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