Update of /cvsroot/fink/dists/10.4-transitional/stable/main/finkinfo/sci
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv23740
Added Files:
arb.info arb.patch
Log Message:
Stable.
--- NEW FILE: arb.patch ---
--- Makefile 2005-07-17 18:09:22.000000000 -0700
+++ Makefile 2005-07-17 19:22:47.000000000 -0700
@@ -135,12 +135,12 @@
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
@@ -153,7 +153,7 @@
MOTIF_LIBNAME = libXm.3.dylib
MOTIF_LIBPATH = $(LIBDIR)/$(MOTIF_LIBNAME)
XINCLUDES = -I/usr/X11R6/include
- XLIBS = -L$(XHOME)/lib -lXm -lXt -lX11 -lXext -lXp -lc
+ XLIBS = -L$(XHOME)/lib -L$(LIBDIR) -lXm -lXt -lX11 -lXext -lXp -lc
PERLBIN = /usr/bin
PERLLIB = /usr/lib
@@ -343,7 +343,7 @@
# ---------------------------------------- check gcc version
-GCC_VERSION_FOUND=$(shell $(GCC) --version | head -1 | sed
's/^[^0-9]*\([0-9.]\+\).*/\1/' )
+GCC_VERSION_FOUND=4.0.0
GCC_VERSION_ALLOWED=$(strip $(subst ___,,$(foreach
version,$(ALLOWED_GCC_VERSIONS),$(findstring
___$(version)___,___$(GCC_VERSION_FOUND)___))))
check_same_GCC_VERSION:
@@ -860,7 +860,7 @@
# MOTIF_LIBPATH
ifndef MOTIF_LIBNAME
-MOTIF_LIBNAME=libXm.so.2
+MOTIF_LIBNAME=libXm.so.3
endif
ifndef MOTIF_LIBPATH
MOTIF_LIBPATH=Motif/$(MOTIF_LIBNAME)
@@ -1295,7 +1295,7 @@
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
--- ARBDB/arbdb.h 2005-07-17 18:09:19.000000000 -0700
+++ ARBDB/arbdb.h 2005-07-17 18:44:40.000000000 -0700
@@ -2,8 +2,10 @@
#define ARBDB_H
#ifndef _STDIO_H
+#ifndef _STDIO_H_
#error "arbdb.h needs stdio.h included"
#endif
+#endif
#define NOT4PERL
/* function definitions starting with NOT4PERL are not included into the
ARB-perl-interface */
--- 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 <stdio.h> */
+#include <stdio.h>
#include <stdlib.h>
#include <string.h>
/* #include <malloc.h> */
@@ -1325,7 +1325,7 @@
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) */
@@ -1359,8 +1359,8 @@
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 <list>
#include <string>
+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 ********
--- NEW FILE: arb.info ---
Package: arb
Version: 20050526
Revision: 2
Source:
http://www2.mikro.biologie.tu-muenchen.de/download/ARB/pre_release/2005_05_26/arbsrc.tgz
#http://www2.mikro.biologie.tu-muenchen.de/download/ARB/src/%nsrc_2003_08_22.tgz
Source-MD5: 4efc37b69eb2cf5ca24c42bf26e9ee25
SourceDirectory: .
PatchScript: <<
#!/bin/sh -ex
cp config.makefile.template config.makefile; patch -p0 < %a/%n.patch
<<
BuildDepends: sed, openmotif3 (>= 2.2.2-3), x11-dev
Depends: x11, openmotif3-shlibs (>= 2.2.2-3), xfig, ghostscript, app-defaults
Conflicts: clustalw, afni
NoSetCXXFLAGS: true
CompileScript: <<
#!/bin/sh -ex
export CCACHE_DISABLE=1
export ARBHOME=%b
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/usr/X11R6/include
-I%p/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
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 <[EMAIL PROTECTED]>
Homepage: http://www.arb-home.de/
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