emboss-6.3.1-3 stable port information

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=${java_home} \
--with-javaos=${java_home}/include \
--disable-dependency-tracking \
--libdir=%p/lib/EMBOSS \
--docdir=%p/share/EMBOSS
<<
CompileScript: <<
#!/bin/sh -ev
%p/bin/autoreconf -fi
if [ -x /usr/libexec/java_home ]; then
export java_home=`/usr/libexec/java_home`
else
export java_home=/System/Library/Frameworks/JavaVM.framework/Versions/1.5.0/Home
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
<<
Maintainer: None
Homepage: http://emboss.sourceforge.net
License: GPL

emboss-6.3.1-3 stable port .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
#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 \

emboss-6.3.1-3 _unstable_ port .patch