[med-svn] r17529 - in trunk/packages/arb/trunk/debian: . patches
Andreas Tille
tille at moszumanska.debian.org
Mon Jul 28 14:03:55 UTC 2014
Author: tille
Date: 2014-07-28 14:03:55 +0000 (Mon, 28 Jul 2014)
New Revision: 17529
Removed:
trunk/packages/arb/trunk/debian/patches/20_tmpfile_issue.patch
trunk/packages/arb/trunk/debian/patches/30_phyml
trunk/packages/arb/trunk/debian/patches/50_build_naligner.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/30_Makefile_main
trunk/packages/arb/trunk/debian/patches/40_add_libGLU.patch
trunk/packages/arb/trunk/debian/patches/50_fix_gcc-4.8.patch
trunk/packages/arb/trunk/debian/patches/60_use_debian_packaged_raxml.patch
trunk/packages/arb/trunk/debian/patches/hardening.patch
trunk/packages/arb/trunk/debian/patches/series
trunk/packages/arb/trunk/debian/patches/tmpfile_CVE-2008-5378.patch
trunk/packages/arb/trunk/debian/rules
Log:
Adapted patches to new upstream version (does not build yet!)
Modified: trunk/packages/arb/trunk/debian/changelog
===================================================================
--- trunk/packages/arb/trunk/debian/changelog 2014-07-28 12:38:39 UTC (rev 17528)
+++ trunk/packages/arb/trunk/debian/changelog 2014-07-28 14:03:55 UTC (rev 17529)
@@ -2,6 +2,7 @@
* New upstream version
* debian/upstream -> debian/upstream/metadata
+ * Build-Depends: libglib2.0-dev
TODO: Run test suite
-- Andreas Tille <tille at debian.org> Mon, 28 Jul 2014 14:36:39 +0200
Modified: trunk/packages/arb/trunk/debian/control
===================================================================
--- trunk/packages/arb/trunk/debian/control 2014-07-28 12:38:39 UTC (rev 17528)
+++ trunk/packages/arb/trunk/debian/control 2014-07-28 14:03:55 UTC (rev 17529)
@@ -9,6 +9,7 @@
freeglut3-dev | libglu-dev,
libbio-perl-perl,
libglew-dev,
+ libglib2.0-dev,
libglw1-mesa-dev,
libglu1-mesa-dev,
libmotif-dev,
Modified: trunk/packages/arb/trunk/debian/patches/20_Makefiles
===================================================================
--- trunk/packages/arb/trunk/debian/patches/20_Makefiles 2014-07-28 12:38:39 UTC (rev 17528)
+++ trunk/packages/arb/trunk/debian/patches/20_Makefiles 2014-07-28 14:03:55 UTC (rev 17529)
@@ -1,51 +1,22 @@
Author: Andreas Tille <tille at debian.org>
+Last-Update: Mon, 28 Jul 2014 15:06:57 +0200
Description: Fix various clean targets
---- a/ARBDB2/Makefile
-+++ b/ARBDB2/Makefile
-@@ -1,7 +1,11 @@
- # INCLUDE und GLOBALS MAIN CC cflags werden von aussen uebergeben
- .SUFFIXES: .o .c .depend
-
--include AD_MOBJECTS.h
-+HeaderFile = AD_MOBJECTS.h
-+CheckHEADER := $(shell if [ -e $(HeaderFile) ] ; then echo 1 ; else echo 0 ; fi)
-+ifeq ($(CheckHEADER),1)
-+ include $(HeaderFile)
-+endif
-
- ACC_OBJECTS = $(GB_O) $(GB_T) $(GB_X)
-
---- 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
-
--include AD_MOBJECTS.h
-+HeaderFile = AD_MOBJECTS.h
-+CheckHEADER := $(shell if [ -e $(HeaderFile) ] ; then echo 1 ; else echo 0 ; fi)
-+ifeq ($(CheckHEADER),1)
-+ include $(HeaderFile)
-+endif
-
-
- OBJECTS = $(GB_O) $(GB_T) $(GB_PP) $(GB_X)
--- 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)
+@@ -20,7 +20,7 @@ AISC_COMPILER=../AISC/aisc
+ AISC_PROTOTYPER=../AISC_MKPTPS/aisc_mkpt
+ AISC_DEPENDS = $(wildcard AISC/*.pa) $(AISC_COMPILER) $(AISC_PROTOTYPER)
-include AISC/export2sub
-+include $(ARBHOME)/AISC_COM//AISC/export2sub
++include $(ARBHOME)/AISC_COM/AISC/export2sub
- server.a: $(MAIN_SOURCE) $(PRIVATE_SERVER_OBJECTS:.o=.c) $(PUBLIC_SOURCES) $(AISC_DEPENDS)
- @$(MAKE) -r -f AISC/Makefile
-@@ -27,7 +27,7 @@ depends:
- @$(MAKE) -r -f AISC/Makefile pregenerate
+ $(MAIN): server.a
+@@ -33,7 +33,7 @@ depends:
+
clean:
+ @rm -f .depends
- @$(MAKE) -r -f AISC/Makefile clean
+ @$(MAKE) -r -f ../AISC/Makefile clean
@@ -53,96 +24,36 @@
--- 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)
+@@ -20,7 +20,7 @@ AISC_COMPILER=../AISC/aisc
+ AISC_PROTOTYPER=../AISC_MKPTPS/aisc_mkpt
+ AISC_DEPENDS = $(wildcard AISC/*.pa) $(AISC_COMPILER) $(AISC_PROTOTYPER)
-include AISC/export2sub
-+include $(ARBHOME)/AISC_COM//AISC/export2sub
++include $(ARBHOME)/AISC_COM/AISC/export2sub
- server.a: $(MAIN_SOURCE) $(PRIVATE_SERVER_OBJECTS:.o=.c) $(PUBLIC_SOURCES) $(AISC_DEPENDS)
- @$(MAKE) -r -f AISC/Makefile
-@@ -27,7 +27,7 @@ depends:
- @$(MAKE) -r -f AISC/Makefile pregenerate
+ $(MAIN): server.a
- clean:
-- @$(MAKE) -r -f AISC/Makefile clean
-+ @$(MAKE) -r -f ../AISC/Makefile clean
+@@ -33,7 +33,7 @@ depends:
- # DO NOT DELETE
-
---- a/GENOM_IMPORT/Makefile
-+++ b/GENOM_IMPORT/Makefile
-@@ -30,12 +30,12 @@ $(MAIN): $(CPP_OBJECTS)
- $(ACC) $(cflags) -c $< $(CPPINCLUDES)
-
clean:
-- -rm *.o
-- -rm *.a
-- -rm *.bak
-- -rm *~
-- -rm *#
-- -rm *\%
-+ -rm -f *.o
-+ -rm -f *.a
-+ -rm -f *.bak
-+ -rm -f *~
-+ -rm -f *#
-+ -rm -f *\%
+ @rm -f .depends
+- @$(MAKE) -r -f AISC/Makefile clean
++ @$(MAKE) -r -f ../AISC/Makefile clean
- #.IGNORE:
- # clean
---- a/HELP_SOURCE/Makefile
-+++ b/HELP_SOURCE/Makefile
-@@ -151,7 +151,7 @@ $(HLP_DEST)/%.pdf.gz : $(HLP_SOURCE)/%.p
- # --------------------------------------------------------------------------------
-
- delzerohtml:
-- -find $(HTML_LOCATION) -name "*.html" -size -1 -exec rm {} \;
-+ -if [ -d $(HTML_LOCATION) ] ; then find $(HTML_LOCATION) -name "*.html" -size -1 -exec rm {} \; ; fi
-
- date :
- $(MAKE) date.xsl.tmp
+ # DO NOT DELETE
+
--- a/GDEHELP/Makefile.helpfiles
+++ b/GDEHELP/Makefile.helpfiles
@@ -2,9 +2,9 @@
-
+
.SUFFIXES: .doc .help .html
-
+
-# GENHELPDEST, GENDOCDEST and HELPFILELIST are passed from 'Makefile'
+# GENHELPDEST, GENDOCDEST and HELP_NAMES are passed from 'Makefile'
-
+
-HELP_NAMES=$(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) $(MENUS) $(HELPFILELIST)
-- @$(MAKE) -f Makefile.helpfiles \
-- "GENHELPDEST=$(GENHELPDEST)" \
-- "GENDOCDEST=$(GENDOCDEST)" \
-- "HELPFILELIST=$(HELPFILELIST)" \
-- clean
-- rm -f $(GENMENUS) $(MENUS) $(HELPFILELIST)
-+ rm -f $(GENMENUS) $(MENUS)
-+ @if [ -e $(HELPFILELIST) ] ; then \
-+ $(MAKE) -f Makefile.helpfiles \
-+ "GENHELPDEST=$(GENHELPDEST)" \
-+ "GENDOCDEST=$(GENDOCDEST)" \
-+ "HELPFILELIST=$(HELPFILELIST)" \
-+ clean ; \
-+ else \
-+ $(MAKE) -f Makefile.helpfiles \
-+ "GENHELPDEST=$(GENHELPDEST)" \
-+ "GENDOCDEST=$(GENDOCDEST)" \
-+ "HELPFILELIST=$(HELPFILELIST)" \
-+ clean ; \
-+ fi
-+ rm -f $(HELPFILELIST)
-
Deleted: trunk/packages/arb/trunk/debian/patches/20_tmpfile_issue.patch
===================================================================
--- trunk/packages/arb/trunk/debian/patches/20_tmpfile_issue.patch 2014-07-28 12:38:39 UTC (rev 17528)
+++ trunk/packages/arb/trunk/debian/patches/20_tmpfile_issue.patch 2014-07-28 14:03:55 UTC (rev 17529)
@@ -1,69 +0,0 @@
-Author: Andreas Tille <tille at debian.org>
-Description: Proper use of tempfiles in scripts
-
---- a/SH/arb_fastdnaml
-+++ b/SH/arb_fastdnaml
-@@ -1,5 +1,5 @@
- #!/bin/sh
--tmp=/tmp/arb_fdnaml_${USER}_$$
-+tmp=`mktemp -t arb_fdnaml_XXXXXXXXXX`
- mv infile $tmp
- nice -19 $1 < $tmp &
- sig=$!
---- a/SH/dszmconnect.pl
-+++ b/SH/dszmconnect.pl
-@@ -20,7 +20,7 @@ use LWP::Simple;
- use HTTP::Request::Common qw(POST);
- use LWP::UserAgent;
-
--
-+use File::Temp qw/ tempfile tempdir /;
-
-
-
-@@ -51,9 +51,12 @@ Last modified: Mon Sep 8 14:25:42 CEST
- </body>
- </html>";
-
-+my $TMPOUT;
-+my $template = 'arbdsmz_XXXXXX';
-+(undef, $TMPOUT) = tempfile($template, OPEN => 0);
-+$TMPOUT = $TMPOUT . ".html";
-
--
--open (OUTPUT , "> /tmp/arbdsmz.html") or die "cannot open input file /tmp/arbdsmz.html";
-+open (OUTPUT , "> $TMPOUT") or die "cannot open temporary input file $TMPOUT";
-
- if (scalar(@ARGV) == 0)
- {print OUTPUT $errordocument;
-@@ -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
-- my $res_selection = $ua_selection -> request($req_selection, '/tmp/arbdsmz.htm');
-+ my $TMPUSEROUT;
-+ (undef, $TMPUSEROUT) = tempfile($template, OPEN => 0);
-+ $TMPUSEROUT = $TMPUSEROUT . ".htm";
-+ my $res_selection = $ua_selection -> request($req_selection, $TMPUSEROUT);
-
-
-
-@@ -95,7 +101,7 @@ print STDERR "Searching for '$item2'\n";
- else {die "Bad luck this time, request failed\n";};
-
-
--open (INPUT , "< /tmp/arbdsmz.htm") or die "cannot open input file /tmp/arbdsmz.htm";
-+open (INPUT , "< $TMPUSEROUT") or die "cannot open input file $TMPUSEROUT";
-
-
- my $htmlcontent;
-@@ -111,7 +117,7 @@ $htmlcontent =~ s{HREF=[^"]}{HREF=http:/
-
- print OUTPUT $htmlcontent ;
-
--#exec ('netscape', '/tmp/arbdsmz.html');
--print "file:///tmp/arbdsmz.html";
-+#exec ('netscape', $TMPOUT);
-+print "file://" . $TMPOUT;
-
- ##print "$htmlcontent\n";
Modified: trunk/packages/arb/trunk/debian/patches/30_Makefile_main
===================================================================
--- trunk/packages/arb/trunk/debian/patches/30_Makefile_main 2014-07-28 12:38:39 UTC (rev 17528)
+++ trunk/packages/arb/trunk/debian/patches/30_Makefile_main 2014-07-28 14:03:55 UTC (rev 17529)
@@ -2,65 +2,15 @@
Date: Thu, 26 Jul 2012 12:15:21 +0200
Description: Some adaptations to Debian
* Enable building with Debian default compiler
- * Enable fixing rpath issue when build under Debian
- * Fix X11 path
- * Enable propagation of hardening flags
--- a/Makefile
+++ b/Makefile
-@@ -67,8 +67,9 @@ ALLOWED_GCC_4xx_VERSIONS=\
- 4.2.0 4.2.1 4.2.3 4.2.4 \
- 4.3.1 4.3.2 4.3.3 \
- 4.4.1 4.4.3 \
-- 4.6.1 \
-- 4.7.1
-+ 4.6.1 4.6.2 4.6.3 \
-+ 4.7.1 4.7.2 4.7.3 \
-+ 4.8.0 4.8.1 4.8.2 4.8.3
+@@ -96,7 +96,7 @@ ALLOWED_gcc_VERSIONS=\
+ 4.6.1 4.6.2 4.6.3 \
+ 4.7.1 4.7.2 4.7.3 \
+ 4.8.0 4.8.1 4.8.2 4.8.3 \
+- 4.9.0 \
++ 4.9.0 4.9.1 \
- ALLOWED_GCC_VERSIONS=$(ALLOWED_GCC_3xx_VERSIONS) $(ALLOWED_GCC_4xx_VERSIONS)
-
-@@ -105,7 +106,12 @@ ifeq ($(DEBUG),0)
- dflags := -DNDEBUG# defines
- cflags := -O4# compiler flags (C and C++)
- ifndef DARWIN
-- 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# linker flags
-+ endif
- endif
- endif
-
-@@ -208,7 +214,7 @@ cflags += -fPIC
-
- #---------------------- X11 location
-
--ifdef DARWIN
-+ifdef DEBIAN
- XHOME:=$(PREFIX)
- else
- XHOME:=/usr/X11R6
-@@ -285,9 +291,9 @@ endif
- # (instead define variables above)
- # -------------------------------------------------------------------------
-
--cflags += -W -Wall $(dflags) $(extended_warnings) $(cdynamic)
-+cflags += $(CFLAGS) -W -Wall $(dflags) $(extended_warnings) $(cdynamic)
-
--cppflags := $(extended_cpp_warnings)
-+cppflags := $(extended_cpp_warnings) $(CPPFLAGS)
-
- ifeq ($(DEVELOPER),RALF)
- HAVE_GNUPP0X=`SOURCE_TOOLS/requireVersion.pl 4.3 $(GCC_VERSION_FOUND)`
-@@ -304,7 +310,7 @@ CPP := $(GPP) $(cppflags)# compile C++
- ACCLIB := $(ACC) $(shared_cflags)# compile C (shared libs)
- CPPLIB := $(CPP) $(shared_cflags)# compile C++ (shared libs)
-
--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)
+ # supported clang versions:
+ ALLOWED_clang_VERSIONS=\
Deleted: trunk/packages/arb/trunk/debian/patches/30_phyml
===================================================================
--- trunk/packages/arb/trunk/debian/patches/30_phyml 2014-07-28 12:38:39 UTC (rev 17528)
+++ trunk/packages/arb/trunk/debian/patches/30_phyml 2014-07-28 14:03:55 UTC (rev 17529)
@@ -1,15 +0,0 @@
-Author: Andreas Tille <tille at debian.org>
-Description: Prevent static linking of phyml
-
---- a/GDE/PHYML/Makefile
-+++ b/GDE/PHYML/Makefile
-@@ -13,7 +13,8 @@ ifndef ARB
- # original compilation
-
- CC = gcc #cc
--CFLAGS = -O4 -fomit-frame-pointer -Wall -static
-+CFLAGS = -O4 -fomit-frame-pointer -Wall
-+# -static
- # CFLAGS = -Wall
- # CFLAGS = -g -Wall
- # CFLAGS = -pg -Wall -fprofile-arcs -static
Modified: trunk/packages/arb/trunk/debian/patches/40_add_libGLU.patch
===================================================================
--- trunk/packages/arb/trunk/debian/patches/40_add_libGLU.patch 2014-07-28 12:38:39 UTC (rev 17528)
+++ trunk/packages/arb/trunk/debian/patches/40_add_libGLU.patch 2014-07-28 14:03:55 UTC (rev 17529)
@@ -1,14 +1,17 @@
Author: Andreas Tille <tille at debian.org>
+Last-Update: Mon, 28 Jul 2014 15:35:40 +0200
Description: Add missing libGLU
--- a/Makefile
+++ b/Makefile
-@@ -747,7 +747,7 @@ $(EDIT4): $(ARCHS_EDIT4:.a=.dummy) share
- @SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_EDIT4) $(GUI_LIBS) || ( \
- echo Link $@ ; \
- echo "$(LINK_EXECUTABLE) $@ $(LIBPATH) $(ARCHS_EDIT4) $(GUI_LIBS) $(LIBS_EDIT4)" ; \
-- $(LINK_EXECUTABLE) $@ $(LIBPATH) $(ARCHS_EDIT4) $(GUI_LIBS) $(LIBS_EDIT4) \
-+ $(LINK_EXECUTABLE) $@ $(LIBPATH) $(ARCHS_EDIT4) $(GUI_LIBS) -lGLU $(LIBS_EDIT4) \
+@@ -968,8 +968,8 @@ ARCHS_NTREE = \
+ $(NTREE): $(ARCHS_NTREE:.a=.dummy) link_awt
+ @SOURCE_TOOLS/binuptodate.pl $@ $(ARCHS_NTREE) $(GUI_LIBS) $(use_ARB_main) || ( \
+ echo "$(SEP) Link $@"; \
+- echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_NTREE) $(ARCHS_CLIENT_PROBE) $(GUI_LIBS) $(EXECLIBS)" ; \
+- $(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_NTREE) $(ARCHS_CLIENT_PROBE) $(GUI_LIBS) $(EXECLIBS) && \
++ echo "$(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_NTREE) $(ARCHS_CLIENT_PROBE) $(GUI_LIBS) -lGLU $(EXECLIBS)" ; \
++ $(LINK_EXECUTABLE) $@ $(use_ARB_main) $(LIBPATH) $(ARCHS_NTREE) $(ARCHS_CLIENT_PROBE) $(GUI_LIBS) -lGLU $(EXECLIBS) && \
+ echo "$(SEP) Link $@ [done]"; \
)
- #*********************************** arb_pgt **************************************
Deleted: trunk/packages/arb/trunk/debian/patches/50_build_naligner.patch
===================================================================
--- trunk/packages/arb/trunk/debian/patches/50_build_naligner.patch 2014-07-28 12:38:39 UTC (rev 17528)
+++ trunk/packages/arb/trunk/debian/patches/50_build_naligner.patch 2014-07-28 14:03:55 UTC (rev 17529)
@@ -1,14 +0,0 @@
-Author: Andreas Tille <tille at debian.org>
-Description: Some build flags were simply not propagated in $(CFLAGS) - use $(cflags)
-
---- a/NALIGNER/Makefile
-+++ b/NALIGNER/Makefile
-@@ -22,7 +22,7 @@ $(MAIN): $(CPP_OBJECTS)
- $(LINK_STATIC_LIB) $(MAIN) $(CPP_OBJECTS)
-
- .cxx.o:
-- $(CPP) $(CFLAGS) -c -o $@ $< $(CPPINCLUDES)
-+ $(CPP) $(cflags) -c -o $@ $< $(CPPINCLUDES)
-
- clean:
- rm -f $(CPP_OBJECTS) *.a
Modified: trunk/packages/arb/trunk/debian/patches/50_fix_gcc-4.8.patch
===================================================================
--- trunk/packages/arb/trunk/debian/patches/50_fix_gcc-4.8.patch 2014-07-28 12:38:39 UTC (rev 17528)
+++ trunk/packages/arb/trunk/debian/patches/50_fix_gcc-4.8.patch 2014-07-28 14:03:55 UTC (rev 17529)
@@ -1,47 +1,15 @@
Author: Andreas Tille <tille at debian.org>
-Description: Fix some gcc-4.8 issues
+Last-Update: Mon, 28 Jul 2014 15:42:56 +0200
+Description: Propagate hardening options
---- a/GDE/SUPPORT/varpos.c
-+++ b/GDE/SUPPORT/varpos.c
-@@ -1,3 +1,4 @@
-+#include "stdlib.h"
- #include "Flatio.c"
- #define MAX(a,b) ((a)>(b)?(a):(b))
-
---- a/GDE/AxML/axml.c
-+++ b/GDE/AxML/axml.c
-@@ -9,6 +9,8 @@
- #include <sys/types.h>
- #include <sys/time.h>
- #include <time.h>
-+#include <stdlib.h>
-+#include <string.h>
- double accTime = 0.0;
- double globTime = 0.0;
- struct timeval ttime;
---- a/GDE/AxML/axml.h
-+++ b/GDE/AxML/axml.h
-@@ -266,12 +266,6 @@ typedef struct {
-
- void exit();
-
--#if ANSI || MALLOC_VOID
-- void *malloc();
--#else
-- char *malloc();
--#endif
--
- #define Malloc(x) malloc((unsigned) (x)) /* BSD */
- /* #define Malloc(x) malloc((size_t) (x)) */ /* System V */
-
--- a/GDE/AxML/Makefile
+++ b/GDE/AxML/Makefile
-@@ -33,7 +33,7 @@ endif
+@@ -31,7 +31,7 @@ endif
all : $(TARGET)
$(TARGET) : $(OBJECTS)
-- $(CC) $(CFLAGS) -o $@ $< $(LDFLAGS)
-+ $(CC) $(CFLAGS) -o $@ $< -lm
+- $(CC) $(CFLAGS) -o $@ $< -lm
++ $(CC) $(CFLAGS) -o $@ $< $(LDFLAGS)
.c.o:
$(CC) $(CFLAGS) -c -o $@ $<
Modified: trunk/packages/arb/trunk/debian/patches/60_use_debian_packaged_raxml.patch
===================================================================
--- trunk/packages/arb/trunk/debian/patches/60_use_debian_packaged_raxml.patch 2014-07-28 12:38:39 UTC (rev 17528)
+++ trunk/packages/arb/trunk/debian/patches/60_use_debian_packaged_raxml.patch 2014-07-28 14:03:55 UTC (rev 17529)
@@ -3,15 +3,15 @@
--- a/GDE/Makefile
+++ b/GDE/Makefile
-@@ -3,7 +3,6 @@ ARCHS_ALL = \
+@@ -3,7 +3,6 @@ ARCHS_COMMON = \
CLUSTAL/CLUSTAL.dummy \
SUPPORT/SUPPORT.dummy \
AxML/AxML.dummy \
- RAxML/RAxML.dummy \
PHYML/PHYML.dummy \
+ MrBAYES/MrBAYES.dummy \
- # --------------------------------------------------------------------------------
-@@ -15,6 +14,7 @@ ARCHS_ALL = \
+@@ -23,6 +22,7 @@ ARCHS_NO_DEPENDS = \
ARCHS_NON_DEBIAN = \
CLUSTALW/CLUSTALW.dummy \
PHYLIP/PHYLIP.dummy \
Modified: trunk/packages/arb/trunk/debian/patches/hardening.patch
===================================================================
--- trunk/packages/arb/trunk/debian/patches/hardening.patch 2014-07-28 12:38:39 UTC (rev 17528)
+++ trunk/packages/arb/trunk/debian/patches/hardening.patch 2014-07-28 14:03:55 UTC (rev 17529)
@@ -4,12 +4,14 @@
--- a/Makefile
+++ b/Makefile
-@@ -107,7 +107,7 @@ ifeq ($(DEBUG),0)
- cflags := -O4# compiler flags (C and C++)
- ifndef DARWIN
- ifdef DEBIAN
-- lflags += -O2 -Wl,-rpath=/usr/lib/arb/lib # linker flags
-+ lflags += -O2 -Wl,-rpath=/usr/lib/arb/lib $(LDFLAGS) # linker flags
- # remark: --strip-all option breaks g++ 4.6 and it's unwanted anyway
- else
- lflags += -O99# linker flags
+@@ -196,8 +196,8 @@ ifeq ($(DEBUG),0)
+ endif
+
+ ifeq ($(DEBIAN),1)
+- lflags += -rpath=/usr/lib/arb/lib -z relro
+- clflags += -Wl,-rpath=/usr/lib/arb/lib -Wl,-z,relro
++ lflags += -rpath=/usr/lib/arb/lib $(LDFLAGS)
++ clflags += -Wl,-rpath=/usr/lib/arb/lib
+ endif
+
+ ifeq ($(DEBUG),1)
Modified: trunk/packages/arb/trunk/debian/patches/series
===================================================================
--- trunk/packages/arb/trunk/debian/patches/series 2014-07-28 12:38:39 UTC (rev 17528)
+++ trunk/packages/arb/trunk/debian/patches/series 2014-07-28 14:03:55 UTC (rev 17529)
@@ -1,11 +1,8 @@
-30_phyml
20_config.makefiles
30_Makefile_main
20_Makefiles
-20_tmpfile_issue.patch
tmpfile_CVE-2008-5378.patch
40_add_libGLU.patch
-50_build_naligner.patch
50_fix_gcc-4.8.patch
60_use_debian_packaged_raxml.patch
hardening.patch
Modified: trunk/packages/arb/trunk/debian/patches/tmpfile_CVE-2008-5378.patch
===================================================================
--- trunk/packages/arb/trunk/debian/patches/tmpfile_CVE-2008-5378.patch 2014-07-28 12:38:39 UTC (rev 17528)
+++ trunk/packages/arb/trunk/debian/patches/tmpfile_CVE-2008-5378.patch 2014-07-28 14:03:55 UTC (rev 17529)
@@ -1,42 +1,11 @@
+Author: Andreas Tille <tille at debian.org>
BugClosed: http://bugs.debian.org/508942
+Last-Update: Mon, 28 Jul 2014 15:31:20 +0200
Description: This patch fixes tmpfile issues reported in CVE-2008-5378
---- a/SH/arb_fastdnaml
-+++ b/SH/arb_fastdnaml
-@@ -1,9 +1,10 @@
- #!/bin/sh
- tmp=`mktemp -t arb_fdnaml_XXXXXXXXXX`
-+pidfile=`mktemp -p /tmp foo_${USER}_${PPID}_XXXXXX`
- mv infile $tmp
- nice -19 $1 < $tmp &
- sig=$!
--/bin/echo "$sig $$ \c" >>/tmp/arb_pids_${USER}_${ARB_PID}
-+/bin/echo "$sig $$ \c" >>"$pidfile"
- wait
- # echo $tmp not deleted for debugging purposes
- rm -f $tmp
---- a/SH/arb_clean
-+++ b/SH/arb_clean
-@@ -9,9 +9,14 @@ else
- pidfiles=/tmp/arb_pids_${USER}_${ARB_PID}
- fi
-
--if [ "\"X$pidfiles\"" != "X" ]; then
-+# Make sure files to remove are no symbolic links
-+if [ "\"X$pidfiles\"" != "X" -a -f "$pidfiles" ]; then
- kill -9 `cat $pidfiles` >/dev/null 2>&1
- rm -f $pidfiles
- fi
-
--rm -f /tmp/arb_*_${USER}_${ARB_PID}*
-+for pidfile in /tmp/arb_*_${USER}_${ARB_PID}* ; do
-+ if [ -f "$pidfile" ] ; then
-+ rm -f "$pidfile"
-+ fi
-+done
--- a/SH/arb_panic
+++ b/SH/arb_panic
-@@ -21,7 +21,9 @@ echo " There may be more than one datab
+@@ -22,7 +22,9 @@ echo " There may be more than one datab
echo " --------------------------------"
for i in $chooser ; do
@@ -47,30 +16,3 @@
done
echo " --------------------------------"
-@@ -29,19 +31,21 @@ seperator
- echo "Please choose one line and enter the rightmost number"
-
- read ARB_PID
--if [ ! -f /tmp/arb_pids_${USER}_${ARB_PID} ]; then
-- err "Incorrect Choice"
--fi
-+for arbpid in /tmp/arb_pids_${USER}_${ARB_PID}* ; do
-+ if [ ! -f "$arbpid" ]; then
-+ err "Incorrect Choice"
-+ fi
-+done
-
- seperator
- echo "Please enter full path (to save DB):"
- read FILE
-
--panicfile="/tmp/arb_panic_${USER}_${ARB_PID}"
-+panicfile=`mktemp -p /tmp arb_panic_${USER}_${ARB_PID}_XXXXXX`
- rm -f $panicfile
- echo "$FILE" >$panicfile
- ok=false
--for i in `cat /tmp/arb_pids_${USER}_${ARB_PID}`; do
-+for i in `cat /tmp/arb_pids_${USER}_${ARB_PID}*`; do
- echo "[Sending SIGHUP to pid $i]"
- if kill -HUP $i 2>/dev/null; then
- ok=true
Modified: trunk/packages/arb/trunk/debian/rules
===================================================================
--- trunk/packages/arb/trunk/debian/rules 2014-07-28 12:38:39 UTC (rev 17528)
+++ trunk/packages/arb/trunk/debian/rules 2014-07-28 14:03:55 UTC (rev 17529)
@@ -80,6 +80,7 @@
rm -fr $(DIRSTOREMOVE)
for dtc in $(DIRSTOCLEAN); do if [ -d $${dtc} ] ; then cd $${dtc}; make clean ; fi; done
find . -name "*.stamp" -o -name "*.bs" -o -name ".exists" -delete
+ rm -f UNIT_TESTER/Makefile.setup.local
override_dh_install:
dh_install
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