From 05e3865e07f76de24d4d98351043f2d0ad73a6a8 Mon Sep 17 00:00:00 2001
From: ng0 <ng0@we.make.ritual.n0.is>
Date: Wed, 2 Nov 2016 20:13:46 +0000
Subject: gnu: gnurl: Update to 7.51.0 [fixes CVE-2016-{8615..8625}].

* gnu/packages/gnunet.scm (gnurl): Update to 7.51.0.

Signed-off-by: Leo Famulari <leo@famulari.name>
---
 gnu/packages/gnunet.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/gnunet.scm b/gnu/packages/gnunet.scm
index 6d9c3c8f33..bcefa42d11 100644
--- a/gnu/packages/gnunet.scm
+++ b/gnu/packages/gnunet.scm
@@ -163,7 +163,7 @@ (define-public libmicrohttpd
 (define-public gnurl
   (package
    (name "gnurl")
-   (version "7.50.3")
+   (version "7.51.0")
    (source (origin
             (method url-fetch)
             (uri (let ((version-with-underscores
@@ -172,7 +172,7 @@ (define-public gnurl
                                   name "-" version-with-underscores ".tar.bz2")))
             (sha256
              (base32
-              "07ij9mj60kpfrmi0436k14b1d1idsj79nk4w5h3bia69arzp2cnk"))))
+              "1rgl4agrzghvyfz1afk1p5ryq4b9cz28lavx8ikrav6aiv9h00ig"))))
    (build-system gnu-build-system)
    (inputs `(("gnutls" ,gnutls)
              ("libidn" ,libidn)
-- 
cgit v1.2.3


From 5d68e9d6204333e7ce9d43645a7a49f0dca23270 Mon Sep 17 00:00:00 2001
From: Arun Isaac <arunisaac@systemreboot.net>
Date: Sun, 30 Oct 2016 16:37:28 +0530
Subject: gnu: Add pdf2svg.
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

* gnu/packages/pdf.scm (pdf2svg): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
---
 gnu/packages/pdf.scm | 26 ++++++++++++++++++++++++++
 1 file changed, 26 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/pdf.scm b/gnu/packages/pdf.scm
index 42547dff9b..8aabacc9cc 100644
--- a/gnu/packages/pdf.scm
+++ b/gnu/packages/pdf.scm
@@ -8,6 +8,7 @@
 ;;; Coypright © 2016 Marius Bakke <mbakke@fastmail.com>
 ;;; Coypright © 2016 Ludovic Courtès <ludo@gnu.org>
 ;;; Coypright © 2016 Julien Lepiller <julien@lepiller.eu>
+;;; Copyright © 2016 Arun Isaac <arunisaac@systemreboot.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -751,3 +752,28 @@ (define-public fbida
 the framebuffer.")
 
     (license license:gpl2+)))
+
+(define-public pdf2svg
+  (package
+    (name "pdf2svg")
+    (version "0.2.3")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append
+                    "https://github.com/dawbarton/pdf2svg/archive/v"
+                    version ".tar.gz"))
+              (file-name (string-append name "-" version ".tar.gz"))
+              (sha256
+               (base32
+                "12pa1pajirnlrkz2il3h4l30lc2prryk1qr132jk6z9y1c3qdcag"))))
+    (build-system gnu-build-system)
+    (inputs
+     `(("cairo" ,cairo)
+       ("poppler" ,poppler)))
+    (native-inputs
+     `(("pkg-config" ,pkg-config)))
+    (home-page "http://www.cityinthesky.co.uk/opensource/pdf2svg/")
+    (synopsis "PDF to SVG converter")
+    (description "@command{pdf2svg} is a simple command-line PDF to SVG
+converter using the Poppler and Cairo libraries.")
+    (license license:gpl2+)))
-- 
cgit v1.2.3


From b054b26a481e2e6609f6050b1bed5c2518bfb832 Mon Sep 17 00:00:00 2001
From: Danny Milosavljevic <dannym@scratchpost.org>
Date: Thu, 3 Nov 2016 00:58:56 +0100
Subject: gnu: sunxi-tools: Update to 1.4.1.
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

* gnu/packages/admin.scm (sunxi-tools): Update to 1.4.1.
[arguments]: Add "CC=gcc" "all" to #:make-flags.  Remove 'fix-Makefile'
phase.  Add 'install' phase.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
---
 gnu/packages/admin.scm | 24 +++++++++++-------------
 1 file changed, 11 insertions(+), 13 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/admin.scm b/gnu/packages/admin.scm
index c9563a16ed..1d577c73bc 100644
--- a/gnu/packages/admin.scm
+++ b/gnu/packages/admin.scm
@@ -1859,14 +1859,14 @@ (define-public pam-krb5
 (define-public sunxi-tools
   (package
     (name "sunxi-tools")
-    (version "1.3")
+    (version "1.4.1")
     (source
      (origin
        (method url-fetch)
        (uri (string-append "https://github.com/linux-sunxi/"
                            "sunxi-tools/archive/v" version ".tar.gz"))
        (sha256
-        (base32 "1iazm28gws1i8sls3gxwc5p108n56ags287zmh1rpvkn2k1az81a"))
+        (base32 "06qd2b4dlzbmzfy4q9n8v5rkkbmgcfdbv4nkkcp4nysi10k7cpfs"))
        (modules '((guix build utils)))
        (snippet
         ;; Remove binaries contained in the tarball which are only for the
@@ -1882,19 +1882,16 @@ (define-public sunxi-tools
      `(#:tests? #f ; no tests exist
        #:make-flags (list (string-append "PREFIX="
                                          (assoc-ref %outputs "out"))
-                          "TARGET_TOOLS=sunxi-pio sunxi-meminfo"
-                          "CROSS_COMPILE=")
+                          "CROSS_COMPILE="
+                          "CC=gcc"
+                          "all")
        #:phases
        (modify-phases %standard-phases
-         (add-after 'unpack 'fix-Makefile
-           (lambda _
-             (substitute* "Makefile"
-               ;; Upstream adds Makefile and config.h as dependencies
-               ;; of all their tools which means $^ would pass them to gcc.
-               ;; gcc won't know what to do with a Makefile.
-               (("-o [$][@] [$]\\^") "-o $@ meminfo.c"))
-             #t))
-         (delete 'configure))))
+         (delete 'configure)
+         (replace 'install
+           (lambda* (#:key make-flags #:allow-other-keys)
+             (zero? (apply system* "make" "install-all" "install-misc"
+                           make-flags)))))))
     (home-page "https://github.com/linux-sunxi/sunxi-tools")
     (synopsis "Hardware management tools for Allwinner computers")
     (description "This package contains tools for Allwinner devices:
@@ -1910,5 +1907,6 @@ (define-public sunxi-tools
 @item @command{sunxi-pio}: Sets GPIO parameters and oscillates a GPIO
 in order to be able to find it.
 @item @command{sunxi-meminfo}: Prints memory bus settings.
+@item @command{sunxi-nand-image-builder}: Prepares raw NAND images.
 @end enumerate")
     (license license:gpl2+)))
-- 
cgit v1.2.3


From b81245ccb38dc16d115519dd3166d8bb2c295bb8 Mon Sep 17 00:00:00 2001
From: Kei Kebreau <kei@openmailbox.org>
Date: Thu, 3 Nov 2016 13:36:02 -0400
Subject: [PATCH] gnu: Add libjxr.

* gnu/packages/image.scm (libjxr): New variable.
* gnu/packages/patches/libjxr-fix-function-signature.patch: New file.
* gnu/packages/patches/libjxr-fix-typos.patch: New file.
* gnu/local.mk (dist_patch_DATA): Register patches.
---
 gnu/local.mk                                       |  2 +
 gnu/packages/image.scm                             | 57 ++++++++++++++++++++++
 .../patches/libjxr-fix-function-signature.patch    | 16 ++++++
 gnu/packages/patches/libjxr-fix-typos.patch        | 29 +++++++++++
 4 files changed, 104 insertions(+)
 create mode 100644 gnu/packages/patches/libjxr-fix-function-signature.patch
 create mode 100644 gnu/packages/patches/libjxr-fix-typos.patch

(limited to 'gnu/packages')

diff --git a/gnu/local.mk b/gnu/local.mk
index 5fe6be5190..a23d536394 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -639,6 +639,8 @@ dist_patch_DATA =						\
   %D%/packages/patches/libdrm-symbol-check.patch		\
   %D%/packages/patches/libevent-dns-tests.patch			\
   %D%/packages/patches/libextractor-ffmpeg-3.patch		\
+  %D%/packages/patches/libjxr-fix-function-signature.patch	\
+  %D%/packages/patches/libjxr-fix-typos.patch			\
   %D%/packages/patches/liboop-mips64-deplibs-fix.patch		\
   %D%/packages/patches/libotr-test-auth-fix.patch		\
   %D%/packages/patches/liblxqt-include.patch			\
diff --git a/gnu/packages/image.scm b/gnu/packages/image.scm
index 3a1209f4b1..6f83fc4be4 100644
--- a/gnu/packages/image.scm
+++ b/gnu/packages/image.scm
@@ -11,6 +11,7 @@
 ;;; Copyright © 2016 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2016 Eric Bavier <bavier@member.fsf.org>
 ;;; Copyright © 2016 Arun Isaac <arunisaac@systemreboot.net>
+;;; Copyright © 2016 Kei Kebreau <kei@openmailbox.org>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -129,6 +130,62 @@ (define-public libjpeg-8
             (sha256 (base32
                      "1cz0dy05mgxqdgjf52p54yxpyy95rgl30cnazdrfmw7hfca9n0h0"))))))
 
+(define-public libjxr
+  (package
+    (name "libjxr")
+    (version "1.1")
+    (source (origin
+              ;; We are using the Debian source because CodePlex does not
+              ;; deliver an easily downloadable tarball.
+              (method url-fetch)
+              (uri (string-append "mirror://debian/pool/main/j/jxrlib/jxrlib_"
+                                  version ".orig.tar.gz"))
+              (sha256
+               (base32
+                "00w3f3cmjsm3fiaxq5mxskmp5rl3mki8psrf9y8s1vqbg237na67"))
+              (patch-flags '("-p1" "--binary"))
+              (patches (search-patches "libjxr-fix-function-signature.patch"
+                                       "libjxr-fix-typos.patch"))))
+    (build-system gnu-build-system)
+    (arguments '(#:make-flags '("CC=gcc")
+                 #:tests? #f ; no check target
+                 #:phases
+                 (modify-phases %standard-phases
+                   (delete 'configure) ; no configure script
+                   ;; The upstream makefile does not include an install phase.
+                   (replace 'install
+                     (lambda* (#:key outputs #:allow-other-keys)
+                       (let* ((out (assoc-ref outputs "out"))
+                              (bin (string-append out "/bin"))
+                              (lib (string-append out "/lib"))
+                              (include (string-append out "/include/jxrlib")))
+                         (for-each (lambda (file)
+                                     (install-file file include)
+                                     (delete-file file))
+                                   (append
+                                    '("jxrgluelib/JXRGlue.h"
+                                      "jxrgluelib/JXRMeta.h"
+                                      "jxrtestlib/JXRTest.h"
+                                      "image/sys/windowsmediaphoto.h")
+                                    (find-files "common/include" "\\.h$")))
+                         (for-each (lambda (file)
+                                     (install-file file lib)
+                                     (delete-file file))
+                                   (find-files "." "\\.a$"))
+                         (for-each (lambda (file)
+                                     (install-file file bin)
+                                     (delete-file file))
+                                   '("JxrDecApp" "JxrEncApp")))
+                       #t)))))
+    (synopsis "Implementation of the JPEG XR standard")
+    (description "JPEG XR is an approved ISO/IEC International standard (its
+official designation is ISO/IEC 29199-2). This library is an implementation of that standard.")
+    (license
+     (license:non-copyleft
+      "file://Makefile"
+      "See the header of the Makefile in the distribution."))
+    (home-page "https://jxrlib.codeplex.com/")))
+
 (define-public jpegoptim
   (package
    (name "jpegoptim")
diff --git a/gnu/packages/patches/libjxr-fix-function-signature.patch b/gnu/packages/patches/libjxr-fix-function-signature.patch
new file mode 100644
index 0000000000..32f5f64512
--- /dev/null
+++ b/gnu/packages/patches/libjxr-fix-function-signature.patch
@@ -0,0 +1,16 @@
+Description: Fix function signature
+Author: Mathieu Malaterre <malat@debian.org>
+Origin: upstream, https://jxrlib.codeplex.com/SourceControl/changeset/04cf339385b8196f98025b43a366a0790deac994
+Bug-Debian: http://bugs.debian.org/748590
+
+--- jxrlib-1.1.orig/image/decode/JXRTranscode.c
++++ jxrlib-1.1/image/decode/JXRTranscode.c
+@@ -47,7 +47,7 @@ EXTERN_C Void FreeCodingContextDec(CWMIm
+ EXTERN_C Int StrEncInit(CWMImageStrCodec *);
+ EXTERN_C Void StrIOEncTerm(CWMImageStrCodec *);
+ EXTERN_C Void FreeCodingContextEnc(CWMImageStrCodec *);
+-EXTERN_C Void encodeMB(CWMImageStrCodec *, Int, Int);
++EXTERN_C Int encodeMB(CWMImageStrCodec *, Int, Int);
+ EXTERN_C Int  writeIndexTableNull(CWMImageStrCodec *);
+ EXTERN_C Void writePacketHeader(BitIOInfo *, U8, U8);
+ 
diff --git a/gnu/packages/patches/libjxr-fix-typos.patch b/gnu/packages/patches/libjxr-fix-typos.patch
new file mode 100644
index 0000000000..819db34900
--- /dev/null
+++ b/gnu/packages/patches/libjxr-fix-typos.patch
@@ -0,0 +1,29 @@
+Description: Fix typos and remove some warnings
+Author: Mathieu Malaterre <malat@debian.org>
+
+Index: jxrlib-1.1/jxrencoderdecoder/JxrEncApp.c
+===================================================================
+--- jxrlib-1.1.orig/jxrencoderdecoder/JxrEncApp.c
++++ jxrlib-1.1/jxrencoderdecoder/JxrEncApp.c
+@@ -578,7 +578,7 @@ main(int argc, char* argv[])
+ 
+     //================================
+     Call(PKCreateCodecFactory(&pCodecFactory, WMP_SDK_VERSION));
+-    Call(pCodecFactory->CreateCodec(&IID_PKImageWmpEncode, &pEncoder));
++    Call(pCodecFactory->CreateCodec(&IID_PKImageWmpEncode, (void**)&pEncoder));
+ 
+     //----------------------------------------------------------------
+     Call(PKCreateTestFactory(&pTestFactory, WMP_SDK_VERSION));
+Index: jxrlib-1.1/jxrgluelib/JXRMeta.h
+===================================================================
+--- jxrlib-1.1.orig/jxrgluelib/JXRMeta.h
++++ jxrlib-1.1/jxrgluelib/JXRMeta.h
+@@ -34,7 +34,7 @@
+ 
+ #ifndef UNREFERENCED_PARAMETER
+ #define UNREFERENCED_PARAMETER(P) { (P) = (P); }
+-#endif UNREFERENCED_PARAMETER
++#endif /*UNREFERENCED_PARAMETER*/
+ 
+ //================================================================
+ // Container
-- 
cgit v1.2.3


From ac3265abada4c55080008c964fec85e684094183 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 3 Nov 2016 17:43:47 +0100
Subject: gnu: Add r-htmltable.

* gnu/packages/web.scm (r-htmltable): New variable.
---
 gnu/packages/web.scm | 29 +++++++++++++++++++++++++++++
 1 file changed, 29 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm
index 976820171b..9ea9503521 100644
--- a/gnu/packages/web.scm
+++ b/gnu/packages/web.scm
@@ -3309,6 +3309,35 @@ (define-public r-htmlwidgets
 applications.")
     (license l:expat)))
 
+(define-public r-htmltable
+  (package
+    (name "r-htmltable")
+    (version "1.7")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "htmlTable" version))
+       (sha256
+        (base32
+         "0x2f2hrbhvm53zqwn0ny9wxbk34nwf6zww8cx4bjy5ax15asdllm"))))
+    (properties `((upstream-name . "htmlTable")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-knitr" ,r-knitr)
+       ("r-magrittr" ,r-magrittr)
+       ("r-stringr" ,r-stringr)))
+    (home-page "http://gforge.se/packages/")
+    (synopsis "Advanced tables for Markdown/HTML")
+    (description
+     "This package provides functions to build tables with advanced layout
+elements such as row spanners, column spanners, table spanners, zebra
+striping, and more.  While allowing advanced layout, the underlying
+CSS-structure is simple in order to maximize compatibility with word
+processors such as LibreOffice.  The package also contains a few text
+formatting functions that help outputting text compatible with HTML or
+LaTeX.")
+    (license l:gpl3+)))
+
 (define-public r-curl
   (package
     (name "r-curl")
-- 
cgit v1.2.3


From ebbd4d0bfdc7d23996762ad86700f02b77b08cf3 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 3 Nov 2016 18:57:21 +0100
Subject: gnu: Add r-survival.

* gnu/packages/statistics.scm (r-survival): New variable.
---
 gnu/packages/statistics.scm | 20 ++++++++++++++++++++
 1 file changed, 20 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index b15f9cf45e..c595f965bf 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -3230,6 +3230,26 @@ (define-public r-rpart
 classification, regression and survival trees.")
     (license (list license:gpl2+ license:gpl3+))))
 
+(define-public r-survival
+  (package
+    (name "r-survival")
+    (version "2.40-1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "survival" version))
+       (sha256
+        (base32
+         "10pf0kq0g66k5rgizrvh29mq3r84acljw2jgrv5yp6z38xw23mci"))))
+    (build-system r-build-system)
+    (home-page "https://github.com/therneau/survival")
+    (synopsis "Survival analysis")
+    (description
+     "This package contains the core survival analysis routines, including
+definition of Surv objects, Kaplan-Meier and Aalen-Johansen (multi-state)
+curves, Cox models, and parametric accelerated failure time models.")
+    (license license:lgpl2.0+)))
+
 (define-public r-hmisc
   (package
     (name "r-hmisc")
-- 
cgit v1.2.3


From d13a4e25754888d3f233e67bd4968279fa9a4dd2 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 3 Nov 2016 17:44:10 +0100
Subject: gnu: r-proto: Update to 1.0.0.

* gnu/packages/statistics.scm (r-proto): Update to 1.0.0.
---
 gnu/packages/statistics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index c595f965bf..50f8671804 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -504,13 +504,13 @@ (define-public r-plyr
 (define-public r-proto
   (package
     (name "r-proto")
-    (version "0.3-10")
+    (version "1.0.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "proto" version))
        (sha256
-        (base32 "03mvzi529y6kjcp9bkpk7zlgpcakb3iz73hca6rpjy14pyzl3nfh"))))
+        (base32 "1l843p8vckjckdhgv37ngv47fga5jzy0n00pmipvp05nnaixk54j"))))
     (build-system r-build-system)
     (home-page "http://r-proto.googlecode.com")
     (synopsis "Prototype object-based programming")
-- 
cgit v1.2.3


From 054a9a786b587265bf2a6facb4598929ccbac989 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 3 Nov 2016 17:44:31 +0100
Subject: gnu: r-gdtools: Update to 0.1.1.

* gnu/packages/statistics.scm (r-gdtools): Update to 0.1.1.
[propagated-inputs]: Add r-withr.
---
 gnu/packages/statistics.scm | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 50f8671804..d1436fd611 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -692,20 +692,22 @@ (define-public r-ggplot2
 (define-public r-gdtools
   (package
     (name "r-gdtools")
-    (version "0.0.7")
+    (version "0.1.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "gdtools" version))
        (sha256
         (base32
-         "1bmnf9d677f2jy8jnb9ymjz1qzm4yrd0qp6k5qrrly06jfffyx7g"))))
+         "1l9d759x9s4ddz51sls8kcjps2i9kwfbc72dnagrdavh82h0al8n"))))
     (build-system r-build-system)
     (native-inputs
      `(("r-rcpp" ,r-rcpp)
        ("pkg-config" ,pkg-config)))
     (inputs
      `(("cairo" ,cairo)))
+    (propagated-inputs
+     `(("r-withr" ,r-withr)))
     (home-page "http://cran.r-project.org/web/packages/gdtools")
     (synopsis "Utilities for graphical rendering")
     (description
-- 
cgit v1.2.3


From 572e1a0ca7cc8ec96fd65f16c57441d82ad79fa4 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 3 Nov 2016 17:45:57 +0100
Subject: gnu: r-acepack: Update to 1.4.1.

* gnu/packages/statistics.scm (r-acepack): Update to 1.4.1.
---
 gnu/packages/statistics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index d1436fd611..de53d7261f 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -1217,14 +1217,14 @@ (define-public r-dplyr
 (define-public r-acepack
   (package
     (name "r-acepack")
-    (version "1.4.0")
+    (version "1.4.1")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "acepack" version))
        (sha256
         (base32
-         "0brivhr0imf2qq1flc9qxibybg1zi5m8pxz8cjn5a8gb42bcv96n"))))
+         "1f98rpfjmhd92rdc3j004plyfpjailz6j0ycysbac0kgj83haxc2"))))
     (build-system r-build-system)
     (inputs
      `(("gfortran" ,gfortran)))
-- 
cgit v1.2.3


From fbe5161c7d93eedc49debda5b05e4431f938076e Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 3 Nov 2016 17:46:17 +0100
Subject: gnu: r-checkmate: Update to 1.8.2.

* gnu/packages/statistics.scm (r-checkmate): Update to 1.8.2.
---
 gnu/packages/statistics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index de53d7261f..02c0cb8c42 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -1646,14 +1646,14 @@ (define-public r-backports
 (define-public r-checkmate
   (package
     (name "r-checkmate")
-    (version "1.8.1")
+    (version "1.8.2")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "checkmate" version))
        (sha256
         (base32
-         "1nqyi58jl33af82y8kw8iy9xbna2080y1khhy90kf6lim6q74024"))))
+         "1zqcggl9m7slvc0q6zyhssdypb7jzf3l9byl5vxh1qdwjiw2y64g"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-backports" ,r-backports)))
-- 
cgit v1.2.3


From f890981690c2f23b9609438b510b079f5b6e23ce Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 3 Nov 2016 17:46:39 +0100
Subject: gnu: r-openssl: Update to 0.9.5.

* gnu/packages/statistics.scm (r-openssl): Update to 0.9.5.
---
 gnu/packages/statistics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 02c0cb8c42..b5c27c0dc7 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -1786,14 +1786,14 @@ (define-public r-roxygen2
 (define-public r-openssl
   (package
     (name "r-openssl")
-    (version "0.9.4")
+    (version "0.9.5")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "openssl" version))
        (sha256
         (base32
-         "0rpb3xdzab453yjddr8ryad53ll27zss8abnj30aqa2lzbg4jwyb"))))
+         "1lal8mmcwjhhln10mfi96ipv3d364k0wiviiln220wvhddcpr9pp"))))
     (build-system r-build-system)
     (inputs
      `(("openssl" ,openssl)))
-- 
cgit v1.2.3


From f158b92caff10d285879045a713eadf56889bd64 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 3 Nov 2016 17:47:01 +0100
Subject: gnu: r-r-oo: Update to 1.21.0.

* gnu/packages/statistics.scm (r-r-oo): Update to 1.21.0.
---
 gnu/packages/statistics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index b5c27c0dc7..43b5634a68 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -2884,13 +2884,13 @@ (define-public r-r-methodss3
 (define-public r-r-oo
   (package
     (name "r-r-oo")
-    (version "1.20.0")
+    (version "1.21.0")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "R.oo" version))
               (sha256
                (base32
-                "1l1x4r69mdchjyi6sq52p580fz3b3bqv6dpn1706y9n4vq47qx24"))))
+                "0723gxjazgqq7v3lwnl7axw3brzcnizvhbd71ijkkv8mz31fwp34"))))
     (properties `((upstream-name . "R.oo")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From e71659162b9a10a4ba60373edb147c660327b23d Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 3 Nov 2016 17:47:26 +0100
Subject: gnu: r-hmisc: Update to 4.0.0.

* gnu/packages/statistics.scm (r-hmisc): Update to 4.0.0.
[propagated-inputs]: Add r-htmltable, r-htmltools, r-viridis,
r-survival.
---
 gnu/packages/statistics.scm | 10 ++++++++--
 1 file changed, 8 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 43b5634a68..5566ce7359 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -3255,14 +3255,14 @@ (define-public r-survival
 (define-public r-hmisc
   (package
     (name "r-hmisc")
-    (version "3.17-4")
+    (version "4.0-0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "Hmisc" version))
        (sha256
         (base32
-         "1hr2kycpm0h3li9gnlbx9pl6h13das7g2wqfk6cip1kx6lv00ypw"))))
+         "0azxmg9h9c456biydc0wpi9xhljmd37m8bv0zaadbvc93g7x0l4b"))))
     (properties `((upstream-name . "Hmisc")))
     (build-system r-build-system)
     (native-inputs
@@ -3277,7 +3277,13 @@ (define-public r-hmisc
        ("r-gridextra" ,r-gridextra)
        ("r-gtable" ,r-gtable)
        ("r-lattice" ,r-lattice)
+       ;; Hmisc needs survival >= 2.40.1, so it cannot use the survival
+       ;; package that comes with R 3.3.1.
+       ("r-survival" ,r-survival)
        ("r-latticeextra" ,r-latticeextra)
+       ("r-htmltable" ,r-htmltable)
+       ("r-htmltools" ,r-htmltools)
+       ("r-viridis" ,r-viridis)
        ("r-nnet" ,r-nnet)
        ("r-rpart" ,r-rpart)))
     (home-page "http://biostat.mc.vanderbilt.edu/Hmisc")
-- 
cgit v1.2.3


From ed3054231d4513d714565e6a8f94a5d8a259d51c Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 3 Nov 2016 17:48:22 +0100
Subject: gnu: r-edger: Update to 3.16.1.

* gnu/packages/bioinformatics.scm (r-edger): Update to 3.16.1.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 4750cb97bf..028a07bad6 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -6171,13 +6171,13 @@ (define-public r-genomeinfodb
 (define-public r-edger
   (package
     (name "r-edger")
-    (version "3.16.0")
+    (version "3.16.1")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "edgeR" version))
               (sha256
                (base32
-                "1qr20j55m35dwzqyzzmla69gk5bzff8v1v2qjh7yd3362wq1ch49"))))
+                "1r6hhwkqp13m022hjajzr1lnjsbai0yjhykwn0kp1f0la990a808"))))
     (properties `((upstream-name . "edgeR")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From 5b3b2d2f025126cea405e642ca77e4d087e141fe Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 3 Nov 2016 17:48:46 +0100
Subject: gnu: r-limma: Update to 3.30.2.

* gnu/packages/bioinformatics.scm (r-limma): Update to 3.30.2.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 028a07bad6..f188e827ae 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -6235,13 +6235,13 @@ (define-public r-variantannotation
 (define-public r-limma
   (package
     (name "r-limma")
-    (version "3.30.0")
+    (version "3.30.2")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "limma" version))
               (sha256
                (base32
-                "0d8wp7b7nymawf4czwsg27k4c61i4ij2lhv7phi6cb3hdd8c76yf"))))
+                "04jris7wk2lxksrrvrjsysznsdb2k04lfgrnp18ic49sazva0hfy"))))
     (build-system r-build-system)
     (home-page "http://bioinf.wehi.edu.au/limma")
     (synopsis "Package for linear models for microarray and RNA-seq data")
-- 
cgit v1.2.3


From c15ae9b00882a69eb3e95b3c720312ac4de3a742 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 3 Nov 2016 17:49:15 +0100
Subject: gnu: r-biocparallel: Update to 1.8.1.

* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.8.1.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index f188e827ae..7116399b57 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -6398,13 +6398,13 @@ (define-public r-biomart
 (define-public r-biocparallel
   (package
     (name "r-biocparallel")
-    (version "1.8.0")
+    (version "1.8.1")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "BiocParallel" version))
               (sha256
                (base32
-                "0vz23i14f7wjygr5d4y1hp8ki6l6igwcsjscfpr6dcigmknyi55c"))))
+                "123i928rwi4h4sy4fpysv6pinw5nns0sm3myxi2ghqhm34ws8gyl"))))
     (properties
      `((upstream-name . "BiocParallel")))
     (build-system r-build-system)
-- 
cgit v1.2.3


From 16a8bd319467b3677e345290f2ed29a64301db82 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 3 Nov 2016 17:49:46 +0100
Subject: gnu: r-rtracklayer: Update to 1.34.1.

* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.34.1.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 7116399b57..0fc679d228 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -6554,13 +6554,13 @@ (define-public r-genomicalignments
 (define-public r-rtracklayer
   (package
     (name "r-rtracklayer")
-    (version "1.34.0")
+    (version "1.34.1")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "rtracklayer" version))
               (sha256
                (base32
-                "0mix5k75j70mwplbdipqw71n8qic75ny6y8w2f5jj0pqg1k0327d"))))
+                "0x59k2fd0iaqi93gy6bm58p2j2z90z1b7a6w5b4c098y98n096rc"))))
     (build-system r-build-system)
     (arguments
      `(#:phases
-- 
cgit v1.2.3


From ed8fbe5e62bc04c56b848f84236a65471b13ea28 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 3 Nov 2016 18:30:43 +0100
Subject: gnu: r-rcas: Update to 1.0.0.

* gnu/packages/bioinformatics.scm (r-rcas): Update to 1.0.0.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 0fc679d228..4dfac15040 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7312,7 +7312,7 @@ (define-public r-bamsignals
 (define-public r-rcas
   (package
     (name "r-rcas")
-    (version "0.99.6")
+    (version "1.0.0")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://github.com/BIMSBbioinfo/RCAS/archive/v"
@@ -7320,7 +7320,7 @@ (define-public r-rcas
               (file-name (string-append name "-" version ".tar.gz"))
               (sha256
                (base32
-                "1ljgl2b4r6w2n0i9i04d9xaphajsvhfkjdj2i2z830nha4m3w8f0"))))
+                "1h7di822ihgkhmmmlfbfz3c2dkjyjxl307i6mx8w0cwjqbna1kp6"))))
     (build-system r-build-system)
     (native-inputs
      `(("r-knitr" ,r-knitr)
-- 
cgit v1.2.3


From 043f1535c2668e417a67971afc91abf634e269b6 Mon Sep 17 00:00:00 2001
From: Kei Kebreau <kei@openmailbox.org>
Date: Thu, 3 Nov 2016 15:40:17 -0400
Subject: gnu: starfighter: Update to 1.6.

* gnu/packages/games.scm (starfighter): Update to 1.6.
---
 gnu/packages/games.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/games.scm b/gnu/packages/games.scm
index e209cfbdbe..941e3a0852 100644
--- a/gnu/packages/games.scm
+++ b/gnu/packages/games.scm
@@ -2518,7 +2518,7 @@ (define-public warzone2100
 (define-public starfighter
   (package
     (name "starfighter")
-    (version "1.5.1.1")
+    (version "1.6")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -2527,7 +2527,7 @@ (define-public starfighter
                     name "-" version "-src.tar.gz"))
               (sha256
                (base32
-                "1qc0hhw9m8sy3n9fips52c7aph3w8a8pdl4n45yaasgxzbvpn9xg"))))
+                "1qb5nk0b3d0ia5zszmg4a3ydf4fiy39fmymb66vwkqn4djajdhzq"))))
     (build-system gnu-build-system)
     (arguments
      '(#:tests? #f ; no check target
-- 
cgit v1.2.3


From ccbc575824d575459f5449f3b852294f2f6443c0 Mon Sep 17 00:00:00 2001
From: Kei Kebreau <kei@openmailbox.org>
Date: Thu, 3 Nov 2016 16:14:05 -0400
Subject: gnu: maxima: Update to 5.38.1.

* gnu/packages/maths.scm (maxima): Update to 5.38.1.
---
 gnu/packages/maths.scm | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 64e53e2dd7..96ade5deac 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -1847,7 +1847,7 @@ (define-public gsegrafix
 (define-public maxima
   (package
     (name "maxima")
-    (version "5.36.1")
+    (version "5.38.1")
     (source
      (origin
        (method url-fetch)
@@ -1855,7 +1855,7 @@ (define-public maxima
                            version "-source/" name "-" version ".tar.gz"))
        (sha256
         (base32
-         "0x1rk659sn3cq0n5c90848ilzr1gb1wf0072fl6jhkdq00qgh2s0"))
+         "1p6646rvq43hk09msyp0dk50cqpkh07mf4x0bc2fqisqmcv6b1hf"))
        (patches (search-patches "maxima-defsystem-mkdir.patch"))))
     (build-system gnu-build-system)
     (inputs
@@ -1864,7 +1864,8 @@ (define-public maxima
        ("tk" ,tk)))                               ;Tcl/Tk is used by 'xmaxima'
     (native-inputs
      `(("texinfo" ,texinfo)
-       ("perl" ,perl)))
+       ("perl" ,perl)
+       ("python" ,python)))
     (arguments
      `(#:configure-flags
        (list "--enable-gcl"
-- 
cgit v1.2.3


From b4edcd28cf0bc55e3768d1be3044370f9d45ad73 Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Tue, 1 Nov 2016 13:46:44 +0000
Subject: gnu: Add geteltorito.

* gnu/packages/cdrom.scm (geteltorito): New variable.
---
 gnu/packages/cdrom.scm | 36 ++++++++++++++++++++++++++++++++++++
 1 file changed, 36 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/cdrom.scm b/gnu/packages/cdrom.scm
index 39c7b52426..99b7d3465f 100644
--- a/gnu/packages/cdrom.scm
+++ b/gnu/packages/cdrom.scm
@@ -5,6 +5,7 @@
 ;;; Copyright © 2015 Paul van der Walt <paul@denknerd.org>
 ;;; Copyright © 2015, 2016 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2016 Alex Kost <alezost@gmail.com>
+;;; Copyright © 2016 Marius Bakke <mbakke@fastmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -359,3 +360,38 @@ (define (wrap file)
 that grabs tracks off a CD, encodes them to Ogg/Vorbis, MP3, FLAC, Ogg/Speex
 and/or MPP/MP+ (Musepack) format, and tags them, all in one go.")
     (license gpl2+)))
+
+(define-public geteltorito
+  (package
+    (name "geteltorito")
+    (version "0.6")
+    (home-page
+     "https://userpages.uni-koblenz.de/~krienke/ftp/noarch/geteltorito/")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append home-page name "-" version ".tar.gz"))
+              (sha256
+               (base32
+                "1gkbm9ahj2mgqrkrfpibzclsriqgsbsvjh19fr815vpd9f6snkxv"))))
+    (build-system gnu-build-system)
+    (arguments
+     `(#:tests? #f ; No tests.
+       #:phases
+       (modify-phases %standard-phases
+         (delete 'configure)
+         (delete 'build)
+         (replace 'install
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let ((out (assoc-ref outputs "out")))
+               (install-file "geteltorito"
+                             (string-append out "/bin"))))))))
+    (inputs `(("perl" ,perl)))
+    (synopsis "Extract the boot image from a CD-ROM")
+    (description
+     "@command{geteltorito} can extract the initial/default boot
+image from CDs (and ISOs) that follow the El Torito specification
+for bootable CD-ROMs.
+
+Image data is written to standard output by default and all other
+information is written to standard error.")
+    (license gpl2+)))
-- 
cgit v1.2.3


From 6e1d7aa94e6acb5ede8b69586c4d3fb393096ff2 Mon Sep 17 00:00:00 2001
From: Marius Bakke <mbakke@fastmail.com>
Date: Sun, 9 Oct 2016 22:26:12 +0100
Subject: gnu: Add font-adobe-source-code-pro.

* gnu/packages/fonts.scm (font-adobe-source-code-pro): New variable.
---
 gnu/packages/fonts.scm | 46 ++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 46 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/fonts.scm b/gnu/packages/fonts.scm
index c8642b72ae..3022d9a474 100644
--- a/gnu/packages/fonts.scm
+++ b/gnu/packages/fonts.scm
@@ -11,6 +11,7 @@
 ;;; Copyright © 2016 Jookia <166291@gmail.com>
 ;;; Copyright © 2016 Eric Bavier <bavier@member.fsf.org>
 ;;; Copyright © 2016 Dmitry Nikolaev <cameltheman@gmail.com>
+;;; Copyright © 2016 Marius Bakke <mbakke@fastmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -28,6 +29,7 @@
 ;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
 
 (define-module (gnu packages fonts)
+  #:use-module (ice-9 regex)
   #:use-module (guix utils)
   #:use-module ((guix licenses) #:prefix license:)
   #:use-module (guix packages)
@@ -851,3 +853,47 @@ (define-public font-hack
     (license (license:x11-style
               "https://github.com/chrissimpkins/Hack/blob/master/LICENSE.md"
               "Hack Open Font License v2.0"))))
+
+(define-public font-adobe-source-code-pro
+  (package
+    (name "font-adobe-source-code-pro")
+    (version "2.030R-ro-1.050R-it")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append
+                    "https://github.com/adobe-fonts/source-code-pro/archive/"
+                    (regexp-substitute/global
+                     ;; The upstream tag uses "/" between the roman and italic
+                     ;; versions, so substitute our "-" separator here.
+                     #f "R-ro-" version 'pre "R-ro/" 'post) ".tar.gz"))
+              (file-name (string-append name "-" version ".tar.gz"))
+              (sha256
+               (base32
+                "0arhhsf3i7ss39ykn73d1j8k4n8vx7115xph6jwkd970p1cxvr54"))))
+    (build-system trivial-build-system)
+    (arguments
+     `(#:modules ((guix build utils))
+       #:builder
+       (begin
+         (use-modules (guix build utils))
+         (let ((tar  (string-append (assoc-ref %build-inputs "tar")
+                                    "/bin/tar"))
+               (PATH (string-append (assoc-ref %build-inputs "gzip")
+                                    "/bin"))
+               (font-dir (string-append %output "/share/fonts/opentype")))
+           (setenv "PATH" PATH)
+           (mkdir-p font-dir)
+           (zero? (system* tar "-C" font-dir "--strip-components=2"
+                           "-xvf" (assoc-ref %build-inputs "source")
+                           (string-append "source-code-pro-"
+                                          ,version "/OTF")))))))
+    (native-inputs
+     `(("gzip" ,gzip)
+       ("tar" ,tar)))
+    (home-page "https://github.com/adobe-fonts/source-code-pro")
+    (synopsis
+     "Monospaced font family for user interface and coding environments")
+    (description
+     "Source Code Pro is a set of monospaced OpenType fonts that have been
+designed to work well in user interface environments.")
+    (license license:silofl1.1)))
-- 
cgit v1.2.3


From a5ba14811ab7657ac895235b91b0f64f959ee2d8 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Tue, 1 Nov 2016 13:20:31 +0100
Subject: gnu: python-traitlets: Update to 4.2.0.

* gnu/packages/python.scm (python-traitlets): Update to 4.2.0.
---
 gnu/packages/python.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index b7c9e110c5..c612846349 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -4467,14 +4467,14 @@ (define-public python2-ipython-genutils
 (define-public python-traitlets
   (package
     (name "python-traitlets")
-    (version "4.1.0")
+    (version "4.2.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "traitlets" version))
        (sha256
         (base32
-         "0nxgj8jxlm1kqf8cx2x7vjid05zdgbxpqhjbdl46r8njlpgkh3j4"))))
+         "1afy08sa5n9gnkvh3da49c16zkyv598vchv0p1hp7zzjy8895hz4"))))
     (build-system python-build-system)
     (arguments
      `(#:phases
-- 
cgit v1.2.3


From 4263b06fa2bf3e25ec21fa39822b548fc3a6e8ca Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Tue, 1 Nov 2016 13:20:32 +0100
Subject: gnu: Add python-jupyter-core.

* gnu/packages/python.scm (python-jupyter-core, python2-jupyter-core):
New variables.
---
 gnu/packages/python.scm | 25 +++++++++++++++++++++++++
 1 file changed, 25 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index c612846349..da16647c2d 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -4500,6 +4500,31 @@ (define-public python-traitlets
 (define-public python2-traitlets
   (package-with-python2 python-traitlets))
 
+(define-public python-jupyter-core
+  (package
+    (name "python-jupyter-core")
+    (version "4.2.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append (pypi-uri "jupyter_core" version)))
+       (sha256
+        (base32
+         "177d9csqldzhsh6xs1p4nf6lzvhzyg6gklqjf69lxgxyadx87v24"))))
+    (build-system python-build-system)
+    ;; FIXME: not sure how to run the tests
+    (arguments `(#:tests? #f))
+    (propagated-inputs
+     `(("python-traitlets" ,python-traitlets)))
+    (home-page "http://jupyter.org/")
+    (synopsis "Jupyter base package")
+    (description
+     "Jupyter core is the base package on which Jupyter projects rely.")
+    (license license:bsd-3)))
+
+(define-public python2-jupyter-core
+  (package-with-python2 python-jupyter-core))
+
 (define-public python-ipython
   (package
     (name "python-ipython")
-- 
cgit v1.2.3


From 9ff01f2d018d65f01b1a6a66bd28c26f196719bc Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Tue, 1 Nov 2016 13:20:33 +0100
Subject: gnu: Add python-jupyter-client.

* gnu/packages/python.scm (python-jupyter-client,
python2-jupyter-client): New variables.
---
 gnu/packages/python.scm | 32 ++++++++++++++++++++++++++++++++
 1 file changed, 32 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index da16647c2d..0f1697820d 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -4525,6 +4525,38 @@ (define-public python-jupyter-core
 (define-public python2-jupyter-core
   (package-with-python2 python-jupyter-core))
 
+(define-public python-jupyter-client
+  (package
+    (name "python-jupyter-client")
+    (version "4.4.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "jupyter_client" version))
+       (sha256
+        (base32
+         "1vjjrpjw7k5sh982pbjnslv7byfbfazjw9g92jvs7dz5qbx556n9"))))
+    (build-system python-build-system)
+    ;; Tests fail because of missing native python kernel which I assume is
+    ;; provided by the ipython package, which we cannot use because it would
+    ;; cause a dependency cycle.
+    (arguments `(#:tests? #f))
+    (propagated-inputs
+     `(("python-pyzmq" ,python-pyzmq)
+       ("python-traitlets" ,python-traitlets)
+       ("python-jupyter-core" ,python-jupyter-core)))
+    (home-page "http://jupyter.org/")
+    (synopsis "Jupyter protocol implementation and client libraries")
+    (description
+     "The @code{jupyter_client} package contains the reference implementation
+of the Jupyter protocol.  It also provides client and kernel management APIs
+for working with kernels, and the @code{jupyter kernelspec} entrypoint for
+installing @code{kernelspec}s for use with Jupyter frontends.")
+    (license license:bsd-3)))
+
+(define-public python2-jupyter-client
+  (package-with-python2 python-jupyter-client))
+
 (define-public python-ipython
   (package
     (name "python-ipython")
-- 
cgit v1.2.3


From ab526102ed7f0af0fe607cb2d1ba1fbd7f791582 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Tue, 1 Nov 2016 13:20:34 +0100
Subject: gnu: Add python-ipykernel.

* gnu/packages/python.scm (python-ipykernel, python2-ipykernel): New
variables.
---
 gnu/packages/python.scm | 26 ++++++++++++++++++++++++++
 1 file changed, 26 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 0f1697820d..da2d48417b 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -4557,6 +4557,32 @@ (define-public python-jupyter-client
 (define-public python2-jupyter-client
   (package-with-python2 python-jupyter-client))
 
+(define-public python-ipykernel
+  (package
+    (name "python-ipykernel")
+    (version "4.5.0")
+    (source
+     (origin
+      (method url-fetch)
+      (uri (pypi-uri "ipykernel" version))
+      (sha256
+       (base32 "15c2bp1x3i6s4xb7vz7742h3kmvdfdfn9n2haywm3mwgvf77jni4"))))
+    (build-system python-build-system)
+    ;; The tests load a submodule of IPython.  However, IPython itself depends
+    ;; on ipykernel.
+    (arguments `(#:tests? #f))
+    (propagated-inputs
+     ;; imported at runtime during connect
+     `(("python-jupyter-client" ,python-jupyter-client)))
+    (home-page "http://ipython.org")
+    (synopsis "IPython Kernel for Jupyter")
+    (description
+     "This package provides the IPython kernel for Jupyter.")
+    (license license:bsd-3)))
+
+(define-public python2-ipykernel
+  (package-with-python2 python-ipykernel))
+
 (define-public python-ipython
   (package
     (name "python-ipython")
-- 
cgit v1.2.3


From 5ff6effcc08fdd2cf1d668fd7bd849a05a649eaa Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Tue, 1 Nov 2016 13:20:35 +0100
Subject: gnu: Add python-testpath.

* gnu/packages/python.scm (python-testpath, python2-testpath): New
variables.
---
 gnu/packages/python.scm | 41 +++++++++++++++++++++++++++++++++++++++++
 1 file changed, 41 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index da2d48417b..25c52467fc 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -4583,6 +4583,47 @@ (define-public python-ipykernel
 (define-public python2-ipykernel
   (package-with-python2 python-ipykernel))
 
+(define-public python-testpath
+  (package
+    (name "python-testpath")
+    (version "0.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://github.com/jupyter/testpath/archive/"
+                           version ".tar.gz"))
+       (file-name (string-append name "-" version ".tar.gz"))
+       (sha256
+        (base32
+         "04kh3fgvmqz6cfcw79q70qwjz7ib7lxm27cc548iy2rpr33qqf55"))))
+    (build-system python-build-system)
+    (arguments
+     `(#:tests? #f ; this package does not even have a setup.py
+       #:phases
+       (modify-phases %standard-phases
+         (delete 'install)
+         (replace 'build
+                  (lambda* (#:key inputs outputs #:allow-other-keys)
+                    (let ((dir (string-append
+                                (assoc-ref outputs "out")
+                                "/lib/python"
+                                (string-take (string-take-right
+                                              (assoc-ref inputs "python") 5) 3)
+                                "/site-packages/testpath")))
+                      (mkdir-p dir)
+                      (copy-recursively "testpath" dir))
+                    #t)))))
+    (home-page "https://github.com/takluyver/testpath")
+    (synopsis "Test utilities for code working with files and commands")
+    (description
+     "Testpath is a collection of utilities for Python code working with files
+and commands.  It contains functions to check things on the filesystem, and
+tools for mocking system commands and recording calls to those.")
+    (license license:expat)))
+
+(define-public python2-testpath
+  (package-with-python2 python-testpath))
+
 (define-public python-ipython
   (package
     (name "python-ipython")
-- 
cgit v1.2.3


From 8ee62c97f659c6b288c76efe621969b9535a3542 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Tue, 1 Nov 2016 13:20:36 +0100
Subject: gnu: Add python-html5lib-0.9.

* gnu/packages/python.scm (python-html5lib-0.9, python2-html5lib-0.9):
New variables.
---
 gnu/packages/python.scm | 16 ++++++++++++++++
 1 file changed, 16 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 25c52467fc..5234dba2d2 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -4788,6 +4788,22 @@ (define-public python-html5lib
 (define-public python2-html5lib
   (package-with-python2 python-html5lib))
 
+;; Needed for python-bleach, a dependency of python-notebook
+(define-public python-html5lib-0.9
+  (package
+    (inherit python-html5lib)
+    (version "0.999")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "html5lib" version))
+       (sha256
+        (base32
+         "17n4zfsj6ynmbwdwviywmj8r6nzr3xvfx2zs0xhndmvm51z7z263"))))))
+
+(define-public python2-html5lib-0.9
+  (package-with-python2 python-html5lib-0.9))
+
 (define-public python-urwid
   (package
     (name "python-urwid")
-- 
cgit v1.2.3


From 2d321bb2c572ca91830da2790aa6883e6218b42a Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Tue, 1 Nov 2016 13:20:37 +0100
Subject: gnu: Add python-nbformat.

* gnu/packages/python.scm (python-nbformat, python2-nbformat): New
variables.
---
 gnu/packages/python.scm | 29 +++++++++++++++++++++++++++++
 1 file changed, 29 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 5234dba2d2..28b38cfae6 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -6664,6 +6664,35 @@ (define-public python-debian
 (define-public python2-debian
   (package-with-python2 python-debian))
 
+(define-public python-nbformat
+  (package
+    (name "python-nbformat")
+    (version "4.1.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "nbformat" version))
+       (sha256
+        (base32
+         "0mq8iki3d4mnx7wy05phss7x98mds4fqydin8lcagidp1knw1xnv"))))
+    (build-system python-build-system)
+    (arguments `(#:tests? #f)) ; no test target
+    (propagated-inputs
+     `(("python-ipython-genutils" ,python-ipython-genutils)
+       ("python-jsonschema" ,python-jsonschema)
+       ("python-jupyter-core" ,python-jupyter-core)
+       ("python-traitlets" ,python-traitlets)))
+    (native-inputs
+     `(("python-setuptools" ,python-setuptools)))
+    (home-page "http://jupyter.org")
+    (synopsis "Jupyter Notebook format")
+    (description "This package provides the reference implementation of the
+Jupyter Notebook format and Python APIs for working with notebooks.")
+    (license license:bsd-3)))
+
+(define-public python2-nbformat
+  (package-with-python2 python-nbformat))
+
 (define-public python-chardet
   (package
     (name "python-chardet")
-- 
cgit v1.2.3


From 55436048d8aea6eb287c90ca4879304b5998724f Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Tue, 1 Nov 2016 13:20:38 +0100
Subject: gnu: Add python-bleach.

* gnu/packages/python.scm (python-bleach, python2-bleach): New
variables.
---
 gnu/packages/python.scm | 26 ++++++++++++++++++++++++++
 1 file changed, 26 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 28b38cfae6..8987450d5b 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -6693,6 +6693,32 @@ (define-public python-nbformat
 (define-public python2-nbformat
   (package-with-python2 python-nbformat))
 
+(define-public python-bleach
+  (package
+    (name "python-bleach")
+    (version "1.4.3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "bleach" version))
+       (sha256
+        (base32
+         "0jvg3jxrvnx7xmm9gj262v60ib452xlnwlb0navyp7jsvcd0d4qj"))))
+    (build-system python-build-system)
+    (propagated-inputs
+     `(("python-html5lib" ,python-html5lib-0.9)
+       ("python-setuptools" ,python-setuptools)
+       ("python-six" ,python-six)))
+    (native-inputs
+     `(("python-nose" ,python-nose)))
+    (home-page "http://github.com/jsocol/bleach")
+    (synopsis "Whitelist-based HTML-sanitizing tool")
+    (description "Bleach is an easy whitelist-based HTML-sanitizing tool.")
+    (license license:asl2.0)))
+
+(define-public python2-bleach
+  (package-with-python2 python-bleach))
+
 (define-public python-chardet
   (package
     (name "python-chardet")
-- 
cgit v1.2.3


From 18f3d92b39faaa881c65e5838434059f2f8ced75 Mon Sep 17 00:00:00 2001
From: Florian Paul Schmidt <mista.tapas@gmx.net>
Date: Thu, 10 Dec 2015 15:13:36 +0100
Subject: gnu: Add swh-plugins-lv2.

* gnu/packages/audio.scm (swh-plugins-lv2): New variable.

Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
---
 gnu/packages/audio.scm | 44 ++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 44 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm
index e6670fa8b5..e81e1bf34f 100644
--- a/gnu/packages/audio.scm
+++ b/gnu/packages/audio.scm
@@ -385,6 +385,50 @@ (define-public infamous-plugins
 envelope follower, distortion effects, tape effects and more.")
     (license license:gpl2+)))
 
+(define-public swh-plugins-lv2
+  (package
+    (name "swh-plugins-lv2")
+    (version "1.0.16")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "https://github.com/swh/"
+                                  "lv2/archive/v" version ".tar.gz"))
+              (file-name (string-append name "-" version ".tar.gz"))
+              (sha256
+               (base32
+                "0j1mih0lp4fds07knp5i32in515sh0df1qi6694pmyz2wqnm295w"))))
+    (build-system gnu-build-system)
+    (arguments
+     `(#:tests? #f ; no check target
+       #:make-flags (list "CC=gcc"
+                          (string-append "PREFIX="
+                                         (assoc-ref %outputs "out")))
+       #:phases
+       (modify-phases %standard-phases
+         ;; no configure script
+         (delete 'configure)
+         (add-after 'unpack 'patch-makefile-and-enter-directory
+           ;; The default install target doesn't install, but the
+           ;; "install-system" target does.
+           (lambda _
+             (substitute* "Makefile"
+               (("install:") "install: install-system"))
+             #t)))))
+    (inputs
+     `(("lv2" ,lv2)
+       ("fftwf" ,fftwf)))
+    (native-inputs
+     `(("libxslt" ,libxslt)
+       ("pkg-config" ,pkg-config)))
+    (home-page "http://plugin.org.uk")
+    (synopsis "SWH plugins in LV2 format")
+    (description
+     "Swh-plugins-lv2 is a collection of audio plugins in LV2 format.  Plugin
+classes include: dynamics (compressor, limiter), time (delay, chorus,
+flanger), ringmodulator, distortion, filters, pitchshift, oscillators,
+emulation (valve, tape), bit fiddling (decimator, pointer-cast), etc.")
+    (license license:gpl3+)))
+
 (define-public csound
   (package
     (name "csound")
-- 
cgit v1.2.3


From 2784fca032e59a87ce92225c1ae039703832b411 Mon Sep 17 00:00:00 2001
From: 宋文武 <iyzsong@gmail.com>
Date: Fri, 4 Nov 2016 20:20:54 +0800
Subject: gnu: libxmp: Update to 4.4.1.

* gnu/packages/audio.scm (libxmp): Update to 4.4.1.
---
 gnu/packages/audio.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm
index e81e1bf34f..e9360bb87f 100644
--- a/gnu/packages/audio.scm
+++ b/gnu/packages/audio.scm
@@ -2029,14 +2029,14 @@ (define-public libmodplug
 (define-public libxmp
   (package
     (name "libxmp")
-    (version "4.3.10")
+    (version "4.4.1")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://sourceforge/xmp/libxmp/" version "/"
                                   name "-" version ".tar.gz"))
               (sha256
                (base32
-                "1gm5xa0ca7ypcbj3bkmj3k1vvzl7nkch8gjyrm8p1a9vgzr0n761"))))
+                "1kycz4jsyvmf7ny9227b497wc7y5ligydi6fvvldmkf8hk63ad9m"))))
     (build-system gnu-build-system)
     (home-page "http://xmp.sourceforge.net/")
     (synopsis "Module player library")
-- 
cgit v1.2.3


From 1a79d4767a36ae3427b4d1d1519101ffddc57cf6 Mon Sep 17 00:00:00 2001
From: 宋文武 <iyzsong@gmail.com>
Date: Fri, 4 Nov 2016 20:21:21 +0800
Subject: gnu: xmp: Update to 4.1.0.

* gnu/packages/audio.scm (xmp): Update to 4.1.0.
---
 gnu/packages/audio.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm
index e9360bb87f..b9034c9225 100644
--- a/gnu/packages/audio.scm
+++ b/gnu/packages/audio.scm
@@ -2049,14 +2049,14 @@ (define-public libxmp
 (define-public xmp
   (package
     (name "xmp")
-    (version "4.0.10")
+    (version "4.1.0")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://sourceforge/xmp/xmp/" version "/"
                                   name "-" version ".tar.gz"))
               (sha256
                (base32
-                "0gjylvvmq7ha0nhcjg56qfp0xxpsrcsj7y5r914svd5x1ppmzm5n"))))
+                "17i8fc7x7yn3z1x963xp9iv108gxfakxmdgmpv3mlm438w3n3g8x"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("pkg-config" ,pkg-config)))
-- 
cgit v1.2.3


From c6105d69c0a78c3b0880679370e70f17427a43e0 Mon Sep 17 00:00:00 2001
From: Roel Janssen <roel@gnu.org>
Date: Fri, 4 Nov 2016 14:35:04 +0100
Subject: gnu: Add r-bigmemory-sri.

gnu/packages/statistics.scm (r-bigmemory-sri): New variable.
---
 gnu/packages/statistics.scm | 20 ++++++++++++++++++++
 1 file changed, 20 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 5566ce7359..b7f9b9a9c1 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -2789,6 +2789,26 @@ (define-public r-e1071
 computation, bagged clustering, naive Bayes classifier, and more.")
     (license license:gpl2+)))
 
+(define-public r-bigmemory-sri
+  (package
+    (name "r-bigmemory-sri")
+    (version "0.1.3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "bigmemory.sri" version))
+       (sha256
+        (base32 "0mg14ilwdkd64q2ri9jdwnk7mp55dqim7xfifrs65sdsv1934h2m"))))
+    (properties
+     `((upstream-name . "bigmemory.sri")))
+    (build-system r-build-system)
+    (home-page "http://cran.r-project.org/web/packages/bigmemory.sri")
+    (synopsis "Shared resource interface for the bigmemory package")
+    (description "This package provides a shared resource interface for the
+bigmemory and synchronicity packages.")
+    ;; Users can choose either LGPLv3 or ASL2.0.
+    (license (list license:lgpl3 license:asl2.0))))
+
 (define-public r-nmf
   (package
     (name "r-nmf")
-- 
cgit v1.2.3


From 4a838652862cc849b799cb7f7c3d302d5337483f Mon Sep 17 00:00:00 2001
From: Roel Janssen <roel@gnu.org>
Date: Fri, 4 Nov 2016 14:40:13 +0100
Subject: gnu: Add r-synchronicity.

* gnu/packages/statistics.scm (r-synchronicity): New variable.
---
 gnu/packages/statistics.scm | 24 ++++++++++++++++++++++++
 1 file changed, 24 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index b7f9b9a9c1..29809ea219 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -2809,6 +2809,30 @@ (define-public r-bigmemory-sri
     ;; Users can choose either LGPLv3 or ASL2.0.
     (license (list license:lgpl3 license:asl2.0))))
 
+(define-public r-synchronicity
+  (package
+    (name "r-synchronicity")
+    (version "1.1.9.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "synchronicity" version))
+       (sha256
+        (base32
+         "0d9skpwmsnkn4xb3f2kgyyv8bhdi0r9p1kj3cvi0s92fjjnpi00c"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-bh" ,r-bh)
+       ("r-bigmemory-sri" ,r-bigmemory-sri)
+       ("r-rcpp" ,r-rcpp)))
+    (home-page "http://www.bigmemory.org")
+    (synopsis "Boost mutex functionality in R")
+    (description "This package provides support for synchronization
+via mutexes and may eventually support interprocess communication and
+message passing.")
+    ;; Users can choose either LGPLv3 or ASL2.0.
+    (license (list license:lgpl3 license:asl2.0))))
+
 (define-public r-nmf
   (package
     (name "r-nmf")
-- 
cgit v1.2.3


From 59523c4cf53d6c650da71c1e71bb6c6cccadd2e6 Mon Sep 17 00:00:00 2001
From: Roel Janssen <roel@gnu.org>
Date: Fri, 4 Nov 2016 14:46:47 +0100
Subject: gnu: Add r-bigmemory.

* gnu/packages/statistics.scm (r-bigmemory): New variable.
---
 gnu/packages/statistics.scm | 25 +++++++++++++++++++++++++
 1 file changed, 25 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 29809ea219..5b478c2ed7 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -2833,6 +2833,31 @@ (define-public r-synchronicity
     ;; Users can choose either LGPLv3 or ASL2.0.
     (license (list license:lgpl3 license:asl2.0))))
 
+(define-public r-bigmemory
+  (package
+    (name "r-bigmemory")
+    (version "4.5.19")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "bigmemory" version))
+       (sha256
+        (base32
+         "191gbzca557kpk7mdsg716vfyqpr7j5din6qb8hin4g1nkzzwmg6"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-bh" ,r-bh)
+       ("r-rcpp" ,r-rcpp)
+       ("r-bigmemory-sri" ,r-bigmemory-sri)
+       ("r-r-utils" ,r-r-utils)))
+    (home-page "http://www.bigmemory.org")
+    (synopsis "Manage large matrices with shared memory or memory-mapped files")
+    (description "This package provides methods to create, store, access, and
+manipulate large matrices.  Matrices are allocated to shared memory and may use
+memory-mapped files.")
+    ;; Users can choose either LGPLv3 or ASL2.0.
+    (license (list license:lgpl3 license:asl2.0))))
+
 (define-public r-nmf
   (package
     (name "r-nmf")
-- 
cgit v1.2.3


From 8af47ef603aeea6efbcfe9ab2c4adefefad2f6fb Mon Sep 17 00:00:00 2001
From: Roel Janssen <roel@gnu.org>
Date: Fri, 4 Nov 2016 14:53:24 +0100
Subject: gnu: r-nmf: Use bigmemory.

* gnu/packages/statistics.scm (r-nmf)[propagated-inputs]: Add
r-bigmemory and r-synchronicity.
---
 gnu/packages/statistics.scm | 2 ++
 1 file changed, 2 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 5b478c2ed7..c2761207e3 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -2873,6 +2873,8 @@ (define-public r-nmf
     (build-system r-build-system)
     (propagated-inputs
      `(("r-cluster" ,r-cluster)
+       ("r-bigmemory" ,r-bigmemory)
+       ("r-synchronicity" ,r-synchronicity)
        ("r-colorspace" ,r-colorspace)
        ("r-digest" ,r-digest)
        ("r-doparallel" ,r-doparallel)
-- 
cgit v1.2.3


From fb77c61422ae2d03c0bf655d96b0e88f5f8001da Mon Sep 17 00:00:00 2001
From: Ludovic Courtès <ludo@gnu.org>
Date: Fri, 4 Nov 2016 15:16:11 +0100
Subject: gnu: Remove '%final-inputs' references at the top level.

Due to circular dependencies, referring to bindings exported by other
modules from the top level is frowned upon.  This patch addresses one of
the remaining cases.

* gnu/packages/base.scm (%final-inputs): New procedure.
* gnu/packages/cross-base.scm: Remove (gnu packages commencement) import.
(cross-gcc): Use the new '%final-inputs'.
* gnu/packages/make-bootstrap.scm: Remove (gnu packages commencement) import.
(package-with-relocatable-glibc): Use the new '%final-inputs'.
---
 gnu/packages/base.scm           | 6 ++++++
 gnu/packages/cross-base.scm     | 5 ++---
 gnu/packages/make-bootstrap.scm | 5 ++---
 3 files changed, 10 insertions(+), 6 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/base.scm b/gnu/packages/base.scm
index a476837102..012a807bab 100644
--- a/gnu/packages/base.scm
+++ b/gnu/packages/base.scm
@@ -1003,4 +1003,10 @@ (define-public (canonical-package package)
          (proc  (module-ref iface 'canonical-package)))
     (proc package)))
 
+(define-public (%final-inputs)
+  "Return the list of \"final inputs\"."
+  ;; Avoid circular dependency by lazily resolving 'commencement'.
+  (let ((iface (resolve-interface '(gnu packages commencement))))
+    (module-ref iface '%final-inputs)))
+
 ;;; base.scm ends here
diff --git a/gnu/packages/cross-base.scm b/gnu/packages/cross-base.scm
index 3bd30fd78c..0000a3adcb 100644
--- a/gnu/packages/cross-base.scm
+++ b/gnu/packages/cross-base.scm
@@ -23,7 +23,6 @@ (define-module (gnu packages cross-base)
   #:use-module (gnu packages)
   #:use-module (gnu packages gcc)
   #:use-module (gnu packages base)
-  #:use-module (gnu packages commencement)
   #:use-module (gnu packages linux)
   #:use-module (guix packages)
   #:use-module (guix download)
@@ -257,11 +256,11 @@ (define* (cross-gcc target
 
        ;; Call it differently so that the builder can check whether the "libc"
        ;; input is #f.
-       ("libc-native" ,@(assoc-ref %final-inputs "libc"))
+       ("libc-native" ,@(assoc-ref (%final-inputs) "libc"))
 
        ;; Remaining inputs.
        ,@(let ((inputs (append (package-inputs %xgcc)
-                               (alist-delete "libc" %final-inputs))))
+                               (alist-delete "libc" (%final-inputs)))))
            (if libc
                `(("libc" ,libc)
                  ("xkernel-headers"                ;the target headers
diff --git a/gnu/packages/make-bootstrap.scm b/gnu/packages/make-bootstrap.scm
index 336ad2ee13..f2bae7753f 100644
--- a/gnu/packages/make-bootstrap.scm
+++ b/gnu/packages/make-bootstrap.scm
@@ -23,7 +23,6 @@ (define-module (gnu packages make-bootstrap)
   #:use-module (guix build-system trivial)
   #:use-module (guix build-system gnu)
   #:use-module ((gnu packages) #:select (search-patch))
-  #:use-module ((gnu packages commencement) #:select (%final-inputs))
   #:use-module (gnu packages base)
   #:use-module (gnu packages cross-base)
   #:use-module (gnu packages bash)
@@ -101,14 +100,14 @@ (define (native-inputs)
                                           (cross-binutils target)
                                           (cross-bootstrap-libc)))
             ("cross-binutils" ,(cross-binutils target))
-            ,@%final-inputs))
+            ,@(%final-inputs)))
         `(("libc" ,(glibc-for-bootstrap))
           ("gcc" ,(package (inherit gcc)
                     (outputs '("out")) ; all in one so libgcc_s is easily found
                     (inputs
                      `(("libc",(glibc-for-bootstrap))
                        ,@(package-inputs gcc)))))
-          ,@(fold alist-delete %final-inputs '("libc" "gcc")))))
+          ,@(fold alist-delete (%final-inputs) '("libc" "gcc")))))
 
   (package-with-explicit-inputs p inputs
                                 (current-source-location)
-- 
cgit v1.2.3


From bd2e1a8cb07088bdc54b9bb05d9b2e99f78e5b28 Mon Sep 17 00:00:00 2001
From: Ludovic Courtès <ludo@gnu.org>
Date: Fri, 4 Nov 2016 15:29:01 +0100
Subject: gnu: cross-base: Remove exports of cross compilers.

They were never really needed and caused troubles in the presence of
circular module dependencies as reported by
Danny Milosavljevic <dannym@scratchpost.org> at
<https://lists.gnu.org/archive/html/guix-devel/2016-11/msg00144.html>.

* gnu/packages/cross-base.scm (xgcc-mips64el, xgcc-xtensa, xgcc-armhf):
Remove.
* gnu/packages/firmware.scm (ath9k-htc-firmware)[native-inputs]: Use
'cross-gcc' instead of XGCC-XTENSA.
---
 gnu/packages/cross-base.scm | 38 ++++++++------------------------------
 gnu/packages/firmware.scm   |  4 ++--
 2 files changed, 10 insertions(+), 32 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/cross-base.scm b/gnu/packages/cross-base.scm
index 0000a3adcb..4b720ba4e9 100644
--- a/gnu/packages/cross-base.scm
+++ b/gnu/packages/cross-base.scm
@@ -368,36 +368,14 @@ (define xlinux-headers
                      ,@(package-native-inputs glibc)))))
 
 
-;;;
-;;; Concrete cross toolchains.
-;;;
-
-(define-public xgcc-mips64el
-  (let* ((triplet "mips64el-linux-gnuabi64")      ;N64 ABI
-         (xgcc    (cross-gcc triplet
-                             (cross-binutils triplet)
-                             (cross-libc triplet))))
-    ;; Don't attempt to build this cross-compiler on i686;
-    ;; see <http://bugs.gnu.org/19598>.
-    (package (inherit xgcc)
-      (supported-systems (fold delete
-                               (package-supported-systems xgcc)
-                               '("mips64el-linux" "i686-linux"))))))
-
-(define-public xgcc-xtensa
-  ;; Bare-bones Xtensa cross-compiler, used to build the Atheros firmware.
-  (cross-gcc "xtensa-elf"))
-
-(define-public xgcc-armhf
-  (let* ((triplet "arm-linux-gnueabihf")
-         (xgcc    (cross-gcc triplet
-                             (cross-binutils triplet)
-                             (cross-libc triplet))))
-    (package (inherit xgcc)
-      (supported-systems (delete "armhf-linux" %supported-systems)))))
-
-;; (define-public xgcc-armel
-;;   (let ((triplet "armel-linux-gnueabi"))
+;;; Concrete cross tool chains are instantiated like this:
+;;
+;; (define-public xgcc-armhf
+;;   (let ((triplet "arm-linux-gnueabihf"))
 ;;     (cross-gcc triplet
 ;;                (cross-binutils triplet)
 ;;                (cross-libc triplet))))
+;;
+;;; We don't do that here because we'd be referring to bindings from (gnu
+;;; packages gcc) from the top level, which doesn't play well with circular
+;;; dependencies among modules.
diff --git a/gnu/packages/firmware.scm b/gnu/packages/firmware.scm
index 45b7bf7ab1..484896f592 100644
--- a/gnu/packages/firmware.scm
+++ b/gnu/packages/firmware.scm
@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2014, 2015 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2014, 2015, 2016 Ludovic Courtès <ludo@gnu.org>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -71,7 +71,7 @@ (define-public ath9k-htc-firmware
 
     ;; The firmware is cross-compiled using a "bare bones" compiler (no libc.)
     ;; Use our own tool chain for that.
-    (native-inputs `(("cross-gcc" ,xgcc-xtensa)
+    (native-inputs `(("cross-gcc" ,(cross-gcc "xtensa-elf"))
                      ("cross-binutils" ,(cross-binutils "xtensa-elf"))
                      ("cmake" ,cmake)
                      ("perl" ,perl)))
-- 
cgit v1.2.3


From 08722837b048e7d0b416e414f7e695a380e7784b Mon Sep 17 00:00:00 2001
From: Kei Kebreau <kei@openmailbox.org>
Date: Fri, 4 Nov 2016 11:17:09 -0400
Subject: gnu: chromium-bsu: Update to 0.9.16.1.

* gnu/packages/games.scm (chromium-bsu): Update to 0.9.16.1.
[arguments]: Remove 'set-sdl-paths phase.
[inputs]: Add gnu-gettext.
---
 gnu/packages/games.scm | 15 ++++-----------
 1 file changed, 4 insertions(+), 11 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/games.scm b/gnu/packages/games.scm
index 941e3a0852..a6633961b3 100644
--- a/gnu/packages/games.scm
+++ b/gnu/packages/games.scm
@@ -2563,7 +2563,7 @@ (define-public starfighter
 (define-public chromium-bsu
   (package
     (name "chromium-bsu")
-    (version "0.9.15.1")
+    (version "0.9.16.1")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://sourceforge/" name
@@ -2571,18 +2571,11 @@ (define-public chromium-bsu
                                   name "-" version ".tar.gz"))
               (sha256
                (base32
-                "01c4mki0rpz6wrqbf18fj4vd7axln5v0xqm80cyksbv63g04s6w6"))))
+                "0jk2w5b6s6nkzri585bbz16cif2fhqcnl5l1mq3rd98r9nil3hd1"))))
     (build-system gnu-build-system)
-    (arguments
-     `(#:phases (modify-phases %standard-phases
-                  (add-after 'set-paths 'set-sdl-paths
-                             (lambda* (#:key inputs #:allow-other-keys)
-                               (setenv "CPATH"
-                                       (string-append (assoc-ref inputs "sdl-union")
-                                                      "/include/SDL"))
-                               #t)))))
     (native-inputs `(("pkg-config" ,pkg-config)))
-    (inputs `(("glu" ,glu)
+    (inputs `(("gettext" ,gnu-gettext)
+              ("glu" ,glu)
               ("quesoglc" ,quesoglc)
               ("sdl-union" ,(sdl-union (list sdl sdl-image sdl-mixer)))))
     (home-page "http://chromium-bsu.sourceforge.net/")
-- 
cgit v1.2.3


From 60590a3ae8952ff0b5c77a722981aef514e3de66 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Tue, 1 Nov 2016 13:20:39 +0100
Subject: gnu: Add python-entrypoints.

* gnu/packages/python.scm (python-entrypoints, python2-entrypoints): New
variables.
---
 gnu/packages/python.scm | 40 ++++++++++++++++++++++++++++++++++++++++
 1 file changed, 40 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 8987450d5b..9aa3e49f58 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -6719,6 +6719,46 @@ (define-public python-bleach
 (define-public python2-bleach
   (package-with-python2 python-bleach))
 
+(define-public python-entrypoints
+  (package
+    (name "python-entrypoints")
+    (version "0.2.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://github.com/takluyver/entrypoints/archive/"
+                           version ".tar.gz"))
+       (file-name (string-append name "-" version ".tar.gz"))
+       (sha256
+        (base32
+         "0azqlkh3j0za080lsf5crnhaxx3c93k9dpv5ihkhf5cppgw5sjz5"))))
+    (build-system python-build-system)
+    ;; The package does not come with a setup.py file, so we have to generate
+    ;; one ourselves.
+    (arguments
+     `(#:tests? #f
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'create-setup.py
+           (lambda _
+             (call-with-output-file "setup.py"
+               (lambda (port)
+                 (format port "\
+from setuptools import setup
+setup(name='entrypoints', version='~a', py_modules=['entrypoints'])
+" ,version))))))))
+    (home-page "https://github.com/takluyver/entrypoints")
+    (synopsis "Discover and load entry points from installed Python packages")
+    (description "Entry points are a way for Python packages to advertise
+objects with some common interface.  The most common examples are
+@code{console_scripts} entry points, which define shell commands by
+identifying a Python function to run.  The @code{entrypoints} module contains
+functions to find and load entry points.")
+    (license license:expat)))
+
+(define-public python2-entrypoints
+  (package-with-python2 python-entrypoints))
+
 (define-public python-chardet
   (package
     (name "python-chardet")
-- 
cgit v1.2.3


From c60898a845301f2ac1c8845c843907cb6e98224e Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Tue, 1 Nov 2016 13:20:40 +0100
Subject: gnu: Add python-nbconvert.

* gnu/packages/python.scm (python-nbconvert, python2-nbconvert): New
variables.
---
 gnu/packages/python.scm | 45 +++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 45 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 9aa3e49f58..7a5f3a3aba 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -6759,6 +6759,51 @@ (define-public python-entrypoints
 (define-public python2-entrypoints
   (package-with-python2 python-entrypoints))
 
+(define-public python-nbconvert
+  (package
+    (name "python-nbconvert")
+    (version "5.0.0b1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "nbconvert" version))
+       (sha256
+        (base32
+         "0brclbb18l4nmd5qy3dl9wn05rjdh1fz4rmzdlfqacj12rcdvdgp"))))
+    (build-system python-build-system)
+    ;; The "bdist_egg" target is disabled by default, causing the installation
+    ;; to fail.
+    (arguments `(#:configure-flags (list "bdist_egg")))
+    (propagated-inputs
+     `(("python-bleach" ,python-bleach)
+       ("python-entrypoints" ,python-entrypoints)
+       ("python-jinja2" ,python-jinja2)
+       ("python-jupyter-core" ,python-jupyter-core)
+       ("python-mistune" ,python-mistune)
+       ("python-nbformat" ,python-nbformat)
+       ("python-pygments" ,python-pygments)
+       ("python-setuptools" ,python-setuptools)
+       ("python-traitlets" ,python-traitlets)))
+    (home-page "http://jupyter.org")
+    (synopsis "Converting Jupyter Notebooks")
+    (description "The @code{nbconvert} tool, @{jupyter nbconvert}, converts
+notebooks to various other formats via Jinja templates.  It allows you to
+convert an @code{.ipynb} notebook file into various static formats including:
+
+@enumerate
+@item HTML
+@item LaTeX
+@item PDF
+@item Reveal JS
+@item Markdown (md)
+@item ReStructured Text (rst)
+@item executable script
+@end enumerate\n")
+    (license license:bsd-3)))
+
+(define-public python2-nbconvert
+  (package-with-python2 python-nbconvert))
+
 (define-public python-chardet
   (package
     (name "python-chardet")
-- 
cgit v1.2.3


From a0d62280f56050848b8f021db28c857a56d6f7dc Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Tue, 1 Nov 2016 13:20:41 +0100
Subject: gnu: Add python-notebook.

* gnu/packages/python.scm (python-notebook, python2-notebook): New
variables.
---
 gnu/packages/python.scm | 38 ++++++++++++++++++++++++++++++++++++++
 1 file changed, 38 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 7a5f3a3aba..453e7e689a 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -6804,6 +6804,44 @@ (define-public python-nbconvert
 (define-public python2-nbconvert
   (package-with-python2 python-nbconvert))
 
+(define-public python-notebook
+  (package
+    (name "python-notebook")
+    (version "4.2.3")
+    (source (origin
+              (method url-fetch)
+              (uri (pypi-uri "notebook" version))
+              (sha256
+               (base32
+                "0laq5c2f21frq6xcdckgq7raqhznbjb0qs0357g612z87wyn1a9r"))))
+    (build-system python-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (replace 'check
+           (lambda _
+             ;; HOME must be set for tests
+             (setenv "HOME" "/tmp")
+             (zero? (system* "nosetests")))))))
+    (propagated-inputs
+     `(("python-jupyter-core" ,python-jupyter-core)
+       ("python-nbformat" ,python-nbformat)
+       ("python-nbconvert" ,python-nbconvert)
+       ("python-ipython" ,python-ipython)))
+    (native-inputs
+     `(("python-nose" ,python-nose)
+       ("python-sphinx" ,python-sphinx)
+       ("python-requests" ,python-requests)))
+    (home-page "http://jupyter.org/")
+    (synopsis "Web-based notebook environment for interactive computing")
+    (description
+     "The Jupyter HTML notebook is a web-based notebook environment for
+interactive computing.")
+    (license license:bsd-3)))
+
+(define-public python2-notebook
+  (package-with-python2 python-notebook))
+
 (define-public python-chardet
   (package
     (name "python-chardet")
-- 
cgit v1.2.3


From d55724ed5b07b218131dcffcdf694ce98a87da5e Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Tue, 1 Nov 2016 13:20:42 +0100
Subject: gnu: Add python-widgetsnbextension.

* gnu/packages/python.scm (python-widgetsnbextension,
python2-widgetsnbextension): New variables.
---
 gnu/packages/python.scm | 26 ++++++++++++++++++++++++++
 1 file changed, 26 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 453e7e689a..8145938d05 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -6842,6 +6842,32 @@ (define-public python-notebook
 (define-public python2-notebook
   (package-with-python2 python-notebook))
 
+(define-public python-widgetsnbextension
+  (package
+    (name "python-widgetsnbextension")
+    (version "1.2.6")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "widgetsnbextension" version))
+       (sha256
+        (base32
+         "0lff2mrwrgsa1mxmwx3phl9xvy0jqfpg6khbmxy53jbq56rwy666"))))
+    (build-system python-build-system)
+    (propagated-inputs
+     `(("python-notebook" ,python-notebook)))
+    (native-inputs
+     `(("python-nose" ,python-nose)
+       ("python-setuptools" ,python-setuptools)))
+    (home-page "http://ipython.org")
+    (synopsis "IPython HTML widgets for Jupyter")
+    (description "This package provides interactive HTML widgets for Jupyter
+notebooks.")
+    (license license:bsd-3)))
+
+(define-public python2-widgetsnbextension
+  (package-with-python2 python-widgetsnbextension))
+
 (define-public python-chardet
   (package
     (name "python-chardet")
-- 
cgit v1.2.3


From 4fe2e34409cb1aad6a19e2cf93ebeb7f555a703f Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Tue, 1 Nov 2016 13:20:43 +0100
Subject: gnu: Add python-ipywidgets.

* gnu/packages/python.scm (python-ipywidgets, python2-ipywidgets): New
variables.
---
 gnu/packages/python.scm | 31 +++++++++++++++++++++++++++++++
 1 file changed, 31 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 8145938d05..3f0b2b3dd5 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -6868,6 +6868,37 @@ (define-public python-widgetsnbextension
 (define-public python2-widgetsnbextension
   (package-with-python2 python-widgetsnbextension))
 
+(define-public python-ipywidgets
+  (package
+    (name "python-ipywidgets")
+    (version "5.2.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "ipywidgets" version))
+       (sha256
+        (base32
+         "1lk0qrr5l9a0z7qkkn30hv5832whxwxymf1l576fmmad0n7hkxms"))))
+    (build-system python-build-system)
+    ;; FIXME: it's not clear how to run the tests.
+    (arguments `(#:tests? #f))
+    (propagated-inputs
+     `(("python-ipykernel" ,python-ipykernel)
+       ("python-ipython" ,python-ipython)
+       ("python-setuptools" ,python-setuptools)
+       ("python-traitlets" ,python-traitlets)
+       ("python-widgetsnbextension" ,python-widgetsnbextension)))
+    (home-page "http://ipython.org")
+    (synopsis "IPython HTML widgets for Jupyter")
+    (description "Ipywidgets are interactive HTML widgets for Jupyter
+notebooks and the IPython kernel.  Notebooks come alive when interactive
+widgets are used.  Users gain control of their data and can visualize changes
+in the data.")
+    (license license:bsd-3)))
+
+(define-public python2-ipywidgets
+  (package-with-python2 python-ipywidgets))
+
 (define-public python-chardet
   (package
     (name "python-chardet")
-- 
cgit v1.2.3


From 8ceebf8fa6d513e86e3292727678b0d21b885d08 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Tue, 1 Nov 2016 13:20:44 +0100
Subject: gnu: Add python-jupyter-console.

* gnu/packages/python.scm (python-jupyter-console,
python2-jupyter-console): New variable.
---
 gnu/packages/python.scm | 31 +++++++++++++++++++++++++++++++
 1 file changed, 31 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 3f0b2b3dd5..09fab7b17c 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -6899,6 +6899,37 @@ (define-public python-ipywidgets
 (define-public python2-ipywidgets
   (package-with-python2 python-ipywidgets))
 
+(define-public python-jupyter-console
+  (package
+    (name "python-jupyter-console")
+    (version "5.0.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "jupyter_console" version))
+       (sha256
+        (base32
+         "04acmkwsi99rcg3vb54c6n492zv35s92h2ahabc0w6wj976cipvx"))))
+    (build-system python-build-system)
+    ;; FIXME: it's not clear how to run the tests.
+    (arguments `(#:tests? #f))
+    (propagated-inputs
+     `(("python-ipykernel" ,python-ipykernel)
+       ("python-ipython" ,python-ipython)
+       ("python-jupyter-client" ,python-jupyter-client)
+       ("python-prompt-toolkit" ,python-prompt-toolkit)
+       ("python-pygments" ,python-pygments)
+       ("python-setuptools" ,python-setuptools)))
+    (home-page "https://jupyter.org")
+    (synopsis "Jupyter terminal console")
+    (description "This package provides a terminal-based console frontend for
+Jupyter kernels.  It also allows for console-based interaction with non-Python
+Jupyter kernels such as IJulia and IRKernel.")
+    (license license:bsd-3)))
+
+(define-public python2-jupyter-console
+  (package-with-python2 python-jupyter-console))
+
 (define-public python-chardet
   (package
     (name "python-chardet")
-- 
cgit v1.2.3


From accd5f996e2cfda656dee3cba97de5fd3cec3ad9 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Tue, 1 Nov 2016 13:20:45 +0100
Subject: gnu: python-ipython: Update to 4.0.0.

* gnu/packages/python.scm (python-ipython): Update to 4.0.0.
[inputs]: Keep only "readline" and "which"; move the remaining inputs
to propagated-inputs, except for "python-requests" and "python-nose"
which are moved to native-inputs.
[propagated-inputs]: Add "python-pexpect", "python-pickleshare",
"python-simplegeneric", "python-traitlets", "python-ipykernel".
[native-inputs]: Add "python-testpath".
[arguments]: Enable building of HTML documentation.
[source]: Remove patch.
* gnu/packages/patches/python-ipython-inputhook-ctype.patch: Remove
patch.
* gnu/local.mk (dist_patch_DATA): Remove it.
---
 gnu/local.mk                                       |  2 +-
 .../patches/python-ipython-inputhook-ctype.patch   | 41 ----------------------
 gnu/packages/python.scm                            | 36 ++++++++++---------
 3 files changed, 21 insertions(+), 58 deletions(-)
 delete mode 100644 gnu/packages/patches/python-ipython-inputhook-ctype.patch

(limited to 'gnu/packages')

diff --git a/gnu/local.mk b/gnu/local.mk
index a23d536394..27848ac805 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -6,6 +6,7 @@
 # Copyright © 2016 Chris Marusich <cmmarusich@gmail.com>
 # Copyright © 2016 Kei Kebreau <kei@openmailbox.org>
 # Copyright © 2016 Adonay "adfeno" Felipe Nogueira <https://libreplanet.org/wiki/User:Adfeno> <adfeno@openmailbox.org>
+# Copyright © 2016 Ricardo Wurmus <rekado@elephly.net>
 #
 # This file is part of GNU Guix.
 #
@@ -807,7 +808,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/python-dendropy-exclude-failing-tests.patch \
   %D%/packages/patches/python-disable-ssl-test.patch		\
   %D%/packages/patches/python-fix-tests.patch			\
-  %D%/packages/patches/python-ipython-inputhook-ctype.patch	\
   %D%/packages/patches/python-rarfile-fix-tests.patch		\
   %D%/packages/patches/python2-rdflib-drop-sparqlwrapper.patch	\
   %D%/packages/patches/python-statsmodels-fix-tests.patch	\
diff --git a/gnu/packages/patches/python-ipython-inputhook-ctype.patch b/gnu/packages/patches/python-ipython-inputhook-ctype.patch
deleted file mode 100644
index c77e310542..0000000000
--- a/gnu/packages/patches/python-ipython-inputhook-ctype.patch
+++ /dev/null
@@ -1,41 +0,0 @@
-From 04c5d358c7ab74d3ddab4f7662e539393d8604c6 Mon Sep 17 00:00:00 2001
-From: Lucretiel <Lucretiel@users.noreply.github.com>
-Date: Wed, 13 May 2015 13:12:43 -0400
-Subject: [PATCH] register now checks for missing ctypes
-
-If ctypes is None, then no input hooks may be registered; `InputHookManager.register` skips registration of input hook classes. Also updated `__init__` to no longer skip creating the instance attributes, to prevent AttributeError exceptions at load time.
----
- IPython/lib/inputhook.py | 13 +++++++------
- 1 file changed, 7 insertions(+), 6 deletions(-)
-
-diff --git a/IPython/lib/inputhook.py b/IPython/lib/inputhook.py
-index 4ae2cb3..6578365 100644
---- a/IPython/lib/inputhook.py
-+++ b/IPython/lib/inputhook.py
-@@ -107,8 +107,8 @@ class InputHookManager(object):
-     def __init__(self):
-         if ctypes is None:
-             warn("IPython GUI event loop requires ctypes, %gui will not be available")
--            return
--        self.PYFUNC = ctypes.PYFUNCTYPE(ctypes.c_int)
-+        else:
-+            self.PYFUNC = ctypes.PYFUNCTYPE(ctypes.c_int)
-         self.guihooks = {}
-         self.aliases = {}
-         self.apps = {}
-@@ -197,10 +197,11 @@ def enable(self, app=None):
-                     ...
-         """
-         def decorator(cls):
--            inst = cls(self)
--            self.guihooks[toolkitname] = inst
--            for a in aliases:
--                self.aliases[a] = toolkitname
-+            if ctypes is not None:
-+                inst = cls(self)
-+                self.guihooks[toolkitname] = inst
-+                for a in aliases:
-+                    self.aliases[a] = toolkitname
-             return cls
-         return decorator
- 
diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 09fab7b17c..a1148b1c38 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -4627,34 +4627,38 @@ (define-public python2-testpath
 (define-public python-ipython
   (package
     (name "python-ipython")
-    (version "3.2.1")
+    (version "4.0.0")
     (source
      (origin
        (method url-fetch)
-       (patches (search-patches "python-ipython-inputhook-ctype.patch"))
-       (uri (string-append "https://pypi.python.org/packages/source/i/"
-                           "ipython/ipython-" version ".tar.gz"))
+       (uri (pypi-uri "ipython" version ".tar.gz"))
        (sha256
-        (base32 "0xwin0sa9n0cabx4cq1ibf5ldsiw5dyimibla82kicz5gbpas4y9"))))
+        (base32 "1npl8g6bfsff9j938ypx0q5fyzy2l8lp0jl8skjjj2zv0z27dlig"))))
     (build-system python-build-system)
     (outputs '("out" "doc"))
     (propagated-inputs
      `(("python-pyzmq" ,python-pyzmq)
-       ("python-terminado" ,python-terminado)))
-    (inputs
-     `(("readline" ,readline)
-       ("which" ,which)
+       ("python-terminado" ,python-terminado)
        ("python-matplotlib" ,python-matplotlib)
        ("python-numpy" ,python-numpy)
        ("python-numpydoc" ,python-numpydoc)
        ("python-jinja2" ,python-jinja2)
        ("python-mistune" ,python-mistune)
+       ("python-pexpect" ,python-pexpect)
+       ("python-pickleshare" ,python-pickleshare)
+       ("python-simplegeneric" ,python-simplegeneric)
        ("python-jsonschema" ,python-jsonschema)
-       ("python-pygments" ,python-pygments)
-       ("python-requests" ,python-requests) ;; for tests
-       ("python-nose" ,python-nose)))
+       ("python-traitlets" ,python-traitlets)
+       ("python-ipykernel" ,python-ipykernel)
+       ("python-pygments" ,python-pygments)))
+    (inputs
+     `(("readline" ,readline)
+       ("which" ,which)))
     (native-inputs
      `(("pkg-config" ,pkg-config)
+       ("python-requests" ,python-requests) ;; for tests
+       ("python-testpath" ,python-testpath)
+       ("python-nose" ,python-nose)
        ("python-sphinx" ,python-sphinx)
        ("texlive" ,texlive)
        ("texinfo" ,texinfo)
@@ -4673,13 +4677,13 @@ (define-public python-ipython
                    (examples (string-append doc "/examples")))
               (setenv "LANG" "en_US.utf8")
               (with-directory-excursion "docs"
-                ;; FIXME: html and pdf fail to build
-                ;; (system* "make" "html")
-                ;; (system* "make" "pdf" "PAPER=a4")
+                ;; FIXME: pdf fails to build
+                ;;(system* "make" "pdf" "PAPER=a4")
+                (system* "make" "html")
                 (system* "make" "info"))
               (copy-recursively "docs/man" man1)
               (copy-recursively "examples" examples)
-              ;; (copy-recursively "docs/build/html" html)
+              (copy-recursively "docs/build/html" html)
               ;; (copy-file "docs/build/latex/ipython.pdf"
               ;;            (string-append doc "/ipython.pdf"))
               (mkdir-p info)
-- 
cgit v1.2.3


From c27ae827da71dffcbc42f813a9b59c4114d7869b Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Tue, 1 Nov 2016 13:20:46 +0100
Subject: gnu: Add jupyter.

* gnu/packages/python.scm (jupyter): New variable.
---
 gnu/packages/python.scm | 30 ++++++++++++++++++++++++++++++
 1 file changed, 30 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index a1148b1c38..518ab3a50c 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -6934,6 +6934,36 @@ (define-public python-jupyter-console
 (define-public python2-jupyter-console
   (package-with-python2 python-jupyter-console))
 
+(define-public jupyter
+  (package
+    (name "jupyter")
+    (version "1.0.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "jupyter" version))
+       (sha256
+        (base32
+         "0pwf3pminkzyzgx5kcplvvbvwrrzd3baa7lmh96f647k30rlpp6r"))))
+    (build-system python-build-system)
+    ;; FIXME: it's not clear how to run the tests.
+    (arguments `(#:tests? #f))
+    (propagated-inputs
+     `(("python-ipykernel" ,python-ipykernel)
+       ("python-ipywidgets" ,python-ipywidgets)
+       ("python-jupyter-console" ,python-jupyter-console)
+       ("python-nbconvert" ,python-nbconvert)
+       ("python-notebook" ,python-notebook)
+       ("python-setuptools" ,python-setuptools)))
+    (home-page "http://jupyter.org")
+    (synopsis "Web application for interactive documents")
+    (description
+     "The Jupyter Notebook is a web application that allows you to create and
+share documents that contain live code, equations, visualizations and
+explanatory text.  Uses include: data cleaning and transformation, numerical
+simulation, statistical modeling, machine learning and much more.")
+    (license license:bsd-3)))
+
 (define-public python-chardet
   (package
     (name "python-chardet")
-- 
cgit v1.2.3


From 682bfb8124508c016b93f2d1d6696e5e06699e0c Mon Sep 17 00:00:00 2001
From: Leo Famulari <leo@famulari.name>
Date: Fri, 4 Nov 2016 19:47:47 -0400
Subject: gnu: webkitgtk: Update to 2.14.2.

* gnu/packages/webkit.scm (webkitgtk): Update to 2.14.1.
---
 gnu/packages/webkit.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/webkit.scm b/gnu/packages/webkit.scm
index 46ae30aa9a..facdb050ab 100644
--- a/gnu/packages/webkit.scm
+++ b/gnu/packages/webkit.scm
@@ -53,14 +53,14 @@ (define-module (gnu packages webkit)
 (define-public webkitgtk
   (package
     (name "webkitgtk")
-    (version "2.14.1")
+    (version "2.14.2")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://www.webkitgtk.org/releases/"
                                   name "-" version ".tar.xz"))
               (sha256
                (base32
-                "1dffnz20psgc604azhbzn9a6cdhafar9dw74w3bbwrfy531pcb9f"))))
+                "0mjmcxhafh6l6j062z2nwfqbbvfyx16iqrzrbajswijh23awpnrf"))))
     (build-system cmake-build-system)
     (arguments
      '(#:tests? #f ; no tests
-- 
cgit v1.2.3


From 674a0f955809d40c2fe3e5092b2927c4c96e8351 Mon Sep 17 00:00:00 2001
From: Kei Kebreau <kei@openmailbox.org>
Date: Fri, 4 Nov 2016 20:06:03 -0400
Subject: gnu: w3m: Switch to Debian's actively maintained fork of w3m.

Fixes some security issues seen here:
<http://www.openwall.com/lists/oss-security/2016/11/03/3>

* gnu/packages/w3m.scm (w3m): Switch it.
[source]: Use Debian's git tree. Remove obsolete patches.
[arguments]: Remove an unneeded substitute* function.
* gnu/packages/patches/w3m-disable-sslv2-and-sslv3.patch,
gnu/packages/patches/w3m-disable-weak-ciphers.patch,
gnu/packages/patches/w3m-force-ssl_verify_server-on.patch,
gnu/packages/patches/w3m-libgc.patch: Delete files.
* gnu/local.mk (dist_patch_DATA): Remove them.
---
 gnu/local.mk                                       |  4 ---
 .../patches/w3m-disable-sslv2-and-sslv3.patch      | 24 ----------------
 .../patches/w3m-disable-weak-ciphers.patch         | 24 ----------------
 .../patches/w3m-force-ssl_verify_server-on.patch   | 24 ----------------
 gnu/packages/patches/w3m-libgc.patch               | 28 ------------------
 gnu/packages/w3m.scm                               | 33 +++++++++-------------
 6 files changed, 13 insertions(+), 124 deletions(-)
 delete mode 100644 gnu/packages/patches/w3m-disable-sslv2-and-sslv3.patch
 delete mode 100644 gnu/packages/patches/w3m-disable-weak-ciphers.patch
 delete mode 100644 gnu/packages/patches/w3m-force-ssl_verify_server-on.patch
 delete mode 100644 gnu/packages/patches/w3m-libgc.patch

(limited to 'gnu/packages')

diff --git a/gnu/local.mk b/gnu/local.mk
index 27848ac805..49b672111f 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -891,10 +891,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/vte-CVE-2012-2738-pt1.patch			\
   %D%/packages/patches/vte-CVE-2012-2738-pt2.patch			\
   %D%/packages/patches/vtk-mesa-10.patch			\
-  %D%/packages/patches/w3m-libgc.patch				\
-  %D%/packages/patches/w3m-force-ssl_verify_server-on.patch	\
-  %D%/packages/patches/w3m-disable-sslv2-and-sslv3.patch	\
-  %D%/packages/patches/w3m-disable-weak-ciphers.patch		\
   %D%/packages/patches/weechat-python.patch			\
   %D%/packages/patches/weex-vacopy.patch			\
   %D%/packages/patches/wicd-bitrate-none-fix.patch		\
diff --git a/gnu/packages/patches/w3m-disable-sslv2-and-sslv3.patch b/gnu/packages/patches/w3m-disable-sslv2-and-sslv3.patch
deleted file mode 100644
index 5b78f2d909..0000000000
--- a/gnu/packages/patches/w3m-disable-sslv2-and-sslv3.patch
+++ /dev/null
@@ -1,24 +0,0 @@
-Subject: Disable SSLv2 and SSLv3.
-
-The only remaining methods are TLSv1.* (the code never distinguishes
-between TLSv1.0, TLSv1.1, and TLSv1.2).
----
- fm.h | 2 +-
- 1 file changed, 1 insertion(+), 1 deletion(-)
-
-diff --git a/fm.h b/fm.h
-index 320906c..ddcd4fc 100644
---- a/fm.h
-+++ b/fm.h
-@@ -1144,7 +1144,7 @@ global int ssl_path_modified init(FALSE);
- #endif				/* defined(USE_SSL) &&
- 				 * defined(USE_SSL_VERIFY) */
- #ifdef USE_SSL
--global char *ssl_forbid_method init(NULL);
-+global char *ssl_forbid_method init("2, 3");
- #endif
- 
- global int is_redisplay init(FALSE);
--- 
-2.6.4
-
diff --git a/gnu/packages/patches/w3m-disable-weak-ciphers.patch b/gnu/packages/patches/w3m-disable-weak-ciphers.patch
deleted file mode 100644
index 4780d54cb6..0000000000
--- a/gnu/packages/patches/w3m-disable-weak-ciphers.patch
+++ /dev/null
@@ -1,24 +0,0 @@
-Subject: Disable weak ciphers
-
-Disable RC4, "export ciphers", and all keys < 128 bits.
-
-Bug-Ubuntu: https://bugs.launchpad.net/ubuntu/+source/w3m/+bug/1325674
----
- url.c | 1 +
- 1 file changed, 1 insertion(+)
-
-diff --git a/url.c b/url.c
-index ed6062e..e86b1f3 100644
---- a/url.c
-+++ b/url.c
-@@ -326,6 +326,7 @@ openSSLHandle(int sock, char *hostname, char **p_cert)
- 	SSL_load_error_strings();
- 	if (!(ssl_ctx = SSL_CTX_new(SSLv23_client_method())))
- 	    goto eend;
-+	SSL_CTX_set_cipher_list(ssl_ctx, "DEFAULT:!LOW:!RC4:!EXP");
- 	option = SSL_OP_ALL;
- 	if (ssl_forbid_method) {
- 	    if (strchr(ssl_forbid_method, '2'))
--- 
-2.6.4
-
diff --git a/gnu/packages/patches/w3m-force-ssl_verify_server-on.patch b/gnu/packages/patches/w3m-force-ssl_verify_server-on.patch
deleted file mode 100644
index dc9f117f9d..0000000000
--- a/gnu/packages/patches/w3m-force-ssl_verify_server-on.patch
+++ /dev/null
@@ -1,24 +0,0 @@
-Subject: Force ssl_verify_server on.
-
-By default, SSL/TLS certificates are not verified. This enables the
-verification.
----
- fm.h | 2 +-
- 1 file changed, 1 insertion(+), 1 deletion(-)
-
-diff --git a/fm.h b/fm.h
-index 8378939..320906c 100644
---- a/fm.h
-+++ b/fm.h
-@@ -1135,7 +1135,7 @@ global int view_unseenobject init(TRUE);
- #endif
- 
- #if defined(USE_SSL) && defined(USE_SSL_VERIFY)
--global int ssl_verify_server init(FALSE);
-+global int ssl_verify_server init(TRUE);
- global char *ssl_cert_file init(NULL);
- global char *ssl_key_file init(NULL);
- global char *ssl_ca_path init(NULL);
--- 
-2.6.4
-
diff --git a/gnu/packages/patches/w3m-libgc.patch b/gnu/packages/patches/w3m-libgc.patch
deleted file mode 100644
index 0dc6a4027c..0000000000
--- a/gnu/packages/patches/w3m-libgc.patch
+++ /dev/null
@@ -1,28 +0,0 @@
-This patch fixes w3m compilation with libgc > 7.2.
-
-Reported:
-https://bugs.archlinux.org/task/33397
-
-Patch with explanation:
-http://anonscm.debian.org/cgit/collab-maint/w3m.git/commit/?id=770eec8304bdbe458
----
- main.c | 3 ++-
- 1 file changed, 2 insertions(+), 1 deletion(-)
-
-diff --git a/main.c b/main.c
-index b421943..249eb1a 100644
---- a/main.c
-+++ b/main.c
-@@ -833,7 +833,8 @@ main(int argc, char **argv, char **envp)
-     mySignal(SIGPIPE, SigPipe);
- #endif
- 
--    orig_GC_warn_proc = GC_set_warn_proc(wrap_GC_warn_proc);
-+    orig_GC_warn_proc = GC_get_warn_proc();
-+    GC_set_warn_proc(wrap_GC_warn_proc);
-     err_msg = Strnew();
-     if (load_argc == 0) {
- 	/* no URL specified */
--- 
-2.6.4
-
diff --git a/gnu/packages/w3m.scm b/gnu/packages/w3m.scm
index e7dd583c11..54d4a119f5 100644
--- a/gnu/packages/w3m.scm
+++ b/gnu/packages/w3m.scm
@@ -1,6 +1,7 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2013 Nikita Karetnikov <nikita@karetnikov.org>
 ;;; Copyright © 2016 Leo Famulari <leo@famulari.name>
+;;; Copyright © 2016 Kei Kebreau <kei@openmailbox.org>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -28,37 +29,29 @@ (define-module (gnu packages w3m)
   #:use-module (gnu packages tls)
   #:use-module (gnu packages)
   #:use-module (guix packages)
-  #:use-module (guix download)
+  #:use-module (guix git-download)
   #:use-module (guix build-system gnu))
 
 (define-public w3m
   (package
     (name "w3m")
-    (version "0.5.3")
+    (version "0.5.3+git20161031")
     (source (origin
-             (method url-fetch)
-             (uri (string-append "mirror://sourceforge/" name "/" name "/"
-                                 name "-" version "/"
-                                 name "-" version ".tar.gz"))
-             (sha256
-              (base32
-               "1qx9f0kprf92r1wxl3sacykla0g04qsi0idypzz24b7xy9ix5579"))
-
-             ;; cf. https://bugs.archlinux.org/task/33397
-             (patches (search-patches "w3m-libgc.patch"
-                                      "w3m-force-ssl_verify_server-on.patch"
-                                      "w3m-disable-sslv2-and-sslv3.patch"
-                                      "w3m-disable-weak-ciphers.patch"))))
+              (method git-fetch)
+              ;; Debian's fork of w3m is the only one that is still
+              ;; maintained.
+              (uri (git-reference
+                    (url "https://anonscm.debian.org/cgit/collab-maint/w3m.git")
+                    (commit version)))
+              (file-name (string-append "w3m-" version "-checkout"))
+              (sha256
+               (base32
+                "142vkkmsk76wj9w6r4y2pa1hmy1kkzmc73an9zchx0ikm2z92x6s"))))
     (build-system gnu-build-system)
     (arguments `(#:tests? #f  ; no check target
                  #:phases (alist-cons-before
                            'configure 'fix-perl
                            (lambda _
-                             ;; https://launchpad.net/bugs/935540
-                             ;; 'struct file_handle' is used by 'glibc'
-                             (substitute* '("istream.c" "istream.h")
-                              (("struct[[:blank:]]+file_handle")
-                               "struct w3m_file_handle"))
                              (substitute* '("scripts/w3mmail.cgi.in"
                                             "scripts/dirlist.cgi.in")
                                (("@PERL@") (which "perl"))))
-- 
cgit v1.2.3


From 250a8abc6634291334029b689b89058ba33b0ec4 Mon Sep 17 00:00:00 2001
From: Leo Famulari <leo@famulari.name>
Date: Fri, 4 Nov 2016 11:19:45 -0400
Subject: gnu: Add libidn2.

* gnu/packages/libidn.scm (libidn2): New variable.
---
 gnu/packages/libidn.scm | 22 ++++++++++++++++++++++
 1 file changed, 22 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/libidn.scm b/gnu/packages/libidn.scm
index 432c1fe675..141ad7a831 100644
--- a/gnu/packages/libidn.scm
+++ b/gnu/packages/libidn.scm
@@ -59,3 +59,25 @@ (define libidn-1.33
           (sha256
            (base32
             "068fjg2arlppjqqpzd714n1lf6gxkpac9v5yyvp1qwmv6nvam9s4")))))))
+
+(define-public libidn2
+  (package
+    (name "libidn2")
+    (version "0.11")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "ftp://alpha.gnu.org/gnu/libidn/libidn2-"
+                                  version ".tar.gz"))
+              (sha256
+               (base32
+                "1zxzhzx14q2b1xkx746pz4lawvqd8d055yy84n52ndwb4pf7nfax"))))
+    (build-system gnu-build-system)
+    (synopsis "Internationalized domain name library for IDNA2008")
+    (description "Libidn2 is an internationalized domain library implementing
+the IDNA2008 specifications.   Libidn2 is believed to be a complete IDNA2008
+implementation, but has yet to be as extensively used as the original Libidn
+library.")
+    (home-page "https://www.gnu.org/software/libidn/#libidn2")
+    ;; The command-line tool 'idn2' is GPL3+, while the library is dual-licensed
+    ;; GPL2+ or LGPL3+.
+    (license (list gpl2+ gpl3+ lgpl3+))))
-- 
cgit v1.2.3


From c2f4cab9a062bdd01af48584424f38ccebb7c29d Mon Sep 17 00:00:00 2001
From: Leo Famulari <leo@famulari.name>
Date: Fri, 4 Nov 2016 20:06:10 -0400
Subject: gnu: libidn: Distinguish from libidn2.

* gnu/packages/libidn.scm (libidn)[description]: Add detail to help distinguish
from libidn2.
---
 gnu/packages/libidn.scm | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/libidn.scm b/gnu/packages/libidn.scm
index 141ad7a831..79baa39a21 100644
--- a/gnu/packages/libidn.scm
+++ b/gnu/packages/libidn.scm
@@ -41,7 +41,8 @@ (define-public libidn
    (description
      "libidn is a library implementing of the Stringprep, Punycode and IDNA
 specifications.  These are used to encode and decode internationalized domain
-names.  It includes native C, C# and Java libraries.")
+names according to the IDNA2003 specifications.  It includes native C, C# and
+Java libraries.")
    ;; The C code is dual-licensed gpl2+ lgpl3+, the manual is fdl1.3+,
    ;; the command line tool is gpl3+.
    (license (list gpl2+ gpl3+ lgpl3+ fdl1.3+))
-- 
cgit v1.2.3


From 02f8f804f0242df885311715412a1e3ee5436f3b Mon Sep 17 00:00:00 2001
From: ng0 <ng0@we.make.ritual.n0.is>
Date: Fri, 4 Nov 2016 19:23:01 +0000
Subject: gnu: Add python-pafy.

* gnu/packages/python.scm (python-pafy): New variable.

Signed-off-by: Marius Bakke <mbakke@fastmail.com>
---
 gnu/packages/python.scm | 23 +++++++++++++++++++++++
 1 file changed, 23 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 518ab3a50c..ed4a078e05 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -86,6 +86,7 @@ (define-module (gnu packages python)
   #:use-module (gnu packages texinfo)
   #:use-module (gnu packages tls)
   #:use-module (gnu packages version-control)
+  #:use-module (gnu packages video)
   #:use-module (gnu packages web)
   #:use-module (gnu packages base)
   #:use-module (gnu packages xml)
@@ -1583,6 +1584,28 @@ (define-public python2-unittest2
      `(#:python ,python-2
        #:tests? #f)))) ; no setup.py test command
 
+(define-public python-pafy
+  (package
+    (name "python-pafy")
+    (version "0.5.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "pafy" version))
+       (sha256
+        (base32
+         "1ckvrypyvb7jbqlgwdz0y337ajagjv7dgxyns326nqwypn1wpq0i"))))
+    (build-system python-build-system)
+    (propagated-inputs
+     ;; Youtube-dl is a python package which is imported in the file
+     ;; "backend_youtube_dl.py", therefore it needs to be propagated.
+     `(("youtube-dl" ,youtube-dl)))
+    (home-page "https://np1.github.io/pafy/")
+    (synopsis "Retrieve YouTube content and metadata")
+    (description
+     "@code{pafy} is a python library to retrieve YouTube content and metadata.")
+    (license license:lgpl3+)))
+
 (define-public python-py
   (package
     (name "python-py")
-- 
cgit v1.2.3


From 05234973c79f26d7f38189b771976c3bb6643930 Mon Sep 17 00:00:00 2001
From: ng0 <ng0@we.make.ritual.n0.is>
Date: Fri, 4 Nov 2016 19:23:02 +0000
Subject: gnu: Add mps-youtube.

* gnu/packages/video.scm (mps-youtube): New variable.

Signed-off-by: Marius Bakke <mbakke@fastmail.com>
---
 gnu/packages/video.scm | 29 +++++++++++++++++++++++++++++
 1 file changed, 29 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/video.scm b/gnu/packages/video.scm
index 6ce03f7bcc..e7c90e13de 100644
--- a/gnu/packages/video.scm
+++ b/gnu/packages/video.scm
@@ -11,6 +11,7 @@
 ;;; Copyright © 2016 Kei Kebreau <kei@openmailbox.org>
 ;;; Copyright © 2016 Dmitry Nikolaev <cameltheman@gmail.com>
 ;;; Copyright © 2016 Andy Patterson <ajpatter@uwaterloo.ca>
+;;; Copyright © 2016 ng0 <ng0@we.make.ritual.n0.is>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -1683,3 +1684,31 @@ (define-public libaacs
     (description "libaacs is a library which implements the Advanced Access
 Content System specification.")
     (license license:lgpl2.1+)))
+
+(define-public mps-youtube
+  (package
+    (name "mps-youtube")
+    (version "0.2.7.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://github.com/mps-youtube/mps-youtube/"
+                           "archive/v" version ".tar.gz"))
+       (file-name (string-append name "-" version ".tar.gz"))
+       (sha256
+        (base32
+         "1s7h35yx6f0szf8mm8612ic913w3v05m2kwphjfcxnpq0ammhyci"))))
+    (build-system python-build-system)
+    (propagated-inputs
+     `(("python-pafy" ,python-pafy)
+       ("python-pygobject" ,python-pygobject))) ; For mpris2 support
+    (home-page "https://github.com/mps-youtube/mps-youtube")
+    (synopsis "Terminal based YouTube player and downloader")
+    (description
+     "@code{mps-youtube} is based on mps, a terminal based program to
+search, stream and download music.  This implementation uses YouTube as
+a source of content and can play and download video as well as audio.
+It can use either mpv or mplayer for playback, and for conversion of
+formats ffmpeg or libav is used.  Users should install one of the
+supported players in addition to this package.")
+    (license license:gpl3+)))
-- 
cgit v1.2.3


From e2a2eeecced33e9e02bee0ed834a3296289528cb Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Thu, 3 Nov 2016 20:39:23 +0200
Subject: gnu: gstreamer: Update to 1.10.0.

* gnu/packages/gstreamer.scm (gstreamer): Update to 1.10.0.
---
 gnu/packages/gstreamer.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/gstreamer.scm b/gnu/packages/gstreamer.scm
index 4aea514411..765345ef6c 100644
--- a/gnu/packages/gstreamer.scm
+++ b/gnu/packages/gstreamer.scm
@@ -97,7 +97,7 @@ (define-public orc
 (define-public gstreamer
   (package
     (name "gstreamer")
-    (version "1.8.2")
+    (version "1.10.0")
     (source
      (origin
       (method url-fetch)
@@ -106,7 +106,7 @@ (define-public gstreamer
             version ".tar.xz"))
       (sha256
        (base32
-        "0hc3j684nx209p10ampvnkza3gna2yiryr7jyx701ciakh3vxglx"))))
+        "01vjsgz58n6nrmnahs4ac7v4656yc042ymffqjzqa0a8pvx7hxqy"))))
     (build-system gnu-build-system)
     (outputs '("out" "doc"))
     (arguments
-- 
cgit v1.2.3


From 74e6c84444b47651ef6db0b8f7691979c7d57a13 Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Thu, 3 Nov 2016 20:40:18 +0200
Subject: gnu: gst-plugins-base: Update to 1.10.0.

* gnu/packages/gstreamer.scm (gst-plugins-base): Update to 1.10.0.
---
 gnu/packages/gstreamer.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/gstreamer.scm b/gnu/packages/gstreamer.scm
index 765345ef6c..431d54dc52 100644
--- a/gnu/packages/gstreamer.scm
+++ b/gnu/packages/gstreamer.scm
@@ -145,7 +145,7 @@ (define-public gstreamer
 (define-public gst-plugins-base
   (package
     (name "gst-plugins-base")
-    (version "1.8.2")
+    (version "1.10.0")
     (source
      (origin
       (method url-fetch)
@@ -153,7 +153,7 @@ (define-public gst-plugins-base
                           name "-" version ".tar.xz"))
       (sha256
        (base32
-        "13fk751vvfrfhbm4ip28vxyvlsm4b4y0bc0pvf7fqp8azg40jwcx"))))
+        "0jp9rwv0am8qv32q3dzhdcbyygg5wjm4fg20njyhp6n6vybyzkdz"))))
     (build-system gnu-build-system)
     (outputs '("out" "doc"))
     (propagated-inputs
-- 
cgit v1.2.3


From 49eddefbf0dc82a74a8720fb3076348aacbc89f0 Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Thu, 3 Nov 2016 20:41:01 +0200
Subject: gnu: gst-plugins-good: Update to 1.10.0.

* gnu/packages/gstreamer.scm (gst-plugins-good): Update to 1.10.0.
---
 gnu/packages/gstreamer.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/gstreamer.scm b/gnu/packages/gstreamer.scm
index 431d54dc52..97022a7b68 100644
--- a/gnu/packages/gstreamer.scm
+++ b/gnu/packages/gstreamer.scm
@@ -199,7 +199,7 @@ (define-public gst-plugins-base
 (define-public gst-plugins-good
   (package
     (name "gst-plugins-good")
-    (version "1.8.2")
+    (version "1.10.0")
     (source
      (origin
       (method url-fetch)
@@ -208,7 +208,7 @@ (define-public gst-plugins-good
             name "-" version ".tar.xz"))
       (sha256
        (base32
-        "0i1rlbbx3m6ykvcdyaidsd8wa2b7nq2qmcvbrsg00yivi88ljxcd"))))
+        "1qhx6x3ax1qqbvm20zhqax3dsas4yzlx7vdjnjqllqzmcfbma0vs"))))
     (build-system gnu-build-system)
     (inputs
      `(("aalib" ,aalib)
-- 
cgit v1.2.3


From 7aa083e58140df20153fad96a1e48913333e49ab Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Thu, 3 Nov 2016 20:41:35 +0200
Subject: gnu: gst-plugins-ugly: Update to 1.10.0.

* gnu/packages/gstreamer.scm (gst-plugins-ugly): Update to 1.10.0.
---
 gnu/packages/gstreamer.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/gstreamer.scm b/gnu/packages/gstreamer.scm
index 97022a7b68..3d4630f0b5 100644
--- a/gnu/packages/gstreamer.scm
+++ b/gnu/packages/gstreamer.scm
@@ -340,7 +340,7 @@ (define-public gst-plugins-bad
 (define-public gst-plugins-ugly
   (package
     (name "gst-plugins-ugly")
-    (version "1.8.2")
+    (version "1.10.0")
     (source
      (origin
        (method url-fetch)
@@ -348,7 +348,7 @@ (define-public gst-plugins-ugly
                            name "/" name "-" version ".tar.xz"))
        (sha256
         (base32
-         "1b58s7z430cbbaw8mgy87kslbpmj3xmm66wsr7bddhcgm6i36nww"))))
+         "1q2m3bl8kh9q3grshj55lb2mqby4r20qfsrffc2l7ddb0ccqvplp"))))
     (build-system gnu-build-system)
     (inputs
      `(("gst-plugins-base" ,gst-plugins-base)
-- 
cgit v1.2.3


From 81fc4b20c7104c37fe2db021090ab6a468784e95 Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Thu, 3 Nov 2016 20:42:28 +0200
Subject: gnu: gst-libav: Update to 1.10.0.

* gnu/packages/gstreamer.scm (gst-libav): Update to 1.10.0.
---
 gnu/packages/gstreamer.scm | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/gstreamer.scm b/gnu/packages/gstreamer.scm
index 3d4630f0b5..452e0d165d 100644
--- a/gnu/packages/gstreamer.scm
+++ b/gnu/packages/gstreamer.scm
@@ -379,7 +379,7 @@ (define-public gst-plugins-ugly
 (define-public gst-libav
   (package
     (name "gst-libav")
-    (version "1.8.2")
+    (version "1.10.0")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -387,7 +387,7 @@ (define-public gst-libav
                     name "-" version ".tar.xz"))
               (sha256
                (base32
-                "0yk8pxg3xi26ndj7pliqdfphy0jmqsq4dmdzy31gbd9rgficgwxm"))))
+                "0nyqkggcxfrbflcf4jyj0h9l1rkbi3r5h61w4fcbp2n72522165g"))))
     (build-system gnu-build-system)
     (arguments
      '(#:configure-flags '("--with-system-libav")
@@ -397,7 +397,8 @@ (define-public gst-libav
                      (lambda _
                        (substitute* "gst-libs/ext/libav/configure"
                          (("#! /bin/sh")
-                          (string-append "#! "(which "sh")))))))))
+                          (string-append "#! "(which "sh"))))
+                       #t)))))
     (native-inputs
      `(("pkg-config" ,pkg-config)
        ("python" ,python)))
-- 
cgit v1.2.3


From 96451462c51fd54fd3c1e4df312e005b12cdde40 Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Thu, 3 Nov 2016 20:43:57 +0200
Subject: gnu: python-gst: Update to 1.10.0.

* gnu/packages/gstreamer.scm (python-gst): Update to 1.10.0.
---
 gnu/packages/gstreamer.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/gstreamer.scm b/gnu/packages/gstreamer.scm
index 452e0d165d..310e4d1d56 100644
--- a/gnu/packages/gstreamer.scm
+++ b/gnu/packages/gstreamer.scm
@@ -417,7 +417,7 @@ (define-public gst-libav
 (define-public python-gst
   (package
     (name "python-gst")
-    (version "1.8.2")
+    (version "1.10.0")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -425,7 +425,7 @@ (define-public python-gst
                     "gst-python-" version ".tar.xz"))
               (sha256
                (base32
-                "15sdfa6lq5pswvi09vk51cs30yf8wr2rlm9myhb4q0c2jhiial2g"))))
+                "0hf71m0vqnd5sdj14li935xzzmqxh606qgw744a25w3vwj9v8nfy"))))
     (build-system gnu-build-system)
     (arguments
      ;; XXX: Factorize python-sitedir with python-build-system.
-- 
cgit v1.2.3


From 378a0535e17cbcba686fc776e63838c01999ba43 Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Sat, 5 Nov 2016 17:37:58 +0200
Subject: gnu: freeipmi: Update to 1.5.5.

* gnu/packages/freeipmi.scm (freeipmi): Update to 1.5.5.
---
 gnu/packages/freeipmi.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/freeipmi.scm b/gnu/packages/freeipmi.scm
index cd97d52f99..fc11bbd2b9 100644
--- a/gnu/packages/freeipmi.scm
+++ b/gnu/packages/freeipmi.scm
@@ -28,14 +28,14 @@ (define-module (gnu packages freeipmi)
 (define-public freeipmi
   (package
     (name "freeipmi")
-    (version "1.5.4")
+    (version "1.5.5")
     (source (origin
              (method url-fetch)
              (uri (string-append "mirror://gnu/freeipmi/freeipmi-"
                                  version ".tar.gz"))
              (sha256
               (base32
-               "1m8zvnyjyjap07vvc5z90nyghabbb6bjcyyc7qswj66qsmssf135"))))
+               "0lzzvhzbdl1cxin4xz3lirqxsjwmjr5ac0qr4g21cqsv2j6vj85f"))))
     (build-system gnu-build-system)
     (inputs
      `(("readline" ,readline)
-- 
cgit v1.2.3


From 18a9a7ef384063bb30e8e1ed197ee4d03400db40 Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Sat, 5 Nov 2016 17:39:11 +0200
Subject: gnu: jasper: Update to 1.900.19.

* gnu/packages/image.scm (jasper): Update to 1.900.19.
[arguments]: Remove custom make-flags.
---
 gnu/packages/image.scm | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/image.scm b/gnu/packages/image.scm
index 6f83fc4be4..601e81805b 100644
--- a/gnu/packages/image.scm
+++ b/gnu/packages/image.scm
@@ -841,17 +841,15 @@ (define-public devil
 (define-public jasper
   (package
     (name "jasper")
-    (version "1.900.16")
+    (version "1.900.19")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://www.ece.uvic.ca/~frodo/jasper"
                                   "/software/jasper-" version ".tar.gz"))
               (sha256
                (base32
-                "0wgrz6970sf8apyld35vrxamzx46fq15l0ipkvjsjlbwfrhj57rl"))))
+                "0dm3k0wdny3s37zxm9s9riv46p69c14bnn532fv6cv5b6l1b0pwb"))))
     (build-system gnu-build-system)
-    (arguments
-     '(#:make-flags '("CFLAGS=-std=c99"))) ; 1.900.13 added c++ style comments
     (synopsis "JPEG-2000 library")
     (description "The JasPer Project is an initiative to provide a reference
 implementation of the codec specified in the JPEG-2000 Part-1 standard (i.e.,
-- 
cgit v1.2.3


From 0cee33ac9694fa67ed0de795ddc2cb5a26e39d15 Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Sat, 5 Nov 2016 17:40:13 +0200
Subject: gnu: gst-plugins-bad: Update to 1.10.0.

* gnu/packages/gstreamer.scm (gst-plugins-bad): Update to 1.10.0.
[inputs]: Remove wayland.
[tests]: Update comment about failing tests.
[home-page]: Use https.
---
 gnu/packages/gstreamer.scm | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/gstreamer.scm b/gnu/packages/gstreamer.scm
index 310e4d1d56..0b73fd14e2 100644
--- a/gnu/packages/gstreamer.scm
+++ b/gnu/packages/gstreamer.scm
@@ -264,18 +264,18 @@ (define-public gst-plugins-good
 (define-public gst-plugins-bad
   (package
     (name "gst-plugins-bad")
-    (version "1.6.3")
+    (version "1.10.0")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://gstreamer.freedesktop.org/src/"
                                   name "/" name "-" version ".tar.xz"))
               (sha256
                (base32
-                "0q9s5da54819gwncmdi95l5qzx97l9vxk6adx4zmx73a3l82j6wp"))))
+                "0kqwh5r4j05f2w9m353grvypn0106hxcr52409f7rvm3w4b9sprx"))))
     (outputs '("out" "doc"))
     (build-system gnu-build-system)
     (arguments
-     '(#:tests? #f ; XXX: 11 of 54 tests fail
+     '(#:tests? #f ; XXX: 18 of 65 tests fail
        #:configure-flags
        (list (string-append "--with-html-dir="
                             (assoc-ref %outputs "doc")
@@ -329,8 +329,9 @@ (define-public gst-plugins-bad
        ;("qtx11extras" ,qtx11extras)
        ("soundtouch" ,soundtouch)
        ("x265" ,x265)
-       ("wayland" ,wayland)))
-    (home-page "http://gstreamer.freedesktop.org/")
+       ;("wayland" ,wayland) ; needs wayland-protocols
+       ))
+    (home-page "https://gstreamer.freedesktop.org/")
     (synopsis "Plugins for the GStreamer multimedia library")
     (description
      "GStreamer Bad Plug-ins is a set of plug-ins whose quality aren't up to
-- 
cgit v1.2.3


From 268b3802e9bb5336b087039d75eb0db7280f156f Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Sat, 5 Nov 2016 17:46:55 +0200
Subject: gnu: whois: Update to 5.2.13.

* gnu/packages/networking.scm (whois): Update to 5.2.13.
---
 gnu/packages/networking.scm | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/networking.scm b/gnu/packages/networking.scm
index 1f6ed77ae2..2c51aeaac4 100644
--- a/gnu/packages/networking.scm
+++ b/gnu/packages/networking.scm
@@ -428,7 +428,7 @@ (define-public iodine
 (define-public whois
   (package
     (name "whois")
-    (version "5.2.12")
+    (version "5.2.13")
     (source
      (origin
        (method url-fetch)
@@ -436,7 +436,7 @@ (define-public whois
                            name "_" version ".tar.xz"))
        (sha256
         (base32
-         "1wfdyqi64l5x56j259jrrlbh19b7q7i6r83a8q8rjzcqp0kl0vdj"))))
+         "0r3bbxpwsxssa99d8dcjnp79mw1cjwqxgmqjm1537q277jwsk0yc"))))
     (build-system gnu-build-system)
     ;; TODO: unbundle mkpasswd binary + its po files.
     (arguments
@@ -449,7 +449,8 @@ (define-public whois
          (add-before 'build 'setenv
            (lambda _
              (setenv "HAVE_ICONV" "1")
-             (setenv "HAVE_LIBIDN" "1"))))))
+             (setenv "HAVE_LIBIDN" "1")
+             #t)))))
     (inputs
      `(("libidn" ,libidn)))
     (native-inputs
-- 
cgit v1.2.3


From 2d125a9b21306919e6123f76c0970988b14dadcf Mon Sep 17 00:00:00 2001
From: Leo Famulari <leo@famulari.name>
Date: Sat, 5 Nov 2016 13:28:42 -0400
Subject: gnu: weex: Update to 2.8.2 [fixes CVE-2005-3150].

* gnu/packages/ftp.scm (weex): Update to 2.8.2.
[source]: Use new URL. Remove obsolete 'weex-vacopy.patch'.
[arguments]: Remove custom 'configure' phase and add 'bootstrap' phase.
[native-inputs]: Add autoconf, automake, and gnu-gettext.
* gnu/packages/patches/weex-vacopy.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove it.
---
 gnu/local.mk                           |  1 -
 gnu/packages/ftp.scm                   | 27 ++++++++++++---------------
 gnu/packages/patches/weex-vacopy.patch | 13 -------------
 3 files changed, 12 insertions(+), 29 deletions(-)
 delete mode 100644 gnu/packages/patches/weex-vacopy.patch

(limited to 'gnu/packages')

diff --git a/gnu/local.mk b/gnu/local.mk
index 49b672111f..1ac336196d 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -892,7 +892,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/vte-CVE-2012-2738-pt2.patch			\
   %D%/packages/patches/vtk-mesa-10.patch			\
   %D%/packages/patches/weechat-python.patch			\
-  %D%/packages/patches/weex-vacopy.patch			\
   %D%/packages/patches/wicd-bitrate-none-fix.patch		\
   %D%/packages/patches/wicd-get-selected-profile-fix.patch	\
   %D%/packages/patches/wicd-urwid-1.3.patch			\
diff --git a/gnu/packages/ftp.scm b/gnu/packages/ftp.scm
index a11265532a..eb622dd17c 100644
--- a/gnu/packages/ftp.scm
+++ b/gnu/packages/ftp.scm
@@ -25,6 +25,8 @@ (define-module (gnu packages ftp)
   #:use-module (guix download)
   #:use-module (guix packages)
   #:use-module (gnu packages)
+  #:use-module (gnu packages autotools)
+  #:use-module (gnu packages gettext)
   #:use-module (gnu packages ncurses)
   #:use-module (gnu packages readline)
   #:use-module (gnu packages pkg-config)
@@ -126,31 +128,26 @@ (define-public ncftp
 (define-public weex
   (package
     (name "weex")
-    (version "2.6.1.5")
+    (version "2.8.2")
     (source
       (origin
         (method url-fetch)
         (uri
-          (string-append "mirror://sourceforge/weex/weex/" version
-                         "/weex-" version ".tar.gz"))
+          (string-append "mirror://sourceforge/weex/weex/"
+                         "/weex_" version ".tar.gz"))
         (sha256
           (base32
-            "0f5cj5p852wkm24mzy2sxgxyahv2p9rk4wlq21j310pi7wlhgwyl"))
-        (patches (search-patches "weex-vacopy.patch"))))
+            "1ir761hjncr1bamaqcw9j7x57xi3s9jax3223bxwbq30a0vsw1pd"))))
     (build-system gnu-build-system)
+    (native-inputs
+     `(("automake" ,automake)
+       ("autoconf" ,autoconf)
+       ("gettext" ,gnu-gettext)))
     (arguments
      `(#:phases
        (modify-phases %standard-phases
-         (replace 'configure
-                  ;; configure does not work followed by both "SHELL=..." and
-                  ;; "CONFIG_SHELL=..."; set environment variables instead
-                  (lambda* (#:key outputs #:allow-other-keys)
-                    (let* ((out (assoc-ref outputs "out"))
-                           (bash (which "bash")))
-                      (setenv "SHELL" bash)
-                      (setenv "CONFIG_SHELL" bash)
-                      (zero? (system* bash "./configure"
-                                      (string-append "--prefix=" out)))))))))
+         (add-before 'configure 'bootstrap
+           (lambda _ (zero? (system* "autoreconf" "-vfi")))))))
     (home-page "http://weex.sourceforge.net/")
     (synopsis "Non-interactive client for FTP synchronization")
     (description
diff --git a/gnu/packages/patches/weex-vacopy.patch b/gnu/packages/patches/weex-vacopy.patch
deleted file mode 100644
index f593e86c08..0000000000
--- a/gnu/packages/patches/weex-vacopy.patch
+++ /dev/null
@@ -1,13 +0,0 @@
-Taken from the Debian 2.8.0 package.
-
---- weex-2.6.1.5/src/strlib.c	2003-08-18 11:52:38.000000000 +0200
-+++ weex-2.8.0/src/strlib.c	2007-12-04 14:22:02.000000000 +0100
-@@ -42,6 +42,8 @@
- #  define G_VA_COPY(ap1, ap2)     (*(ap1) = *(ap2))
- #  elif defined (G_VA_COPY_AS_ARRAY)
- #  define G_VA_COPY(ap1, ap2)     g_memmove ((ap1), (ap2), sizeof (va_list))
-+#  elif defined (__x86_64__)
-+#  define G_VA_COPY(ap1, ap2)     memmove ((ap1), (ap2), sizeof (va_list))
- #  else /* va_list is a pointer */
- #  define G_VA_COPY(ap1, ap2)     ((ap1) = (ap2))
- #  endif /* va_list is a pointer */
-- 
cgit v1.2.3


From 2f6dd9cdef58c01668f89e046b182b8235f9c556 Mon Sep 17 00:00:00 2001
From: Arun Isaac <arunisaac@systemreboot.net>
Date: Thu, 20 Oct 2016 15:45:03 +0530
Subject: gnu: Add python-axolotl-curve25519.

* gnu/packages/python.scm (python-axolotl-curve25519,
  python2-axolotl-curve25519): New variables.

Signed-off-by: Leo Famulari <leo@famulari.name>
---
 gnu/packages/python.scm | 34 ++++++++++++++++++++++++++++++++++
 1 file changed, 34 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index ed4a078e05..b656a1e32b 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -30,6 +30,7 @@
 ;;; Copyright © 2016 Stefan Reichoer <stefan@xsteve.at>
 ;;; Copyright © 2016 Dylan Jeffers <sapientech@sapientech@openmailbox.org>
 ;;; Copyright © 2016 Alex Vong <alexvong1995@gmail.com>
+;;; Copyright © 2016 Arun Isaac <arunisaac@systemreboot.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -11909,3 +11910,36 @@ (define-public python2-imagesize
       (inherit base)
       (native-inputs `(("python2-setuptools" ,python2-setuptools)
                        ,@(package-native-inputs base))))))
+
+(define-public python-axolotl-curve25519
+  (package
+    (name "python-axolotl-curve25519")
+    (version "0.1")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "git://github.com/tgalal/python-axolotl-curve25519")
+             (commit "e4a9c4de0eae27223200579c58d1f8f6d20637e2")))
+       (file-name (string-append name "-" version "-checkout"))
+       (sha256
+        (base32
+         "0agap5q0hmvf6cwzjqc05kw53pjgf6942pcivpazksmg1vk400ra"))))
+    (build-system python-build-system)
+    (arguments
+     `(;; Prevent creation of the egg. This works around
+       ;; https://debbugs.gnu.org/cgi/bugreport.cgi?bug=20765
+       #:configure-flags '("--root=/")))
+    (native-inputs
+     `(("python-setuptools" ,python-setuptools)))
+    (home-page "https://github.com/tgalal/python-axolotl-curve25519")
+    (synopsis "Python wrapper for curve25519 library")
+    (description "This is a python wrapper for the curve25519 library
+with ed25519 signatures.  The C code was pulled from
+libaxolotl-android.  At the moment this wrapper is meant for use by
+python-axolotl.")
+    (license (list license:gpl3    ; Most files
+                   license:isc)))) ; curve/curve25519-donna.c
+
+(define-public python2-axolotl-curve25519
+  (package-with-python2 python-axolotl-curve25519))
-- 
cgit v1.2.3


From 06ff0837548899fb5a5ee2ce29396db45f5925a1 Mon Sep 17 00:00:00 2001
From: Arun Isaac <arunisaac@systemreboot.net>
Date: Thu, 20 Oct 2016 15:45:04 +0530
Subject: gnu: Add python-axolotl.

* gnu/packages/python.scm (python-axolotl, python2-axolotl): New variables.

Signed-off-by: Leo Famulari <leo@famulari.name>
---
 gnu/packages/python.scm | 44 ++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 44 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index b656a1e32b..5c26906bda 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -80,6 +80,7 @@ (define-module (gnu packages python)
   #:use-module (gnu packages pcre)
   #:use-module (gnu packages perl)
   #:use-module (gnu packages pkg-config)
+  #:use-module (gnu packages protobuf)
   #:use-module (gnu packages readline)
   #:use-module (gnu packages sdl)
   #:use-module (gnu packages statistics)
@@ -11943,3 +11944,46 @@ (define-public python-axolotl-curve25519
 
 (define-public python2-axolotl-curve25519
   (package-with-python2 python-axolotl-curve25519))
+
+(define-public python-axolotl
+  (package
+    (name "python-axolotl")
+    (version "0.1.35")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append
+             "https://github.com/tgalal/python-axolotl/archive/"
+             version ".tar.gz"))
+       (file-name (string-append name "-" version ".tar.gz"))
+       (sha256
+        (base32 "1z8d89p7v40p4bwywjm9h4z28fdvra79ddw06azlkrfjbl7dxmz8"))))
+    (build-system python-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         ;; Don't install tests
+         (add-before 'install 'remove-tests
+           (lambda _
+             (for-each delete-file-recursively
+                       '("axolotl/tests" "build/lib/axolotl/tests"))
+             #t)))
+       ;; Prevent creation of the egg. This works around
+       ;; https://debbugs.gnu.org/cgi/bugreport.cgi?bug=20765
+       #:configure-flags '("--root=/")))
+    (native-inputs
+     `(("python-setuptools" ,python-setuptools)))
+    (propagated-inputs
+     `(("python-axolotl-curve25519" ,python-axolotl-curve25519)
+       ("python-dateutil" ,python-dateutil)
+       ("python-protobuf" ,python-protobuf)
+       ("python-pycrypto" ,python-pycrypto)))
+    (home-page "https://github.com/tgalal/python-axolotl")
+    (synopsis "Python port of libaxolotl-android")
+    (description "This is a python port of libaxolotl-android.  This
+is a ratcheting forward secrecy protocol that works in synchronous and
+asynchronous messaging environments.")
+    (license license:gpl3)))
+
+(define-public python2-axolotl
+  (package-with-python2 python-axolotl))
-- 
cgit v1.2.3


From 683cdbf51b1f1d194f661272c34b91384e6f44e5 Mon Sep 17 00:00:00 2001
From: Leo Famulari <leo@famulari.name>
Date: Sat, 5 Nov 2016 16:33:32 -0400
Subject: gnu: python-axolotl-curve25519: Fix license.

* gnu/packages/python.scm (python-axolotl-curve25519,
python2-axolotl-curve25519)[license]: Replace ISC with BSD-3.
---
 gnu/packages/python.scm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 5c26906bda..54360b3c71 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -11940,7 +11940,7 @@ (define-public python-axolotl-curve25519
 libaxolotl-android.  At the moment this wrapper is meant for use by
 python-axolotl.")
     (license (list license:gpl3    ; Most files
-                   license:isc)))) ; curve/curve25519-donna.c
+                   license:bsd-3)))) ; curve/curve25519-donna.c
 
 (define-public python2-axolotl-curve25519
   (package-with-python2 python-axolotl-curve25519))
-- 
cgit v1.2.3


From 2c62b31619eb4ba6033a0c879751f8d094f26fa2 Mon Sep 17 00:00:00 2001
From: ng0 <ng0@we.make.ritual.n0.is>
Date: Sat, 5 Nov 2016 21:07:48 +0000
Subject: gnu: w3m: Fix the commit string.

* gnu/packages/w3m.scm (w3m)[source]: Fix the commit string.

Signed-off-by: Leo Famulari <leo@famulari.name>
---
 gnu/packages/w3m.scm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/w3m.scm b/gnu/packages/w3m.scm
index 54d4a119f5..216ae657b0 100644
--- a/gnu/packages/w3m.scm
+++ b/gnu/packages/w3m.scm
@@ -42,7 +42,7 @@ (define-public w3m
               ;; maintained.
               (uri (git-reference
                     (url "https://anonscm.debian.org/cgit/collab-maint/w3m.git")
-                    (commit version)))
+                    (commit (string-append "v" version))))
               (file-name (string-append "w3m-" version "-checkout"))
               (sha256
                (base32
-- 
cgit v1.2.3


From 7acc2a3eb394373ab89e25a9fd70e3df918ffd24 Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Sat, 5 Nov 2016 22:10:56 +0200
Subject: gnu: libkate: Update upstream location.

* gnu/packages/xiph.scm (libkate)[source]: Update source uri.
[home-page]: Update project's home-page.
---
 gnu/packages/xiph.scm | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/xiph.scm b/gnu/packages/xiph.scm
index 81e0934889..708b31bf8e 100644
--- a/gnu/packages/xiph.scm
+++ b/gnu/packages/xiph.scm
@@ -229,8 +229,8 @@ (define libkate
    (version "0.4.1")
    (source (origin
             (method url-fetch)
-            (uri (string-append "http://libkate.googlecode.com/files/libkate-"
-                                version ".tar.gz"))
+            (uri (string-append "http://downloads.xiph.org/releases/kate/"
+                                "libkate-" version ".tar.gz"))
             (sha256
              (base32
               "0s3vr2nxfxlf1k75iqpp4l78yf4gil3f0v778kvlngbchvaq23n4"))))
@@ -241,7 +241,7 @@ (define libkate
    (inputs `(("bison" ,bison)
              ("libogg" ,libogg)
              ("libpng" ,libpng)
-("python" ,python-wrapper)
+             ("python" ,python-wrapper)
              ("zlib" ,zlib)))
    (synopsis "Karaoke and text codec for embedding in ogg")
    (description
@@ -257,7 +257,7 @@ (define libkate
 to draw arbitrary shapes, so hand drawing can also be represented by a
 Kate stream.")
    (license license:bsd-3)
-   (home-page "http://code.google.com/p/libkate/")))
+   (home-page "https://wiki.xiph.org/OggKate")))
 
 (define vorbis-tools
   (package
-- 
cgit v1.2.3


From 569fc290b303892128719c53b8f5f15bf6dafd88 Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Sat, 5 Nov 2016 23:14:09 +0200
Subject: gnu: ibus: Update to 1.5.14.

* gnu/packages/ibus.scm (ibus): Update to 1.5.14.
[arguments]: Disable emojis.
[inputs]: Add json-glib.
[home-page]: Use project's new home-page.
---
 gnu/packages/ibus.scm | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/ibus.scm b/gnu/packages/ibus.scm
index 814984f16f..39752bf0c4 100644
--- a/gnu/packages/ibus.scm
+++ b/gnu/packages/ibus.scm
@@ -42,7 +42,7 @@ (define-module (gnu packages ibus)
 (define-public ibus
   (package
    (name "ibus")
-   (version "1.5.11")
+   (version "1.5.14")
    (source (origin
              (method url-fetch)
              (uri (string-append "https://github.com/ibus/ibus/"
@@ -50,10 +50,11 @@ (define-public ibus
                                  version "/ibus-" version ".tar.gz"))
              (sha256
               (base32
-               "1g26llizd26h9sfz4xdq8krhz19hn08pirvfbkk3g89ri8lmm6a9"))))
+               "0g4x02d7j5w1lfn4zvmzsq93h17lajgn9d7hlvr6pws28vz40ax4"))))
    (build-system glib-or-gtk-build-system)
    (arguments
     `(#:tests? #f  ; tests fail because there's no connection to dbus
+      #:configure-flags '("--disable-emoji-dict") ; cannot find emoji.json path
       #:make-flags
       (list "CC=gcc"
             (string-append "pyoverridesdir="
@@ -106,6 +107,7 @@ (define-public ibus
       ("gtk2" ,gtk+-2)
       ("gtk+" ,gtk+)
       ("intltool" ,intltool)
+      ("json-glib" ,json-glib)
       ("libnotify" ,libnotify)
       ("libx11" ,libx11)
       ("setxkbmap" ,setxkbmap)
@@ -127,7 +129,7 @@ (define-public ibus
     "IBus is an input framework providing a full-featured and user-friendly
 input method user interface.  It comes with multilingual input support.  It
 may also simplify input method development.")
-   (home-page "http://ibus.googlecode.com/")
+   (home-page "https://github.com/ibus/ibus/wiki")
    (license lgpl2.1+)))
 
 (define-public ibus-libpinyin
-- 
cgit v1.2.3


From 7f4658983a742072be4e28b227d6349461e9a68b Mon Sep 17 00:00:00 2001
From: Mark H Weaver <mhw@netris.org>
Date: Sun, 6 Nov 2016 02:55:52 -0500
Subject: gnu: epiphany: Update to 3.22.1.

* gnu/packages/gnome.scm (epiphany): Update to 3.22.1.
---
 gnu/packages/gnome.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/gnome.scm b/gnu/packages/gnome.scm
index d5995e5d22..359175f27f 100644
--- a/gnu/packages/gnome.scm
+++ b/gnu/packages/gnome.scm
@@ -3581,7 +3581,7 @@ (define-public simple-scan
 (define-public epiphany
   (package
     (name "epiphany")
-    (version "3.22.0")
+    (version "3.22.1")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://gnome/sources/" name "/"
@@ -3589,7 +3589,7 @@ (define-public epiphany
                                   name "-" version ".tar.xz"))
               (sha256
                (base32
-                "09rscbmyjxzd8wlibn1fbmbwmlwnahzfl1kkcka6dhm121yd2id6"))))
+                "03ncqmb8n06qr88rlwa2rph833gjcwsmxaw2wf1yawadwpnn5cda"))))
     (build-system glib-or-gtk-build-system)
     (arguments
      ;; FIXME: tests run under Xvfb, but fail with:
-- 
cgit v1.2.3