Merge branch 'master' into core-updates

3 files changed, 130 insertions, 0 deletions

diff --git a/gnu/packages/patches/arb-ldconfig.patch b/gnu/packages/patches/arb-ldconfig.patch
new file mode 100644
index 0000000000..478ec5a6f0
--- /dev/null
+++ b/gnu/packages/patches/arb-ldconfig.patch
@@ -0,0 +1,22 @@
+diff -u -r arb-2.8.1.orig/configure arb-2.8.1/configure
+--- arb-2.8.1.orig/configure	2015-12-31 17:30:01.000000000 +0100
++++ arb-2.8.1/configure	2016-01-20 16:41:41.336726596 +0100
+@@ -647,6 +647,7 @@
+ echo "ARB_SHARED=$SHARED" >> Makefile
+ echo "ARB_LIB=$ARB_LIB" >> Makefile
+ echo "ARB_LIBNAME=$ARB_LIBNAME" >> Makefile
++echo "ARB_MAJOR=$ARB_MAJOR" >> Makefile
+ echo "ARB_SOLIB=$ARB_SOLIB" >> Makefile
+ echo "EXEEXT=$EXEEXT" >> Makefile
+ echo "PREFIX=$PREFIX" >> Makefile
+diff -u -r arb-2.8.1.orig/Makefile.in arb-2.8.1/Makefile.in
+--- arb-2.8.1.orig/Makefile.in	2015-12-31 17:30:01.000000000 +0100
++++ arb-2.8.1/Makefile.in	2016-01-20 16:30:32.575298517 +0100
+@@ -101,6 +101,7 @@
+ 		$(LDCONFIG) -n "$(CURDIR)"; \
+ 	fi
+ 	ln -sf "$(ARB_LIB)" "$(ARB_LIBNAME)"; \
++	ln -sf "$(ARB_LIB)" "$(ARB_LIBNAME).$(ARB_MAJOR)"; \
+ 
+ libarb.a: $(OBJS) $(LIB_SOURCES) $(EXT_SOURCES) $(HEADERS) $(EXT_HEADERS) | build build/interfaces
+ 	$(AT)$(foreach ext, $(EXTENSIONS), $(foreach dir, $(patsubst $(ext)/%.h, %, $(wildcard $(ext)/*.h)), mkdir -p build/$(dir); BUILD_DIR=$(CURDIR)/build/$(dir); export BUILD_DIR; MOD_DIR=$(dir); export MOD_DIR; $(MAKE) -f $(CURDIR)/Makefile.subdirs -C $(ext)/$(dir) static || exit $$?;))
diff --git a/gnu/packages/patches/linux-libre-CVE-2016-0728.patch b/gnu/packages/patches/linux-libre-CVE-2016-0728.patch
new file mode 100644
index 0000000000..254d6c1aea
--- /dev/null
+++ b/gnu/packages/patches/linux-libre-CVE-2016-0728.patch
@@ -0,0 +1,84 @@
+Copied from
+https://git.kernel.org/cgit/linux/kernel/git/torvalds/linux.git/patch/?id=23567fd052a9abb6d67fe8e7a9ccdd9800a540f2
+
+From 23567fd052a9abb6d67fe8e7a9ccdd9800a540f2 Mon Sep 17 00:00:00 2001
+From: Yevgeny Pats <yevgeny@perception-point.io>
+Date: Tue, 19 Jan 2016 22:09:04 +0000
+Subject: KEYS: Fix keyring ref leak in join_session_keyring()
+
+This fixes CVE-2016-0728.
+
+If a thread is asked to join as a session keyring the keyring that's already
+set as its session, we leak a keyring reference.
+
+This can be tested with the following program:
+
+	#include <stddef.h>
+	#include <stdio.h>
+	#include <sys/types.h>
+	#include <keyutils.h>
+
+	int main(int argc, const char *argv[])
+	{
+		int i = 0;
+		key_serial_t serial;
+
+		serial = keyctl(KEYCTL_JOIN_SESSION_KEYRING,
+				"leaked-keyring");
+		if (serial < 0) {
+			perror("keyctl");
+			return -1;
+		}
+
+		if (keyctl(KEYCTL_SETPERM, serial,
+			   KEY_POS_ALL | KEY_USR_ALL) < 0) {
+			perror("keyctl");
+			return -1;
+		}
+
+		for (i = 0; i < 100; i++) {
+			serial = keyctl(KEYCTL_JOIN_SESSION_KEYRING,
+					"leaked-keyring");
+			if (serial < 0) {
+				perror("keyctl");
+				return -1;
+			}
+		}
+
+		return 0;
+	}
+
+If, after the program has run, there something like the following line in
+/proc/keys:
+
+3f3d898f I--Q---   100 perm 3f3f0000     0     0 keyring   leaked-keyring: empty
+
+with a usage count of 100 * the number of times the program has been run,
+then the kernel is malfunctioning.  If leaked-keyring has zero usages or
+has been garbage collected, then the problem is fixed.
+
+Reported-by: Yevgeny Pats <yevgeny@perception-point.io>
+Signed-off-by: David Howells <dhowells@redhat.com>
+Acked-by: Don Zickus <dzickus@redhat.com>
+Acked-by: Prarit Bhargava <prarit@redhat.com>
+Acked-by: Jarod Wilson <jarod@redhat.com>
+Signed-off-by: James Morris <james.l.morris@oracle.com>
+---
+ security/keys/process_keys.c | 1 +
+ 1 file changed, 1 insertion(+)
+
+diff --git a/security/keys/process_keys.c b/security/keys/process_keys.c
+index a3f85d2..e6d50172 100644
+--- a/security/keys/process_keys.c
++++ b/security/keys/process_keys.c
+@@ -794,6 +794,7 @@ long join_session_keyring(const char *name)
+ 		ret = PTR_ERR(keyring);
+ 		goto error2;
+ 	} else if (keyring == new->session_keyring) {
++		key_put(keyring);
+ 		ret = 0;
+ 		goto error2;
+ 	}
+-- 
+cgit v0.12
+
diff --git a/gnu/packages/patches/tophat-build-with-later-seqan.patch b/gnu/packages/patches/tophat-build-with-later-seqan.patch
new file mode 100644
index 0000000000..fc742e2a7d
--- /dev/null
+++ b/gnu/packages/patches/tophat-build-with-later-seqan.patch
@@ -0,0 +1,24 @@
+This patch resolves a build failure when building TopHat 2.1.0 with SeqAn 1.4.
+This is the relevant part of a patch originally posted here:
+https://lists.fu-berlin.de/pipermail/seqan-dev/2014-July/msg00001.html
+
+--- a/src/segment_juncs.cpp
++++ b/src/segment_juncs.cpp
+@@ -2050,10 +2050,13 @@ void juncs_from_ref_segs(RefSequenceTabl
+     typedef map<uint32_t, IntronMotifs> MotifMap;
+     
+     MotifMap ims;
+-	
+-    seqan::DnaStringReverseComplement rev_donor_dinuc(donor_dinuc);
+-    seqan::DnaStringReverseComplement rev_acceptor_dinuc(acceptor_dinuc);
+-    
++
++    typedef seqan::ModifiedString<
++                    seqan::ModifiedString<seqan::DnaString const, seqan::ModView<seqan::FunctorComplement<seqan::Dna> > >,  
++                    seqan::ModReverse>   ConstDnaStringReverseComplement;
++    ConstDnaStringReverseComplement rev_donor_dinuc(donor_dinuc);
++    ConstDnaStringReverseComplement rev_acceptor_dinuc(acceptor_dinuc);
++     
+     if (talkative)
+         fprintf(stderr, "Collecting potential splice sites in islands\n");
+