[med-svn] r8533 - in trunk/packages/arb/trunk/debian: . patches
Andreas Tille
tille at alioth.debian.org
Fri Nov 11 13:30:25 UTC 2011
Author: tille
Date: 2011-11-11 13:30:24 +0000 (Fri, 11 Nov 2011)
New Revision: 8533
Removed:
trunk/packages/arb/trunk/debian/patches/20_perlscripts
trunk/packages/arb/trunk/debian/patches/no_xview_dependency.patch
Modified:
trunk/packages/arb/trunk/debian/arb-common.install
trunk/packages/arb/trunk/debian/changelog
trunk/packages/arb/trunk/debian/compat
trunk/packages/arb/trunk/debian/control
trunk/packages/arb/trunk/debian/copyright
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:
Several adpatations to new upstrem version; needs further testing
Modified: trunk/packages/arb/trunk/debian/arb-common.install
===================================================================
--- trunk/packages/arb/trunk/debian/arb-common.install 2011-11-11 12:38:27 UTC (rev 8532)
+++ trunk/packages/arb/trunk/debian/arb-common.install 2011-11-11 13:30:24 UTC (rev 8533)
@@ -10,7 +10,6 @@
demo.arb usr/share/doc/arb/examples
lib/[d-gi-kmoqt-z]* usr/lib/arb/lib
lib/arb_default/* usr/lib/arb/lib/arb_default
-lib/config.Linux usr/lib/arb/lib
lib/help usr/lib/arb/lib
lib/nas/names.dat* var/lib/arb/nas
lib/pi* usr/share/arb/lib
Modified: trunk/packages/arb/trunk/debian/changelog
===================================================================
--- trunk/packages/arb/trunk/debian/changelog 2011-11-11 12:38:27 UTC (rev 8532)
+++ trunk/packages/arb/trunk/debian/changelog 2011-11-11 13:30:24 UTC (rev 8533)
@@ -1,11 +1,21 @@
-arb (5.2-2) UNRELEASED; urgency=low
+arb (5.3-1) UNRELEASED; urgency=low
+ [ Nelson A. de Oliveira ]
* Fix FTBFS: replaced sablotron by xsltproc in debian/control
(Closes: #634999)
* Replaced arb dependency on the ssh metapackage by openssh-client only
- -- Nelson A. de Oliveira <naoliv at debian.org> Thu, 21 Jul 2011 13:03:55 -0300
+ [ Andreas Tille ]
+ * New upstream version (including updateing debian/patches/*)
+ This version doese not depend from molphy any more
+ * debian/control
+ - Do not depend from molphy which is removed from Debian any more
+ - Standards-Version: 3.9.2 (no changes needed)
+ - Fixed Vcs fields
+ * Debhelper 8 (control+compat)
+ -- Andreas Tille <tille at debian.org> Fri, 11 Nov 2011 11:46:22 +0100
+
arb (5.2-1) unstable; urgency=low
* New upstream version
Modified: trunk/packages/arb/trunk/debian/compat
===================================================================
--- trunk/packages/arb/trunk/debian/compat 2011-11-11 12:38:27 UTC (rev 8532)
+++ trunk/packages/arb/trunk/debian/compat 2011-11-11 13:30:24 UTC (rev 8533)
@@ -1 +1 @@
-7
+8
Modified: trunk/packages/arb/trunk/debian/control
===================================================================
--- trunk/packages/arb/trunk/debian/control 2011-11-11 12:38:27 UTC (rev 8532)
+++ trunk/packages/arb/trunk/debian/control 2011-11-11 13:30:24 UTC (rev 8533)
@@ -5,7 +5,7 @@
DM-Upload-Allowed: yes
Uploaders: Andreas Tille <tille at debian.org>
Build-Depends: chrpath,
- debhelper (>= 7.1),
+ debhelper (>= 8),
dpkg-dev (>= 1.15.4),
freeglut3-dev | libglu-dev,
libglew1.5-dev,
@@ -24,10 +24,10 @@
x11proto-print-dev,
xsltproc,
xutils-dev
-Standards-Version: 3.9.1
+Standards-Version: 3.9.2
Homepage: http://www.arb-home.de/
-Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/arb/trunk/?rev=0&sc=0
-Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/arb/trunk/
+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/
XS-Autobuild: yes
Package: arb
@@ -35,7 +35,6 @@
Depends: arb-common (= ${source:Version}),
fastdnaml (>= 1.2.2-4),
libarb (= ${binary:Version}),
- molphy,
openssh-client,
phylip (>= 3.6b),
readseq (>= 1-1),
Modified: trunk/packages/arb/trunk/debian/copyright
===================================================================
--- trunk/packages/arb/trunk/debian/copyright 2011-11-11 12:38:27 UTC (rev 8532)
+++ trunk/packages/arb/trunk/debian/copyright 2011-11-11 13:30:24 UTC (rev 8533)
@@ -1,9 +1,10 @@
-Format-Specification: http://wiki.debian.org/Proposals/CopyrightFormat
-Upstream-Author: Arb development team <devel at arb-home.de>,
+Format: http://dep.debian.net/deps/dep5/
+Upstream-Name: Arb
+Upstream-Contact: Arb development team <devel at arb-home.de>,
Ralf Westram <ralf at arb-home.de>
+Source: http://download.arb-home.de/release/
Packaged-By: Andreas Tille <tille at debian.org>
Packaged-Date: Thu, 03 Jun 2004 11:17:55 +0200
-Upstream-Source: http://download.arb-home.de/src/
Files: debian/*
Copyright: (C) 2008 Andreas Tille <tille at debian.org>
Modified: trunk/packages/arb/trunk/debian/patches/20_Makefiles
===================================================================
--- trunk/packages/arb/trunk/debian/patches/20_Makefiles 2011-11-11 12:38:27 UTC (rev 8532)
+++ trunk/packages/arb/trunk/debian/patches/20_Makefiles 2011-11-11 13:30:24 UTC (rev 8533)
@@ -1,5 +1,5 @@
---- arbsrc_6779.orig/ARBDB2/Makefile
-+++ arbsrc_6779/ARBDB2/Makefile
+--- arbsrc_8210.orig/ARBDB2/Makefile
++++ arbsrc_8210/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)
---- arbsrc_6779.orig/ARBDBS/Makefile
-+++ arbsrc_6779/ARBDBS/Makefile
+--- arbsrc_8210.orig/ARBDBS/Makefile
++++ arbsrc_8210/ARBDBS/Makefile
@@ -1,7 +1,11 @@
# INCLUDE und GLOBALS MAIN CC cflags werden von aussen uebergeben
.SUFFIXES: .o .c .cxx .depend
@@ -28,8 +28,8 @@
OBJECTS = $(GB_O) $(GB_T) $(GB_PP) $(GB_X)
---- arbsrc_6779.orig/NAMES_COM/Makefile
-+++ arbsrc_6779/NAMES_COM/Makefile
+--- arbsrc_8210.orig/NAMES_COM/Makefile
++++ arbsrc_8210/NAMES_COM/Makefile
@@ -18,7 +18,7 @@
AISC_COMPILER=../MAKEBIN/aisc
AISC_DEPENDS = $(wildcard AISC/*.pa) $(AISC_COMPILER)
@@ -48,8 +48,8 @@
# DO NOT DELETE
---- arbsrc_6779.orig/PROBE_COM/Makefile
-+++ arbsrc_6779/PROBE_COM/Makefile
+--- arbsrc_8210.orig/PROBE_COM/Makefile
++++ arbsrc_8210/PROBE_COM/Makefile
@@ -18,7 +18,7 @@
AISC_COMPILER=../MAKEBIN/aisc
AISC_DEPENDS = $(wildcard AISC/*.pa) $(AISC_COMPILER)
@@ -68,8 +68,8 @@
# DO NOT DELETE
---- arbsrc_6779.orig/GENOM_IMPORT/Makefile
-+++ arbsrc_6779/GENOM_IMPORT/Makefile
+--- arbsrc_8210.orig/GENOM_IMPORT/Makefile
++++ arbsrc_8210/GENOM_IMPORT/Makefile
@@ -30,12 +30,12 @@
$(ACC) $(cflags) -c $< $(CPPINCLUDES)
@@ -89,9 +89,9 @@
#.IGNORE:
# clean
---- arbsrc_6779.orig/HELP_SOURCE/Makefile
-+++ arbsrc_6779/HELP_SOURCE/Makefile
-@@ -160,7 +160,7 @@
+--- arbsrc_8210.orig/HELP_SOURCE/Makefile
++++ arbsrc_8210/HELP_SOURCE/Makefile
+@@ -151,7 +151,7 @@
# --------------------------------------------------------------------------------
delzerohtml:
@@ -100,20 +100,8 @@
date :
$(MAKE) date.xsl.tmp
-@@ -232,9 +232,9 @@
- clean:
- rm -f $(TOOL_OBJECTS) $(BINARIES)
- rm -f $(HTML_IDX) `find $(HLP_DEST) -name "*.hlp"`
-- rm -f html.list `find $(HTML_LOCATION) -name "*.html"`
-+ rm -rf html.list $(HTML_LOCATION)
- ifeq ($(CONVERT_FROM_OLD_HELP),1)
-- rm -f $(XML_DEPEND) dummy `find $(XML_LOCATION) -name "*.xml"`
-+ rm -rf $(XML_DEPEND) dummy $(XML_LOCATION)
- endif
- $(MAKE) -C $(HLP_GENERATED) clean
-
---- arbsrc_6779.orig/GDEHELP/Makefile
-+++ arbsrc_6779/GDEHELP/Makefile
+--- arbsrc_8210.orig/GDEHELP/Makefile
++++ arbsrc_8210/GDEHELP/Makefile
@@ -37,10 +37,18 @@
tar cvf - MENUS ARB_GDEmenus* |gzip >`date '+arbgdemnus_%d_%m_%y.tar.gz'`
@@ -139,8 +127,8 @@
+ fi
+ rm -f $(HELPFILELIST)
---- arbsrc_6779.orig/GDEHELP/Makefile.helpfiles
-+++ arbsrc_6779/GDEHELP/Makefile.helpfiles
+--- arbsrc_8210.orig/GDEHELP/Makefile.helpfiles
++++ arbsrc_8210/GDEHELP/Makefile.helpfiles
@@ -2,9 +2,9 @@
.SUFFIXES: .doc .help .html
Modified: trunk/packages/arb/trunk/debian/patches/20_config.makefiles
===================================================================
--- trunk/packages/arb/trunk/debian/patches/20_config.makefiles 2011-11-11 12:38:27 UTC (rev 8532)
+++ trunk/packages/arb/trunk/debian/patches/20_config.makefiles 2011-11-11 13:30:24 UTC (rev 8533)
@@ -1,5 +1,5 @@
--- /dev/null
-+++ arbsrc_6779/config.makefile
++++ arbsrc_8210/config.makefile
@@ -0,0 +1,27 @@
+# --------------------------------------------------------------------------------
+# If this file is named config.makefile.template then copy it to config.makefile
Deleted: trunk/packages/arb/trunk/debian/patches/20_perlscripts
===================================================================
--- trunk/packages/arb/trunk/debian/patches/20_perlscripts 2011-11-11 12:38:27 UTC (rev 8532)
+++ trunk/packages/arb/trunk/debian/patches/20_perlscripts 2011-11-11 13:30:24 UTC (rev 8533)
@@ -1,7 +0,0 @@
---- arb-0.0.20071207.1.orig/PERL_SCRIPTS/IFTHELP/genbank_gen_long_features.pl
-+++ arb-0.0.20071207.1/PERL_SCRIPTS/IFTHELP/genbank_gen_long_features.pl
-@@ -1,4 +1,3 @@
--
- #!/usr/bin/perl
- # ================================================================ #
- # #
Modified: trunk/packages/arb/trunk/debian/patches/20_tmpfile_issue.patch
===================================================================
--- trunk/packages/arb/trunk/debian/patches/20_tmpfile_issue.patch 2011-11-11 12:38:27 UTC (rev 8532)
+++ trunk/packages/arb/trunk/debian/patches/20_tmpfile_issue.patch 2011-11-11 13:30:24 UTC (rev 8533)
@@ -1,5 +1,5 @@
---- arb-0.0.20071207.1.orig/SH/arb_fastdnaml
-+++ arb-0.0.20071207.1/SH/arb_fastdnaml
+--- arbsrc_8210.orig/SH/arb_fastdnaml
++++ arbsrc_8210/SH/arb_fastdnaml
@@ -1,5 +1,5 @@
#!/bin/sh
-tmp=/tmp/arb_fdnaml_${USER}_$$
@@ -7,8 +7,8 @@
mv infile $tmp
nice -19 $1 < $tmp &
sig=$!
---- arb-0.0.20071207.1.orig/SH/dszmconnect.pl
-+++ arb-0.0.20071207.1/SH/dszmconnect.pl
+--- arbsrc_8210.orig/SH/dszmconnect.pl
++++ arbsrc_8210/SH/dszmconnect.pl
@@ -20,7 +20,7 @@
use HTTP::Request::Common qw(POST);
use LWP::UserAgent;
Modified: trunk/packages/arb/trunk/debian/patches/30_Makefile_main
===================================================================
--- trunk/packages/arb/trunk/debian/patches/30_Makefile_main 2011-11-11 12:38:27 UTC (rev 8532)
+++ trunk/packages/arb/trunk/debian/patches/30_Makefile_main 2011-11-11 13:30:24 UTC (rev 8533)
@@ -1,26 +1,31 @@
---- arbsrc_6779.orig/Makefile
-+++ arbsrc_6779/Makefile
-@@ -58,7 +58,7 @@
+--- arbsrc_8210.orig/Makefile
++++ arbsrc_8210/Makefile
+@@ -58,7 +58,8 @@
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
-+ 4.4.1 4.4.3 4.4.5
+- 4.4.1 4.4.3 \
++ 4.4.1 4.4.3 4.4.5 \
++ 4.6
ALLOWED_GCC_VERSIONS=$(ALLOWED_GCC_3xx_VERSIONS) $(ALLOWED_GCC_4xx_VERSIONS)
-@@ -86,7 +86,8 @@
+@@ -95,7 +96,12 @@
+ dflags := -DNDEBUG# defines
+ cflags := -O4# compiler flags (C and C++)
+ ifndef DARWIN
+- lflags += -O99 --strip-all# linker flags
++ ifdef DEBIAN
++ lflags += -O2 -Wl,-rpath=/usr/lib/arb/lib # linker flags
++ # remark: --strip-all option breaks g++ 4.6 and it's unwanted anyway
++ else
++ lflags += -O99 --strip-all# linker flags
++ endif
+ endif
endif
- shared_cflags :=# flags for shared lib compilation
--lflags :=# linker flags
-+# lflags := -Wl,-rpath,/usr/lib/arb/lib # linker flags
-+lflags := -rpath=/usr/lib/arb/lib # linker flags
- extended_warnings :=# warning flags for C and C++-compiler
- extended_cpp_warnings :=# warning flags for C++-compiler only
+@@ -199,7 +205,11 @@
-@@ -199,7 +200,11 @@
-
#---------------------- X11 location
-XHOME:=/usr/X11R6
@@ -32,3 +37,12 @@
XINCLUDES:=-I$(XHOME)/include
ifdef DARWIN
+@@ -304,7 +314,7 @@
+
+ lflags += $(ldynamic)
+
+-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_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 2011-11-11 12:38:27 UTC (rev 8532)
+++ trunk/packages/arb/trunk/debian/patches/30_phyml 2011-11-11 13:30:24 UTC (rev 8533)
@@ -1,5 +1,5 @@
---- arbsrc_6182.orig/GDE/PHYML/Makefile
-+++ arbsrc_6182/GDE/PHYML/Makefile
+--- arbsrc_8210.orig/GDE/PHYML/Makefile
++++ arbsrc_8210/GDE/PHYML/Makefile
@@ -13,7 +13,8 @@
# original compilation
Deleted: trunk/packages/arb/trunk/debian/patches/no_xview_dependency.patch
===================================================================
--- trunk/packages/arb/trunk/debian/patches/no_xview_dependency.patch 2011-11-11 12:38:27 UTC (rev 8532)
+++ trunk/packages/arb/trunk/debian/patches/no_xview_dependency.patch 2011-11-11 13:30:24 UTC (rev 8533)
@@ -1,81 +0,0 @@
-Author: Andreas Tille <tille at debian.org>
-Date: Wed, 09 Feb 2011 16:56:15 +0100
-Description: Make sure we do not have a hidden Dependency
- from xview-clients via the usage of texteditor
-
---- arbsrc_6779.orig/lib/arb_default/edit.arb
-+++ arbsrc_6779/lib/arb_default/edit.arb
-@@ -155,7 +155,7 @@
- %) /*tools*/
-
- textedit %% (%
-- command "textedit * &"
-+ command "editor * &"
- %) /*textedit*/
-
- submission %% (%
---- arbsrc_6779.orig/lib/arb_default/ntree.arb
-+++ arbsrc_6779/lib/arb_default/ntree.arb
-@@ -491,7 +491,7 @@
-
- etc_check_gcg %% (%
- fetch "fetch"
-- textedit "textedit"
-+ textedit "editor"
- minlen %i 400
- exclude_0 ""
- exclude_1 ""
---- arbsrc_6779.orig/SH/arb_hindex
-+++ arbsrc_6779/SH/arb_hindex
-@@ -5,4 +5,4 @@
- rm -f $file
- grep TITLE *.hlp | sed -e "s/^\(.\{1,15\}\)TITLE/\1 TITLE/g" -e "s/TITLE/ TITLE/g" >$file
- ls *.ps >>$file
--textedit $file&
-+editor $file&
---- arbsrc_6779.orig/SH/arb_textedit
-+++ arbsrc_6779/SH/arb_textedit
-@@ -4,16 +4,19 @@
- echo '$ARB_TEXTEDIT not set! Searching for an editor..'
- echo ''
-
-- # try to find an editor (order = basic to convinient; last found is used):
--
-- if [ -x "`which edit`" ] ; then ARB_TEXTEDIT=edit ; fi
-- if [ -x "`which vi`" ] ; then ARB_TEXTEDIT=vi ; fi
-- if [ -x "`which emacs`" ] ; then ARB_TEXTEDIT=emacs ; fi
-- if [ -x "`which xemacs`" ] ; then ARB_TEXTEDIT=xemacs ; fi
-- if [ -x "`which textedit`" ] ; then ARB_TEXTEDIT=textedit ; fi
-- if [ -x "`which xedit`" ] ; then ARB_TEXTEDIT=xedit ; fi
-- if [ -x "`which gedit`" ] ; then ARB_TEXTEDIT=gedit ; fi
-- if [ -x "`which kwrite`" ] ; then ARB_TEXTEDIT=kwrite ; fi
-+ # prefer Debian default editor
-+ if [ -x "`which editor`" ] ; then
-+ ARB_TEXTEDIT=editor
-+ else
-+ # try to find an editor (order = basic to convinient; last found is used):
-+ if [ -x "`which edit`" ] ; then ARB_TEXTEDIT=edit ; fi
-+ if [ -x "`which vi`" ] ; then ARB_TEXTEDIT=vi ; fi
-+ if [ -x "`which emacs`" ] ; then ARB_TEXTEDIT=emacs ; fi
-+ if [ -x "`which xemacs`" ] ; then ARB_TEXTEDIT=xemacs ; fi
-+ if [ -x "`which xedit`" ] ; then ARB_TEXTEDIT=xedit ; fi
-+ if [ -x "`which gedit`" ] ; then ARB_TEXTEDIT=gedit ; fi
-+ if [ -x "`which kwrite`" ] ; then ARB_TEXTEDIT=kwrite ; fi
-+ fi
-
- if [ -z "$ARB_TEXTEDIT" ]; then
- echo "Can't guess an editor. Even 'vi' seems to be absent."
---- arbsrc_6779.orig/SH/arb_history
-+++ arbsrc_6779/SH/arb_history
-@@ -1,2 +1,2 @@
- #!/bin/sh
--textedit $ARBHOME/lib/history &
-+editor $ARBHOME/lib/history &
---- arbsrc_6779.orig/SH/arb_index
-+++ arbsrc_6779/SH/arb_index
-@@ -6,4 +6,4 @@
- arb_replace 'TITLE\t=\t\t\tTITLE:UP=\t\t\t\tUP:SUB=\t\t\t\tSUB' index
-
- ls ../ps/*.ps >>index
--textedit index &
-+editor index &
Modified: trunk/packages/arb/trunk/debian/patches/series
===================================================================
--- trunk/packages/arb/trunk/debian/patches/series 2011-11-11 12:38:27 UTC (rev 8532)
+++ trunk/packages/arb/trunk/debian/patches/series 2011-11-11 13:30:24 UTC (rev 8533)
@@ -4,4 +4,3 @@
20_Makefiles
20_tmpfile_issue.patch
tmpfile_CVE-2008-5378.patch
-no_xview_dependency.patch
Modified: trunk/packages/arb/trunk/debian/patches/tmpfile_CVE-2008-5378.patch
===================================================================
--- trunk/packages/arb/trunk/debian/patches/tmpfile_CVE-2008-5378.patch 2011-11-11 12:38:27 UTC (rev 8532)
+++ trunk/packages/arb/trunk/debian/patches/tmpfile_CVE-2008-5378.patch 2011-11-11 13:30:24 UTC (rev 8533)
@@ -1,6 +1,6 @@
This patch fixes tmpfile issues reported in CVE-2008-5378
---- arbsrc_6779.orig/SH/arb_fastdnaml
-+++ arbsrc_6779/SH/arb_fastdnaml
+--- arbsrc_8210.orig/SH/arb_fastdnaml
++++ arbsrc_8210/SH/arb_fastdnaml
@@ -1,9 +1,10 @@
#!/bin/sh
tmp=`mktemp -t arb_fdnaml_XXXXXXXXXX`
@@ -13,8 +13,8 @@
wait
# echo $tmp not deleted for debugging purposes
rm -f $tmp
---- arbsrc_6779.orig/SH/arb_clean
-+++ arbsrc_6779/SH/arb_clean
+--- arbsrc_8210.orig/SH/arb_clean
++++ arbsrc_8210/SH/arb_clean
@@ -9,9 +9,14 @@
pidfiles=/tmp/arb_pids_${USER}_${ARB_PID}
fi
@@ -32,8 +32,8 @@
+ rm -f "$pidfile"
+ fi
+done
---- arbsrc_6779.orig/SH/arb_panic
-+++ arbsrc_6779/SH/arb_panic
+--- arbsrc_8210.orig/SH/arb_panic
++++ arbsrc_8210/SH/arb_panic
@@ -21,7 +21,9 @@
echo " --------------------------------"
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