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-rw-r--r--gnu/packages/patches/awesome-reproducible-png.patch4
-rw-r--r--gnu/packages/patches/chicken-CVE-2016-6830+CVE-2016-6831.patch81
-rw-r--r--gnu/packages/patches/cracklib-fix-buffer-overflow.patch39
-rw-r--r--gnu/packages/patches/gnupg-test-segfault-on-32bit-arch.patch40
-rw-r--r--gnu/packages/patches/inkscape-drop-wait-for-targets.patch68
-rw-r--r--gnu/packages/patches/kdbusaddons-kinit-file-name.patch15
-rw-r--r--gnu/packages/patches/khal-disable-failing-tests.patch33
-rw-r--r--gnu/packages/patches/libpng-CVE-2016-10087.patch37
-rw-r--r--gnu/packages/patches/libtiff-CVE-2016-10092.patch42
-rw-r--r--gnu/packages/patches/libtiff-CVE-2016-10093.patch53
-rw-r--r--gnu/packages/patches/libtiff-CVE-2016-10094.patch34
-rw-r--r--gnu/packages/patches/libtiff-assertion-failure.patch60
-rw-r--r--gnu/packages/patches/libtiff-divide-by-zero-ojpeg.patch63
-rw-r--r--gnu/packages/patches/libtiff-divide-by-zero-tiffcp.patch104
-rw-r--r--gnu/packages/patches/libtiff-divide-by-zero-tiffcrop.patch57
-rw-r--r--gnu/packages/patches/libtiff-divide-by-zero.patch67
-rw-r--r--gnu/packages/patches/libtiff-heap-overflow-pixarlog-luv.patch131
-rw-r--r--gnu/packages/patches/libtiff-heap-overflow-tif-dirread.patch132
-rw-r--r--gnu/packages/patches/libtiff-heap-overflow-tiffcp.patch67
-rw-r--r--gnu/packages/patches/libtiff-heap-overflow-tiffcrop.patch60
-rw-r--r--gnu/packages/patches/libtiff-invalid-read.patch64
-rw-r--r--gnu/packages/patches/libtiff-null-dereference.patch42
-rw-r--r--gnu/packages/patches/libtiff-tiffcp-underflow.patch41
-rw-r--r--gnu/packages/patches/libupnp-CVE-2016-8863.patch72
-rw-r--r--gnu/packages/patches/libxml2-CVE-2016-4658.patch257
-rw-r--r--gnu/packages/patches/libxml2-CVE-2016-5131.patch218
-rw-r--r--gnu/packages/patches/libxt-guix-search-paths.patch126
-rw-r--r--gnu/packages/patches/mcrypt-CVE-2012-4409.patch35
-rw-r--r--gnu/packages/patches/mcrypt-CVE-2012-4527.patch198
-rw-r--r--gnu/packages/patches/multiqc-fix-git-subprocess-error.patch16
-rw-r--r--gnu/packages/patches/ocaml-Add-a-.file-directive.patch96
-rw-r--r--gnu/packages/patches/ocaml-bisect-fix-camlp4-in-another-directory.patch125
-rw-r--r--gnu/packages/patches/ocaml-bitstring-fix-configure.patch53
-rw-r--r--gnu/packages/patches/openssh-memory-exhaustion.patch39
-rw-r--r--gnu/packages/patches/python-dendropy-exclude-failing-tests.patch21
-rw-r--r--gnu/packages/patches/python-pycrypto-CVE-2013-7459.patch97
-rw-r--r--gnu/packages/patches/python-pygpgme-fix-pinentry-tests.patch69
-rw-r--r--gnu/packages/patches/qemu-CVE-2016-8576.patch62
-rw-r--r--gnu/packages/patches/qemu-CVE-2016-8577.patch36
-rw-r--r--gnu/packages/patches/qemu-CVE-2016-8578.patch27
-rw-r--r--gnu/packages/patches/ruby-yard-fix-skip-of-markdown-tests.patch17
-rw-r--r--gnu/packages/patches/slock-CVE-2016-6866.patch51
-rw-r--r--gnu/packages/patches/unrtf-CVE-2016-10091.patch189
43 files changed, 2686 insertions, 452 deletions
diff --git a/gnu/packages/patches/awesome-reproducible-png.patch b/gnu/packages/patches/awesome-reproducible-png.patch
index 0fae65bc71..d8e92c70f9 100644
--- a/gnu/packages/patches/awesome-reproducible-png.patch
+++ b/gnu/packages/patches/awesome-reproducible-png.patch
@@ -7,8 +7,8 @@ See <https://wiki.debian.org/ReproducibleBuilds/TimestampsInPNG>.
set(ALL_ICONS ${ALL_ICONS} ${output})
add_custom_command(
-- COMMAND ${CONVERT_EXECUTABLE} ${input} ${ARGN} ${output}
-+ COMMAND ${CONVERT_EXECUTABLE} +set date:create +set date:modify -define png:exclude-chunk=time ${input} ${ARGN} ${output}
+- COMMAND ${CONVERT_EXECUTABLE} ${input} -strip ${ARGN} ${output}
++ COMMAND ${CONVERT_EXECUTABLE} +set date:create +set date:modify -define png:exclude-chunk=time ${input} -strip ${ARGN} ${output}
OUTPUT ${output}
DEPENDS ${input}
VERBATIM)
diff --git a/gnu/packages/patches/chicken-CVE-2016-6830+CVE-2016-6831.patch b/gnu/packages/patches/chicken-CVE-2016-6830+CVE-2016-6831.patch
new file mode 100644
index 0000000000..59decde0e9
--- /dev/null
+++ b/gnu/packages/patches/chicken-CVE-2016-6830+CVE-2016-6831.patch
@@ -0,0 +1,81 @@
+diff -ur a/irregex-core.scm b/irregex-core.scm
+--- a/irregex-core.scm 2016-09-11 19:03:00.000000000 -0400
++++ b/irregex-core.scm 2017-01-01 22:24:08.000000000 -0500
+@@ -30,6 +30,8 @@
+
+ ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
+ ;;;; History
++;; 0.9.6: 2016/12/05 - fixed exponential memory use of + in compilation
++;; of backtracking matcher.
+ ;; 0.9.5: 2016/09/10 - fixed a bug in irregex-fold handling of bow
+ ;; 0.9.4: 2015/12/14 - performance improvement for {n,m} matches
+ ;; 0.9.3: 2014/07/01 - R7RS library
+@@ -3170,16 +3172,7 @@
+ ((sre-empty? (sre-sequence (cdr sre)))
+ (error "invalid sre: empty *" sre))
+ (else
+- (letrec
+- ((body
+- (lp (sre-sequence (cdr sre))
+- n
+- flags
+- (lambda (cnk init src str i end matches fail)
+- (body cnk init src str i end matches
+- (lambda ()
+- (next cnk init src str i end matches fail)
+- ))))))
++ (let ((body (rec (list '+ (sre-sequence (cdr sre))))))
+ (lambda (cnk init src str i end matches fail)
+ (body cnk init src str i end matches
+ (lambda ()
+@@ -3204,10 +3197,21 @@
+ (lambda ()
+ (body cnk init src str i end matches fail))))))))
+ ((+)
+- (lp (sre-sequence (cdr sre))
+- n
+- flags
+- (rec (list '* (sre-sequence (cdr sre))))))
++ (cond
++ ((sre-empty? (sre-sequence (cdr sre)))
++ (error "invalid sre: empty +" sre))
++ (else
++ (letrec
++ ((body
++ (lp (sre-sequence (cdr sre))
++ n
++ flags
++ (lambda (cnk init src str i end matches fail)
++ (body cnk init src str i end matches
++ (lambda ()
++ (next cnk init src str i end matches fail)
++ ))))))
++ body))))
+ ((=)
+ (rec `(** ,(cadr sre) ,(cadr sre) ,@(cddr sre))))
+ ((>=)
+diff -ur a/irregex-utils.scm b/irregex-utils.scm
+--- a/irregex-utils.scm 2016-09-11 19:03:00.000000000 -0400
++++ b/irregex-utils.scm 2017-01-01 22:25:25.000000000 -0500
+@@ -89,7 +89,7 @@
+ (case (car x)
+ ((: seq)
+ (cond
+- ((and (pair? (cddr x)) (pair? (cddr x)) (not (eq? x obj)))
++ ((and (pair? (cdr x)) (pair? (cddr x)) (not (eq? x obj)))
+ (display "(?:" out) (for-each lp (cdr x)) (display ")" out))
+ (else (for-each lp (cdr x)))))
+ ((submatch)
+diff -ur "a/manual-html/Unit irregex.html" "b/manual-html/Unit irregex.html"
+--- "a/manual-html/Unit irregex.html" 2016-09-11 19:10:47.000000000 -0400
++++ "b/manual-html/Unit irregex.html" 2017-01-01 22:26:05.000000000 -0500
+@@ -353,6 +353,6 @@
+ <dd class="defsig"><p>Returns an optimized SRE matching any of the literal strings in the list, like Emacs' <tt>regexp-opt</tt>. Note this optimization doesn't help when irregex is able to build a DFA.</p></dd>
+ </dl>
+ <h5 id="sec:sre-.3estring"><a href="#sec:sre-.3estring">sre-&gt;string</a></h5><dl class="defsig"><dt class="defsig" id="def:sre-.3estring"><span class="sig"><tt>(sre-&gt;string &lt;sre&gt;)</tt></span> <span class="type">procedure</span></dt>
+-<dd class="defsig"><p>Convert an SRE to a POSIX-style regular expression string, if possible.</p></dd>
++<dd class="defsig"><p>Convert an SRE to a PCRE-style regular expression string, if possible.</p></dd>
+ </dl>
+-<hr /><p>Previous: <a href="Unit%20extras.html">Unit extras</a></p><p>Next: <a href="Unit%20srfi-1.html">Unit srfi-1</a></p></div></div></body>
+\ No newline at end of file
++<hr /><p>Previous: <a href="Unit%20extras.html">Unit extras</a></p><p>Next: <a href="Unit%20srfi-1.html">Unit srfi-1</a></p></div></div></body>
diff --git a/gnu/packages/patches/cracklib-fix-buffer-overflow.patch b/gnu/packages/patches/cracklib-fix-buffer-overflow.patch
new file mode 100644
index 0000000000..b1c990f282
--- /dev/null
+++ b/gnu/packages/patches/cracklib-fix-buffer-overflow.patch
@@ -0,0 +1,39 @@
+Fix buffer overflow processing long words in Mangle().
+
+Patch adpated from upstream commit, omitting changes to 'NEWS':
+
+https://github.com/cracklib/cracklib/commit/33d7fa4585247cd2247a1ffa032ad245836c6edb
+
+From 33d7fa4585247cd2247a1ffa032ad245836c6edb Mon Sep 17 00:00:00 2001
+From: Jan Dittberner <jan@dittberner.info>
+Date: Thu, 25 Aug 2016 17:17:53 +0200
+Subject: [PATCH] Fix a buffer overflow processing long words
+
+A buffer overflow processing long words has been discovered. This commit
+applies the patch from
+https://build.opensuse.org/package/view_file/Base:System/cracklib/0004-overflow-processing-long-words.patch
+by Howard Guo.
+
+See https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=835386 and
+http://www.openwall.com/lists/oss-security/2016/08/23/8
+---
+ src/NEWS | 1 +
+ src/lib/rules.c | 5 ++---
+ 2 files changed, 3 insertions(+), 3 deletions(-)
+
+diff --git a/src/lib/rules.c b/src/lib/rules.c
+index d193cc0..3a2aa46 100644
+--- a/lib/rules.c
++++ b/lib/rules.c
+@@ -434,9 +434,8 @@ Mangle(input, control) /* returns a pointer to a controlled Mangle */
+ {
+ int limit;
+ register char *ptr;
+- static char area[STRINGSIZE];
+- char area2[STRINGSIZE];
+- area[0] = '\0';
++ static char area[STRINGSIZE * 2] = {0};
++ char area2[STRINGSIZE * 2] = {0};
+ strcpy(area, input);
+
+ for (ptr = control; *ptr; ptr++)
diff --git a/gnu/packages/patches/gnupg-test-segfault-on-32bit-arch.patch b/gnu/packages/patches/gnupg-test-segfault-on-32bit-arch.patch
new file mode 100644
index 0000000000..79bb41caaa
--- /dev/null
+++ b/gnu/packages/patches/gnupg-test-segfault-on-32bit-arch.patch
@@ -0,0 +1,40 @@
+This fixes a segfault on 32-bit architectures. Upstream discussion:
+
+https://lists.gnupg.org/pipermail/gnupg-devel/2016-December/032364.html
+
+Guix thread: https://lists.gnu.org/archive/html/guix-devel/2016-12/msg00631.html
+
+Patch copied from upstream source repository:
+
+https://git.gnupg.org/cgi-bin/gitweb.cgi?p=gnupg.git;a=commitdiff;h=6e96cdd41a0e55b672309431062f37c4a4a9f485
+
+From 6e96cdd41a0e55b672309431062f37c4a4a9f485 Mon Sep 17 00:00:00 2001
+From: Justus Winter <justus@g10code.com>
+Date: Wed, 21 Dec 2016 16:14:45 +0100
+Subject: [PATCH] gpgscm: Guard use of union member.
+
+* tests/gpgscm/scheme.c (opexe_5): Check that we have a file port
+before accessing filename. Fixes a crash on 32-bit architectures.
+
+Fixes-commit: e7429b1ced0c69fa7901f888f8dc25f00fc346a4
+Signed-off-by: Justus Winter <justus@g10code.com>
+---
+ tests/gpgscm/scheme.c | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/tests/gpgscm/scheme.c b/tests/gpgscm/scheme.c
+index a5b7691..2844545 100644
+--- a/tests/gpgscm/scheme.c
++++ b/tests/gpgscm/scheme.c
+@@ -4838,7 +4838,7 @@ static pointer opexe_5(scheme *sc, enum scheme_opcodes op) {
+ } else {
+ sc->nesting_stack[sc->file_i]++;
+ #if USE_TAGS && SHOW_ERROR_LINE
+- {
++ if (sc->load_stack[sc->file_i].kind & port_file) {
+ const char *filename =
+ sc->load_stack[sc->file_i].rep.stdio.filename;
+ int lineno =
+--
+2.8.0.rc3
+
diff --git a/gnu/packages/patches/inkscape-drop-wait-for-targets.patch b/gnu/packages/patches/inkscape-drop-wait-for-targets.patch
deleted file mode 100644
index 3dbe6641e2..0000000000
--- a/gnu/packages/patches/inkscape-drop-wait-for-targets.patch
+++ /dev/null
@@ -1,68 +0,0 @@
-Copied from Fedora.
-
-http://pkgs.fedoraproject.org/cgit/rpms/inkscape.git/plain/inkscape-0.91-drop-wait-for-targets.patch?id=eb5340800b563d6b05aa5f11a2f24f2cc0d8c80e
-
-=== modified file 'src/ui/clipboard.cpp'
---- src/ui/clipboard.cpp 2016-04-02 15:15:43 +0000
-+++ src/ui/clipboard.cpp 2016-04-07 16:30:32 +0000
-@@ -146,8 +146,6 @@
- void _setClipboardColor(guint32);
- void _userWarn(SPDesktop *, char const *);
-
-- void _inkscape_wait_for_targets(std::list<Glib::ustring> &);
--
- // private properites
- SPDocument *_clipboardSPDoc; ///< Document that stores the clipboard until someone requests it
- Inkscape::XML::Node *_defs; ///< Reference to the clipboard document's defs node
-@@ -1302,9 +1300,7 @@
- */
- Glib::ustring ClipboardManagerImpl::_getBestTarget()
- {
-- // GTKmm's wait_for_targets() is broken, see the comment in _inkscape_wait_for_targets()
-- std::list<Glib::ustring> targets; // = _clipboard->wait_for_targets();
-- _inkscape_wait_for_targets(targets);
-+ std::list<Glib::ustring> targets = _clipboard->wait_for_targets();
-
- // clipboard target debugging snippet
- /*
-@@ -1456,39 +1452,6 @@
- desktop->messageStack()->flash(Inkscape::WARNING_MESSAGE, msg);
- }
-
--
--// GTKMM's clipboard::wait_for_targets is buggy and might return bogus, see
--//
--// https://bugs.launchpad.net/inkscape/+bug/296778
--// http://mail.gnome.org/archives/gtk-devel-list/2009-June/msg00062.html
--//
--// for details. Until this has been fixed upstream we will use our own implementation
--// of this method, as copied from /gtkmm-2.16.0/gtk/gtkmm/clipboard.cc.
--void ClipboardManagerImpl::_inkscape_wait_for_targets(std::list<Glib::ustring> &listTargets)
--{
-- //Get a newly-allocated array of atoms:
-- GdkAtom* targets = NULL;
-- gint n_targets = 0;
-- gboolean test = gtk_clipboard_wait_for_targets( gtk_clipboard_get(GDK_SELECTION_CLIPBOARD), &targets, &n_targets );
-- if (!test || (targets == NULL)) {
-- return;
-- }
--
-- //Add the targets to the C++ container:
-- for (int i = 0; i < n_targets; i++)
-- {
-- //Convert the atom to a string:
-- gchar* const atom_name = gdk_atom_name(targets[i]);
--
-- Glib::ustring target;
-- if (atom_name) {
-- target = Glib::ScopedPtr<char>(atom_name).get(); //This frees the gchar*.
-- }
--
-- listTargets.push_back(target);
-- }
--}
--
- /* #######################################
- ClipboardManager class
- ####################################### */
-
diff --git a/gnu/packages/patches/kdbusaddons-kinit-file-name.patch b/gnu/packages/patches/kdbusaddons-kinit-file-name.patch
new file mode 100644
index 0000000000..ffed88e043
--- /dev/null
+++ b/gnu/packages/patches/kdbusaddons-kinit-file-name.patch
@@ -0,0 +1,15 @@
+Add placeholder for kinit's store file name.
+
+diff --git a/src/kdeinitinterface.cpp b/src/kdeinitinterface.cpp
+index 22fa5e5..3d40937 100644
+--- a/src/kdeinitinterface.cpp
++++ b/src/kdeinitinterface.cpp
+@@ -52,7 +52,7 @@ void KDEInitInterface::ensureKdeinitRunning()
+ // If not found in system paths, search other paths
+ if (srv.isEmpty()) {
+ const QStringList searchPaths = QStringList()
+- << QCoreApplication::applicationDirPath() // then look where our application binary is located
++ << QString::fromUtf8("@SUBSTITUTEME@/bin") // using QStringLiteral would be more efficient, but breaks guix store reference detection.
+ << QLibraryInfo::location(QLibraryInfo::BinariesPath); // look where exec path is (can be set in qt.conf)
+ srv = QStandardPaths::findExecutable(QStringLiteral("kdeinit5"), searchPaths);
+ if (srv.isEmpty()) {
diff --git a/gnu/packages/patches/khal-disable-failing-tests.patch b/gnu/packages/patches/khal-disable-failing-tests.patch
new file mode 100644
index 0000000000..e2c65df8ce
--- /dev/null
+++ b/gnu/packages/patches/khal-disable-failing-tests.patch
@@ -0,0 +1,33 @@
+Disable some tests that are known to fail:
+
+https://github.com/pimutils/khal/issues/546
+https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=844081
+
+diff --git a/tests/khalendar_test.py b/tests/khalendar_test.py
+index fd8dcc6..17732bf 100644
+--- a/tests/khalendar_test.py
++++ b/tests/khalendar_test.py
+@@ -65,6 +65,7 @@ class TestCalendar(object):
+ else:
+ mtimes[cal] = mtime
+
++ @pytest.mark.xfail
+ def test_db_needs_update(self, coll_vdirs):
+ coll, vdirs = coll_vdirs
+
+@@ -321,6 +322,7 @@ class TestDbCreation(object):
+ CalendarCollection(calendars, dbpath=dbpath, locale=aux.locale)
+
+
++@pytest.mark.xfail
+ def test_default_calendar(coll_vdirs):
+ """test if an update to the vdir is detected by the CalendarCollection"""
+ coll, vdirs = coll_vdirs
+@@ -341,6 +343,7 @@ def test_default_calendar(coll_vdirs):
+ assert len(list(coll.get_events_on(today))) == 0
+
+
++@pytest.mark.xfail
+ def test_only_update_old_event(coll_vdirs, monkeypatch):
+ coll, vdirs = coll_vdirs
+
diff --git a/gnu/packages/patches/libpng-CVE-2016-10087.patch b/gnu/packages/patches/libpng-CVE-2016-10087.patch
new file mode 100644
index 0000000000..8093b3e448
--- /dev/null
+++ b/gnu/packages/patches/libpng-CVE-2016-10087.patch
@@ -0,0 +1,37 @@
+Fix CVE-2016-10087, a null pointer dereference in png_set_text_2():
+
+https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2016-10087
+http://seclists.org/oss-sec/2016/q4/777
+
+Patch adapted from upstream source repository:
+
+https://sourceforge.net/p/libpng/code/ci/812768d7a9c973452222d454634496b25ed415eb/
+
+From 812768d7a9c973452222d454634496b25ed415eb Mon Sep 17 00:00:00 2001
+From: Glenn Randers-Pehrson <glennrp at users.sourceforge.net>
+Date: Thu, 29 Dec 2016 07:51:33 -0600
+Subject: [PATCH] [libpng16] Fixed a potential null pointer dereference in
+ png_set_text_2()
+
+(bug report and patch by Patrick Keshishian).
+---
+ ANNOUNCE | 2 ++
+ CHANGES | 2 ++
+ png.c | 1 +
+ 3 files changed, 5 insertions(+)
+
+diff --git a/png.c b/png.c
+index 8afc28fc2..2e05de159 100644
+--- a/png.c
++++ b/png.c
+@@ -477,6 +477,7 @@ png_free_data(png_const_structrp png_ptr, png_inforp info_ptr, png_uint_32 mask,
+ png_free(png_ptr, info_ptr->text);
+ info_ptr->text = NULL;
+ info_ptr->num_text = 0;
++ info_ptr->max_text = 0;
+ }
+ }
+ #endif
+--
+2.11.0
+
diff --git a/gnu/packages/patches/libtiff-CVE-2016-10092.patch b/gnu/packages/patches/libtiff-CVE-2016-10092.patch
new file mode 100644
index 0000000000..d5fd796169
--- /dev/null
+++ b/gnu/packages/patches/libtiff-CVE-2016-10092.patch
@@ -0,0 +1,42 @@
+Fix CVE-2016-10092:
+
+http://bugzilla.maptools.org/show_bug.cgi?id=2620
+https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2016-10092
+https://security-tracker.debian.org/tracker/CVE-2016-10092
+
+2016-12-03 Even Rouault <even.rouault at spatialys.com>
+
+ * tools/tiffcrop.c: fix readContigStripsIntoBuffer() in -i (ignore)
+ mode so that the output buffer is correctly incremented to avoid write
+ outside bounds.
+ Reported by Agostino Sarubbo.
+ Fixes http://bugzilla.maptools.org/show_bug.cgi?id=2620
+
+/cvs/maptools/cvsroot/libtiff/ChangeLog,v <-- ChangeLog
+new revision: 1.1178; previous revision: 1.1177
+/cvs/maptools/cvsroot/libtiff/tools/tiffcrop.c,v <-- tools/tiffcrop.c
+new revision: 1.47; previous revision: 1.46
+
+Index: libtiff/tools/tiffcrop.c
+===================================================================
+RCS file: /cvs/maptools/cvsroot/libtiff/tools/tiffcrop.c,v
+retrieving revision 1.46
+retrieving revision 1.47
+diff -u -r1.46 -r1.47
+--- libtiff/tools/tiffcrop.c 18 Nov 2016 14:58:46 -0000 1.46
++++ libtiff/tools/tiffcrop.c 3 Dec 2016 11:35:56 -0000 1.47
+@@ -1,4 +1,4 @@
+-/* $Id: tiffcrop.c,v 1.46 2016-11-18 14:58:46 erouault Exp $ */
++/* $Id: tiffcrop.c,v 1.47 2016-12-03 11:35:56 erouault Exp $ */
+
+ /* tiffcrop.c -- a port of tiffcp.c extended to include manipulations of
+ * the image data through additional options listed below
+@@ -3698,7 +3698,7 @@
+ (unsigned long) strip, (unsigned long)rows);
+ return 0;
+ }
+- bufp += bytes_read;
++ bufp += stripsize;
+ }
+
+ return 1;
diff --git a/gnu/packages/patches/libtiff-CVE-2016-10093.patch b/gnu/packages/patches/libtiff-CVE-2016-10093.patch
new file mode 100644
index 0000000000..5897ec1029
--- /dev/null
+++ b/gnu/packages/patches/libtiff-CVE-2016-10093.patch
@@ -0,0 +1,53 @@
+Fix CVE-2016-10093:
+
+http://bugzilla.maptools.org/show_bug.cgi?id=2610
+https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2016-10093
+https://security-tracker.debian.org/tracker/CVE-2016-10093
+
+2016-12-03 Even Rouault <even.rouault at spatialys.com>
+
+ * tools/tiffcp.c: fix uint32 underflow/overflow that can cause
+ heap-based buffer overflow.
+ Reported by Agostino Sarubbo.
+ Fixes http://bugzilla.maptools.org/show_bug.cgi?id=2610
+
+/cvs/maptools/cvsroot/libtiff/ChangeLog,v <-- ChangeLog
+new revision: 1.1187; previous revision: 1.1186
+/cvs/maptools/cvsroot/libtiff/tools/tiffcp.c,v <-- tools/tiffcp.c
+new revision: 1.59; previous revision: 1.58
+
+Index: libtiff/tools/tiffcp.c
+===================================================================
+RCS file: /cvs/maptools/cvsroot/libtiff/tools/tiffcp.c,v
+retrieving revision 1.58
+retrieving revision 1.59
+diff -u -r1.58 -r1.59
+--- libtiff/tools/tiffcp.c 3 Dec 2016 15:44:15 -0000 1.58
++++ libtiff/tools/tiffcp.c 3 Dec 2016 16:40:01 -0000 1.59
+@@ -1163,7 +1163,7 @@
+
+ static void
+ cpStripToTile(uint8* out, uint8* in,
+- uint32 rows, uint32 cols, int outskew, int inskew)
++ uint32 rows, uint32 cols, int outskew, int64 inskew)
+ {
+ while (rows-- > 0) {
+ uint32 j = cols;
+@@ -1320,7 +1320,7 @@
+ tdata_t tilebuf;
+ uint32 imagew = TIFFScanlineSize(in);
+ uint32 tilew = TIFFTileRowSize(in);
+- int iskew = imagew - tilew;
++ int64 iskew = (int64)imagew - (int64)tilew;
+ uint8* bufp = (uint8*) buf;
+ uint32 tw, tl;
+ uint32 row;
+@@ -1348,7 +1348,7 @@
+ status = 0;
+ goto done;
+ }
+- if (colb + tilew > imagew) {
++ if (colb > iskew) {
+ uint32 width = imagew - colb;
+ uint32 oskew = tilew - width;
+ cpStripToTile(bufp + colb,
diff --git a/gnu/packages/patches/libtiff-CVE-2016-10094.patch b/gnu/packages/patches/libtiff-CVE-2016-10094.patch
new file mode 100644
index 0000000000..9018773565
--- /dev/null
+++ b/gnu/packages/patches/libtiff-CVE-2016-10094.patch
@@ -0,0 +1,34 @@
+Fix CVE-2016-10094:
+
+http://bugzilla.maptools.org/show_bug.cgi?id=2640
+https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2016-10094
+https://security-tracker.debian.org/tracker/CVE-2016-10094
+
+2016-12-20 Even Rouault <even.rouault at spatialys.com>
+
+ * tools/tiff2pdf.c: avoid potential heap-based overflow in
+ t2p_readwrite_pdf_image_tile().
+ Fixes http://bugzilla.maptools.org/show_bug.cgi?id=2640
+
+/cvs/maptools/cvsroot/libtiff/ChangeLog,v <-- ChangeLog
+new revision: 1.1199; previous revision: 1.1198
+/cvs/maptools/cvsroot/libtiff/tools/tiff2pdf.c,v <-- tools/tiff2pdf.c
+new revision: 1.101; previous revision: 1.100
+
+Index: libtiff/tools/tiff2pdf.c
+===================================================================
+RCS file: /cvs/maptools/cvsroot/libtiff/tools/tiff2pdf.c,v
+retrieving revision 1.100
+retrieving revision 1.101
+diff -u -r1.100 -r1.101
+--- libtiff/tools/tiff2pdf.c 20 Dec 2016 17:24:35 -0000 1.100
++++ libtiff/tools/tiff2pdf.c 20 Dec 2016 17:28:17 -0000 1.101
+@@ -2895,7 +2895,7 @@
+ return(0);
+ }
+ if(TIFFGetField(input, TIFFTAG_JPEGTABLES, &count, &jpt) != 0) {
+- if (count >= 4) {
++ if (count > 4) {
+ int retTIFFReadRawTile;
+ /* Ignore EOI marker of JpegTables */
+ _TIFFmemcpy(buffer, jpt, count - 2);
diff --git a/gnu/packages/patches/libtiff-assertion-failure.patch b/gnu/packages/patches/libtiff-assertion-failure.patch
new file mode 100644
index 0000000000..ef747fbdd7
--- /dev/null
+++ b/gnu/packages/patches/libtiff-assertion-failure.patch
@@ -0,0 +1,60 @@
+Fix assertion failure in readSeparateTilesIntoBuffer():
+
+http://bugzilla.maptools.org/show_bug.cgi?id=2605
+
+2016-12-03 Even Rouault <even.rouault at spatialys.com>
+
+ * tools/tiffcp.c: replace assert( (bps % 8) == 0 ) by a non assert
+check.
+ Reported by Agostino Sarubbo.
+ Fixes http://bugzilla.maptools.org/show_bug.cgi?id=2605
+
+/cvs/maptools/cvsroot/libtiff/ChangeLog,v <-- ChangeLog
+new revision: 1.1188; previous revision: 1.1187
+/cvs/maptools/cvsroot/libtiff/tools/tiffcp.c,v <-- tools/tiffcp.c
+new revision: 1.60; previous revision: 1.59
+
+Index: libtiff/tools/tiffcp.c
+===================================================================
+RCS file: /cvs/maptools/cvsroot/libtiff/tools/tiffcp.c,v
+retrieving revision 1.59
+retrieving revision 1.60
+diff -u -r1.59 -r1.60
+--- libtiff/tools/tiffcp.c 3 Dec 2016 16:40:01 -0000 1.59
++++ libtiff/tools/tiffcp.c 3 Dec 2016 16:50:02 -0000 1.60
+@@ -45,7 +45,6 @@
+ #include <string.h>
+
+ #include <ctype.h>
+-#include <assert.h>
+
+ #ifdef HAVE_UNISTD_H
+ # include <unistd.h>
+@@ -1393,7 +1392,12 @@
+ status = 0;
+ goto done;
+ }
+- assert( bps % 8 == 0 );
++ if( (bps % 8) != 0 )
++ {
++ TIFFError(TIFFFileName(in), "Error, cannot handle BitsPerSample that is not a multiple of 8");
++ status = 0;
++ goto done;
++ }
+ bytes_per_sample = bps/8;
+
+ for (row = 0; row < imagelength; row += tl) {
+@@ -1584,7 +1588,12 @@
+ _TIFFfree(obuf);
+ return 0;
+ }
+- assert( bps % 8 == 0 );
++ if( (bps % 8) != 0 )
++ {
++ TIFFError(TIFFFileName(out), "Error, cannot handle BitsPerSample that is not a multiple of 8");
++ _TIFFfree(obuf);
++ return 0;
++ }
+ bytes_per_sample = bps/8;
+
+ for (row = 0; row < imagelength; row += tl) {
diff --git a/gnu/packages/patches/libtiff-divide-by-zero-ojpeg.patch b/gnu/packages/patches/libtiff-divide-by-zero-ojpeg.patch
new file mode 100644
index 0000000000..2a96b68521
--- /dev/null
+++ b/gnu/packages/patches/libtiff-divide-by-zero-ojpeg.patch
@@ -0,0 +1,63 @@
+Fix divide-by-zero in OJPEGDecodeRaw():
+
+http://bugzilla.maptools.org/show_bug.cgi?id=2611
+
+2016-12-03 Even Rouault <even.rouault at spatialys.com>
+
+ * libtiff/tif_ojpeg.c: make OJPEGDecode() early exit in case of failure
+in
+ OJPEGPreDecode(). This will avoid a divide by zero, and potential other
+issues.
+ Reported by Agostino Sarubbo.
+ Fixes http://bugzilla.maptools.org/show_bug.cgi?id=2611
+
+/cvs/maptools/cvsroot/libtiff/ChangeLog,v <-- ChangeLog
+new revision: 1.1177; previous revision: 1.1176
+/cvs/maptools/cvsroot/libtiff/libtiff/tif_ojpeg.c,v <-- libtiff/tif_ojpeg.c
+new revision: 1.66; previous revision: 1.65
+
+Index: libtiff/libtiff/tif_ojpeg.c
+===================================================================
+RCS file: /cvs/maptools/cvsroot/libtiff/libtiff/tif_ojpeg.c,v
+retrieving revision 1.65
+retrieving revision 1.66
+diff -u -r1.65 -r1.66
+--- libtiff/libtiff/tif_ojpeg.c 4 Sep 2016 21:32:56 -0000 1.65
++++ libtiff/libtiff/tif_ojpeg.c 3 Dec 2016 11:15:18 -0000 1.66
+@@ -1,4 +1,4 @@
+-/* $Id: tif_ojpeg.c,v 1.65 2016-09-04 21:32:56 erouault Exp $ */
++/* $Id: tif_ojpeg.c,v 1.66 2016-12-03 11:15:18 erouault Exp $ */
+
+ /* WARNING: The type of JPEG encapsulation defined by the TIFF Version 6.0
+ specification is now totally obsolete and deprecated for new applications and
+@@ -244,6 +244,7 @@
+
+ typedef struct {
+ TIFF* tif;
++ int decoder_ok;
+ #ifndef LIBJPEG_ENCAP_EXTERNAL
+ JMP_BUF exit_jmpbuf;
+ #endif
+@@ -722,6 +723,7 @@
+ }
+ sp->write_curstrile++;
+ }
++ sp->decoder_ok = 1;
+ return(1);
+ }
+
+@@ -784,8 +786,14 @@
+ static int
+ OJPEGDecode(TIFF* tif, uint8* buf, tmsize_t cc, uint16 s)
+ {
++ static const char module[]="OJPEGDecode";
+ OJPEGState* sp=(OJPEGState*)tif->tif_data;
+ (void)s;
++ if( !sp->decoder_ok )
++ {
++ TIFFErrorExt(tif->tif_clientdata,module,"Cannot decode: decoder not correctly initialized");
++ return 0;
++ }
+ if (sp->libjpeg_jpeg_query_style==0)
+ {
+ if (OJPEGDecodeRaw(tif,buf,cc)==0)
diff --git a/gnu/packages/patches/libtiff-divide-by-zero-tiffcp.patch b/gnu/packages/patches/libtiff-divide-by-zero-tiffcp.patch
new file mode 100644
index 0000000000..d3f1c2b60e
--- /dev/null
+++ b/gnu/packages/patches/libtiff-divide-by-zero-tiffcp.patch
@@ -0,0 +1,104 @@
+Fix two divide-by-zero bugs in readSeparateTilesIntoBuffer():
+
+http://bugzilla.maptools.org/show_bug.cgi?id=2597
+http://bugzilla.maptools.org/show_bug.cgi?id=2607
+
+2016-12-03 Even Rouault <even.rouault at spatialys.com>
+
+ * tools/tiffcp.c: avoid potential division by zero is BitsPerSamples
+tag is
+ missing.
+ Reported by Agostino sarubbo.
+ Fixes http://bugzilla.maptools.org/show_bug.cgi?id=2597
+
+/cvs/maptools/cvsroot/libtiff/ChangeLog,v <-- ChangeLog
+new revision: 1.1183; previous revision: 1.1182
+/cvs/maptools/cvsroot/libtiff/tools/tiffcp.c,v <-- tools/tiffcp.c
+new revision: 1.57; previous revision: 1.56
+
+Index: libtiff/tools/tiffcp.c
+===================================================================
+RCS file: /cvs/maptools/cvsroot/libtiff/tools/tiffcp.c,v
+retrieving revision 1.56
+retrieving revision 1.57
+diff -u -r1.56 -r1.57
+--- libtiff/tools/tiffcp.c 2 Dec 2016 22:13:32 -0000 1.56
++++ libtiff/tools/tiffcp.c 3 Dec 2016 14:42:40 -0000 1.57
+@@ -1,4 +1,4 @@
+-/* $Id: tiffcp.c,v 1.56 2016-12-02 22:13:32 erouault Exp $ */
++/* $Id: tiffcp.c,v 1.57 2016-12-03 14:42:40 erouault Exp $ */
+
+ /*
+ * Copyright (c) 1988-1997 Sam Leffler
+@@ -1378,7 +1378,7 @@
+ uint8* bufp = (uint8*) buf;
+ uint32 tw, tl;
+ uint32 row;
+- uint16 bps, bytes_per_sample;
++ uint16 bps = 0, bytes_per_sample;
+
+ tilebuf = _TIFFmalloc(tilesize);
+ if (tilebuf == 0)
+@@ -1387,6 +1387,12 @@
+ (void) TIFFGetField(in, TIFFTAG_TILEWIDTH, &tw);
+ (void) TIFFGetField(in, TIFFTAG_TILELENGTH, &tl);
+ (void) TIFFGetField(in, TIFFTAG_BITSPERSAMPLE, &bps);
++ if( bps == 0 )
++ {
++ TIFFError(TIFFFileName(in), "Error, cannot read BitsPerSample");
++ status = 0;
++ goto done;
++ }
+ assert( bps % 8 == 0 );
+ bytes_per_sample = bps/8;
+
+2016-12-03 Even Rouault <even.rouault at spatialys.com>
+
+ * tools/tiffcp.c: avoid potential division by zero is BitsPerSamples
+tag is
+ missing.
+ Reported by Agostino Sarubbo.
+ Fixes http://bugzilla.maptools.org/show_bug.cgi?id=2607
+
+
+/cvs/maptools/cvsroot/libtiff/ChangeLog,v <-- ChangeLog
+new revision: 1.1186; previous revision: 1.1185
+/cvs/maptools/cvsroot/libtiff/tools/tiffcp.c,v <-- tools/tiffcp.c
+new revision: 1.58; previous revision: 1.57
+
+Index: libtiff/tools/tiffcp.c
+===================================================================
+RCS file: /cvs/maptools/cvsroot/libtiff/tools/tiffcp.c,v
+retrieving revision 1.57
+retrieving revision 1.58
+diff -u -r1.57 -r1.58
+--- libtiff/tools/tiffcp.c 3 Dec 2016 14:42:40 -0000 1.57
++++ libtiff/tools/tiffcp.c 3 Dec 2016 15:44:15 -0000 1.58
+@@ -1,4 +1,4 @@
+-/* $Id: tiffcp.c,v 1.57 2016-12-03 14:42:40 erouault Exp $ */
++/* $Id: tiffcp.c,v 1.58 2016-12-03 15:44:15 erouault Exp $ */
+
+ /*
+ * Copyright (c) 1988-1997 Sam Leffler
+@@ -1569,7 +1569,7 @@
+ uint8* bufp = (uint8*) buf;
+ uint32 tl, tw;
+ uint32 row;
+- uint16 bps, bytes_per_sample;
++ uint16 bps = 0, bytes_per_sample;
+
+ obuf = _TIFFmalloc(TIFFTileSize(out));
+ if (obuf == NULL)
+@@ -1578,6 +1578,12 @@
+ (void) TIFFGetField(out, TIFFTAG_TILELENGTH, &tl);
+ (void) TIFFGetField(out, TIFFTAG_TILEWIDTH, &tw);
+ (void) TIFFGetField(out, TIFFTAG_BITSPERSAMPLE, &bps);
++ if( bps == 0 )
++ {
++ TIFFError(TIFFFileName(out), "Error, cannot read BitsPerSample");
++ _TIFFfree(obuf);
++ return 0;
++ }
+ assert( bps % 8 == 0 );
+ bytes_per_sample = bps/8;
+
diff --git a/gnu/packages/patches/libtiff-divide-by-zero-tiffcrop.patch b/gnu/packages/patches/libtiff-divide-by-zero-tiffcrop.patch
new file mode 100644
index 0000000000..823293f1cf
--- /dev/null
+++ b/gnu/packages/patches/libtiff-divide-by-zero-tiffcrop.patch
@@ -0,0 +1,57 @@
+Fix divide-by-zero in readSeparateStripsIntoBuffer():
+
+http://bugzilla.maptools.org/show_bug.cgi?id=2619
+
+2016-12-03 Even Rouault <even.rouault at spatialys.com>
+
+ * tools/tiffcrop.c: fix integer division by zero when BitsPerSample is
+missing.
+ Reported by Agostina Sarubo.
+ Fixes http://bugzilla.maptools.org/show_bug.cgi?id=2619
+
+/cvs/maptools/cvsroot/libtiff/ChangeLog,v <-- ChangeLog
+new revision: 1.1180; previous revision: 1.1179
+/cvs/maptools/cvsroot/libtiff/tools/tiffcrop.c,v <-- tools/tiffcrop.c
+new revision: 1.49; previous revision: 1.48
+
+Index: libtiff/tools/tiffcrop.c
+===================================================================
+RCS file: /cvs/maptools/cvsroot/libtiff/tools/tiffcrop.c,v
+retrieving revision 1.48
+retrieving revision 1.49
+diff -u -r1.48 -r1.49
+--- libtiff/tools/tiffcrop.c 3 Dec 2016 12:19:32 -0000 1.48
++++ libtiff/tools/tiffcrop.c 3 Dec 2016 13:00:04 -0000 1.49
+@@ -1,4 +1,4 @@
+-/* $Id: tiffcrop.c,v 1.48 2016-12-03 12:19:32 erouault Exp $ */
++/* $Id: tiffcrop.c,v 1.49 2016-12-03 13:00:04 erouault Exp $ */
+
+ /* tiffcrop.c -- a port of tiffcp.c extended to include manipulations of
+ * the image data through additional options listed below
+@@ -1164,7 +1164,7 @@
+ tdata_t obuf;
+
+ (void) TIFFGetFieldDefaulted(out, TIFFTAG_ROWSPERSTRIP, &rowsperstrip);
+- (void) TIFFGetField(out, TIFFTAG_BITSPERSAMPLE, &bps);
++ (void) TIFFGetFieldDefaulted(out, TIFFTAG_BITSPERSAMPLE, &bps);
+ bytes_per_sample = (bps + 7) / 8;
+ if( width == 0 ||
+ (uint32)bps * (uint32)spp > TIFF_UINT32_MAX / width ||
+@@ -4760,7 +4760,7 @@
+ int i, bytes_per_sample, bytes_per_pixel, shift_width, result = 1;
+ uint32 j;
+ int32 bytes_read = 0;
+- uint16 bps, planar;
++ uint16 bps = 0, planar;
+ uint32 nstrips;
+ uint32 strips_per_sample;
+ uint32 src_rowsize, dst_rowsize, rows_processed, rps;
+@@ -4780,7 +4780,7 @@
+ }
+
+ memset (srcbuffs, '\0', sizeof(srcbuffs));
+- TIFFGetField(in, TIFFTAG_BITSPERSAMPLE, &bps);
++ TIFFGetFieldDefaulted(in, TIFFTAG_BITSPERSAMPLE, &bps);
+ TIFFGetFieldDefaulted(in, TIFFTAG_PLANARCONFIG, &planar);
+ TIFFGetFieldDefaulted(in, TIFFTAG_ROWSPERSTRIP, &rps);
+ if (rps > length)
diff --git a/gnu/packages/patches/libtiff-divide-by-zero.patch b/gnu/packages/patches/libtiff-divide-by-zero.patch
new file mode 100644
index 0000000000..6dbd4666cd
--- /dev/null
+++ b/gnu/packages/patches/libtiff-divide-by-zero.patch
@@ -0,0 +1,67 @@
+Fix an integer overflow in TIFFReadEncodedStrip() that led to division-by-zero:
+
+http://bugzilla.maptools.org/show_bug.cgi?id=2596
+
+2016-12-02 Even Rouault <even.rouault at spatialys.com>
+
+ * libtiff/tif_read.c, libtiff/tiffiop.h: fix uint32 overflow in
+ TIFFReadEncodedStrip() that caused an integer division by zero.
+ Reported by Agostino Sarubbo.
+ Fixes http://bugzilla.maptools.org/show_bug.cgi?id=2596
+
+
+/cvs/maptools/cvsroot/libtiff/ChangeLog,v <-- ChangeLog
+new revision: 1.1173; previous revision: 1.1172
+/cvs/maptools/cvsroot/libtiff/libtiff/tif_read.c,v <-- libtiff/tif_read.c
+new revision: 1.50; previous revision: 1.49
+/cvs/maptools/cvsroot/libtiff/libtiff/tiffiop.h,v <-- libtiff/tiffiop.h
+new revision: 1.90; previous revision: 1.89
+
+Index: libtiff/libtiff/tif_read.c
+===================================================================
+RCS file: /cvs/maptools/cvsroot/libtiff/libtiff/tif_read.c,v
+retrieving revision 1.49
+retrieving revision 1.50
+diff -u -r1.49 -r1.50
+--- libtiff/libtiff/tif_read.c 10 Jul 2016 18:00:21 -0000 1.49
++++ libtiff/libtiff/tif_read.c 2 Dec 2016 21:56:56 -0000 1.50
+@@ -1,4 +1,4 @@
+-/* $Id: tif_read.c,v 1.49 2016-07-10 18:00:21 erouault Exp $ */
++/* $Id: tif_read.c,v 1.50 2016-12-02 21:56:56 erouault Exp $ */
+
+ /*
+ * Copyright (c) 1988-1997 Sam Leffler
+@@ -346,7 +346,7 @@
+ rowsperstrip=td->td_rowsperstrip;
+ if (rowsperstrip>td->td_imagelength)
+ rowsperstrip=td->td_imagelength;
+- stripsperplane=((td->td_imagelength+rowsperstrip-1)/rowsperstrip);
++ stripsperplane= TIFFhowmany_32_maxuint_compat(td->td_imagelength, rowsperstrip);
+ stripinplane=(strip%stripsperplane);
+ plane=(uint16)(strip/stripsperplane);
+ rows=td->td_imagelength-stripinplane*rowsperstrip;
+Index: libtiff/libtiff/tiffiop.h
+===================================================================
+RCS file: /cvs/maptools/cvsroot/libtiff/libtiff/tiffiop.h,v
+retrieving revision 1.89
+retrieving revision 1.90
+diff -u -r1.89 -r1.90
+--- libtiff/libtiff/tiffiop.h 23 Jan 2016 21:20:34 -0000 1.89
++++ libtiff/libtiff/tiffiop.h 2 Dec 2016 21:56:56 -0000 1.90
+@@ -1,4 +1,4 @@
+-/* $Id: tiffiop.h,v 1.89 2016-01-23 21:20:34 erouault Exp $ */
++/* $Id: tiffiop.h,v 1.90 2016-12-02 21:56:56 erouault Exp $ */
+
+ /*
+ * Copyright (c) 1988-1997 Sam Leffler
+@@ -250,6 +250,10 @@
+ #define TIFFhowmany_32(x, y) (((uint32)x < (0xffffffff - (uint32)(y-1))) ? \
+ ((((uint32)(x))+(((uint32)(y))-1))/((uint32)(y))) : \
+ 0U)
++/* Variant of TIFFhowmany_32() that doesn't return 0 if x close to MAXUINT. */
++/* Caution: TIFFhowmany_32_maxuint_compat(x,y)*y might overflow */
++#define TIFFhowmany_32_maxuint_compat(x, y) \
++ (((uint32)(x) / (uint32)(y)) + ((((uint32)(x) % (uint32)(y)) != 0) ? 1 : 0))
+ #define TIFFhowmany8_32(x) (((x)&0x07)?((uint32)(x)>>3)+1:(uint32)(x)>>3)
+ #define TIFFroundup_32(x, y) (TIFFhowmany_32(x,y)*(y))
+ #define TIFFhowmany_64(x, y) ((((uint64)(x))+(((uint64)(y))-1))/((uint64)(y)))
diff --git a/gnu/packages/patches/libtiff-heap-overflow-pixarlog-luv.patch b/gnu/packages/patches/libtiff-heap-overflow-pixarlog-luv.patch
new file mode 100644
index 0000000000..2d5e23586d
--- /dev/null
+++ b/gnu/packages/patches/libtiff-heap-overflow-pixarlog-luv.patch
@@ -0,0 +1,131 @@
+Fix heap-based buffer overflow in _TIFFmemcpy():
+
+http://bugzilla.maptools.org/show_bug.cgi?id=2604
+
+2016-12-03 Even Rouault <even.rouault at spatialys.com>
+
+ * libtiff/tif_pixarlog.c, libtiff/tif_luv.c: fix heap-based buffer
+ overflow on generation of PixarLog / LUV compressed files, with
+ ColorMap, TransferFunction attached and nasty plays with bitspersample.
+ The fix for LUV has not been tested, but suffers from the same kind
+ of issue of PixarLog.
+ Reported by Agostino Sarubbo.
+ Fixes http://bugzilla.maptools.org/show_bug.cgi?id=2604
+
+/cvs/maptools/cvsroot/libtiff/ChangeLog,v <-- ChangeLog
+new revision: 1.1175; previous revision: 1.1174
+/cvs/maptools/cvsroot/libtiff/libtiff/tif_luv.c,v <-- libtiff/tif_luv.c
+new revision: 1.44; previous revision: 1.43
+/cvs/maptools/cvsroot/libtiff/libtiff/tif_pixarlog.c,v <--
+libtiff/tif_pixarlog.c
+new revision: 1.49; previous revision: 1.48
+
+Index: libtiff/libtiff/tif_luv.c
+===================================================================
+RCS file: /cvs/maptools/cvsroot/libtiff/libtiff/tif_luv.c,v
+retrieving revision 1.43
+retrieving revision 1.44
+diff -u -r1.43 -r1.44
+--- libtiff/libtiff/tif_luv.c 4 Sep 2016 21:32:56 -0000 1.43
++++ libtiff/libtiff/tif_luv.c 2 Dec 2016 23:05:51 -0000 1.44
+@@ -1,4 +1,4 @@
+-/* $Id: tif_luv.c,v 1.43 2016-09-04 21:32:56 erouault Exp $ */
++/* $Id: tif_luv.c,v 1.44 2016-12-02 23:05:51 erouault Exp $ */
+
+ /*
+ * Copyright (c) 1997 Greg Ward Larson
+@@ -158,6 +158,7 @@
+ typedef struct logLuvState LogLuvState;
+
+ struct logLuvState {
++ int encoder_state; /* 1 if encoder correctly initialized */
+ int user_datafmt; /* user data format */
+ int encode_meth; /* encoding method */
+ int pixel_size; /* bytes per pixel */
+@@ -1552,6 +1553,7 @@
+ td->td_photometric, "must be either LogLUV or LogL");
+ break;
+ }
++ sp->encoder_state = 1;
+ return (1);
+ notsupported:
+ TIFFErrorExt(tif->tif_clientdata, module,
+@@ -1563,19 +1565,27 @@
+ static void
+ LogLuvClose(TIFF* tif)
+ {
++ LogLuvState* sp = (LogLuvState*) tif->tif_data;
+ TIFFDirectory *td = &tif->tif_dir;
+
++ assert(sp != 0);
+ /*
+ * For consistency, we always want to write out the same
+ * bitspersample and sampleformat for our TIFF file,
+ * regardless of the data format being used by the application.
+ * Since this routine is called after tags have been set but
+ * before they have been recorded in the file, we reset them here.
++ * Note: this is really a nasty approach. See PixarLogClose
+ */
+- td->td_samplesperpixel =
+- (td->td_photometric == PHOTOMETRIC_LOGL) ? 1 : 3;
+- td->td_bitspersample = 16;
+- td->td_sampleformat = SAMPLEFORMAT_INT;
++ if( sp->encoder_state )
++ {
++ /* See PixarLogClose. Might avoid issues with tags whose size depends
++ * on those below, but not completely sure this is enough. */
++ td->td_samplesperpixel =
++ (td->td_photometric == PHOTOMETRIC_LOGL) ? 1 : 3;
++ td->td_bitspersample = 16;
++ td->td_sampleformat = SAMPLEFORMAT_INT;
++ }
+ }
+
+ static void
+Index: libtiff/libtiff/tif_pixarlog.c
+===================================================================
+RCS file: /cvs/maptools/cvsroot/libtiff/libtiff/tif_pixarlog.c,v
+retrieving revision 1.48
+retrieving revision 1.49
+diff -u -r1.48 -r1.49
+--- libtiff/libtiff/tif_pixarlog.c 23 Sep 2016 22:12:18 -0000 1.48
++++ libtiff/libtiff/tif_pixarlog.c 2 Dec 2016 23:05:51 -0000 1.49
+@@ -1,4 +1,4 @@
+-/* $Id: tif_pixarlog.c,v 1.48 2016-09-23 22:12:18 erouault Exp $ */
++/* $Id: tif_pixarlog.c,v 1.49 2016-12-02 23:05:51 erouault Exp $ */
+
+ /*
+ * Copyright (c) 1996-1997 Sam Leffler
+@@ -1233,8 +1233,10 @@
+ static void
+ PixarLogClose(TIFF* tif)
+ {
++ PixarLogState* sp = (PixarLogState*) tif->tif_data;
+ TIFFDirectory *td = &tif->tif_dir;
+
++ assert(sp != 0);
+ /* In a really sneaky (and really incorrect, and untruthful, and
+ * troublesome, and error-prone) maneuver that completely goes against
+ * the spirit of TIFF, and breaks TIFF, on close, we covertly
+@@ -1243,8 +1245,19 @@
+ * readers that don't know about PixarLog, or how to set
+ * the PIXARLOGDATFMT pseudo-tag.
+ */
+- td->td_bitspersample = 8;
+- td->td_sampleformat = SAMPLEFORMAT_UINT;
++
++ if (sp->state&PLSTATE_INIT) {
++ /* We test the state to avoid an issue such as in
++ * http://bugzilla.maptools.org/show_bug.cgi?id=2604
++ * What appends in that case is that the bitspersample is 1 and
++ * a TransferFunction is set. The size of the TransferFunction
++ * depends on 1<<bitspersample. So if we increase it, an access
++ * out of the buffer will happen at directory flushing.
++ * Another option would be to clear those targs.
++ */
++ td->td_bitspersample = 8;
++ td->td_sampleformat = SAMPLEFORMAT_UINT;
++ }
+ }
+
+ static void
diff --git a/gnu/packages/patches/libtiff-heap-overflow-tif-dirread.patch b/gnu/packages/patches/libtiff-heap-overflow-tif-dirread.patch
new file mode 100644
index 0000000000..68889b121b
--- /dev/null
+++ b/gnu/packages/patches/libtiff-heap-overflow-tif-dirread.patch
@@ -0,0 +1,132 @@
+Fix heap-based buffer overflow in TIFFFillStrip():
+
+http://bugzilla.maptools.org/show_bug.cgi?id=2608
+
+2016-12-03 Even Rouault <even.rouault at spatialys.com>
+
+ * libtiff/tif_dirread.c: modify ChopUpSingleUncompressedStrip() to
+ instanciate compute ntrips as TIFFhowmany_32(td->td_imagelength,
+rowsperstrip),
+ instead of a logic based on the total size of data. Which is faulty is
+ the total size of data is not sufficient to fill the whole image, and
+thus
+ results in reading outside of the StripByCounts/StripOffsets arrays
+when
+ using TIFFReadScanline().
+ Reported by Agostino Sarubbo.
+ Fixes http://bugzilla.maptools.org/show_bug.cgi?id=2608.
+
+ * libtiff/tif_strip.c: revert the change in TIFFNumberOfStrips() done
+ for http://bugzilla.maptools.org/show_bug.cgi?id=2587 / CVE-2016-9273
+since
+ the above change is a better fix that makes it unnecessary.
+
+/cvs/maptools/cvsroot/libtiff/ChangeLog,v <-- ChangeLog
+new revision: 1.1176; previous revision: 1.1175
+/cvs/maptools/cvsroot/libtiff/libtiff/tif_dirread.c,v <--
+libtiff/tif_dirread.c
+new revision: 1.205; previous revision: 1.204
+/cvs/maptools/cvsroot/libtiff/libtiff/tif_strip.c,v <-- libtiff/tif_strip.c
+new revision: 1.38; previous revision: 1.37
+
+Index: libtiff/libtiff/tif_dirread.c
+===================================================================
+RCS file: /cvs/maptools/cvsroot/libtiff/libtiff/tif_dirread.c,v
+retrieving revision 1.204
+retrieving revision 1.205
+diff -u -r1.204 -r1.205
+--- libtiff/libtiff/tif_dirread.c 16 Nov 2016 15:14:15 -0000 1.204
++++ libtiff/libtiff/tif_dirread.c 3 Dec 2016 11:02:15 -0000 1.205
+@@ -1,4 +1,4 @@
+-/* $Id: tif_dirread.c,v 1.204 2016-11-16 15:14:15 erouault Exp $ */
++/* $Id: tif_dirread.c,v 1.205 2016-12-03 11:02:15 erouault Exp $ */
+
+ /*
+ * Copyright (c) 1988-1997 Sam Leffler
+@@ -5502,8 +5502,7 @@
+ uint64 rowblockbytes;
+ uint64 stripbytes;
+ uint32 strip;
+- uint64 nstrips64;
+- uint32 nstrips32;
++ uint32 nstrips;
+ uint32 rowsperstrip;
+ uint64* newcounts;
+ uint64* newoffsets;
+@@ -5534,18 +5533,17 @@
+ return;
+
+ /*
+- * never increase the number of strips in an image
++ * never increase the number of rows per strip
+ */
+ if (rowsperstrip >= td->td_rowsperstrip)
+ return;
+- nstrips64 = TIFFhowmany_64(bytecount, stripbytes);
+- if ((nstrips64==0)||(nstrips64>0xFFFFFFFF)) /* something is wonky, do nothing. */
+- return;
+- nstrips32 = (uint32)nstrips64;
++ nstrips = TIFFhowmany_32(td->td_imagelength, rowsperstrip);
++ if( nstrips == 0 )
++ return;
+
+- newcounts = (uint64*) _TIFFCheckMalloc(tif, nstrips32, sizeof (uint64),
++ newcounts = (uint64*) _TIFFCheckMalloc(tif, nstrips, sizeof (uint64),
+ "for chopped \"StripByteCounts\" array");
+- newoffsets = (uint64*) _TIFFCheckMalloc(tif, nstrips32, sizeof (uint64),
++ newoffsets = (uint64*) _TIFFCheckMalloc(tif, nstrips, sizeof (uint64),
+ "for chopped \"StripOffsets\" array");
+ if (newcounts == NULL || newoffsets == NULL) {
+ /*
+@@ -5562,18 +5560,18 @@
+ * Fill the strip information arrays with new bytecounts and offsets
+ * that reflect the broken-up format.
+ */
+- for (strip = 0; strip < nstrips32; strip++) {
++ for (strip = 0; strip < nstrips; strip++) {
+ if (stripbytes > bytecount)
+ stripbytes = bytecount;
+ newcounts[strip] = stripbytes;
+- newoffsets[strip] = offset;
++ newoffsets[strip] = stripbytes ? offset : 0;
+ offset += stripbytes;
+ bytecount -= stripbytes;
+ }
+ /*
+ * Replace old single strip info with multi-strip info.
+ */
+- td->td_stripsperimage = td->td_nstrips = nstrips32;
++ td->td_stripsperimage = td->td_nstrips = nstrips;
+ TIFFSetField(tif, TIFFTAG_ROWSPERSTRIP, rowsperstrip);
+
+ _TIFFfree(td->td_stripbytecount);
+Index: libtiff/libtiff/tif_strip.c
+===================================================================
+RCS file: /cvs/maptools/cvsroot/libtiff/libtiff/tif_strip.c,v
+retrieving revision 1.37
+retrieving revision 1.38
+diff -u -r1.37 -r1.38
+--- libtiff/libtiff/tif_strip.c 9 Nov 2016 23:00:49 -0000 1.37
++++ libtiff/libtiff/tif_strip.c 3 Dec 2016 11:02:15 -0000 1.38
+@@ -1,4 +1,4 @@
+-/* $Id: tif_strip.c,v 1.37 2016-11-09 23:00:49 erouault Exp $ */
++/* $Id: tif_strip.c,v 1.38 2016-12-03 11:02:15 erouault Exp $ */
+
+ /*
+ * Copyright (c) 1991-1997 Sam Leffler
+@@ -63,15 +63,6 @@
+ TIFFDirectory *td = &tif->tif_dir;
+ uint32 nstrips;
+
+- /* If the value was already computed and store in td_nstrips, then return it,
+- since ChopUpSingleUncompressedStrip might have altered and resized the
+- since the td_stripbytecount and td_stripoffset arrays to the new value
+- after the initial affectation of td_nstrips = TIFFNumberOfStrips() in
+- tif_dirread.c ~line 3612.
+- See http://bugzilla.maptools.org/show_bug.cgi?id=2587 */
+- if( td->td_nstrips )
+- return td->td_nstrips;
+-
+ nstrips = (td->td_rowsperstrip == (uint32) -1 ? 1 :
+ TIFFhowmany_32(td->td_imagelength, td->td_rowsperstrip));
+ if (td->td_planarconfig == PLANARCONFIG_SEPARATE)
diff --git a/gnu/packages/patches/libtiff-heap-overflow-tiffcp.patch b/gnu/packages/patches/libtiff-heap-overflow-tiffcp.patch
new file mode 100644
index 0000000000..f0fef08bf3
--- /dev/null
+++ b/gnu/packages/patches/libtiff-heap-overflow-tiffcp.patch
@@ -0,0 +1,67 @@
+Fix heap buffer overflow in tiffcp when parsing number of inks:
+
+http://bugzilla.maptools.org/show_bug.cgi?id=2599
+
+2016-12-03 Even Rouault <even.rouault at spatialys.com>
+
+ * tools/tif_dir.c: when TIFFGetField(, TIFFTAG_NUMBEROFINKS, ) is
+called,
+ limit the return number of inks to SamplesPerPixel, so that code that
+parses
+ ink names doesn't go past the end of the buffer.
+ Reported by Agostino Sarubbo.
+ Fixes http://bugzilla.maptools.org/show_bug.cgi?id=2599
+
+
+/cvs/maptools/cvsroot/libtiff/ChangeLog,v <-- ChangeLog
+new revision: 1.1184; previous revision: 1.1183
+/cvs/maptools/cvsroot/libtiff/libtiff/tif_dir.c,v <-- libtiff/tif_dir.c
+new revision: 1.128; previous revision: 1.127
+
+Index: libtiff/libtiff/tif_dir.c
+===================================================================
+RCS file: /cvs/maptools/cvsroot/libtiff/libtiff/tif_dir.c,v
+retrieving revision 1.127
+retrieving revision 1.128
+diff -u -r1.127 -r1.128
+--- libtiff/libtiff/tif_dir.c 25 Oct 2016 21:35:15 -0000 1.127
++++ libtiff/libtiff/tif_dir.c 3 Dec 2016 15:30:31 -0000 1.128
+@@ -1,4 +1,4 @@
+-/* $Id: tif_dir.c,v 1.127 2016-10-25 21:35:15 erouault Exp $ */
++/* $Id: tif_dir.c,v 1.128 2016-12-03 15:30:31 erouault Exp $ */
+
+ /*
+ * Copyright (c) 1988-1997 Sam Leffler
+@@ -854,6 +854,32 @@
+ if( fip == NULL ) /* cannot happen since TIFFGetField() already checks it */
+ return 0;
+
++ if( tag == TIFFTAG_NUMBEROFINKS )
++ {
++ int i;
++ for (i = 0; i < td->td_customValueCount; i++) {
++ uint16 val;
++ TIFFTagValue *tv = td->td_customValues + i;
++ if (tv->info->field_tag != tag)
++ continue;
++ val = *(uint16 *)tv->value;
++ /* Truncate to SamplesPerPixel, since the */
++ /* setting code for INKNAMES assume that there are SamplesPerPixel */
++ /* inknames. */
++ /* Fixes http://bugzilla.maptools.org/show_bug.cgi?id=2599 */
++ if( val > td->td_samplesperpixel )
++ {
++ TIFFWarningExt(tif->tif_clientdata,"_TIFFVGetField",
++ "Truncating NumberOfInks from %u to %u",
++ val, td->td_samplesperpixel);
++ val = td->td_samplesperpixel;
++ }
++ *va_arg(ap, uint16*) = val;
++ return 1;
++ }
++ return 0;
++ }
++
+ /*
+ * We want to force the custom code to be used for custom
+ * fields even if the tag happens to match a well known
diff --git a/gnu/packages/patches/libtiff-heap-overflow-tiffcrop.patch b/gnu/packages/patches/libtiff-heap-overflow-tiffcrop.patch
new file mode 100644
index 0000000000..8166c55758
--- /dev/null
+++ b/gnu/packages/patches/libtiff-heap-overflow-tiffcrop.patch
@@ -0,0 +1,60 @@
+Fix heap-based buffer overflow in combineSeparateSamples16bits():
+
+http://bugzilla.maptools.org/show_bug.cgi?id=2621
+
+2016-12-03 Even Rouault <even.rouault at spatialys.com>
+
+ * tools/tiffcrop.c: add 3 extra bytes at end of strip buffer in
+ readSeparateStripsIntoBuffer() to avoid read outside of heap allocated
+buffer.
+ Reported by Agostina Sarubo.
+ Fixes http://bugzilla.maptools.org/show_bug.cgi?id=2621
+
+/cvs/maptools/cvsroot/libtiff/ChangeLog,v <-- ChangeLog
+new revision: 1.1179; previous revision: 1.1178
+/cvs/maptools/cvsroot/libtiff/tools/tiffcrop.c,v <-- tools/tiffcrop.c
+new revision: 1.48; previous revision: 1.47
+
+Index: libtiff/tools/tiffcrop.c
+===================================================================
+RCS file: /cvs/maptools/cvsroot/libtiff/tools/tiffcrop.c,v
+retrieving revision 1.47
+retrieving revision 1.48
+diff -u -r1.47 -r1.48
+--- libtiff/tools/tiffcrop.c 3 Dec 2016 11:35:56 -0000 1.47
++++ libtiff/tools/tiffcrop.c 3 Dec 2016 12:19:32 -0000 1.48
+@@ -1,4 +1,4 @@
+-/* $Id: tiffcrop.c,v 1.47 2016-12-03 11:35:56 erouault Exp $ */
++/* $Id: tiffcrop.c,v 1.48 2016-12-03 12:19:32 erouault Exp $ */
+
+ /* tiffcrop.c -- a port of tiffcp.c extended to include manipulations of
+ * the image data through additional options listed below
+@@ -4815,10 +4815,17 @@
+ nstrips = TIFFNumberOfStrips(in);
+ strips_per_sample = nstrips /spp;
+
++ /* Add 3 padding bytes for combineSeparateSamples32bits */
++ if( (size_t) stripsize > 0xFFFFFFFFU - 3U )
++ {
++ TIFFError("readSeparateStripsIntoBuffer", "Integer overflow when calculating buffer size.");
++ exit(-1);
++ }
++
+ for (s = 0; (s < spp) && (s < MAX_SAMPLES); s++)
+ {
+ srcbuffs[s] = NULL;
+- buff = _TIFFmalloc(stripsize);
++ buff = _TIFFmalloc(stripsize + 3);
+ if (!buff)
+ {
+ TIFFError ("readSeparateStripsIntoBuffer",
+@@ -4827,6 +4834,9 @@
+ _TIFFfree (srcbuffs[i]);
+ return 0;
+ }
++ buff[stripsize] = 0;
++ buff[stripsize+1] = 0;
++ buff[stripsize+2] = 0;
+ srcbuffs[s] = buff;
+ }
+
diff --git a/gnu/packages/patches/libtiff-invalid-read.patch b/gnu/packages/patches/libtiff-invalid-read.patch
new file mode 100644
index 0000000000..92742d8757
--- /dev/null
+++ b/gnu/packages/patches/libtiff-invalid-read.patch
@@ -0,0 +1,64 @@
+Fix invalid read in t2p_writeproc():
+
+http://bugzilla.maptools.org/show_bug.cgi?id=2639
+
+2016-12-20 Even Rouault <even.rouault at spatialys.com>
+
+ * tools/tiff2pdf.c: avoid potential invalid memory read in
+ t2p_writeproc.
+ Fixes http://bugzilla.maptools.org/show_bug.cgi?id=2639
+
+
+/cvs/maptools/cvsroot/libtiff/ChangeLog,v <-- ChangeLog
+new revision: 1.1198; previous revision: 1.1197
+/cvs/maptools/cvsroot/libtiff/tools/tiff2pdf.c,v <-- tools/tiff2pdf.c
+new revision: 1.100; previous revision: 1.99
+
+Index: libtiff/tools/tiff2pdf.c
+===================================================================
+RCS file: /cvs/maptools/cvsroot/libtiff/tools/tiff2pdf.c,v
+retrieving revision 1.99
+retrieving revision 1.100
+diff -u -r1.99 -r1.100
+--- libtiff/tools/tiff2pdf.c 20 Dec 2016 17:13:26 -0000 1.99
++++ libtiff/tools/tiff2pdf.c 20 Dec 2016 17:24:35 -0000 1.100
+@@ -2896,6 +2896,7 @@
+ }
+ if(TIFFGetField(input, TIFFTAG_JPEGTABLES, &count, &jpt) != 0) {
+ if (count >= 4) {
++ int retTIFFReadRawTile;
+ /* Ignore EOI marker of JpegTables */
+ _TIFFmemcpy(buffer, jpt, count - 2);
+ bufferoffset += count - 2;
+@@ -2903,22 +2904,23 @@
+ table_end[0] = buffer[bufferoffset-2];
+ table_end[1] = buffer[bufferoffset-1];
+ xuint32 = bufferoffset;
+- bufferoffset -= 2;
+- bufferoffset += TIFFReadRawTile(
++ bufferoffset -= 2;
++ retTIFFReadRawTile= TIFFReadRawTile(
+ input,
+ tile,
+ (tdata_t) &(((unsigned char*)buffer)[bufferoffset]),
+ -1);
++ if( retTIFFReadRawTile < 0 )
++ {
++ _TIFFfree(buffer);
++ t2p->t2p_error = T2P_ERR_ERROR;
++ return(0);
++ }
++ bufferoffset += retTIFFReadRawTile;
+ /* Overwrite SOI marker of image scan with previously */
+ /* saved end of JpegTables */
+ buffer[xuint32-2]=table_end[0];
+ buffer[xuint32-1]=table_end[1];
+- } else {
+- bufferoffset += TIFFReadRawTile(
+- input,
+- tile,
+- (tdata_t) &(((unsigned char*)buffer)[bufferoffset]),
+- -1);
+ }
+ }
+ t2pWriteFile(output, (tdata_t) buffer, bufferoffset);
diff --git a/gnu/packages/patches/libtiff-null-dereference.patch b/gnu/packages/patches/libtiff-null-dereference.patch
new file mode 100644
index 0000000000..8c6345b804
--- /dev/null
+++ b/gnu/packages/patches/libtiff-null-dereference.patch
@@ -0,0 +1,42 @@
+Fix NULL pointer dereference in TIFFReadRawData():
+
+http://bugzilla.maptools.org/show_bug.cgi?id=2594
+
+
+2016-12-03 Even Rouault <even.rouault at spatialys.com>
+
+ * tools/tiffinfo.c: fix null pointer dereference in -r mode when
+ * the
+image has
+ no StripByteCount tag.
+ Reported by Agostino Sarubbo.
+ Fixes http://bugzilla.maptools.org/show_bug.cgi?id=2594
+
+/cvs/maptools/cvsroot/libtiff/ChangeLog,v <-- ChangeLog
+new revision: 1.1182; previous revision: 1.1181
+/cvs/maptools/cvsroot/libtiff/tools/tiffinfo.c,v <-- tools/tiffinfo.c
+new revision: 1.26; previous revision: 1.25
+
+Index: libtiff/tools/tiffinfo.c
+===================================================================
+RCS file: /cvs/maptools/cvsroot/libtiff/tools/tiffinfo.c,v
+retrieving revision 1.25
+retrieving revision 1.26
+diff -u -r1.25 -r1.26
+--- libtiff/tools/tiffinfo.c 12 Nov 2016 20:06:05 -0000 1.25
++++ libtiff/tools/tiffinfo.c 3 Dec 2016 14:18:49 -0000 1.26
+@@ -1,4 +1,4 @@
+-/* $Id: tiffinfo.c,v 1.25 2016-11-12 20:06:05 bfriesen Exp $ */
++/* $Id: tiffinfo.c,v 1.26 2016-12-03 14:18:49 erouault Exp $ */
+
+ /*
+ * Copyright (c) 1988-1997 Sam Leffler
+@@ -417,7 +417,7 @@
+ uint64* stripbc=NULL;
+
+ TIFFGetField(tif, TIFFTAG_STRIPBYTECOUNTS, &stripbc);
+- if (nstrips > 0) {
++ if (stripbc != NULL && nstrips > 0) {
+ uint32 bufsize = (uint32) stripbc[0];
+ tdata_t buf = _TIFFmalloc(bufsize);
+ tstrip_t s;
diff --git a/gnu/packages/patches/libtiff-tiffcp-underflow.patch b/gnu/packages/patches/libtiff-tiffcp-underflow.patch
new file mode 100644
index 0000000000..5615cbb3e1
--- /dev/null
+++ b/gnu/packages/patches/libtiff-tiffcp-underflow.patch
@@ -0,0 +1,41 @@
+Fix a integer underflow in tiffcp that led to heap overflows in
+TIFFReverseBits():
+
+http://bugzilla.maptools.org/show_bug.cgi?id=2598
+
+2016-12-02 Even Rouault <even.rouault at spatialys.com>
+
+ * tools/tiffcp.c: avoid uint32 underflow in cpDecodedStrips that
+ can cause various issues, such as buffer overflows in the library.
+ Reported by Agostino Sarubbo.
+ Fixes http://bugzilla.maptools.org/show_bug.cgi?id=2598
+
+
+/cvs/maptools/cvsroot/libtiff/ChangeLog,v <-- ChangeLog
+new revision: 1.1174; previous revision: 1.1173
+/cvs/maptools/cvsroot/libtiff/tools/tiffcp.c,v <-- tools/tiffcp.c
+new revision: 1.56; previous revision: 1.55
+
+Index: libtiff/tools/tiffcp.c
+===================================================================
+RCS file: /cvs/maptools/cvsroot/libtiff/tools/tiffcp.c,v
+retrieving revision 1.55
+retrieving revision 1.56
+diff -u -r1.55 -r1.56
+--- libtiff/tools/tiffcp.c 8 Oct 2016 15:54:57 -0000 1.55
++++ libtiff/tools/tiffcp.c 2 Dec 2016 22:13:32 -0000 1.56
+@@ -1,4 +1,4 @@
+-/* $Id: tiffcp.c,v 1.55 2016-10-08 15:54:57 erouault Exp $ */
++/* $Id: tiffcp.c,v 1.56 2016-12-02 22:13:32 erouault Exp $ */
+
+ /*
+ * Copyright (c) 1988-1997 Sam Leffler
+@@ -985,7 +985,7 @@
+ tstrip_t s, ns = TIFFNumberOfStrips(in);
+ uint32 row = 0;
+ _TIFFmemset(buf, 0, stripsize);
+- for (s = 0; s < ns; s++) {
++ for (s = 0; s < ns && row < imagelength; s++) {
+ tsize_t cc = (row + rowsperstrip > imagelength) ?
+ TIFFVStripSize(in, imagelength - row) : stripsize;
+ if (TIFFReadEncodedStrip(in, s, buf, cc) < 0
diff --git a/gnu/packages/patches/libupnp-CVE-2016-8863.patch b/gnu/packages/patches/libupnp-CVE-2016-8863.patch
new file mode 100644
index 0000000000..9978b39487
--- /dev/null
+++ b/gnu/packages/patches/libupnp-CVE-2016-8863.patch
@@ -0,0 +1,72 @@
+Fix CVE-2016-8863:
+
+https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2016-8863
+https://sourceforge.net/p/pupnp/bugs/133/
+
+Patch copied from upstream source repository:
+
+https://sourceforge.net/p/pupnp/code/ci/9c099c2923ab4d98530ab5204af1738be5bddba7/
+
+From 9c099c2923ab4d98530ab5204af1738be5bddba7 Mon Sep 17 00:00:00 2001
+From: =?UTF-8?q?Uwe=20Kleine-K=C3=B6nig?= <ukleinek@debian.org>
+Date: Thu, 8 Dec 2016 17:11:53 +0100
+Subject: [PATCH] Fix out-of-bound access in create_url_list() (CVE-2016-8863)
+
+If there is an invalid URL in URLS->buf after a valid one, uri_parse is
+called with out pointing after the allocated memory. As uri_parse writes
+to *out before returning an error the loop in create_url_list must be
+stopped early to prevent an out-of-bound access
+
+Bug: https://sourceforge.net/p/pupnp/bugs/133/
+Bug-CVE: https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2016-8863
+Bug-Debian: https://bugs.debian.org/842093
+Bug-Redhat: https://bugzilla.redhat.com/show_bug.cgi?id=1388771
+(cherry picked from commit a0f6e719bc03c4d2fe6a4a42ef6b8761446f520b)
+---
+ upnp/src/gena/gena_device.c | 17 ++++++++++++-----
+ 1 file changed, 12 insertions(+), 5 deletions(-)
+
+diff --git a/upnp/src/gena/gena_device.c b/upnp/src/gena/gena_device.c
+index fb04a29..245c56b 100644
+--- a/upnp/src/gena/gena_device.c
++++ b/upnp/src/gena/gena_device.c
+@@ -1113,7 +1113,7 @@ static int create_url_list(
+ /*! [out] . */
+ URL_list *out)
+ {
+- size_t URLcount = 0;
++ size_t URLcount = 0, URLcount2 = 0;
+ size_t i;
+ int return_code = 0;
+ uri_type temp;
+@@ -1155,16 +1155,23 @@ static int create_url_list(
+ }
+ memcpy( out->URLs, URLS->buff, URLS->size );
+ out->URLs[URLS->size] = 0;
+- URLcount = 0;
+ for( i = 0; i < URLS->size; i++ ) {
+ if( ( URLS->buff[i] == '<' ) && ( i + 1 < URLS->size ) ) {
+ if( ( ( return_code =
+ parse_uri( &out->URLs[i + 1], URLS->size - i + 1,
+- &out->parsedURLs[URLcount] ) ) ==
++ &out->parsedURLs[URLcount2] ) ) ==
+ HTTP_SUCCESS )
+- && ( out->parsedURLs[URLcount].hostport.text.size !=
++ && ( out->parsedURLs[URLcount2].hostport.text.size !=
+ 0 ) ) {
+- URLcount++;
++ URLcount2++;
++ if (URLcount2 >= URLcount)
++ /*
++ * break early here in case there is a bogus URL that
++ * was skipped above. This prevents to access
++ * out->parsedURLs[URLcount] which is beyond the
++ * allocation.
++ */
++ break;
+ } else {
+ if( return_code == UPNP_E_OUTOF_MEMORY ) {
+ free( out->URLs );
+--
+2.11.0
+
diff --git a/gnu/packages/patches/libxml2-CVE-2016-4658.patch b/gnu/packages/patches/libxml2-CVE-2016-4658.patch
new file mode 100644
index 0000000000..a4e1f31fae
--- /dev/null
+++ b/gnu/packages/patches/libxml2-CVE-2016-4658.patch
@@ -0,0 +1,257 @@
+Fix CVE-2016-4658:
+
+https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2016-4658
+
+Patch copied from upstream source repository:
+
+https://git.gnome.org/browse/libxml2/commit/?id=c1d1f7121194036608bf555f08d3062a36fd344b
+
+From c1d1f7121194036608bf555f08d3062a36fd344b Mon Sep 17 00:00:00 2001
+From: Nick Wellnhofer <wellnhofer@aevum.de>
+Date: Tue, 28 Jun 2016 18:34:52 +0200
+Subject: [PATCH] Disallow namespace nodes in XPointer ranges
+
+Namespace nodes must be copied to avoid use-after-free errors.
+But they don't necessarily have a physical representation in a
+document, so simply disallow them in XPointer ranges.
+
+Found with afl-fuzz.
+
+Fixes CVE-2016-4658.
+---
+ xpointer.c | 149 +++++++++++++++++++++++--------------------------------------
+ 1 file changed, 56 insertions(+), 93 deletions(-)
+
+diff --git a/xpointer.c b/xpointer.c
+index a7b03fbd..694d120e 100644
+--- a/xpointer.c
++++ b/xpointer.c
+@@ -320,6 +320,45 @@ xmlXPtrRangesEqual(xmlXPathObjectPtr range1, xmlXPathObjectPtr range2) {
+ }
+
+ /**
++ * xmlXPtrNewRangeInternal:
++ * @start: the starting node
++ * @startindex: the start index
++ * @end: the ending point
++ * @endindex: the ending index
++ *
++ * Internal function to create a new xmlXPathObjectPtr of type range
++ *
++ * Returns the newly created object.
++ */
++static xmlXPathObjectPtr
++xmlXPtrNewRangeInternal(xmlNodePtr start, int startindex,
++ xmlNodePtr end, int endindex) {
++ xmlXPathObjectPtr ret;
++
++ /*
++ * Namespace nodes must be copied (see xmlXPathNodeSetDupNs).
++ * Disallow them for now.
++ */
++ if ((start != NULL) && (start->type == XML_NAMESPACE_DECL))
++ return(NULL);
++ if ((end != NULL) && (end->type == XML_NAMESPACE_DECL))
++ return(NULL);
++
++ ret = (xmlXPathObjectPtr) xmlMalloc(sizeof(xmlXPathObject));
++ if (ret == NULL) {
++ xmlXPtrErrMemory("allocating range");
++ return(NULL);
++ }
++ memset(ret, 0, sizeof(xmlXPathObject));
++ ret->type = XPATH_RANGE;
++ ret->user = start;
++ ret->index = startindex;
++ ret->user2 = end;
++ ret->index2 = endindex;
++ return(ret);
++}
++
++/**
+ * xmlXPtrNewRange:
+ * @start: the starting node
+ * @startindex: the start index
+@@ -344,17 +383,7 @@ xmlXPtrNewRange(xmlNodePtr start, int startindex,
+ if (endindex < 0)
+ return(NULL);
+
+- ret = (xmlXPathObjectPtr) xmlMalloc(sizeof(xmlXPathObject));
+- if (ret == NULL) {
+- xmlXPtrErrMemory("allocating range");
+- return(NULL);
+- }
+- memset(ret, 0 , (size_t) sizeof(xmlXPathObject));
+- ret->type = XPATH_RANGE;
+- ret->user = start;
+- ret->index = startindex;
+- ret->user2 = end;
+- ret->index2 = endindex;
++ ret = xmlXPtrNewRangeInternal(start, startindex, end, endindex);
+ xmlXPtrRangeCheckOrder(ret);
+ return(ret);
+ }
+@@ -381,17 +410,8 @@ xmlXPtrNewRangePoints(xmlXPathObjectPtr start, xmlXPathObjectPtr end) {
+ if (end->type != XPATH_POINT)
+ return(NULL);
+
+- ret = (xmlXPathObjectPtr) xmlMalloc(sizeof(xmlXPathObject));
+- if (ret == NULL) {
+- xmlXPtrErrMemory("allocating range");
+- return(NULL);
+- }
+- memset(ret, 0 , (size_t) sizeof(xmlXPathObject));
+- ret->type = XPATH_RANGE;
+- ret->user = start->user;
+- ret->index = start->index;
+- ret->user2 = end->user;
+- ret->index2 = end->index;
++ ret = xmlXPtrNewRangeInternal(start->user, start->index, end->user,
++ end->index);
+ xmlXPtrRangeCheckOrder(ret);
+ return(ret);
+ }
+@@ -416,17 +436,7 @@ xmlXPtrNewRangePointNode(xmlXPathObjectPtr start, xmlNodePtr end) {
+ if (start->type != XPATH_POINT)
+ return(NULL);
+
+- ret = (xmlXPathObjectPtr) xmlMalloc(sizeof(xmlXPathObject));
+- if (ret == NULL) {
+- xmlXPtrErrMemory("allocating range");
+- return(NULL);
+- }
+- memset(ret, 0 , (size_t) sizeof(xmlXPathObject));
+- ret->type = XPATH_RANGE;
+- ret->user = start->user;
+- ret->index = start->index;
+- ret->user2 = end;
+- ret->index2 = -1;
++ ret = xmlXPtrNewRangeInternal(start->user, start->index, end, -1);
+ xmlXPtrRangeCheckOrder(ret);
+ return(ret);
+ }
+@@ -453,17 +463,7 @@ xmlXPtrNewRangeNodePoint(xmlNodePtr start, xmlXPathObjectPtr end) {
+ if (end->type != XPATH_POINT)
+ return(NULL);
+
+- ret = (xmlXPathObjectPtr) xmlMalloc(sizeof(xmlXPathObject));
+- if (ret == NULL) {
+- xmlXPtrErrMemory("allocating range");
+- return(NULL);
+- }
+- memset(ret, 0 , (size_t) sizeof(xmlXPathObject));
+- ret->type = XPATH_RANGE;
+- ret->user = start;
+- ret->index = -1;
+- ret->user2 = end->user;
+- ret->index2 = end->index;
++ ret = xmlXPtrNewRangeInternal(start, -1, end->user, end->index);
+ xmlXPtrRangeCheckOrder(ret);
+ return(ret);
+ }
+@@ -486,17 +486,7 @@ xmlXPtrNewRangeNodes(xmlNodePtr start, xmlNodePtr end) {
+ if (end == NULL)
+ return(NULL);
+
+- ret = (xmlXPathObjectPtr) xmlMalloc(sizeof(xmlXPathObject));
+- if (ret == NULL) {
+- xmlXPtrErrMemory("allocating range");
+- return(NULL);
+- }
+- memset(ret, 0 , (size_t) sizeof(xmlXPathObject));
+- ret->type = XPATH_RANGE;
+- ret->user = start;
+- ret->index = -1;
+- ret->user2 = end;
+- ret->index2 = -1;
++ ret = xmlXPtrNewRangeInternal(start, -1, end, -1);
+ xmlXPtrRangeCheckOrder(ret);
+ return(ret);
+ }
+@@ -516,17 +506,7 @@ xmlXPtrNewCollapsedRange(xmlNodePtr start) {
+ if (start == NULL)
+ return(NULL);
+
+- ret = (xmlXPathObjectPtr) xmlMalloc(sizeof(xmlXPathObject));
+- if (ret == NULL) {
+- xmlXPtrErrMemory("allocating range");
+- return(NULL);
+- }
+- memset(ret, 0 , (size_t) sizeof(xmlXPathObject));
+- ret->type = XPATH_RANGE;
+- ret->user = start;
+- ret->index = -1;
+- ret->user2 = NULL;
+- ret->index2 = -1;
++ ret = xmlXPtrNewRangeInternal(start, -1, NULL, -1);
+ return(ret);
+ }
+
+@@ -541,6 +521,8 @@ xmlXPtrNewCollapsedRange(xmlNodePtr start) {
+ */
+ xmlXPathObjectPtr
+ xmlXPtrNewRangeNodeObject(xmlNodePtr start, xmlXPathObjectPtr end) {
++ xmlNodePtr endNode;
++ int endIndex;
+ xmlXPathObjectPtr ret;
+
+ if (start == NULL)
+@@ -549,7 +531,12 @@ xmlXPtrNewRangeNodeObject(xmlNodePtr start, xmlXPathObjectPtr end) {
+ return(NULL);
+ switch (end->type) {
+ case XPATH_POINT:
++ endNode = end->user;
++ endIndex = end->index;
++ break;
+ case XPATH_RANGE:
++ endNode = end->user2;
++ endIndex = end->index2;
+ break;
+ case XPATH_NODESET:
+ /*
+@@ -557,39 +544,15 @@ xmlXPtrNewRangeNodeObject(xmlNodePtr start, xmlXPathObjectPtr end) {
+ */
+ if (end->nodesetval->nodeNr <= 0)
+ return(NULL);
++ endNode = end->nodesetval->nodeTab[end->nodesetval->nodeNr - 1];
++ endIndex = -1;
+ break;
+ default:
+ /* TODO */
+ return(NULL);
+ }
+
+- ret = (xmlXPathObjectPtr) xmlMalloc(sizeof(xmlXPathObject));
+- if (ret == NULL) {
+- xmlXPtrErrMemory("allocating range");
+- return(NULL);
+- }
+- memset(ret, 0 , (size_t) sizeof(xmlXPathObject));
+- ret->type = XPATH_RANGE;
+- ret->user = start;
+- ret->index = -1;
+- switch (end->type) {
+- case XPATH_POINT:
+- ret->user2 = end->user;
+- ret->index2 = end->index;
+- break;
+- case XPATH_RANGE:
+- ret->user2 = end->user2;
+- ret->index2 = end->index2;
+- break;
+- case XPATH_NODESET: {
+- ret->user2 = end->nodesetval->nodeTab[end->nodesetval->nodeNr - 1];
+- ret->index2 = -1;
+- break;
+- }
+- default:
+- STRANGE
+- return(NULL);
+- }
++ ret = xmlXPtrNewRangeInternal(start, -1, endNode, endIndex);
+ xmlXPtrRangeCheckOrder(ret);
+ return(ret);
+ }
+--
+2.11.0
+
diff --git a/gnu/packages/patches/libxml2-CVE-2016-5131.patch b/gnu/packages/patches/libxml2-CVE-2016-5131.patch
new file mode 100644
index 0000000000..38938c8e3e
--- /dev/null
+++ b/gnu/packages/patches/libxml2-CVE-2016-5131.patch
@@ -0,0 +1,218 @@
+Fix CVE-2016-5131:
+
+https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2016-5131
+
+Patches copied from upstream source repository (the test suite fails
+without the 2nd patch):
+
+https://git.gnome.org/browse/libxml2/commit/?id=9ab01a277d71f54d3143c2cf333c5c2e9aaedd9e
+https://git.gnome.org/browse/libxml2/commit/?id=a005199330b86dada19d162cae15ef9bdcb6baa8
+
+From 9ab01a277d71f54d3143c2cf333c5c2e9aaedd9e Mon Sep 17 00:00:00 2001
+From: Nick Wellnhofer <wellnhofer@aevum.de>
+Date: Tue, 28 Jun 2016 14:22:23 +0200
+Subject: [PATCH] Fix XPointer paths beginning with range-to
+
+The old code would invoke the broken xmlXPtrRangeToFunction. range-to
+isn't really a function but a special kind of location step. Remove
+this function and always handle range-to in the XPath code.
+
+The old xmlXPtrRangeToFunction could also be abused to trigger a
+use-after-free error with the potential for remote code execution.
+
+Found with afl-fuzz.
+
+Fixes CVE-2016-5131.
+---
+ result/XPath/xptr/vidbase | 13 ++++++++
+ test/XPath/xptr/vidbase | 1 +
+ xpath.c | 7 ++++-
+ xpointer.c | 76 ++++-------------------------------------------
+ 4 files changed, 26 insertions(+), 71 deletions(-)
+
+diff --git a/result/XPath/xptr/vidbase b/result/XPath/xptr/vidbase
+index 8b9e92d6..f19193e7 100644
+--- a/result/XPath/xptr/vidbase
++++ b/result/XPath/xptr/vidbase
+@@ -17,3 +17,16 @@ Object is a Location Set:
+ To node
+ ELEMENT p
+
++
++========================
++Expression: xpointer(range-to(id('chapter2')))
++Object is a Location Set:
++1 : Object is a range :
++ From node
++ /
++ To node
++ ELEMENT chapter
++ ATTRIBUTE id
++ TEXT
++ content=chapter2
++
+diff --git a/test/XPath/xptr/vidbase b/test/XPath/xptr/vidbase
+index b1463830..884b1065 100644
+--- a/test/XPath/xptr/vidbase
++++ b/test/XPath/xptr/vidbase
+@@ -1,2 +1,3 @@
+ xpointer(id('chapter1')/p)
+ xpointer(id('chapter1')/p[1]/range-to(following-sibling::p[2]))
++xpointer(range-to(id('chapter2')))
+diff --git a/xpath.c b/xpath.c
+index d992841e..5a01b1b3 100644
+--- a/xpath.c
++++ b/xpath.c
+@@ -10691,13 +10691,18 @@ xmlXPathCompPathExpr(xmlXPathParserContextPtr ctxt) {
+ lc = 1;
+ break;
+ } else if ((NXT(len) == '(')) {
+- /* Note Type or Function */
++ /* Node Type or Function */
+ if (xmlXPathIsNodeType(name)) {
+ #ifdef DEBUG_STEP
+ xmlGenericError(xmlGenericErrorContext,
+ "PathExpr: Type search\n");
+ #endif
+ lc = 1;
++#ifdef LIBXML_XPTR_ENABLED
++ } else if (ctxt->xptr &&
++ xmlStrEqual(name, BAD_CAST "range-to")) {
++ lc = 1;
++#endif
+ } else {
+ #ifdef DEBUG_STEP
+ xmlGenericError(xmlGenericErrorContext,
+diff --git a/xpointer.c b/xpointer.c
+index 676c5105..d74174a3 100644
+--- a/xpointer.c
++++ b/xpointer.c
+@@ -1332,8 +1332,6 @@ xmlXPtrNewContext(xmlDocPtr doc, xmlNodePtr here, xmlNodePtr origin) {
+ ret->here = here;
+ ret->origin = origin;
+
+- xmlXPathRegisterFunc(ret, (xmlChar *)"range-to",
+- xmlXPtrRangeToFunction);
+ xmlXPathRegisterFunc(ret, (xmlChar *)"range",
+ xmlXPtrRangeFunction);
+ xmlXPathRegisterFunc(ret, (xmlChar *)"range-inside",
+@@ -2243,76 +2241,14 @@ xmlXPtrRangeInsideFunction(xmlXPathParserContextPtr ctxt, int nargs) {
+ * @nargs: the number of args
+ *
+ * Implement the range-to() XPointer function
++ *
++ * Obsolete. range-to is not a real function but a special type of location
++ * step which is handled in xpath.c.
+ */
+ void
+-xmlXPtrRangeToFunction(xmlXPathParserContextPtr ctxt, int nargs) {
+- xmlXPathObjectPtr range;
+- const xmlChar *cur;
+- xmlXPathObjectPtr res, obj;
+- xmlXPathObjectPtr tmp;
+- xmlLocationSetPtr newset = NULL;
+- xmlNodeSetPtr oldset;
+- int i;
+-
+- if (ctxt == NULL) return;
+- CHECK_ARITY(1);
+- /*
+- * Save the expression pointer since we will have to evaluate
+- * it multiple times. Initialize the new set.
+- */
+- CHECK_TYPE(XPATH_NODESET);
+- obj = valuePop(ctxt);
+- oldset = obj->nodesetval;
+- ctxt->context->node = NULL;
+-
+- cur = ctxt->cur;
+- newset = xmlXPtrLocationSetCreate(NULL);
+-
+- for (i = 0; i < oldset->nodeNr; i++) {
+- ctxt->cur = cur;
+-
+- /*
+- * Run the evaluation with a node list made of a single item
+- * in the nodeset.
+- */
+- ctxt->context->node = oldset->nodeTab[i];
+- tmp = xmlXPathNewNodeSet(ctxt->context->node);
+- valuePush(ctxt, tmp);
+-
+- xmlXPathEvalExpr(ctxt);
+- CHECK_ERROR;
+-
+- /*
+- * The result of the evaluation need to be tested to
+- * decided whether the filter succeeded or not
+- */
+- res = valuePop(ctxt);
+- range = xmlXPtrNewRangeNodeObject(oldset->nodeTab[i], res);
+- if (range != NULL) {
+- xmlXPtrLocationSetAdd(newset, range);
+- }
+-
+- /*
+- * Cleanup
+- */
+- if (res != NULL)
+- xmlXPathFreeObject(res);
+- if (ctxt->value == tmp) {
+- res = valuePop(ctxt);
+- xmlXPathFreeObject(res);
+- }
+-
+- ctxt->context->node = NULL;
+- }
+-
+- /*
+- * The result is used as the new evaluation set.
+- */
+- xmlXPathFreeObject(obj);
+- ctxt->context->node = NULL;
+- ctxt->context->contextSize = -1;
+- ctxt->context->proximityPosition = -1;
+- valuePush(ctxt, xmlXPtrWrapLocationSet(newset));
++xmlXPtrRangeToFunction(xmlXPathParserContextPtr ctxt,
++ int nargs ATTRIBUTE_UNUSED) {
++ XP_ERROR(XPATH_EXPR_ERROR);
+ }
+
+ /**
+--
+2.11.0
+
+From a005199330b86dada19d162cae15ef9bdcb6baa8 Mon Sep 17 00:00:00 2001
+From: Nick Wellnhofer <wellnhofer@aevum.de>
+Date: Tue, 28 Jun 2016 14:19:58 +0200
+Subject: [PATCH] Fix comparison with root node in xmlXPathCmpNodes
+
+This change has already been made in xmlXPathCmpNodesExt but not in
+xmlXPathCmpNodes.
+---
+ xpath.c | 4 ++--
+ 1 file changed, 2 insertions(+), 2 deletions(-)
+
+diff --git a/xpath.c b/xpath.c
+index 751665b8..d992841e 100644
+--- a/xpath.c
++++ b/xpath.c
+@@ -3342,13 +3342,13 @@ xmlXPathCmpNodes(xmlNodePtr node1, xmlNodePtr node2) {
+ * compute depth to root
+ */
+ for (depth2 = 0, cur = node2;cur->parent != NULL;cur = cur->parent) {
+- if (cur == node1)
++ if (cur->parent == node1)
+ return(1);
+ depth2++;
+ }
+ root = cur;
+ for (depth1 = 0, cur = node1;cur->parent != NULL;cur = cur->parent) {
+- if (cur == node2)
++ if (cur->parent == node2)
+ return(-1);
+ depth1++;
+ }
+--
+2.11.0
+
diff --git a/gnu/packages/patches/libxt-guix-search-paths.patch b/gnu/packages/patches/libxt-guix-search-paths.patch
new file mode 100644
index 0000000000..c618f48da5
--- /dev/null
+++ b/gnu/packages/patches/libxt-guix-search-paths.patch
@@ -0,0 +1,126 @@
+--- libXt-1.1.5/src/Intrinsic.c 2015-05-01 07:36:20.000000000 +0200
++++ Intrinsic.c 2016-12-12 00:42:16.567388450 +0100
+@@ -1303,21 +1303,101 @@
+ } else (void) strcpy(*rest, string);
+ }
+
+-/*
+- * default path used if environment variable XFILESEARCHPATH
+- * is not defined. Also substitued for %D.
+- * The exact value should be documented in the implementation
+- * notes for any Xt implementation.
++
++
++/*
++ Return the default search path for the function
++ XtResolvePathname to use if XFILESEARCHPATH is
++ not defined.
++
++ It returns the combination the set of values which are the 6 "stems" below,
++ prepended with "/run/current-system/profile", and $GUIX_PROFILE and
++ "$HOME/.guix-profile"
++
++ These values provide the default paths where Guix/GuixSD can expect
++ to find resources for installed packages.
+ */
+-static const char *implementation_default_path(void)
++static const char *guix_default_path(void)
+ {
+-#if defined(WIN32)
+- static char xfilesearchpath[] = "";
+-
+- return xfilesearchpath;
+-#else
+- return XFILESEARCHPATHDEFAULT;
+-#endif
++ static const char *search_path_default_stem[] = {
++ "/lib/X11/%L/%T/%N%C%S",
++ "/lib/X11/%l/%T/%N%C%S",
++ "/lib/X11/%T/%N%C%S",
++ "/lib/X11/%L/%T/%N%S",
++ "/lib/X11/%l/%T/%N%S",
++ "/lib/X11/%T/%N%S"
++ };
++
++#define SIZEOF_STEMS (strlen (search_path_default_stem[0]) \
++ + strlen (search_path_default_stem[1]) \
++ + strlen (search_path_default_stem[2]) \
++ + strlen (search_path_default_stem[3]) \
++ + strlen (search_path_default_stem[4]) \
++ + strlen (search_path_default_stem[5]))
++
++
++ int i;
++ const char *current_profile = "/run/current-system/profile";
++ char *home = getenv ("HOME");
++ char *guix_profile = getenv ("GUIX_PROFILE");
++
++ size_t bytesAllocd = SIZEOF_STEMS + 1;
++
++ /* This function is evaluated multiple times and the calling
++ code assumes that it is idempotent. So we must not allow
++ (say) a changed environment variable to cause it to return
++ something different. */
++ static char *path = NULL;
++ if (path)
++ return path;
++
++ bytesAllocd += 6 * (1 + strlen (current_profile));
++
++ if (guix_profile != NULL)
++ {
++ bytesAllocd += SIZEOF_STEMS;
++ bytesAllocd += 6 * (1 + strlen (guix_profile));
++ }
++
++ if (home != NULL)
++ {
++ bytesAllocd += SIZEOF_STEMS;
++ bytesAllocd += 6 * (1 + strlen(home) + strlen ("/.guix-profile"));
++ }
++
++ path = XtMalloc(bytesAllocd);
++ if (path == NULL) _XtAllocError(NULL);
++
++ memset (path, 0, bytesAllocd);
++
++ for (i = 0 ; i < 6 ; ++i)
++ {
++ strcat (path, current_profile);
++ strcat (path, search_path_default_stem[i]);
++ strcat (path, ":");
++ }
++
++ if (guix_profile != NULL)
++ for (i = 0 ; i < 6 ; ++i)
++ {
++ strcat (path, guix_profile);
++ strcat (path, search_path_default_stem[i]);
++ strcat (path, ":");
++ }
++
++ if (home != NULL)
++ for (i = 0 ; i < 6 ; ++i)
++ {
++ strcat (path, home);
++ strcat (path, "/.guix-profile");
++ strcat (path, search_path_default_stem[i]);
++ strcat (path, ":");
++ }
++
++ /* Remove final : */
++ path[strlen(path) - 1] = '\0';
++
++ return path;
+ }
+
+
+@@ -1345,7 +1425,7 @@
+ {
+ XtPerDisplay pd;
+ static const char *defaultPath = NULL;
+- const char *impl_default = implementation_default_path();
++ const char *impl_default = guix_default_path();
+ int idef_len = strlen(impl_default);
+ char *massagedPath;
+ int bytesAllocd, bytesLeft;
diff --git a/gnu/packages/patches/mcrypt-CVE-2012-4409.patch b/gnu/packages/patches/mcrypt-CVE-2012-4409.patch
index 60cf8e0430..3089f962f7 100644
--- a/gnu/packages/patches/mcrypt-CVE-2012-4409.patch
+++ b/gnu/packages/patches/mcrypt-CVE-2012-4409.patch
@@ -3,30 +3,17 @@ From: Tom Callaway <spot@fedoraproject.org>
Date: Fri, 7 Sep 2012 11:39:29 -0400
Subject: apply fix for CVE-2012-4409 (thanks to Raphael Geissert)
----
- mcrypt-CVE-2012-4409.patch | 12 ++++++++++++
- mcrypt.spec | 10 +++++++++-
- 2 files changed, 21 insertions(+), 1 deletion(-)
- create mode 100644 mcrypt-CVE-2012-4409.patch
-
-diff --git a/mcrypt-CVE-2012-4409.patch b/mcrypt-CVE-2012-4409.patch
-new file mode 100644
-index 0000000..747f428
---- /dev/null
-+++ b/mcrypt-CVE-2012-4409.patch
-@@ -0,0 +1,12 @@
-+diff -up mcrypt-2.6.8/src/extra.c.CVE-2012-4409 mcrypt-2.6.8/src/extra.c
-+--- mcrypt-2.6.8/src/extra.c.CVE-2012-4409 2012-09-07 11:00:55.906870746 -0400
-++++ mcrypt-2.6.8/src/extra.c 2012-09-07 11:00:27.967858365 -0400
-+@@ -242,6 +242,8 @@ int check_file_head(FILE * fstream, char
-+ if (m_getbit(0, sflag) != 0) { /* if the first bit is set */
-+ *salt_size = m_setbit(0, sflag, 0);
-+ if (*salt_size > 0) {
-++ if (*salt_size > sizeof(tmp_buf))
-++ err_quit(_("Salt is too long\n"));
-+ fread(tmp_buf, 1, *salt_size,
-+ fstream);
-+ memmove(salt, tmp_buf, *salt_size);
+--- mcrypt-2.6.8/src/extra.c.CVE-2012-4409 2012-09-07 11:00:55.906870746 -0400
++++ mcrypt-2.6.8/src/extra.c 2012-09-07 11:00:27.967858365 -0400
+@@ -242,6 +242,8 @@ int check_file_head(FILE * fstream, char
+ if (m_getbit(0, sflag) != 0) { /* if the first bit is set */
+ *salt_size = m_setbit(0, sflag, 0);
+ if (*salt_size > 0) {
++ if (*salt_size > sizeof(tmp_buf))
++ err_quit(_("Salt is too long\n"));
+ fread(tmp_buf, 1, *salt_size,
+ fstream);
+ memmove(salt, tmp_buf, *salt_size);
--
cgit v0.12
diff --git a/gnu/packages/patches/mcrypt-CVE-2012-4527.patch b/gnu/packages/patches/mcrypt-CVE-2012-4527.patch
index d931dd174b..dfbf048583 100644
--- a/gnu/packages/patches/mcrypt-CVE-2012-4527.patch
+++ b/gnu/packages/patches/mcrypt-CVE-2012-4527.patch
@@ -3,109 +3,97 @@ From: Tom Callaway <spot@fedoraproject.org>
Date: Tue, 30 Oct 2012 15:39:24 -0400
Subject: apply workaround to CVE-2012-4527
----
- mcrypt-CVE-2012-4527-80-width-patch | 91 +++++++++++++++++++++++++++++++++++++
- mcrypt.spec | 10 +++-
- 2 files changed, 100 insertions(+), 1 deletion(-)
- create mode 100644 mcrypt-CVE-2012-4527-80-width-patch
-
-diff --git a/mcrypt-CVE-2012-4527-80-width-patch b/mcrypt-CVE-2012-4527-80-width-patch
-new file mode 100644
-index 0000000..0eb94d8
---- /dev/null
-+++ b/mcrypt-CVE-2012-4527-80-width-patch
-@@ -0,0 +1,91 @@
-+--- mcrypt-2.6.8.orig/src/mcrypt.c
-++++ mcrypt-2.6.8/src/mcrypt.c
-+@@ -41,6 +41,8 @@
-+ # include <time.h>
-+ #endif
-+
-++#define WIDTH 80
-++
-+ static char rcsid[] =
-+ "$Id: mcrypt.c,v 1.2 2007/11/07 17:10:21 nmav Exp $";
-+
-+@@ -482,7 +484,7 @@
-+ #ifdef HAVE_STAT
-+ if (stream_flag == FALSE) {
-+ if (is_normal_file(file[i]) == FALSE) {
-+- sprintf(tmperr,
-++ snprintf(tmperr, WIDTH,
-+ _
-+ ("%s: %s is not a regular file. Skipping...\n"),
-+ program_name, file[i]);
-+@@ -501,7 +503,7 @@
-+ dinfile = file[i];
-+ if ((isatty(fileno((FILE *) (stdin))) == 1)
-+ && (stream_flag == TRUE) && (force == 0)) { /* not a tty */
-+- sprintf(tmperr,
-++ snprintf(tmperr, WIDTH,
-+ _
-+ ("%s: Encrypted data will not be read from a terminal.\n"),
-+ program_name);
-+@@ -520,7 +522,7 @@
-+ einfile = file[i];
-+ if ((isatty(fileno((FILE *) (stdout))) == 1)
-+ && (stream_flag == TRUE) && (force == 0)) { /* not a tty */
-+- sprintf(tmperr,
-++ snprintf(tmperr, WIDTH,
-+ _
-+ ("%s: Encrypted data will not be written to a terminal.\n"),
-+ program_name);
-+@@ -544,7 +546,7 @@
-+ strcpy(outfile, einfile);
-+ /* if file has already the .nc ignore it */
-+ if (strstr(outfile, ".nc") != NULL) {
-+- sprintf(tmperr,
-++ snprintf(tmperr, WIDTH,
-+ _
-+ ("%s: file %s has the .nc suffix... skipping...\n"),
-+ program_name, outfile);
-+@@ -590,10 +592,10 @@
-+
-+ if (x == 0) {
-+ if (stream_flag == FALSE) {
-+- sprintf(tmperr, _("File %s was decrypted.\n"), dinfile);
-++ snprintf(tmperr, WIDTH, _("File %s was decrypted.\n"), dinfile);
-+ err_warn(tmperr);
-+ } else {
-+- sprintf(tmperr, _("Stdin was decrypted.\n"));
-++ snprintf(tmperr, WIDTH, _("Stdin was decrypted.\n"));
-+ err_warn(tmperr);
-+ }
-+ #ifdef HAVE_STAT
-+@@ -610,7 +612,7 @@
-+
-+ } else {
-+ if (stream_flag == FALSE) {
-+- sprintf(tmperr,
-++ snprintf(tmperr, WIDTH,
-+ _
-+ ("File %s was NOT decrypted successfully.\n"),
-+ dinfile);
-+@@ -636,10 +638,10 @@
-+
-+ if (x == 0) {
-+ if (stream_flag == FALSE) {
-+- sprintf(tmperr, _("File %s was encrypted.\n"), einfile);
-++ snprintf(tmperr, WIDTH, _("File %s was encrypted.\n"), einfile);
-+ err_warn(tmperr);
-+ } else {
-+- sprintf(tmperr, _("Stdin was encrypted.\n"));
-++ snprintf(tmperr, WIDTH, _("Stdin was encrypted.\n"));
-+ err_warn(tmperr);
-+ }
-+ #ifdef HAVE_STAT
-+@@ -655,7 +657,7 @@
-+
-+ } else {
-+ if (stream_flag == FALSE) {
-+- sprintf(tmperr,
-++ snprintf(tmperr, WIDTH,
-+ _
-+ ("File %s was NOT encrypted successfully.\n"),
-+ einfile);
---
-cgit v0.12
+--- mcrypt-2.6.8.orig/src/mcrypt.c
++++ mcrypt-2.6.8/src/mcrypt.c
+@@ -41,6 +41,8 @@
+ # include <time.h>
+ #endif
+
++#define WIDTH 80
++
+ static char rcsid[] =
+ "$Id: mcrypt.c,v 1.2 2007/11/07 17:10:21 nmav Exp $";
+
+@@ -482,7 +484,7 @@
+ #ifdef HAVE_STAT
+ if (stream_flag == FALSE) {
+ if (is_normal_file(file[i]) == FALSE) {
+- sprintf(tmperr,
++ snprintf(tmperr, WIDTH,
+ _
+ ("%s: %s is not a regular file. Skipping...\n"),
+ program_name, file[i]);
+@@ -501,7 +503,7 @@
+ dinfile = file[i];
+ if ((isatty(fileno((FILE *) (stdin))) == 1)
+ && (stream_flag == TRUE) && (force == 0)) { /* not a tty */
+- sprintf(tmperr,
++ snprintf(tmperr, WIDTH,
+ _
+ ("%s: Encrypted data will not be read from a terminal.\n"),
+ program_name);
+@@ -520,7 +522,7 @@
+ einfile = file[i];
+ if ((isatty(fileno((FILE *) (stdout))) == 1)
+ && (stream_flag == TRUE) && (force == 0)) { /* not a tty */
+- sprintf(tmperr,
++ snprintf(tmperr, WIDTH,
+ _
+ ("%s: Encrypted data will not be written to a terminal.\n"),
+ program_name);
+@@ -544,7 +546,7 @@
+ strcpy(outfile, einfile);
+ /* if file has already the .nc ignore it */
+ if (strstr(outfile, ".nc") != NULL) {
+- sprintf(tmperr,
++ snprintf(tmperr, WIDTH,
+ _
+ ("%s: file %s has the .nc suffix... skipping...\n"),
+ program_name, outfile);
+@@ -590,10 +592,10 @@
+
+ if (x == 0) {
+ if (stream_flag == FALSE) {
+- sprintf(tmperr, _("File %s was decrypted.\n"), dinfile);
++ snprintf(tmperr, WIDTH, _("File %s was decrypted.\n"), dinfile);
+ err_warn(tmperr);
+ } else {
+- sprintf(tmperr, _("Stdin was decrypted.\n"));
++ snprintf(tmperr, WIDTH, _("Stdin was decrypted.\n"));
+ err_warn(tmperr);
+ }
+ #ifdef HAVE_STAT
+@@ -610,7 +612,7 @@
+
+ } else {
+ if (stream_flag == FALSE) {
+- sprintf(tmperr,
++ snprintf(tmperr, WIDTH,
+ _
+ ("File %s was NOT decrypted successfully.\n"),
+ dinfile);
+@@ -636,10 +638,10 @@
+
+ if (x == 0) {
+ if (stream_flag == FALSE) {
+- sprintf(tmperr, _("File %s was encrypted.\n"), einfile);
++ snprintf(tmperr, WIDTH, _("File %s was encrypted.\n"), einfile);
+ err_warn(tmperr);
+ } else {
+- sprintf(tmperr, _("Stdin was encrypted.\n"));
++ snprintf(tmperr, WIDTH, _("Stdin was encrypted.\n"));
+ err_warn(tmperr);
+ }
+ #ifdef HAVE_STAT
+@@ -655,7 +657,7 @@
+
+ } else {
+ if (stream_flag == FALSE) {
+- sprintf(tmperr,
++ snprintf(tmperr, WIDTH,
+ _
+ ("File %s was NOT encrypted successfully.\n"),
+ einfile);
+-
+git v0.12
diff --git a/gnu/packages/patches/multiqc-fix-git-subprocess-error.patch b/gnu/packages/patches/multiqc-fix-git-subprocess-error.patch
new file mode 100644
index 0000000000..87be6142f4
--- /dev/null
+++ b/gnu/packages/patches/multiqc-fix-git-subprocess-error.patch
@@ -0,0 +1,16 @@
+Without this patch, the incorrect exception is caught when 'git' is not in
+PATH. See https://github.com/ewels/MultiQC/pull/377.
+
+diff --git a/multiqc/utils/config.py b/multiqc/utils/config.py
+index 01fa554..4a11793 100755
+--- a/multiqc/utils/config.py
++++ b/multiqc/utils/config.py
+@@ -28,7 +28,7 @@ try:
+ git_hash = subprocess.check_output(['git', 'rev-parse', 'HEAD'], stderr=subprocess.STDOUT)
+ git_hash_short = git_hash[:7]
+ version = '{} ({})'.format(version, git_hash_short)
+-except subprocess.CalledProcessError:
++except (subprocess.CalledProcessError, FileNotFoundError):
+ pass
+ os.chdir(cwd)
+
diff --git a/gnu/packages/patches/ocaml-Add-a-.file-directive.patch b/gnu/packages/patches/ocaml-Add-a-.file-directive.patch
new file mode 100644
index 0000000000..07842e9c32
--- /dev/null
+++ b/gnu/packages/patches/ocaml-Add-a-.file-directive.patch
@@ -0,0 +1,96 @@
+From: Stephane Glondu <steph@glondu.net>
+Date: Sun, 16 Aug 2015 20:59:14 +0200
+Subject: Add a .file directive to generated .s files
+
+When no .file directive is given, the toolchain records the filename
+of the .o file, which is sometimes random, making generated objects
+non-deterministic.
+
+We use Location.input_name for adding .file directives to assembly
+files. Note: when the file is preprocessed, this reference holds the
+name of the temporary file. Hence, files compiled with -pp are still
+not deterministic.
+
+Bug-Debian: https://bugs.debian.org/795784
+Bug-Debian: https://bugs.debian.org/796336
+---
+ asmcomp/amd64/emit.mlp | 1 +
+ asmcomp/arm/emit.mlp | 1 +
+ asmcomp/arm64/emit.mlp | 1 +
+ asmcomp/i386/emit.mlp | 1 +
+ asmcomp/power/emit.mlp | 1 +
+ asmcomp/sparc/emit.mlp | 1 +
+ 6 files changed, 6 insertions(+)
+
+diff --git a/asmcomp/amd64/emit.mlp b/asmcomp/amd64/emit.mlp
+index d56d0f5..4d7aa30 100644
+--- a/asmcomp/amd64/emit.mlp
++++ b/asmcomp/amd64/emit.mlp
+@@ -794,6 +794,7 @@ let data l =
+ let begin_assembly() =
+ reset_debug_info(); (* PR#5603 *)
+ float_constants := [];
++ ` .file \"{emit_string (String.escaped !Location.input_name)}\"\n`;
+ if !Clflags.dlcode then begin
+ (* from amd64.S; could emit these constants on demand *)
+ if macosx then
+diff --git a/asmcomp/arm/emit.mlp b/asmcomp/arm/emit.mlp
+index 4948fb2..6f30fba 100644
+--- a/asmcomp/arm/emit.mlp
++++ b/asmcomp/arm/emit.mlp
+@@ -892,6 +892,7 @@ let data l =
+
+ let begin_assembly() =
+ reset_debug_info();
++ ` .file \"{emit_string (String.escaped !Location.input_name)}\"\n`;
+ ` .syntax unified\n`;
+ begin match !arch with
+ | ARMv4 -> ` .arch armv4t\n`
+diff --git a/asmcomp/arm64/emit.mlp b/asmcomp/arm64/emit.mlp
+index 750c2b2..5afbb8a 100644
+--- a/asmcomp/arm64/emit.mlp
++++ b/asmcomp/arm64/emit.mlp
+@@ -942,6 +942,7 @@ let data l =
+
+ let begin_assembly() =
+ reset_debug_info();
++ ` .file \"{emit_string (String.escaped !Location.input_name)}\"\n`;
+ let lbl_begin = Compilenv.make_symbol (Some "data_begin") in
+ ` .data\n`;
+ ` .globl {emit_symbol lbl_begin}\n`;
+diff --git a/asmcomp/i386/emit.mlp b/asmcomp/i386/emit.mlp
+index 98df5f9..531150f 100644
+--- a/asmcomp/i386/emit.mlp
++++ b/asmcomp/i386/emit.mlp
+@@ -986,6 +986,7 @@ let data l =
+ let begin_assembly() =
+ reset_debug_info(); (* PR#5603 *)
+ float_constants := [];
++ ` .file \"{emit_string (String.escaped !Location.input_name)}\"\n`;
+ let lbl_begin = Compilenv.make_symbol (Some "data_begin") in
+ ` .data\n`;
+ ` .globl {emit_symbol lbl_begin}\n`;
+diff --git a/asmcomp/power/emit.mlp b/asmcomp/power/emit.mlp
+index 4344085..343132b 100644
+--- a/asmcomp/power/emit.mlp
++++ b/asmcomp/power/emit.mlp
+@@ -887,6 +887,7 @@ let data l =
+ let begin_assembly() =
+ defined_functions := StringSet.empty;
+ external_functions := StringSet.empty;
++ ` .file \"{emit_string (String.escaped !Location.input_name)}\"\n`;
+ (* Emit the beginning of the segments *)
+ let lbl_begin = Compilenv.make_symbol (Some "data_begin") in
+ emit_string data_space;
+diff --git a/asmcomp/sparc/emit.mlp b/asmcomp/sparc/emit.mlp
+index 877a3d5..7b041e9 100644
+--- a/asmcomp/sparc/emit.mlp
++++ b/asmcomp/sparc/emit.mlp
+@@ -727,6 +727,7 @@ let data l =
+ (* Beginning / end of an assembly file *)
+
+ let begin_assembly() =
++ ` .file \"{emit_string (String.escaped !Location.input_name)}\"\n`;
+ let lbl_begin = Compilenv.make_symbol (Some "data_begin") in
+ ` .data\n`;
+ ` .global {emit_symbol lbl_begin}\n`;
diff --git a/gnu/packages/patches/ocaml-bisect-fix-camlp4-in-another-directory.patch b/gnu/packages/patches/ocaml-bisect-fix-camlp4-in-another-directory.patch
new file mode 100644
index 0000000000..2056b42356
--- /dev/null
+++ b/gnu/packages/patches/ocaml-bisect-fix-camlp4-in-another-directory.patch
@@ -0,0 +1,125 @@
+From 26cac62fe0154cf65c06faaee10805531e9dade8 Mon Sep 17 00:00:00 2001
+From: Julien Lepiller <julien@lepiller.eu>
+Date: Wed, 14 Dec 2016 14:14:59 +0100
+Subject: [PATCH] fix camlp4 in another directory
+
+---
+ Makefile | 11 ++++++-----
+ configure | 13 ++++++++++++-
+ myocamlbuild.ml | 2 +-
+ 3 files changed, 19 insertions(+), 7 deletions(-)
+
+diff --git a/Makefile b/Makefile
+index 4a8ce17..d94a6d5 100644
+--- a/Makefile
++++ b/Makefile
+@@ -25,7 +25,7 @@ PATH_BUILD=$(PATH_BASE)/_build
+ PATH_OCAMLDOC=$(PATH_BASE)/ocamldoc
+ PATH_SRC=$(PATH_BASE)/src
+ PATH_TESTS=$(PATH_BASE)/tests
+-PATH_INSTALL=$(PATH_OCAML_PREFIX)/lib/ocaml/bisect
++PATH_INSTALL=$(PREFIX)/lib/ocaml/bisect
+
+
+ # DEFINITIONS
+@@ -33,7 +33,8 @@ PATH_INSTALL=$(PATH_OCAML_PREFIX)/lib/ocaml/bisect
+ PROJECT_NAME=bisect
+ OCAMLBUILD=$(PATH_OCAML_PREFIX)/bin/ocamlbuild
+ OCAMLBUILD_ENV=WARNINGS=$(WARNINGS) PATH_OCAML_PREFIX=$(PATH_OCAML_PREFIX)
+-OCAMLBUILD_FLAGS=-classic-display -no-links
++CAMLP4_INCLUDE=$(shell test -z $(CAMLP4_LIBDIR) || echo "-cflags -I,$(CAMLP4_LIBDIR)")
++OCAMLBUILD_FLAGS=-classic-display -no-links $(CAMLP4_INCLUDE)
+ MODULES_ODOCL=$(PROJECT_NAME).odocl
+ MODULES_MLPACK=$(PROJECT_NAME).mlpack
+ MODULES_MLPACK_PP=$(PROJECT_NAME)_pp.mlpack
+@@ -80,11 +81,11 @@ veryclean: clean
+ rm -f $(PATH_OCAMLDOC)/*.html $(PATH_OCAMLDOC)/*.css
+
+ install: FORCE
+- cp $(PATH_BUILD)/src/report/report.byte $(PATH_OCAML_PREFIX)/bin/bisect-report; \
++ cp $(PATH_BUILD)/src/report/report.byte $(PREFIX)/bin/bisect-report; \
+ if [ "$(PPX)" = "TRUE" ]; then \
+- cp $(PATH_BUILD)/src/syntax/bisect_ppx.byte $(PATH_OCAML_PREFIX)/bin; \
++ cp $(PATH_BUILD)/src/syntax/bisect_ppx.byte $(PREFIX)/bin; \
+ fi; \
+- (test -x $(PATH_OCAML_PREFIX)/bin/ocamlopt && cp $(PATH_BUILD)/src/report/report.native $(PATH_OCAML_PREFIX)/bin/bisect-report.opt || true); \
++ (test -x $(PATH_OCAML_PREFIX)/bin/ocamlopt && cp $(PATH_BUILD)/src/report/report.native $(PREFIX)/bin/bisect-report.opt || true); \
+ if [ -x "$(PATH_OCAMLFIND)" ]; then \
+ $(PATH_OCAMLFIND) query $(PROJECT_NAME) && $(PATH_OCAMLFIND) remove $(PROJECT_NAME) || true; \
+ $(PATH_OCAMLFIND) install $(PROJECT_NAME) META -optional \
+diff --git a/configure b/configure
+index bb7ebf4..61a3095 100755
+--- a/configure
++++ b/configure
+@@ -21,7 +21,9 @@
+ # default values
+ ocamlbuild=`which ocamlbuild || echo '/usr/local/bin/ocamlbuild'`
+ bin_path=`dirname $ocamlbuild`
++prefix=''
+ ocaml_prefix=`dirname $bin_path`
++camlp4_prefix=`dirname $(dirname $(which camlp4of))`
+ ocamlfind=`which ocamlfind 2> /dev/null || echo ''`
+ native_dynlink='TRUE'
+ devel='FALSE'
+@@ -32,8 +34,12 @@ ppx='FALSE'
+ while [ $# -gt 0 ]
+ do
+ case "$1" in
++ -prefix)
++ prefix="$2"; shift;;
+ -ocaml-prefix)
+ ocaml_prefix="$2"; shift;;
++ -camlp4-prefix)
++ camlp4_prefix="$2"; shift;;
+ -ocamlfind)
+ ocamlfind="$2"; shift;;
+ -no-native-dynlink)
+@@ -45,7 +51,7 @@ do
+ -ppx)
+ ppx='TRUE';;
+ *)
+- echo "usage: $0 [-ocaml-prefix <path>] [-ocamlfind <path>] [-no-native-dynlink] [-devel]";
++ echo "usage: $0 [-prefix <path>] [-ocaml-prefix <path>] [-ocamlfind <path>] [-no-native-dynlink] [-devel]";
+ exit 1;;
+ esac
+ shift
+@@ -57,6 +63,9 @@ if [ "$no_camlp4" = "TRUE" -a "$ppx" = "FALSE" ]; then
+ exit 1
+ fi
+
++# prefix default value
++test -z $prefix && prefix=$ocaml_prefix
++
+ # make options
+ make_quiet=`make -f - <<EOF
+ default: gnumake
+@@ -67,11 +76,13 @@ EOF`
+ # file creation
+ echo "# timestamp: `date`" > Makefile.config
+ echo "PATH_OCAML_PREFIX=$ocaml_prefix" >> Makefile.config
++echo "PATH_CAMLP4_PREFIX=$camlp4_prefix" >> Makefile.config
+ echo "PATH_OCAMLFIND=$ocamlfind" >> Makefile.config
+ echo "NATIVE_DYNLINK=$native_dynlink" >> Makefile.config
+ echo "WARNINGS=$devel" >> Makefile.config
+ echo "NO_CAMLP4=$no_camlp4" >> Makefile.config
+ echo "PPX=$ppx" >> Makefile.config
+ echo "MAKE_QUIET=$make_quiet" >> Makefile.config
++echo "PREFIX=$prefix" >> Makefile.config
+ echo "" >> Makefile.config
+ echo 'Makefile.config successfully created'
+diff --git a/myocamlbuild.ml b/myocamlbuild.ml
+index 8aa25fd..09a7d48 100644
+--- a/myocamlbuild.ml
++++ b/myocamlbuild.ml
+@@ -70,7 +70,7 @@ let () =
+ | After_rules ->
+ let camlp4of =
+ try
+- let path_bin = Filename.concat (Sys.getenv "PATH_OCAML_PREFIX") "bin" in
++ let path_bin = Filename.concat (Sys.getenv "PATH_CAMLP4_PREFIX") "bin" in
+ Filename.concat path_bin "camlp4of"
+ with _ -> "camlp4of" in
+ flag ["ocaml"; "compile"; "pp_camlp4of"] (S[A"-pp"; A camlp4of]);
+--
+2.7.4
+
diff --git a/gnu/packages/patches/ocaml-bitstring-fix-configure.patch b/gnu/packages/patches/ocaml-bitstring-fix-configure.patch
new file mode 100644
index 0000000000..c358bf3d6b
--- /dev/null
+++ b/gnu/packages/patches/ocaml-bitstring-fix-configure.patch
@@ -0,0 +1,53 @@
+From 0aaddfceeea3e89df196ab1846da54d09713a512 Mon Sep 17 00:00:00 2001
+From: Julien Lepiller <julien@lepiller.eu>
+Date: Thu, 15 Dec 2016 21:17:31 +0100
+Subject: [PATCH] fix configure
+
+---
+ Makefile.in | 9 +++++----
+ 1 file changed, 5 insertions(+), 4 deletions(-)
+
+diff --git a/Makefile.in b/Makefile.in
+index d040f4c..85e0b38 100644
+--- a/Makefile.in
++++ b/Makefile.in
+@@ -32,6 +32,7 @@ BISECT_REPORT = @BISECT_REPORT@
+ BYTESWAP_H = @BYTESWAP_H@
+
+ OCAMLLIB = @OCAMLLIB@
++BISECTLIB = $(shell if test -z $${BISECTLIB}; then echo $(OCAMLLIB); else echo $${BISECTLIB}; fi)
+ top_srcdir = @top_srcdir@
+
+ pkg_cil = @OCAML_PKG_cil@
+@@ -47,9 +48,9 @@ OCAMLOPTPACKAGES = $(OCAMLCPACKAGES)
+ OCAMLOPTLIBS = -linkpkg
+
+ ifneq ($(enable_coverage),no)
+-OCAMLCFLAGS += -I +bisect -pp 'camlp4o $(OCAMLLIB)/bisect/instrument.cma'
++OCAMLCFLAGS += -I +bisect -pp 'camlp4o $(BISECTLIB)/bisect/instrument.cma'
+ OCAMLCLIBS += -I +bisect bisect.cma
+-OCAMLOPTFLAGS += -I +bisect -pp 'camlp4o $(OCAMLLIB)/bisect/instrument.cma'
++OCAMLOPTFLAGS += -I +bisect -pp 'camlp4o $(BISECTLIB)/bisect/instrument.cma'
+ OCAMLOPTLIBS += -I +bisect bisect.cmxa
+ endif
+
+@@ -110,7 +111,7 @@ bitstring_persistent.cmi: bitstring_persistent.mli
+ -I +camlp4 -pp camlp4of -c $<
+
+ pa_bitstring.cmo: pa_bitstring.ml bitstring.cma bitstring_persistent.cma
+- $(OCAMLFIND) ocamlc bitstring.cma -I +camlp4 dynlink.cma camlp4lib.cma \
++ $(OCAMLFIND) ocamlc $(OCAMLCFLAGS) bitstring.cma -I +camlp4 dynlink.cma camlp4lib.cma \
+ -pp camlp4of -c $< -o $@
+
+ bitstring-objinfo: bitstring_objinfo.cmo bitstring.cma bitstring_persistent.cma
+@@ -133,7 +134,7 @@ byteswap.h: byteswap.in.h
+ ifeq ($(enable_coverage),no)
+ PP = -pp 'camlp4o bitstring.cma bitstring_persistent.cma pa_bitstring.cmo'
+ else
+-PP = -pp 'camlp4o $(OCAMLLIB)/bisect/bisect.cma bitstring.cma bitstring_persistent.cma pa_bitstring.cmo'
++PP = -pp 'camlp4o $(BISECTLIB)/bisect/bisect.cma bitstring.cma bitstring_persistent.cma pa_bitstring.cmo'
+ endif
+
+ check: test
+--
+2.11.0
diff --git a/gnu/packages/patches/openssh-memory-exhaustion.patch b/gnu/packages/patches/openssh-memory-exhaustion.patch
deleted file mode 100644
index 91fe294ca4..0000000000
--- a/gnu/packages/patches/openssh-memory-exhaustion.patch
+++ /dev/null
@@ -1,39 +0,0 @@
-Fix a memory exhaustion bug in the key exchange, whereby an unauthenticated user
-could potentially consume 38400 MB of memory on the server:
-
-http://seclists.org/oss-sec/2016/q4/185
-
-Patch adapted from upstream source repository:
-
-https://github.com/openssh/openssh-portable/commit/ec165c392ca54317dbe3064a8c200de6531e89ad
-
-From ec165c392ca54317dbe3064a8c200de6531e89ad Mon Sep 17 00:00:00 2001
-From: "markus@openbsd.org" <markus@openbsd.org>
-Date: Mon, 10 Oct 2016 19:28:48 +0000
-Subject: [PATCH] upstream commit
-
-Unregister the KEXINIT handler after message has been
-received. Otherwise an unauthenticated peer can repeat the KEXINIT and cause
-allocation of up to 128MB -- until the connection is closed. Reported by
-shilei-c at 360.cn
-
-Upstream-ID: 43649ae12a27ef94290db16d1a98294588b75c05
----
- kex.c | 3 ++-
- 1 file changed, 2 insertions(+), 1 deletion(-)
-
-diff --git a/kex.c b/kex.c
-index 3f97f8c..6a94bc5 100644
---- a/kex.c
-+++ b/kex.c
-@@ -481,6 +481,7 @@ kex_input_kexinit(int type, u_int32_t seq, void *ctxt)
- if (kex == NULL)
- return SSH_ERR_INVALID_ARGUMENT;
-
-+ ssh_dispatch_set(ssh, SSH2_MSG_KEXINIT, NULL);
- ptr = sshpkt_ptr(ssh, &dlen);
- if ((r = sshbuf_put(kex->peer, ptr, dlen)) != 0)
- return r;
---
-2.10.1
-
diff --git a/gnu/packages/patches/python-dendropy-exclude-failing-tests.patch b/gnu/packages/patches/python-dendropy-exclude-failing-tests.patch
deleted file mode 100644
index 288a58b06f..0000000000
--- a/gnu/packages/patches/python-dendropy-exclude-failing-tests.patch
+++ /dev/null
@@ -1,21 +0,0 @@
-diff --git a/dendropy/test/test_phylogenetic_distance_matrix.py b/dendropy/test/test_phylogenetic_distance_matrix.py
-index 10c05f5..a18ba52 100644
---- a/dendropy/test/test_phylogenetic_distance_matrix.py
-+++ b/dendropy/test/test_phylogenetic_distance_matrix.py
-@@ -793,7 +793,7 @@ class PdmUpgmaTree(PdmTreeChecker, unittest.TestCase):
- expected_tree=expected_tree)
-
- class NodeToNodeDistancesTest(unittest.TestCase):
--
-+ @unittest.expectedFailure
- def test_distances(self):
- ## get distances from ape
- # library(ape)
-@@ -825,6 +825,7 @@ class NodeToNodeDistancesTest(unittest.TestCase):
- e = reference_table[nd1.label, nd2.label]
- self.assertAlmostEqual(d, e)
-
-+ @unittest.expectedFailure
- def test_mrca(self):
- test_runs = [
- "hiv1.newick",
diff --git a/gnu/packages/patches/python-pycrypto-CVE-2013-7459.patch b/gnu/packages/patches/python-pycrypto-CVE-2013-7459.patch
new file mode 100644
index 0000000000..3570b94e9b
--- /dev/null
+++ b/gnu/packages/patches/python-pycrypto-CVE-2013-7459.patch
@@ -0,0 +1,97 @@
+Fix CVE-2013-7459:
+
+https://github.com/dlitz/pycrypto/issues/176
+https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2013-7459
+
+Copied from Debian:
+
+https://anonscm.debian.org/cgit/collab-maint/python-crypto.git/commit/?id=0de2243837ed369a086f15c50cca2be85bdfab9d
+
+Debian adapts this upstream commit:
+
+https://github.com/dlitz/pycrypto/commit/8dbe0dc3eea5c689d4f76b37b93fe216cf1f00d4
+
+From 8dbe0dc3eea5c689d4f76b37b93fe216cf1f00d4 Mon Sep 17 00:00:00 2001
+From: Legrandin <helderijs@gmail.com>
+Date: Sun, 22 Dec 2013 22:24:46 +0100
+Subject: [PATCH] Throw exception when IV is used with ECB or CTR
+
+The IV parameter is currently ignored when initializing
+a cipher in ECB or CTR mode.
+
+For CTR mode, it is confusing: it takes some time to see
+that a different parameter is needed (the counter).
+
+For ECB mode, it is outright dangerous.
+
+This patch forces an exception to be raised.
+---
+ lib/Crypto/SelfTest/Cipher/common.py | 31 +++++++++++++++++++++++--------
+ src/block_template.c | 11 +++++++++++
+ 2 files changed, 34 insertions(+), 8 deletions(-)
+
+--- a/lib/Crypto/SelfTest/Cipher/common.py
++++ b/lib/Crypto/SelfTest/Cipher/common.py
+@@ -239,19 +239,34 @@ class RoundtripTest(unittest.TestCase):
+ return """%s .decrypt() output of .encrypt() should not be garbled""" % (self.module_name,)
+
+ def runTest(self):
+- for mode in (self.module.MODE_ECB, self.module.MODE_CBC, self.module.MODE_CFB, self.module.MODE_OFB, self.module.MODE_OPENPGP):
++
++ ## ECB mode
++ mode = self.module.MODE_ECB
++ encryption_cipher = self.module.new(a2b_hex(self.key), mode)
++ ciphertext = encryption_cipher.encrypt(self.plaintext)
++ decryption_cipher = self.module.new(a2b_hex(self.key), mode)
++ decrypted_plaintext = decryption_cipher.decrypt(ciphertext)
++ self.assertEqual(self.plaintext, decrypted_plaintext)
++
++ ## OPENPGP mode
++ mode = self.module.MODE_OPENPGP
++ encryption_cipher = self.module.new(a2b_hex(self.key), mode, self.iv)
++ eiv_ciphertext = encryption_cipher.encrypt(self.plaintext)
++ eiv = eiv_ciphertext[:self.module.block_size+2]
++ ciphertext = eiv_ciphertext[self.module.block_size+2:]
++ decryption_cipher = self.module.new(a2b_hex(self.key), mode, eiv)
++ decrypted_plaintext = decryption_cipher.decrypt(ciphertext)
++ self.assertEqual(self.plaintext, decrypted_plaintext)
++
++ ## All other non-AEAD modes (but CTR)
++ for mode in (self.module.MODE_CBC, self.module.MODE_CFB, self.module.MODE_OFB):
+ encryption_cipher = self.module.new(a2b_hex(self.key), mode, self.iv)
+ ciphertext = encryption_cipher.encrypt(self.plaintext)
+-
+- if mode != self.module.MODE_OPENPGP:
+- decryption_cipher = self.module.new(a2b_hex(self.key), mode, self.iv)
+- else:
+- eiv = ciphertext[:self.module.block_size+2]
+- ciphertext = ciphertext[self.module.block_size+2:]
+- decryption_cipher = self.module.new(a2b_hex(self.key), mode, eiv)
++ decryption_cipher = self.module.new(a2b_hex(self.key), mode, self.iv)
+ decrypted_plaintext = decryption_cipher.decrypt(ciphertext)
+ self.assertEqual(self.plaintext, decrypted_plaintext)
+
++
+ class PGPTest(unittest.TestCase):
+ def __init__(self, module, params):
+ unittest.TestCase.__init__(self)
+--- a/src/block_template.c
++++ b/src/block_template.c
+@@ -170,6 +170,17 @@ ALGnew(PyObject *self, PyObject *args, P
+ "Key cannot be the null string");
+ return NULL;
+ }
++ if (IVlen != 0 && mode == MODE_ECB)
++ {
++ PyErr_Format(PyExc_ValueError, "ECB mode does not use IV");
++ return NULL;
++ }
++ if (IVlen != 0 && mode == MODE_CTR)
++ {
++ PyErr_Format(PyExc_ValueError,
++ "CTR mode needs counter parameter, not IV");
++ return NULL;
++ }
+ if (IVlen != BLOCK_SIZE && mode != MODE_ECB && mode != MODE_CTR)
+ {
+ PyErr_Format(PyExc_ValueError,
diff --git a/gnu/packages/patches/python-pygpgme-fix-pinentry-tests.patch b/gnu/packages/patches/python-pygpgme-fix-pinentry-tests.patch
new file mode 100644
index 0000000000..1f7a4cadb7
--- /dev/null
+++ b/gnu/packages/patches/python-pygpgme-fix-pinentry-tests.patch
@@ -0,0 +1,69 @@
+Fix test failure of test_XXX caused by upgrade of gpgme from 1.6.0 to
+1.8.0:
+
+======================================================================
+FAIL: test_encrypt_to_signonly (tests.test_encrypt_decrypt.EncryptDecryptTestCase)
+----------------------------------------------------------------------
+Traceback (most recent call last):
+ File "/tmp/guix-build-python2-pygpgme-0.3.drv-0/pygpgme-0.3/tests/test_encrypt_decrypt.py", line 185, in test_encrypt_to_signonly
+ self.assertEqual(exc.args[0], gpgme.ERR_SOURCE_UNKNOWN)
+AssertionError: 7 != 0
+
+----------------------------------------------------------------------
+
+Patch copied from the Debian package pygpgme-0.3-1.2:
+
+https://sources.debian.net/src/pygpgme/0.3-1.2/debian/patches/0005-Fix-test-failures-with-pinentry.patch/
+
+From: "Dr. Tobias Quathamer" <toddy@debian.org>
+Date: Thu, 24 Nov 2016 12:20:54 +0100
+Subject: Fix test failures with pinentry
+
+---
+ tests/test_encrypt_decrypt.py | 5 +++--
+ tests/test_passphrase.py | 2 ++
+ 2 files changed, 5 insertions(+), 2 deletions(-)
+
+diff --git a/tests/test_encrypt_decrypt.py b/tests/test_encrypt_decrypt.py
+index 21ae83e..05707e1 100644
+--- a/tests/test_encrypt_decrypt.py
++++ b/tests/test_encrypt_decrypt.py
+@@ -132,6 +132,7 @@ class EncryptDecryptTestCase(GpgHomeTestCase):
+ os.write(fd, b'Symmetric passphrase\n')
+ ctx = gpgme.Context()
+ ctx.armor = True
++ ctx.pinentry_mode = gpgme.PINENTRY_MODE_LOOPBACK
+ ctx.passphrase_cb = passphrase
+ ctx.encrypt(None, 0, plaintext, ciphertext)
+ self.assertTrue(
+@@ -182,8 +183,8 @@ class EncryptDecryptTestCase(GpgHomeTestCase):
+ ctx.encrypt([recipient], gpgme.ENCRYPT_ALWAYS_TRUST,
+ plaintext, ciphertext)
+ except gpgme.GpgmeError as exc:
+- self.assertEqual(exc.args[0], gpgme.ERR_SOURCE_UNKNOWN)
+- self.assertEqual(exc.args[1], gpgme.ERR_GENERAL)
++ self.assertEqual(exc.args[0], gpgme.ERR_SOURCE_GPGME)
++ self.assertEqual(exc.args[1], gpgme.ERR_UNUSABLE_PUBKEY)
+ else:
+ self.fail('gpgme.GpgmeError not raised')
+
+diff --git a/tests/test_passphrase.py b/tests/test_passphrase.py
+index 35b3c59..05e6811 100644
+--- a/tests/test_passphrase.py
++++ b/tests/test_passphrase.py
+@@ -34,6 +34,7 @@ class PassphraseTestCase(GpgHomeTestCase):
+ ctx = gpgme.Context()
+ key = ctx.get_key('EFB052B4230BBBC51914BCBB54DCBBC8DBFB9EB3')
+ ctx.signers = [key]
++ ctx.pinentry_mode = gpgme.PINENTRY_MODE_LOOPBACK
+ plaintext = BytesIO(b'Hello World\n')
+ signature = BytesIO()
+
+@@ -55,6 +56,7 @@ class PassphraseTestCase(GpgHomeTestCase):
+ ctx = gpgme.Context()
+ key = ctx.get_key('EFB052B4230BBBC51914BCBB54DCBBC8DBFB9EB3')
+ ctx.signers = [key]
++ ctx.pinentry_mode = gpgme.PINENTRY_MODE_LOOPBACK
+ ctx.passphrase_cb = self.passphrase_cb
+ plaintext = BytesIO(b'Hello World\n')
+ signature = BytesIO()
diff --git a/gnu/packages/patches/qemu-CVE-2016-8576.patch b/gnu/packages/patches/qemu-CVE-2016-8576.patch
deleted file mode 100644
index 5031b59d81..0000000000
--- a/gnu/packages/patches/qemu-CVE-2016-8576.patch
+++ /dev/null
@@ -1,62 +0,0 @@
-From 20009bdaf95d10bf748fa69b104672d3cfaceddf Mon Sep 17 00:00:00 2001
-From: Gerd Hoffmann <kraxel@redhat.com>
-Date: Fri, 7 Oct 2016 10:15:29 +0200
-Subject: [PATCH] xhci: limit the number of link trbs we are willing to process
-
-Signed-off-by: Gerd Hoffmann <kraxel@redhat.com>
----
- hw/usb/hcd-xhci.c | 10 ++++++++++
- 1 file changed, 10 insertions(+)
-
-diff --git a/hw/usb/hcd-xhci.c b/hw/usb/hcd-xhci.c
-index 726435c..ee4fa48 100644
---- a/hw/usb/hcd-xhci.c
-+++ b/hw/usb/hcd-xhci.c
-@@ -54,6 +54,8 @@
- * to the specs when it gets them */
- #define ER_FULL_HACK
-
-+#define TRB_LINK_LIMIT 4
-+
- #define LEN_CAP 0x40
- #define LEN_OPER (0x400 + 0x10 * MAXPORTS)
- #define LEN_RUNTIME ((MAXINTRS + 1) * 0x20)
-@@ -1000,6 +1002,7 @@ static TRBType xhci_ring_fetch(XHCIState *xhci, XHCIRing *ring, XHCITRB *trb,
- dma_addr_t *addr)
- {
- PCIDevice *pci_dev = PCI_DEVICE(xhci);
-+ uint32_t link_cnt = 0;
-
- while (1) {
- TRBType type;
-@@ -1026,6 +1029,9 @@ static TRBType xhci_ring_fetch(XHCIState *xhci, XHCIRing *ring, XHCITRB *trb,
- ring->dequeue += TRB_SIZE;
- return type;
- } else {
-+ if (++link_cnt > TRB_LINK_LIMIT) {
-+ return 0;
-+ }
- ring->dequeue = xhci_mask64(trb->parameter);
- if (trb->control & TRB_LK_TC) {
- ring->ccs = !ring->ccs;
-@@ -1043,6 +1049,7 @@ static int xhci_ring_chain_length(XHCIState *xhci, const XHCIRing *ring)
- bool ccs = ring->ccs;
- /* hack to bundle together the two/three TDs that make a setup transfer */
- bool control_td_set = 0;
-+ uint32_t link_cnt = 0;
-
- while (1) {
- TRBType type;
-@@ -1058,6 +1065,9 @@ static int xhci_ring_chain_length(XHCIState *xhci, const XHCIRing *ring)
- type = TRB_TYPE(trb);
-
- if (type == TR_LINK) {
-+ if (++link_cnt > TRB_LINK_LIMIT) {
-+ return -length;
-+ }
- dequeue = xhci_mask64(trb.parameter);
- if (trb.control & TRB_LK_TC) {
- ccs = !ccs;
---
-1.8.3.1
-
diff --git a/gnu/packages/patches/qemu-CVE-2016-8577.patch b/gnu/packages/patches/qemu-CVE-2016-8577.patch
deleted file mode 100644
index c4132d2fb1..0000000000
--- a/gnu/packages/patches/qemu-CVE-2016-8577.patch
+++ /dev/null
@@ -1,36 +0,0 @@
-Subject: [Qemu-devel] [PATCH] 9pfs: fix potential host memory leak in v9fs_read
-From: Li Qiang <liq3ea@gmail.com>
-
-In 9pfs read dispatch function, it doesn't free two QEMUIOVector
-object thus causing potential memory leak. This patch avoid this.
-
-Signed-off-by: Li Qiang <liq3ea@gmail.com>
----
- hw/9pfs/9p.c | 5 +++--
- 1 file changed, 3 insertions(+), 2 deletions(-)
-
-diff --git a/hw/9pfs/9p.c b/hw/9pfs/9p.c
-index 119ee58..543a791 100644
---- a/hw/9pfs/9p.c
-+++ b/hw/9pfs/9p.c
-@@ -1826,14 +1826,15 @@ static void v9fs_read(void *opaque)
- if (len < 0) {
- /* IO error return the error */
- err = len;
-- goto out;
-+ goto out_free_iovec;
- }
- } while (count < max_count && len > 0);
- err = pdu_marshal(pdu, offset, "d", count);
- if (err < 0) {
-- goto out;
-+ goto out_free_iovec;
- }
- err += offset + count;
-+out_free_iovec:
- qemu_iovec_destroy(&qiov);
- qemu_iovec_destroy(&qiov_full);
- } else if (fidp->fid_type == P9_FID_XATTR) {
---
-1.8.3.1
-
diff --git a/gnu/packages/patches/qemu-CVE-2016-8578.patch b/gnu/packages/patches/qemu-CVE-2016-8578.patch
deleted file mode 100644
index 92ba365727..0000000000
--- a/gnu/packages/patches/qemu-CVE-2016-8578.patch
+++ /dev/null
@@ -1,27 +0,0 @@
-From: Li Qiang <liq3ea@gmail.com>
-
-In 9pfs function v9fs_iov_vunmarshal, it will not allocate space
-for empty string. This will cause several NULL pointer dereference
-issues. this patch fix this issue.
-
-Signed-off-by: Li Qiang <liq3ea@gmail.com>
----
- fsdev/9p-iov-marshal.c | 2 +-
- 1 file changed, 1 insertion(+), 1 deletion(-)
-
-diff --git a/fsdev/9p-iov-marshal.c b/fsdev/9p-iov-marshal.c
-index 663cad5..1d16f8d 100644
---- a/fsdev/9p-iov-marshal.c
-+++ b/fsdev/9p-iov-marshal.c
-@@ -125,7 +125,7 @@ ssize_t v9fs_iov_vunmarshal(struct iovec *out_sg, int out_num, size_t offset,
- str->data = g_malloc(str->size + 1);
- copied = v9fs_unpack(str->data, out_sg, out_num, offset,
- str->size);
-- if (copied > 0) {
-+ if (copied >= 0) {
- str->data[str->size] = 0;
- } else {
- v9fs_string_free(str);
---
-1.8.3.1
-
diff --git a/gnu/packages/patches/ruby-yard-fix-skip-of-markdown-tests.patch b/gnu/packages/patches/ruby-yard-fix-skip-of-markdown-tests.patch
deleted file mode 100644
index f592f5cd51..0000000000
--- a/gnu/packages/patches/ruby-yard-fix-skip-of-markdown-tests.patch
+++ /dev/null
@@ -1,17 +0,0 @@
-The tests currently fail due to use of 'skip' rather than 'pending' to skip a
-test usually not skipped by upstream. This patch has been proposed upstream
-at https://github.com/lsegal/yard/pull/1033
-
-diff --git a/spec/templates/helpers/html_helper_spec.rb b/spec/templates/helpers/html_helper_spec.rb
-index 84624c3..9c4fc2b 100644
---- a/spec/templates/helpers/html_helper_spec.rb
-+++ b/spec/templates/helpers/html_helper_spec.rb
-@@ -184,7 +184,7 @@ describe YARD::Templates::Helpers::HtmlHelper do
- it "creates tables (markdown specific)" do
- log.enter_level(Logger::FATAL) do
- unless markup_class(:markdown).to_s == "RedcarpetCompat"
-- skip "This test depends on a markdown engine that supports tables"
-+ pending "This test depends on a markdown engine that supports tables"
- end
- end
-
diff --git a/gnu/packages/patches/slock-CVE-2016-6866.patch b/gnu/packages/patches/slock-CVE-2016-6866.patch
deleted file mode 100644
index 2f94b8c1a9..0000000000
--- a/gnu/packages/patches/slock-CVE-2016-6866.patch
+++ /dev/null
@@ -1,51 +0,0 @@
-Fix CVE-2016-6866.
-
-https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2016-6866
-https://security-tracker.debian.org/tracker/CVE-2016-6866
-
-Copied from upstream source repository:
-http://git.suckless.org/slock/commit/?id=d8bec0f6fdc8a246d78cb488a0068954b46fcb29
-
-From d8bec0f6fdc8a246d78cb488a0068954b46fcb29 Mon Sep 17 00:00:00 2001
-From: Markus Teich <markus.teich@stusta.mhn.de>
-Date: Tue, 30 Aug 2016 22:59:06 +0000
-Subject: fix CVE-2016-6866
-
----
-diff --git a/slock.c b/slock.c
-index 847b328..8ed59ca 100644
---- a/slock.c
-+++ b/slock.c
-@@ -123,7 +123,7 @@ readpw(Display *dpy)
- readpw(Display *dpy, const char *pws)
- #endif
- {
-- char buf[32], passwd[256];
-+ char buf[32], passwd[256], *encrypted;
- int num, screen;
- unsigned int len, color;
- KeySym ksym;
-@@ -159,7 +159,11 @@ readpw(Display *dpy, const char *pws)
- #ifdef HAVE_BSD_AUTH
- running = !auth_userokay(getlogin(), NULL, "auth-slock", passwd);
- #else
-- running = !!strcmp(crypt(passwd, pws), pws);
-+ errno = 0;
-+ if (!(encrypted = crypt(passwd, pws)))
-+ fprintf(stderr, "slock: crypt: %s\n", strerror(errno));
-+ else
-+ running = !!strcmp(encrypted, pws);
- #endif
- if (running) {
- XBell(dpy, 100);
-@@ -312,6 +316,8 @@ main(int argc, char **argv) {
-
- #ifndef HAVE_BSD_AUTH
- pws = getpw();
-+ if (strlen(pws) < 2)
-+ die("slock: failed to get user password hash.\n");
- #endif
-
- if (!(dpy = XOpenDisplay(NULL)))
---
-cgit v0.9.0.3-65-g4555
diff --git a/gnu/packages/patches/unrtf-CVE-2016-10091.patch b/gnu/packages/patches/unrtf-CVE-2016-10091.patch
new file mode 100644
index 0000000000..badd1b8ed6
--- /dev/null
+++ b/gnu/packages/patches/unrtf-CVE-2016-10091.patch
@@ -0,0 +1,189 @@
+Fix CVE-2016-10091 (stack-based buffer overflows in cmd_* functions):
+
+https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2016-10091
+https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=849705
+http://seclists.org/oss-sec/2016/q4/787
+
+Patch adapted from Debian:
+
+https://anonscm.debian.org/cgit/collab-maint/unrtf.git/commit/?h=jessie&id=7500a48fb0fbad3ab963fb17560b2f90a8a485c8
+
+The Debian patch adapts this upstream commit so that it can be applied
+to the 0.21.9 release tarball:
+
+http://hg.savannah.gnu.org/hgweb/unrtf/rev/3b16893a6406
+
+From 7dd568ed8a6a5acb6c04f2b40f457d63a00435f3 Mon Sep 17 00:00:00 2001
+From: Willi Mann <willi@debian.org>
+Date: Sat, 31 Dec 2016 20:31:38 +0100
+Subject: [PATCH] Add patch from upstream to fix CVE-2016-10091 (buffer
+ overflow in various cmd_ functions)
+
+diff --git a/src/attr.c b/src/attr.c
+index 02b5c81..e2951ea 100644
+--- a/src/attr.c
++++ b/src/attr.c
+@@ -746,7 +746,7 @@ char *
+ assemble_string(char *string, int nr)
+ {
+
+- char *s, tmp[12];/* Number of characters that can be in int type (including '\0') - AF */
++ char *s, tmp[20];
+ int i = 0, j = 0;
+
+ if (string == NULL)
+@@ -762,7 +762,7 @@ assemble_string(char *string, int nr)
+ }
+
+ if (string[i] != '\0') {
+- sprintf(tmp, "%d", nr);
++ snprintf(tmp, 20, "%d", nr);
+ strcpy(&s[j], tmp);
+ j = j + strlen(tmp);
+ }
+diff --git a/src/convert.c b/src/convert.c
+index c76d7d6..8eacdcb 100644
+--- a/src/convert.c
++++ b/src/convert.c
+@@ -472,7 +472,7 @@ static const int fcharsetparmtocp(int parm)
+ }
+
+ // Translate code page to encoding name hopefully suitable as iconv input
+-static char *cptoencoding(parm)
++static char *cptoencoding(int parm)
+ {
+ // Note that CP0 is supposed to mean current system default, which does
+ // not make any sense as a stored value, we don't handle it.
+@@ -964,7 +964,7 @@ cmd_cf (Word *w, int align, char has_param, int num)
+ }
+ else
+ {
+- sprintf(str,"#%02x%02x%02x",
++ snprintf(str, 40, "#%02x%02x%02x",
+ color_table[num].r,
+ color_table[num].g,
+ color_table[num].b);
+@@ -993,7 +993,7 @@ cmd_cb (Word *w, int align, char has_param, int num)
+ }
+ else
+ {
+- sprintf(str,"#%02x%02x%02x",
++ snprintf(str, 40, "#%02x%02x%02x",
+ color_table[num].r,
+ color_table[num].g,
+ color_table[num].b);
+@@ -1018,7 +1018,7 @@ cmd_fs (Word *w, int align, char has_param, int points) {
+ /* Note, fs20 means 10pt */
+ points /= 2;
+
+- sprintf(str,"%d",points);
++ snprintf(str, 20, "%d", points);
+ attr_push(ATTR_FONTSIZE,str);
+
+ return FALSE;
+@@ -1166,7 +1166,7 @@ cmd_f (Word *w, int align, char has_param, int num)
+ {
+ // TOBEDONE: WHAT'S THIS ???
+ name = my_malloc(12);
+- sprintf(name, "%d", num);
++ snprintf(name, 12, "%d", num);
+ }
+
+ /* we are going to output entities, so should not output font */
+@@ -1218,7 +1218,7 @@ cmd_highlight (Word *w, int align, char has_param, int num)
+ }
+ else
+ {
+- sprintf(str,"#%02x%02x%02x",
++ snprintf(str, 40, "#%02x%02x%02x",
+ color_table[num].r,
+ color_table[num].g,
+ color_table[num].b);
+@@ -1373,9 +1373,9 @@ cmd_ftech (Word *w, int align, char has_param, int param) {
+
+ static int
+ cmd_expand (Word *w, int align, char has_param, int param) {
+- char str[10];
++ char str[20];
+ if (has_param) {
+- sprintf(str, "%d", param/4);
++ snprintf(str, 20, "%d", param / 4);
+ if (!param)
+ attr_pop(ATTR_EXPAND);
+ else
+@@ -1394,7 +1394,7 @@ cmd_expand (Word *w, int align, char has_param, int param) {
+
+ static int
+ cmd_emboss (Word *w, int align, char has_param, int param) {
+- char str[10];
++ char str[20];
+ if (has_param && !param)
+ #ifdef SUPPORT_UNNESTED
+ attr_find_pop(ATTR_EMBOSS);
+@@ -1403,7 +1403,7 @@ cmd_emboss (Word *w, int align, char has_param, int param) {
+ #endif
+ else
+ {
+- sprintf(str, "%d", param);
++ snprintf(str, 20, "%d", param);
+ attr_push(ATTR_EMBOSS, str);
+ }
+ return FALSE;
+@@ -1419,12 +1419,12 @@ cmd_emboss (Word *w, int align, char has_param, int param) {
+
+ static int
+ cmd_engrave (Word *w, int align, char has_param, int param) {
+- char str[10];
++ char str[20];
+ if (has_param && !param)
+ attr_pop(ATTR_ENGRAVE);
+ else
+ {
+- sprintf(str, "%d", param);
++ snprintf(str, 20, "%d", param);
+ attr_push(ATTR_ENGRAVE, str);
+ }
+ return FALSE;
+@@ -1976,7 +1976,7 @@ static int cmd_u (Word *w, int align, char has_param, int param) {
+
+ short done=0;
+ long unicode_number = (long) param; /* On 16bit architectures int is too small to store unicode characters. - AF */
+- char tmp[12]; /* Number of characters that can be in int type (including '\0'). If int size is greater than 4 bytes change this value. - AF */
++ char tmp[20]; /* Number of characters that can be in int type (including '\0'). If int size is greater than 4 bytes change this value. - AF */
+ const char *alias;
+ #define DEBUG 0
+ #if DEBUG
+@@ -2006,7 +2006,7 @@ static int cmd_u (Word *w, int align, char has_param, int param) {
+ /* RTF spec: Unicode values beyond 32767 are represented by negative numbers */
+ unicode_number += 65536;
+ }
+- sprintf(tmp, "%ld", unicode_number);
++ snprintf(tmp, 20, "%ld", unicode_number);
+
+ if (safe_printf(1, op->unisymbol_print, tmp)) fprintf(stderr, TOO_MANY_ARGS, "unisymbol_print");
+ done++;
+diff --git a/src/output.c b/src/output.c
+index 86d8b5c..4cdbfa6 100644
+--- a/src/output.c
++++ b/src/output.c
+@@ -320,7 +320,7 @@ op_begin_std_fontsize (OutputPersonality *op, int size)
+ if (!found_std_expr) {
+ if (op->fontsize_begin) {
+ char expr[16];
+- sprintf (expr, "%d", size);
++ snprintf(expr, 16, "%d", size);
+ if (safe_printf (1, op->fontsize_begin, expr)) fprintf(stderr, TOO_MANY_ARGS, "fontsize_begin");
+ } else {
+ /* If we cannot write out a change for the exact
+@@ -440,7 +440,7 @@ op_end_std_fontsize (OutputPersonality *op, int size)
+ if (!found_std_expr) {
+ if (op->fontsize_end) {
+ char expr[16];
+- sprintf (expr, "%d", size);
++ snprintf(expr, 16, "%d", size);
+ if (safe_printf(1, op->fontsize_end, expr)) fprintf(stderr, TOO_MANY_ARGS, "fontsize_end");
+ } else {
+ /* If we cannot write out a change for the exact
+-
+.11.0
+