[med-svn] r3917 - in trunk/packages/arb/trunk/debian: . patches
Andreas Tille
tille at alioth.debian.org
Mon Sep 7 12:15:08 UTC 2009
Author: tille
Date: 2009-09-07 12:15:07 +0000 (Mon, 07 Sep 2009)
New Revision: 3917
Removed:
trunk/packages/arb/trunk/debian/patches/20_64bit_support_-fPIC.patch
Modified:
trunk/packages/arb/trunk/debian/changelog
trunk/packages/arb/trunk/debian/patches/series
trunk/packages/arb/trunk/debian/patches/tmpfile_CVE-2008-5378.patch
Log:
Overworked old patches to make sure all apply correctly
Modified: trunk/packages/arb/trunk/debian/changelog
===================================================================
--- trunk/packages/arb/trunk/debian/changelog 2009-09-07 12:04:58 UTC (rev 3916)
+++ trunk/packages/arb/trunk/debian/changelog 2009-09-07 12:15:07 UTC (rev 3917)
@@ -2,16 +2,15 @@
[ Andreas Tille ]
* New upstream version
- * Package arb-doc in non-free/doc
- * patches/20_64bit_support_-fPIC.patch: Add -fPIC option where it
- seems to be missing.
Closes: #522021
+ * Package arb-doc in non-free/doc
* Standards-Version: 3.8.3 (Added README.source)
* Build-Depends: dpkg-dev (>= 1.15.4) to make use of
`dpkg-architecture -qDEB_BUILD_ARCH_BITS` in Makefile
- * Removed patches which were applied upstream
- - debian/patches/ARB_release200712_gcc4.3.1.patch
- - debian/patches/20_replace_rxp_by_xmllint.patch
+ * Removed / changed patches which were applied upstream
+ - debian/patches/ARB_release200712_gcc4.3.1.patch removed
+ - debian/patches/20_replace_rxp_by_xmllint.patch removed
+ - debian/patches/tmpfile_CVE-2008-5378.patch removed applied part
[ David Paleino ]
* Removed myself from Uploaders
Deleted: trunk/packages/arb/trunk/debian/patches/20_64bit_support_-fPIC.patch
===================================================================
--- trunk/packages/arb/trunk/debian/patches/20_64bit_support_-fPIC.patch 2009-09-07 12:04:58 UTC (rev 3916)
+++ trunk/packages/arb/trunk/debian/patches/20_64bit_support_-fPIC.patch 2009-09-07 12:15:07 UTC (rev 3917)
@@ -1,13 +0,0 @@
-This patch solves an issue when building arb on 64 bit machines. In some
-Makefiles the -fPIC option was just not included.
---- arb-0.0.20071207.1.orig/Makefile
-+++ arb-0.0.20071207.1/Makefile
-@@ -207,7 +207,7 @@
- f77_flags = $(fflags) -W -N9 -e
- F77LIB = -lU77
-
-- ARCPPLIB = $(GPP) -Wall -shared $(LINUX_SPECIALS) -o
-+ ARCPPLIB = $(GPP) -Wall -shared $(LINUX_SPECIALS) -fPIC -o
- ARLIB = $(GCC) -Wall -shared $(LINUX_SPECIALS) -o
- GMAKE = make -j 3 -r
- SYSLIBS = -lm
Modified: trunk/packages/arb/trunk/debian/patches/series
===================================================================
--- trunk/packages/arb/trunk/debian/patches/series 2009-09-07 12:04:58 UTC (rev 3916)
+++ trunk/packages/arb/trunk/debian/patches/series 2009-09-07 12:15:07 UTC (rev 3917)
@@ -4,4 +4,3 @@
20_Makefiles
20_tmpfile_issue.patch
tmpfile_CVE-2008-5378.patch
-20_64bit_support_-fPIC.patch
Modified: trunk/packages/arb/trunk/debian/patches/tmpfile_CVE-2008-5378.patch
===================================================================
--- trunk/packages/arb/trunk/debian/patches/tmpfile_CVE-2008-5378.patch 2009-09-07 12:04:58 UTC (rev 3916)
+++ trunk/packages/arb/trunk/debian/patches/tmpfile_CVE-2008-5378.patch 2009-09-07 12:15:07 UTC (rev 3917)
@@ -1,6 +1,6 @@
This patch fixes tmpfile issues reported in CVE-2008-5378
---- arb-0.0.20071207.1.orig/SH/arb_fastdnaml
-+++ arb-0.0.20071207.1/SH/arb_fastdnaml
+--- arbsrc_6182.orig/SH/arb_fastdnaml
++++ arbsrc_6182/SH/arb_fastdnaml
@@ -1,9 +1,10 @@
#!/bin/sh
tmp=`mktemp -t arb_fdnaml_XXXXXXXXXX`
@@ -13,71 +13,8 @@
wait
# echo $tmp not deleted for debugging purposes
rm -f $tmp
---- arb-0.0.20071207.1.orig/ARBDB/adcomm.c
-+++ arb-0.0.20071207.1/ARBDB/adcomm.c
-@@ -126,19 +126,30 @@
- ***************************************************************************************/
- GBCONTAINER *gbcms_gb_main;
- void *gbcms_sighup(void){
-- char buffer[1024];
-+ char buffer[1024], lsbuffer[1024];
- char *fname;
- GB_ERROR error;
- int translevel;
- GB_MAIN_TYPE *Main;
-+ FILE *fp;
-
- {
- const char *ap = GB_getenv("ARB_PID");
- if (!ap ) ap = "";
-- sprintf(buffer,"/tmp/arb_panic_%s_%s",GB_getenvUSER(),ap);
-+ sprintf(lsbuffer,"ls /tmp/arb_panic_%s_%s_*",GB_getenvUSER(),ap);
- }
-+ /* TODO:
-+ * We have to open an existing file so we have to use scandir(2) for any file *
-+ * which matches the template instead inventing a new name using mktemp! */
- fprintf(stderr,"**** ARB DATABASE SERVER GOT a HANGUP SIGNAL ****\n");
- fprintf(stderr,"- Looking for file '%s'\n",buffer);
-+
-+ fp = popen(lsbuffer, "r");
-+ if ( fscanf(fp, "%s", buffer) == EOF ) {
-+ fprintf(stderr,"- File matching '%s' not found - exiting!\n",lsbuffer);
-+ exit(EXIT_FAILURE);
-+ }
-+
- fname = GB_read_file(buffer);
- if (!fname) {
- fprintf(stderr,"- File '%s' not found - exiting!\n",buffer);
-@@ -2066,7 +2077,8 @@
- {
- static long lastpid = 0;
- long pid = getpid();
-- FILE *pidfile;
-+ char buffer[1000];
-+ int fh;
- char filename[1000];
- const char *user = GB_getenvUSER();
- const char *arb_pid = GB_getenv("ARB_PID");
-@@ -2076,10 +2088,12 @@
- if (lastpid == pid) return 0;
- if (lastpid == -25) return 0; /* never install */
- lastpid = pid;
-- sprintf(filename,"/tmp/arb_pids_%s_%s",user,arb_pid);
-- pidfile = fopen(filename,"a");
-- if (!pidfile) return GB_export_error("Cannot open pid file '%s'",filename);
-- fprintf(pidfile,"%li ",pid);
-- fclose(pidfile);
-+ sprintf(filename,"/tmp/arb_pids_%s_%s_XXXXXX",user,arb_pid);
-+ fh = mkstemp(filename);
-+ /* pidfile = fopen(filename,"a"); */
-+ if (!fh) return GB_export_error("Cannot open pid file '%s'",filename);
-+ snprintf(buffer,256,"%li ",pid);
-+ write(fh, buffer, sizeof(buffer));
-+ close(fh);
- return 0;
- }
---- arb-0.0.20071207.1.orig/SH/arb_clean
-+++ arb-0.0.20071207.1/SH/arb_clean
+--- arbsrc_6182.orig/SH/arb_clean
++++ arbsrc_6182/SH/arb_clean
@@ -9,9 +9,14 @@
pidfiles=/tmp/arb_pids_${USER}_${ARB_PID}
fi
@@ -95,33 +32,34 @@
+ rm -f "$pidfile"
+ fi
+done
---- arb-0.0.20071207.1.orig/SH/arb_panic
-+++ arb-0.0.20071207.1/SH/arb_panic
-@@ -22,26 +22,30 @@
- echo " --------------------------------"
+--- arbsrc_6182.orig/SH/arb_panic
++++ arbsrc_6182/SH/arb_panic
+@@ -21,7 +21,9 @@
+ echo " --------------------------------"
for i in $chooser ; do
-- /bin/echo " - >" `ls $i` "<";
-+ if [ ! -L "$i" ] ; then
-+ /bin/echo " - >" `ls $i` "<";
-+ fi
+- /bin/echo " - >" `ls $i` "<";
++ if [ ! -L "$i" ] ; then
++ /bin/echo " - >" `ls $i` "<";
++ fi
done
- echo " --------------------------------"
+ echo " --------------------------------"
+@@ -29,19 +31,21 @@
echo "Please choose one line and enter the rightmost number"
read ARB_PID
-if [ ! -f /tmp/arb_pids_${USER}_${ARB_PID} ]; then
-- err "Incorrect Choice"
+- err "Incorrect Choice"
-fi
+for arbpid in /tmp/arb_pids_${USER}_${ARB_PID}* ; do
-+ if [ ! -f "$arbpid" ]; then
-+ err "Incorrect Choice"
-+ fi
++ if [ ! -f "$arbpid" ]; then
++ err "Incorrect Choice"
++ fi
+done
seperator
- echo "Please enter file name (full path):"
+ echo "Please enter full path (to save DB):"
read FILE
-panicfile="/tmp/arb_panic_${USER}_${ARB_PID}"
@@ -131,6 +69,6 @@
ok=false
-for i in `cat /tmp/arb_pids_${USER}_${ARB_PID}`; do
+for i in `cat /tmp/arb_pids_${USER}_${ARB_PID}*`; do
- if kill -1 $i 2>/dev/null; then
- ok=true
- break
+ echo "[Sending SIGHUP to pid $i]"
+ if kill -HUP $i 2>/dev/null; then
+ ok=true
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