[med-svn] r12611 - in trunk/packages/arb/trunk/debian: . patches

Andreas Tille tille at alioth.debian.org
Wed Dec 12 18:42:45 UTC 2012 

Author: tille
Date: 2012-12-12 18:42:44 +0000 (Wed, 12 Dec 2012)
New Revision: 12611

Removed:
   trunk/packages/arb/trunk/debian/patches/gcc-4.7.patch
Modified:
   trunk/packages/arb/trunk/debian/changelog
   trunk/packages/arb/trunk/debian/control
   trunk/packages/arb/trunk/debian/patches/20_Makefiles
   trunk/packages/arb/trunk/debian/patches/20_config.makefiles
   trunk/packages/arb/trunk/debian/patches/20_tmpfile_issue.patch
   trunk/packages/arb/trunk/debian/patches/30_Makefile_main
   trunk/packages/arb/trunk/debian/patches/30_phyml
   trunk/packages/arb/trunk/debian/patches/series
   trunk/packages/arb/trunk/debian/patches/tmpfile_CVE-2008-5378.patch
Log:
New upstream version + adapted patches


Modified: trunk/packages/arb/trunk/debian/changelog
===================================================================
--- trunk/packages/arb/trunk/debian/changelog	2012-12-12 13:55:17 UTC (rev 12610)
+++ trunk/packages/arb/trunk/debian/changelog	2012-12-12 18:42:44 UTC (rev 12611)
@@ -1,3 +1,10 @@
+arb (5.5-1) UNRELEASED; urgency=low
+
+  * New upstream version (+adapted patches)
+  * Standards-Version: 3.9.4 (no changes needed)
+
+ -- Andreas Tille <tille at debian.org>  Tue, 11 Dec 2012 09:59:08 +0100
+
 arb (5.3-4) unstable; urgency=low
 
   * debian/upstream: Add citations

Modified: trunk/packages/arb/trunk/debian/control
===================================================================
--- trunk/packages/arb/trunk/debian/control	2012-12-12 13:55:17 UTC (rev 12610)
+++ trunk/packages/arb/trunk/debian/control	2012-12-12 18:42:44 UTC (rev 12611)
@@ -23,7 +23,7 @@
                perl-doc,
                xsltproc,
                xutils-dev
-Standards-Version: 3.9.3
+Standards-Version: 3.9.4
 Homepage: http://www.arb-home.de/
 Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/arb/trunk/
 Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/arb/trunk/

Modified: trunk/packages/arb/trunk/debian/patches/20_Makefiles
===================================================================
--- trunk/packages/arb/trunk/debian/patches/20_Makefiles	2012-12-12 13:55:17 UTC (rev 12610)
+++ trunk/packages/arb/trunk/debian/patches/20_Makefiles	2012-12-12 18:42:44 UTC (rev 12611)
@@ -1,5 +1,5 @@
---- arb-5.3.orig/ARBDB2/Makefile
-+++ arb-5.3/ARBDB2/Makefile
+--- a/ARBDB2/Makefile
++++ b/ARBDB2/Makefile
 @@ -1,7 +1,11 @@
  # INCLUDE und GLOBALS MAIN CC cflags werden von aussen uebergeben
  .SUFFIXES: .o .c .depend
@@ -13,8 +13,8 @@
  
  ACC_OBJECTS = $(GB_O) $(GB_T) $(GB_X)
  
---- arb-5.3.orig/ARBDBS/Makefile
-+++ arb-5.3/ARBDBS/Makefile
+--- a/ARBDBS/Makefile
++++ b/ARBDBS/Makefile
 @@ -1,7 +1,11 @@
  # INCLUDE und GLOBALS MAIN CC cflags werden von aussen uebergeben
  .SUFFIXES: .o .c .cxx .depend
@@ -28,9 +28,9 @@
  
  
  OBJECTS = $(GB_O) $(GB_T) $(GB_PP) $(GB_X)
---- arb-5.3.orig/NAMES_COM/Makefile
-+++ arb-5.3/NAMES_COM/Makefile
-@@ -18,7 +18,7 @@
+--- a/NAMES_COM/Makefile
++++ b/NAMES_COM/Makefile
+@@ -18,7 +18,7 @@ CLIENTCOMPILER = $(COMPILER)
  AISC_COMPILER=../MAKEBIN/aisc
  AISC_DEPENDS = $(wildcard AISC/*.pa) $(AISC_COMPILER)
  
@@ -39,7 +39,7 @@
  
  server.a: $(MAIN_SOURCE) $(PRIVATE_SERVER_OBJECTS:.o=.c) $(PUBLIC_SOURCES) $(AISC_DEPENDS)
  	@$(MAKE) -r -f AISC/Makefile
-@@ -27,7 +27,7 @@
+@@ -27,7 +27,7 @@ depends:
  	@$(MAKE) -r -f AISC/Makefile pregenerate
  
  clean:
@@ -48,9 +48,9 @@
  
  # DO NOT DELETE
  
---- arb-5.3.orig/PROBE_COM/Makefile
-+++ arb-5.3/PROBE_COM/Makefile
-@@ -18,7 +18,7 @@
+--- a/PROBE_COM/Makefile
++++ b/PROBE_COM/Makefile
+@@ -18,7 +18,7 @@ CLIENTCOMPILER := $(COMPILER)
  AISC_COMPILER=../MAKEBIN/aisc
  AISC_DEPENDS = $(wildcard AISC/*.pa) $(AISC_COMPILER)
  
@@ -59,7 +59,7 @@
  
  server.a:	$(MAIN_SOURCE)	$(PRIVATE_SERVER_OBJECTS:.o=.c) $(PUBLIC_SOURCES) $(AISC_DEPENDS)
  		@$(MAKE) -r -f AISC/Makefile
-@@ -27,7 +27,7 @@
+@@ -27,7 +27,7 @@ depends:
  		@$(MAKE) -r -f AISC/Makefile pregenerate
  
  clean:
@@ -68,9 +68,9 @@
  
  # DO NOT DELETE
  
---- arb-5.3.orig/GENOM_IMPORT/Makefile
-+++ arb-5.3/GENOM_IMPORT/Makefile
-@@ -30,12 +30,12 @@
+--- a/GENOM_IMPORT/Makefile
++++ b/GENOM_IMPORT/Makefile
+@@ -30,12 +30,12 @@ $(MAIN): $(CPP_OBJECTS)
  	$(ACC) $(cflags) -c $< $(CPPINCLUDES)
  
  clean:
@@ -89,9 +89,9 @@
  
  #.IGNORE:
  #	clean
---- arb-5.3.orig/HELP_SOURCE/Makefile
-+++ arb-5.3/HELP_SOURCE/Makefile
-@@ -151,7 +151,7 @@
+--- a/HELP_SOURCE/Makefile
++++ b/HELP_SOURCE/Makefile
+@@ -151,7 +151,7 @@ $(HLP_DEST)/%.pdf.gz : $(HLP_SOURCE)/%.p
  # --------------------------------------------------------------------------------
  
  delzerohtml:
@@ -100,19 +100,34 @@
  
  date :
  	$(MAKE) date.xsl.tmp
---- arb-5.3.orig/GDEHELP/Makefile
-+++ arb-5.3/GDEHELP/Makefile
-@@ -37,10 +37,18 @@
+--- a/GDEHELP/Makefile.helpfiles
++++ b/GDEHELP/Makefile.helpfiles
+@@ -2,9 +2,9 @@
+ 
+ .SUFFIXES: .doc .help .html
+ 
+-# GENHELPDEST, GENDOCDEST and HELPFILELIST are passed from 'Makefile'
++# GENHELPDEST, GENDOCDEST and HELP_NAMES are passed from 'Makefile'
+ 
+-HELP_NAMES=$(shell cat $(HELPFILELIST))
++# HELP_NAMES=$(shell cat $(HELPFILELIST))
+ HELP_TARGETS=$(addprefix $(GENHELPDEST)/,$(HELP_NAMES))
+ HELP_PLAIN=./HELP_PLAIN
+ HELP_WRITTEN=./HELP_WRITTEN
+--- a/GDEHELP/Makefile
++++ b/GDEHELP/Makefile
+@@ -47,11 +47,19 @@ save:
  	tar cvf - MENUS ARB_GDEmenus* |gzip >`date '+arbgdemnus_%d_%m_%y.tar.gz'`
  
  clean:
--	rm -f $(GENMENUS) $(TARGET) $(HELPFILELIST)
+-	rm -f $(GENMENUS) $(MENUS) $(HELPFILELIST)
 -	@$(MAKE) -f Makefile.helpfiles \
 -		"GENHELPDEST=$(GENHELPDEST)" \
 -		"GENDOCDEST=$(GENDOCDEST)" \
 -		"HELPFILELIST=$(HELPFILELIST)" \
 -		clean
-+	rm -f $(GENMENUS) $(TARGET)
+-	rm -f $(GENMENUS) $(MENUS) $(HELPFILELIST)
++	rm -f $(GENMENUS) $(MENUS)
 +	@if [ -e $(HELPFILELIST) ] ; then \
 +		$(MAKE) -f Makefile.helpfiles \
 +			"GENHELPDEST=$(GENHELPDEST)" \
@@ -123,21 +138,8 @@
 +		$(MAKE) -f Makefile.helpfiles \
 +			"GENHELPDEST=$(GENHELPDEST)" \
 +			"GENDOCDEST=$(GENDOCDEST)" \
++			"HELPFILELIST=$(HELPFILELIST)" \
 +			clean ; \
 +	fi
- 
 +	rm -f $(HELPFILELIST)
---- arb-5.3.orig/GDEHELP/Makefile.helpfiles
-+++ arb-5.3/GDEHELP/Makefile.helpfiles
-@@ -2,9 +2,9 @@
  
- .SUFFIXES: .doc .help .html
- 
--# GENHELPDEST, GENDOCDEST and HELPFILELIST are passed from 'Makefile'
-+# GENHELPDEST, GENDOCDEST and HELP_NAMES are passed from 'Makefile'
- 
--HELP_NAMES=$(shell cat $(HELPFILELIST))
-+# HELP_NAMES=$(shell cat $(HELPFILELIST))
- HELP_TARGETS=$(addprefix $(GENHELPDEST)/,$(HELP_NAMES))
- HELP_PLAIN=./HELP_PLAIN
- HELP_WRITTEN=./HELP_WRITTEN

Modified: trunk/packages/arb/trunk/debian/patches/20_config.makefiles
===================================================================
--- trunk/packages/arb/trunk/debian/patches/20_config.makefiles	2012-12-12 13:55:17 UTC (rev 12610)
+++ trunk/packages/arb/trunk/debian/patches/20_config.makefiles	2012-12-12 18:42:44 UTC (rev 12611)
@@ -1,5 +1,5 @@
 --- /dev/null
-+++ arb-5.3/config.makefile
++++ b/config.makefile
 @@ -0,0 +1,27 @@
 +# --------------------------------------------------------------------------------
 +# If this file is named config.makefile.template then copy it to config.makefile

Modified: trunk/packages/arb/trunk/debian/patches/20_tmpfile_issue.patch
===================================================================
--- trunk/packages/arb/trunk/debian/patches/20_tmpfile_issue.patch	2012-12-12 13:55:17 UTC (rev 12610)
+++ trunk/packages/arb/trunk/debian/patches/20_tmpfile_issue.patch	2012-12-12 18:42:44 UTC (rev 12611)
@@ -1,5 +1,5 @@
---- arb-5.3.orig/SH/arb_fastdnaml
-+++ arb-5.3/SH/arb_fastdnaml
+--- a/SH/arb_fastdnaml
++++ b/SH/arb_fastdnaml
 @@ -1,5 +1,5 @@
  #!/bin/sh
 -tmp=/tmp/arb_fdnaml_${USER}_$$
@@ -7,9 +7,9 @@
  mv infile $tmp
  nice -19 $1 < $tmp &
  sig=$!
---- arb-5.3.orig/SH/dszmconnect.pl
-+++ arb-5.3/SH/dszmconnect.pl
-@@ -20,7 +20,7 @@
+--- a/SH/dszmconnect.pl
++++ b/SH/dszmconnect.pl
+@@ -20,7 +20,7 @@ use LWP::Simple;
  use HTTP::Request::Common qw(POST);
  use LWP::UserAgent;
  
@@ -18,7 +18,7 @@
  
  
  
-@@ -51,9 +51,12 @@
+@@ -51,9 +51,12 @@ Last modified: Mon Sep  8 14:25:42 CEST
    </body>
  </html>";
  
@@ -33,7 +33,7 @@
  
  if (scalar(@ARGV) == 0)
    {print OUTPUT $errordocument;
-@@ -86,7 +89,10 @@
+@@ -86,7 +89,10 @@ print STDERR "Searching for '$item2'\n";
   $req_selection->content($selection_content);
  
   # Pass request to the user agent and get a response back
@@ -45,7 +45,7 @@
  
  
  
-@@ -95,7 +101,7 @@
+@@ -95,7 +101,7 @@ print STDERR "Searching for '$item2'\n";
   else  {die "Bad luck this time, request failed\n";};
  
  
@@ -54,7 +54,7 @@
  
  
   my $htmlcontent;
-@@ -111,7 +117,7 @@
+@@ -111,7 +117,7 @@ $htmlcontent =~ s{HREF=[^"]}{HREF=http:/
  
  print OUTPUT $htmlcontent ;
  

Modified: trunk/packages/arb/trunk/debian/patches/30_Makefile_main
===================================================================
--- trunk/packages/arb/trunk/debian/patches/30_Makefile_main	2012-12-12 13:55:17 UTC (rev 12610)
+++ trunk/packages/arb/trunk/debian/patches/30_Makefile_main	2012-12-12 18:42:44 UTC (rev 12611)
@@ -6,47 +6,41 @@
   * Fix X11 path
   * Enable propagation of hardening flags
 
---- arb-5.3.orig/Makefile
-+++ arb-5.3/Makefile
-@@ -58,7 +58,9 @@
- 	4.1.1 4.1.2 4.1.3 \
- 	4.2.0 4.2.1 4.2.3 4.2.4 \
- 	4.3 4.3.1 4.3.2 4.3.3 \
--	4.4.1 4.4.3 \
-+	4.4.1 4.4.3 4.4.5 \
-+	4.6 \
-+	4.7
+--- a/Makefile
++++ b/Makefile
+@@ -68,7 +68,7 @@ ALLOWED_GCC_4xx_VERSIONS=\
+ 	      4.3.1 4.3.2 4.3.3 \
+ 	      4.4.1       4.4.3 \
+ 	      4.6.1 \
+-	      4.7.1
++	      4.7.1 4.7.2
  
  ALLOWED_GCC_VERSIONS=$(ALLOWED_GCC_3xx_VERSIONS) $(ALLOWED_GCC_4xx_VERSIONS)
  
-@@ -95,7 +97,12 @@
+@@ -105,7 +105,12 @@ ifeq ($(DEBUG),0)
  	dflags := -DNDEBUG# defines
  	cflags := -O4# compiler flags (C and C++)
   ifndef DARWIN
--	lflags += -O99 --strip-all# linker flags
+-	lflags += -O99# linker flags
 +	ifdef DEBIAN
 +		lflags += -O2 -Wl,-rpath=/usr/lib/arb/lib # linker flags
 +		# remark:  --strip-all option breaks g++ 4.6 and it's unwanted anyway
 +	else
-+		lflags += -O99 --strip-all# linker flags
++		lflags += -O99# linker flags
 +	endif
   endif
  endif
  
-@@ -199,7 +206,11 @@
+@@ -208,7 +213,7 @@ cflags += -fPIC
  
  #---------------------- X11 location
  
--XHOME:=/usr/X11R6
+-ifdef DARWIN
 +ifdef DEBIAN
-+	XHOME:=/usr
-+else
-+	XHOME:=/usr/X11R6
-+endif
- XINCLUDES:=-I$(XHOME)/include
- 
- ifdef DARWIN
-@@ -281,9 +292,9 @@
+ 	XHOME:=$(PREFIX)
+ else
+ 	XHOME:=/usr/X11R6
+@@ -285,9 +290,9 @@ endif
  #	(instead define variables above)
  # -------------------------------------------------------------------------
  
@@ -58,15 +52,12 @@
  
  ifeq ($(DEVELOPER),RALF)
  HAVE_GNUPP0X=`SOURCE_TOOLS/requireVersion.pl 4.3 $(GCC_VERSION_FOUND)`
-@@ -302,9 +313,9 @@
+@@ -304,7 +309,7 @@ CPP := $(GPP) $(cppflags)# compile C++
+ ACCLIB := $(ACC) $(shared_cflags)# compile C (shared libs)
+ CPPLIB := $(CPP) $(shared_cflags)# compile C++ (shared libs)
  
- PP := $(CPPreal)# preprocessor
- 
--lflags += $(ldynamic)
-+lflags += $(ldynamic) $(LDFLAGS)
- 
--LINK_STATIC_LIB := ld $(lflags) -r -o# link static lib
-+LINK_STATIC_LIB := ld -rpath=/usr/lib/arb/lib -r -o# link static lib
+-LINK_STATIC_LIB := ld $(lflags) $(ldynamic) -r -o# link static lib
++LINK_STATIC_LIB := ld -rpath=/usr/lib/arb/lib -z relro -r -o# link static lib
  LINK_EXECUTABLE := $(GPP) $(lflags) $(cdynamic) -o# link executable (c++)
  
  ifeq ($(LINK_STATIC),1)

Modified: trunk/packages/arb/trunk/debian/patches/30_phyml
===================================================================
--- trunk/packages/arb/trunk/debian/patches/30_phyml	2012-12-12 13:55:17 UTC (rev 12610)
+++ trunk/packages/arb/trunk/debian/patches/30_phyml	2012-12-12 18:42:44 UTC (rev 12611)
@@ -1,6 +1,6 @@
---- arb-5.3.orig/GDE/PHYML/Makefile
-+++ arb-5.3/GDE/PHYML/Makefile
-@@ -13,7 +13,8 @@
+--- a/GDE/PHYML/Makefile
++++ b/GDE/PHYML/Makefile
+@@ -13,7 +13,8 @@ ifndef ARB
  # original compilation
  
  CC = gcc #cc
@@ -10,12 +10,3 @@
  # CFLAGS = -Wall
  # CFLAGS = -g -Wall
  # CFLAGS = -pg -Wall -fprofile-arcs -static
-@@ -30,8 +31,6 @@
- 
- ifdef DARWIN
- CFLAGS += -fPIC
--else
--CFLAGS += -static
- endif
- 
- # ARBs standard target

Deleted: trunk/packages/arb/trunk/debian/patches/gcc-4.7.patch
===================================================================
--- trunk/packages/arb/trunk/debian/patches/gcc-4.7.patch	2012-12-12 13:55:17 UTC (rev 12610)
+++ trunk/packages/arb/trunk/debian/patches/gcc-4.7.patch	2012-12-12 18:42:44 UTC (rev 12611)
@@ -1,14 +0,0 @@
-Author: Andreas Tille <tille at debian.org>
-Date: Thu, 26 Jul 2012 12:15:21 +0200
-Description: Fix gcc-4.7 build issue
-
---- arb-5.3.orig/AWTI/AWTI_import.cxx
-+++ arb-5.3/AWTI/AWTI_import.cxx
-@@ -12,6 +12,7 @@
- #include <GEN.hxx>
- 
- #include <climits>
-+#include <unistd.h>
- 
- using namespace std;
- 

Modified: trunk/packages/arb/trunk/debian/patches/series
===================================================================
--- trunk/packages/arb/trunk/debian/patches/series	2012-12-12 13:55:17 UTC (rev 12610)
+++ trunk/packages/arb/trunk/debian/patches/series	2012-12-12 18:42:44 UTC (rev 12611)
@@ -4,4 +4,3 @@
 20_Makefiles
 20_tmpfile_issue.patch
 tmpfile_CVE-2008-5378.patch
-gcc-4.7.patch

Modified: trunk/packages/arb/trunk/debian/patches/tmpfile_CVE-2008-5378.patch
===================================================================
--- trunk/packages/arb/trunk/debian/patches/tmpfile_CVE-2008-5378.patch	2012-12-12 13:55:17 UTC (rev 12610)
+++ trunk/packages/arb/trunk/debian/patches/tmpfile_CVE-2008-5378.patch	2012-12-12 18:42:44 UTC (rev 12611)
@@ -1,6 +1,6 @@
 This patch fixes tmpfile issues reported in CVE-2008-5378
---- arb-5.3.orig/SH/arb_fastdnaml
-+++ arb-5.3/SH/arb_fastdnaml
+--- a/SH/arb_fastdnaml
++++ b/SH/arb_fastdnaml
 @@ -1,9 +1,10 @@
  #!/bin/sh
  tmp=`mktemp -t arb_fdnaml_XXXXXXXXXX`
@@ -13,9 +13,9 @@
  wait
  # echo $tmp not deleted for debugging purposes
  rm -f $tmp
---- arb-5.3.orig/SH/arb_clean
-+++ arb-5.3/SH/arb_clean
-@@ -9,9 +9,14 @@
+--- a/SH/arb_clean
++++ b/SH/arb_clean
+@@ -9,9 +9,14 @@ else
  	pidfiles=/tmp/arb_pids_${USER}_${ARB_PID}
  fi
  
@@ -32,9 +32,9 @@
 +		rm -f "$pidfile"
 +	fi
 +done
---- arb-5.3.orig/SH/arb_panic
-+++ arb-5.3/SH/arb_panic
-@@ -21,7 +21,9 @@
+--- a/SH/arb_panic
++++ b/SH/arb_panic
+@@ -21,7 +21,9 @@ echo "  There may be more than one datab
  echo "          --------------------------------"
  
  for i in $chooser ; do
@@ -45,7 +45,7 @@
  done
  echo "          --------------------------------"
  
-@@ -29,19 +31,21 @@
+@@ -29,19 +31,21 @@ seperator
  echo "Please choose one line and enter the rightmost number"
  
  read ARB_PID

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