[med-svn] r11913 - in trunk/packages/arb/trunk/debian: . patches po

Andreas Tille tille at alioth.debian.org
Fri Jul 27 12:51:29 UTC 2012 

Author: tille
Date: 2012-07-27 12:51:29 +0000 (Fri, 27 Jul 2012)
New Revision: 11913

Added:
   trunk/packages/arb/trunk/debian/patches/gcc-4.7.patch
   trunk/packages/arb/trunk/debian/po/nl.po
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:
Mass changes to fix all open bugs and hopefully finally also build properly with gcc-4.7


Modified: trunk/packages/arb/trunk/debian/changelog
===================================================================
--- trunk/packages/arb/trunk/debian/changelog	2012-07-27 07:18:28 UTC (rev 11912)
+++ trunk/packages/arb/trunk/debian/changelog	2012-07-27 12:51:29 UTC (rev 11913)
@@ -1,8 +1,18 @@
 arb (5.3-4) UNRELEASED; urgency=low
 
   * debian/upstream: Add citations
+  * debian/control:
+     - Build-Depends: libpng-dev instead of libpng12-dev
+       Closes: #662270
+     - Standards-Version: 3.9.3 (no changes needed)
+  * debian/po/nl.po: Add Dutch translation of debconf templates
+    Thanks for the translation to Jeroen Schot <schot at A-Eskwadraat.nl>
+    Closes: #654763
+  * debian/patches/30_Makefile_main: Enable gcc-4.7 as well
+    Closes: #682404
+  * debian/patches/gcc-4.7.patch: Fix gcc-4.7 build issue
 
- -- Andreas Tille <tille at debian.org>  Mon, 21 May 2012 21:49:47 +0200
+ -- Andreas Tille <tille at debian.org>  Thu, 26 Jul 2012 12:15:21 +0200
 
 arb (5.3-3) unstable; urgency=low
 

Modified: trunk/packages/arb/trunk/debian/control
===================================================================
--- trunk/packages/arb/trunk/debian/control	2012-07-27 07:18:28 UTC (rev 11912)
+++ trunk/packages/arb/trunk/debian/control	2012-07-27 12:51:29 UTC (rev 11913)
@@ -1,6 +1,6 @@
 Source: arb
 Section: non-free/science
-Priority: extra
+Priority: optional
 Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
 DM-Upload-Allowed: yes
 Uploaders: Andreas Tille <tille at debian.org>
@@ -12,7 +12,7 @@
                libglew1.5-dev,
                libglw1-mesa-dev,
                libmotif-dev,
-               libpng12-dev,
+               libpng-dev,
                libtiff4-dev,
                libxaw7-dev,
                libxml2-utils,
@@ -23,7 +23,7 @@
                perl-doc,
                xsltproc,
                xutils-dev
-Standards-Version: 3.9.2
+Standards-Version: 3.9.3
 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	2012-07-27 07:18:28 UTC (rev 11912)
+++ trunk/packages/arb/trunk/debian/patches/20_Makefiles	2012-07-27 12:51:29 UTC (rev 11913)
@@ -1,5 +1,5 @@
---- arbsrc_8210.orig/ARBDB2/Makefile
-+++ arbsrc_8210/ARBDB2/Makefile
+--- arb-5.3.orig/ARBDB2/Makefile
++++ arb-5.3/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_8210.orig/ARBDBS/Makefile
-+++ arbsrc_8210/ARBDBS/Makefile
+--- arb-5.3.orig/ARBDBS/Makefile
++++ arb-5.3/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_8210.orig/NAMES_COM/Makefile
-+++ arbsrc_8210/NAMES_COM/Makefile
+--- arb-5.3.orig/NAMES_COM/Makefile
++++ arb-5.3/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_8210.orig/PROBE_COM/Makefile
-+++ arbsrc_8210/PROBE_COM/Makefile
+--- arb-5.3.orig/PROBE_COM/Makefile
++++ arb-5.3/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_8210.orig/GENOM_IMPORT/Makefile
-+++ arbsrc_8210/GENOM_IMPORT/Makefile
+--- arb-5.3.orig/GENOM_IMPORT/Makefile
++++ arb-5.3/GENOM_IMPORT/Makefile
 @@ -30,12 +30,12 @@
  	$(ACC) $(cflags) -c $< $(CPPINCLUDES)
  
@@ -89,8 +89,8 @@
  
  #.IGNORE:
  #	clean
---- arbsrc_8210.orig/HELP_SOURCE/Makefile
-+++ arbsrc_8210/HELP_SOURCE/Makefile
+--- arb-5.3.orig/HELP_SOURCE/Makefile
++++ arb-5.3/HELP_SOURCE/Makefile
 @@ -151,7 +151,7 @@
  # --------------------------------------------------------------------------------
  
@@ -100,8 +100,8 @@
  
  date :
  	$(MAKE) date.xsl.tmp
---- arbsrc_8210.orig/GDEHELP/Makefile
-+++ arbsrc_8210/GDEHELP/Makefile
+--- arb-5.3.orig/GDEHELP/Makefile
++++ arb-5.3/GDEHELP/Makefile
 @@ -37,10 +37,18 @@
  	tar cvf - MENUS ARB_GDEmenus* |gzip >`date '+arbgdemnus_%d_%m_%y.tar.gz'`
  
@@ -127,8 +127,8 @@
 +	fi
  
 +	rm -f $(HELPFILELIST)
---- arbsrc_8210.orig/GDEHELP/Makefile.helpfiles
-+++ arbsrc_8210/GDEHELP/Makefile.helpfiles
+--- arb-5.3.orig/GDEHELP/Makefile.helpfiles
++++ arb-5.3/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	2012-07-27 07:18:28 UTC (rev 11912)
+++ trunk/packages/arb/trunk/debian/patches/20_config.makefiles	2012-07-27 12:51:29 UTC (rev 11913)
@@ -1,5 +1,5 @@
 --- /dev/null
-+++ arbsrc_8210/config.makefile
++++ arb-5.3/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	2012-07-27 07:18:28 UTC (rev 11912)
+++ trunk/packages/arb/trunk/debian/patches/20_tmpfile_issue.patch	2012-07-27 12:51:29 UTC (rev 11913)
@@ -1,5 +1,5 @@
---- arbsrc_8210.orig/SH/arb_fastdnaml
-+++ arbsrc_8210/SH/arb_fastdnaml
+--- arb-5.3.orig/SH/arb_fastdnaml
++++ arb-5.3/SH/arb_fastdnaml
 @@ -1,5 +1,5 @@
  #!/bin/sh
 -tmp=/tmp/arb_fdnaml_${USER}_$$
@@ -7,8 +7,8 @@
  mv infile $tmp
  nice -19 $1 < $tmp &
  sig=$!
---- arbsrc_8210.orig/SH/dszmconnect.pl
-+++ arbsrc_8210/SH/dszmconnect.pl
+--- arb-5.3.orig/SH/dszmconnect.pl
++++ arb-5.3/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	2012-07-27 07:18:28 UTC (rev 11912)
+++ trunk/packages/arb/trunk/debian/patches/30_Makefile_main	2012-07-27 12:51:29 UTC (rev 11913)
@@ -1,16 +1,17 @@
---- arbsrc_8210.orig/Makefile
-+++ arbsrc_8210/Makefile
-@@ -58,7 +58,8 @@
+--- 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
++	4.6 \
++	4.7
  
  ALLOWED_GCC_VERSIONS=$(ALLOWED_GCC_3xx_VERSIONS) $(ALLOWED_GCC_4xx_VERSIONS)
  
-@@ -95,7 +96,12 @@
+@@ -95,7 +97,12 @@
  	dflags := -DNDEBUG# defines
  	cflags := -O4# compiler flags (C and C++)
   ifndef DARWIN
@@ -24,7 +25,7 @@
   endif
  endif
  
-@@ -199,7 +205,11 @@
+@@ -199,7 +206,11 @@
  
  #---------------------- X11 location
  
@@ -37,7 +38,7 @@
  XINCLUDES:=-I$(XHOME)/include
  
  ifdef DARWIN
-@@ -304,7 +314,7 @@
+@@ -304,7 +315,7 @@
  
  lflags += $(ldynamic)
  

Modified: trunk/packages/arb/trunk/debian/patches/30_phyml
===================================================================
--- trunk/packages/arb/trunk/debian/patches/30_phyml	2012-07-27 07:18:28 UTC (rev 11912)
+++ trunk/packages/arb/trunk/debian/patches/30_phyml	2012-07-27 12:51:29 UTC (rev 11913)
@@ -1,5 +1,5 @@
---- arbsrc_8210.orig/GDE/PHYML/Makefile
-+++ arbsrc_8210/GDE/PHYML/Makefile
+--- arb-5.3.orig/GDE/PHYML/Makefile
++++ arb-5.3/GDE/PHYML/Makefile
 @@ -13,7 +13,8 @@
  # original compilation
  

Added: trunk/packages/arb/trunk/debian/patches/gcc-4.7.patch
===================================================================
--- trunk/packages/arb/trunk/debian/patches/gcc-4.7.patch	                        (rev 0)
+++ trunk/packages/arb/trunk/debian/patches/gcc-4.7.patch	2012-07-27 12:51:29 UTC (rev 11913)
@@ -0,0 +1,14 @@
+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	2012-07-27 07:18:28 UTC (rev 11912)
+++ trunk/packages/arb/trunk/debian/patches/series	2012-07-27 12:51:29 UTC (rev 11913)
@@ -4,3 +4,4 @@
 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	2012-07-27 07:18:28 UTC (rev 11912)
+++ trunk/packages/arb/trunk/debian/patches/tmpfile_CVE-2008-5378.patch	2012-07-27 12:51:29 UTC (rev 11913)
@@ -1,6 +1,6 @@
 This patch fixes tmpfile issues reported in CVE-2008-5378
---- arbsrc_8210.orig/SH/arb_fastdnaml
-+++ arbsrc_8210/SH/arb_fastdnaml
+--- arb-5.3.orig/SH/arb_fastdnaml
++++ arb-5.3/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 $tmp
---- arbsrc_8210.orig/SH/arb_clean
-+++ arbsrc_8210/SH/arb_clean
+--- arb-5.3.orig/SH/arb_clean
++++ arb-5.3/SH/arb_clean
 @@ -9,9 +9,14 @@
  	pidfiles=/tmp/arb_pids_${USER}_${ARB_PID}
  fi
@@ -32,8 +32,8 @@
 +		rm -f "$pidfile"
 +	fi
 +done
---- arbsrc_8210.orig/SH/arb_panic
-+++ arbsrc_8210/SH/arb_panic
+--- arb-5.3.orig/SH/arb_panic
++++ arb-5.3/SH/arb_panic
 @@ -21,7 +21,9 @@
  echo "          --------------------------------"
  

Added: trunk/packages/arb/trunk/debian/po/nl.po
===================================================================
--- trunk/packages/arb/trunk/debian/po/nl.po	                        (rev 0)
+++ trunk/packages/arb/trunk/debian/po/nl.po	2012-07-27 12:51:29 UTC (rev 11913)
@@ -0,0 +1,33 @@
+# Dutch translation of arb debconf templates.
+# Copyright (C) 2012 THE PACKAGE'S COPYRIGHT HOLDER
+# This file is distributed under the same license as the arb package.
+# Jeroen Schot <schot at a-eskwadraat.nl>, 2012.
+#
+msgid ""
+msgstr ""
+"Project-Id-Version: arb 5.3-2\n"
+"Report-Msgid-Bugs-To: arb at packages.debian.org\n"
+"POT-Creation-Date: 2009-03-20 08:21+0100\n"
+"PO-Revision-Date: 2012-01-05 16:31+0100\n"
+"Last-Translator: Jeroen Schot <schot at a-eskwadraat.nl>\n"
+"Language-Team: Debian l10n Dutch <debian-l10n-dutch at lists.debian.org>\n"
+"Language: nl\n"
+"MIME-Version: 1.0\n"
+"Content-Type: text/plain; charset=UTF-8\n"
+"Content-Transfer-Encoding: 8bit\n"
+
+#. Type: multiselect
+#. Description
+#: ../arb-common.templates:1001
+msgid "Arb users:"
+msgstr "Gebruikers van arb:"
+
+#. Type: multiselect
+#. Description
+#: ../arb-common.templates:1001
+msgid ""
+"Please choose, among the list of all unprivileged users of the system, those "
+"who will be allowed running ${pkg}."
+msgstr ""
+"Geef in lijst van alle normale gebruikers van het systeem aan welke ${pkg} "
+"mogen uitvoeren."

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