Merge branch 'master' into core-updates

3 files changed, 62 insertions, 89 deletions

diff --git a/gnu/packages/patches/gemma-intel-compat.patch b/gnu/packages/patches/gemma-intel-compat.patch
deleted file mode 100644
index f12ec56d9b..0000000000
--- a/gnu/packages/patches/gemma-intel-compat.patch
+++ /dev/null
@@ -1,44 +0,0 @@
-From da1ed24209121f7b0f03f360b1029d7125a38e70 Mon Sep 17 00:00:00 2001
-From: Efraim Flashner <efraim@flashner.co.il>
-Date: Tue, 4 Jul 2017 12:44:53 +0300
-Subject: [PATCH] Add NO_INTEL_COMPAT flag to Makefile.
-
-see also: https://github.com/xiangzhou/GEMMA/pull/47
-
----
- Makefile | 12 ++++++++----
- 1 file changed, 8 insertions(+), 4 deletions(-)
-
-diff --git a/Makefile b/Makefile
-index 5bb8748..712b1ad 100644
---- a/Makefile
-+++ b/Makefile
-@@ -11,6 +11,7 @@
- SYS = LNX
- # Leave blank after "=" to disable; put "= 1" to enable
- WITH_LAPACK = 1
-+NO_INTEL_COMPAT = 
- FORCE_32BIT = 
- FORCE_DYNAMIC = 
- DIST_NAME = gemma-0.96
-@@ -64,10 +65,13 @@ endif
-   HDR += $(SRC_DIR)/lapack.h
- endif
- 
--ifdef FORCE_32BIT
--  CPPFLAGS += -m32
--else
--  CPPFLAGS += -m64
-+ifdef NO_INTEL_COMPAT
-+  else
-+  ifdef FORCE_32BIT
-+    CPPFLAGS += -m32
-+  else
-+    CPPFLAGS += -m64
-+  endif
- endif
- 
- ifdef FORCE_DYNAMIC
--- 
-2.13.2
-
diff --git a/gnu/packages/patches/jq-CVE-2015-8863.patch b/gnu/packages/patches/jq-CVE-2015-8863.patch
deleted file mode 100644
index 20b3bb3f06..0000000000
--- a/gnu/packages/patches/jq-CVE-2015-8863.patch
+++ /dev/null
@@ -1,45 +0,0 @@
-Fix CVE-2015-8863 (Off-by-one error in the tokenadd function in
-jv_parse.c in jq allows remote attackers to cause a denial of service
-(crash) via a long JSON-encoded number, which triggers a heap-based
-buffer overflow):
-
-<https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2015-8863>
-
-Copied from upstream code repository:
-
-<https://github.com/stedolan/jq/commit/8eb1367ca44e772963e704a700ef72ae2e12babd>
-
-From 8eb1367ca44e772963e704a700ef72ae2e12babd Mon Sep 17 00:00:00 2001
-From: Nicolas Williams <nico@cryptonector.com>
-Date: Sat, 24 Oct 2015 17:24:57 -0500
-Subject: [PATCH] Heap buffer overflow in tokenadd() (fix #105)
-
-This was an off-by one: the NUL terminator byte was not allocated on
-resize.  This was triggered by JSON-encoded numbers longer than 256
-bytes.
----
- jv_parse.c | 4 ++--
- 1 file changed, 2 insertions(+), 2 deletions(-)
-
-diff --git a/jv_parse.c b/jv_parse.c
-index 3102ed4..84245b8 100644
---- a/jv_parse.c
-+++ b/jv_parse.c
-@@ -383,7 +383,7 @@ static pfunc stream_token(struct jv_parser* p, char ch) {
- 
- static void tokenadd(struct jv_parser* p, char c) {
-   assert(p->tokenpos <= p->tokenlen);
--  if (p->tokenpos == p->tokenlen) {
-+  if (p->tokenpos >= (p->tokenlen - 1)) {
-     p->tokenlen = p->tokenlen*2 + 256;
-     p->tokenbuf = jv_mem_realloc(p->tokenbuf, p->tokenlen);
-   }
-@@ -485,7 +485,7 @@ static pfunc check_literal(struct jv_parser* p) {
-     TRY(value(p, v));
-   } else {
-     // FIXME: better parser
--    p->tokenbuf[p->tokenpos] = 0; // FIXME: invalid
-+    p->tokenbuf[p->tokenpos] = 0;
-     char* end = 0;
-     double d = jvp_strtod(&p->dtoa, p->tokenbuf, &end);
-     if (end == 0 || *end != 0)
diff --git a/gnu/packages/patches/libgit2-oom-test.patch b/gnu/packages/patches/libgit2-oom-test.patch
new file mode 100644
index 0000000000..9667d1c0da
--- /dev/null
+++ b/gnu/packages/patches/libgit2-oom-test.patch
@@ -0,0 +1,62 @@
+Fix a test failure on 32-bit platforms as reported
+at <https://github.com/libgit2/libgit2/issues/4868>.
+
+From 415a8ae9c9b6ac18f0524b6af8e58408b426457d Mon Sep 17 00:00:00 2001
+From: Edward Thomson <ethomson@edwardthomson.com>
+Date: Thu, 13 Sep 2018 13:27:07 +0100
+Subject: [PATCH] tests: don't run buf::oom on 32-bit systems
+
+On a 32-bit Linux systems, the value large enough to make malloc
+guarantee a failure is also large enough that valgrind considers it
+"fishy".  Skip this test on those systems entirely.
+---
+ tests/buf/oom.c | 14 +++++++++-----
+ 1 file changed, 9 insertions(+), 5 deletions(-)
+
+diff --git a/tests/buf/oom.c b/tests/buf/oom.c
+index 2741a8ddf2..ec3bad9979 100644
+--- a/tests/buf/oom.c
++++ b/tests/buf/oom.c
+@@ -11,12 +11,8 @@
+  */
+ #if defined(GIT_ARCH_64) && defined(__linux__)
+ # define TOOBIG 0x0fffffffffffffff
+-#elif defined(__linux__)
+-# define TOOBIG 0x0fffffff
+ #elif defined(GIT_ARCH_64)
+ # define TOOBIG 0xffffffffffffff00
+-#else
+-# define TOOBIG 0xffffff00
+ #endif
+ 
+ /**
+@@ -25,13 +21,18 @@
+  * will fail.  And because the git_buf_grow() wrapper always
+  * sets mark_oom, the code in git_buf_try_grow() will free
+  * the internal buffer and set it to git_buf__oom.
+- * 
++ *
+  * We initialized the internal buffer to (the static variable)
+  * git_buf__initbuf.  The purpose of this test is to make sure
+  * that we don't try to free the static buffer.
++ *
++ * Skip this test entirely on 32-bit platforms; a buffer large enough
++ * to guarantee malloc failures is so large that valgrind considers
++ * it likely to be an error.
+  */
+ void test_buf_oom__grow(void)
+ {
++#ifdef GIT_ARCH_64
+ 	git_buf buf = GIT_BUF_INIT;
+ 
+ 	git_buf_clear(&buf);
+@@ -40,6 +41,9 @@ void test_buf_oom__grow(void)
+ 	cl_assert(git_buf_oom(&buf));
+ 
+ 	git_buf_free(&buf);
++#else
++    cl_skip();
++#endif
+ }
+ 
+ void test_buf_oom__grow_by(void)