rpms/EMBOSS/devel README.fixes, 1.3, 1.4 .cvsignore, 1.4, 1.5 EMBOSS.spec, 1.5, 1.6 sources, 1.4, 1.5
belegdol
belegdol at fedoraproject.org
Wed Apr 7 21:34:23 UTC 2010
Author: belegdol
Update of /cvs/pkgs/rpms/EMBOSS/devel
In directory cvs01.phx2.fedoraproject.org:/tmp/cvs-serv20816
Modified Files:
.cvsignore EMBOSS.spec sources
Added Files:
README.fixes
Log Message:
* Wed Apr 07 2010 Julian Sikorski <belegdol at fedoraproject.org> - 6.2.0-3
- Added upstream 1-18 patch
Index: README.fixes
===================================================================
RCS file: README.fixes
diff -N README.fixes
--- /dev/null 1 Jan 1970 00:00:00 -0000
+++ README.fixes 7 Apr 2010 21:34:23 -0000 1.4
@@ -0,0 +1,160 @@
+The files in this directory are bugfix replacements for files in
+the EMBOSS-6.2.0 distribution. Just drop the replacement files in
+the location shown and redo the 'make install.'
+
+Fix 1. EMBOSS-6.2.0/emboss/jembossctl.c
+ EMBOSS-6.2.0/jemboss/lib/jemboss.jar
+ EMBOSS-6.2.0/jemboss/org/emboss/jemboss/gui/filetree/DragTree.java
+ EMBOSS-6.2.0/jemboss/org/emboss/jemboss/gui/filetree/RemoteDragTree.java
+ EMBOSS-6.2.0/jemboss/org/emboss/jemboss/gui/form/BuildJembossForm.java
+ EMBOSS-6.2.0/jemboss/org/emboss/jemboss/gui/ShowResultSet.java
+ EMBOSS-6.2.0/jemboss/org/emboss/jemboss/JembossParams.java
+ EMBOSS-6.2.0/jemboss/org/emboss/jemboss/programs/RunEmbossApplication2.java
+ EMBOSS-6.2.0/jemboss/org/emboss/jemboss/server/JembossAuthServer.java
+ EMBOSS-6.2.0/jemboss/org/emboss/jemboss/server/JembossServer.java
+ EMBOSS-6.2.0/jemboss/org/emboss/jemboss/server/JembossThread.java
+ EMBOSS-6.2.0/jemboss/org/emboss/jemboss/soap/AuthPopup.java
+ EMBOSS-6.2.0/jemboss/org/emboss/jemboss/soap/JembossRun.java
+ EMBOSS-6.2.0/jemboss/org/emboss/jemboss/soap/PrivateRequest.java
+ EMBOSS-6.2.0/jemboss/utils/install-jemboss-server.sh
+
+26 Feb 2010: Various Jemboss fixes including allowing multiple
+ parameters to "wossname" and reporting of stderr
+ output
+
+
+Fix 2. EMBOSS-6.2.0/emboss/acd/jaspextract.acd
+ EMBOSS-6.2.0/emboss/acd/jaspscan.acd
+ EMBOSS-6.2.0/emboss/jaspextract.c
+ EMBOSS-6.2.0/emboss/jaspscan.c
+
+26 Feb 2010: jaspextract and jaspscan can use the latest-format data at
+ http://jaspar.genereg.net/html/DOWNLOAD/Archive.zip
+ jaspextract uses the data in the "all_data/FlatFileDir"
+ directory. It is advisable to clear delete any old data files
+ from your EMBOSS data file area e.g. from the
+ /usr/local/emboss/share/EMBOSS/data/JASPAR_* directories
+
+
+Fix 3. EMBOSS-6.2.0/emboss/emma.c
+
+26 Feb 2010: Takes note once again of any EMBOSS_CLUSTALW environment variable
+ setting.
+
+
+Fix 4. EMBOSS-6.2.0/emboss/acd/trimseq.acd
+
+26 Feb 2010: Place limit on the maximum window size
+
+
+Fix 5. EMBOSS-6.2.0/ajax/core/ajpat.c
+ EMBOSS-6.2.0/nucleus/embpat.c
+
+26 Feb 2010: Fix crash when excessive mismatches requested in one of the
+ fuzzpro search algorithms.
+
+
+Fix 6. EMBOSS-6.2.0/emboss/coderet.c
+ EMBOSS-6.2.0/emboss/splitter.c
+
+26 Feb 2010: Fix crash if no features in the source sequence
+
+
+Fix 7. EMBOSS-6.2.0/emboss/matcher.c
+
+26 Feb 2010: Fix memory allocation problem
+
+
+Fix 8. EMBOSS-6.2.0/ajax/core/ajseqread.c
+ EMBOSS-6.2.0/ajax/core/ajseqwrite.c
+
+01-Mar-2010: Fix sequence format 'refseqp' to be a valid protein
+ output format and to preserve more fields from refseqp input.
+
+
+Fix 9. EMBOSS-6.2.0/ajax/core/ajlist.c
+ EMBOSS-6.2.0/ajax/core/ajlist.h
+ EMBOSS-6.2.0/emboss/showfeat.c
+
+01-Mar-2010: Fix showfeat sorted feature output to correctly sort exons
+ for 'join' feature locations.
+
+
+Fix 10.EMBOSS-6.2.0/ajax/graphics/ajgraph.c
+ EMBOSS-6.2.0/emboss/prettyplot.c
+
+01-Mar-2010: Fix PNG graphics output format to remove large blank
+ margins added by the plplot driver. Improve prettyplot
+ output to better centre sequence characters within boxes.
+
+
+Fix 11.EMBOSS-6.2.0/emboss/recoder.c
+ EMBOSS-6.2.0/emboss/remap.c
+ EMBOSS-6.2.0/emboss/restrict.c
+ EMBOSS-6.2.0/emboss/showseq.c
+ EMBOSS-6.2.0/emboss/silent.c
+
+01-Mar-2010: Skip bad enzyme file records
+
+
+Fix 12.EMBOSS-6.2.0/emboss/showpep.c
+ EMBOSS-6.2.0/emboss/showseq.c
+
+01-Mar-2010: Correct HTML output closing tag.
+
+
+Fix 13.EMBOSS-6.2.0/ajax/core/ajfeat.c
+
+01-Mar-2010: Remove warnings for accessions and repeat features in
+ ensembl format EMBL files.
+
+
+Fix 14.EMBOSS-6.2.0/emboss/acd/cirdna.acd
+ EMBOSS-6.2.0/emboss/acd/knowntypes.standard
+
+01-Mar-2010: Fix description of cirdna input
+
+
+Fix 15.EMBOSS-6.2.0/emboss/acd/extractfeat.acd
+ EMBOSS-6.2.0/emboss/acd/maskfeat.acd
+ EMBOSS-6.2.0/emboss/acd/showfeat.acd
+ EMBOSS-6.2.0/emboss/acd/showpep.acd
+ EMBOSS-6.2.0/emboss/acd/showseq.acd
+ EMBOSS-6.2.0/emboss/acd/twofeat.acd
+ EMBOSS-6.2.0/doc/programs/html/extractfeat.html
+ EMBOSS-6.2.0/doc/programs/html/maskfeat.html
+ EMBOSS-6.2.0/doc/programs/html/showfeat.html
+ EMBOSS-6.2.0/doc/programs/html/showpep.html
+ EMBOSS-6.2.0/doc/programs/html/showseq.html
+ EMBOSS-6.2.0/doc/programs/html/twofeat.html
+ EMBOSS-6.2.0/doc/programs/text/extractfeat.txt
+ EMBOSS-6.2.0/doc/programs/text/maskfeat.txt
+ EMBOSS-6.2.0/doc/programs/text/showfeat.txt
+ EMBOSS-6.2.0/doc/programs/text/showpep.txt
+ EMBOSS-6.2.0/doc/programs/text/showseq.txt
+ EMBOSS-6.2.0/doc/programs/text/twofeat.txt
+
+01-Mar-2010: Fix URLs for EMBL/GenBank and SwissProt feature table
+ descriptions in help and documentation.
+
+
+Fix 16.EMBOSS-6.2.0/emboss/acd/remap.acd
+ EMBOSS-6.2.0/emboss/acd/restover.acd
+ EMBOSS-6.2.0/emboss/acd/restrict.acd
+ EMBOSS-6.2.0/emboss/acd/showseq.acd
+
+01-Mar-2010: Remove artificial upper limit on number of restriction cuts
+
+
+Fix 17.EMBOSS-6.2.0/doc/programs/html/density.2.density.gif
+ EMBOSS-6.2.0/doc/programs/html/density.3.density.gif
+ EMBOSS-6.2.0/doc/programs/html/Makefile.am
+ EMBOSS-6.2.0/doc/programs/html/Makefile.in
+ EMBOSS-6.2.0/doc/programs/html/Makefile
+
+01-Mar-2010: Missing images for density usage examples
+
+
+Fix 18. EMBOSS-6.2.0/ajax/core/ajsys.c
+
+02-Mar-2010: Add .exe extension when searching for CYGWIN executables
Index: .cvsignore
===================================================================
RCS file: /cvs/pkgs/rpms/EMBOSS/devel/.cvsignore,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -p -r1.4 -r1.5
--- .cvsignore 24 Feb 2010 20:29:23 -0000 1.4
+++ .cvsignore 7 Apr 2010 21:34:23 -0000 1.5
@@ -1 +1,2 @@
EMBOSS-6.2.0.tar.gz
+patch-1-18.gz
Index: EMBOSS.spec
===================================================================
RCS file: /cvs/pkgs/rpms/EMBOSS/devel/EMBOSS.spec,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -p -r1.5 -r1.6
--- EMBOSS.spec 7 Apr 2010 20:52:16 -0000 1.5
+++ EMBOSS.spec 7 Apr 2010 21:34:23 -0000 1.6
@@ -18,7 +18,7 @@
Name: EMBOSS
Version: 6.2.0
-Release: 2%{?dist}
+Release: 3%{?dist}
Summary: The European Molecular Biology Open Software Suite
Group: Applications/Engineering
@@ -33,12 +33,12 @@ Group: Applications/Engineering
License: GPLv2+ and LGPLv2+
URL: http://emboss.sf.net/
Source0: ftp://emboss.open-bio.org/pub/EMBOSS/%{name}-%{version}.tar.gz
-#Source1: README.fixes
+Source1: ftp://emboss.open-bio.org/pub/EMBOSS/fixes/README.fixes
%if %{with jemboss}
Source2: jemboss.desktop
%endif
# Upstream patch
-# Patch0: ftp://emboss.open-bio.org/pub/EMBOSS/fixes/patches/patch-1-3.gz
+Patch0: ftp://emboss.open-bio.org/pub/EMBOSS/fixes/patches/patch-1-18.gz
# Use system-wide pcre. Sent upstream.
Patch1: EMBOSS-6.2.0-system-pcre.patch
# Use system-wide zlib.
@@ -127,7 +127,7 @@ http://www.hgmp.mrc.ac.uk/Software/EMBOS
%prep
%setup -q
-#%patch0 -p1
+%patch0 -p1
%patch1 -p1 -b .system-pcre
%patch2 -p1 -b .system-zlib
%patch3 -p1 -b .system-plplot
@@ -289,6 +289,9 @@ rm -rf $RPM_BUILD_ROOT
%changelog
+* Wed Apr 07 2010 Julian Sikorski <belegdol at fedoraproject.org> - 6.2.0-3
+- Added upstream 1-18 patch
+
* Wed Apr 7 2010 Tom "spot" Callaway <tcallawa at redhat.com> - 6.2.0-2
- fix pcre patch, use system pcre
- add patch to use system zlib
Index: sources
===================================================================
RCS file: /cvs/pkgs/rpms/EMBOSS/devel/sources,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -p -r1.4 -r1.5
--- sources 24 Feb 2010 20:29:24 -0000 1.4
+++ sources 7 Apr 2010 21:34:23 -0000 1.5
@@ -1 +1,2 @@
2e2937dd0493814ca0f64981f4c79319 EMBOSS-6.2.0.tar.gz
+562038e587099462869c45fda2e9628d patch-1-18.gz
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