Hi,
after quite some time, the fedora package review for emboss is complete.
Several minor issues have been pointed out:
1. Several files lack a license header. The list of these files is attached.
2. The destdir is missing in runJemboss.sh installation command. Patch
fixing the problem is attached.
3. The reviewer has provided a patch which enables using the system-wide
pcre. Patch attached.
I would be very grateful if you could look into these issues, as well
the exit call I mentioned earlier [1].
Best regards,
Julian
[1] http://article.gmane.org/gmane.science.biology.emboss/1412
EMBOSS-6.1.0/jemboss/contrib/jaligner/examples/hbb.sh: *No copyright* UNKNOWN
EMBOSS-6.1.0/jemboss/api/getClasses.pl: *No copyright* UNKNOWN
EMBOSS-6.1.0/jemboss/utils/keys.sh: *No copyright* UNKNOWN
EMBOSS-6.1.0/jemboss/org/emboss/jemboss/editor/GroutAlignJFrameEvent.java: *No
copyright* UNKNOWN
EMBOSS-6.1.0/jemboss/org/emboss/jemboss/editor/GroutGraphicSequenceCollectionListener.java:
*No copyright* UNKNOWN
EMBOSS-6.1.0/jemboss/org/emboss/jemboss/editor/GroutGraphicSequenceCollectionEvent.java:
*No copyright* UNKNOWN
EMBOSS-6.1.0/jemboss/org/emboss/jemboss/editor/GroutAlignJFrameListener.java:
*No copyright* UNKNOWN
EMBOSS-6.1.0/jemboss/runJemboss.sh: *No copyright* UNKNOWN
EMBOSS-6.1.0/plplot/plwind.c: UNKNOWN
EMBOSS-6.1.0/plplot/plsdef.c: UNKNOWN
EMBOSS-6.1.0/plplot/plctrl.c: UNKNOWN
EMBOSS-6.1.0/plplot/ps.h: *No copyright* UNKNOWN
EMBOSS-6.1.0/plplot/plvect.c: UNKNOWN
EMBOSS-6.1.0/plplot/null.c: *No copyright* UNKNOWN
EMBOSS-6.1.0/plplot/plbuf.c: UNKNOWN
EMBOSS-6.1.0/plplot/plcore.c: UNKNOWN
EMBOSS-6.1.0/plplot/hpgl.c: *No copyright* UNKNOWN
EMBOSS-6.1.0/plplot/ljiip.c: *No copyright* UNKNOWN
EMBOSS-6.1.0/plplot/pdf.h: UNKNOWN
EMBOSS-6.1.0/plplot/xfig.c: *No copyright* UNKNOWN
EMBOSS-6.1.0/plplot/pldebug.h: UNKNOWN
EMBOSS-6.1.0/plplot/plxwd.h: *No copyright* UNKNOWN
EMBOSS-6.1.0/plplot/metadefs.h: *No copyright* UNKNOWN
EMBOSS-6.1.0/plplot/impress.c: *No copyright* UNKNOWN
EMBOSS-6.1.0/plplot/plbox.c: UNKNOWN
EMBOSS-6.1.0/plplot/plcont.c: UNKNOWN
EMBOSS-6.1.0/plplot/tek.c: *No copyright* UNKNOWN
EMBOSS-6.1.0/plplot/plpage.c: UNKNOWN
EMBOSS-6.1.0/plplot/plsym.c: UNKNOWN
EMBOSS-6.1.0/plplot/plcvt.c: UNKNOWN
EMBOSS-6.1.0/plplot/plstripc.c: UNKNOWN
EMBOSS-6.1.0/plplot/plplotP.h: UNKNOWN
EMBOSS-6.1.0/plplot/pdfutils.c: UNKNOWN
EMBOSS-6.1.0/plplot/plfill.c: UNKNOWN
EMBOSS-6.1.0/plplot/plhist.c: UNKNOWN
EMBOSS-6.1.0/plplot/pbm.c: *No copyright* UNKNOWN
EMBOSS-6.1.0/plplot/ljii.c: *No copyright* UNKNOWN
EMBOSS-6.1.0/plplot/plunicode-type1.h: UNKNOWN
EMBOSS-6.1.0/plplot/plimage.c: UNKNOWN
EMBOSS-6.1.0/plplot/pltick.c: UNKNOWN
EMBOSS-6.1.0/plplot/ps.c: UNKNOWN
EMBOSS-6.1.0/plplot/gd.c: UNKNOWN
EMBOSS-6.1.0/plplot/data.c: *No copyright* UNKNOWN
EMBOSS-6.1.0/plplot/plvpor.c: UNKNOWN
EMBOSS-6.1.0/plplot/pldtik.c: UNKNOWN
EMBOSS-6.1.0/plplot/plfci-type1.h: UNKNOWN
EMBOSS-6.1.0/plplot/pldll.h: *No copyright* UNKNOWN
EMBOSS-6.1.0/plplot/plshade.c: UNKNOWN
EMBOSS-6.1.0/plplot/xwin.c: UNKNOWN
EMBOSS-6.1.0/plplot/disptab.h: *No copyright* UNKNOWN
EMBOSS-6.1.0/plplot/plevent.h: UNKNOWN
EMBOSS-6.1.0/emboss/seqretsingle.c: *No copyright* UNKNOWN
EMBOSS-6.1.0/emboss/ajtest.c: *No copyright* UNKNOWN
EMBOSS-6.1.0/scripts/embossdoc.pl: *No copyright* UNKNOWN
EMBOSS-6.1.0/scripts/makesummary.pl: *No copyright* UNKNOWN
EMBOSS-6.1.0/scripts/dbfetch.pl: *No copyright* UNKNOWN
EMBOSS-6.1.0/scripts/qatest.pl: *No copyright* UNKNOWN
EMBOSS-6.1.0/scripts/third.pl: *No copyright* UNKNOWN
EMBOSS-6.1.0/scripts/embossdatadoc.pl: *No copyright* UNKNOWN
EMBOSS-6.1.0/scripts/dovalidclean.pl: *No copyright* UNKNOWN
EMBOSS-6.1.0/scripts/fixdeprecated.pl: *No copyright* UNKNOWN
EMBOSS-6.1.0/scripts/embossdatacheck.pl: *No copyright* UNKNOWN
EMBOSS-6.1.0/scripts/makeMake.pl: *No copyright* UNKNOWN
EMBOSS-6.1.0/scripts/dbitest.pl: *No copyright* UNKNOWN
EMBOSS-6.1.0/scripts/emblmini.pl: *No copyright* UNKNOWN
EMBOSS-6.1.0/scripts/embossdoccheck.pl: *No copyright* UNKNOWN
EMBOSS-6.1.0/scripts/edithtml.pl: *No copyright* UNKNOWN
EMBOSS-6.1.0/scripts/cleannew.pl: *No copyright* UNKNOWN
EMBOSS-6.1.0/scripts/acdstats.pl: *No copyright* UNKNOWN
EMBOSS-6.1.0/scripts/efuncrel.pl: *No copyright* UNKNOWN
EMBOSS-6.1.0/scripts/autodoc.pl: *No copyright* UNKNOWN
EMBOSS-6.1.0/scripts/codestandard.pl: *No copyright* UNKNOWN
EMBOSS-6.1.0/scripts/sections.pl: *No copyright* UNKNOWN
EMBOSS-6.1.0/scripts/sourceforgevalid.pl: *No copyright* UNKNOWN
EMBOSS-6.1.0/scripts/knowntypevalid.pl: *No copyright* UNKNOWN
EMBOSS-6.1.0/scripts/docnucleusindex.pl: *No copyright* UNKNOWN
EMBOSS-6.1.0/scripts/dbxref.pl: *No copyright* UNKNOWN
EMBOSS-6.1.0/scripts/makeexample.pl: *No copyright* UNKNOWN
EMBOSS-6.1.0/scripts/embossdocreport.pl: *No copyright* UNKNOWN
EMBOSS-6.1.0/scripts/docindex.pl: *No copyright* UNKNOWN
EMBOSS-6.1.0/scripts/eiprscan-sort.pl: *No copyright* UNKNOWN
EMBOSS-6.1.0/scripts/embassytestconfig.pl: *No copyright* UNKNOWN
EMBOSS-6.1.0/scripts/soextract.pl: *No copyright* UNKNOWN
EMBOSS-6.1.0/scripts/acdvalidreport.pl: *No copyright* UNKNOWN
EMBOSS-6.1.0/scripts/makefilestest.pl: *No copyright* UNKNOWN
EMBOSS-6.1.0/scripts/valgrindreport.pl: *No copyright* UNKNOWN
EMBOSS-6.1.0/scripts/logreport1.pl: *No copyright* UNKNOWN
EMBOSS-6.1.0/scripts/acdsyntax.pl: *No copyright* UNKNOWN
EMBOSS-6.1.0/scripts/purify.pl: *No copyright* UNKNOWN
EMBOSS-6.1.0/scripts/checkc.pl: *No copyright* UNKNOWN
EMBOSS-6.1.0/scripts/emblsplit.pl: *No copyright* UNKNOWN
EMBOSS-6.1.0/scripts/dbilist.pl: *No copyright* UNKNOWN
EMBOSS-6.1.0/scripts/unused_functions.pl: *No copyright* UNKNOWN
EMBOSS-6.1.0/scripts/embossdoccategories.pl: *No copyright* UNKNOWN
EMBOSS-6.1.0/scripts/valgrind.pl: *No copyright* UNKNOWN
EMBOSS-6.1.0/scripts/makehistory.pl: *No copyright* UNKNOWN
EMBOSS-6.1.0/scripts/qatomemtest.pl: *No copyright* UNKNOWN
EMBOSS-6.1.0/scripts/createnewdocumentation.pl: *No copyright* UNKNOWN
EMBOSS-6.1.0/scripts/embllocations.pl: *No copyright* UNKNOWN
EMBOSS-6.1.0/scripts/embossdoccatreport.pl: *No copyright* UNKNOWN
EMBOSS-6.1.0/nucleus/emboss.h: *No copyright* UNKNOWN
EMBOSS-6.1.0/nucleus/embnmer.h: *No copyright* UNKNOWN
EMBOSS-6.1.0/nucleus/embshow.h: *No copyright* UNKNOWN
EMBOSS-6.1.0/nucleus/embiep.h: *No copyright* UNKNOWN
EMBOSS-6.1.0/nucleus/embexit.h: *No copyright* UNKNOWN
EMBOSS-6.1.0/nucleus/embprop.h: *No copyright* UNKNOWN
EMBOSS-6.1.0/nucleus/embinit.h: *No copyright* UNKNOWN
EMBOSS-6.1.0/nucleus/embmisc.h: *No copyright* UNKNOWN
EMBOSS-6.1.0/nucleus/embcom.h: *No copyright* UNKNOWN
EMBOSS-6.1.0/nucleus/embcons.h: *No copyright* UNKNOWN
EMBOSS-6.1.0/nucleus/embpatlist.h: *No copyright* UNKNOWN
EMBOSS-6.1.0/nucleus/embest.h: *No copyright* UNKNOWN
EMBOSS-6.1.0/nucleus/embdata.h: *No copyright* UNKNOWN
EMBOSS-6.1.0/nucleus/embmat.h: *No copyright* UNKNOWN
EMBOSS-6.1.0/nucleus/embword.h: *No copyright* UNKNOWN
EMBOSS-6.1.0/nucleus/embaln.h: *No copyright* UNKNOWN
EMBOSS-6.1.0/nucleus/embpat.h: *No copyright* UNKNOWN
EMBOSS-6.1.0/nucleus/embmol.h: *No copyright* UNKNOWN
EMBOSS-6.1.0/nucleus/embgroup.h: *No copyright* UNKNOWN
EMBOSS-6.1.0/nucleus/embindex.h: *No copyright* UNKNOWN
EMBOSS-6.1.0/nucleus/embread.h: *No copyright* UNKNOWN
EMBOSS-6.1.0/nucleus/embdbi.h: *No copyright* UNKNOWN
EMBOSS-6.1.0/ajax/ajarr.h: *No copyright* UNKNOWN
EMBOSS-6.1.0/ajax/ajalign.h: *No copyright* UNKNOWN
EMBOSS-6.1.0/ajax/ajmem.h: *No copyright* UNKNOWN
EMBOSS-6.1.0/ajax/ajtranslate.h: *No copyright* UNKNOWN
EMBOSS-6.1.0/ajax/ajreport.h: *No copyright* UNKNOWN
EMBOSS-6.1.0/ajax/pcre_chartables.c: *No copyright* UNKNOWN
EMBOSS-6.1.0/ajax/ajassert.h: *No copyright* UNKNOWN
EMBOSS-6.1.0/ajax/ajtable.h: *No copyright* UNKNOWN
EMBOSS-6.1.0/ajax/ajsort.h: *No copyright* UNKNOWN
EMBOSS-6.1.0/ajax/ajfeatdata.h: *No copyright* UNKNOWN
EMBOSS-6.1.0/ajax/ajfile.h: *No copyright* UNKNOWN
EMBOSS-6.1.0/ajax/ajcall.c: *No copyright* UNKNOWN
EMBOSS-6.1.0/ajax/ajjava.h: *No copyright* UNKNOWN
EMBOSS-6.1.0/ajax/ajarch.h: *No copyright* UNKNOWN
EMBOSS-6.1.0/ajax/ajseqabi.h: *No copyright* UNKNOWN
EMBOSS-6.1.0/ajax/ajseqdata.h: *No copyright* UNKNOWN
EMBOSS-6.1.0/ajax/ajphylo.h: *No copyright* UNKNOWN
EMBOSS-6.1.0/ajax/ajmath.h: *No copyright* UNKNOWN
EMBOSS-6.1.0/ajax/ajtree.h: *No copyright* UNKNOWN
EMBOSS-6.1.0/ajax/ajlist.h: *No copyright* UNKNOWN
EMBOSS-6.1.0/ajax/pcre_internal.h: UNKNOWN
EMBOSS-6.1.0/ajax/ajseq.h: *No copyright* UNKNOWN
EMBOSS-6.1.0/ajax/ajreg.h: *No copyright* UNKNOWN
EMBOSS-6.1.0/ajax/ajtime.h: *No copyright* UNKNOWN
EMBOSS-6.1.0/ajax/ajsys.h: *No copyright* UNKNOWN
EMBOSS-6.1.0/ajax/ajbase.h: *No copyright* UNKNOWN
EMBOSS-6.1.0/ajax/ajdan.h: *No copyright* UNKNOWN
EMBOSS-6.1.0/ajax/ajrange.h: *No copyright* UNKNOWN
EMBOSS-6.1.0/ajax/pcre.c: UNKNOWN
EMBOSS-6.1.0/ajax/ajnexus.h: *No copyright* UNKNOWN
EMBOSS-6.1.0/ajax/ajdefine.h: *No copyright* UNKNOWN
EMBOSS-6.1.0/ajax/ajseqdb.h: *No copyright* UNKNOWN
EMBOSS-6.1.0/ajax/ajpat.h: *No copyright* UNKNOWN
EMBOSS-6.1.0/ajax/pcre_study.c: UNKNOWN
EMBOSS-6.1.0/ajax/ajutil.h: *No copyright* UNKNOWN
EMBOSS-6.1.0/ajax/ajcod.h: *No copyright* UNKNOWN
EMBOSS-6.1.0/ajax/ajseqtype.h: *No copyright* UNKNOWN
EMBOSS-6.1.0/ajax/ajindex.h: *No copyright* UNKNOWN
EMBOSS-6.1.0/ajax/pcre_printint.c: UNKNOWN
EMBOSS-6.1.0/ajax/ajexcept.h: *No copyright* UNKNOWN
EMBOSS-6.1.0/ajax/ajnam.h: *No copyright* UNKNOWN
EMBOSS-6.1.0/ajax/ajmatrices.h: *No copyright* UNKNOWN
EMBOSS-6.1.0/ajax/ajmess.h: *No copyright* UNKNOWN
EMBOSS-6.1.0/ajax/pcreposix.h: UNKNOWN
EMBOSS-6.1.0/ajax/ajvector.h: *No copyright* UNKNOWN
EMBOSS-6.1.0/ajax/ajfmt.h: *No copyright* UNKNOWN
EMBOSS-6.1.0/ajax/ajfiledata.h: *No copyright* UNKNOWN
EMBOSS-6.1.0/ajax/ajax.h: *No copyright* UNKNOWN
EMBOSS-6.1.0/ajax/pcre_get.c: UNKNOWN
EMBOSS-6.1.0/ajax/ajstr.h: *No copyright* UNKNOWN
EMBOSS-6.1.0/ajax/ajfileio.h: *No copyright* UNKNOWN
EMBOSS-6.1.0/ajax/ajcall.h: *No copyright* UNKNOWN
EMBOSS-6.1.0/ajax/ajacd.h: *No copyright* UNKNOWN
EMBOSS-6.1.0/ajax/pcreposix.c: UNKNOWN
EMBOSS-6.1.0/ajax/ajdom.h: *No copyright* UNKNOWN
EMBOSS-6.1.0/ajax/ajseqread.h: *No copyright* UNKNOWN
EMBOSS-6.1.0/ajax/ajgraphstruct.h: *No copyright* UNKNOWN
EMBOSS-6.1.0/ajax/ajseqwrite.h: *No copyright* UNKNOWN
EMBOSS-6.1.0/ajax/ajfeat.h: *No copyright* UNKNOWN
EMBOSS-6.1.0/ajax/ajgraphxml.h: *No copyright* UNKNOWN
--- 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 -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_fa...@am_libajax_la_objects = $(am__objects_1)
@iscygwin_t...@am_libajax_la_objects = $(am__objects_1) \
@@ -159,7 +159,6 @@ EXEEXT = @EXEEXT@
FGREP = @FGREP@
GREP = @GREP@
HAVE_MEMMOVE = @HAVE_MEMMOVE@
-HAVE_STRERROR = @HAVE_STRERROR@
INSTALL = @INSTALL@
INSTALL_DATA = @INSTALL_DATA@
INSTALL_PROGRAM = @INSTALL_PROGRAM@
@@ -172,7 +171,7 @@ LD = @LD@
LDFLAGS = @LDFLAGS@
LIBOBJS = @LIBOBJS@
#LDFLAGS = -no-undefined
-LIBS =
+LIBS = @LIBS@
LIBTOOL = @LIBTOOL@
LIPO = @LIPO@
LN_S = @LN_S@
@@ -193,13 +192,6 @@ PACKAGE_STRING = @PACKAGE_STRING@
PACKAGE_TARNAME = @PACKAGE_TARNAME@
PACKAGE_VERSION = @PACKAGE_VERSION@
PATH_SEPARATOR = @PATH_SEPARATOR@
-PCRE_DATE = @PCRE_DATE@
-PCRE_LIB_VERSION = @PCRE_LIB_VERSION@
-PCRE_MAJOR = @PCRE_MAJOR@
-PCRE_MINOR = @PCRE_MINOR@
-PCRE_POSIXLIB_VERSION = @PCRE_POSIXLIB_VERSION@
-PCRE_VERSION = @PCRE_VERSION@
-POSIX_MALLOC_THRESHOLD = @POSIX_MALLOC_THRESHOLD@
RANLIB = @RANLIB@
SED = @SED@
SET_MAKE = @SET_MAKE@
@@ -272,8 +264,6 @@ top_srcdir = @top_srcdir@
@ISAIXIA64_TRUE@@ISSHARED_TRUE@@needajax_fa...@am_cflags = -Wl,-G -L../plplot/.libs -L.libs -leplplot -lm
@ISAIXIA64_TRUE@@ISSHARED_TRUE@@needajax_t...@am_cflags = -Wl,-G -L../plplot/.libs -L.libs -lajax -leplplot -lm
@iscygwin_t...@am_ldflags = -no-undefined -Wl,--add-stdcall-alias -Wl,--export-all-symbols -Wl,--enable-auto-import -L../plplot -leplplot
-PCRELIBVERSION = @PCRE_LIB_VERSION@
-PCREPOSIXLIBVERSION = @PCRE_POSIXLIB_VERSION@
INCLUDES = -DAJAX_FIXED_ROOT=$(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_fa...@libajax_la_sources = $(AJAXSRC)
@iscygwin_t...@libajax_la_sources = $(AJAXSRC) $(AJAXGSRC)
@@ -440,9 +427,6 @@ distclean-compile:
@AMDEP_TRUE@@am__include@ @am__qu...@./$(DEPDIR)/ajtree....@am__quote@
@AMDEP_TRUE@@am__include@ @am__qu...@./$(DEPDIR)/ajutil....@am__quote@
@AMDEP_TRUE@@am__include@ @am__qu...@./$(DEPDIR)/ajvector....@am__quote@
-...@amdep_true@@am__include@ @am__qu...@./$(DEPDIR)/pcre....@am__quote@
-...@amdep_true@@am__include@ @am__qu...@./$(DEPDIR)/pcre_study....@am__quote@
-...@amdep_true@@am__include@ @am__qu...@./$(DEPDIR)/pcreposix....@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
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