rpms/EMBOSS/F-11 EMBOSS.spec,1.1,1.2
belegdol
belegdol at fedoraproject.org
Thu Dec 24 08:16:54 UTC 2009
- Previous message (by thread): rpms/EMBOSS/F-11 EMBOSS-6.1.0-rebuild.patch, NONE, 1.1 jemboss.desktop, NONE, 1.1 .cvsignore, 1.2, 1.3 README.fixes, 1.1, 1.2 sources, 1.2, 1.3
- Next message (by thread): rpms/lohit-assamese-fonts/devel bug-549319.patch, NONE, 1.1 lohit-assamese-fonts.spec, 1.2, 1.3
- Messages sorted by:
[ date ]
[ thread ]
[ subject ]
[ author ]
Author: belegdol
Update of /cvs/pkgs/rpms/EMBOSS/F-11
In directory cvs1.fedora.phx.redhat.com:/tmp/cvs-serv17506
Modified Files:
EMBOSS.spec
Log Message:
Commit the spec as well
Index: EMBOSS.spec
===================================================================
RCS file: /cvs/pkgs/rpms/EMBOSS/F-11/EMBOSS.spec,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -p -r1.1 -r1.2
--- EMBOSS.spec 17 Oct 2009 22:50:58 -0000 1.1
+++ EMBOSS.spec 24 Dec 2009 08:16:54 -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
- Previous message (by thread): rpms/EMBOSS/F-11 EMBOSS-6.1.0-rebuild.patch, NONE, 1.1 jemboss.desktop, NONE, 1.1 .cvsignore, 1.2, 1.3 README.fixes, 1.1, 1.2 sources, 1.2, 1.3
- Next message (by thread): rpms/lohit-assamese-fonts/devel bug-549319.patch, NONE, 1.1 lohit-assamese-fonts.spec, 1.2, 1.3
- Messages sorted by:
[ date ]
[ thread ]
[ subject ]
[ author ]
More information about the fedora-extras-commits
mailing list