- d[i][j] = delta[i][j] + rnorm()*estd;
-- return;
-+ return 0;
- }
- for(i=2; i<=n; i++)
- for(j=1; j<i; j++)
- d[i][j] = delta[i][j];
-- if(start==3 && nempty==0) return;
-+ if(start==3 && nempty==0) return 0;
- emp=nempty;
- nemp=0;
- while(nemp<emp)
-@@ -576,7 +576,7 @@
- for(j=1; j<i; j++)
- d[i][j]+= rnorm()*estd;
- }
-- return;
-+ return 0;
- }
-
- static int nm0, nm1, nm2, nm3;
-@@ -735,7 +735,7 @@
- {
- prc = 0;
- print_iter(maxfnc, f);
-- return;
-+ return 0;
- }
- if(itcrs>m)
- {
-@@ -813,7 +813,7 @@
- {
- prc = 0;
- print_iter(maxfnc, f);
-- return;
-+ return 0;
- }
- }
- if(maxfnc==maxfn)
Modified: trunk/dports/science/arb/files/patch-ARB-makefile.diff
===================================================================
--- trunk/dports/science/arb/files/patch-ARB-makefile.diff 2011-12-13 17:52:05 UTC (rev 87940)
+++ trunk/dports/science/arb/files/patch-ARB-makefile.diff 2011-12-13 18:02:01 UTC (rev 87941)
@@ -59,7 +59,7 @@
endif
ifdef DARWIN
-- XLIBS := -L/usr/OpenMotif/lib -lXm -L$(XHOME)/lib -lpng -lXt -lX11 -lXext -lXp -lc -lXmu -lXi
+- XLIBS := -L/usr/OpenMotif/lib -lXm -L$(XHOME)/lib -lpng -lXt -lX11 -lXext -lc -lXmu -lXi
+ XLIBS := -L$(XHOME)/lib -lXm -lpng -lz -lXt -lX11 -lXext -lXp -lXmu -lXi
XLIBS += -lGLU -lGL -Wl,-dylib_file,$(OSX_FW_OPENGL)/libGL.dylib:$(OSX_FW_OPENGL)/libGL.dylib
else
Added: trunk/dports/science/arb/files/patch-ARB_GDEmenus.source.diff
===================================================================
--- trunk/dports/science/arb/files/patch-ARB_GDEmenus.source.diff (rev 0)
+++ trunk/dports/science/arb/files/patch-ARB_GDEmenus.source.diff 2011-12-13 18:02:01 UTC (rev 87941)
@@ -0,0 +1,11 @@
+--- GDEHELP/ARB_GDEmenus.source.orig 2011-11-10 10:19:41.000000000 -0500
++++ GDEHELP/ARB_GDEmenus.source 2011-11-14 18:25:17.000000000 -0500
+@@ -6,7 +6,7 @@
+ #define GEN_INFILE(in1) GOTO_LOCAL_DIR ; arb_convert_aln -GenBank in1 -phylip infile
+ #define RM_LOCAL_FILES(in1) RM_LOCAL_DIR(in1)
+
+-#define RUN_IN_WINDOW(cmd) ${ARB_XCMD:-cmdtool} bash -x -c ''LD_LIBRARY_PATH="${ARB_LIBRARY_PATH:-/usr/arb/lib}";export LD_LIBRARY_PATH; cmd ;arb_wait''
++#define RUN_IN_WINDOW(cmd) ${ARB_XCMD:-cmdtool} bash -x -c LD_LIBRARY_PATH="${ARB_LIBRARY_PATH:-/usr/arb/lib}";export LD_LIBRARY_PATH; cmd ;arb_wait
+
+ #include <warning.genmenu>
+
Added: trunk/dports/science/arb/files/patch-GDEHELP-Makefile.diff
===================================================================
--- trunk/dports/science/arb/files/patch-GDEHELP-Makefile.diff (rev 0)
+++ trunk/dports/science/arb/files/patch-GDEHELP-Makefile.diff 2011-12-13 18:02:01 UTC (rev 87941)
@@ -0,0 +1,11 @@
+--- GDEHELP/Makefile.orig 2011-11-13 09:47:34.000000000 -0500
++++ GDEHELP/Makefile 2011-11-13 11:03:22.000000000 -0500
+@@ -17,7 +17,7 @@
+
+ $(TARGET) : $(SOURCE) $(GENMENUS)
+ -chmod a+w $(TARGET)
+- $(PP) -IMENUS $(SOURCE) >$(TARGET)
++ $(GCC) -E -x c-header -IMENUS $(SOURCE) >$(TARGET)
+ chmod a-w $(TARGET)
+
+ # ------------------------------------------------------------
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