Update of /cvsroot/fink/dists/10.4/stable/main/finkinfo/sci
In directory sfp-cvsdas-3.v30.ch3.sourceforge.com:/tmp/cvs-serv15109/sci
Modified Files:
dx.info easychem.info gperiodic.info gperiodic.patch
Added Files:
dx-10.4.info emboss-6.3.1-3.info emboss-6.3.1-3.patch
emboss.info emboss.patch libplplot10-shlibs.info
libplplot10-shlibs.patch
Removed Files:
dx-10.6.info emboss-6.0.1-4.info emboss-6.0.1-4.patch
Log Message:
latest gnome and kde3 to stable, along with .la cleaning and associated build
fixes and others uncovered while working on it, and other related packages
--- dx-10.6.info DELETED ---
--- emboss-6.0.1-4.patch DELETED ---
--- NEW FILE: emboss-6.3.1-3.info ---
Package: emboss
Version: 6.3.1
Revision: 3
Depends: <<
%N-ajax6-shlibs (>= %v-%r),
%N-nucleus6-shlibs (>= %v-%r),
%N-plplot3-shlibs (>= %v-%r),
freetype219-shlibs (>= 2.3.8-2),
fontconfig2-shlibs (>= 2.4.1-1),
gd2-shlibs,
libiconv,
libjpeg-shlibs,
libpng3-shlibs,
system-java (>= 1.5.0),
x11,
x11-shlibs
<<
BuildDepends: <<
autoconf2.6,
automake1.11,
fink (>= 0.24.12),
fontconfig2-dev (>= 2.4.1-1),
freetype219 (>= 2.3.8-2),
gd2,
libiconv-dev,
libjpeg,
libpng3,
libtool2,
system-java-dev (>= 1.5.0),
x11-dev
<<
Source: mirror:custom:EMBOSS-%v.tar.gz
CustomMirror: <<
Primary: ftp://emboss.open-bio.org/pub/EMBOSS/
<<
Source-MD5: 04d1179b6261103a77e396d54f8ac38e
#SetCPPFLAGS: -Dstat64=stat
PatchFile: %n-%v-%r.patch
PatchFile-MD5: 381f5ca50a03fee61b7a24baf5cd87cf
ConfigureParams: <<
--with-java=/System/Library/Frameworks/JavaVM.framework/Versions/1.5.0/Home \
--with-javaos=/System/Library/Frameworks/JavaVM.framework/Versions/1.5.0/Home/include
\
--disable-dependency-tracking \
--libdir=%p/lib/EMBOSS \
--docdir=%p/share/EMBOSS
<<
CompileScript: <<
%p/bin/autoreconf -fi
./configure %c
make
<<
Installscript: <<
make install DESTDIR=%d
mkdir -p %i/include/EMBOSS
mv %i/include/*.* %i/include/EMBOSS/
ln -s
EMBOSS/lib{ajax,ajaxg,ajaxdb,nucleus,eplplot,acd,eexpat,ensembl,epcre,ezlib}.dylib
%i/lib
mv %i/lib/EMBOSS/*.*a %i/lib
<<
SplitOff10: <<
Package: %N-ajax6-shlibs
Depends: <<
%N-plplot3-shlibs (>= %v-%r),
fontconfig2-shlibs (>= 2.4.1-1),
freetype219-shlibs (>= 2.3.8-2),
gd2-shlibs,
libiconv,
libjpeg-shlibs,
libpng3-shlibs,
x11-shlibs
<<
DocFiles: ChangeLog COPYING README
Files: <<
lib/EMBOSS/libajax.6*.dylib
lib/EMBOSS/libajaxdb.6*.dylib
lib/EMBOSS/libajaxg.6*.dylib
lib/EMBOSS/libacd.6*.dylib
lib/EMBOSS/libensembl.6*.dylib
lib/EMBOSS/libeexpat.1*.dylib
lib/EMBOSS/libepcre.7*.dylib
lib/EMBOSS/libezlib.1*.dylib
<<
Shlibs: <<
%p/lib/EMBOSS/libajax.6.dylib 7.0.0 %n (>= 6.2.0-1)
%p/lib/EMBOSS/libajaxdb.6.dylib 7.0.0 %n (>= 6.2.0-1)
%p/lib/EMBOSS/libajaxg.6.dylib 7.0.0 %n (>= 6.2.0-1)
%p/lib/EMBOSS/libacd.6.dylib 7.0.0 %n (>= 6.2.0-1)
%p/lib/EMBOSS/libensembl.6.dylib 7.0.0 %n (>= 6.2.0-1)
%p/lib/EMBOSS/libeexpat.1.dylib 3.0.0 %n (>= 6.2.0-1)
%p/lib/EMBOSS/libepcre.7.dylib 8.0.0 %n (>= 6.2.0-1)
%p/lib/EMBOSS/libezlib.1.dylib 3.0.0 %n (>= 6.2.0-1)
<<
<<
SplitOff11: <<
Package: %N-ajax6-dev
Depends: %N-ajax6-shlibs (= %v-%r)
Conflicts: %N-dev, %N-ajax4-dev, %N-ajax5-dev
Replaces: %N-dev, %N-ajax4-dev, %N-ajax5-dev
DocFiles: ChangeLog COPYING README
Files: <<
lib/libajax*
lib/libacd*
lib/libensembl*
lib/libeexpat*
lib/libepcre*
lib/libezlib*
lib/EMBOSS/libajax*
lib/EMBOSS/libacd*
lib/EMBOSS/libensembl*
lib/EMBOSS/libeexpat*
lib/EMBOSS/libepcre*
lib/EMBOSS/libezlib*
include/EMBOSS/aj*.h
include/EMBOSS/ens*.h
include/eexpat
include/epcre
include/ezlib
<<
BuildDependsOnly: True
<<
SplitOff20: <<
Package: %N-nucleus6-shlibs
Depends: %N-ajax6-shlibs (>= %v-%r)
Replaces: %N (<< 6.0.0-1)
DocFiles: ChangeLog COPYING README
Files: <<
lib/EMBOSS/libnucleus.6*.dylib
<<
Shlibs: <<
%p/lib/EMBOSS/libnucleus.6.dylib 7.0.0 %n (>= 6.2.0-1)
<<
<<
SplitOff21: <<
Package: %N-nucleus6-dev
Depends: %N-nucleus6-shlibs (= %v-%r)
Conflicts: %N-dev, %N-nucleus4-dev, %N-nucleus5-dev
Replaces: %N-dev, %N (<< 5.0.0-3), %N-nucleus4-dev, %N-nucleus5-dev
DocFiles: ChangeLog COPYING README
Files: <<
lib/libnucleus*
lib/EMBOSS/libnucleus*
include/EMBOSS/em*.h
<<
BuildDependsOnly: True
<<
SplitOff30: <<
Package: %N-plplot3-shlibs
Depends: <<
fontconfig2-shlibs (>= 2.4.1-1),
freetype219-shlibs (>= 2.3.8-2),
gd2-shlibs,
libpng3-shlibs,
libjpeg-shlibs,
libiconv,
x11-shlibs
<<
# identical Shlibs-supplier package was previously named as "5" and "6"
# uses "3" as of 6.1.0-4 to match .dylib filename
Replaces: %N (<< 5.0.0-1), %N-plplot5-shlibs, %N-plplot6-shlibs
DocFiles: ChangeLog COPYING README
Files: <<
lib/EMBOSS/libeplplot.3*.dylib
<<
Shlibs: <<
%p/lib/EMBOSS/libeplplot.3.dylib 6.0.0 %n (>= 6.2.0-1)
<<
<<
SplitOff31: <<
Package: %N-plplot3-dev
Depends: %N-plplot3-shlibs (= %v-%r)
Conflicts: %N-dev, %N-plplot5-dev, %N-plplot6-dev
Replaces: %N-dev, %N (<< 6.0.0-1), %N-plplot5-dev, %N-plplot6-dev
DocFiles: ChangeLog COPYING README
Files: <<
lib/libeplplot*
lib/EMBOSS/libeplplot*
include/eplplot
<<
BuildDependsOnly: True
<<
RunTimeVars: <<
# PLPLOT_LIB: %p/share/EMBOSS/
EMBOSS_DATA: %p/share/EMBOSS/data
<<
DocFiles: <<
AUTHORS ChangeLog COMPAT COPYING FAQ INSTALL KNOWN_BUGS LICENSE NEWS PROBLEMS
README README.fixes THANKS
<<
Description: Molecular Biology Open Software Suite
DescDetail: <<
EMBOSS is a free Open Source software analysis package specially
developed for the needs of the molecular biology (e.g. EMBnet) user
community. The software automatically copes with data in a variety of
formats and even allows transparent retrieval of sequence data from the
web. Also, as extensive libraries are provided with the package, it is a
platform to allow other scientists to develop and release software in
true open source spirit. EMBOSS also integrates a range of currently
available packages and tools for sequence analysis into a seamless
whole.
<<
DescUsage: <<
See the README file for other environment variables you may need to
configure. See http://emboss.sourceforge.net/Jemboss/ for
information on using the Jemboss GUI for EMBOSS. To prevent conflicts,
the headers are located in %p/include/EMBOSS instead of %p/include.
Install kemboss-qt4 for a GUI that works either in Aqua or X11.
<<
DescPort: <<
dmacks added explicit linking to libs that supply symbols used by
the shared libraries here. This prevents things that link against
the shared libraries from having to know to pass additional flags
when the linker requires all symbols be defined.
dmacks overhauled splitoff layout so that lib versions can float
against each other and patched to assure use of EMBOSS's own pcre
headers (libpcre doesn't understand ABI compatibility rules:(
<<
DescPackaging: <<
Former Maintainer: Koen van der Drift <drift...@users.sourceforge.net>
<<
Maintainer: None <fink-de...@lists.sourceforge.net>
Homepage: http://emboss.sourceforge.net
License: GPL
--- NEW FILE: libplplot10-shlibs.info ---
Info2: <<
Package: libplplot10-shlibs
Version: 5.9.6
Revision: 2
BuildDepends: <<
aquaterm-dev,
cairo (>= 1.8.8-3),
cmake,
fink (>= 0.27.2),
fink-package-precedence,
fontconfig2-dev (>= 2.8.0-4),
freetype219 (>= 2.3.12-1),
glib2-dev (>= 2.22.0-1),
lasi-dev,
libtool2,
pango1-xft2-ft219-dev (>= 1.24.5-4),
pixman (>= 0.16.0-1),
pkgconfig,
qhull,
readline5,
swig,
x11-dev
<<
Depends: <<
aquaterm-shlibs,
cairo-shlibs (>= 1.8.8-3),
fontconfig2-shlibs (>= 2.8.0-4),
freetype219-shlibs (>= 2.3.12-1),
glib2-shlibs (>= 2.22.0-1),
lasi-shlibs,
libcsiro1-shlibs (>= %v-%r),
libtool2-shlibs,
pango1-xft2-ft219-shlibs (>= 1.24.5-4),
x11
<<
GCC: 4.0
Source: mirror:sourceforge:plplot/plplot-%v.tar.gz
Source-MD5: 772c772bde3a107e5f06d21cefa7f6b6
PatchFile: %n.patch
PatchFile-MD5: 46e139e1b9ad6eb0fec90480b0db37ba
PatchScript: <<
sed -e 's,@PREFIX@,%p,g' < %{PatchFile} | patch -p1
perl -pi.bak -e 's/(set\(\S+_SOVERSION\s+)(\d+)/"$1".(1+$2);/e'
cmake/modules/plplot_version.cmake
perl -pi -e 's,/usr/local,%p,g' cmake/modules/FindLTDL.cmake
<<
NoSetMAKEFLAGS: true
SetMAKEFLAGS: -j1
SetCFLAGS: -MD
SetCXXFLAGS: -MD
CompileScript: <<
#!/bin/sh -ev
export CCACHE_DISABLE=1
export
PKG_CONFIG_PATH=%p/lib/glib-2.0/pkgconfig-strict:%p/lib/fontconfig2/lib/pkgconfig:$PKG_CONFIG_PATH
%p/bin/cmake -DCMAKE_VERBOSE_MAKEFILE:BOOL=ON \
-DCMAKE_INSTALL_PREFIX:PATH=%p \
-DCMAKE_INSTALL_LIBDIR:PATH=%p/lib/plplot \
-DBUILD_SHARED_LIBS:BOOL=ON \
-DDEFAULT_NO_BINDINGS:BOOL=ON \
-DENABLE_cxx:BOOL=ON \
-DPLD_wxwidgets:BOOL=OFF \
-DLTDL_LIBRARIES:FILEPATH=%p/lib/libltdl.dylib \
.
make
fink-package-precedence \
--prohibit-bdep=plplot-dev,plplot-nognome-dev \
--prohibit-bdep=libplplot10-dev \
--prohibit-bdep=libcsiro1-dev \
--depfile-ext='\.d' \
.
<<
InstallScript: <<
#!/bin/sh -ev
make install DESTDIR=%d
# can't find cmake flag to control this location
# (overriding default based on libdir)
mv %i/lib/plplot/pkgconfig %i/lib
## remove silliness from pkg-config data
#perl -pi -e 's,-L/usr/lib,,g' %i/lib/pkgconfig/plplotd.pc
# aw heck, remove *everything* except direct link (Requires:
# gets plplot sublibs, not need internal implementation libs)
perl -pi -e 's/^Libs:.*/Libs: -L\${libdir} -lplplotd/'
%i/lib/pkgconfig/plplotd.pc
# fix installation of docfiles to use upstream set but in
# fink-policy-required location: save and restore automatic
mv %i/share/doc/plplot TARGET_DOC_FILES
<<
DocFiles: TARGET_DOC_FILES/*
Shlibs: <<
%p/lib/plplot/libplplotd.10.dylib 10.0.0 %n (>= 5.9.6-1)
%p/lib/plplot/libplplotcxxd.10.dylib 10.0.0 %n (>= 5.9.6-1)
%p/lib/plplot/libqsastime.1.dylib 1.0.0 %n (>= 5.9.6-1)
<<
SplitOff: <<
Package: libplplot10-dev
Depends: libplplot10-shlibs (= %v-%r)
Replaces: <<
plplot-dev, plplot-nognome-dev
<<
BuildDependsOnly: true
Files: <<
include
lib/pkgconfig
lib/plplot/libplplotd.dylib
lib/plplot/libplplotcxxd.dylib
lib/plplot/libqsastime.dylib
share/plplot5.9.6/examples
<<
DocFiles: TARGET_DOC_FILES/*
<<
SplitOff10: <<
Package: libcsiro1-shlibs
Files: <<
lib/plplot/libcsirocsa.*.dylib
lib/plplot/libcsironn.*.dylib
<<
Shlibs: <<
%p/lib/plplot/libcsirocsa.1.dylib 1.0.0 %n (>= 5.9.6-1)
%p/lib/plplot/libcsironn.1.dylib 1.0.0 %n (>= 5.9.6-1)
<<
DocFiles: TARGET_DOC_FILES/*
<<
SplitOff11: <<
Package: libcsiro1-dev
Depends: libcsiro1-shlibs (= %v-%r)
BuildDependsOnly: true
Files: <<
lib/plplot/libcsirocsa.dylib
lib/plplot/libcsironn.dylib
<<
DocFiles: TARGET_DOC_FILES/*
<<
SplitOff2: <<
Package: plplot-bin
Depends: <<
libcsiro1-shlibs (>= %v-%r),
libplplot10-shlibs (>= %v-%r)
<<
Replaces: plplot, plplot-nognome
Files: <<
bin
share/man
<<
DocFiles: TARGET_DOC_FILES/*
<<
Description: Scientific plotting package
DescDetail: <<
PLplot is relatively small, portable, freely distributable, and is rich
enough to satisfy most users. It has a wide range of plot types
including line (linear, log), contour, 3D, fill, and almost 1000
characters (including Greek and mathematical) in its extended font set.
The package is designed to make it easy to quickly get graphical output;
only a handful of function calls is typically required. For more
advanced use, virtually all aspects of plotting are configurable.
"plplot-bin" is some useful utility programs (plm2gif, plpr,
pltex). Some formerly-supplied programs are no longer available
because they were buggy and/or obsolete (plrender, pltex), or
specifically related to certain bindings sets (pltcl, plserver).
This packaging is just the basic libraries (no bindings for languages
that are themselves large fink package trees).
<<
DescUsage: <<
<<
DescPackaging: <<
Fix aqt.cmake to use fink's aquaterm package instead of
non-fink Framework installation of it.
Try to fix ldtl detection to look in fink dir (cmake tests
don't know to look in "nothing special" (use-test) rather than
searching for file by name?) but mainly hardcode it because
cmake library detection is an opaque mess.
Bump all SOVERSION by 1 so that none are zero because
compatibility_version 0.0.0 has a special meaning that cmake
doesn't understand (libtool was smart enough to do this
automatically). There does not appear to be a separate
variable for c_v and VERSION only affects the .x.y.z.dylib
filename not the .x.filename (WTF?)
No idea why default installation with certain features
disabled installs headers specifically for them (gcw.h), but
not fixing it for now. That and the splitoff divisions based
on debian's packaging.
All symbols are resolved, so neuter un-needed linking from .pc
Libs. The csiro stuff looks like only used internally and by
own binaries (no public .h).
Old plplot suite layout was a disaster, with multiple
providers of same libs that could not swap cleanly (removing
one left hole in other!) because of Provides, and Replaces
without Conflicts. Even with new %n for headers, we cannot
Replaces/Conflicts to eject the old -dev packages because
there are runtime Depends on them (BDO:false) and having the
same name in a Provides and a real Package confuses dpkg. So
we just kill old .info and Replaces much of it, hopefully old
will eventually fade away from users' systems.
<<
License: LGPL
Maintainer: None <fink-de...@lists.sourceforge.net>
Homepage: http://plplot.sourceforge.net
<<
Index: easychem.info
===================================================================
RCS file: /cvsroot/fink/dists/10.4/stable/main/finkinfo/sci/easychem.info,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -d -r1.4 -r1.5
--- easychem.info 6 Jan 2010 01:08:02 -0000 1.4
+++ easychem.info 2 Nov 2010 15:46:18 -0000 1.5
@@ -1,37 +1,35 @@
Package: easychem
Version: 0.6
-Revision: 3
+Revision: 4
BuildDepends: <<
- atk1 (>= 1.20.0-1),
- cairo (>= 1.6-1),
- expat1,
+ atk1 (>= 1.28.0-1),
+ cairo (>= 1.8.8-3),
fink (>= 0.24.12-1),
- fontconfig2-dev (>= 2.4.1-1),
- freetype219 (>= 2.3.5-1),
+ fink-package-precedence,
+ fontconfig2-dev (>= 2.8.0-4),
+ freetype219 (>= 2.3.12-1),
gettext-tools,
- glib2-dev (>= 2.14.0-1),
+ glib2-dev (>= 2.22.0-1),
glitz,
- gtk+2 (>= 2.12.0-1),
- gtk+2-dev (>= 2.12.0-1),
- libgettext3-dev,
- libiconv-dev,
- libpng3,
- pango1-xft2-ft219-dev (>= 1.18.4-4),
- pixman (>= 0.10.0-1),
- pkgconfig (>= 0.21-1),
+ gtk+2-dev (>= 2.18.0-1),
+ libgettext8-dev,
+ pango1-xft2-ft219-dev (>= 1.24.5-4),
+ pixman (>= 0.16.0-1),
+ pkgconfig (>= 0.23),
sed,
- x11-dev,
- xft2-dev
+ x11-dev
<<
Depends: <<
- atk1-shlibs (>= 1.20.0-1),
+ atk1-shlibs (>= 1.28.0-1),
+ cairo-shlibs (>= 1.8.8-3),
+ fontconfig2-shlibs (>= 2.8.0-4),
+ freetype219-shlibs (>= 2.3.12-1),
ghostscript,
- glib2-shlibs (>= 2.14.0-1),
- gtk+2-shlibs (>= 2.12.0-1),
- libgettext3-shlibs,
- libiconv,
- pstoedit-bin,
- x11-shlibs
+ glib2-shlibs (>= 2.22.0-1),
+ gtk+2-shlibs (>= 2.18.0-1),
+ libgettext8-shlibs,
+ pango1-xft2-ft219-shlibs (>= 1.24.5-4),
+ pstoedit-bin
<<
Source: mirror:sourceforge:easychem/%n-%v.tar.gz
Source-MD5: e3c9a7fb7807b6abc592a3472a65d969
@@ -41,7 +39,14 @@
%{default_script}
perl -pi -e 's,sed,gsed,g' postscript/Makefile
<<
-CompileScript:
PKG_CONFIG_PATH="%p/lib/pango-ft219/lib/pkgconfig:%p/lib/fontconfig2/lib/pkgconfig:%p/lib/freetype219/lib/pkgconfig:$PKG_CONFIG_PATH"
FREETYPE_CONFIG=%p/lib/freetype219/bin/freetype-config make -j1 -f
Makefile.linux PREFIX=%p
+SetCPPFLAGS: -MD
+SetLDFLAGS: -lintl
+CompileScript: <<
+#!/bin/sh -ev
+ export
PKG_CONFIG_PATH="%p/lib/glib-2.0/pkgconfig-strict:%p/lib/fontconfig2/lib/pkgconfig:$PKG_CONFIG_PATH"
+ make -j1 -f Makefile.linux PREFIX=%p
+ fink-package-precedence --depfile-ext='\.d' .
+<<
InstallScript: <<
mkdir -p %i/bin
cp easychem %i/bin
--- NEW FILE: emboss.patch ---
diff -Nurd -x'*~' EMBOSS-6.3.1.orig/Makefile.am EMBOSS-6.3.1/Makefile.am
--- EMBOSS-6.3.1.orig/Makefile.am 2010-01-11 08:15:41.000000000 -0500
+++ EMBOSS-6.3.1/Makefile.am 2010-08-04 12:15:15.000000000 -0400
@@ -5,7 +5,10 @@
AUTOMAKE_OPTIONS = gnits
-SUBDIRS = plplot ajax nucleus emboss test doc jemboss
+if !ESYSTEMLIBS
+EXTRA_DIRS = plplot
+endif
+SUBDIRS = $(EXTRA_DIRS) ajax nucleus emboss test doc jemboss
# AJAX_FIXED_ROOT = \"`pwd`/emboss/acd\"
diff -Nurd -x'*~' EMBOSS-6.3.1.orig/ajax/Makefile.am
EMBOSS-6.3.1/ajax/Makefile.am
--- EMBOSS-6.3.1.orig/ajax/Makefile.am 2010-06-16 06:26:45.000000000 -0400
+++ EMBOSS-6.3.1/ajax/Makefile.am 2010-08-04 19:07:47.000000000 -0400
@@ -1,6 +1,6 @@
## Process this file with automake to produce Makefile.in
if !ESYSTEMLIBS
-EXTRA_DIRS = expat zlib
+EXTRA_DIRS = pcre expat zlib
endif
-SUBDIRS = pcre $(EXTRA_DIRS) core graphics ensembl ajaxdb acd
+SUBDIRS = $(EXTRA_DIRS) core graphics ensembl ajaxdb acd
diff -Nurd -x'*~' EMBOSS-6.3.1.orig/ajax/acd/Makefile.am
EMBOSS-6.3.1/ajax/acd/Makefile.am
--- EMBOSS-6.3.1.orig/ajax/acd/Makefile.am 2010-06-16 07:36:00.000000000
-0400
+++ EMBOSS-6.3.1/ajax/acd/Makefile.am 2010-08-06 04:31:47.000000000 -0400
@@ -13,10 +13,13 @@
endif
if !ESYSTEMLIBS
-EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib
+EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib \
+-I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre
+else
+EXTRA_INCLUDES = $(PLPLOT_CFLAGS)
endif
-INCLUDES = -I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre \
+INCLUDES = \
$(EXTRA_INCLUDES) \
-I$(top_srcdir)/ajax/core \
-I$(top_srcdir)/ajax/graphics \
@@ -38,3 +41,4 @@
endif
libacd_la_LDFLAGS = $(LINKFLAGS)
+libacd_la_LIBADD = ../core/libajax.la ../graphics/libajaxg.la
../ajaxdb/libajaxdb.la
diff -Nurd -x'*~' EMBOSS-6.3.1.orig/ajax/ajaxdb/Makefile.am
EMBOSS-6.3.1/ajax/ajaxdb/Makefile.am
--- EMBOSS-6.3.1.orig/ajax/ajaxdb/Makefile.am 2010-06-16 07:36:00.000000000
-0400
+++ EMBOSS-6.3.1/ajax/ajaxdb/Makefile.am 2010-08-06 04:19:18.000000000
-0400
@@ -13,11 +13,12 @@
endif
if !ESYSTEMLIBS
-EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib
+EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib \
+-I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre
endif
-INCLUDES = -I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre \
+INCLUDES = \
$(EXTRA_INCLUDES) \
-I$(top_srcdir)/ajax/core -I$(top_srcdir)/ajax/ensembl
@@ -37,3 +38,4 @@
endif
libajaxdb_la_LDFLAGS = $(LINKFLAGS)
+libajaxdb_la_LIBADD = ../core/libajax.la ../ensembl/libensembl.la
diff -Nurd -x'*~' EMBOSS-6.3.1.orig/ajax/core/Makefile.am
EMBOSS-6.3.1/ajax/core/Makefile.am
--- EMBOSS-6.3.1.orig/ajax/core/Makefile.am 2010-06-16 07:36:00.000000000
-0400
+++ EMBOSS-6.3.1/ajax/core/Makefile.am 2010-08-06 08:16:54.000000000 -0400
@@ -12,13 +12,18 @@
endif
if !ESYSTEMLIBS
-EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib
+EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib \
+-I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre
+else
+EXTRA_LIBS = -lexpat -lpcre
endif
+EXTRA_DIST = ajax-pcre-config.h.in
+DISTCLEAN = ajax-pcre-config.h
INCLUDES = -DAJAX_FIXED_ROOT=$(AJAX_FIXED_ROOT) \
-DAJAX_SYSTEM="$(AJAX_SYSTEM)" -DPREFIX=\"$(prefix)\" \
--I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre $(EXTRA_INCLUDES)
+$(EXTRA_INCLUDES) $(POSTGRESQL_CFLAGS) $(MYSQL_CFLAGS)
AJAXSRC = ajalign.c ajarr.c ajassert.c \
ajbase.c ajcall.c ajcod.c \
@@ -44,7 +49,7 @@
ajmath.h ajmatrices.h ajmem.h ajmess.h \
ajnam.h ajnexus.h ajobo.h \
ajpat.h ajpdb.h ajpdbio.h ajphylo.h \
-ajrange.h ajreg.h ajreport.h ajresource.h \
+ajrange.h ajreg.h ajax-pcre-config.h ajreport.h ajresource.h \
ajseq.h ajseqabi.h ajseqbam.h ajseqdata.h ajseqread.h ajseqtype.h ajseqwrite.h
\
ajsort.h ajsql.h ajstr.h ajsys.h \
ajtable.h ajtax.h ajtime.h ajtranslate.h ajtree.h ajutil.h ajvector.h
@@ -61,3 +66,4 @@
endif
libajax_la_LDFLAGS = $(LINKFLAGS)
+libajax_la_LIBADD = $(EXTRA_LIBS) $(POSTGRESQL_LDFLAGS) $(MYSQL_LDFLAGS)
diff -Nurd -x'*~' EMBOSS-6.3.1.orig/ajax/core/ajax-pcre-config.h.in
EMBOSS-6.3.1/ajax/core/ajax-pcre-config.h.in
--- EMBOSS-6.3.1.orig/ajax/core/ajax-pcre-config.h.in 1969-12-31
19:00:00.000000000 -0500
+++ EMBOSS-6.3.1/ajax/core/ajax-pcre-config.h.in 2010-08-04
20:21:16.000000000 -0400
@@ -0,0 +1 @@
+...@define_use_system_pcre@ AJAX_USE_SYSTEM_PCRE
diff -Nurd -x'*~' EMBOSS-6.3.1.orig/ajax/core/ajreg.h
EMBOSS-6.3.1/ajax/core/ajreg.h
--- EMBOSS-6.3.1.orig/ajax/core/ajreg.h 2010-04-14 03:44:20.000000000 -0400
+++ EMBOSS-6.3.1/ajax/core/ajreg.h 2010-08-04 20:29:22.000000000 -0400
@@ -16,9 +16,14 @@
#define ajreg_h
#include "ajax.h"
+#include "ajax-pcre-config.h"
+#ifndef AJAX_USE_SYSTEM_PCRE
#include "pcre_config.h"
#include "pcre_internal.h"
#include "pcreposix.h"
+#else
+#include <pcre.h>
+#endif
#define AJREG_OVECSIZE 30
@@ -41,7 +46,11 @@
******************************************************************************/
typedef struct AjSRegexp {
+#ifndef AJAX_USE_SYSTEM_PCRE
real_pcre *pcre;
+#else
+ pcre *pcre;
+#endif
pcre_extra *extra;
int *ovector;
const char* orig;
diff -Nurd -x'*~' EMBOSS-6.3.1.orig/ajax/ensembl/Makefile.am
EMBOSS-6.3.1/ajax/ensembl/Makefile.am
--- EMBOSS-6.3.1.orig/ajax/ensembl/Makefile.am 2010-06-16 07:36:00.000000000
-0400
+++ EMBOSS-6.3.1/ajax/ensembl/Makefile.am 2010-08-06 04:16:49.000000000
-0400
@@ -10,12 +10,13 @@
endif
if !ESYSTEMLIBS
-EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat
+EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat \
+-I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre
endif
-INCLUDES = -I$(top_srcdir)/plplot $(EXTRA_INCLUDES) \
--I$(top_srcdir)/ajax/pcre -I$(top_srcdir)/ajax/core
+INCLUDES = $(EXTRA_INCLUDES) \
+-I$(top_srcdir)/ajax/core
ENSEMBLSRC = ensanalysis.c ensassembly.c ensassemblyexception.c \
ensassemblymapper.c ensattribute.c ensbaseadaptor.c enscache.c \
@@ -56,3 +57,4 @@
endif
libensembl_la_LDFLAGS = $(LINKFLAGS)
+libensembl_la_LIBADD = ../core/libajax.la
diff -Nurd -x'*~' EMBOSS-6.3.1.orig/ajax/graphics/Makefile.am
EMBOSS-6.3.1/ajax/graphics/Makefile.am
--- EMBOSS-6.3.1.orig/ajax/graphics/Makefile.am 2010-06-16 07:36:00.000000000
-0400
+++ EMBOSS-6.3.1/ajax/graphics/Makefile.am 2010-08-06 04:09:10.000000000
-0400
@@ -10,11 +10,15 @@
endif
if !ESYSTEMLIBS
-EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat
+EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat \
+-I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre
+else
+EXTRA_INCLUDES = $(PLPLOT_CFLAGS) -DUSE_PLXSFNAM_SHIM
+EXTRA_LIBS = $(PLPLOT_LIBS)
endif
-INCLUDES = -I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre \
+INCLUDES = \
$(EXTRA_INCLUDES) -I$(top_srcdir)/ajax/core
AJAXGSRC = ajgraph.c ajhist.c
@@ -32,3 +36,4 @@
endif
libajaxg_la_LDFLAGS = $(LINKFLAGS)
+libajaxg_la_LIBADD = ../core/libajax.la $(EXTRA_LIBS)
diff -Nurd -x'*~' EMBOSS-6.3.1.orig/ajax/graphics/ajgraph.c
EMBOSS-6.3.1/ajax/graphics/ajgraph.c
--- EMBOSS-6.3.1.orig/ajax/graphics/ajgraph.c 2010-07-19 07:40:00.000000000
-0400
+++ EMBOSS-6.3.1/ajax/graphics/ajgraph.c 2010-08-06 04:11:20.000000000
-0400
@@ -1054,8 +1054,18 @@
{
if(!thys->ready)
{
+#ifdef USE_PLXSFNAM_SHIM
+ char *fullname;
+#endif
ajDebug("=g= plxsfnam ('%S', '%s')\n", txt, ext);
+#ifdef USE_PLXSFNAM_SHIM
+ fullname = asprintf(fullname,"%s%s", ajStrGetPtr(txt), ext);
+ ajDebug("=g= plsfnam ('%S') instead\n", fullname);
+ plsfnam(fullname);
+ free(fullname);
+#else
plxsfnam(ajStrGetPtr(txt), ext);
+#endif
ajStrAssignS(&graphBasename, txt);
ajStrAssignC(&graphExtension, ext);
if(ajStrGetCharFirst(graphExtension) == '.')
diff -Nurd -x'*~' EMBOSS-6.3.1.orig/configure.in EMBOSS-6.3.1/configure.in
--- EMBOSS-6.3.1.orig/configure.in 2010-07-19 07:45:34.000000000 -0400
+++ EMBOSS-6.3.1/configure.in 2010-08-06 07:20:07.000000000 -0400
@@ -235,15 +235,6 @@
AC_PROG_LN_S
AC_PROG_MAKE_SET
-dnl Intel MacOSX 10.6 puts X11 in a non-standard place
-if test "${with_x}" != "no" ; then
-if test "`uname -a | grep Darwin`"; then
-OSXX=`sw_vers -productVersion | sed 's/\(10\.[[0-9]]*\).*/\1/'`
-if test ${OSXX} '>' '10.4'; then
-CFLAGS="$CFLAGS -I/usr/X11/include -L/usr/X11/lib"
-fi
-fi
-fi
# Checks for header files.
#as# AC_PATH_X
@@ -292,9 +283,6 @@
#as# select socket sqrt strchr strcspn strdup strerror strpbrk \
#as# strrchr strspn strstr strtol])
-if test "${with_x}" != "no" ; then
-LF_EMBOSS_PATH_XLIB
-fi
dnl Library checks
AC_CHECK_LIB(c, socket, LIBS="$LIBS" , LIBS="$LIBS -lsocket")
@@ -322,8 +310,8 @@
CFLAGS="$CFLAGS $MYSQL_CFLAGS"
LDFLAGS="$LDFLAGS $MYSQL_LDFLAGS"
-CFLAGS="$CFLAGS $POSTGRESQL_CFLAGS"
-LDFLAGS="$LDFLAGS $POSTGRESQL_LDFLAGS"
+CFLAGS="$POSTGRESQL_CFLAGS $CFLAGS"
+LDFLAGS="$POSTGRESQL_LDFLAGS $LDFLAGS"
dnl Check for 'ant' for packaging Jemboss and export result
@@ -443,13 +431,33 @@
dnl Test if --enable-systemlibs given
have_systemlibs=no
+DEFINE_USE_SYSTEM_PCRE="#undef"
AC_ARG_ENABLE(systemlibs,
AS_HELP_STRING([--enable-systemlibs], [utility for RPM/dpkg bundles]))
if test "${enable_systemlibs}" = "yes" ; then
have_systemlibs=yes
+ DEFINE_USE_SYSTEM_PCRE="#define"
+ PKG_CHECK_MODULES(PLPLOT, [plplotd])
+else
+ dnl X11 is only used by plplot
+ dnl Intel MacOSX 10.6 puts X11 in a non-standard place
+ if test "${with_x}" != "no" ; then
+ if test "`uname -a | grep Darwin`"; then
+ OSXX=`sw_vers -productVersion | sed 's/\(10\.[[0-9]]*\).*/\1/'`
+ if test ${OSXX} '>' '10.4'; then
+ CFLAGS="$CFLAGS -I/usr/X11/include -L/usr/X11/lib"
+ fi
+ fi
+ fi
+ if test "${with_x}" != "no" ; then
+ LF_EMBOSS_PATH_XLIB
+ fi
fi
AM_CONDITIONAL(ESYSTEMLIBS, test "$have_systemlibs" = "yes")
AC_SUBST(ESYSTEMLIBS)
+AC_SUBST(DEFINE_USE_SYSTEM_PCRE)
+AC_SUBST(PLPLOT_CFLAGS)
+AC_SUBST(PLPLOT_LIBS)
@@ -683,6 +691,7 @@
AC_OUTPUT([plplot/Makefile plplot/lib/Makefile nucleus/Makefile ajax/Makefile
+ajax/core/ajax-pcre-config.h
ajax/pcre/Makefile ajax/expat/Makefile ajax/zlib/Makefile ajax/core/Makefile
ajax/graphics/Makefile ajax/ensembl/Makefile ajax/ajaxdb/Makefile
ajax/acd/Makefile
diff -Nurd -x'*~' EMBOSS-6.3.1.orig/emboss/Makefile.am
EMBOSS-6.3.1/emboss/Makefile.am
--- EMBOSS-6.3.1.orig/emboss/Makefile.am 2010-06-16 06:26:45.000000000
-0400
+++ EMBOSS-6.3.1/emboss/Makefile.am 2010-08-06 05:50:53.000000000 -0400
@@ -79,14 +79,17 @@
yank
if !ESYSTEMLIBS
-EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib
+EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib \
+-I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre
+else
+EXTRA_INCLUDES = $(PLPLOT_CFLAGS)
endif
-INCLUDES = -I$(top_srcdir)/nucleus -I$(top_srcdir)/ajax/pcre \
+INCLUDES = -I$(top_srcdir)/nucleus \
$(EXTRA_INCLUDES) \
-I$(top_srcdir)/ajax/core -I$(top_srcdir)/ajax/graphics \
-I$(top_srcdir)/ajax/ensembl -I$(top_srcdir)/ajax/ajaxdb \
- -I$(top_srcdir)/ajax/acd -I$(top_srcdir)/plplot
+ -I$(top_srcdir)/ajax/acd
aaindexextract_SOURCES = aaindexextract.c
@@ -319,7 +322,7 @@
treetypedisplay_SOURCES = treetypedisplay.c
if !ESYSTEMLIBS
-EXTRA_LDS = ../ajax/zlib/libezlib.la ../ajax/expat/libeexpat.la
+EXTRA_LDS = ../ajax/zlib/libezlib.la ../ajax/expat/libeexpat.la
../plplot/libeplplot.la ../ajax/pcre/libepcre.la
endif
@@ -327,7 +330,6 @@
../ajax/ajaxdb/libajaxdb.la ../ajax/ensembl/libensembl.la \
../ajax/graphics/libajaxg.la ../ajax/core/libajax.la \
$(EXTRA_LDS) \
- ../ajax/pcre/libepcre.la ../plplot/libeplplot.la \
$(XLIB)
pkgdata_DATA = emboss.default.template
diff -Nurd -x'*~' EMBOSS-6.3.1.orig/nucleus/Makefile.am
EMBOSS-6.3.1/nucleus/Makefile.am
--- EMBOSS-6.3.1.orig/nucleus/Makefile.am 2010-06-16 07:36:00.000000000
-0400
+++ EMBOSS-6.3.1/nucleus/Makefile.am 2010-08-06 05:20:16.000000000 -0400
@@ -19,13 +19,16 @@
-lezlib -leplplot
else
if !ESYSTEMLIBS
-EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib
+EXTRA_INCLUDES = -I$(top_srcdir)/ajax/expat -I$(top_srcdir)/ajax/zlib \
+-I$(top_srcdir)/plplot -I$(top_srcdir)/ajax/pcre
+else
+EXTRA_INCLUDES = $(PLPLOT_CFLAGS)
endif
endif
-INCLUDES = -I$(top_srcdir)/plplot $(X_CFLAGS) -I$(srcdir)/ \
- -I$(top_srcdir)/ajax -I$(top_srcdir)/ajax/pcre \
+INCLUDES = $(X_CFLAGS) -I$(srcdir)/ \
+ -I$(top_srcdir)/ajax \
$(EXTRA_INCLUDES) \
-I$(top_srcdir)/ajax/core -I$(top_srcdir)/ajax/graphics \
-I$(top_srcdir)/ajax/ensembl -I$(top_srcdir)/ajax/ajaxdb \
@@ -55,3 +58,4 @@
endif
libnucleus_la_LDFLAGS = $(LINKFLAGS)
+libnucleus_la_LIBADD = ../ajax/core/libajax.la ../ajax/graphics/libajaxg.la
../ajax/acd/libacd.la
--- NEW FILE: emboss-6.3.1-3.patch ---
diff -Nurd EMBOSS-6.3.1/README.fixes EMBOSS-6.3.1-patched/README.fixes
--- EMBOSS-6.3.1/README.fixes 1969-12-31 19:00:00.000000000 -0500
+++ EMBOSS-6.3.1-patched/README.fixes 2010-07-21 05:25:27.000000000 -0400
@@ -0,0 +1,9 @@
+The files in this directory are bugfix replacements for files in
+the EMBOSS-6.3.1 distribution. Just drop the replacement files in
+the location shown and redo the 'make install.'
+
+Fix 1. EMBOSS-6.3.1/configure
+ EMBOSS-6.3.1/m4/mysql.m4
+
+21 Jul 2010: Addresses a problem whereby, in some circumstances, inclusion of
+ hpdf support prevented inclusion of MySQL support.
diff -Nurd EMBOSS-6.3.1/ajax/acd/Makefile.in
EMBOSS-6.3.1-patched/ajax/acd/Makefile.in
--- EMBOSS-6.3.1/ajax/acd/Makefile.in 2010-07-19 07:55:40.000000000 -0400
+++ EMBOSS-6.3.1-patched/ajax/acd/Makefile.in 2010-07-24 10:57:13.000000000
-0400
@@ -73,7 +73,7 @@
sed '$$!N;$$!N;$$!N;$$!N;s/\n/ /g'
am__installdirs = "$(DESTDIR)$(libdir)" "$(DESTDIR)$(includedir)"
LTLIBRARIES = $(lib_LTLIBRARIES)
-libacd_la_LIBADD =
+libacd_la_LIBADD = ../core/libajax.la ../graphics/libajaxg.la
../ajaxdb/libajaxdb.la
am__objects_1 = ajacd.lo
am_libacd_la_OBJECTS = $(am__objects_1)
libacd_la_OBJECTS = $(am_libacd_la_OBJECTS)
diff -Nurd EMBOSS-6.3.1/ajax/ajaxdb/Makefile.in
EMBOSS-6.3.1-patched/ajax/ajaxdb/Makefile.in
--- EMBOSS-6.3.1/ajax/ajaxdb/Makefile.in 2010-07-19 07:55:40.000000000
-0400
+++ EMBOSS-6.3.1-patched/ajax/ajaxdb/Makefile.in 2010-07-24
10:57:47.000000000 -0400
@@ -73,7 +73,7 @@
sed '$$!N;$$!N;$$!N;$$!N;s/\n/ /g'
am__installdirs = "$(DESTDIR)$(libdir)" "$(DESTDIR)$(includedir)"
LTLIBRARIES = $(lib_LTLIBRARIES)
-libajaxdb_la_LIBADD =
+libajaxdb_la_LIBADD = ../core/libajax.la
am__objects_1 = ajmart.lo ajseqdb.lo
am_libajaxdb_la_OBJECTS = $(am__objects_1)
libajaxdb_la_OBJECTS = $(am_libajaxdb_la_OBJECTS)
diff -Nurd EMBOSS-6.3.1/ajax/core/Makefile.in
EMBOSS-6.3.1-patched/ajax/core/Makefile.in
--- EMBOSS-6.3.1/ajax/core/Makefile.in 2010-07-19 07:55:40.000000000 -0400
+++ EMBOSS-6.3.1-patched/ajax/core/Makefile.in 2010-07-24 13:04:41.000000000
-0400
@@ -73,7 +73,7 @@
sed '$$!N;$$!N;$$!N;$$!N;s/\n/ /g'
am__installdirs = "$(DESTDIR)$(libdir)" "$(DESTDIR)$(includedir)"
LTLIBRARIES = $(lib_LTLIBRARIES)
-libajax_la_LIBADD =
+libajax_la_LIBADD = ../pcre/libepcre.la
am__objects_1 = ajalign.lo ajarr.lo ajassert.lo ajbase.lo ajcall.lo \
ajcod.lo ajdan.lo ajdmx.lo ajdom.lo ajdomain.lo ajexcept.lo \
ajfeat.lo ajfile.lo ajfiledata.lo ajfileio.lo ajfmt.lo \
diff -Nurd EMBOSS-6.3.1/ajax/graphics/Makefile.in
EMBOSS-6.3.1-patched/ajax/graphics/Makefile.in
--- EMBOSS-6.3.1/ajax/graphics/Makefile.in 2010-07-19 07:55:40.000000000
-0400
+++ EMBOSS-6.3.1-patched/ajax/graphics/Makefile.in 2010-07-24
13:05:30.000000000 -0400
@@ -73,7 +73,7 @@
sed '$$!N;$$!N;$$!N;$$!N;s/\n/ /g'
am__installdirs = "$(DESTDIR)$(libdir)" "$(DESTDIR)$(includedir)"
LTLIBRARIES = $(lib_LTLIBRARIES)
-libajaxg_la_LIBADD =
+libajaxg_la_LIBADD = ../core/libajax.la ../../plplot/libeplplot.la
am__objects_1 = ajgraph.lo ajhist.lo
am_libajaxg_la_OBJECTS = $(am__objects_1)
libajaxg_la_OBJECTS = $(am_libajaxg_la_OBJECTS)
diff -Nurd EMBOSS-6.3.1/configure EMBOSS-6.3.1-patched/configure
--- EMBOSS-6.3.1/configure 2010-07-19 07:55:36.000000000 -0400
+++ EMBOSS-6.3.1-patched/configure 2010-07-21 05:25:34.000000000 -0400
@@ -14481,8 +14481,8 @@
EMBCFLAGS=$CFLAGS
EMBLDFLAGS=$LDFLAGS
- CFLAGS=$MYSQL_CFLAGS
- LDFLAGS=$MYSQL_LDFLAGS
+ CFLAGS="$MYSQL_CFLAGS $EMBCFLAGS"
+ LDFLAGS="$MYSQL_LDFLAGS $EMBLDFLAGS"
cat confdefs.h - <<_ACEOF >conftest.$ac_ext
/* end confdefs.h. */
diff -Nurd EMBOSS-6.3.1/m4/mysql.m4 EMBOSS-6.3.1-patched/m4/mysql.m4
--- EMBOSS-6.3.1/m4/mysql.m4 2010-05-18 18:12:06.000000000 -0400
+++ EMBOSS-6.3.1-patched/m4/mysql.m4 2010-07-21 05:25:41.000000000 -0400
@@ -96,8 +96,8 @@
EMBCFLAGS=$CFLAGS
EMBLDFLAGS=$LDFLAGS
- CFLAGS=$MYSQL_CFLAGS
- LDFLAGS=$MYSQL_LDFLAGS
+ CFLAGS="$MYSQL_CFLAGS $EMBCFLAGS"
+ LDFLAGS="$MYSQL_LDFLAGS $EMBLDFLAGS"
AC_LINK_IFELSE([AC_LANG_PROGRAM([[#include <stdio.h>
#include "mysql.h"]],
diff -Nurd EMBOSS-6.3.1/nucleus/Makefile.in
EMBOSS-6.3.1-patched/nucleus/Makefile.in
--- EMBOSS-6.3.1/nucleus/Makefile.in 2010-07-19 07:55:42.000000000 -0400
+++ EMBOSS-6.3.1-patched/nucleus/Makefile.in 2010-07-24 13:06:08.000000000
-0400
@@ -73,7 +73,7 @@
sed '$$!N;$$!N;$$!N;$$!N;s/\n/ /g'
am__installdirs = "$(DESTDIR)$(libdir)" "$(DESTDIR)$(includedir)"
LTLIBRARIES = $(lib_LTLIBRARIES)
-libnucleus_la_LIBADD =
+libnucleus_la_LIBADD = ../ajax/core/libajax.la ../ajax/graphics/libajaxg.la
../ajax/ajaxdb/libajaxdb.la ../ajax/acd/libacd.la
am__objects_1 = embaln.lo embcom.lo embcons.lo embdata.lo embdbi.lo \
embdmx.lo embdomain.lo embest.lo embexit.lo embgroup.lo \
embiep.lo embindex.lo embinit.lo embmat.lo embmisc.lo \
diff -Nurd EMBOSS-6.3.1/plplot/Makefile.in
EMBOSS-6.3.1-patched/plplot/Makefile.in
--- EMBOSS-6.3.1/plplot/Makefile.in 2010-07-19 07:55:42.000000000 -0400
+++ EMBOSS-6.3.1-patched/plplot/Makefile.in 2010-07-24 13:06:33.000000000
-0400
@@ -72,7 +72,7 @@
sed '$$!N;$$!N;$$!N;$$!N;s/\n/ /g'
am__installdirs = "$(DESTDIR)$(libdir)" "$(DESTDIR)$(pkgincludedir)"
LTLIBRARIES = $(lib_LTLIBRARIES)
-libeplplot_la_LIBADD =
+libeplplot_la_LIBADD = = $(XLIB) -lgd
am__objects_1 = pdfutils.lo plargs.lo plbox.lo plcont.lo plcore.lo \
plctrl.lo plcvt.lo pldtik.lo plfill.lo plhist.lo plline.lo \
plmap.lo plot3d.lo plpage.lo plsdef.lo plshade.lo plsym.lo \
Index: gperiodic.patch
===================================================================
RCS file: /cvsroot/fink/dists/10.4/stable/main/finkinfo/sci/gperiodic.patch,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -d -r1.2 -r1.3
--- gperiodic.patch 16 Jul 2008 03:01:48 -0000 1.2
+++ gperiodic.patch 2 Nov 2010 15:46:18 -0000 1.3
@@ -1,10 +1,12 @@
-diff -uNr gperiodic-2.0.10/Makefile gperiodic-2.0.10-new/Makefile
---- gperiodic-2.0.10/Makefile 2007-07-11 08:58:05.000000000 -0400
-+++ gperiodic-2.0.10-new/Makefile 2007-09-27 22:47:56.000000000 -0400
-@@ -1,5 +1,5 @@
+diff -Nurd -x'*~' gperiodic-2.0.10.orig/Makefile gperiodic-2.0.10/Makefile
+--- gperiodic-2.0.10.orig/Makefile 2007-07-11 08:58:05.000000000 -0400
++++ gperiodic-2.0.10/Makefile 2010-05-04 00:26:50.000000000 -0400
+@@ -1,6 +1,6 @@
CC := gcc
-CFLAGS := `pkg-config --cflags gtk+-2.0` -I. -DG_DISABLE_DEPRECATED
-DGDK_DISABLE_DEPRECATED -DGDK_PIXBUF_DISABLE_DEPRECATED
-DGTK_DISABLE_DEPRECATED
+-LIBS :=`pkg-config --libs gtk+-2.0`
+CFLAGS := -I. `pkg-config --cflags gtk+-2.0`
- LIBS :=`pkg-config --libs gtk+-2.0`
++LIBS :=`pkg-config --libs gtk+-2.0` -lintl
bindir ?= /usr/bin
datadir ?= /usr/share
+ enable_nls ?= 1
--- NEW FILE: libplplot10-shlibs.patch ---
diff -Nurd -x'*~' plplot-5.9.6.orig/cmake/modules/aqt.cmake
plplot-5.9.6/cmake/modules/aqt.cmake
--- plplot-5.9.6.orig/cmake/modules/aqt.cmake 2010-06-05 12:11:39.000000000
-0400
+++ plplot-5.9.6/cmake/modules/aqt.cmake 2010-08-11 15:36:30.000000000
-0400
@@ -36,8 +36,8 @@
include(FindAQT)
if(AQT_FOUND)
message(STATUS "Found AQT: ${AQT_FRAMEWORK}")
- set(aqt_COMPILE_FLAGS "-ObjC")
- set(aqt_LINK_FLAGS "-framework AquaTerm -framework Foundation")
+ set(aqt_COMPILE_FLAGS "-ObjC -...@prefix@/include")
+ set(aqt_LINK_FLAGS "-lobjc -laquaterm -...@prefix@/lib -framework
Foundation")
set(DRIVERS_LINK_FLAGS ${DRIVERS_LINK_FLAGS} ${aqt_LINK_FLAGS})
else(AQT_FOUND)
set(PLD_aqt OFF CACHE BOOL "Enable aqt device" FORCE)
Index: dx.info
===================================================================
RCS file: /cvsroot/fink/dists/10.4/stable/main/finkinfo/sci/dx.info,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -d -r1.5 -r1.6
--- dx.info 12 Feb 2010 21:27:24 -0000 1.5
+++ dx.info 2 Nov 2010 15:46:18 -0000 1.6
@@ -1,34 +1,29 @@
Package: dx
Version: 4.4.4
-Revision: 1004
-Architecture: i386, powerpc
-Distribution: 10.4, 10.5
+Revision: 1504
+Distribution: 10.5, 10.6
Source: http://opendx.sdsc.edu/source/%n-%v.tar.gz
Source-MD5: 6da0c4cd21d3c08f97b7662e3aee5b7b
PatchFile: %n.patch
PatchFile-MD5: 96c2f7a9fa3e39018c345fc05adbd441
-BuildDepends: autoconf, automake1.9, bzip2, expat1, fink (>= 0.24.12-1),
fontconfig2-dev, freetype219, gcc42, imagemagick1-dev (>= 6.4.0-1011), lcms,
libiconv-dev, libjpeg, libpng3, libtiff (>= 3.7.2-1001), libtool14, libxml2,
netcdf (>= 3.6.2-6), openmotif3 (>= 2.2.3-11), x11-dev
-Depends: bzip2-shlibs, expat1-shlibs, fontconfig2-shlibs, freetype219-shlibs,
gcc42-shlibs, hdf (>= 4.2r1-1001), imagemagick1-shlibs (>= 6.4.0-1011),
lcms-shlibs, libiconv, libjpeg-shlibs, libpng3-shlibs, libtiff-shlibs (>=
3.7.2-1001), libtool14-shlibs, libxml2-shlibs, netcdf-shlibs (>= 3.6.2-6),
openmotif3-shlibs (>= 2.2.3-11), x11
-ConfigureParams: --prefix=%p/share --exec_prefix=%p --with-motif-libs=%p/lib
--with-motif-includes=%p/include --without-javadx --with-large-arenas
--disable-dependency-tracking --x-includes=/usr/X11R6/include
--x-libraries=/usr/X11R6/lib
+PatchScript: <<
+ %{default_script}
+ perl -pi -e "s|LIB_HDF\=\'\-ldf\'|LIB_HDF='-ldf -ljpeg'|" configure.ac
+<<
+BuildDepends: autoconf, automake1.9, bzip2, expat1, fink (>= 0.24.12-1),
fontconfig2-dev, freetype219, gcc4.2, imagemagick1-dev (>= 6.4.0-1011), lcms,
libiconv-dev, libjpeg, libpng3, libtiff (>= 3.7.2-1001), libtool14, libxml2,
netcdf (>= 3.6.2-6), openmotif3 (>= 2.2.3-11), x11-dev
+Depends: bzip2-shlibs, expat1-shlibs, fontconfig2-shlibs, freetype219-shlibs,
hdf (>= 4.2r1-1001), imagemagick1-shlibs (>= 6.4.0-1011), lcms-shlibs,
libiconv, libjpeg-shlibs, libpng3-shlibs, libtiff-shlibs (>= 3.7.2-1001),
libtool14-shlibs, libxml2-shlibs, netcdf-shlibs (>= 3.6.2-6), openmotif3-shlibs
(>= 2.2.3-11), x11
+ConfigureParams: --prefix=%p/share --exec_prefix=%p --with-motif-libs=%p/lib
--with-motif-includes=%p/include --without-javadx --with-large-arenas
--disable-dependency-tracking --x-includes=/usr/X11R6/include
--x-libraries=/usr/X11R6/lib
+SetCXX:g++-4.2
+SetCC:gcc-4.2
GCC:4.0
-SetCXX:/usr/bin/g++-4.2
-SetCC:/usr/bin/gcc-4.2
CompileScript:<<
%p/bin/autoreconf -f -i
-./configure %c
+./configure ac_cv_exeext='' %c
make
<<
InstallScript: <<
make install DESTDIR=%d
ln -s %p/include %i/share/dx
-ln %i/share/dx/bin_macos/builder.dSYM %i/share/dx/bin_macos/builder
-ln %i/share/dx/bin_macos/prompter.dSYM %i/share/dx/bin_macos/prompter
-ln %i/share/dx/bin_macos/dxexec.dSYM %i/share/dx/bin_macos/dxexec
-ln %i/share/dx/bin_macos/startupui.dSYM %i/share/dx/bin_macos/startupui
-ln %i/share/dx/bin_macos/dxui.dSYM %i/share/dx/bin_macos/dxui
-ln %i/share/dx/bin_macos/tutor.dSYM %i/share/dx/bin_macos/tutor
-
-
<<
DocFiles: <<
LICENSE NEWS README doc/README COPYING doc/README_SMP
@@ -81,6 +76,9 @@
written with argc as an unsigned int instead of int, so then
passing pointers to it give invalid conversion...too deeply
embedded to make a simple change to solve it.
+
+ drm: The 10.6 version of dx uses /usr/bin/gcc-4.2 rather than
+ fink's gcc42 package (which is not available in 10.6).
<<
Homepage: http://www.opendx.org
-Maintainer: Jeremy Erwin <jer...@ponymail.com>
+Maintainer: Jeremy Erwin <jer...@ponymail.com>
--- emboss-6.0.1-4.info DELETED ---
Index: gperiodic.info
===================================================================
RCS file: /cvsroot/fink/dists/10.4/stable/main/finkinfo/sci/gperiodic.info,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -d -r1.4 -r1.5
--- gperiodic.info 16 Jul 2008 03:01:48 -0000 1.4
+++ gperiodic.info 2 Nov 2010 15:46:18 -0000 1.5
@@ -1,47 +1,38 @@
Package: gperiodic
Version: 2.0.10
-Revision: 2
+Revision: 3
Maintainer: The Gnome Core Team <fink-gnome-c...@lists.sourceforge.net>
Source: http://www.frantz.fi/software/%n-%v.tar.gz
Source-MD5: 9680f8a4850bdafad113fd4af7c57e45
Depends: <<
- atk1-shlibs (>= 1.20.0-1),
- cairo-shlibs (>= 1.6-1),
- expat1-shlibs,
- fontconfig2-shlibs (>= 2.4.1-1),
- freetype219-shlibs (>= 2.3.5-1),
- glib2-shlibs (>= 2.14.0-1),
- glitz-shlibs,
- gtk+2-shlibs (>= 2.12.0-1),
- libgettext3-shlibs,
- libiconv,
- libpng3-shlibs,
- pango1-xft2-ft219-shlibs (>= 1.18.4-4),
- x11-shlibs,
- xft2-shlibs
+ atk1-shlibs (>= 1.28.0-1),
+ cairo-shlibs (>= 1.8.8-3),
+ fontconfig2-shlibs (>= 2.8.0-4),
+ freetype219-shlibs (>= 2.3.12-1),
+ glib2-shlibs (>= 2.22.0-1),
+ gtk+2-shlibs (>= 2.18.0-1),
+ libgettext8-shlibs,
+ pango1-xft2-ft219-shlibs (>= 1.24.5-4)
<<
BuildDepends: <<
- atk1 (>= 1.20.0-1),
- cairo (>= 1.6-1),
- expat1,
+ atk1 (>= 1.28.0-1),
+ cairo (>= 1.8.8-3),
fink (>= 0.24.12-1),
+ fink-package-precedence,
fontconfig2-dev (>= 2.4.1-1),
freetype219 (>= 2.3.5-1),
gettext-tools,
- glib2-dev (>= 2.14.0-1),
+ glib2-dev (>= 2.22.0-1),
glitz,
- gtk+2-dev (>= 2.12.0-1),
- libgettext3-dev,
- libiconv-dev,
- libpng3,
- pango1-xft2-ft219-dev (>= 1.18.4-4),
- pixman (>= 0.10.0-1),
- pkgconfig (>= 0.21-1),
- x11-dev,
- xft2-dev
+ gtk+2-dev (>= 2.18.0-1),
+ libgettext8-dev,
+ pango1-xft2-ft219-dev (>= 1.24.5-4),
+ pixman (>= 0.16.0-1),
+ pkgconfig (>= 0.23),
+ x11-dev
<<
PatchFile: %n.patch
-PatchFile-MD5: bf7156da596ada44be19058b0a15f095
+PatchFile-MD5: 7fade9c06cd77819e59fecfb574884b8
PatchScript: <<
%{default_script}
rm INSTALL
@@ -49,16 +40,18 @@
<<
NoSetMAKEFLAGS: true
SetMAKEFLAGS: -j1
+SetCPPFLAGS: -MD
CompileScript: <<
#!/bin/sh -ev
- export
PKG_CONFIG_PATH="%p/lib/pango-ft219/lib/pkgconfig:%p/lib/fontconfig2/lib/pkgconfig:%p/lib/freetype219/lib/pkgconfig:$PKG_CONFIG_PATH"
+ export
PKG_CONFIG_PATH="%p/lib/glib-2.0/pkgconfig-strict:%p/lib/fontconfig2/lib/pkgconfig:$PKG_CONFIG_PATH"
make bindir=%p/bin datadir=%p/share
+ fink-package-precedence --depfile-ext='\.d' .
<<
InstallScript: <<
#!/bin/sh -ev
- export
PKG_CONFIG_PATH="%p/lib/pango-ft219/lib/pkgconfig:%p/lib/fontconfig2/lib/pkgconfig:%p/lib/freetype219/lib/pkgconfig:$PKG_CONFIG_PATH"
+ export
PKG_CONFIG_PATH="%p/lib/glib-2.0/pkgconfig-strict:%p/lib/fontconfig2/lib/pkgconfig:$PKG_CONFIG_PATH"
make bindir=%i/bin datadir=%i/share install
<<
DocFiles: AUTHORS ChangeLog NEWS README gpl.txt
@@ -71,11 +64,15 @@
DescPort: <<
Have to remove INSTALL in order to have 'make install' work on
case-insensitive filesystem.
+
+ Recent glib doesn't publish -lintl, so pass it directly.
<<
DescPackaging: <<
Originally packaged by Matt Stephenson.
Create directories before installing files into them.
+
+ Enable dependency tracking so can check for coherent fink deps
<<
License: GPL
Homepage: http://www.frantz.fi/software/gperiodic.php
--- NEW FILE: dx-10.4.info ---
Package: dx
Version: 4.4.4
Revision: 1004
Architecture: i386, powerpc
Distribution: 10.4
Source: http://opendx.sdsc.edu/source/%n-%v.tar.gz
Source-MD5: 6da0c4cd21d3c08f97b7662e3aee5b7b
PatchFile: %n.patch
PatchFile-MD5: 96c2f7a9fa3e39018c345fc05adbd441
PatchScript: <<
%{default_script}
perl -pi -e "s|LIB_HDF\=\'\-ldf\'|LIB_HDF='-ldf -ljpeg'|" configure.ac
<<
BuildDepends: autoconf, automake1.9, bzip2, expat1, fink (>= 0.24.12-1),
fontconfig2-dev, freetype219, gcc42, imagemagick1-dev (>= 6.4.0-1011), lcms,
libiconv-dev, libjpeg, libpng3, libtiff (>= 3.7.2-1001), libtool14, libxml2,
netcdf (>= 3.6.2-6), openmotif3 (>= 2.2.3-11), x11-dev
Depends: bzip2-shlibs, expat1-shlibs, fontconfig2-shlibs, freetype219-shlibs,
gcc42-shlibs, hdf (>= 4.2r1-1001), imagemagick1-shlibs (>= 6.4.0-1011),
lcms-shlibs, libiconv, libjpeg-shlibs, libpng3-shlibs, libtiff-shlibs (>=
3.7.2-1001), libtool14-shlibs, libxml2-shlibs, netcdf-shlibs (>= 3.6.2-6),
openmotif3-shlibs (>= 2.2.3-11), x11
ConfigureParams: --prefix=%p/share --exec_prefix=%p --with-motif-libs=%p/lib
--with-motif-includes=%p/include --without-javadx --with-large-arenas
--disable-dependency-tracking --x-includes=/usr/X11R6/include
--x-libraries=/usr/X11R6/lib
GCC:4.0
SetCXX:%p/lib/gcc4.2/bin/g++
SetCC:%p/lib/gcc4.2/bin/gcc
CompileScript:<<
%p/bin/autoreconf -f -i
./configure ac_cv_exeext='' %c
make
<<
InstallScript: <<
make install DESTDIR=%d
ln -s %p/include %i/share/dx
<<
DocFiles: <<
LICENSE NEWS README doc/README COPYING doc/README_SMP
<<
License: OSI-Approved
Description: Open Visualization Data Explorer
DescDetail: <<
Open Visualization Data Explorer is a full visualization environment that
gives users the ability to apply advanced visualization and analysis
techniques to their data. These techniques can be applied to help users
gain new insights into data from applications in a wide variety of fields
including science, engineering, medicine and business. Data Explorer
provides a full set of tools for manipulating, transforming, processing,
realizing, rendering and animating data and allow for visualization and
analysis methods based on points, lines, areas, volumes, images or geometric
primitives in any combination. Data Explorer is discipline-independent and
easily adapts to new applications and data. The integrated object-oriented
graphical user interface is intuitive to learn and easy to use.
(http://www.research.ibm.com/dx/dxDescription.html)
<<
DescPort: <<
The original program installed itself in %p/dx, which is against fink policy.
Various makefile.am were modified so that fink installed the bulk of the
program in %p/share/dx, while installing binaries, includes, manfiles, etc.
in %p/bin, %p/include, %p/share/man etc. Using %p/lib breaks things, so
I've left the "libraries" in %/p/share/dx/lib.
Disables java dx.
Fixed the -morehelp option.
Now uses openmotif3, as lesstif doesn't render some widgets correctly.
Corrected configure.ac so all necesary hdf libaries are compiled in.
Placed a symbolic link between %p/include and %p/share/dx/include to aid in
porting downstream packages with "smart" configure scripts.
Adds work around discussed in Apple Technical Q&A 1567:Compiling X11/ OpenGL
applications on Mac OS X v.10.5 Leopard. Fixes StartWebBrowser.C to compile
with Leopard's ApplicationServices.h
Patch to allow compiling if ImageMagick was built with --enable-hdri
(require positive int for array subscript in _im_image.c). See:
http://www.imagemagick.org/script/high-dynamic-range.php
<<
DescPackaging: <<
dmacks: Hack configure to use moderner check for ImageMagick.
dmacks: hdf (v4) requires g95, but switching dx to use hdf5
seems non-trivial. Use dx-hdf5 to add support for newer hdf*
functionality into dx.
Can't move to gcc43 because it won't tolerate that main() is
written with argc as an unsigned int instead of int, so then
passing pointers to it give invalid conversion...too deeply
embedded to make a simple change to solve it.
<<
Homepage: http://www.opendx.org
Maintainer: Jeremy Erwin <jer...@ponymail.com>
--- NEW FILE: emboss.info ---
Package: emboss
Version: 6.3.1
Revision: 102
Depends: <<
%N-libajax6-shlibs (>= %v-%r),
%N-libnucleus6-shlibs (>= %v-%r),
dpkg-base-files,
expat1-shlibs,
freetype219-shlibs (>= 2.3.12-1),
gd2-shlibs,
libpng14-shlibs,
libtool2-shlibs,
mysql-unified-shlibs,
pcre-shlibs,
libplplot10-shlibs,
postgresql84-shlibs,
system-java (>= 1.5.0)
<<
BuildDepends: <<
autoconf2.6,
automake1.11,
fink (>= 0.24.12),
fink-package-precedence,
expat1,
freetype219 (>= 2.3.12-1),
gd2,
libpng14,
libtool2,
mysql-unified-dev,
pcre,
pkgconfig,
libplplot10-dev,
postgresql84-dev,
system-java-dev (>= 1.5.0)
<<
Source: ftp://emboss.open-bio.org/pub/EMBOSS/EMBOSS-%v.tar.gz
Source-MD5: 04d1179b6261103a77e396d54f8ac38e
PatchFile: %n.patch
PatchFile-MD5: 714dcd80c41343a1e0c4bc0e90e36718
PatchScript: <<
%{default_script}
find . -name Makefile.am | xargs perl -pi -e 's/(_la_LDFLAGS.*)/\1
-no-undefined/'
<<
ConfigureParams: <<
--with-java=/System/Library/Frameworks/JavaVM.framework/Versions/1.5.0/Home \
--with-javaos=/System/Library/Frameworks/JavaVM.framework/Versions/1.5.0/Home/include
\
--enable-dependency-tracking --disable-static \
--includedir=%p/lib/EMBOSS/include --libdir=%p/lib/EMBOSS/lib \
--docdir=%p/share/EMBOSS \
--enable-systemlibs --with-postgresql=%p/opt/postgresql-8.4/bin/pg_config
<<
CompileScript: <<
#!/bin/sh -ev
%p/bin/autoreconf -fi
./configure %c
make
fink-package-precedence \
--prohibit-bdep=%N-libajax6-dev,%N-libnucleus6-dev \
--prohibit-bdep=emboss-ajax6-dev,emboss-nucleus6-dev,emboss-plplot3-dev,emboss-plplot6-dev
\
.
<<
Installscript: <<
make install DESTDIR=%d
<<
DocFiles: AUTHORS COMPAT COPYING ChangeLog FAQ INSTALL KNOWN_BUGS LICENSE NEWS
ONEWS PROBLEMS README THANKS
RunTimeVars: <<
# EMBOSS_ROOT: %p/share/EMBOSS
EMBOSS_DATA: %p/share/EMBOSS/data
<<
SplitOff10: <<
Package: %N-libajax6-shlibs
Depends: <<
expat1-shlibs,
freetype219-shlibs (>= 2.3.12-1),
gd2-shlibs,
libpng14-shlibs,
libtool2-shlibs,
mysql-unified-shlibs,
pcre-shlibs,
libplplot10-shlibs,
postgresql84-shlibs
<<
Files: <<
lib/EMBOSS/lib/libacd.6*.dylib
lib/EMBOSS/lib/libajax.6*.dylib
lib/EMBOSS/lib/libajaxdb.6*.dylib
lib/EMBOSS/lib/libajaxg.6*.dylib
lib/EMBOSS/lib/libensembl.6*.dylib
<<
Shlibs: <<
%p/lib/EMBOSS/lib/libacd.6.dylib 7.0.0 %n (>= 6.3.1-101)
%p/lib/EMBOSS/lib/libajax.6.dylib 7.0.0 %n (>= 6.3.1-101)
%p/lib/EMBOSS/lib/libajaxdb.6.dylib 7.0.0 %n (>= 6.3.1-101)
%p/lib/EMBOSS/lib/libajaxg.6.dylib 7.0.0 %n (>= 6.3.1-101)
%p/lib/EMBOSS/lib/libensembl.6.dylib 7.0.0 %n (>= 6.3.1-101)
<<
DocFiles: AUTHORS COMPAT COPYING ChangeLog FAQ INSTALL KNOWN_BUGS
LICENSE NEWS ONEWS PROBLEMS README THANKS
<<
SplitOff11: <<
Package: %N-libajax6-dev
Depends: %N-libajax6-shlibs (= %v-%r)
BuildDependsOnly: True
Files: <<
lib/EMBOSS/lib/libacd.*
lib/EMBOSS/lib/libajax.*
lib/EMBOSS/lib/libajaxdb.*
lib/EMBOSS/lib/libajaxg.*
lib/EMBOSS/lib/libensembl.*
lib/EMBOSS/include/aj*.h
lib/EMBOSS/include/ens*.h
<<
DocFiles: AUTHORS COMPAT COPYING ChangeLog FAQ INSTALL KNOWN_BUGS
LICENSE NEWS ONEWS PROBLEMS README THANKS
<<
SplitOff20: <<
Package: %N-libnucleus6-shlibs
Depends: <<
%N-libajax6-shlibs (>= %v-%r),
expat1-shlibs,
freetype219-shlibs (>= 2.3.12-1),
gd2-shlibs,
libpng14-shlibs,
libtool2-shlibs,
mysql-unified-shlibs,
pcre-shlibs,
libplplot10-shlibs,
postgresql84-shlibs
<<
Files: <<
lib/EMBOSS/lib/libnucleus.6*.dylib
<<
Shlibs: <<
%p/lib/EMBOSS/lib/libnucleus.6.dylib 7.0.0 %n (>= 6.3.1-101)
<<
DocFiles: AUTHORS COMPAT COPYING ChangeLog FAQ INSTALL KNOWN_BUGS
LICENSE NEWS ONEWS PROBLEMS README THANKS
<<
SplitOff21: <<
Package: %N-libnucleus6-dev
Depends: %N-libnucleus6-shlibs (= %v-%r)
BuildDependsOnly: True
Files: <<
lib/EMBOSS/lib/libnucleus.*
lib/EMBOSS/include/em*.h
<<
DocFiles: AUTHORS COMPAT COPYING ChangeLog FAQ INSTALL KNOWN_BUGS
LICENSE NEWS ONEWS PROBLEMS README THANKS
<<
Description: Molecular Biology Open Software Suite
DescDetail: <<
EMBOSS is a free Open Source software analysis package specially
developed for the needs of the molecular biology (e.g. EMBnet) user
community. The software automatically copes with data in a variety of
formats and even allows transparent retrieval of sequence data from the
web. Also, as extensive libraries are provided with the package, it is a
platform to allow other scientists to develop and release software in
true open source spirit. EMBOSS also integrates a range of currently
available packages and tools for sequence analysis into a seamless
whole.
<<
DescUsage: <<
See the README file for other environment variables you may need to
configure. See http://emboss.sourceforge.net/Jemboss/ for
information on using the Jemboss GUI for EMBOSS. To prevent conflicts,
the headers are located in %p/lib/EMBOSS/include instead of %p/include.
Install kemboss-qt4-mac or kemboss-qt4-x11 for a GUI that works either
in Aqua or X11 respectively or emboss-kaptain for a different X11 GUI.
<<
DescPort: <<
Add explicit linking to libs that supply symbols used by the
shared libraries here. This prevents things that link against
the shared libraries from having to know to pass additional
flags when the linker requires all symbols be defined.
Home-grown hack mis-passes things and isn't portable. But we
don't need it because we're using system plplot so omit rather
than fix.
Fink plplot doesn't have plxsfnam(), which takes separate
filename and extension, so hack ajgraph.c to use plfnam(),
which takes single filename.
<<
DescPackaging: <<
Former Maintainer: Koen van der Drift <drift...@users.sourceforge.net>
There have been a ton of Shlibs Policy problems. As of
6.3.1-101, making clean break with new library package-names
and install_names (via never-before-used --libdir and parallel
--includedir) and no attempt to retain symlinks for -dev or
-shlibs since old pkgs are not necessarily compatible with
these new ones.
Hack configure and Makefiles to consider external plplot and
expat library as other systemlibs.
Make sure pg flags get passed early so specific-version buried
-I and -L supercede unpredictably-versioned ones in default
locations.
<<
Maintainer: Daniel Macks <dma...@netspace.org>
Homepage: http://emboss.sourceforge.net
License: GPL
------------------------------------------------------------------------------
Nokia and AT&T present the 2010 Calling All Innovators-North America contest
Create new apps & games for the Nokia N8 for consumers in U.S. and Canada
$10 million total in prizes - $4M cash, 500 devices, nearly $6M in marketing
Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store
http://p.sf.net/sfu/nokia-dev2dev
_______________________________________________
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