rpms/EMBOSS/F-12 EMBOSS-6.1.0-destdir.patch, NONE, 1.1 EMBOSS-fedora.patch, NONE, 1.1 EMBOSS-system-pcre.patch, NONE, 1.1 EMBOSS.spec, NONE, 1.1 README.fixes, NONE, 1.1 import.log, NONE, 1.1 .cvsignore, 1.1, 1.2 sources, 1.1, 1.2
belegdol
belegdol at fedoraproject.org
Sat Oct 17 22:49:37 UTC 2009
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Author: belegdol
Update of /cvs/pkgs/rpms/EMBOSS/F-12
In directory cvs1.fedora.phx.redhat.com:/tmp/cvs-serv29305/F-12
Modified Files:
.cvsignore sources
Added Files:
EMBOSS-6.1.0-destdir.patch EMBOSS-fedora.patch
EMBOSS-system-pcre.patch EMBOSS.spec README.fixes import.log
Log Message:
Initial import
EMBOSS-6.1.0-destdir.patch:
Makefile.am | 2 +-
Makefile.in | 2 +-
2 files changed, 2 insertions(+), 2 deletions(-)
--- NEW FILE EMBOSS-6.1.0-destdir.patch ---
--- jemboss/Makefile.am.destdir 2009-06-15 13:08:19.000000000 +0200
+++ jemboss/Makefile.am 2009-07-29 12:52:37.000000000 +0200
@@ -64,7 +64,7 @@
echo "(cd $(prefix)/share/$(PACKAGE)/jemboss; java org/emboss/jemboss/Jemboss &)" >> $(DESTDIR)$(bindir)/runJemboss.csh; \
chmod 755 $(DESTDIR)$(bindir)/runJemboss.csh; \
(cd $(DESTDIR)$(prefix)/share/$(PACKAGE)/jemboss/resources; sed "s|user.auth=true|user.auth=false|" jemboss.properties | sed "s|jemboss.server=true|jemboss.server=false|" | sed "s|/packages/emboss/STABLE|$(prefix)|" > jemboss.properties.new; mv -f jemboss.properties.new jemboss.properties; cd -); \
- sed "s|JEMBOSS_HOME=.|JEMBOSS_HOME=$(DESTDIR)$(prefix)/share/$(PACKAGE)/jemboss/|" runJemboss.sh > $(DESTDIR)$(prefix)/share/$(PACKAGE)/jemboss/runJemboss.sh; \
+ sed "s|JEMBOSS_HOME=.|JEMBOSS_HOME=$(prefix)/share/$(PACKAGE)/jemboss/|" runJemboss.sh > $(DESTDIR)$(prefix)/share/$(PACKAGE)/jemboss/runJemboss.sh; \
chmod 755 $(DESTDIR)$(prefix)/share/$(PACKAGE)/jemboss/runJemboss.sh;
pkgdata_DATA = LICENSE readme.html README
--- jemboss/Makefile.in.destdir 2009-07-15 01:16:00.000000000 +0200
+++ jemboss/Makefile.in 2009-07-29 12:52:39.000000000 +0200
@@ -682,7 +682,7 @@
echo "(cd $(prefix)/share/$(PACKAGE)/jemboss; java org/emboss/jemboss/Jemboss &)" >> $(DESTDIR)$(bindir)/runJemboss.csh; \
chmod 755 $(DESTDIR)$(bindir)/runJemboss.csh; \
(cd $(DESTDIR)$(prefix)/share/$(PACKAGE)/jemboss/resources; sed "s|user.auth=true|user.auth=false|" jemboss.properties | sed "s|jemboss.server=true|jemboss.server=false|" | sed "s|/packages/emboss/STABLE|$(prefix)|" > jemboss.properties.new; mv -f jemboss.properties.new jemboss.properties; cd -); \
- sed "s|JEMBOSS_HOME=.|JEMBOSS_HOME=$(DESTDIR)$(prefix)/share/$(PACKAGE)/jemboss/|" runJemboss.sh > $(DESTDIR)$(prefix)/share/$(PACKAGE)/jemboss/runJemboss.sh; \
+ sed "s|JEMBOSS_HOME=.|JEMBOSS_HOME=$(prefix)/share/$(PACKAGE)/jemboss/|" runJemboss.sh > $(DESTDIR)$(prefix)/share/$(PACKAGE)/jemboss/runJemboss.sh; \
chmod 755 $(DESTDIR)$(prefix)/share/$(PACKAGE)/jemboss/runJemboss.sh;
# tar to pick up the other directories
EMBOSS-fedora.patch:
jemboss.properties | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
--- NEW FILE EMBOSS-fedora.patch ---
--- jemboss/resources/jemboss.properties.fedora 2008-05-02 15:27:28.000000000 +0200
+++ jemboss/resources/jemboss.properties 2009-04-16 20:11:28.000000000 +0200
@@ -5,8 +5,8 @@
service.public=JembossAuthServer
service.private=JembossAuthServer
plplot=/packages/emboss/STABLE/share/EMBOSS/
-embossData=/packages/emboss/STABLE/share/EMBOSS/data/
-embossBin=/packages/emboss/STABLE/bin/
+embossData=/usr/share/EMBOSS/data/
+embossBin=/usr/bin/
embossPath=/usr/bin:/bin:/packages/clustal/:/packages/primer3/bin:/data/jobqueue/bin/:/usr/ucb/
-acdDirToParse=/packages/emboss/STABLE/share/EMBOSS/acd/
+acdDirToParse=/usr/share/EMBOSS/acd/
embossURL=http://emboss.sourceforge.net/
EMBOSS-system-pcre.patch:
ajax/Makefile.in | 26 ++++-----------------
ajax/ajreg.h | 6 ++--
configure | 67 +++++++++++++++++++++++++++++++++++++++++++++++++++++++
3 files changed, 75 insertions(+), 24 deletions(-)
--- NEW FILE EMBOSS-system-pcre.patch ---
diff -up EMBOSS-6.1.0/ajax/ajreg.h.pcre EMBOSS-6.1.0/ajax/ajreg.h
--- EMBOSS-6.1.0/ajax/ajreg.h.pcre 2007-02-09 19:30:59.000000000 +0100
+++ EMBOSS-6.1.0/ajax/ajreg.h 2009-09-27 03:17:19.000000000 +0200
@@ -16,8 +16,8 @@ extern "C"
#define ajreg_h
#include "ajax.h"
-#include "pcre_internal.h"
-#include "pcreposix.h"
+#include <pcre.h>
+#include <pcreposix.h>
#define AJREG_OVECSIZE 30
@@ -37,7 +37,7 @@ extern "C"
******************************************************************************/
typedef struct AjSRegexp {
- real_pcre *pcre;
+ struct real_pcre *pcre;
pcre_extra *extra;
int *ovector;
const char* orig;
diff -up EMBOSS-6.1.0/ajax/Makefile.in.pcre EMBOSS-6.1.0/ajax/Makefile.in
--- EMBOSS-6.1.0/ajax/Makefile.in.pcre 2009-07-15 01:15:58.000000000 +0200
+++ EMBOSS-6.1.0/ajax/Makefile.in 2009-09-27 03:17:19.000000000 +0200
@@ -81,7 +81,7 @@ am__libajax_la_SOURCES_DIST = ajacd.c aj
ajphylo.c ajrange.c ajreg.c ajreport.c ajseq.c ajseqabi.c \
ajseqdb.c ajseqread.c ajseqtype.c ajseqwrite.c ajsort.c \
ajstr.c ajsys.c ajtable.c ajtime.c ajtranslate.c ajtree.c \
- ajutil.c ajvector.c pcre.c pcre_study.c pcreposix.c ajgraph.c \
+ ajutil.c ajvector.c \
ajhist.c
am__objects_1 = ajacd.lo ajalign.lo ajarr.lo ajassert.lo ajbase.lo \
ajcall.lo ajcod.lo ajdan.lo ajdmx.lo ajdom.lo ajdomain.lo \
@@ -92,7 +92,7 @@ am__objects_1 = ajacd.lo ajalign.lo ajar
ajreport.lo ajseq.lo ajseqabi.lo ajseqdb.lo ajseqread.lo \
ajseqtype.lo ajseqwrite.lo ajsort.lo ajstr.lo ajsys.lo \
ajtable.lo ajtime.lo ajtranslate.lo ajtree.lo ajutil.lo \
- ajvector.lo pcre.lo pcre_study.lo pcreposix.lo
+ ajvector.lo
am__objects_2 = ajgraph.lo ajhist.lo
@ISCYGWIN_FALSE at am_libajax_la_OBJECTS = $(am__objects_1)
@ISCYGWIN_TRUE at am_libajax_la_OBJECTS = $(am__objects_1) \
@@ -159,7 +159,6 @@ EXEEXT = @EXEEXT@
FGREP = @FGREP@
GREP = @GREP@
HAVE_MEMMOVE = @HAVE_MEMMOVE@
-HAVE_STRERROR = @HAVE_STRERROR@
INSTALL = @INSTALL@
INSTALL_DATA = @INSTALL_DATA@
INSTALL_PROGRAM = @INSTALL_PROGRAM@
@@ -172,7 +171,7 @@ LD = @LD@
LDFLAGS = @LDFLAGS@
LIBOBJS = @LIBOBJS@
#LDFLAGS = -no-undefined
-LIBS =
+LIBS = @LIBS@
LIBTOOL = @LIBTOOL@
LIPO = @LIPO@
LN_S = @LN_S@
@@ -193,13 +192,6 @@ PACKAGE_STRING = @PACKAGE_STRING@
PACKAGE_TARNAME = @PACKAGE_TARNAME@
PACKAGE_VERSION = @PACKAGE_VERSION@
PATH_SEPARATOR = @PATH_SEPARATOR@
-PCRE_DATE = @PCRE_DATE@
-PCRE_LIB_VERSION = @PCRE_LIB_VERSION@
-PCRE_MAJOR = @PCRE_MAJOR@
-PCRE_MINOR = @PCRE_MINOR@
-PCRE_POSIXLIB_VERSION = @PCRE_POSIXLIB_VERSION@
-PCRE_VERSION = @PCRE_VERSION@
-POSIX_MALLOC_THRESHOLD = @POSIX_MALLOC_THRESHOLD@
RANLIB = @RANLIB@
SED = @SED@
SET_MAKE = @SET_MAKE@
@@ -272,8 +264,6 @@ top_srcdir = @top_srcdir@
@ISAIXIA64_TRUE@@ISSHARED_TRUE@@NEEDAJAX_FALSE at AM_CFLAGS = -Wl,-G -L../plplot/.libs -L.libs -leplplot -lm
@ISAIXIA64_TRUE@@ISSHARED_TRUE@@NEEDAJAX_TRUE at AM_CFLAGS = -Wl,-G -L../plplot/.libs -L.libs -lajax -leplplot -lm
@ISCYGWIN_TRUE at AM_LDFLAGS = -no-undefined -Wl,--add-stdcall-alias -Wl,--export-all-symbols -Wl,--enable-auto-import -L../plplot -leplplot
-PCRELIBVERSION = @PCRE_LIB_VERSION@
-PCREPOSIXLIBVERSION = @PCRE_POSIXLIB_VERSION@
INCLUDES = -DAJAX_FIXED_ROOT=$(AJAX_FIXED_ROOT) -DPREFIX=\"$(prefix)\" -I$(top_srcdir)/plplot $(POSIX_MALLOC_THRESHOLD)
AJAXSRC = ajacd.c ajalign.c ajarr.c ajassert.c \
ajbase.c ajcall.c ajcod.c \
@@ -288,8 +278,7 @@ ajrange.c ajreg.c ajreport.c \
ajseq.c ajseqabi.c ajseqdb.c ajseqread.c ajseqtype.c ajseqwrite.c \
ajsort.c ajstr.c ajsys.c \
ajtable.c ajtime.c ajtranslate.c ajtree.c \
-ajutil.c ajvector.c \
-pcre.c pcre_study.c pcreposix.c
+ajutil.c ajvector.c
AJAXGSRC = ajgraph.c ajhist.c
include_HEADERS = ajax.h ajarch.h ajdefine.h \
@@ -303,9 +292,7 @@ ajpat.h ajpdb.h ajpdbio.h ajphylo.h \
ajrange.h ajreg.h ajreport.h \
ajseq.h ajseqabi.h ajseqdata.h ajseqdb.h ajseqread.h ajseqtype.h ajseqwrite.h \
ajsort.h ajstr.h ajsys.h \
-ajtable.h ajtime.h ajtranslate.h ajtree.h ajutil.h ajvector.h \
-pcre.h pcre_chartables.c pcre_config.h pcre_get.c pcre_printint.c \
-pcre_internal.h pcreposix.h
+ajtable.h ajtime.h ajtranslate.h ajtree.h ajutil.h ajvector.h
@ISCYGWIN_FALSE at libajax_la_SOURCES = $(AJAXSRC)
@ISCYGWIN_TRUE at libajax_la_SOURCES = $(AJAXSRC) $(AJAXGSRC)
@@ -440,9 +427,6 @@ distclean-compile:
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/ajtree.Plo at am__quote@
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/ajutil.Plo at am__quote@
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/ajvector.Plo at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/pcre.Plo at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/pcre_study.Plo at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/pcreposix.Plo at am__quote@
.c.o:
@am__fastdepCC_TRUE@ $(COMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $<
diff -up EMBOSS-6.1.0/configure.pcre EMBOSS-6.1.0/configure
--- EMBOSS-6.1.0/configure.pcre 2009-07-15 01:15:56.000000000 +0200
+++ EMBOSS-6.1.0/configure 2009-09-27 03:21:32.000000000 +0200
@@ -16724,6 +16724,73 @@ _ACEOF
fi
+{ echo "$as_me:$LINENO: checking for pcre_compile in -lpcre" >&5
+echo $ECHO_N "checking for pcre_compile in -lpcre... $ECHO_C" >&6; }
+if test "${ac_cv_lib_pcre_pcre_compile+set}" = set; then
+ echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+ ac_check_lib_save_LIBS=$LIBS
+LIBS="-lpcre $LIBS"
+cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+
+/* Override any GCC internal prototype to avoid an error.
+ Use char because int might match the return type of a GCC
+ builtin and then its argument prototype would still apply. */
+#ifdef __cplusplus
+extern "C"
+#endif
+char pcre_compile ();
+int
+main ()
+{
+return pcre_compile ();
+ ;
+ return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext conftest$ac_exeext
+if { (ac_try="$ac_link"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5
+ (eval "$ac_link") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } && {
+ test -z "$ac_c_werror_flag" ||
+ test ! -s conftest.err
+ } && test -s conftest$ac_exeext &&
+ $as_test_x conftest$ac_exeext; then
+ ac_cv_lib_pcre_pcre_compile=yes
+else
+ echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ ac_cv_lib_pcre_pcre_compile=no
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \
+ conftest$ac_exeext conftest.$ac_ext
+LIBS=$ac_check_lib_save_LIBS
+fi
+{ echo "$as_me:$LINENO: result: $ac_cv_lib_pcre_pcre_compile" >&5
+echo "${ECHO_T}$ac_cv_lib_pcre_pcre_compile" >&6; }
+if test "x$ac_cv_lib_pcre_pcre_compile" = x""yes; then
+ LIBS="-lpcre $LIBS"
+else
+ LIBS="$LIBS"
+fi
+
if test "`uname`" = "FreeBSD" && ${with_pngdriver} != "no"; then
{ $as_echo "$as_me:$LINENO: checking for main in -liconv" >&5
--- NEW FILE EMBOSS.spec ---
# TODO:
# fix jemboss and enable it
%define emhome %{_datadir}/EMBOSS
Name: EMBOSS
Version: 6.1.0
Release: 5%{?dist}
Summary: The European Molecular Biology Open Software Suite
Group: Applications/Engineering
License: GPLv2+
URL: http://emboss.sf.net/
Source0: ftp://emboss.open-bio.org/pub/EMBOSS/%{name}-%{version}.tar.gz
Source1: README.fixes
#Upstream patch
Patch0: ftp://emboss.open-bio.org/pub/EMBOSS/fixes/patches/patch-1-2.gz
#Use system-wide pcre. Sent upstream.
Patch1: %{name}-system-pcre.patch
#Fedora-specific. Not sent upstream.
Patch2: %{name}-fedora.patch
#Add missing destdir. Sent upstream.
Patch3: %{name}-6.1.0-destdir.patch
BuildRoot: %{_tmppath}/%{name}-%{version}-%{release}-root-%(%{__id_u} -n)
BuildRequires: gd-devel
#BuildRequires: java-devel
BuildRequires: pam-devel
BuildRequires: pcre-devel
#BuildRequires: axis classpathx-jaf jakarta-commons-discovery
#BuildRequires: jakarta-commons-logging log4j wsdl4j
%description
EMBOSS is a new, 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.
Reference for EMBOSS: Rice,P. Longden,I. and Bleasby,A.
"EMBOSS: The European Molecular Biology Open Software Suite"
Trends in Genetics June 2000, vol 16, No 6. pp.276-277
%package devel
Summary: Development tools for programs which will use the %{name} library
Group: Development/Libraries
Requires: %{name}-libs = %{version}-%{release}
%description devel
The %{name}-devel package includes the header files and static libraries
necessary for developing programs which will use the %{name} library.
%package libs
Summary: Shared libraries for %{name}
Group: System Environment/Libraries
%description libs
The %{name}-libs package includes the dynamic libraries
necessary for %{name}.
#%package java
#Summary: Java interface to %{name}
#Group: Applications/Engineering
#Requires: %{name} = %{version}-%{release}
#Requires: axis classpathx-jaf jakarta-commons-discovery
#Requires: jakarta-commons-logging log4j wsdl4j
#%description java
#Jemboss is a Java interface to EMBOSS, developed at
#the HGMP-RC and in close collaboration with the EMBOSS
#development team. It is distributed as part of the EMBOSS
#software.
#Documentation on Jemboss can be found at:
#http://www.hgmp.mrc.ac.uk/Software/EMBOSS/Jemboss/
%prep
%setup -q
%patch0 -p1
%patch1 -p1 -b .pcre
%patch2 -p0 -b .fedora
%patch3 -p0 -b .destdir
#install the patch readme
install -pm 644 %{SOURCE1} README.fixes
#these files were executable for some reason
chmod 644 emboss/prettyplot.c emboss/polydot.c emboss/supermatcher.c
#use system java libraries
#pushd jemboss/lib
#rm activation.jar;
#ln -s %{_javadir}/activation.jar activation.jar;
#pushd axis
#for i in axis-ant axis jaxrpc saaj;
#do
# rm $i.jar;
# ln -s %{_javadir}/axis/$i.jar $i.jar;
#done
#for i in commons-discovery commons-logging wsdl4j;
#do
# rm $i.jar;
# ln -s %{_javadir}/$i.jar $i.jar;
#done
#rm log4j-1.2.8.jar
#ln -s %{_javadir}/log4j.jar log4j-1.2.8.jar
#popd
#popd
%build
%configure \
--without-java \
--disable-static \
--with-x \
--with-auth \
--with-thread \
--includedir=%{_includedir}/EMBOSS \
%ifarch ppc64 sparc64 x86_64
--enable-64 \
%endif
%{__make} %{?_smp_mflags}
%install
rm -rf $RPM_BUILD_ROOT
%{__make} install DESTDIR=$RPM_BUILD_ROOT
install -m 755 -d $RPM_BUILD_ROOT/%{_sysconfdir}/profile.d
cat << __EOF__ >> $RPM_BUILD_ROOT/%{_sysconfdir}/profile.d/emboss.sh
export PLPLOT_LIB=%{emhome}
export EMBOSS_ACDROOT=%{emhome}/acd
export EMBOSS_DOCROOT=%{emhome}/doc
export EMBOSS_DATABASE_DIR=%{emhome}/data
export EMBOSS_DATA=%{emhome}/data
__EOF__
cat << __EOF__ >> $RPM_BUILD_ROOT/%{_sysconfdir}/profile.d/emboss.csh
setenv PLPLOT_LIB %{emhome}
setenv EMBOSS_ACDROOT %{emhome}/acd
setenv EMBOSS_DOCROOT %{emhome}/doc
setenv EMBOSS_DATABASE_DIR %{emhome}/data
setenv EMBOSS_DATA %{emhome}/data
__EOF__
rm $RPM_BUILD_ROOT%{_libdir}/*.la
#this file has zero length, so kill it
rm $RPM_BUILD_ROOT%{_datadir}/EMBOSS/test/data/dna.aln
#fix executable permissions
pushd $RPM_BUILD_ROOT%{_datadir}/EMBOSS/jemboss/utils
chmod +x install-jemboss-server.sh keys.sh makeFileManagerJNLP.sh makeJar.csh \
makeJNLP.sh
popd
pushd $RPM_BUILD_ROOT%{_datadir}/EMBOSS/jemboss/api
chmod +x getClasses.pl makeDocs.csh
popd
#rename conflicting binaries
mv $RPM_BUILD_ROOT%{_bindir}/chaos $RPM_BUILD_ROOT%{_bindir}/em_chaos
%clean
rm -rf $RPM_BUILD_ROOT
%post libs -p /sbin/ldconfig
%postun libs -p /sbin/ldconfig
%files
%defattr(-,root,root,-)
%doc AUTHORS ChangeLog COPYING FAQ INSTALL LICENSE NEWS README README.fixes THANKS
%{_bindir}/*
%exclude %{_bindir}/runJemboss.csh
%exclude %{_bindir}/jembossctl
%{_datadir}/EMBOSS
%exclude %{_datadir}/EMBOSS/jemboss
%config %{_sysconfdir}/profile.d/*
%files devel
%defattr(-,root,root,-)
%{_libdir}/*.so
%{_includedir}/EMBOSS
%files libs
%defattr(-,root,root,-)
%{_libdir}/*.so.*
#%files java
#%defattr(-,root,root,-)
#%doc jemboss/README jemboss/resources jemboss/api
#%{_bindir}/runJemboss.csh
#%{_bindir}/jembossctl
#%{_datadir}/EMBOSS/jemboss
%changelog
* Sat Oct 17 2009 Julian Sikorski <belegdol at fedoraproject.org> - 6.1.0-5
- Added comments explaining the purpose of each patch
* Mon Oct 05 2009 Julian Sikorski <belegdol at fedoraproject.org> - 6.1.0-4
- Renamed conflicting binaries
- Disabled jemboss
* Tue Sep 29 2009 Julian Sikorski <belegdol at fedoraproject.org> - 6.1.0-3
- Re-enabled system pcre usage
- Initial attempt at using system-wide .jar files
* Tue Sep 22 2009 Julian Sikorski <belegdol at fedoraproject.org> - 6.1.0-2
- Added the upstream 1-2 patch
* Wed Jul 29 2009 Julian Sikorski <belegdol at fedoraproject.org> - 6.1.0-1
- Updated to 6.1.0
- Dropped pcre-devel from BuildRequires for the time being
- Ditto --with-java and --with-javaos
- Patched jemboss/Makefile.am not to include DESTDIR in runJemboss.sh
- Install the header files in EMBOSS subdir
- Added the missing executable bits
* Fri Jun 12 2009 Julian Sikorski <belegdol at fedoraproject.org> - 6.0.1-3
- Updated the upstream patch to 1-12
- Added the patch readme to %%doc
* Thu Apr 16 2009 Julian Sikorski <belegdol at fedoraproject.org> - 6.0.1-2
- Own %%{_datadir}/EMBOSS
- Don't use %%{name} macro in %%files
- Updated the upstream patch to 1-7
- Use dist instead of dist_tag
- Adjusted whitespaces
- Added pcre-devel to BuildRequires
- Fixed spurious executable permissions
- Removed the empty dna.aln file
- Patched jemboss.properties to include the paths this package uses
- Made the -java package require the main one
* Mon Sep 29 2008 Dominik Mierzejewski <rpm at greysector.net> 6.0.1-1
- updated to 6.0.1
- applied upstream patch 1-1
- patched to use system pcre
* Tue Jan 08 2008 Dominik Mierzejewski <rpm at greysector.net> 5.0.0-1
- Cleaned up BioRPMs' spec
- Updated to 5.0.0
* Thu Mar 17 2005 Bent Terp <Bent.Terp at biosci.ki.se>
- Upped to 2.10.0
* Fri Jul 16 2004 Bent Terp <Bent.Terp at biosci.ki.se>
- Had forgotten the emboss_database_dir env var
* Wed Feb 18 2004 Bent Terp <Bent.Terp at biosci.ki.se>
- Tried to make the building more dynamic. Added Requires and BuildRequires
* Thu Dec 04 2003 Luc Ducazu <luc at biolinux.org>
- Build for EMBOSS 2.8.0
- subpackage jemboss
* Wed Jun 11 2003 Luc Ducazu <luc at biolinux.org>
- Build for EMBOSS 2.7.1
* Tue Jan 28 2003 Luc Ducazu <luc at biolinux.org>
- Build for EMBOSS 2.6.0
- Programs moved to /usr/local/bin
- Adopted many ideas from Guillaume Rousse <g.rousse at linux-mandrake.com>
* Wed Nov 27 2002 Luc Ducazu <luc at biolinux.org>
- Initial build for EMBOSS 2.5.1
--- NEW FILE README.fixes ---
The files in this directory are bugfix replacements for files in
the EMBOSS-6.1.0 distribution. Just drop the replacement files in
the location shown and redo the 'make install.'
Fix 1. EMBOSS-6.1.0/ajax/ajfeat.c
EMBOSS-6.1.0/ajax/ajseqread.c
EMBOSS-6.1.0/ajax/ajseqwrite.c
EMBOSS-6.1.0/jemboss/org/emboss/jemboss/gui/Browser.java
EMBOSS-6.1.0/jemboss/org/emboss/jemboss/gui/BuildProgramMenu.java
EMBOSS-6.1.0/jemboss/org/emboss/jemboss/gui/form/BuildJembossForm.java
EMBOSS-6.1.0/jemboss/org/emboss/jemboss/gui/sequenceChooser/InputSequenceAttributes.java
EMBOSS-6.1.0/jemboss/org/emboss/jemboss/soap/GetVersion.java
EMBOSS-6.1.0/jemboss/org/emboss/jemboss/soap/ShowDB.java
EMBOSS-6.1.0/jemboss/utils/install-jemboss-server.sh
EMBOSS-6.1.0/jemboss/lib/client.jar
29 Jul 2009: Fix feature specification problems in Jemboss.
Use version number to point to documentation URLs
Remove standalone option from server script.
Correct FASTQ input searching for '@' to start next sequence
Standardize FASTQ sequence formats with other OpenBio projects
Correct issues in igstrict, genpept and refseqp formats
Fix 2. EMBOSS-6.1.0/ajax/ajmem.h
EMBOSS-6.1.0/ajax/ajstr.c
EMBOSS-6.1.0/ajax/ajstr.h
EMBOSS-6.1.0/nucleus/embaln.c
24-Aug-2009: Fix string extension so that pointers in lists remain valid.
This fixes a bug in processing SwissProt complex descriptions.
Fix definition of AJRESIZE0 macro.
Fix processing of first match in a profile alignment (prophet).
--- NEW FILE import.log ---
EMBOSS-6_1_0-5_fc11:F-12:EMBOSS-6.1.0-5.fc11.src.rpm:1255819735
Index: .cvsignore
===================================================================
RCS file: /cvs/pkgs/rpms/EMBOSS/F-12/.cvsignore,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -p -r1.1 -r1.2
--- .cvsignore 17 Oct 2009 20:39:05 -0000 1.1
+++ .cvsignore 17 Oct 2009 22:49:35 -0000 1.2
@@ -0,0 +1,2 @@
+EMBOSS-6.1.0.tar.gz
+patch-1-2.gz
Index: sources
===================================================================
RCS file: /cvs/pkgs/rpms/EMBOSS/F-12/sources,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -p -r1.1 -r1.2
--- sources 17 Oct 2009 20:39:05 -0000 1.1
+++ sources 17 Oct 2009 22:49:36 -0000 1.2
@@ -0,0 +1,2 @@
+6c5163c571bc0be94d64420ce0d71824 EMBOSS-6.1.0.tar.gz
+faec6ddd399ef243f4d6ffbcc878b009 patch-1-2.gz
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