| 1 |
commit: 15848c4175bd2c42967e5f09128a600f376febd3 |
| 2 |
Author: Justin Lecher <jlec <AT> gentoo <DOT> org> |
| 3 |
AuthorDate: Fri Dec 25 10:38:04 2015 +0000 |
| 4 |
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org> |
| 5 |
CommitDate: Fri Dec 25 10:38:04 2015 +0000 |
| 6 |
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=15848c41 |
| 7 |
|
| 8 |
sci-biology/t-coffee: Import fix for CVE-2015-8621 |
| 9 |
|
| 10 |
Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=569650 |
| 11 |
|
| 12 |
Package-Manager: portage-2.2.26 |
| 13 |
Signed-off-by: Justin Lecher <jlec <AT> gentoo.org> |
| 14 |
|
| 15 |
.../t-coffee/files/t-coffee-11.00-mayhem.patch | 25 ++++++++++++++++ |
| 16 |
...t-coffee-11.00-set_proper_dir_permissions.patch | 35 ++++++++++++++++++++++ |
| 17 |
...offee-11.00.ebuild => t-coffee-11.00-r1.ebuild} | 3 ++ |
| 18 |
3 files changed, 63 insertions(+) |
| 19 |
|
| 20 |
diff --git a/sci-biology/t-coffee/files/t-coffee-11.00-mayhem.patch b/sci-biology/t-coffee/files/t-coffee-11.00-mayhem.patch |
| 21 |
new file mode 100644 |
| 22 |
index 0000000..cbfeeab |
| 23 |
--- /dev/null |
| 24 |
+++ b/sci-biology/t-coffee/files/t-coffee-11.00-mayhem.patch |
| 25 |
@@ -0,0 +1,25 @@ |
| 26 |
+Author: Andreas Tille <tille@××××××.org> |
| 27 |
+Last-Update: Mon, 21 Dec 2015 21:30:36 +0100 |
| 28 |
+Bug-Debian: https://bugs.debian.org/716373 |
| 29 |
+Description: Fix Mayhem issue |
| 30 |
+ The idea behind this patch is that if there is a problem to set the HOME |
| 31 |
+ directories no additional processes can exist and so we should *really* |
| 32 |
+ exit. Somehow the printf_exit() function does some logic which ends up |
| 33 |
+ in an endless loop and thus forcing the exit will help here. |
| 34 |
+ . |
| 35 |
+ Unfortunately this does not solve the issue completely since inside the |
| 36 |
+ Exit call a "Segmentation fault" happens - so some broken pointer handling |
| 37 |
+ seems to happen somewhere before. |
| 38 |
+ |
| 39 |
+--- a/t_coffee_source/util_lib/util.c |
| 40 |
++++ b/t_coffee_source/util_lib/util.c |
| 41 |
+@@ -4642,7 +4642,8 @@ char *get_home_4_tcoffee () |
| 42 |
+ } |
| 43 |
+ else |
| 44 |
+ { |
| 45 |
+- 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); |
| 46 |
++ 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); |
| 47 |
++ exit(EXIT_FAILURE); |
| 48 |
+ } |
| 49 |
+ |
| 50 |
+ |
| 51 |
|
| 52 |
diff --git a/sci-biology/t-coffee/files/t-coffee-11.00-set_proper_dir_permissions.patch b/sci-biology/t-coffee/files/t-coffee-11.00-set_proper_dir_permissions.patch |
| 53 |
new file mode 100644 |
| 54 |
index 0000000..a3f47cd |
| 55 |
--- /dev/null |
| 56 |
+++ b/sci-biology/t-coffee/files/t-coffee-11.00-set_proper_dir_permissions.patch |
| 57 |
@@ -0,0 +1,35 @@ |
| 58 |
+Author: Andreas Tille <tille@××××××.org> |
| 59 |
+Last-Update: Mon, 21 Dec 2015 21:30:36 +0100 |
| 60 |
+Bug-Debian: https://bugs.debian.org/751579 |
| 61 |
+Description: When creating subdirectories in $HOME do not |
| 62 |
+ make these world writable but keep users umask |
| 63 |
+ |
| 64 |
+--- a/t_coffee_source/util_lib/util.c |
| 65 |
++++ b/t_coffee_source/util_lib/util.c |
| 66 |
+@@ -7714,6 +7714,10 @@ int my_mkdir ( char *dir_in) |
| 67 |
+ int a, buf; |
| 68 |
+ char *dir; |
| 69 |
+ |
| 70 |
++ static char *home = getenv ("HOME"); |
| 71 |
++ static mode_t oldmask = umask(0); |
| 72 |
++ int change_umask = 0; |
| 73 |
++ if (strncmp (dir_in, home, strlen(home))==0) change_umask = 1; |
| 74 |
+ |
| 75 |
+ dir=(char*)vcalloc ( strlen (dir_in)+strlen (get_home_4_tcoffee())+100, sizeof (char)); |
| 76 |
+ sprintf ( dir, "%s", dir_in); |
| 77 |
+@@ -7733,10 +7737,11 @@ int my_mkdir ( char *dir_in) |
| 78 |
+ |
| 79 |
+ if (access(dir, F_OK)==-1) |
| 80 |
+ { |
| 81 |
+- mode_t oldmask = umask(0); |
| 82 |
+- mkdir (dir, S_IRWXU | S_IRWXG | S_IRWXO); |
| 83 |
+- umask(oldmask); |
| 84 |
+- |
| 85 |
++ if ( change_umask == 1 ) mkdir (dir, 0777-oldmask); |
| 86 |
++ else { |
| 87 |
++ mkdir (dir, S_IRWXU | S_IRWXG | S_IRWXO); |
| 88 |
++ umask(oldmask); |
| 89 |
++ } |
| 90 |
+ if ( access (dir, F_OK)==-1) |
| 91 |
+ { |
| 92 |
+ myexit(fprintf_error ( stderr, "\nERROR: Could Not Create Directory %s [FATAL:%s]", dir, PROGRAM)); } |
| 93 |
|
| 94 |
diff --git a/sci-biology/t-coffee/t-coffee-11.00.ebuild b/sci-biology/t-coffee/t-coffee-11.00-r1.ebuild |
| 95 |
similarity index 92% |
| 96 |
rename from sci-biology/t-coffee/t-coffee-11.00.ebuild |
| 97 |
rename to sci-biology/t-coffee/t-coffee-11.00-r1.ebuild |
| 98 |
index 62e8b70..3f2861c 100644 |
| 99 |
--- a/sci-biology/t-coffee/t-coffee-11.00.ebuild |
| 100 |
+++ b/sci-biology/t-coffee/t-coffee-11.00-r1.ebuild |
| 101 |
@@ -31,6 +31,9 @@ src_prepare() { |
| 102 |
-e '/@/s:.*;:\t:g' \ |
| 103 |
-e '/Linking/s:$(CC):$(CC) $(CFLAGS) $(LDFLAGS):g' \ |
| 104 |
-i t_coffee_source/makefile || die |
| 105 |
+ epatch \ |
| 106 |
+ "${FILESDIR}"/${P}-mayhem.patch \ |
| 107 |
+ "${FILESDIR}"/${P}-set_proper_dir_permissions.patch |
| 108 |
} |
| 109 |
|
| 110 |
src_compile() { |
Archives