[med-svn] r20865 - in trunk/packages/t-coffee/trunk/debian: . patches

[Andreas Tille]

Author: tille
Date: 2015-12-22 16:41:15 +0000 (Tue, 22 Dec 2015)
New Revision: 20865

Added:
   trunk/packages/t-coffee/trunk/debian/patches/set_proper_dir_permissions.patch
Removed:
   trunk/packages/t-coffee/trunk/debian/README.source
Modified:
   trunk/packages/t-coffee/trunk/debian/changelog
   trunk/packages/t-coffee/trunk/debian/patches/series
Log:
Set proper dir permissions, clean up packaging, notice that Mayhem issue is not finally fixed :-(


Deleted: trunk/packages/t-coffee/trunk/debian/README.source
===================================================================
--- trunk/packages/t-coffee/trunk/debian/README.source	2015-12-22 15:51:41 UTC (rev 20864)
+++ trunk/packages/t-coffee/trunk/debian/README.source	2015-12-22 16:41:15 UTC (rev 20865)
@@ -1,4 +0,0 @@
-This packages uses the quilt patch system. Please read
-/usr/share/doc/quilt/README.source for more information.
-
- -- Andreas Tille <tille at debian.org>  Fri, 25 Sep 2009 14:41:41 +0200

Modified: trunk/packages/t-coffee/trunk/debian/changelog
===================================================================
--- trunk/packages/t-coffee/trunk/debian/changelog	2015-12-22 15:51:41 UTC (rev 20864)
+++ trunk/packages/t-coffee/trunk/debian/changelog	2015-12-22 16:41:15 UTC (rev 20865)
@@ -6,10 +6,15 @@
   * compress changelog with '-n' option
   * propagate hardening options
   * Do not build unused TMalign
-  * Fix Mayhem issue
-    Closes: #716373
+  * When creating subdirectories in $HOME do not make these world
+    writable but keep users umask
+    Closes: #751579
+  * Drop redundant debian/README.source
+  * Package builds for all architectures so this
+    Closes: #631249
+    (feel free to reopen if tests might keep on failing on armel)
 
- -- Andreas Tille <tille at debian.org>  Mon, 21 Dec 2015 21:30:36 +0100
+ -- Andreas Tille <tille at debian.org>  Tue, 22 Dec 2015 17:16:01 +0100
 
 t-coffee (11.00.8cbe486-1) unstable; urgency=low
 

Modified: trunk/packages/t-coffee/trunk/debian/patches/series
===================================================================
--- trunk/packages/t-coffee/trunk/debian/patches/series	2015-12-22 15:51:41 UTC (rev 20864)
+++ trunk/packages/t-coffee/trunk/debian/patches/series	2015-12-22 16:41:15 UTC (rev 20865)
@@ -1,2 +1,6 @@
 probconsrna.patch
 ncbi-blast++_has_dropped_pl_extension.patch
+use_debian_packaged_TMalign.patch
+hardening.patch
+set_proper_dir_permissions.patch
+mayhem.patch

Added: trunk/packages/t-coffee/trunk/debian/patches/set_proper_dir_permissions.patch
===================================================================
--- trunk/packages/t-coffee/trunk/debian/patches/set_proper_dir_permissions.patch	                        (rev 0)
+++ trunk/packages/t-coffee/trunk/debian/patches/set_proper_dir_permissions.patch	2015-12-22 16:41:15 UTC (rev 20865)
@@ -0,0 +1,35 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Mon, 21 Dec 2015 21:30:36 +0100
+Bug-Debian: https://bugs.debian.org/751579
+Description: When creating subdirectories in $HOME do not
+ make these world writable but keep users umask
+
+--- a/t_coffee_source/util_lib/util.c
++++ b/t_coffee_source/util_lib/util.c
+@@ -7714,6 +7714,10 @@ int my_mkdir ( char *dir_in)
+   int a, buf;
+   char *dir;
+ 
++  static char *home = getenv ("HOME");
++  static mode_t oldmask = umask(0);
++  int change_umask = 0;
++  if (strncmp (dir_in, home, strlen(home))==0) change_umask = 1;
+ 
+   dir=(char*)vcalloc ( strlen (dir_in)+strlen (get_home_4_tcoffee())+100, sizeof (char));
+   sprintf ( dir, "%s", dir_in);
+@@ -7733,10 +7737,11 @@ int my_mkdir ( char *dir_in)
+ 
+ 	  if (access(dir, F_OK)==-1)
+ 	    {
+-		  mode_t oldmask = umask(0);
+-	      mkdir (dir, S_IRWXU | S_IRWXG | S_IRWXO);
+-	      umask(oldmask);
+-
++	      if ( change_umask == 1 ) mkdir (dir, 0777-oldmask);
++	      else {
++	        mkdir (dir, S_IRWXU | S_IRWXG | S_IRWXO);
++	        umask(oldmask);
++	      }
+ 	      if ( access (dir, F_OK)==-1)
+ 		{
+ 		  myexit(fprintf_error ( stderr, "\nERROR: Could Not Create Directory %s [FATAL:%s]", dir, PROGRAM));	}