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authorJustin Lecher <jlec@gentoo.org>2015-12-25 11:38:04 +0100
committerJustin Lecher <jlec@gentoo.org>2015-12-25 11:38:04 +0100
commit15848c4175bd2c42967e5f09128a600f376febd3 (patch)
tree89fe75f28508231b1744bf09851648def86c2826 /sci-biology
parentsci-chemistry/tm-align: Version Bump (diff)
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sci-biology/t-coffee: Import fix for CVE-2015-8621
Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=569650 Package-Manager: portage-2.2.26 Signed-off-by: Justin Lecher <jlec@gentoo.org>
Diffstat (limited to 'sci-biology')
-rw-r--r--sci-biology/t-coffee/files/t-coffee-11.00-mayhem.patch25
-rw-r--r--sci-biology/t-coffee/files/t-coffee-11.00-set_proper_dir_permissions.patch35
-rw-r--r--sci-biology/t-coffee/t-coffee-11.00-r1.ebuild (renamed from sci-biology/t-coffee/t-coffee-11.00.ebuild)3
3 files changed, 63 insertions, 0 deletions
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
new file mode 100644
index 00000000000..cbfeeabc181
--- /dev/null
+++ b/sci-biology/t-coffee/files/t-coffee-11.00-mayhem.patch
@@ -0,0 +1,25 @@
+Author: Andreas Tille <tille@debian.org>
+Last-Update: Mon, 21 Dec 2015 21:30:36 +0100
+Bug-Debian: https://bugs.debian.org/716373
+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
+@@ -4642,7 +4642,8 @@ char *get_home_4_tcoffee ()
+ }
+ 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);
++ exit(EXIT_FAILURE);
+ }
+
+
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
new file mode 100644
index 00000000000..a3f47cd9fce
--- /dev/null
+++ b/sci-biology/t-coffee/files/t-coffee-11.00-set_proper_dir_permissions.patch
@@ -0,0 +1,35 @@
+Author: Andreas Tille <tille@debian.org>
+Last-Update: Mon, 21 Dec 2015 21:30:36 +0100
+Bug-Debian: https://bugs.debian.org/751579
+Description: When creating subdirectories in $HOME do not
+ make these world writable but keep users umask
+
+--- a/t_coffee_source/util_lib/util.c
++++ b/t_coffee_source/util_lib/util.c
+@@ -7714,6 +7714,10 @@ int my_mkdir ( char *dir_in)
+ int a, buf;
+ char *dir;
+
++ static char *home = getenv ("HOME");
++ static mode_t oldmask = umask(0);
++ int change_umask = 0;
++ if (strncmp (dir_in, home, strlen(home))==0) change_umask = 1;
+
+ dir=(char*)vcalloc ( strlen (dir_in)+strlen (get_home_4_tcoffee())+100, sizeof (char));
+ sprintf ( dir, "%s", dir_in);
+@@ -7733,10 +7737,11 @@ int my_mkdir ( char *dir_in)
+
+ if (access(dir, F_OK)==-1)
+ {
+- mode_t oldmask = umask(0);
+- mkdir (dir, S_IRWXU | S_IRWXG | S_IRWXO);
+- umask(oldmask);
+-
++ if ( change_umask == 1 ) mkdir (dir, 0777-oldmask);
++ else {
++ mkdir (dir, S_IRWXU | S_IRWXG | S_IRWXO);
++ umask(oldmask);
++ }
+ if ( access (dir, F_OK)==-1)
+ {
+ myexit(fprintf_error ( stderr, "\nERROR: Could Not Create Directory %s [FATAL:%s]", dir, PROGRAM)); }
diff --git a/sci-biology/t-coffee/t-coffee-11.00.ebuild b/sci-biology/t-coffee/t-coffee-11.00-r1.ebuild
index 62e8b7033cb..3f2861c4a47 100644
--- a/sci-biology/t-coffee/t-coffee-11.00.ebuild
+++ b/sci-biology/t-coffee/t-coffee-11.00-r1.ebuild
@@ -31,6 +31,9 @@ src_prepare() {
-e '/@/s:.*;:\t:g' \
-e '/Linking/s:$(CC):$(CC) $(CFLAGS) $(LDFLAGS):g' \
-i t_coffee_source/makefile || die
+ epatch \
+ "${FILESDIR}"/${P}-mayhem.patch \
+ "${FILESDIR}"/${P}-set_proper_dir_permissions.patch
}
src_compile() {