[med-svn] r5519 - in trunk/packages/arb/trunk/debian: . patches
Andreas Tille
tille at alioth.debian.org
Fri Nov 26 11:04:41 UTC 2010
Author: tille
Date: 2010-11-26 11:04:40 +0000 (Fri, 26 Nov 2010)
New Revision: 5519
Removed:
trunk/packages/arb/trunk/debian/patches/10_gcc_4.4.3.patch
Modified:
trunk/packages/arb/trunk/debian/changelog
trunk/packages/arb/trunk/debian/control
trunk/packages/arb/trunk/debian/patches/30_Makefile_main
trunk/packages/arb/trunk/debian/patches/series
trunk/packages/arb/trunk/debian/patches/tmpfile_CVE-2008-5378.patch
Log:
Start working on new upstream release of arb, however, it does not build
Modified: trunk/packages/arb/trunk/debian/changelog
===================================================================
--- trunk/packages/arb/trunk/debian/changelog 2010-11-26 01:18:25 UTC (rev 5518)
+++ trunk/packages/arb/trunk/debian/changelog 2010-11-26 11:04:40 UTC (rev 5519)
@@ -1,3 +1,10 @@
+arb (5.2-1) UNRELEASED; urgency=low
+
+ * New upstream version
+ * Standards-Version: 3.9.1 (no changes needed)
+
+ -- Andreas Tille <tille at debian.org> Fri, 26 Nov 2010 10:54:45 +0100
+
arb (5.1-1) unstable; urgency=low
[ Andreas Tille ]
Modified: trunk/packages/arb/trunk/debian/control
===================================================================
--- trunk/packages/arb/trunk/debian/control 2010-11-26 01:18:25 UTC (rev 5518)
+++ trunk/packages/arb/trunk/debian/control 2010-11-26 11:04:40 UTC (rev 5519)
@@ -8,7 +8,7 @@
libxml2-utils, lynx, sablotron, libtiff4-dev, libxaw7-dev, openjdk-6-jdk | default-jdk,
freeglut3-dev | libglu-dev, libglew1.5-dev, libpng12-dev, x11proto-print-dev,
libxpm-dev, libxp-dev, libglw1-mesa-dev, perl-doc, chrpath, xutils-dev, libmotif-dev
-Standards-Version: 3.8.4
+Standards-Version: 3.9.1
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/
Deleted: trunk/packages/arb/trunk/debian/patches/10_gcc_4.4.3.patch
===================================================================
--- trunk/packages/arb/trunk/debian/patches/10_gcc_4.4.3.patch 2010-11-26 01:18:25 UTC (rev 5518)
+++ trunk/packages/arb/trunk/debian/patches/10_gcc_4.4.3.patch 2010-11-26 11:04:40 UTC (rev 5519)
@@ -1,130 +0,0 @@
---- arbsrc_6213.orig/SL/FILE_BUFFER/FileBuffer.cxx
-+++ arbsrc_6213/SL/FILE_BUFFER/FileBuffer.cxx
-@@ -13,6 +13,7 @@
- #include <cstdlib>
- #include <cstring>
- #include <errno.h>
-+#include <cstdio>
-
- using namespace std;
-
---- arbsrc_6213.orig/SL/FAST_ALIGNER/ClustalV.cxx
-+++ arbsrc_6213/SL/FAST_ALIGNER/ClustalV.cxx
-@@ -286,8 +286,8 @@
- // 2 for improbably mutations
- // -1 if one char is illegal
- {
-- char *p1 = strchr(nucleic_acid_order, c1);
-- char *p2 = strchr(nucleic_acid_order, c2);
-+ char *p1 = (char *)strchr(nucleic_acid_order, c1);
-+ char *p2 = (char *)strchr(nucleic_acid_order, c2);
-
- awtc_assert(c1);
- awtc_assert(c2);
---- arbsrc_6213.orig/AWT/AWT_file_selection.cxx
-+++ arbsrc_6213/AWT/AWT_file_selection.cxx
-@@ -142,7 +142,7 @@
- }
-
- char *AWT_extract_directory(const char *path) {
-- char *lslash = strrchr(path, '/');
-+ char *lslash = (char *)strrchr(path, '/');
- if (!lslash) return 0;
-
- char *result = strdup(path);
---- arbsrc_6213.orig/AWTI/AWTI_import.cxx
-+++ arbsrc_6213/AWTI/AWTI_import.cxx
-@@ -19,7 +19,7 @@
- #define MAX_COMMENT_LINES 2000
-
- inline const char *name_only(const char *fullpath) {
-- char *lslash = strrchr(fullpath, '/');
-+ char *lslash = (char *)strrchr(fullpath, '/');
- return lslash ? lslash+1 : fullpath;
- }
-
---- arbsrc_6213.orig/NTREE/NT_edconf.cxx
-+++ arbsrc_6213/NTREE/NT_edconf.cxx
-@@ -249,7 +249,7 @@
- static long nt_build_sai_string_by_hash(const char *key, long val, void *cd_sai_builder) {
- struct SAI_string_builder *sai_builder = (struct SAI_string_builder*)cd_sai_builder;
-
-- char *sep = strchr(key,1);
-+ char *sep = (char *)strchr(key,1);
- if (!sep) return val; // what's wrong
-
- struct GBS_strstruct *sai_middle = sai_builder->sai_middle;
---- arbsrc_6213.orig/PROBE_DESIGN/probe_design.cxx
-+++ arbsrc_6213/PROBE_DESIGN/probe_design.cxx
-@@ -1848,7 +1848,7 @@
- }
-
- if (!error) { // set pt-server database file to same permissions as pts directory
-- char *dir = strrchr(file,'/');
-+ char *dir = (char *)strrchr(file,'/');
- if (dir) {
- *dir = 0;
- long modi = GB_mode_of_file(file);
---- arbsrc_6213.orig/PROBE_DESIGN/SaiProbeVisualization.cxx
-+++ arbsrc_6213/PROBE_DESIGN/SaiProbeVisualization.cxx
-@@ -526,7 +526,7 @@
-
- if (!tok_suffix) {
- // handle special case where no suffix exists
-- char *end = strchr(probeRegion, 0);
-+ char *end = (char *)strchr(probeRegion, 0);
- if (end>probeRegion && end[-1] == '-') tok_suffix = "";
- }
-
---- arbsrc_6213.orig/HELP_SOURCE/arb_help2xml.cxx
-+++ arbsrc_6213/HELP_SOURCE/arb_help2xml.cxx
-@@ -302,7 +302,7 @@
- // returns NULL if no keyword was found
- // otherwise returns position behind keyword and sets value of 'keyword'
-
-- char *space = strchr(line, ' ');
-+ char *space = (char *)strchr(line, ' ');
- if (space && space>line) {
- keyword = string(line, 0, space-line);
- return space;
---- arbsrc_6213.orig/PROBE/PT_prefixtree.cxx
-+++ arbsrc_6213/PROBE/PT_prefixtree.cxx
-@@ -238,7 +238,7 @@
- int size = p - buffer;
- p = (char *)PTM_get_mem(size);
- memcpy(p,buffer,size);
-- PT_WRITE_PNTR(data,p);
-+ PT_WRITE_PNTR(data,(long)p);
- psg.stat.cut_offs ++;
- return NULL;
- }
-@@ -318,7 +318,7 @@
- gfather = (POS_TREE *)j;
- if (gfather){
- PT_change_father(gfather, father, new_elemfather);
-- PT_WRITE_PNTR(&new_elemfather->data,gfather);
-+ PT_WRITE_PNTR(&new_elemfather->data,(long)gfather);
- }
- sbase = dbase = sizeof(PT_PNTR);
- base2 = 1 << base;
-@@ -328,16 +328,16 @@
- son = (POS_TREE *)j;
- int sontype = PT_GET_TYPE(son);
- if (sontype != PT_NT_SAVED) {
-- PT_WRITE_PNTR((char *) &son->data, new_elemfather);
-+ PT_WRITE_PNTR((char *) &son->data, (long)new_elemfather);
- }
-- PT_WRITE_PNTR(((char *) &new_elemfather->data) + dbase, son);
-+ PT_WRITE_PNTR(((char *) &new_elemfather->data) + dbase, (long)son);
- sbase += sizeof(PT_PNTR);
- dbase += sizeof(PT_PNTR);
- continue;
- }
- if (i & base2) {
-- PT_WRITE_PNTR(((char *) &new_elemfather->data) + dbase, node);
-- PT_WRITE_PNTR((&node->data), (PT_PNTR)new_elemfather);
-+ PT_WRITE_PNTR(((char *) &new_elemfather->data) + dbase, (long)node);
-+ PT_WRITE_PNTR((&node->data), (long)new_elemfather);
- dbase += sizeof(PT_PNTR);
- }
- }
Modified: trunk/packages/arb/trunk/debian/patches/30_Makefile_main
===================================================================
--- trunk/packages/arb/trunk/debian/patches/30_Makefile_main 2010-11-26 01:18:25 UTC (rev 5518)
+++ trunk/packages/arb/trunk/debian/patches/30_Makefile_main 2010-11-26 11:04:40 UTC (rev 5519)
@@ -1,16 +1,15 @@
---- arbsrc_6213.orig/Makefile
-+++ arbsrc_6213/Makefile
-@@ -57,7 +57,8 @@
- 4.0.0 4.0.1 4.0.2 4.0.3 \
+--- arbsrc_6779.orig/Makefile
++++ arbsrc_6779/Makefile
+@@ -58,7 +58,7 @@
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 \
-+ 4.3 4.3.1 4.3.2 4.3.3 4.3.4 \
-+ 4.4.3 \
+ 4.3 4.3.1 4.3.2 4.3.3 \
+- 4.4.1
++ 4.4.1 4.4.3 4.4.5
ALLOWED_GCC_VERSIONS=$(ALLOWED_GCC_3xx_VERSIONS) $(ALLOWED_GCC_4xx_VERSIONS)
-@@ -85,7 +86,8 @@
+@@ -86,7 +86,8 @@
endif
shared_cflags :=# flags for shared lib compilation
@@ -20,7 +19,7 @@
extended_warnings :=# warning flags for C and C++-compiler
extended_cpp_warnings :=# warning flags for C++-compiler only
-@@ -198,7 +200,11 @@
+@@ -199,7 +200,11 @@
#---------------------- X11 location
Modified: trunk/packages/arb/trunk/debian/patches/series
===================================================================
--- trunk/packages/arb/trunk/debian/patches/series 2010-11-26 01:18:25 UTC (rev 5518)
+++ trunk/packages/arb/trunk/debian/patches/series 2010-11-26 11:04:40 UTC (rev 5519)
@@ -4,4 +4,3 @@
20_Makefiles
20_tmpfile_issue.patch
tmpfile_CVE-2008-5378.patch
-10_gcc_4.4.3.patch
Modified: trunk/packages/arb/trunk/debian/patches/tmpfile_CVE-2008-5378.patch
===================================================================
--- trunk/packages/arb/trunk/debian/patches/tmpfile_CVE-2008-5378.patch 2010-11-26 01:18:25 UTC (rev 5518)
+++ trunk/packages/arb/trunk/debian/patches/tmpfile_CVE-2008-5378.patch 2010-11-26 11:04:40 UTC (rev 5519)
@@ -1,6 +1,6 @@
This patch fixes tmpfile issues reported in CVE-2008-5378
---- arbsrc_6182.orig/SH/arb_fastdnaml
-+++ arbsrc_6182/SH/arb_fastdnaml
+--- arbsrc_6779.orig/SH/arb_fastdnaml
++++ arbsrc_6779/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 $tmp
---- arbsrc_6182.orig/SH/arb_clean
-+++ arbsrc_6182/SH/arb_clean
+--- arbsrc_6779.orig/SH/arb_clean
++++ arbsrc_6779/SH/arb_clean
@@ -9,9 +9,14 @@
pidfiles=/tmp/arb_pids_${USER}_${ARB_PID}
fi
@@ -32,8 +32,8 @@
+ rm -f "$pidfile"
+ fi
+done
---- arbsrc_6182.orig/SH/arb_panic
-+++ arbsrc_6182/SH/arb_panic
+--- arbsrc_6779.orig/SH/arb_panic
++++ arbsrc_6779/SH/arb_panic
@@ -21,7 +21,9 @@
echo " --------------------------------"
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