rpms/EMBOSS/F-12 EMBOSS-6.1.0-rebuild.patch, NONE, 1.1 jemboss.desktop, NONE, 1.1 .cvsignore, 1.2, 1.3 EMBOSS.spec, 1.1, 1.2 README.fixes, 1.1, 1.2 sources, 1.2, 1.3

belegdol belegdol at fedoraproject.org
Thu Dec 24 08:01:31 UTC 2009 

Author: belegdol

Update of /cvs/pkgs/rpms/EMBOSS/F-12
In directory cvs1.fedora.phx.redhat.com:/tmp/cvs-serv15608

Modified Files:
	.cvsignore EMBOSS.spec README.fixes sources 
Added Files:
	EMBOSS-6.1.0-rebuild.patch jemboss.desktop 
Log Message:
* Sun Dec 13 2009 Julian Sikorski <belegdol at fedoraproject.org> - 6.1.0-6
- Added the upstream 1-3 patch
- Fixed bogus Patch3 description
- Jemboss is still disabled, but some improvements have been made
  - Backported patch enabling jemboss rebuild from CVS
  - Added ant and jpackage-utils to BuildRequires
  - Made java-devel dependency versioned
  - Switched to build-jar-repository to fill the dependencies
  - Replaced versioned log4j calls with latest version
  - Renamed EMBOSS-java to jemboss
  - Added a desktop entry for jemboss from Debian


EMBOSS-6.1.0-rebuild.patch:
 Makefile.am |    5 +++++
 Makefile.in |   31 +++++++++++++++++--------------
 2 files changed, 22 insertions(+), 14 deletions(-)

--- NEW FILE EMBOSS-6.1.0-rebuild.patch ---
--- jemboss/lib/Makefile.am.rebuild	2009-06-30 10:33:58.000000000 +0200
+++ jemboss/lib/Makefile.am	2009-10-21 07:56:01.000000000 +0200
@@ -1,5 +1,10 @@
 SUBDIRS = axis
 
+all-local:
+if EHAVEANT
+	ant -f ../build.xml package -Demboss.data=../emboss/data -Dname=client -Djar.dir=lib -Dnotformemboss=yes;
+endif
+
 # The install-exec-hook is for the case where a client.jar has
 # been created by the 'ant' packaging for a standalone Jemboss.
 # In that case it needs to be copied to the install dir.
--- jemboss/lib/Makefile.in.rebuild	2009-07-15 01:16:01.000000000 +0200
+++ jemboss/lib/Makefile.in	2009-10-21 07:56:46.000000000 +0200
@@ -507,7 +507,7 @@
 	done
 check-am: all-am
 check: check-recursive
-all-am: Makefile $(DATA)
+all-am: Makefile $(DATA) all-local
 installdirs: installdirs-recursive
 installdirs-am:
 	for dir in "$(DESTDIR)$(pkgdatadir)"; do \
@@ -609,21 +609,24 @@
 	install-am install-exec-am install-strip tags-recursive
 
 .PHONY: $(RECURSIVE_CLEAN_TARGETS) $(RECURSIVE_TARGETS) CTAGS GTAGS \
-	all all-am check check-am clean clean-generic clean-libtool \
-	ctags ctags-recursive distclean distclean-generic \
-	distclean-libtool distclean-tags distdir dvi dvi-am html \
-	html-am info info-am install install-am install-data \
-	install-data-am install-dvi install-dvi-am install-exec \
-	install-exec-am install-exec-hook install-html install-html-am \
-	install-info install-info-am install-man install-pdf \
-	install-pdf-am install-pkgdataDATA install-ps install-ps-am \
-	install-strip installcheck installcheck-am installdirs \
-	installdirs-am maintainer-clean maintainer-clean-generic \
-	mostlyclean mostlyclean-generic mostlyclean-libtool pdf pdf-am \
-	ps ps-am tags tags-recursive uninstall uninstall-am \
-	uninstall-pkgdataDATA
+	all all-am all-local check check-am clean clean-generic \
+	clean-libtool ctags ctags-recursive distclean \
+	distclean-generic distclean-libtool distclean-tags distdir dvi \
+	dvi-am html html-am info info-am install install-am \
+	install-data install-data-am install-dvi install-dvi-am \
+	install-exec install-exec-am install-exec-hook install-html \
+	install-html-am install-info install-info-am install-man \
+	install-pdf install-pdf-am install-pkgdataDATA install-ps \
+	install-ps-am install-strip installcheck installcheck-am \
+	installdirs installdirs-am maintainer-clean \
+	maintainer-clean-generic mostlyclean mostlyclean-generic \
+	mostlyclean-libtool pdf pdf-am ps ps-am tags tags-recursive \
+	uninstall uninstall-am uninstall-pkgdataDATA
 
 
+all-local:
+ at EHAVEANT_TRUE@	ant -f ../build.xml package -Demboss.data=../emboss/data -Dname=client -Djar.dir=lib -Dnotformemboss=yes;
+
 # The install-exec-hook is for the case where a client.jar has
 # been created by the 'ant' packaging for a standalone Jemboss.
 # In that case it needs to be copied to the install dir.


--- NEW FILE jemboss.desktop ---
[Desktop Entry]
Version=1.0
Terminal=false
Icon=jemboss
Exec=runJemboss.csh
Name=Jemboss
GenericName=GUI for EMBOSS
Comment=Graphical user interface for the European Molecular Biology Open Software Suite.
Type=Application
Categories=Biology;Science;Education;


Index: .cvsignore
===================================================================
RCS file: /cvs/pkgs/rpms/EMBOSS/F-12/.cvsignore,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -p -r1.2 -r1.3
--- .cvsignore	17 Oct 2009 22:49:35 -0000	1.2
+++ .cvsignore	24 Dec 2009 08:01:31 -0000	1.3
@@ -1,2 +1,2 @@
 EMBOSS-6.1.0.tar.gz
-patch-1-2.gz
+patch-1-3.gz


Index: EMBOSS.spec
===================================================================
RCS file: /cvs/pkgs/rpms/EMBOSS/F-12/EMBOSS.spec,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -p -r1.1 -r1.2
--- EMBOSS.spec	17 Oct 2009 22:49:35 -0000	1.1
+++ EMBOSS.spec	24 Dec 2009 08:01:31 -0000	1.2
@@ -5,7 +5,7 @@
 
 Name:           EMBOSS
 Version:        6.1.0
-Release:        5%{?dist}
+Release:        6%{?dist}
 Summary:        The European Molecular Biology Open Software Suite
 
 Group:          Applications/Engineering
@@ -13,22 +13,28 @@ License:        GPLv2+
 URL:            http://emboss.sf.net/
 Source0:        ftp://emboss.open-bio.org/pub/EMBOSS/%{name}-%{version}.tar.gz
 Source1:        README.fixes
+Source2:        jemboss.desktop
 #Upstream patch
-Patch0:         ftp://emboss.open-bio.org/pub/EMBOSS/fixes/patches/patch-1-2.gz
+Patch0:         ftp://emboss.open-bio.org/pub/EMBOSS/fixes/patches/patch-1-3.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.
+#Remove extra destdir. Sent upstream.
 Patch3:         %{name}-6.1.0-destdir.patch
+#Patch ensuring jemboss rebuild backported from CVS
+Patch4:         %{name}-6.1.0-rebuild.patch
 BuildRoot:      %{_tmppath}/%{name}-%{version}-%{release}-root-%(%{__id_u} -n)
 
+BuildRequires:  ant
+BuildRequires:  desktop-file-utils
 BuildRequires:  gd-devel
-#BuildRequires:  java-devel
+BuildRequires:  java-devel >= 1:1.6.0
+BuildRequires:  jpackage-utils
 BuildRequires:  pam-devel
 BuildRequires:  pcre-devel
-#BuildRequires:  axis classpathx-jaf jakarta-commons-discovery
-#BuildRequires:  jakarta-commons-logging log4j wsdl4j
+BuildRequires:  axis jaf javamail jakarta-commons-discovery jakarta-commons-logging
+BuildRequires:  log4j regexp servlet xerces-j2 wsdl4j
 
 %description
 EMBOSS is a new, free Open Source software analysis package specially
@@ -64,14 +70,16 @@ The %{name}-libs package includes the dy
 necessary for %{name}.
 
 
-#%package java
+#%package -n jemboss
 #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
+#Requires:       java >= 1:1.6.0
+#Requires:       jpackage-utils    
+#Requires:       axis jaf javamail jakarta-commons-discovery jakarta-commons-logging
+#Requires:       log4j regexp servlet xerces-j2 wsdl4j
 
-#%description java
+#%description -n jemboss
 #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
@@ -87,6 +95,7 @@ necessary for %{name}.
 %patch1 -p1 -b .pcre
 %patch2 -p0 -b .fedora
 %patch3 -p0 -b .destdir
+%patch4 -p0 -b .jemboss-rebuild
 
 #install the patch readme
 install -pm 644 %{SOURCE1} README.fixes
@@ -94,30 +103,29 @@ 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 newer log4j version
+sed -i "s at log4j-1.2.8@log4j-1.2.14@" \
+    jemboss/lib/axis/Makefile.am \
+    jemboss/lib/axis/Makefile.in \
+    jemboss/utils/makeFileManagerJNLP.sh \
+    jemboss/utils/makeJNLP.sh
+
 #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 $i.jar;
-#done
-#rm log4j-1.2.8.jar
-#ln -s %{_javadir}/log4j.jar log4j-1.2.8.jar
-#popd
-#popd
+rm jemboss/lib/{activation,client,jakarta-regexp-1.2,mail,xerces}.jar
+build-jar-repository -s -p jemboss/lib activation regexp javamail xerces-j2
+mv jemboss/lib/regexp.jar jemboss/lib/jakarta-regexp-1.2.jar
+mv jemboss/lib/javamail.jar jemboss/lib/mail.jar
+mv jemboss/lib/xerces-j2.jar jemboss/lib/xerces.jar
+rm jemboss/lib/axis/*.jar
+build-jar-repository -s -p jemboss/lib/axis axis/axis-ant axis/axis axis/jaxrpc axis/saaj commons-discovery commons-logging log4j-1.2.14 servlet wsdl4j
+for i in axis axis-ant jaxrpc saaj;
+do
+mv jemboss/lib/axis/axis_$i.jar jemboss/lib/axis/$i.jar;
+done
 
 
 %build
 %configure \
-  --without-java \
   --disable-static \
   --with-x \
   --with-auth \
@@ -126,6 +134,9 @@ chmod 644 emboss/prettyplot.c emboss/pol
 %ifarch ppc64 sparc64 x86_64
   --enable-64 \
 %endif
+  --with-java=/usr/lib/jvm/java/include \
+  --with-javaos=/usr/lib/jvm/java/include/linux \
+
 
 %{__make} %{?_smp_mflags}
 
@@ -169,6 +180,11 @@ popd
 #rename conflicting binaries
 mv $RPM_BUILD_ROOT%{_bindir}/chaos $RPM_BUILD_ROOT%{_bindir}/em_chaos
 
+#install the desktop file
+#desktop-file-install                                    \
+#--dir=${RPM_BUILD_ROOT}%{_datadir}/applications         \
+#%{SOURCE2}
+
 
 %clean
 rm -rf $RPM_BUILD_ROOT
@@ -196,20 +212,34 @@ rm -rf $RPM_BUILD_ROOT
 %{_libdir}/*.so
 %{_includedir}/EMBOSS
 
+
 %files libs
 %defattr(-,root,root,-)
 %{_libdir}/*.so.*
 
 
-#%files java
+#%files -n jemboss
 #%defattr(-,root,root,-)
 #%doc jemboss/README jemboss/resources jemboss/api
 #%{_bindir}/runJemboss.csh
 #%{_bindir}/jembossctl
+#%{_datadir}/applications/jemboss.desktop
 #%{_datadir}/EMBOSS/jemboss
 
 
 %changelog
+* Sun Dec 13 2009 Julian Sikorski <belegdol at fedoraproject.org> - 6.1.0-6
+- Added the upstream 1-3 patch
+- Fixed bogus Patch3 description
+- Jemboss is still disabled, but some improvements have been made
+  - Backported patch enabling jemboss rebuild from CVS
+  - Added ant and jpackage-utils to BuildRequires
+  - Made java-devel dependency versioned
+  - Switched to build-jar-repository to fill the dependencies
+  - Replaced versioned log4j calls with latest version
+  - Renamed EMBOSS-java to jemboss
+  - Added a desktop entry for jemboss from Debian
+
 * Sat Oct 17 2009 Julian Sikorski <belegdol at fedoraproject.org> - 6.1.0-5
 - Added comments explaining the purpose of each patch
 


Index: README.fixes
===================================================================
RCS file: /cvs/pkgs/rpms/EMBOSS/F-12/README.fixes,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -p -r1.1 -r1.2
--- README.fixes	17 Oct 2009 22:49:36 -0000	1.1
+++ README.fixes	24 Dec 2009 08:01:31 -0000	1.2
@@ -30,3 +30,79 @@ Fix 2. EMBOSS-6.1.0/ajax/ajmem.h
              This fixes a bug in processing SwissProt complex descriptions.
              Fix definition of AJRESIZE0 macro.
 	     Fix processing of first match in a profile alignment (prophet).
+
+Fix 3. EMBOSS-6.1.0/ajax/ajfeat.c
+       EMBOSS-6.1.0/ajax/ajfeat.h
+       EMBOSS-6.1.0/ajax/ajgraph.c
+       EMBOSS-6.1.0/ajax/ajmath.c
+       EMBOSS-6.1.0/ajax/ajseq.c
+       EMBOSS-6.1.0/ajax/ajseqread.c
+       EMBOSS-6.1.0/ajax/ajseqwrite.c
+       EMBOSS-6.1.0/nucleus/embmisc.c
+       EMBOSS-6.1.0/nucleus/embmisc.h
+       EMBOSS-6.1.0/nucleus/embpat.c
+       EMBOSS-6.1.0/emboss/coderet.c
+       EMBOSS-6.1.0/emboss/extractfeat.c
+       EMBOSS-6.1.0/emboss/notseq.c
+       EMBOSS-6.1.0/emboss/prettyplot.c
+       EMBOSS-6.1.0/emboss/seqmatchall.c
+       EMBOSS-6.1.0/emboss/showfeat.c
+       EMBOSS-6.1.0/emboss/showpep.c
+       EMBOSS-6.1.0/emboss/showseq.c
+       EMBOSS-6.1.0/emboss/twofeat.c
+       EMBOSS-6.1.0/jemboss/utils/install-jemboss-server.sh
+       EMBOSS-6.1.0/jemboss/org/emboss/jemboss/server/AppendToLogFileThread.java
+       EMBOSS-6.1.0/jemboss/org/emboss/jemboss/server/JembossAuthServer.java
+
+02-Dec-2009: Fixes problems with extractfeat. The fix includes cleaner
+             definitions of functions used to match feature tags and
+             feature types which result in minor updates to 6 other
+             applications.
+
+             Extractfeat in previous versions used its own text parser
+             to extract feature data from only a limited set of
+             formats. In release 6.1.0 it was replaced by the standard
+             EMBOSS feature table. With no options set, extractfeat
+             rejected all features (type '*' was needed to extract
+             features). Extractfeat default settings now extract all
+             features from an entry.
+
+             Features on the reverse strand were incorrectly processed
+             (an effect caused by some of the old extractfeat code
+             remaining). Reverse strand features are now correctly
+             parsed, including both "join(complement())" and
+             "complement(join())" syntax in EMBL/GenBank/DDBJ feature
+             tables.
+
+             Fixes an issue in GenBank parsing where the ORIGIN line is absent.
+
+             Fixes scaling errors in prettyplot, especially in mEMBOSS
+             when plotting to a window on screen (the default
+             output). The plplot library does not report the true
+             width and height for several devices. The assumptions in
+             prettyplot depend on reasonable size estimates. Release
+             6.2.0 will have further corrections to plplot device
+             scaling.
+
+	     Fixes the counting of non-coding features in coderet.
+
+	     Fixes a seqmatchall error for short sequences with perfect matches
+
+	     When reverse-complementing sequences, also reverses
+	     the quality scores.
+
+	     Allows '-' in format names in the USA syntax, to allow
+	     fastq-sanger fastq-illumina and fastq-solexa format names
+	     to be used.
+
+	     When reading protein sequences, a sequence with only a
+	     stop is now recognized as empty (zero length) after
+	     processing ambiguity codes and stops.
+
+	     Fixes a problem writing features in PIR format when the
+	     feature table is empty, for example a report file with no hits.
+
+	     Fixes a dependency on 'ant' to install a Jemboss server.
+
+	     Fixes a problem in logging Jemboss info/error messages.
+


Index: sources
===================================================================
RCS file: /cvs/pkgs/rpms/EMBOSS/F-12/sources,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -p -r1.2 -r1.3
--- sources	17 Oct 2009 22:49:36 -0000	1.2
+++ sources	24 Dec 2009 08:01:31 -0000	1.3
@@ -1,2 +1,2 @@
 6c5163c571bc0be94d64420ce0d71824  EMBOSS-6.1.0.tar.gz
-faec6ddd399ef243f4d6ffbcc878b009  patch-1-2.gz
+4a5f96d849409fdecf39e92380e5381e  patch-1-3.gz

More information about the scm-commits mailing list