Update of /cvsroot/fink/dists/10.2/unstable/main/finkinfo/sci
In directory sc8-pr-cvs1:/tmp/cvs-serv21555
Added Files:
arb.info arb.patch
Removed Files:
arb-20030603-3.info arb-20030603-3.patch
Log Message:
update
--- NEW FILE: arb.info ---
Package: arb
Version: 20030822
Revision: 1
Source: http://www2.mikro.biologie.tu-muenchen.de/download/ARB/src/%nsrc_2003_08_22.tgz
Source-MD5: f108ae6629f98d332e3d0a34298b9825
SourceDirectory: .
PatchScript: <<
#!/bin/sh -ex
perl -pi -e 's/ldd \$/otool -L \$/' AISC_COM/AISC/Makefile
cp config.makefile.template config.makefile; patch -p0 < %a/%f.patch
<<
BuildDepends: openmotif3 (>= 2.2.2-3), dlcompat-dev
#, libsablot
Depends: x11, openmotif3-shlibs (>= 2.2.2-3), xfig, ghostscript, app-defaults
Conflicts: clustalw, afni
CompileScript: <<
#!/bin/sh -ex
export CCACHE_DISABLE=1
export ARBHOME=%b
export PATH=$ARBHOME/bin:$PATH
# rm LIBLINK/*
make all PREFIX=%p LDFLAGS=-L%p/lib MOTIF_LIBPATH=%p/lib/libXm.3.dylib
LIBDIR=%p/lib LIBPATH="-LLIBLINK -L%p/lib" XINCLUDES="-I/usr/X11R6/include
-I%p/include/" CFLAGS=-DNDEBUG
<<
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: alignment.txt 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.
<<
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/
--- NEW FILE: arb.patch ---
--- ./config.makefile.orig Fri Aug 15 09:09:51 2003
+++ ./config.makefile Fri Aug 15 09:17:07 2003
@@ -13,9 +13,9 @@
# SEER = 1
#********* LINUX / gcc g++ / static ********
-MACH = LINUX# Linus g++ and gcc
-LINUX = 1
-ECGS = 1# for newer Linux-versions
+# MACH = LINUX# Linus g++ and gcc
+# LINUX = 1
+# ECGS = 1# for newer Linux-versions
# export DEBIAN = 1
@@ -24,8 +24,8 @@
#********* Mac OSX ********
-# MACH = DARWIN#
-# DARWIN = 1
+ MACH = DARWIN#
+ DARWIN = 1
#********* SUN4 / acc CC / dynamic ********
--- AWT/AWT_input_mask.cxx.orig Fri Aug 15 08:29:32 2003
+++ AWT/AWT_input_mask.cxx Fri Aug 15 08:30:32 2003
@@ -692,7 +692,10 @@
for (; b != buttons.end() && v != values.end(); ++b, ++v, ++pos) {
void (AW_window::*ins_togg)(AW_label, const char*, const char*);
- ins_togg = (pos == default_position) ? &AW_window::insert_default_toggle :
&AW_window::insert_toggle;
+ if(pos == default_position)
+ ins_togg = &AW_window::insert_default_toggle;
+ else
+ ins_togg = &AW_window::insert_toggle;
(aws->*ins_togg)(b->c_str(), mask_global()->hotkey(*b), b->c_str());
}
--- ./Makefile~ Wed Aug 13 21:52:41 2003
+++ ./Makefile Fri Aug 15 08:43:40 2003
@@ -848,7 +848,7 @@
# MOTIF_LIBPATH
ifndef MOTIF_LIBNAME
-MOTIF_LIBNAME=libXm.so.2
+MOTIF_LIBNAME=libXm.so.3
endif
ifndef MOTIF_LIBPATH
MOTIF_LIBPATH=Motif/$(MOTIF_LIBNAME)
@@ -1197,7 +1197,7 @@
arbshared: dball aw dp awt
arbapplications: nt pa ed e4 we pr pg na al nal di ph ds trs
-arb: arbbasic arbshared arbapplications help arbxtras
+arb: arbbasic arbshared arbapplications arbxtras
#arb: arbbasic db aw dp awt dbs nt pa ed e4 we pr pg na al nal di db2 ph ds trs help
arbxtras
save: rmbak
--- SECEDIT/SEC_main.cxx.orig Mon Jun 23 22:08:23 2003
+++ SECEDIT/SEC_main.cxx Mon Jun 23 22:06:24 2003
@@ -489,10 +489,10 @@
for (pos=0; ; pos++) {
BI_helix::BI_helix_entry *entry = &(helix->entries[pos]);
- //char *helix_nr = 0;
+ char *helix_nr = 0;
if (entry->pair_type!=HELIX_NONE) {
- char *helix_nr = entry->helix_nr;
+ helix_nr = entry->helix_nr;
if (helix_nr==start_helix_nr) { // same helix_nr as last
end_helix = pos;
@@ -545,10 +545,10 @@
for (pos=0; ; pos++) {
BI_helix::BI_helix_entry *entry = &(helix->entries[pos]);
- //char *helix_nr;
+ char *helix_nr = 0;
if (entry->pair_type!=HELIX_NONE) {
- char *helix_nr = entry->helix_nr;
+ helix_nr = entry->helix_nr;
if (helix_nr==start_helix_nr) { // same helix as last
end_helix = pos;
--- PROBE_GROUP/pg_main.cxx.orig Mon Jun 23 22:11:39 2003
+++ PROBE_GROUP/pg_main.cxx Fri Jul 5 02:56:58 2002
@@ -38,6 +38,7 @@
#define UU 0
#include <arbdbt.h>
+#include <stdarg.h>
using namespace std;
--- arb-20030603-3.info DELETED ---
--- arb-20030603-3.patch DELETED ---
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