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 <[email protected]> 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 <[email protected]> -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 _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
