Merge branch 'master' into core-updates

13 files changed, 511 insertions, 43 deletions

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 2bd71c858b..ed20b562e5 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -1903,7 +1903,7 @@ identify enrichments with functional annotations of the genome.")
 (define-public diamond
   (package
     (name "diamond")
-    (version "0.8.18")
+    (version "0.8.20")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -1912,7 +1912,7 @@ identify enrichments with functional annotations of the genome.")
               (file-name (string-append name "-" version ".tar.gz"))
               (sha256
                (base32
-                "1r8klhbzn5cfzg9g69dd0sk4c0bd8cg1g5id8blsqi273bymm4jl"))))
+                "16bhwpxqzq2nfkh9522rwcc1p97ygszjmhphz69x2jk501jf9wkg"))))
     (build-system cmake-build-system)
     (arguments
      '(#:tests? #f ; no "check" target
diff --git a/gnu/packages/calendar.scm b/gnu/packages/calendar.scm
index 3b5aba72c8..7f3d05d08e 100644
--- a/gnu/packages/calendar.scm
+++ b/gnu/packages/calendar.scm
@@ -3,6 +3,7 @@
 ;;; Copyright © 2015, 2016 Leo Famulari <leo@famulari.name>
 ;;; Copyright © 2016 Kei Kebreau <kei@openmailbox.org>
 ;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2016 Troy Sankey <sankeytms@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -80,42 +81,16 @@ data units.")
 (define-public khal
   (package
     (name "khal")
-    (version "0.7.0")
+    (version "0.8.3")
     (source (origin
              (method url-fetch)
              (uri (pypi-uri "khal" version))
              (sha256
               (base32
-               "00llxj7cv31mjsx0j6zxmyi9s1q20yvfkn025xcy8cv1ylfwic66"))
-             (modules '((guix build utils)))
-             ;; Patch broken path in 'doc' Makefile.
-             ;; Patch sent upstream: https://github.com/geier/khal/pull/307
-             (snippet
-               '(substitute* "doc/source/Makefile"
-                 (("../../../khal/khal/settings/khal.spec")
-                  "../../khal/settings/khal.spec" )))))
+               "1qryqs5d8jsl7j22pjjfkfdi4m8m3nn3n44b890pq85xkw599ihy"))))
     (build-system python-build-system)
     (arguments
      `(#:phases (modify-phases %standard-phases
-        (add-after 'unpack 'disable-tests
-          (lambda _
-            ;; Bug reported for test_only_update_old_event:
-            ;; https://github.com/geier/khal/issues/309
-            (substitute* "tests/khalendar_test.py"
-                         (("test_only_update_old_event")
-                           "disabled_only_update_old_event"))
-
-            ;; Bug reported for test_dt_two_tz:
-            ;; https://github.com/pimutils/khal/issues/382
-            (substitute* "tests/event_test.py"
-                         (("test_dt_two_tz")
-                           "disabled_dt_two_tz"))
-            ;; Another timezone / DST issue:
-            ;; https://github.com/pimutils/khal/issues/146
-            (substitute* "tests/event_test.py"
-                         (("test_raw_dt")
-                           "disabled_raw_dt"))))
-
         ;; Building the manpage requires khal to be installed.
         (add-after 'install 'manpage
           (lambda* (#:key outputs #:allow-other-keys)
@@ -136,9 +111,11 @@ data units.")
             (zero? (system* "py.test" "tests")))))))
     (native-inputs
      `(("python-pytest" ,python-pytest)
+       ("python-pytest-cov" ,python-pytest-cov)
        ("python-setuptools-scm" ,python-setuptools-scm)
        ;; Required for tests
        ("tzdata" ,tzdata)
+       ("python-freezegun" ,python-freezegun)
        ;; Required to build manpage
        ("python-sphinxcontrib-newsfeed" ,python-sphinxcontrib-newsfeed)
        ("python-sphinx" ,python-sphinx)))
diff --git a/gnu/packages/image.scm b/gnu/packages/image.scm
index 7d72492b1a..4fdc4ae252 100644
--- a/gnu/packages/image.scm
+++ b/gnu/packages/image.scm
@@ -150,6 +150,7 @@ maximum quality factor.")
 (define-public libtiff
   (package
    (name "libtiff")
+   (replacement libtiff/fixed)
    (version "4.0.6")
    (source (origin
             (method url-fetch)
@@ -182,6 +183,23 @@ collection of tools for doing simple manipulations of TIFF images.")
                                   "See COPYRIGHT in the distribution."))
    (home-page "http://www.remotesensing.org/libtiff/")))
 
+(define libtiff/fixed
+  (package
+    (inherit libtiff)
+    (source (origin
+              (inherit (package-source libtiff))
+              (patches (search-patches
+                         "libtiff-oob-accesses-in-decode.patch"
+                         "libtiff-oob-write-in-nextdecode.patch"
+                         "libtiff-CVE-2015-8665+CVE-2015-8683.patch"
+                         "libtiff-CVE-2016-3623.patch"
+                         "libtiff-CVE-2016-3945.patch"
+                         "libtiff-CVE-2016-3990.patch"
+                         "libtiff-CVE-2016-3991.patch"
+                         "libtiff-CVE-2016-5314.patch"
+                         "libtiff-CVE-2016-5321.patch"
+                         "libtiff-CVE-2016-5323.patch"))))))
+
 (define-public libwmf
   (package
     (name "libwmf")
diff --git a/gnu/packages/imagemagick.scm b/gnu/packages/imagemagick.scm
index a554b73a4e..f824abf3f4 100644
--- a/gnu/packages/imagemagick.scm
+++ b/gnu/packages/imagemagick.scm
@@ -41,14 +41,14 @@
 (define-public imagemagick
   (package
     (name "imagemagick")
-    (version "6.9.5-7")
+    (version "6.9.5-8")
     (source (origin
              (method url-fetch)
              (uri (string-append "mirror://imagemagick/ImageMagick-"
                                  version ".tar.xz"))
              (sha256
               (base32
-               "00arcvyhsy9i5gp3b0lhfvs04qwhxpmq0bfsv4ipllinb6mjgxf5"))))
+               "0ds21sk1pczf2cwi62rqp6b8x2m24sb6xn82ivzh13m42phzigav"))))
     (build-system gnu-build-system)
     (arguments
      `(#:configure-flags '("--with-frozenpaths" "--without-gcc-arch")
diff --git a/gnu/packages/patches/libtiff-CVE-2016-3623.patch b/gnu/packages/patches/libtiff-CVE-2016-3623.patch
new file mode 100644
index 0000000000..08705861e3
--- /dev/null
+++ b/gnu/packages/patches/libtiff-CVE-2016-3623.patch
@@ -0,0 +1,30 @@
+Fix CVE-2016-3623.
+
+https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2016-3623
+http://bugzilla.maptools.org/show_bug.cgi?id=2569
+
+Patch extracted from upstream CVS repo with:
+$ cvs diff -u -r1.16 -r1.17 tools/rgb2ycbcr.c
+
+Index: tools/rgb2ycbcr.c
+===================================================================
+RCS file: /cvs/maptools/cvsroot/libtiff/tools/rgb2ycbcr.c,v
+retrieving revision 1.16
+retrieving revision 1.17
+diff -u -r1.16 -r1.17
+--- libtiff/tools/rgb2ycbcr.c	21 Jun 2015 01:09:10 -0000	1.16
++++ libtiff/tools/rgb2ycbcr.c	15 Aug 2016 21:26:56 -0000	1.17
+@@ -95,9 +95,13 @@
+ 			break;
+ 		case 'h':
+ 			horizSubSampling = atoi(optarg);
++            if( horizSubSampling != 1 && horizSubSampling != 2 && horizSubSampling != 4 )
++                usage(-1);
+ 			break;
+ 		case 'v':
+ 			vertSubSampling = atoi(optarg);
++            if( vertSubSampling != 1 && vertSubSampling != 2 && vertSubSampling != 4 )
++                usage(-1);
+ 			break;
+ 		case 'r':
+ 			rowsperstrip = atoi(optarg);
diff --git a/gnu/packages/patches/libtiff-CVE-2016-3945.patch b/gnu/packages/patches/libtiff-CVE-2016-3945.patch
new file mode 100644
index 0000000000..8ec62bab99
--- /dev/null
+++ b/gnu/packages/patches/libtiff-CVE-2016-3945.patch
@@ -0,0 +1,94 @@
+Fix CVE-2016-3945 (integer overflow in size of allocated
+buffer, when -b mode is enabled, that could result in out-of-bounds
+write).
+
+https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2016-3945
+http://bugzilla.maptools.org/show_bug.cgi?id=2545
+
+Patch extracted from upstream CVS repo with:
+$ cvs diff -u -r1.21 -r1.22 tools/tiff2rgba.c
+
+Index: tools/tiff2rgba.c
+===================================================================
+RCS file: /cvs/maptools/cvsroot/libtiff/tools/tiff2rgba.c,v
+retrieving revision 1.21
+retrieving revision 1.22
+diff -u -r1.21 -r1.22
+--- libtiff/tools/tiff2rgba.c	21 Jun 2015 01:09:10 -0000	1.21
++++ libtiff/tools/tiff2rgba.c	15 Aug 2016 20:06:41 -0000	1.22
+@@ -147,6 +147,7 @@
+     uint32  row, col;
+     uint32  *wrk_line;
+     int	    ok = 1;
++    uint32  rastersize, wrk_linesize;
+ 
+     TIFFGetField(in, TIFFTAG_IMAGEWIDTH, &width);
+     TIFFGetField(in, TIFFTAG_IMAGELENGTH, &height);
+@@ -163,7 +164,13 @@
+     /*
+      * Allocate tile buffer
+      */
+-    raster = (uint32*)_TIFFmalloc(tile_width * tile_height * sizeof (uint32));
++    rastersize = tile_width * tile_height * sizeof (uint32);
++    if (tile_width != (rastersize / tile_height) / sizeof( uint32))
++    {
++	TIFFError(TIFFFileName(in), "Integer overflow when calculating raster buffer");
++	exit(-1);
++    }
++    raster = (uint32*)_TIFFmalloc(rastersize);
+     if (raster == 0) {
+         TIFFError(TIFFFileName(in), "No space for raster buffer");
+         return (0);
+@@ -173,7 +180,13 @@
+      * Allocate a scanline buffer for swapping during the vertical
+      * mirroring pass.
+      */
+-    wrk_line = (uint32*)_TIFFmalloc(tile_width * sizeof (uint32));
++    wrk_linesize = tile_width * sizeof (uint32);
++    if (tile_width != wrk_linesize / sizeof (uint32))
++    {
++        TIFFError(TIFFFileName(in), "Integer overflow when calculating wrk_line buffer");
++	exit(-1);
++    }
++    wrk_line = (uint32*)_TIFFmalloc(wrk_linesize);
+     if (!wrk_line) {
+         TIFFError(TIFFFileName(in), "No space for raster scanline buffer");
+         ok = 0;
+@@ -249,6 +262,7 @@
+     uint32  row;
+     uint32  *wrk_line;
+     int	    ok = 1;
++    uint32  rastersize, wrk_linesize;
+ 
+     TIFFGetField(in, TIFFTAG_IMAGEWIDTH, &width);
+     TIFFGetField(in, TIFFTAG_IMAGELENGTH, &height);
+@@ -263,7 +277,13 @@
+     /*
+      * Allocate strip buffer
+      */
+-    raster = (uint32*)_TIFFmalloc(width * rowsperstrip * sizeof (uint32));
++    rastersize = width * rowsperstrip * sizeof (uint32);
++    if (width != (rastersize / rowsperstrip) / sizeof( uint32))
++    {
++	TIFFError(TIFFFileName(in), "Integer overflow when calculating raster buffer");
++	exit(-1);
++    }
++    raster = (uint32*)_TIFFmalloc(rastersize);
+     if (raster == 0) {
+         TIFFError(TIFFFileName(in), "No space for raster buffer");
+         return (0);
+@@ -273,7 +293,13 @@
+      * Allocate a scanline buffer for swapping during the vertical
+      * mirroring pass.
+      */
+-    wrk_line = (uint32*)_TIFFmalloc(width * sizeof (uint32));
++    wrk_linesize = width * sizeof (uint32);
++    if (width != wrk_linesize / sizeof (uint32))
++    {
++        TIFFError(TIFFFileName(in), "Integer overflow when calculating wrk_line buffer");
++	exit(-1);
++    }
++    wrk_line = (uint32*)_TIFFmalloc(wrk_linesize);
+     if (!wrk_line) {
+         TIFFError(TIFFFileName(in), "No space for raster scanline buffer");
+         ok = 0;
diff --git a/gnu/packages/patches/libtiff-CVE-2016-3990.patch b/gnu/packages/patches/libtiff-CVE-2016-3990.patch
new file mode 100644
index 0000000000..7641c3073b
--- /dev/null
+++ b/gnu/packages/patches/libtiff-CVE-2016-3990.patch
@@ -0,0 +1,31 @@
+Fix CVE-2016-3990 (write buffer overflow in PixarLogEncode if more input
+samples are provided than expected by PixarLogSetupEncode).
+
+https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2016-3990
+http://bugzilla.maptools.org/show_bug.cgi?id=2544
+
+Patch extracted from upstream CVS repo with:
+$ cvs diff -u -r1.45 -r1.46 libtiff/tif_pixarlog.c
+
+Index: libtiff/tif_pixarlog.c
+===================================================================
+RCS file: /cvs/maptools/cvsroot/libtiff/libtiff/tif_pixarlog.c,v
+retrieving revision 1.45
+retrieving revision 1.46
+diff -u -r1.45 -r1.46
+--- libtiff/libtiff/tif_pixarlog.c	28 Jun 2016 15:37:33 -0000	1.45
++++ libtiff/libtiff/tif_pixarlog.c	15 Aug 2016 20:49:48 -0000	1.46
+@@ -1141,6 +1141,13 @@
+ 	}
+ 
+ 	llen = sp->stride * td->td_imagewidth;
++    /* Check against the number of elements (of size uint16) of sp->tbuf */
++    if( n > td->td_rowsperstrip * llen )
++    {
++        TIFFErrorExt(tif->tif_clientdata, module,
++                     "Too many input bytes provided");
++        return 0;
++    }
+ 
+ 	for (i = 0, up = sp->tbuf; i < n; i += llen, up += llen) {
+ 		switch (sp->user_datafmt)  {
diff --git a/gnu/packages/patches/libtiff-CVE-2016-3991.patch b/gnu/packages/patches/libtiff-CVE-2016-3991.patch
new file mode 100644
index 0000000000..cb05f0007f
--- /dev/null
+++ b/gnu/packages/patches/libtiff-CVE-2016-3991.patch
@@ -0,0 +1,123 @@
+Fix CVE-2016-3991 (out-of-bounds write in loadImage()).
+
+https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2016-3991
+http://bugzilla.maptools.org/show_bug.cgi?id=2543
+
+Patch extracted from upstream CVS repo with:
+$ cvs diff -u -r1.37 -r1.38 tools/tiffcrop.c
+
+Index: tools/tiffcrop.c
+===================================================================
+RCS file: /cvs/maptools/cvsroot/libtiff/tools/tiffcrop.c,v
+retrieving revision 1.37
+retrieving revision 1.38
+diff -u -r1.37 -r1.38
+--- libtiff/tools/tiffcrop.c	11 Jul 2016 21:38:31 -0000	1.37
++++ libtiff/tools/tiffcrop.c	15 Aug 2016 21:05:40 -0000	1.38
+@@ -798,6 +798,11 @@
+     }
+ 
+   tile_buffsize = tilesize;
++  if (tilesize == 0 || tile_rowsize == 0)
++  {
++     TIFFError("readContigTilesIntoBuffer", "Tile size or tile rowsize is zero");
++     exit(-1);
++  }
+ 
+   if (tilesize < (tsize_t)(tl * tile_rowsize))
+     {
+@@ -807,7 +812,12 @@
+               tilesize, tl * tile_rowsize);
+ #endif
+     tile_buffsize = tl * tile_rowsize;
+-    } 
++    if (tl != (tile_buffsize / tile_rowsize))
++    {
++    	TIFFError("readContigTilesIntoBuffer", "Integer overflow when calculating buffer size.");
++        exit(-1);
++    }
++    }
+ 
+   tilebuf = _TIFFmalloc(tile_buffsize);
+   if (tilebuf == 0)
+@@ -1210,6 +1220,12 @@
+       !TIFFGetField(out, TIFFTAG_BITSPERSAMPLE, &bps) )
+       return 1;
+ 
++  if (tilesize == 0 || tile_rowsize == 0 || tl == 0 || tw == 0)
++  {
++    TIFFError("writeBufferToContigTiles", "Tile size, tile row size, tile width, or tile length is zero");
++    exit(-1);
++  }
++  
+   tile_buffsize = tilesize;
+   if (tilesize < (tsize_t)(tl * tile_rowsize))
+     {
+@@ -1219,6 +1235,11 @@
+               tilesize, tl * tile_rowsize);
+ #endif
+     tile_buffsize = tl * tile_rowsize;
++    if (tl != tile_buffsize / tile_rowsize)
++    {
++	TIFFError("writeBufferToContigTiles", "Integer overflow when calculating buffer size");
++	exit(-1);
++    }
+     }
+ 
+   tilebuf = _TIFFmalloc(tile_buffsize);
+@@ -5945,12 +5966,27 @@
+     TIFFGetField(in, TIFFTAG_TILELENGTH, &tl);
+ 
+     tile_rowsize  = TIFFTileRowSize(in);      
++    if (ntiles == 0 || tlsize == 0 || tile_rowsize == 0)
++    {
++	TIFFError("loadImage", "File appears to be tiled, but the number of tiles, tile size, or tile rowsize is zero.");
++	exit(-1);
++    }
+     buffsize = tlsize * ntiles;
++    if (tlsize != (buffsize / ntiles))
++    {
++	TIFFError("loadImage", "Integer overflow when calculating buffer size");
++	exit(-1);
++    }
+ 
+-        
+     if (buffsize < (uint32)(ntiles * tl * tile_rowsize))
+       {
+       buffsize = ntiles * tl * tile_rowsize;
++      if (ntiles != (buffsize / tl / tile_rowsize))
++      {
++	TIFFError("loadImage", "Integer overflow when calculating buffer size");
++	exit(-1);
++      }
++      
+ #ifdef DEBUG2
+       TIFFError("loadImage",
+ 	        "Tilesize %u is too small, using ntiles * tilelength * tilerowsize %lu",
+@@ -5969,8 +6005,25 @@
+     TIFFGetFieldDefaulted(in, TIFFTAG_ROWSPERSTRIP, &rowsperstrip);
+     stsize = TIFFStripSize(in);
+     nstrips = TIFFNumberOfStrips(in);
++    if (nstrips == 0 || stsize == 0)
++    {
++	TIFFError("loadImage", "File appears to be striped, but the number of stipes or stripe size is zero.");
++	exit(-1);
++    }
++
+     buffsize = stsize * nstrips;
+-    
++    if (stsize != (buffsize / nstrips))
++    {
++	TIFFError("loadImage", "Integer overflow when calculating buffer size");
++	exit(-1);
++    }
++    uint32 buffsize_check;
++    buffsize_check = ((length * width * spp * bps) + 7);
++    if (length != ((buffsize_check - 7) / width / spp / bps))
++    {
++	TIFFError("loadImage", "Integer overflow detected.");
++	exit(-1);
++    }
+     if (buffsize < (uint32) (((length * width * spp * bps) + 7) / 8))
+       {
+       buffsize =  ((length * width * spp * bps) + 7) / 8;
diff --git a/gnu/packages/patches/libtiff-CVE-2016-5314.patch b/gnu/packages/patches/libtiff-CVE-2016-5314.patch
new file mode 100644
index 0000000000..e5380f8639
--- /dev/null
+++ b/gnu/packages/patches/libtiff-CVE-2016-5314.patch
@@ -0,0 +1,45 @@
+Fix CVE-2016-5314.
+
+https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2016-5314
+bugzilla.maptools.org/show_bug.cgi?id=2554
+
+Patch extracted from upstream CVS repo with:
+$ cvs diff -u -r1.43 -r1.44 libtiff/tif_pixarlog.c
+
+Index: libtiff/tif_pixarlog.c
+===================================================================
+RCS file: /cvs/maptools/cvsroot/libtiff/libtiff/tif_pixarlog.c,v
+retrieving revision 1.43
+retrieving revision 1.44
+diff -u -r1.43 -r1.44
+--- libtiff/libtiff/tif_pixarlog.c	27 Dec 2015 20:14:11 -0000	1.43
++++ libtiff/libtiff/tif_pixarlog.c	28 Jun 2016 15:12:19 -0000	1.44
+@@ -459,6 +459,7 @@
+ typedef	struct {
+ 	TIFFPredictorState	predict;
+ 	z_stream		stream;
++	tmsize_t		tbuf_size; /* only set/used on reading for now */
+ 	uint16			*tbuf; 
+ 	uint16			stride;
+ 	int			state;
+@@ -694,6 +695,7 @@
+ 	sp->tbuf = (uint16 *) _TIFFmalloc(tbuf_size);
+ 	if (sp->tbuf == NULL)
+ 		return (0);
++	sp->tbuf_size = tbuf_size;
+ 	if (sp->user_datafmt == PIXARLOGDATAFMT_UNKNOWN)
+ 		sp->user_datafmt = PixarLogGuessDataFmt(td);
+ 	if (sp->user_datafmt == PIXARLOGDATAFMT_UNKNOWN) {
+@@ -783,6 +785,12 @@
+ 		TIFFErrorExt(tif->tif_clientdata, module, "ZLib cannot deal with buffers this size");
+ 		return (0);
+ 	}
++	/* Check that we will not fill more than what was allocated */
++	if (sp->stream.avail_out > sp->tbuf_size)
++	{
++		TIFFErrorExt(tif->tif_clientdata, module, "sp->stream.avail_out > sp->tbuf_size");
++		return (0);
++	}
+ 	do {
+ 		int state = inflate(&sp->stream, Z_PARTIAL_FLUSH);
+ 		if (state == Z_STREAM_END) {
diff --git a/gnu/packages/patches/libtiff-CVE-2016-5321.patch b/gnu/packages/patches/libtiff-CVE-2016-5321.patch
new file mode 100644
index 0000000000..2afca18e1d
--- /dev/null
+++ b/gnu/packages/patches/libtiff-CVE-2016-5321.patch
@@ -0,0 +1,25 @@
+Fix CVE-2016-5321. 
+
+https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2016-5321
+http://bugzilla.maptools.org/show_bug.cgi?id=2558
+
+Patch extracted from upstream CVS repo with:
+$ cvs diff -u -r1.35 -r1.36 tools/tiffcrop.c
+
+Index: tools/tiffcrop.c
+===================================================================
+RCS file: /cvs/maptools/cvsroot/libtiff/tools/tiffcrop.c,v
+retrieving revision 1.35
+retrieving revision 1.36
+diff -u -r1.35 -r1.36
+--- libtiff/tools/tiffcrop.c	19 Aug 2015 02:31:04 -0000	1.35
++++ libtiff/tools/tiffcrop.c	11 Jul 2016 21:26:03 -0000	1.36
+@@ -989,7 +989,7 @@
+     nrow = (row + tl > imagelength) ? imagelength - row : tl;
+     for (col = 0; col < imagewidth; col += tw)
+       {
+-      for (s = 0; s < spp; s++)
++      for (s = 0; s < spp && s < MAX_SAMPLES; s++)
+         {  /* Read each plane of a tile set into srcbuffs[s] */
+ 	tbytes = TIFFReadTile(in, srcbuffs[s], col, row, 0, s);
+         if (tbytes < 0  && !ignore)
diff --git a/gnu/packages/patches/libtiff-CVE-2016-5323.patch b/gnu/packages/patches/libtiff-CVE-2016-5323.patch
new file mode 100644
index 0000000000..8b2a043d29
--- /dev/null
+++ b/gnu/packages/patches/libtiff-CVE-2016-5323.patch
@@ -0,0 +1,88 @@
+Fix CVE-2016-5323.
+
+https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2016-5323
+http://bugzilla.maptools.org/show_bug.cgi?id=2559
+
+Patch extracted from upstream CVS repo with:
+$ cvs diff -u -r1.36  -r1.37 tools/tiffcrop.c
+
+Index: tools/tiffcrop.c
+===================================================================
+RCS file: /cvs/maptools/cvsroot/libtiff/tools/tiffcrop.c,v
+retrieving revision 1.36
+retrieving revision 1.37
+diff -u -r1.36 -r1.37
+--- libtiff/tools/tiffcrop.c	11 Jul 2016 21:26:03 -0000	1.36
++++ libtiff/tools/tiffcrop.c	11 Jul 2016 21:38:31 -0000	1.37
+@@ -3738,7 +3738,7 @@
+ 
+       matchbits = maskbits << (8 - src_bit - bps); 
+       /* load up next sample from each plane */
+-      for (s = 0; s < spp; s++)
++      for (s = 0; (s < spp) && (s < MAX_SAMPLES); s++)
+         {
+ 	src = in[s] + src_offset + src_byte;
+         buff1 = ((*src) & matchbits) << (src_bit);
+@@ -3837,7 +3837,7 @@
+       src_bit  = bit_offset % 8;
+ 
+       matchbits = maskbits << (16 - src_bit - bps); 
+-      for (s = 0; s < spp; s++)
++      for (s = 0; (s < spp) && (s < MAX_SAMPLES); s++)
+         {
+ 	src = in[s] + src_offset + src_byte;
+         if (little_endian)
+@@ -3947,7 +3947,7 @@
+       src_bit  = bit_offset % 8;
+ 
+       matchbits = maskbits << (32 - src_bit - bps); 
+-      for (s = 0; s < spp; s++)
++      for (s = 0; (s < spp) && (s < MAX_SAMPLES); s++)
+         {
+ 	src = in[s] + src_offset + src_byte;
+         if (little_endian)
+@@ -4073,7 +4073,7 @@
+       src_bit  = bit_offset % 8;
+ 
+       matchbits = maskbits << (64 - src_bit - bps); 
+-      for (s = 0; s < spp; s++)
++      for (s = 0; (s < spp) && (s < MAX_SAMPLES); s++)
+ 	{
+ 	src = in[s] + src_offset + src_byte;
+ 	if (little_endian)
+@@ -4263,7 +4263,7 @@
+ 
+       matchbits = maskbits << (8 - src_bit - bps); 
+       /* load up next sample from each plane */
+-      for (s = 0; s < spp; s++)
++      for (s = 0; (s < spp) && (s < MAX_SAMPLES); s++)
+         {
+ 	src = in[s] + src_offset + src_byte;
+         buff1 = ((*src) & matchbits) << (src_bit);
+@@ -4362,7 +4362,7 @@
+       src_bit  = bit_offset % 8;
+ 
+       matchbits = maskbits << (16 - src_bit - bps); 
+-      for (s = 0; s < spp; s++)
++      for (s = 0; (s < spp) && (s < MAX_SAMPLES); s++)
+         {
+ 	src = in[s] + src_offset + src_byte;
+         if (little_endian)
+@@ -4471,7 +4471,7 @@
+       src_bit  = bit_offset % 8;
+ 
+       matchbits = maskbits << (32 - src_bit - bps); 
+-      for (s = 0; s < spp; s++)
++      for (s = 0; (s < spp) && (s < MAX_SAMPLES); s++)
+         {
+ 	src = in[s] + src_offset + src_byte;
+         if (little_endian)
+@@ -4597,7 +4597,7 @@
+       src_bit  = bit_offset % 8;
+ 
+       matchbits = maskbits << (64 - src_bit - bps); 
+-      for (s = 0; s < spp; s++)
++      for (s = 0; (s < spp) && (s < MAX_SAMPLES); s++)
+ 	{
+ 	src = in[s] + src_offset + src_byte;
+ 	if (little_endian)
diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index de8f054c5e..c34a2495a6 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -7216,13 +7216,13 @@ processes across test runs.")
 (define-public python-icalendar
   (package
     (name "python-icalendar")
-    (version "3.9.1")
+    (version "3.10")
     (source (origin
              (method url-fetch)
              (uri (pypi-uri "icalendar" version))
              (sha256
               (base32
-               "0fhrczdj3jxy5bvswphp3vys7vwv5c9bpwg7asykqwa3z6253q6q"))))
+               "01amnk3621s7fagfla86npd25knbqirchg7h1jpqxqp103d02bs7"))))
     (build-system python-build-system)
     (propagated-inputs
      `(("python-dateutil-2" ,python-dateutil-2)
@@ -10218,3 +10218,43 @@ List.  Forked from and using the same API as the publicsuffix package.")
       (native-inputs
        `(("python2-setuptools" ,python2-setuptools)
          ,@(package-native-inputs base))))))
+
+(define-public python-freezegun
+  (package
+    (name "python-freezegun")
+    (version "0.3.7")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (pypi-uri "freezegun" version))
+        (sha256
+          (base32
+            "14l19x06v5jkq4rdwbmfyw4x9lrjb2300afrk21r1ash7y1y9a0w"))))
+    (build-system python-build-system)
+    (native-inputs
+     `(("python-mock" ,python-mock)
+       ("python-nose" ,python-nose)
+       ("python-coverage" ,python-coverage)
+       ("python-dateutil-2" ,python-dateutil-2)))
+    (inputs
+     `(("python-six" ,python-six)))
+    (arguments
+     `(#:phases (modify-phases %standard-phases
+        ;; The tests are normally executed via `make test`, but the PyPi
+        ;; package does not include the Makefile.
+        (replace 'check
+          (lambda _
+            (zero? (system* "nosetests" "./tests/")))))))
+    (home-page "https://github.com/spulec/freezegun")
+    (synopsis "Test utility for mocking the datetime module")
+    (description
+      "FreezeGun is a library that allows your python tests to travel through
+time by mocking the datetime module.")
+    (license license:asl2.0)))
+
+(define-public python2-freezegun
+  (let ((base (package-with-python2 (strip-python2-variant python-freezegun))))
+    (package (inherit base)
+      (native-inputs
+       `(("python2-setuptools" ,python2-setuptools)
+         ,@(package-native-inputs base))))))
diff --git a/gnu/packages/ruby.scm b/gnu/packages/ruby.scm
index 52cdef1066..46588dd002 100644
--- a/gnu/packages/ruby.scm
+++ b/gnu/packages/ruby.scm
@@ -4120,21 +4120,18 @@ call.")
      `(#:test-target "spec"
        #:phases
        (modify-phases %standard-phases
-         (add-before 'build 'remove-git-lsfiles-and-extra-gemspecs
-           (lambda _
-             (for-each (lambda (file)
-                         (substitute* file
-                           (("git ls-files") "find * |sort")))
-                       (list "concurrent-ruby.gemspec"
-                             "support/file_map.rb"))
-             #t))
-         (add-before 'build 'remove-extra-gemspecs
+         (add-before 'replace-git-ls-files 'remove-extra-gemspecs
            (lambda _
              ;; Delete extra gemspec files so 'first-gemspec' chooses the
              ;; correct one.
              (delete-file "concurrent-ruby-edge.gemspec")
              (delete-file "concurrent-ruby-ext.gemspec")
              #t))
+         (add-before 'build 'replace-git-ls-files2
+           (lambda _
+             (substitute* "support/file_map.rb"
+               (("git ls-files") "find * |sort"))
+             #t))
          (add-before 'check 'rake-compile
            ;; Fix the test error described at
            ;; https://github.com/ruby-concurrency/concurrent-ruby/pull/408