arb stable port information

Package: arb
Version: 20071207
Revision: 1007
Distribution: 10.4, 10.5
GCC: 4.0
Source: http://download.arb-home.de/src/arbsrc_2007_12_07.tgz
Source-MD5: 74b11d18074d23938823c4e0c6361579
SourceDirectory: .
PatchFile: %n.patch
PatchFile-MD5: 8646b018ea9e81b9d6267e4819fef044
PatchScript: <<
#!/bin/sh -ex
cp config.makefile.template config.makefile; patch -p0 < %{PatchFile}
# perl -pi.bak -e 's|\$\(CPPINCLUDES\)|-I%p/include $&|' RNA3D/Makefile
<<
BuildDepends: mesa-libglw-openmotif3, freeglut, lynx, sed, glew, openmotif3 , x11-dev, libtiff, fink (>= 0.24.12)
Depends: mesa-libglw-openmotif3-shlibs, freeglut-shlibs, x11, glew-shlibs, openmotif3-shlibs (>= 2.2.2-3), xfig, ghostscript, app-defaults, nedit
Conflicts: clustalw, afni
NoSetCXXFLAGS: true
CompileScript: <<
#!/bin/sh -ex
export CCACHE_DISABLE=1
export ARBHOME=%b
export ARB_TEXTEDIT=pico
export PATH=$ARBHOME/bin:$PATH
# rm LIBLINK/*
#MOTIF_LIBPATH=%p/lib/libXm.3.dylib
make all PREFIX=%p LDFLAGS=-L%p/lib LIBDIR=%p/lib \
LIBPATH="-L%b/LIBLINK -L%p/lib" XINCLUDES="-I%p/include -I/usr/X11R6/include"
<<
InstallScript: <<
#!/bin/sh -ex
mkdir -p %i/bin
mkdir -p %i/share/%n/lib/pts
mkdir -p %i/share/doc/%n/GDEHELP
mkdir -p %i/share/%n/PERL_SCRIPTS
mkdir -p %i/share/%n/SH
ln -s %p/bin %i/share/%n/lib/bin
cp -r bin %i
cp -R lib %i/share/%n
cp -r GDEHELP %i/share/%n/GDEHELP
cp -r PERL_SCRIPTS %i/share/%n
cp -r HELP_SOURCE/oldhelp/* %i/share/arb/lib/help
cp -r demo.arb %i/share/%n
find %i/bin -type l -exec rm -rf {} \;
cp -r SH/* %i/bin
<<
ConfFiles: %p/share/arb/lib/arb_tcp.dat
RunTimeVars: ARBHOME: %p/share/arb
DocFiles: README arb_README.txt arb_DEBUG.txt arb_CHANGES.txt arb_MENU_CHANGES.txt arb_LICENSE.txt
License: OSI-Approved
Description: Phylogeny and sequence data management
DescDetail: <<
The ARB software is a graphically oriented package comprising various tools
for sequence
database handling and data analysis. A central database of processed
(aligned) sequences
and any type of additional data linked to the respective sequence entries is
structured
according to phylogeny or other user defined criteria.

NOTE: This version is an experimental beta and is not an official release of
ARB!
<<
DescUsage: <<
ARB works, but the PT_server and "fast save" will NOT work on an HFS+ volume.
The current fix is to specify your PT_server directory on a UFS disk.
A UFS disk image can be used for this purpose.
The default dir is /sw/share/arb/lib/pts/ - symlink this to a writable UFS
image.
Future revisions, this limitation can hopefully be patched around.

Note: The help is currently broken. Disabled.
<<
DescPackaging: <<
bin/count conflicts with the "count" in the afni package. If anyone needs
both, let me know
and I can work around the conflict.
<<
DescPort: <<
ARB does NOT work with lesstif - many images do not display. Thus depends on
openmotif.
Many patches. Shared libraries not building correctly, so i have them building
static.
It wants them in its own lib directory. See the patches to the Makefile.
Thanks to Mike Dyall-Smith for the help in testing this.

Rev 0603:
- Remove ldd from AISC makefile
- Add sys/param.h for MAXPATH
- Help disabled due to incompatible libsablot version in fink
<<
Maintainer: Ben Hines
Homepage: http://www.arb-home.de/

arb stable port .patch

--- ARBDB/arbdb.c 2005-07-17 18:09:19.000000000 -0700
+++ ARBDB/arbdb.c 2005-07-17 18:50:58.000000000 -0700
@@ -1,4 +1,4 @@
-/* #include */
+#include
#include
#include
/* #include */
@@ -1359,7 +1359,7 @@
Get all subfield names
********************************************************************************************/

-static char *stpcpy(char *dest, const char *source)
+static char *arbstpcpy(char *dest, const char *source)
{
while ((*dest++=*source++)) ;
return dest-1; /* return pointer to last copied character (which is \0) */
@@ -1393,8 +1393,8 @@
char *neu_result = (char*)malloc(result_length+keylen+1+1);

if (neu_result) {
- char *p = stpcpy(neu_result, result);
- p = stpcpy(p, key);
+ char *p = arbstpcpy(neu_result, result);
+ p = arbstpcpy(p, key);
*p++ = ';';
p[0] = 0;

--- NAMES/names.cxx 2005-07-17 18:09:22.000000000 -0700
+++ NAMES/names.cxx 2005-07-17 19:13:12.000000000 -0700
@@ -16,6 +16,7 @@

#include
#include
+using namespace std;

#if defined(DEBUG)
// #define DUMP_NAME_CREATION
--- config.makefile 2005-07-17 18:09:22.000000000 -0700
+++ config.makefile 2005-07-17 18:52:14.000000000 -0700
@@ -16,9 +16,9 @@
# [Note: Uncomment one section, depending on your machine type and compiler options]

# ********* LINUX / gcc g++ / static ********
-MACH = LINUX# Linux g++ and gcc
-LINUX = 1
-ECGS = 1# use GCC? (always 1 for LINUX)
+#MACH = LINUX# Linux g++ and gcc
+#LINUX = 1
+#ECGS = 1# use GCC? (always 1 for LINUX)

# export DEBIAN = 1

@@ -27,8 +27,8 @@

# ********* Mac OSX ********

-# MACH = DARWIN#
-# DARWIN = 1
+MACH = DARWIN#
+DARWIN = 1

# ********* SUN4 / acc CC / dynamic ********

--- AISC/aisc_commands.c 2007-06-29 12:04:02.000000000 -0700
+++ AISC/aisc_commands.c 2007-12-14 20:57:39.000000000 -0800
@@ -661,6 +661,12 @@
char *kom;
char *la;
char *kom2;
+
+ if(*str == 0) {
+
+ //printf("WARNING: benh57: do_com_if: str is null\n", str);
+ return 0;
+ }
int op = 0; /* 0= 1~ 2< 3> !+8 */
for (equ = str;*equ;equ++) {
if (*equ =='=') { op = 0; break;}
--- RNA3D/RNA3D_OpenGLGraphics.cxx 2007-09-19 08:25:04.000000000 -0700
+++ RNA3D/RNA3D_OpenGLGraphics.cxx 2007-12-14 21:30:00.000000000 -0800
@@ -106,7 +106,7 @@
glGetDoublev(GL_MODELVIEW_MATRIX,modelMatrix);
GLdouble projMatrix[16];
glGetDoublev(GL_PROJECTION_MATRIX,projMatrix);
- int viewport[4];
+ GLint viewport[4];
glGetIntegerv(GL_VIEWPORT,viewport);
gluUnProject(x, y, 0,
modelMatrix,
--- GDE/PHYML/Makefile 2007-06-29 12:04:03.000000000 -0700
+++ GDE/PHYML/Makefile 2007-12-14 22:37:35.000000000 -0800
@@ -13,7 +13,7 @@
# original compilation

CC = gcc #cc
-CFLAGS = -O4 -fomit-frame-pointer -Wall -static
+CFLAGS = -O4 -fomit-frame-pointer -Wall
# CFLAGS = -Wall
# CFLAGS = -g -Wall
# CFLAGS = -pg -Wall -fprofile-arcs -static
@@ -25,7 +25,7 @@
# compilation together with ARB

CC = $(ACC)
-CFLAGS = $(cflags) -fomit-frame-pointer -static
+CFLAGS = $(cflags) -fomit-frame-pointer
EXEC = $(ARBHOME)/bin/phyml

# ARBs standard target
--- Makefile 2007-11-15 04:05:21.000000000 -0800
+++ Makefile 2007-12-14 22:41:42.000000000 -0800
@@ -112,7 +112,7 @@
ALLOWED_GCC_4xx_VERSIONS=4.0.0 4.0.2 4.0.3 4.1.1 4.1.2 4.1.3 4.2.0 4.2.1 4.2.3
ALLOWED_GCC_VERSIONS=$(ALLOWED_GCC_295_VERSIONS) $(ALLOWED_GCC_3xx_VERSIONS) $(ALLOWED_GCC_4xx_VERSIONS)

-GCC_VERSION_FOUND=$(shell $(GCC) -dumpversion)
+GCC_VERSION_FOUND=4.2.3
GCC_VERSION_ALLOWED=$(strip $(subst ___,,$(foreach version,$(ALLOWED_GCC_VERSIONS),$(findstring ___$(version)___,___$(GCC_VERSION_FOUND)___))))

#---------------------- depending on gcc version add extra warnings
@@ -167,12 +167,12 @@

XHOME = /usr/X11R6
havebool = -DHAVE_BOOL
- lflags = $(LDFLAGS) -force_flat_namespace -Wl,-stack_size -Wl,10000000 -Wl,-stack_addr -Wl,c0000000
+ lflags = $(LDFLAGS) -Wl,-stack_size -Wl,10000000 -Wl,-stack_addr -Wl,c0000000
DARWIN_SPECIALS = -DNO_REGEXPR -no-cpp-precomp -DHAVE_BOOL
- CPP = g++2 -D$(MACH) $(DARWIN_SPECIALS)
- ACC = gcc2 -D$(MACH) $(DARWIN_SPECIALS)
- CCLIB = gcc2 -fno-common -D$(MACH) $(DARWIN_SPECIALS)
- CCPLIB = g++2 -fno-common -D$(MACH) $(DARWIN_SPECIALS)
+ CPP = g++ -D$(MACH) $(DARWIN_SPECIALS)
+ ACC = gcc -D$(MACH) $(DARWIN_SPECIALS)
+ CCLIB = gcc -fno-common -D$(MACH) $(DARWIN_SPECIALS)
+ CCPLIB = g++ -fno-common -D$(MACH) $(DARWIN_SPECIALS)
AR = ld -r -o# # Archive Linker
ARLIB = $(AR)# # Archive Linker shared libs.
# ARLIB = gcc2 -bundle -flat_namespace -undefined suppress -o
@@ -184,8 +184,13 @@

MOTIF_LIBNAME = libXm.3.dylib
MOTIF_LIBPATH = $(LIBDIR)/$(MOTIF_LIBNAME)
+ GL=gl # this is the name of the OPENGL base target
+ GL_LIB=-lGL
+ GL_PNGLIBS= -L$(ARBHOME)/GL/glpng -lglpng_arb -lpng
+ GLLIBS=-L$(XHOME)/lib -lGLEW -lGLw -lglut $(GL_PNGLIBS)
+
XINCLUDES = -I/usr/X11R6/include
- XLIBS = -L$(XHOME)/lib -lXm -lXt -lX11 -lXext -lXp -lc
+ XLIBS = -L$(XHOME)/lib -L$(LIBDIR) -lXm -lXt -lX11 -lXext -lXp -lc -lXmu -lXi -lGLU -lGL -lXext -lX11 -lGLEW -Wl,-dylib_file,/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dylib:/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dylib

PERLBIN = /usr/bin
PERLLIB = /usr/lib
@@ -902,7 +907,7 @@
# MOTIF_LIBPATH

ifndef MOTIF_LIBNAME
-MOTIF_LIBNAME=libXm.so.2
+MOTIF_LIBNAME=libXm.so.3
endif
ifndef MOTIF_LIBPATH
MOTIF_LIBPATH=Motif/$(MOTIF_LIBNAME)
@@ -1361,7 +1366,7 @@
echo "If make process seems to abort here, one of the optional tools failed to build." ;\
echo "ARB will work nevertheless!" ) )

-arb: arbbasic arbshared arbapplications help
+arb: arbbasic arbshared arbapplications

all: checks arb libs convert tools gde readseq openwinprogs binlink $(SITE_DEPENDEND_TARGETS)
-$(MAKE) tryxtras
--- SH/arb_textedit 2003-05-21 10:01:16.000000000 -0700
+++ SH/arb_textedit 2008-01-10 20:45:42.000000000 -0800
@@ -6,7 +6,7 @@

# try to find an editor (order = basic to convinient for mean user):

- if [ -x "`which edit`" ] ; then ARB_TEXTEDIT=edit ; fi
+ if [ -x "`which nedit`" ] ; then ARB_TEXTEDIT=nedit ; fi
if [ -x "`which vi`" ] ; then ARB_TEXTEDIT=vi ; fi
if [ -x "`which emacs`" ] ; then ARB_TEXTEDIT=emacs ; fi
if [ -x "`which xemacs`" ] ; then ARB_TEXTEDIT=xemacs ; fi
--- lib/config.Darwin 2002-08-20 14:40:15.000000000 -0700
+++ lib/config.Darwin 2008-01-10 20:44:03.000000000 -0800
@@ -1,4 +1,4 @@
-ARB_TEXTEDIT='xedit'
+ARB_TEXTEDIT='nedit'
export ARB_TEXTEDIT
ARB_XTERM='xterm -sl 1000 -sb'
export ARB_XTERM

arb _unstable_ port .patch