[med-svn] [Git][med-team/t-coffee][master] Deal with "Segmentation fault" in exit of mayhem patch

[Andreas Tille]

Andreas Tille pushed to branch master at Debian Med / t-coffee


Commits:
9cffa995 by Andreas Tille at 2018-09-28T11:39:33Z
Deal with "Segmentation fault" in exit of mayhem patch

- - - - -


2 changed files:

- debian/changelog
- debian/patches/mayhem.patch


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,10 @@
+t-coffee (11.00.8cbe486-8) UNRELEASED; urgency=medium
+
+  * Deal with "Segmentation fault" in exit of mayhem patch
+    Closes: #909530
+
+ -- Andreas Tille <tille at debian.org>  Fri, 28 Sep 2018 13:13:33 +0200
+
 t-coffee (11.00.8cbe486-7) unstable; urgency=medium
 
   * debhelper 11


=====================================
debian/patches/mayhem.patch
=====================================
@@ -1,15 +1,12 @@
 Author: Andreas Tille <tille at debian.org>
-Last-Update: Mon, 21 Dec 2015 21:30:36 +0100
+Last-Update: Fri, 28 Sep 2018 13:13:33 +0200
 Bug-Debian: https://bugs.debian.org/716373
+            https://bugs.debian.org/909530
 Description: Fix Mayhem issue
  The idea behind this patch is that if there is a problem to set the HOME
  directories no additional processes can exist and so we should *really*
  exit.  Somehow the printf_exit() function does some logic which ends up
  in an endless loop and thus forcing the exit will help here.
- .
- Unfortunately this does not solve the issue completely since inside the
- Exit call a "Segmentation fault" happens - so some broken pointer handling
- seems to happen somewhere before.
 
 --- a/t_coffee_source/util_lib/util.c
 +++ b/t_coffee_source/util_lib/util.c
@@ -18,8 +15,19 @@ Description: Fix Mayhem issue
    else
      {
 -      printf_exit (EXIT_FAILURE, stderr, "ERROR: Could not set a HOME directory.\nSet any of the following environement variables to some suitable location: HOME, HOME_4_TCOFFEE, TMP or TEMP [FATAL:%s]\n", PROGRAM);
-+      fprintf(stderr, "ERROR: Could not set a HOME directory.\nSet any of the following environement variables to some suitable location: HOME, HOME_4_TCOFFEE, TMP or TEMP [FATAL:%s]\n", PROGRAM);
++      fprintf(stderr, "ERROR: Could not set a HOME directory.\nSet any of the following environment variables to some suitable location: HOME, HOME_4_TCOFFEE, TMP or TEMP [FATAL:%s]\n", PROGRAM);
 +      exit(EXIT_FAILURE);
      }
  
  
+@@ -7717,6 +7718,10 @@ int my_mkdir ( char *dir_in)
+   static char *home = getenv ("HOME");
+   static mode_t oldmask = umask(0);
+   int change_umask = 0;
++  if ( ! home ) {
++    /* Do not fiddle around with HOME since we found out that environment variable is not set. */
++    exit(EXIT_FAILURE);
++  }
+   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));



View it on GitLab: https://salsa.debian.org/med-team/t-coffee/commit/9cffa995e4603e396054062c6f3dbff1568bf243

-- 
View it on GitLab: https://salsa.debian.org/med-team/t-coffee/commit/9cffa995e4603e396054062c6f3dbff1568bf243
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