Merge branch 'master' into core-updates

24 files changed, 673 insertions, 93 deletions

diff --git a/gnu/packages/admin.scm b/gnu/packages/admin.scm
index 1f2d0fbf95..953c5b4cf8 100644
--- a/gnu/packages/admin.scm
+++ b/gnu/packages/admin.scm
@@ -6,6 +6,7 @@
 ;;; Copyright © 2015 Taylan Ulrich Bayırlı/Kammer <taylanbayirli@gmail.com>
 ;;; Copyright © 2015 Alex Sassmannshausen <alex.sassmannshausen@gmail.com>
 ;;; Copyright © 2015 Eric Dvorsak <eric@dvorsak.fr>
+;;; Copyright © 2016 Leo Famulari <leo@famulari.name>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -392,7 +393,7 @@ connection alive.")
          (bind-minor-version "9")
          (bind-patch-version "8")
          (bind-release-type "-P")
-         (bind-release-version "2")
+         (bind-release-version "3")
          (bind-version (string-append bind-major-version
                                       "."
                                       bind-minor-version
@@ -508,7 +509,7 @@ connection alive.")
                                         "/bind-" bind-version ".tar.gz"))
                     (sha256
                      (base32
-                      "0agkpmpna7s67la13krn4xlhwhdjpazmljxlq0zbjdwnw4k1k17m"))))
+                      "01qa17479jghy90lb2j8b1bpg3ay6k6aaajpigyirwzsvyc9yj3a"))))
 
                 ;; When cross-compiling, we need the cross Coreutils and sed.
                 ;; Otherwise just use those from %FINAL-INPUTS.
@@ -1377,3 +1378,25 @@ command that learns\".  It works by maintaining a database of the directories
 you use the most from the command line and allows you to \"jump\" to
 frequently used directories by typing only a small pattern.")
     (license license:gpl3+)))
+
+(define-public iftop
+  (package
+    (name "iftop")
+    (version "1.0pre4")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "http://www.ex-parrot.com/~pdw/iftop/download"
+                                  "/iftop-" version ".tar.gz"))
+              (sha256
+               (base32
+                "15sgkdyijb7vbxpxjavh5qm5nvyii3fqcg9mzvw7fx8s6zmfwczp"))))
+    (build-system gnu-build-system)
+    (inputs
+      `(("libpcap" ,libpcap)
+        ("ncurses" ,ncurses)))
+    (synopsis "Monitor network usage")
+    (description "Iftop does for network usage what @command{top} does
+for CPU usage.  It listens to network traffic on a named interface and
+displays a table of current bandwidth usage by pairs of hosts.")
+    (home-page "http://www.ex-parrot.com/~pdw/iftop/")
+    (license license:gpl3)))
diff --git a/gnu/packages/algebra.scm b/gnu/packages/algebra.scm
index dd6838140b..0f17403868 100644
--- a/gnu/packages/algebra.scm
+++ b/gnu/packages/algebra.scm
@@ -238,7 +238,7 @@ fast arithmetic.")
 (define-public arb
   (package
    (name "arb")
-   (version "2.7.0")
+   (version "2.8.1")
    (source (origin
             (method url-fetch)
             (uri (string-append
@@ -247,7 +247,8 @@ fast arithmetic.")
             (file-name (string-append name "-" version ".tar.gz"))
             (sha256
               (base32
-                "1rwkffs57v8mry63rq8l2dyw69zfs9rg5fpbfllqp3nkjnkp1fly"))))
+                "04hhcpshfkcq9fr4hixbhpps50yf9drk62xgkvlcaj5kb4nyrx7l"))
+            (patches (map search-patch '("arb-ldconfig.patch")))))
    (build-system gnu-build-system)
    (propagated-inputs
     `(("flint" ,flint))) ; flint.h is included by arf.h
diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm
index 3cc5cebc2c..0823aad91e 100644
--- a/gnu/packages/audio.scm
+++ b/gnu/packages/audio.scm
@@ -3,7 +3,7 @@
 ;;; Copyright © 2015 Taylan Ulrich Bayırlı/Kammer <taylanbayirli@gmail.com>
 ;;; Copyright © 2015 Andreas Enge <andreas@enge.fr>
 ;;; Copyright © 2015 Alex Kost <alezost@gmail.com>
-;;; Copyright © 2015 Mark H Weaver <mhw@netris.org>
+;;; Copyright © 2015, 2016 Mark H Weaver <mhw@netris.org>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -1535,14 +1535,14 @@ surround and reverb.")
 (define-public libxmp
   (package
     (name "libxmp")
-    (version "4.3.8")
+    (version "4.3.10")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://sourceforge/xmp/libxmp/"
                                   name "-" version ".tar.gz"))
               (sha256
                (base32
-                "0h06091hlpgc6ds4pjmfq8sx4snw7av3nhny180q4pwfyasjb6ny"))))
+                "1gm5xa0ca7ypcbj3bkmj3k1vvzl7nkch8gjyrm8p1a9vgzr0n761"))))
     (build-system gnu-build-system)
     (home-page "http://xmp.sourceforge.net/")
     (synopsis "Module player library")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 314d0ad322..a9df676fc6 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -654,6 +654,73 @@ gapped, local, and paired-end alignment modes.")
     (supported-systems '("x86_64-linux"))
     (license license:gpl3+)))
 
+(define-public tophat
+  (package
+    (name "tophat")
+    (version "2.1.0")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append
+                    "http://ccb.jhu.edu/software/tophat/downloads/tophat-"
+                    version ".tar.gz"))
+              (sha256
+               (base32
+                "168zlzykq622zbgkh90a90f1bdgsxkscq2zxzbj8brq80hbjpyp7"))
+              (patches (list (search-patch "tophat-build-with-later-seqan.patch")))
+              (modules '((guix build utils)))
+              (snippet
+               '(begin
+                  ;; Remove bundled SeqAn and samtools
+                  (delete-file-recursively "src/SeqAn-1.3")
+                  (delete-file-recursively "src/samtools-0.1.18")
+                  #t))))
+    (build-system gnu-build-system)
+    (arguments
+     '(#:parallel-build? #f ; not supported
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'use-system-samtools
+           (lambda* (#:key inputs #:allow-other-keys)
+             (substitute* "src/Makefile.in"
+               (("(noinst_LIBRARIES = )\\$\\(SAMLIB\\)" _ prefix) prefix)
+               (("\\$\\(SAMPROG\\): \\$\\(SAMLIB\\)") "")
+               (("SAMPROG = samtools_0\\.1\\.18") "")
+               (("\\$\\(samtools_0_1_18_SOURCES\\)") "")
+               (("am__EXEEXT_1 = samtools_0\\.1\\.18\\$\\(EXEEXT\\)") ""))
+             (substitute* '("src/common.cpp"
+                            "src/tophat.py")
+               (("samtools_0.1.18") (which "samtools")))
+             (substitute* '("src/common.h"
+                            "src/bam2fastx.cpp")
+               (("#include \"bam.h\"") "#include <samtools/bam.h>")
+               (("#include \"sam.h\"") "#include <samtools/sam.h>"))
+             (substitute* '("src/bwt_map.h"
+                            "src/map2gtf.h"
+                            "src/align_status.h")
+               (("#include <bam.h>") "#include <samtools/bam.h>")
+               (("#include <sam.h>") "#include <samtools/sam.h>"))
+             #t)))))
+    (inputs
+     `(("boost" ,boost)
+       ("bowtie" ,bowtie)
+       ("samtools" ,samtools-0.1)
+       ("ncurses" ,ncurses)
+       ("python" ,python-2)
+       ("perl" ,perl)
+       ("zlib" ,zlib)
+       ("seqan" ,seqan)))
+    (home-page "http://ccb.jhu.edu/software/tophat/index.shtml")
+    (synopsis "Spliced read mapper for RNA-Seq data")
+    (description
+     "TopHat is a fast splice junction mapper for nucleotide sequence
+reads produced by the RNA-Seq method.  It aligns RNA-Seq reads to
+mammalian-sized genomes using the ultra high-throughput short read
+aligner Bowtie, and then analyzes the mapping results to identify
+splice junctions between exons.")
+    ;; TopHat is released under the Boost Software License, Version 1.0
+    ;; See https://github.com/infphilo/tophat/issues/11#issuecomment-121589893
+    (license license:boost1.0)))
+
 (define-public bwa
   (package
     (name "bwa")
@@ -915,6 +982,64 @@ files between different genome assemblies.  It supports most commonly used
 file formats including SAM/BAM, Wiggle/BigWig, BED, GFF/GTF, VCF.")
     (license license:gpl2+)))
 
+(define-public cufflinks
+  (package
+    (name "cufflinks")
+    (version "2.2.1")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "http://cole-trapnell-lab.github.io/"
+                                  "cufflinks/assets/downloads/cufflinks-"
+                                  version ".tar.gz"))
+              (sha256
+               (base32
+                "1bnm10p8m7zq4qiipjhjqb24csiqdm1pwc8c795z253r2xk6ncg8"))))
+    (build-system gnu-build-system)
+    (arguments
+     `(#:make-flags
+       (list
+        ;; The includes for "eigen" are located in a subdirectory.
+        (string-append "EIGEN_CPPFLAGS="
+                       "-I" (assoc-ref %build-inputs "eigen")
+                       "/include/eigen3/")
+        ;; Cufflinks must be linked with various boost libraries.
+        (string-append "LDFLAGS="
+                       (string-join '("-lboost_system"
+                                      "-lboost_serialization"
+                                      "-lboost_thread"))))
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'fix-search-for-bam
+          (lambda _
+            (substitute* '("ax_bam.m4"
+                           "configure"
+                           "src/hits.h")
+              (("<bam/sam\\.h>") "<samtools/sam.h>")
+              (("<bam/bam\\.h>") "<samtools/bam.h>")
+              (("<bam/version\\.hpp>") "<samtools/version.h>"))
+            #t)))
+       #:configure-flags
+       (list (string-append "--with-bam="
+                            (assoc-ref %build-inputs "samtools")))))
+    (inputs
+     `(("eigen" ,eigen)
+       ("samtools" ,samtools-0.1)
+       ("htslib" ,htslib)
+       ("boost" ,boost)
+       ("python" ,python-2)
+       ("zlib" ,zlib)))
+    (home-page "http://cole-trapnell-lab.github.io/cufflinks/")
+    (synopsis "Transcriptome assembly and RNA-Seq expression analysis")
+    (description
+     "Cufflinks assembles RNA transcripts, estimates their abundances,
+and tests for differential expression and regulation in RNA-Seq
+samples.  It accepts aligned RNA-Seq reads and assembles the
+alignments into a parsimonious set of transcripts.  Cufflinks then
+estimates the relative abundances of these transcripts based on how
+many reads support each one, taking into account biases in library
+preparation protocols.")
+    (license license:boost1.0)))
+
 (define-public cutadapt
   (package
     (name "cutadapt")
@@ -3016,40 +3141,107 @@ optimized for modern read lengths of 100 bases or higher, and takes advantage
 of these reads to align data quickly through a hash-based indexing scheme.")
     (license license:asl2.0)))
 
+(define-public sortmerna
+  (package
+    (name "sortmerna")
+    (version "2.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append
+             "https://github.com/biocore/sortmerna/archive/"
+             version ".tar.gz"))
+       (file-name (string-append name "-" version ".tar.gz"))
+       (sha256
+        (base32
+         "1670a92x1vvkacnvgr2i5xac3ls6lp4pc3n0bccnmllsnymggcf0"))))
+    (build-system gnu-build-system)
+    (outputs '("out"      ;for binaries
+               "db"))     ;for sequence databases
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (replace 'install
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let* ((out   (assoc-ref outputs "out"))
+                    (bin   (string-append out "/bin"))
+                    (db    (assoc-ref outputs "db"))
+                    (share
+                     (string-append db "/share/sortmerna/rRNA_databases")))
+               (install-file "sortmerna" bin)
+               (install-file "indexdb_rna" bin)
+               (for-each (lambda (file)
+                           (install-file file share))
+                         (find-files "rRNA_databases" ".*fasta"))
+               #t))))))
+    (home-page "http://bioinfo.lifl.fr/RNA/sortmerna")
+    (synopsis "Biological sequence analysis tool for NGS reads")
+    (description
+     "SortMeRNA is a biological sequence analysis tool for filtering, mapping
+and operational taxonomic unit (OTU) picking of next generation
+sequencing (NGS) reads.  The core algorithm is based on approximate seeds and
+allows for fast and sensitive analyses of nucleotide sequences.  The main
+application of SortMeRNA is filtering rRNA from metatranscriptomic data.")
+    (license license:lgpl3)))
+
 (define-public star
   (package
     (name "star")
-    (version "2.4.2a")
+    (version "2.5.1b")
     (source (origin
               (method url-fetch)
-              (uri (string-append
-                    "https://github.com/alexdobin/STAR/archive/STAR_"
-                    version ".tar.gz"))
+              (uri (string-append "https://github.com/alexdobin/STAR/archive/"
+                                  version ".tar.gz"))
+              (file-name (string-append name "-" version ".tar.gz"))
               (sha256
                (base32
-                "1c3rnm7r5l0kl3d04gl1g7938xqf1c2l0mla87rlplqg1hcns5mc"))
+                "0wzcfhkg10apnh0y73xlarfa79xxwxdizicbdl11wb48awk44iq4"))
               (modules '((guix build utils)))
               (snippet
-               '(substitute* "source/Makefile"
-                  (("/bin/rm") "rm")))))
+               '(begin
+                  (substitute* "source/Makefile"
+                    (("/bin/rm") "rm"))
+                  ;; Remove pre-built binaries and bundled htslib sources.
+                  (delete-file-recursively "bin/MacOSX_x86_64")
+                  (delete-file-recursively "bin/Linux_x86_64")
+                  (delete-file-recursively "source/htslib")
+                  #t))))
     (build-system gnu-build-system)
     (arguments
      '(#:tests? #f ;no check target
        #:make-flags '("STAR")
        #:phases
-       (alist-cons-after
-        'unpack 'enter-source-dir (lambda _ (chdir "source"))
-        (alist-replace
-         'install
-         (lambda* (#:key outputs #:allow-other-keys)
-           (let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
-             (install-file "STAR" bin)))
-         (alist-delete
-          'configure %standard-phases)))))
+       (modify-phases %standard-phases
+         (add-after 'unpack 'enter-source-dir
+           (lambda _ (chdir "source") #t))
+         (add-after 'enter-source-dir 'do-not-use-bundled-htslib
+           (lambda _
+             (substitute* "Makefile"
+               (("(Depend.list: \\$\\(SOURCES\\) parametersDefault\\.xxd) htslib"
+                 _ prefix) prefix))
+             (substitute* '("BAMfunctions.cpp"
+                            "signalFromBAM.h"
+                            "bam_cat.h"
+                            "bam_cat.c"
+                            "STAR.cpp"
+                            "bamRemoveDuplicates.cpp")
+               (("#include \"htslib/([^\"]+\\.h)\"" _ header)
+                (string-append "#include <" header ">")))
+             (substitute* "IncludeDefine.h"
+               (("\"htslib/(htslib/[^\"]+.h)\"" _ header)
+                (string-append "<" header ">")))
+             #t))
+         (replace 'install
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
+               (install-file "STAR" bin))
+             #t))
+         (delete 'configure))))
     (native-inputs
      `(("vim" ,vim))) ; for xxd
     (inputs
-     `(("zlib" ,zlib)))
+     `(("htslib" ,htslib)
+       ("zlib" ,zlib)))
     (home-page "https://github.com/alexdobin/STAR")
     (synopsis "Universal RNA-seq aligner")
     (description
@@ -4002,7 +4194,7 @@ genomic intervals.  In addition, it can use BAM or BigWig files as input.")
 (define-public r-qtl
  (package
   (name "r-qtl")
-  (version "1.37-11")
+  (version "1.38-4")
   (source
    (origin
     (method url-fetch)
@@ -4010,7 +4202,7 @@ genomic intervals.  In addition, it can use BAM or BigWig files as input.")
                         version ".tar.gz"))
     (sha256
      (base32
-      "0h20d36mww7ljp51pfs66xq33yq4b4fwq9nsh02dpmfhlaxgx1xi"))))
+      "0rv9xhp8lyldpgwxqirhyjqvg07dr5x4x1x2jpyj37dada9ccyx3"))))
   (build-system r-build-system)
   (home-page "http://rqtl.org/")
   (synopsis "R package for analyzing QTL experiments in genetics")
diff --git a/gnu/packages/bittorrent.scm b/gnu/packages/bittorrent.scm
index 967580d158..94383dba20 100644
--- a/gnu/packages/bittorrent.scm
+++ b/gnu/packages/bittorrent.scm
@@ -1,6 +1,7 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2014 Taylan Ulrich Bayirli/Kammer <taylanbayirli@gmail.com>
 ;;; Copyright © 2014, 2015 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2016 Leo Famulari <leo@famulari.name>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -21,6 +22,7 @@
   #:use-module (guix packages)
   #:use-module (guix download)
   #:use-module (guix build-system gnu)
+  #:use-module (guix build-system python)
   #:use-module (guix build-system glib-or-gtk)
   #:use-module ((guix licenses) #:prefix l:)
   #:use-module (gnu packages libevent)
@@ -33,6 +35,7 @@
   #:use-module (gnu packages gtk)
   #:use-module (gnu packages check)
   #:use-module (gnu packages ncurses)
+  #:use-module (gnu packages python)
   #:use-module (gnu packages curl)
   #:use-module (gnu packages cyrus-sasl)
   #:use-module (gnu packages tls))
@@ -148,3 +151,44 @@ full encryption, DHT, PEX, and Magnet Links.  It can also be controlled via
 XML-RPC over SCGI.")
     (home-page "https://github.com/rakshasa/rtorrent")
     (license l:gpl2+)))
+
+(define-public transmission-remote-cli
+  (package
+    (name "transmission-remote-cli")
+    (version "1.7.1")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "https://github.com/fagga/"
+                                  "transmission-remote-cli/archive/v"
+                                  version ".tar.gz"))
+              (file-name (string-append name "-" version ".tar.gz"))
+              (sha256
+               (base32
+                "1y0hkpcjf6jw9xig8yf484hbhy63nip0pkchx401yxj81m25l4z9"))))
+    (build-system python-build-system)
+    (arguments
+     `(#:python ,python-2 ; only supports Python 2
+       #:tests? #f ; no test suite
+       #:phases (modify-phases %standard-phases
+                  ;; The software is just a Python script that must be
+                  ;; copied into place.
+                  (delete 'build)
+                  (replace 'install
+                    (lambda* (#:key outputs #:allow-other-keys)
+                      (let* ((out (assoc-ref outputs "out"))
+                             (bin (string-append out "/bin"))
+                             (man (string-append out "/share/man/man1"))
+                             ;; FIXME install zsh completions
+                             (completions (string-append out "/etc/bash_completion.d")))
+                        (install-file "transmission-remote-cli" bin)
+                        (install-file "transmission-remote-cli.1" man)
+                        (install-file
+                          (string-append
+                            "completion/bash/"
+                            "transmission-remote-cli-bash-completion.sh")
+                          completions)))))))
+    (synopsis "Console client for the Transmission BitTorrent daemon")
+    (description "Transmission-remote-cli is a console client, with a curses
+interface, for the Transmission BitTorrent daemon.")
+    (home-page "https://github.com/fagga/transmission-remote-cli")
+    (license l:gpl3+)))
diff --git a/gnu/packages/debug.scm b/gnu/packages/debug.scm
index dc94f97657..72fd993037 100644
--- a/gnu/packages/debug.scm
+++ b/gnu/packages/debug.scm
@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2014, 2015 Eric Bavier <bavier@member.fsf.org>
+;;; Copyright © 2014, 2015, 2016 Eric Bavier <bavier@member.fsf.org>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -169,7 +169,7 @@ tools that process C/C++ code.")
                    (_                "UNSUPPORTED"))))
     (package
       (name "american-fuzzy-lop")
-      (version "1.86b")             ;It seems all releases have the 'b' suffix
+      (version "1.96b")             ;It seems all releases have the 'b' suffix
       (source
        (origin
          (method url-fetch)
@@ -177,7 +177,7 @@ tools that process C/C++ code.")
                              "afl-" version ".tgz"))
          (sha256
           (base32
-           "1by9ncf6lgcyibzqwyla34jv64sd66mn8zhgjz2pcgsds51qwn0r"))))
+           "0z7j231p6v2h1dxxijgdzj1lq1lxr8cxllwf6iyv7p4ki5pv1gh3"))))
       (build-system gnu-build-system)
       (inputs
        `(("custom-qemu"
@@ -190,11 +190,13 @@ tools that process C/C++ code.")
              ;; afl only supports using a single afl-qemu-trace executable, so
              ;; we only build qemu for the native target.
              (arguments
-              `(#:configure-flags
-                (list (string-append "--target-list=" ,machine "-linux-user"))
-                #:modules ((srfi srfi-1)
+              `(#:modules ((srfi srfi-1)
                            ,@%gnu-build-system-modules)
                 ,@(substitute-keyword-arguments (package-arguments qemu-2.3.0)
+                    ((#:configure-flags config-flags)
+                     ``(,(string-append "--target-list=" ,machine "-linux-user")
+                        ,@(remove (λ (f) (string-prefix? "--target-list=" f))
+                                  ,config-flags)))
                     ((#:phases qemu-phases)
                      `(modify-phases ,qemu-phases
                         (add-after
@@ -236,8 +238,8 @@ tools that process C/C++ code.")
                      (lambda* (#:key inputs outputs #:allow-other-keys)
                        (let ((qemu (assoc-ref inputs "custom-qemu"))
                              (out  (assoc-ref outputs "out")))
-                         (copy-file (string-append qemu "/bin/qemu-" ,machine)
-                                    (string-append out "/bin/afl-qemu-trace"))
+                         (symlink (string-append qemu "/bin/qemu-" ,machine)
+                                  (string-append out "/bin/afl-qemu-trace"))
                          #t)))
                     (delete 'check))))
       (supported-systems (fold delete
diff --git a/gnu/packages/dns.scm b/gnu/packages/dns.scm
index 8357dad21e..ef07f30adf 100644
--- a/gnu/packages/dns.scm
+++ b/gnu/packages/dns.scm
@@ -1,5 +1,7 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2015 Taylan Ulrich Bayırlı/Kammer <taylanbayirli@gmail.com>
+;;; Copyright © 2016 Mark H Weaver <mhw@netris.org>
+;;; Copyright © 2016 Ricardo Wurmus <rekado@elephly.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -63,14 +65,14 @@ and BOOTP/TFTP for network booting of diskless machines.")
 (define-public bind-utils
   (package
     (name "bind-utils")
-    (version "9.10.3-P2")
+    (version "9.10.3-P3")
     (source (origin
               (method url-fetch)
               (uri (string-append "http://ftp.isc.org/isc/bind9/" version
                                   "/bind-" version ".tar.gz"))
               (sha256
                (base32
-                "1kbfzml37sx4r2xi4gq48ji8w5kckd1f6gdn6pk6njqdmh8ijv2a"))))
+                "10yblk8qbb85qxakzdjy5qmqvqj4rlcqsqvlkriglampzg8i0239"))))
     (build-system gnu-build-system)
     (inputs
      ;; it would be nice to add GeoIP and gssapi once there is package
@@ -89,20 +91,24 @@ and BOOTP/TFTP for network booting of diskless machines.")
                             (assoc-ref %build-inputs "mysql"))
              (string-append "--with-pkcs11="
                             (assoc-ref %build-inputs "p11-kit")))
+       #:modules ((srfi srfi-1)
+                  (srfi srfi-26)
+                  ,@%gnu-build-system-modules)
        #:phases
-       (alist-replace
-        'build
-        (lambda _
-          (and (zero? (system* "make" "-C" "lib/dns"))
-               (zero? (system* "make" "-C" "lib/isc"))
-               (zero? (system* "make" "-C" "lib/bind9"))
-               (zero? (system* "make" "-C" "lib/isccfg"))
-               (zero? (system* "make" "-C" "lib/lwres"))
-               (zero? (system* "make" "-C" "bin/dig"))))
-        (alist-replace
-         'install
-         (lambda _ (zero? (system* "make" "-C" "bin/dig" "install")))
-         %standard-phases))))
+       (let ((libs '("dns" "isc" "bind9" "isccfg" "lwres"))
+             (bins '("dig" "nsupdate")))
+         (modify-phases %standard-phases
+           (replace 'build
+             (lambda _
+               (every (lambda (dir)
+                        (zero? (system* "make" "-C" dir)))
+                      (append (map (cut string-append "lib/" <>) libs)
+                              (map (cut string-append "bin/" <>) bins)))))
+           (replace 'install
+             (lambda _
+               (every (lambda (dir)
+                        (zero? (system* "make" "-C" dir "install")))
+                      (map (cut string-append "bin/" <>) bins))))))))
     (home-page "https://www.isc.org/downloads/bind/")
     (synopsis "Tools for querying nameservers")
     (description
diff --git a/gnu/packages/ebook.scm b/gnu/packages/ebook.scm
index 718e8b3e50..a551c1d075 100644
--- a/gnu/packages/ebook.scm
+++ b/gnu/packages/ebook.scm
@@ -60,7 +60,7 @@
 (define-public calibre
   (package
     (name "calibre")
-    (version "2.48.0")
+    (version "2.49.0")
     (source
       (origin
         (method url-fetch)
@@ -69,7 +69,7 @@
                             version ".tar.xz"))
         (sha256
           (base32
-           "0bjzw806czqxkhq9qqkhff8bhfc428pijkidb1h6gr47jqdp4hpg"))
+           "0jc476pg07c0nwccprhwgjdlvvb2fdzza9xrjqzc0c42c5v7qzxa"))
         ;; Remove non-free or doubtful code, see
         ;; https://lists.gnu.org/archive/html/guix-devel/2015-02/msg00478.html
         (modules '((guix build utils)))
diff --git a/gnu/packages/enlightenment.scm b/gnu/packages/enlightenment.scm
index 9fdcd42a27..3fec6c6fc7 100644
--- a/gnu/packages/enlightenment.scm
+++ b/gnu/packages/enlightenment.scm
@@ -1,7 +1,7 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2015 Tomáš Čech <sleep_walker@suse.cz>
 ;;; Copyright © 2015 Daniel Pimentel <d4n1@member.fsf.org>
-;;; Copyright © 2015 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2015, 2016 Efraim Flashner <efraim@flashner.co.il>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -271,7 +271,7 @@ Libraries with some extra bells and whistles.")
 (define-public enlightenment
   (package
     (name "enlightenment")
-    (version "0.20.2")
+    (version "0.20.3")
     (source (origin
               (method url-fetch)
               (uri
@@ -279,7 +279,7 @@ Libraries with some extra bells and whistles.")
                               name "/" name "-" version ".tar.xz"))
               (sha256
                (base32
-                 "0faxky7lqd133jjjkr4c40kwwjhqc51ww10l3yy63671rfjhj424"))))
+                 "19z3bwdzwpzwi330l5g5mj7xy6wy8xrc39zivjhm0d1ql3fh649j"))))
     (build-system gnu-build-system)
     (arguments
      `(#:configure-flags '("--enable-mount-eeze")))
diff --git a/gnu/packages/grue-hunter.scm b/gnu/packages/grue-hunter.scm
index 29404fcfb4..71eee96daf 100644
--- a/gnu/packages/grue-hunter.scm
+++ b/gnu/packages/grue-hunter.scm
@@ -32,7 +32,7 @@
     (source
      (origin
       (method url-fetch)
-      (uri (string-append "http://jxself.org/" name ".tar.gz"))
+      (uri (string-append "https://jxself.org/" name ".tar.gz"))
       (sha256
        (base32
         "1hjcpy5439qs3v2zykis7hsi0i17zjs62gks3zd8mnfw9ni4i2h3"))))
diff --git a/gnu/packages/lego.scm b/gnu/packages/lego.scm
new file mode 100644
index 0000000000..d47be5dfb4
--- /dev/null
+++ b/gnu/packages/lego.scm
@@ -0,0 +1,67 @@
+;;; GNU Guix --- Functional package management for GNU
+;;; Copyright © 2016 Eric Bavier <bavier@member.fsf.org>
+;;;
+;;; This file is part of GNU Guix.
+;;;
+;;; GNU Guix is free software; you can redistribute it and/or modify it
+;;; under the terms of the GNU General Public License as published by
+;;; the Free Software Foundation; either version 3 of the License, or (at
+;;; your option) any later version.
+;;;
+;;; GNU Guix is distributed in the hope that it will be useful, but
+;;; WITHOUT ANY WARRANTY; without even the implied warranty of
+;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+;;; GNU General Public License for more details.
+;;;
+;;; You should have received a copy of the GNU General Public License
+;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
+
+(define-module (gnu packages lego)
+  #:use-module ((guix licenses) #:prefix license:)
+  #:use-module (guix download)
+  #:use-module (guix packages)
+  #:use-module (guix build-system gnu)
+  #:use-module (gnu packages)
+  #:use-module (gnu packages bison)
+  #:use-module (gnu packages flex))
+
+(define-public nqc
+  (package
+    (name "nqc")
+    (version "3.1.r6")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "http://bricxcc.sourceforge.net/nqc/release/"
+                                  "nqc-" version ".tgz"))
+              (sha256
+               (base32
+                "0rp7pzr8xrdxpv75c2mi8zszzz2ypli4vvzxiic7mbrryrafdmdz"))))
+    (build-system gnu-build-system)
+    (native-inputs
+     `(("bison" ,bison)
+       ("flex" ,flex)))
+    (arguments
+     '(#:tests? #f                      ;no tests
+       #:make-flags (list (string-append "PREFIX=" %output))
+       #:phases (modify-phases %standard-phases
+                  (delete 'configure)
+                  (add-before 'build 'rm-generated
+                    ;; Regenerating compiler/lexer.cpp avoids an 'undefined
+                    ;; reference to `isatty(int)'' error.
+                    (lambda _
+                      (for-each delete-file
+                                '("compiler/lexer.cpp"
+                                  "compiler/parse.cpp"))
+                      #t))
+                  (add-after 'unpack 'deal-with-tarbomb
+                    (lambda _
+                      (chdir "..")      ;tarbomb
+                      #t)))))
+    (home-page "http://bricxcc.sourceforge.net/nqc/")
+    (synopsis "C-like language for Lego's MINDSTORMS")
+    (description
+     "Not Quite C (NQC) is a simple language for programming several Lego
+MINDSTORMS products.  The preprocessor and control structures of NQC are very
+similar to C.  NQC is not a general purpose language -- there are many
+restrictions that stem from limitations of the standard RCX firmware.")
+    (license license:mpl1.0)))
diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm
index 3ca4ef1868..6500aa51f5 100644
--- a/gnu/packages/linux.scm
+++ b/gnu/packages/linux.scm
@@ -2,10 +2,10 @@
 ;;; Copyright © 2012, 2013, 2014, 2015 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2013, 2014, 2015 Andreas Enge <andreas@enge.fr>
 ;;; Copyright © 2012 Nikita Karetnikov <nikita@karetnikov.org>
-;;; Copyright © 2014, 2015 Mark H Weaver <mhw@netris.org>
+;;; Copyright © 2014, 2015, 2016 Mark H Weaver <mhw@netris.org>
 ;;; Copyright © 2015 Federico Beffa <beffa@fbengineering.ch>
 ;;; Copyright © 2015 Taylan Ulrich Bayırlı/Kammer <taylanbayirli@gmail.com>
-;;; Copyright © 2015 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2015, 2016 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2016 Christopher Allan Webber <cwebber@dustycloud.org>
 ;;;
 ;;; This file is part of GNU Guix.
@@ -286,7 +286,9 @@ for SYSTEM, or #f if there is no configuration for SYSTEM."
              (uri (linux-libre-urls version))
              (sha256
               (base32
-               "1839xsaifs7vvyblzin8jps0gqi10xmz1l9p4x0j27vmdj39jgpm"))))
+               "1839xsaifs7vvyblzin8jps0gqi10xmz1l9p4x0j27vmdj39jgpm"))
+             (patches
+              (list (search-patch "linux-libre-CVE-2016-0728.patch")))))
     (build-system gnu-build-system)
     (supported-systems '("x86_64-linux" "i686-linux"))
     (native-inputs `(("perl" ,perl)
@@ -1234,7 +1236,7 @@ processes currently causing I/O.")
 (define-public fuse
   (package
     (name "fuse")
-    (version "2.9.4")
+    (version "2.9.5")
     (source (origin
               (method url-fetch)
               (uri (let ((version-with-underscores
@@ -1245,7 +1247,7 @@ processes currently causing I/O.")
                        "/fuse-" version ".tar.gz")))
               (sha256
                (base32
-                "1qbwp63a2bp0bchabkwiyzszi9x5krlk2pwk2is6g35gyszw1sbb"))))
+                "1dfvbi1p57svbv2sfnbqwpnsk219spvjnlapf35azhgzqlf3g7sp"))))
     (build-system gnu-build-system)
     (inputs `(("util-linux" ,util-linux)))
     (arguments
diff --git a/gnu/packages/mail.scm b/gnu/packages/mail.scm
index 1057564b39..d41479e83f 100644
--- a/gnu/packages/mail.scm
+++ b/gnu/packages/mail.scm
@@ -8,7 +8,8 @@
 ;;; Copyright © 2015 Paul van der Walt <paul@denknerd.org>
 ;;; Copyright © 2015 Eric Bavier <bavier@member.fsf.org>
 ;;; Copyright © 2015 Andreas Enge <andreas@enge.fr>
-;;; Copyright © 2015 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2015, 2016 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2016 Christopher Allan Webber <cwebber@dustycloud.org>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -519,7 +520,7 @@ MailCore 2.")
 (define-public claws-mail
   (package
     (name "claws-mail")
-    (version "3.13.1")
+    (version "3.13.2")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -527,7 +528,7 @@ MailCore 2.")
                     ".tar.xz"))
               (sha256
                (base32
-                "049av7r0xhjjjm1p93l2ns3xisvn125v3ncqar23cqjzgcichg5d"))))
+                "1l8ankx0qpq1ix1an8viphcf11ksh53jsrm1xjmq8cjbh5910wva"))))
     (build-system gnu-build-system)
     (native-inputs `(("pkg-config" ,pkg-config)))
     (inputs `(("bogofilter" ,bogofilter)
@@ -1014,4 +1015,32 @@ compatibility shims for the @command{sendmail}, @command{mailq}, and
 @command{newaliases} commands.")
     (license gpl2+)))
 
+(define-public fdm
+  (package
+    (name "fdm")
+    (version "1.9")
+    (source (origin
+             (method url-fetch)
+             (uri (string-append "https://github.com/nicm/fdm/releases/download/"
+                                 version "/fdm-"
+                                 version ".tar.gz"))
+             (file-name (string-append name "-" version ".tar.gz"))
+             (sha256
+               (base32 "054rscijahiza5f9qha79rg3siji3bk5mk10f8c2vqx7m4w6qh8n"))))
+    (build-system gnu-build-system)
+    (inputs
+     `(("tdb" ,tdb)
+       ("openssl" ,openssl)
+       ("zlib" ,zlib)))
+    (home-page "https://github.com/nicm/fdm")
+    (synopsis "Mail Retrieval Agent (MRA) and Mail Delivery Agent (MDA)")
+    (description "fdm is a program designed to fetch mail from POP3
+or IMAP servers, or receive local mail from stdin, and
+deliver it in various ways.")
+    (license
+     ;; Why point to a source file?  Well, all the individual files have a
+     ;; copy of this license in their headers, but there's no seprate file
+     ;; with that information.
+     (non-copyleft "https://github.com/nicm/fdm/blob/master/command.c"))))
+
 ;;; mail.scm ends here
diff --git a/gnu/packages/messaging.scm b/gnu/packages/messaging.scm
index 956045d420..23c7a0bbdd 100644
--- a/gnu/packages/messaging.scm
+++ b/gnu/packages/messaging.scm
@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2014, 2015 Mark H Weaver <mhw@netris.org>
+;;; Copyright © 2014, 2015, 2016 Mark H Weaver <mhw@netris.org>
 ;;; Copyright © 2014 Julien Lepiller <julien@lepiller.eu>
 ;;; Copyright © 2015 Taylan Ulrich Bayırlı/Kammer <taylanbayirli@gmail.com>
 ;;; Copyright © 2015 Andreas Enge <andreas@enge.fr>
@@ -425,7 +425,7 @@ was initially a fork of xmpppy, but is using non-blocking sockets.")
 (define-public gajim
   (package
     (name "gajim")
-    (version "0.16.4")
+    (version "0.16.5")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://gajim.org/downloads/"
@@ -433,10 +433,17 @@ was initially a fork of xmpppy, but is using non-blocking sockets.")
                                   "/gajim-" version ".tar.bz2"))
               (sha256
                (base32
-                "0zyfs7q1qg8iqszr8l1gb18gqla6zrrfsgpmbxblpi9maqxas5i1"))))
+                "14fhcqnkqygh91132dnf1idayj4r3iqbwb44sd3mxv20n6ribh55"))))
     (build-system gnu-build-system)
     (arguments
-     `(#:phases
+     `(;; The only check done by gajim-0.16.x is to check that the
+       ;; translations are up-to-date, and in 0.16.5 they are not, so
+       ;; "make check" fails.  Therefore, we disable tests for now.
+       ;;
+       ;; XXX TODO Try re-enabling tests in gajim-0.16.6 or later.
+       ;;
+       #:tests? #f
+       #:phases
        (modify-phases %standard-phases
          (add-after 'install 'wrap-program
           (lambda* (#:key outputs #:allow-other-keys)
diff --git a/gnu/packages/music.scm b/gnu/packages/music.scm
index bfc90c1eeb..a60ba4bccd 100644
--- a/gnu/packages/music.scm
+++ b/gnu/packages/music.scm
@@ -1,6 +1,6 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2014 Eric Bavier <bavier@member.fsf.org>
-;;; Copyright © 2015 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2015, 2016 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2015 Paul van der Walt <paul@denknerd.org>
 ;;;
 ;;; This file is part of GNU Guix.
@@ -328,7 +328,11 @@ you to define complex tempo maps for entire songs or performances.")
 music.  Music is input in a text file containing control sequences which are
 interpreted by LilyPond to produce the final document.  It is extendable with
 Guile.")
-    (license license:gpl3+)))
+    (license license:gpl3+)
+
+    ;; On armhf and mips64el, building the documentation sometimes leads to
+    ;; more than an hour of silence, so double the max silent time.
+    (properties `((max-silent-time . 7200)))))
 
 (define-public non-sequencer
   ;; The latest tagged release is three years old and uses a custom build
@@ -957,7 +961,7 @@ capabilities, custom envelopes, effects, etc.")
 (define-public yoshimi
   (package
     (name "yoshimi")
-    (version "1.3.7.1")
+    (version "1.3.8.2")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://sourceforge/yoshimi/"
@@ -965,7 +969,7 @@ capabilities, custom envelopes, effects, etc.")
                                   "/yoshimi-" version ".tar.bz2"))
               (sha256
                (base32
-                "13xc1x8jrr2rn26jx4dini692ww3771d5j5xf7f56ixqr7mmdhvz"))))
+                "0wl4ln6v1nkkx56kfah23chyrhga2vi93i82g0s200c4s4184xr8"))))
     (build-system cmake-build-system)
     (arguments
      `(#:tests? #f ; there are no tests
@@ -1036,3 +1040,41 @@ graphically in the terminal.  It is built on a full-featured subtractive
 synthesis engine.  Notes and parameter changes may be entered via MIDI or the
 computer's keyboard.")
     (license license:gpl3+)))
+
+(define-public qtractor
+  (package
+    (name "qtractor")
+    (version "0.7.3")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "http://downloads.sourceforge.net/qtractor/"
+                                  "qtractor-" version ".tar.gz"))
+              (sha256
+               (base32
+                "1vy4297myyqk0k58nzybgvgklckhngpdcnmp98k0rq98dirclbl7"))))
+    (build-system gnu-build-system)
+    (arguments `(#:tests? #f)) ; no "check" target
+    (inputs
+     `(("qt" ,qt)
+       ("alsa-lib" ,alsa-lib)
+       ("jack" ,jack-1)
+       ("libsndfile" ,libsndfile)
+       ("ladspa" ,ladspa)
+       ("lv2" ,lv2)
+       ("lilv" ,lilv)
+       ("suil" ,suil)
+       ("libsamplerate" ,libsamplerate)
+       ("libvorbis" ,libvorbis)
+       ("libmad" ,libmad)
+       ("rubberband" ,rubberband)
+       ("liblo" ,liblo)
+       ("zlib" ,zlib)))
+    (native-inputs
+     `(("pkg-config" ,pkg-config)))
+    (home-page "http://qtractor.sourceforge.net/")
+    (synopsis "Audio/MIDI multi-track sequencer")
+    (description
+     "Qtractor is an Audio/MIDI multi-track sequencer application.  It uses
+JACK for audio and ALSA sequencer for MIDI as multimedia infrastructures and
+follows a traditional multi-track tape recorder control paradigm.")
+    (license license:gpl2+)))
diff --git a/gnu/packages/nano.scm b/gnu/packages/nano.scm
index f58f3d9328..352e2b47e0 100644
--- a/gnu/packages/nano.scm
+++ b/gnu/packages/nano.scm
@@ -1,6 +1,6 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2012 Nikita Karetnikov <nikita@karetnikov.org>
-;;; Copyright © 2015 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2015, 2016 Efraim Flashner <efraim@flashner.co.il>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -28,7 +28,7 @@
 (define-public nano
   (package
     (name "nano")
-    (version "2.5.0")
+    (version "2.5.1")
     (source
      (origin
       (method url-fetch)
@@ -36,7 +36,7 @@
                           version ".tar.gz"))
       (sha256
        (base32
-        "1vl9bim56k1b4zwc3icxp46w6pn6gb042j1h4jlz1jklxxpkwcpz"))))
+        "1piv8prj6w3rvsrrx41ra8c10b8fzkgjhnm6399lsgqqpw0wlvz0"))))
     (build-system gnu-build-system)
     (inputs
      `(("gettext" ,gnu-gettext)
diff --git a/gnu/packages/patches/arb-ldconfig.patch b/gnu/packages/patches/arb-ldconfig.patch
new file mode 100644
index 0000000000..478ec5a6f0
--- /dev/null
+++ b/gnu/packages/patches/arb-ldconfig.patch
@@ -0,0 +1,22 @@
+diff -u -r arb-2.8.1.orig/configure arb-2.8.1/configure
+--- arb-2.8.1.orig/configure	2015-12-31 17:30:01.000000000 +0100
++++ arb-2.8.1/configure	2016-01-20 16:41:41.336726596 +0100
+@@ -647,6 +647,7 @@
+ echo "ARB_SHARED=$SHARED" >> Makefile
+ echo "ARB_LIB=$ARB_LIB" >> Makefile
+ echo "ARB_LIBNAME=$ARB_LIBNAME" >> Makefile
++echo "ARB_MAJOR=$ARB_MAJOR" >> Makefile
+ echo "ARB_SOLIB=$ARB_SOLIB" >> Makefile
+ echo "EXEEXT=$EXEEXT" >> Makefile
+ echo "PREFIX=$PREFIX" >> Makefile
+diff -u -r arb-2.8.1.orig/Makefile.in arb-2.8.1/Makefile.in
+--- arb-2.8.1.orig/Makefile.in	2015-12-31 17:30:01.000000000 +0100
++++ arb-2.8.1/Makefile.in	2016-01-20 16:30:32.575298517 +0100
+@@ -101,6 +101,7 @@
+ 		$(LDCONFIG) -n "$(CURDIR)"; \
+ 	fi
+ 	ln -sf "$(ARB_LIB)" "$(ARB_LIBNAME)"; \
++	ln -sf "$(ARB_LIB)" "$(ARB_LIBNAME).$(ARB_MAJOR)"; \
+ 
+ libarb.a: $(OBJS) $(LIB_SOURCES) $(EXT_SOURCES) $(HEADERS) $(EXT_HEADERS) | build build/interfaces
+ 	$(AT)$(foreach ext, $(EXTENSIONS), $(foreach dir, $(patsubst $(ext)/%.h, %, $(wildcard $(ext)/*.h)), mkdir -p build/$(dir); BUILD_DIR=$(CURDIR)/build/$(dir); export BUILD_DIR; MOD_DIR=$(dir); export MOD_DIR; $(MAKE) -f $(CURDIR)/Makefile.subdirs -C $(ext)/$(dir) static || exit $$?;))
diff --git a/gnu/packages/patches/linux-libre-CVE-2016-0728.patch b/gnu/packages/patches/linux-libre-CVE-2016-0728.patch
new file mode 100644
index 0000000000..254d6c1aea
--- /dev/null
+++ b/gnu/packages/patches/linux-libre-CVE-2016-0728.patch
@@ -0,0 +1,84 @@
+Copied from
+https://git.kernel.org/cgit/linux/kernel/git/torvalds/linux.git/patch/?id=23567fd052a9abb6d67fe8e7a9ccdd9800a540f2
+
+From 23567fd052a9abb6d67fe8e7a9ccdd9800a540f2 Mon Sep 17 00:00:00 2001
+From: Yevgeny Pats <yevgeny@perception-point.io>
+Date: Tue, 19 Jan 2016 22:09:04 +0000
+Subject: KEYS: Fix keyring ref leak in join_session_keyring()
+
+This fixes CVE-2016-0728.
+
+If a thread is asked to join as a session keyring the keyring that's already
+set as its session, we leak a keyring reference.
+
+This can be tested with the following program:
+
+	#include <stddef.h>
+	#include <stdio.h>
+	#include <sys/types.h>
+	#include <keyutils.h>
+
+	int main(int argc, const char *argv[])
+	{
+		int i = 0;
+		key_serial_t serial;
+
+		serial = keyctl(KEYCTL_JOIN_SESSION_KEYRING,
+				"leaked-keyring");
+		if (serial < 0) {
+			perror("keyctl");
+			return -1;
+		}
+
+		if (keyctl(KEYCTL_SETPERM, serial,
+			   KEY_POS_ALL | KEY_USR_ALL) < 0) {
+			perror("keyctl");
+			return -1;
+		}
+
+		for (i = 0; i < 100; i++) {
+			serial = keyctl(KEYCTL_JOIN_SESSION_KEYRING,
+					"leaked-keyring");
+			if (serial < 0) {
+				perror("keyctl");
+				return -1;
+			}
+		}
+
+		return 0;
+	}
+
+If, after the program has run, there something like the following line in
+/proc/keys:
+
+3f3d898f I--Q---   100 perm 3f3f0000     0     0 keyring   leaked-keyring: empty
+
+with a usage count of 100 * the number of times the program has been run,
+then the kernel is malfunctioning.  If leaked-keyring has zero usages or
+has been garbage collected, then the problem is fixed.
+
+Reported-by: Yevgeny Pats <yevgeny@perception-point.io>
+Signed-off-by: David Howells <dhowells@redhat.com>
+Acked-by: Don Zickus <dzickus@redhat.com>
+Acked-by: Prarit Bhargava <prarit@redhat.com>
+Acked-by: Jarod Wilson <jarod@redhat.com>
+Signed-off-by: James Morris <james.l.morris@oracle.com>
+---
+ security/keys/process_keys.c | 1 +
+ 1 file changed, 1 insertion(+)
+
+diff --git a/security/keys/process_keys.c b/security/keys/process_keys.c
+index a3f85d2..e6d50172 100644
+--- a/security/keys/process_keys.c
++++ b/security/keys/process_keys.c
+@@ -794,6 +794,7 @@ long join_session_keyring(const char *name)
+ 		ret = PTR_ERR(keyring);
+ 		goto error2;
+ 	} else if (keyring == new->session_keyring) {
++		key_put(keyring);
+ 		ret = 0;
+ 		goto error2;
+ 	}
+-- 
+cgit v0.12
+
diff --git a/gnu/packages/patches/tophat-build-with-later-seqan.patch b/gnu/packages/patches/tophat-build-with-later-seqan.patch
new file mode 100644
index 0000000000..fc742e2a7d
--- /dev/null
+++ b/gnu/packages/patches/tophat-build-with-later-seqan.patch
@@ -0,0 +1,24 @@
+This patch resolves a build failure when building TopHat 2.1.0 with SeqAn 1.4.
+This is the relevant part of a patch originally posted here:
+https://lists.fu-berlin.de/pipermail/seqan-dev/2014-July/msg00001.html
+
+--- a/src/segment_juncs.cpp
++++ b/src/segment_juncs.cpp
+@@ -2050,10 +2050,13 @@ void juncs_from_ref_segs(RefSequenceTabl
+     typedef map<uint32_t, IntronMotifs> MotifMap;
+     
+     MotifMap ims;
+-	
+-    seqan::DnaStringReverseComplement rev_donor_dinuc(donor_dinuc);
+-    seqan::DnaStringReverseComplement rev_acceptor_dinuc(acceptor_dinuc);
+-    
++
++    typedef seqan::ModifiedString<
++                    seqan::ModifiedString<seqan::DnaString const, seqan::ModView<seqan::FunctorComplement<seqan::Dna> > >,  
++                    seqan::ModReverse>   ConstDnaStringReverseComplement;
++    ConstDnaStringReverseComplement rev_donor_dinuc(donor_dinuc);
++    ConstDnaStringReverseComplement rev_acceptor_dinuc(acceptor_dinuc);
++     
+     if (talkative)
+         fprintf(stderr, "Collecting potential splice sites in islands\n");
+ 
diff --git a/gnu/packages/tls.scm b/gnu/packages/tls.scm
index c10d1cbfc7..be48b25c9a 100644
--- a/gnu/packages/tls.scm
+++ b/gnu/packages/tls.scm
@@ -339,13 +339,13 @@ security, and applying best practice development processes.")
 (define-public acme
   (package
     (name "acme")
-    (version "0.1.1")
+    (version "0.2.0")
     (source (origin
       (method url-fetch)
       (uri (pypi-uri "acme" version))
       (sha256
         (base32
-         "1yv0gy8akaqp5p2wjpfj8r5i0da04a9qdmlh06rczdkrmk6q680w"))))
+         "1xcbywzrwrj2cmqhaj4k6b11wfkbm3i7za2k9j1sd74rs1zh5abl"))))
     (build-system python-build-system)
     (arguments
      `(#:python ,python-2))
@@ -371,13 +371,13 @@ security, and applying best practice development processes.")
 (define-public letsencrypt
   (package
     (name "letsencrypt")
-    (version "0.1.1")
+    (version "0.2.0")
     (source (origin
               (method url-fetch)
               (uri (pypi-uri "letsencrypt" version))
               (sha256
                (base32
-                "1kia3wk66lxyi2fghp9sd7cqgr5qiwdfayz153hi4wpa3q1q8rwf"))))
+                "0q57ylx00b6kl9zvawgag5yl03vlv1cjhp18xm96682pdibbgjci"))))
     (build-system python-build-system)
     (arguments
      `(#:python ,python-2))
diff --git a/gnu/packages/tor.scm b/gnu/packages/tor.scm
index e6e8876597..5fb8f954aa 100644
--- a/gnu/packages/tor.scm
+++ b/gnu/packages/tor.scm
@@ -1,6 +1,7 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2013, 2014, 2015 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2014, 2015 Mark H Weaver <mhw@netris.org>
+;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -36,14 +37,14 @@
 (define-public tor
   (package
     (name "tor")
-    (version "0.2.7.5")
+    (version "0.2.7.6")
     (source (origin
              (method url-fetch)
              (uri (string-append "https://www.torproject.org/dist/tor-"
                                  version ".tar.gz"))
              (sha256
               (base32
-               "0pxayvcab4cb107ynbpzx4g0qyr1mjfba2an76wdx6dxn56rwakx"))))
+               "0p8hjlfi8dwghlyjif5s0q98cmpgz9kn9jja25430l04z5wqcfj9"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("python" ,python-2)))  ; for tests
@@ -103,7 +104,7 @@ rejects UDP traffic from the application you're using.")
 (define-public privoxy
   (package
     (name "privoxy")
-    (version "3.0.21")
+    (version "3.0.24")
     (source (origin
              (method url-fetch)
              (uri (string-append "mirror://sourceforge/ijbswa/Sources/"
@@ -111,7 +112,7 @@ rejects UDP traffic from the application you're using.")
                                  version "-stable-src.tar.gz"))
              (sha256
               (base32
-               "1f6xb7aa47p90c26vqaw74y6drs9gpnhxsgby3mx0awdjh0ydisy"))))
+               "04mhkz5g713i2crvjd6s783hhrlsjjjlfb9llbaf13ghg3fgd0d3"))))
     (build-system gnu-build-system)
     (arguments
      '(;; The default 'sysconfdir' is $out/etc; change that to
diff --git a/gnu/packages/version-control.scm b/gnu/packages/version-control.scm
index 1edf9f8d9c..e0626cb3ac 100644
--- a/gnu/packages/version-control.scm
+++ b/gnu/packages/version-control.scm
@@ -6,7 +6,7 @@
 ;;; Copyright © 2015 Mathieu Lirzin <mthl@openmailbox.org>
 ;;; Copyright © 2014, 2015 Mark H Weaver <mhw@netris.org>
 ;;; Copyright © 2014 Eric Bavier <bavier@member.fsf.org>
-;;; Copyright © 2015 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2015, 2016 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2015 Kyle Meyer <kyle@kyleam.com>
 ;;; Copyright © 2015 Ricardo Wurmus <rekado@elephly.net>
 ;;;
@@ -1004,7 +1004,7 @@ modification time.")
 (define-public myrepos
   (package
     (name "myrepos")
-    (version "1.20151022")
+    (version "1.20160123")
     (source
      (origin
        (method url-fetch)
@@ -1013,7 +1013,7 @@ modification time.")
              version ".tar.gz"))
        (file-name (string-append name "-" version ".tar.gz"))
        (sha256
-        (base32 "0c93lqsngpsxsca7nygk4qhidr40ijgih86q81x1mfcwbs0gbds8"))))
+        (base32 "1723cg5haplz2w9dwdzp6ds1ip33cx3awmj4wnb0h4yq171v5lqk"))))
     (build-system gnu-build-system)
     (inputs
      `(("perl" ,perl)))
diff --git a/gnu/packages/video.scm b/gnu/packages/video.scm
index 12f10b9915..636f76584d 100644
--- a/gnu/packages/video.scm
+++ b/gnu/packages/video.scm
@@ -1,6 +1,6 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2013, 2014, 2015 Andreas Enge <andreas@enge.fr>
-;;; Copyright © 2014, 2015 David Thompson <davet@gnu.org>
+;;; Copyright © 2014, 2015, 2016 David Thompson <davet@gnu.org>
 ;;; Copyright © 2014, 2015, 2016 Mark H Weaver <mhw@netris.org>
 ;;; Copyright © 2015 Taylan Ulrich Bayırlı/Kammer <taylanbayirli@gmail.com>
 ;;; Copyright © 2015, 2016 Efraim Flashner <efraim@flashner.co.il>
@@ -1265,6 +1265,39 @@ functionality of the system is provided via an assortment of ready to use
 tools, XML authoring components, and an extensible plug-in based API.")
     (license license:lgpl2.1+)))
 
+(define-public v4l-utils
+  (package
+    (name "v4l-utils")
+    (version "1.8.1")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "http://linuxtv.org/downloads/v4l-utils"
+                                  "/v4l-utils-" version ".tar.bz2"))
+              (sha256
+               (base32
+                "0cqv8drw0z0kfmz4f50a8kzbrz6vbj6j6q78030hgshr7yq1jqig"))))
+    (build-system gnu-build-system)
+    (arguments
+     '(#:configure-flags
+       (list (string-append "--with-udevdir="
+                            (assoc-ref %outputs "out")
+                            "/lib/udev"))))
+    (native-inputs
+     `(("pkg-config" ,pkg-config)))
+    (inputs
+     `(("alsa-lib" ,alsa-lib)
+       ("glu" ,glu)
+       ("libjpeg" ,libjpeg)
+       ("libx11" ,libx11)
+       ("qt" ,qt)
+       ("eudev" ,eudev)))
+    (synopsis "Realtime video capture utilities for Linux")
+    (description "The v4l-utils provide a series of libraries and utilities to
+be used for realtime video capture via Linux-specific APIs.")
+    (home-page "https://linuxtv.org/wiki/index.php/V4l-utils")
+    ;; libv4l2 is LGPL2.1+, while utilities are GPL2 only.
+    (license (list license:lgpl2.1+ license:gpl2))))
+
 (define-public obs
   (package
     (name "obs")
@@ -1293,6 +1326,7 @@ tools, XML authoring components, and an extensible plug-in based API.")
        ("mesa" ,mesa)
        ("pulseaudio" ,pulseaudio)
        ("qt" ,qt)
+       ("v4l-utils" ,v4l-utils)
        ("zlib" ,zlib)))
     (synopsis "Live streaming software")
     (description "Open Broadcaster Software provides a graphical interface for
diff --git a/gnu/packages/xiph.scm b/gnu/packages/xiph.scm
index bc2294e58c..cca0c14c1b 100644
--- a/gnu/packages/xiph.scm
+++ b/gnu/packages/xiph.scm
@@ -5,7 +5,7 @@
 ;;; Copyright © 2014 Sree Harsha Totakura <sreeharsha@totakura.in>
 ;;; Copyright © 2014 Mark H Weaver <mhw@netris.org>
 ;;; Copyright © 2015 Paul van der Walt <paul@denknerd.org>
-;;; Copyright © 2015 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2015, 2016 Efraim Flashner <efraim@flashner.co.il>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -293,7 +293,7 @@ ogginfo, to obtain information (tags, bitrate, length, etc.) about
 (define opus
   (package
     (name "opus")
-    (version "1.1.1")
+    (version "1.1.2")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -301,7 +301,7 @@ ogginfo, to obtain information (tags, bitrate, length, etc.) about
                     ".tar.gz"))
               (sha256
                (base32
-                "07iplfwim26b6k1bqjyciaqvihps9rk5gi8385axa83ppmbgz14v"))))
+                "1z87x5c5x951lhnm70iqr2gqn15wns5cqsw8nnkvl48jwdw00a8f"))))
     (build-system gnu-build-system)
     (synopsis "Versatile audio codec")
     (description
@@ -349,7 +349,7 @@ decoding .opus files.")
 (define opusfile
   (package
     (name "opusfile")
-    (version "0.6")
+    (version "0.7")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -357,7 +357,7 @@ decoding .opus files.")
                     ".tar.gz"))
               (sha256
                (base32
-                "19iys2kld75k0210b807i4illrdmj3cmmnrgxlc9y4vf6mxp2a14"))))
+                "00f3wwjv3hxwg05g22s6mkkxikz80ljsn70g39cmi43jph9ysawy"))))
     (build-system gnu-build-system)
     (propagated-inputs
      `(("opus" ,opus)))
@@ -409,7 +409,7 @@ things in between.")
 (define-public libshout
   (package
     (name "libshout")
-    (version "2.3.1")
+    (version "2.4.1")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -417,7 +417,7 @@ things in between.")
                     name "-" version ".tar.gz"))
               (sha256
                (base32
-                "0vlj4dxfxg06xhvv0z2zjjlrjh5di2m28w7v16zcygsy99mmyg6g"))))
+                "0kgjpf8jkgyclw11nilxi8vyjk4s8878x23qyxnvybbgqbgbib7k"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("pkg-config" ,pkg-config)))