diff --git a/.cvsignore b/.cvsignore index 3c56458..632621c 100644 --- a/.cvsignore +++ b/.cvsignore @@ -1,2 +1,2 @@ -EMBOSS-6.1.0.tar.gz -patch-1-3.gz +EMBOSS-6.2.0.tar.gz +patch-1-18.gz diff --git a/EMBOSS-6.1.0-destdir.patch b/EMBOSS-6.1.0-destdir.patch deleted file mode 100644 index 38b3377..0000000 --- a/EMBOSS-6.1.0-destdir.patch +++ /dev/null @@ -1,22 +0,0 @@ ---- 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 diff --git a/EMBOSS-6.1.0-rebuild.patch b/EMBOSS-6.1.0-rebuild.patch deleted file mode 100644 index 4cacc9f..0000000 --- a/EMBOSS-6.1.0-rebuild.patch +++ /dev/null @@ -1,62 +0,0 @@ ---- 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: -+@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. diff --git a/EMBOSS-system-pcre.patch b/EMBOSS-system-pcre.patch deleted file mode 100644 index 9b0fbfa..0000000 --- a/EMBOSS-system-pcre.patch +++ /dev/null @@ -1,192 +0,0 @@ -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 -+#include - - #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@am_libajax_la_OBJECTS = $(am__objects_1) - @ISCYGWIN_TRUE@am_libajax_la_OBJECTS = $(am__objects_1) \ -@@ -159,7 +159,6 @@ EXEEXT = @EXEEXT@ - FGREP = @FGREP@ - GREP = @GREP@ - HAVE_MEMMOVE = @HAVE_MEMMOVE@ --HAVE_STRERROR = @HAVE_STRERROR@ - INSTALL = @INSTALL@ - INSTALL_DATA = @INSTALL_DATA@ - INSTALL_PROGRAM = @INSTALL_PROGRAM@ -@@ -172,7 +171,7 @@ LD = @LD@ - LDFLAGS = @LDFLAGS@ - LIBOBJS = @LIBOBJS@ - #LDFLAGS = -no-undefined --LIBS = -+LIBS = @LIBS@ - LIBTOOL = @LIBTOOL@ - LIPO = @LIPO@ - LN_S = @LN_S@ -@@ -193,13 +192,6 @@ PACKAGE_STRING = @PACKAGE_STRING@ - PACKAGE_TARNAME = @PACKAGE_TARNAME@ - PACKAGE_VERSION = @PACKAGE_VERSION@ - PATH_SEPARATOR = @PATH_SEPARATOR@ --PCRE_DATE = @PCRE_DATE@ --PCRE_LIB_VERSION = @PCRE_LIB_VERSION@ --PCRE_MAJOR = @PCRE_MAJOR@ --PCRE_MINOR = @PCRE_MINOR@ --PCRE_POSIXLIB_VERSION = @PCRE_POSIXLIB_VERSION@ --PCRE_VERSION = @PCRE_VERSION@ --POSIX_MALLOC_THRESHOLD = @POSIX_MALLOC_THRESHOLD@ - RANLIB = @RANLIB@ - SED = @SED@ - SET_MAKE = @SET_MAKE@ -@@ -272,8 +264,6 @@ top_srcdir = @top_srcdir@ - @ISAIXIA64_TRUE@@ISSHARED_TRUE@@NEEDAJAX_FALSE@AM_CFLAGS = -Wl,-G -L../plplot/.libs -L.libs -leplplot -lm - @ISAIXIA64_TRUE@@ISSHARED_TRUE@@NEEDAJAX_TRUE@AM_CFLAGS = -Wl,-G -L../plplot/.libs -L.libs -lajax -leplplot -lm - @ISCYGWIN_TRUE@AM_LDFLAGS = -no-undefined -Wl,--add-stdcall-alias -Wl,--export-all-symbols -Wl,--enable-auto-import -L../plplot -leplplot --PCRELIBVERSION = @PCRE_LIB_VERSION@ --PCREPOSIXLIBVERSION = @PCRE_POSIXLIB_VERSION@ - INCLUDES = -DAJAX_FIXED_ROOT=$(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@libajax_la_SOURCES = $(AJAXSRC) - @ISCYGWIN_TRUE@libajax_la_SOURCES = $(AJAXSRC) $(AJAXGSRC) -@@ -440,9 +427,6 @@ distclean-compile: - @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/ajtree.Plo@am__quote@ - @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/ajutil.Plo@am__quote@ - @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/ajvector.Plo@am__quote@ --@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/pcre.Plo@am__quote@ --@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/pcre_study.Plo@am__quote@ --@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/pcreposix.Plo@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 diff --git a/EMBOSS.spec b/EMBOSS.spec index fe0cb64..d6263e8 100644 --- a/EMBOSS.spec +++ b/EMBOSS.spec @@ -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/EMBOSS/Jemboss/ %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 - 6.2.0-3 +- Added upstream 1-18 patch + * Wed Apr 7 2010 Tom "spot" Callaway - 6.2.0-2 - fix pcre patch, use system pcre - add patch to use system zlib diff --git a/README.fixes b/README.fixes index fef95d4..dd4d11e 100644 --- a/README.fixes +++ b/README.fixes @@ -1,108 +1,160 @@ The files in this directory are bugfix replacements for files in -the EMBOSS-6.1.0 distribution. Just drop the replacement 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-6.1.0/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). - -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. +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 diff --git a/sources b/sources index a9e48c6..030cbf8 100644 --- a/sources +++ b/sources @@ -1 +1,2 @@ 2e2937dd0493814ca0f64981f4c79319 EMBOSS-6.2.0.tar.gz +562038e587099462869c45fda2e9628d patch-1-18.gz