diff -urN --exclude '*~' --exclude CVS bioperl-ext-1.5.1/Bio/Ext/Align/Makefile.PL bioperl-ext-1.5.2_102/Bio/Ext/Align/Makefile.PL
--- bioperl-ext-1.5.1/Bio/Ext/Align/Makefile.PL	2005-09-27 01:23:53.000000000 +0200
+++ bioperl-ext-1.5.2_102/Bio/Ext/Align/Makefile.PL	2008-11-20 13:59:10.000000000 +0100
@@ -3,7 +3,7 @@
 # the contents of the Makefile that is written.
 WriteMakefile(
     'NAME'	=> 'Bio::Ext::Align',
-    'VERSION'	=> '1.5.1',
+    'VERSION'	=> '1.5.2',
     'LIBS'	=> ['-lm'],   # e.g., '-lm' 
     'DEFINE'	=> '-DPOSIX -DNOERROR',     # e.g., '-DHAVE_SOMETHING' 
     'INC'	=> '-I./libs',     # e.g., '-I/usr/include/other'
@@ -15,7 +15,8 @@
 '
 $(MYEXTLIB): 
 	DEFINE=\'$(DEFINE)\'; CC=\'$(PERLMAINCC)\'; CFLAGS=\'$(CCFLAGS)\'; export DEFINE INC CC CFLAGS; \
-	cd libs && $(MAKE) CC=\'$(PERLMAINCC)\' CFLAGS=\'$(CCFLAGS) $(DEFINE)\' DEFINE=\'$(DEFINE)\' libsw$(LIB_EXT) -e
+	cd libs && $(MAKE) CC=\'$(PERLMAINCC)\' CFLAGS=\'$(CCFLAGS) $(DEFINE)\' DEFINE=\'$(DEFINE)\' libsw$(LIB_EXT) -e ; \
+	$(RANLIB) libsw$(LIB_EXT)
 
 ';
 }
diff -urN --exclude '*~' --exclude CVS bioperl-ext-1.5.1/Bio/Ext/Align/libs/dpalign.c bioperl-ext-1.5.2_102/Bio/Ext/Align/libs/dpalign.c
--- bioperl-ext-1.5.1/Bio/Ext/Align/libs/dpalign.c	2004-04-24 00:09:46.000000000 +0200
+++ bioperl-ext-1.5.2_102/Bio/Ext/Align/libs/dpalign.c	2008-11-19 19:03:19.000000000 +0100
@@ -293,6 +293,5 @@
 	;
     }
 
-    free(waa);
     return score;
 }
diff -urN --exclude '*~' --exclude CVS bioperl-ext-1.5.1/Bio/Ext/Align/libs/makefile bioperl-ext-1.5.2_102/Bio/Ext/Align/libs/makefile
--- bioperl-ext-1.5.1/Bio/Ext/Align/libs/makefile	2004-01-09 16:38:47.000000000 +0100
+++ bioperl-ext-1.5.2_102/Bio/Ext/Align/libs/makefile	2008-11-20 13:58:23.000000000 +0100
@@ -51,3 +51,6 @@
 
 CFLAGS = -c -O
 CC     = cc
+
+clean:
+	rm -f $(OBJS)
diff -urN --exclude '*~' --exclude CVS bioperl-ext-1.5.1/Bio/SeqIO/staden/Makefile.PL bioperl-ext-1.5.2_102/Bio/SeqIO/staden/Makefile.PL
--- bioperl-ext-1.5.1/Bio/SeqIO/staden/Makefile.PL	2005-05-17 00:06:36.000000000 +0200
+++ bioperl-ext-1.5.2_102/Bio/SeqIO/staden/Makefile.PL	2008-11-19 19:09:10.000000000 +0100
@@ -62,14 +62,13 @@
 	if ($ioliblib) {
 	    $prompt = $ioliblib;
 	    $prompt =~ s/lib$/include/;
-	    $prompt = $self->catdir($prompt, "io_lib");
 	} else {
-	    $prompt = "/usr/local/include/io_lib";
+	    $prompt = "/usr/local/include";
 	}
 	$iolibinc = ExtUtils::MakeMaker::prompt("Please tell us where your Staden io_lib \"Read.h\" header is installed: ", $prompt);
     }
 
-    `perl -pi -e 's{(LIBS\\s*=>\\s*")([^"]+)}{\$1-L$ioliblib -lread -lz};' read.pm`;
+    `perl -pi -e 's{(LIBS\\s*=>\\s*")([^"]+)}{\$1-L$ioliblib -lread -lcurl -lz};' read.pm`;
     `perl -pi -e 's{(INC\\s*=>\\s*")([^"]+)}{\$1-I$iolibinc};' read.pm`;
 
     return '';
diff -urN --exclude '*~' --exclude CVS bioperl-ext-1.5.1/Bio/SeqIO/staden/read.pm bioperl-ext-1.5.2_102/Bio/SeqIO/staden/read.pm
--- bioperl-ext-1.5.1/Bio/SeqIO/staden/read.pm	2005-10-09 17:19:43.000000000 +0200
+++ bioperl-ext-1.5.2_102/Bio/SeqIO/staden/read.pm	2008-11-19 19:03:56.000000000 +0100
@@ -75,17 +75,17 @@
 #			);
 
 	use Inline (C => 'DATA',
-		    VERSION => '0.01',
+		    VERSION => '1.52',
 		    NAME => 'Bio::SeqIO::staden::read',
-		    LIBS => "-L/usr/local/lib -lread -lz", # leave these as double quotes - necessary for Makefile.PL function
-		    INC  => "-I/usr/local/include/io_lib", # leave these as double quotes - necessary for Makefile.PL function
+		    LIBS => "-L/projects/gi/staden/io_lib/1.11.4/arch/x86-glibc2.3-linux/lib -lread -lcurl -lz", # leave these as double quotes - necessary for Makefile.PL function
+		    INC  => "-I/projects/gi/staden/io_lib/1.11.4/include", # leave these as double quotes - necessary for Makefile.PL function
 		   );
     } or Bio::Root::Root::throw( -class => 'Bio::Root::SystemException',
 				 -text  => "No Inline::C (or maybe io-lib?) support available",
 			       );
 }
 
-$VERSION = 1.5.1;
+$VERSION = 1.52;
 
 my %formats = ( scf => 1,
 		abi => 2,
@@ -168,7 +168,7 @@
 1;
 __DATA__
 __C__
-#include <Read.h>
+#include <io_lib/Read.h>
 
 int staden_write_trace(SV *self, FILE *fh, int format,
 		       char *seq, int len, SV *qual, char *id, char *desc) {
diff -urN --exclude '*~' --exclude CVS bioperl-ext-1.5.1/Makefile.PL bioperl-ext-1.5.2_102/Makefile.PL
--- bioperl-ext-1.5.1/Makefile.PL	2005-09-27 01:22:49.000000000 +0200
+++ bioperl-ext-1.5.2_102/Makefile.PL	2008-11-19 16:50:37.000000000 +0100
@@ -4,7 +4,7 @@
 WriteMakefile(
     'NAME'      => 'Bio',
     'DISTNAME'  => 'bioperl-ext',
-    'VERSION'	=> '1.5.1-RC1',
+    'VERSION'	=> '1.5.2_102',
     'DIR'       => [ qw( Bio/Ext/Align Bio/SeqIO/staden )],
     'dist'      => {  COMPRESS     => 'gzip -9f',
                       SUFFIX       => '.gz',