~ruther/guix-local

4b4fc92fe59833701b3a023fb4befde8196424cb — Leo Famulari 9 years ago a007d69 + 4e9d505
Merge branch 'master' into core-updates
M gnu/local.mk => gnu/local.mk +7 -0
@@ 626,6 626,13 @@ dist_patch_DATA =						\
  %D%/packages/patches/libtar-CVE-2013-4420.patch \
  %D%/packages/patches/libtheora-config-guess.patch		\
  %D%/packages/patches/libtiff-CVE-2015-8665+CVE-2015-8683.patch \
  %D%/packages/patches/libtiff-CVE-2016-3623.patch		\
  %D%/packages/patches/libtiff-CVE-2016-3945.patch		\
  %D%/packages/patches/libtiff-CVE-2016-3990.patch		\
  %D%/packages/patches/libtiff-CVE-2016-3991.patch		\
  %D%/packages/patches/libtiff-CVE-2016-5314.patch		\
  %D%/packages/patches/libtiff-CVE-2016-5321.patch		\
  %D%/packages/patches/libtiff-CVE-2016-5323.patch		\
  %D%/packages/patches/libtiff-oob-accesses-in-decode.patch	\
  %D%/packages/patches/libtiff-oob-write-in-nextdecode.patch	\
  %D%/packages/patches/libtool-skip-tests2.patch		\

M gnu/packages/bioinformatics.scm => gnu/packages/bioinformatics.scm +2 -2
@@ 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

M gnu/packages/calendar.scm => gnu/packages/calendar.scm +5 -28
@@ 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)))

M gnu/packages/image.scm => gnu/packages/image.scm +18 -0
@@ 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")

M gnu/packages/imagemagick.scm => gnu/packages/imagemagick.scm +2 -2
@@ 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")

A gnu/packages/patches/libtiff-CVE-2016-3623.patch => gnu/packages/patches/libtiff-CVE-2016-3623.patch +30 -0
@@ 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);

A gnu/packages/patches/libtiff-CVE-2016-3945.patch => gnu/packages/patches/libtiff-CVE-2016-3945.patch +94 -0
@@ 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;

A gnu/packages/patches/libtiff-CVE-2016-3990.patch => gnu/packages/patches/libtiff-CVE-2016-3990.patch +31 -0
@@ 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)  {

A gnu/packages/patches/libtiff-CVE-2016-3991.patch => gnu/packages/patches/libtiff-CVE-2016-3991.patch +123 -0
@@ 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;

A gnu/packages/patches/libtiff-CVE-2016-5314.patch => gnu/packages/patches/libtiff-CVE-2016-5314.patch +45 -0
@@ 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) {

A gnu/packages/patches/libtiff-CVE-2016-5321.patch => gnu/packages/patches/libtiff-CVE-2016-5321.patch +25 -0
@@ 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)

A gnu/packages/patches/libtiff-CVE-2016-5323.patch => gnu/packages/patches/libtiff-CVE-2016-5323.patch +88 -0
@@ 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)

M gnu/packages/python.scm => gnu/packages/python.scm +42 -2
@@ 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))))))

M gnu/packages/ruby.scm => gnu/packages/ruby.scm +6 -9
@@ 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

M guix/build/ruby-build-system.scm => guix/build/ruby-build-system.scm +47 -10
@@ 1,7 1,7 @@
;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2015 David Thompson <davet@gnu.org>
;;; Copyright © 2015 Pjotr Prins <pjotr.public01@thebird.nl>
;;; Copyright © 2015 Ben Woodcroft <donttrustben@gmail.com>
;;; Copyright © 2015, 2016 Ben Woodcroft <donttrustben@gmail.com>
;;;
;;; This file is part of GNU Guix.
;;;


@@ 69,6 69,16 @@ directory."
(define (first-gemspec)
  (first-matching-file "\\.gemspec$"))

(define* (replace-git-ls-files #:key source #:allow-other-keys)
  "Many gemspec files downloaded from outside rubygems.org use `git ls-files`
to list of the files to be included in the built gem.  However, since this
operation is not deterministic, we replace it with `find`."
  (when (not (gem-archive? source))
    (let ((gemspec (first-gemspec)))
      (substitute* gemspec
        (("`git ls-files`") "`find . -type f |sort`"))))
  #t)

(define* (extract-gemspec #:key source #:allow-other-keys)
  "Remove the original gemspec, if present, and replace it with a new one.
This avoids issues with upstream gemspecs requiring tools such as git to


@@ 120,27 130,54 @@ GEM-FLAGS are passed to the 'gem' invokation, if present."
                           1))
         (out (assoc-ref outputs "out"))
         (gem-home (string-append out "/lib/ruby/gems/" ruby-version ".0"))
         (gem-name (first-matching-file "\\.gem$")))
         (gem-file (first-matching-file "\\.gem$"))
         (gem-file-basename (basename gem-file))
         (gem-name (substring gem-file-basename
                              0
                              (- (string-length gem-file-basename) 4)))
         (gem-directory (string-append gem-home "/gems/" gem-name)))
    (setenv "GEM_HOME" gem-home)
    (mkdir-p gem-home)
    (and (apply system* "gem" "install" gem-name
    (and (apply system* "gem" "install" gem-file
                "--local" "--ignore-dependencies"
                ;; Executables should go into /bin, not /lib/ruby/gems.
                "--bindir" (string-append out "/bin")
                gem-flags)
         ;; Remove the cached gem file as this is unnecessary and contains
         ;; timestamped files rendering builds not reproducible.
         (begin (delete-file (string-append gem-home "/cache/" gem-name))
                #t))))
         (begin
           ;; Remove the cached gem file as this is unnecessary and contains
           ;; timestamped files rendering builds not reproducible.
           (let ((cached-gem (string-append gem-home "/cache/" gem-file)))
             (log-file-deletion cached-gem)
             (delete-file cached-gem))
           ;; For gems with native extensions, several Makefile-related files
           ;; are created that contain timestamps or other elements making
           ;; them not reproducible.  They are unnecessary so we remove them.
           (if (file-exists? (string-append gem-directory "/ext"))
               (begin
                 (for-each (lambda (file)
                             (log-file-deletion file)
                             (delete-file file))
                           (append
                            (find-files (string-append gem-home "/doc")
                                        "page-Makefile.ri")
                            (find-files (string-append gem-home "/extensions")
                                        "gem_make.out")
                            (find-files (string-append gem-directory "/ext")
                                        "Makefile")))))
           #t))))

(define (log-file-deletion file)
  (display (string-append "deleting '" file "' for reproducibility\n")))

(define %standard-phases
  (modify-phases gnu:%standard-phases
    (delete 'configure)
    (replace 'unpack unpack)
    (add-before 'build 'extract-gemspec extract-gemspec)
    (add-after 'extract-gemspec 'replace-git-ls-files replace-git-ls-files)
    (replace 'build build)
    (replace 'unpack unpack)
    (replace 'install install)
    (replace 'check check)))
    (replace 'check check)
    (replace 'install install)))

(define* (ruby-build #:key inputs (phases %standard-phases)
                     #:allow-other-keys #:rest args)