From 02b067d782323ea2ee6b528f9e5cfcd19d63f01d Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Wed, 22 Mar 2017 12:40:05 +0200
Subject: gnu: perl-compress-raw-zlib: Update to 2.074.

* gnu/packages/compression.scm (perl-compress-raw-zlib): Update to 2.074.
---
 gnu/packages/compression.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu')

diff --git a/gnu/packages/compression.scm b/gnu/packages/compression.scm
index d19ba2290b..d177a6c5c9 100644
--- a/gnu/packages/compression.scm
+++ b/gnu/packages/compression.scm
@@ -616,7 +616,7 @@ compression library.")
 (define-public perl-compress-raw-zlib
   (package
     (name "perl-compress-raw-zlib")
-    (version "2.068")
+    (version "2.074")
     (source
      (origin
        (method url-fetch)
@@ -624,7 +624,7 @@ compression library.")
                            "Compress-Raw-Zlib-" version ".tar.gz"))
        (sha256
         (base32
-         "06q7n87g26nn5gv4z2p31ca32f6zk124hqxc25rfgkjd3qi5798i"))))
+         "08bpx9v6i40n54rdcj6invlj294z20amrl8wvwf9b83aldwdwsd3"))))
     (build-system perl-build-system)
     (inputs
      `(("zlib" ,zlib)))
-- 
cgit v1.2.3


From c0b7b797a2122d1a49d06eff9c230dc84aef9dbf Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Wed, 22 Mar 2017 12:45:55 +0200
Subject: gnu: perl-compress-raw-bzip2: Update to 2.074.

* gnu/packages/compression.scm (perl-compress-raw-bzip2): Update to 2.074.
---
 gnu/packages/compression.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu')

diff --git a/gnu/packages/compression.scm b/gnu/packages/compression.scm
index d177a6c5c9..479daf89a7 100644
--- a/gnu/packages/compression.scm
+++ b/gnu/packages/compression.scm
@@ -596,7 +596,7 @@ decompression of some loosely related file formats used by Microsoft.")
 (define-public perl-compress-raw-bzip2
   (package
     (name "perl-compress-raw-bzip2")
-    (version "2.068")
+    (version "2.074")
     (source
      (origin
        (method url-fetch)
@@ -604,7 +604,7 @@ decompression of some loosely related file formats used by Microsoft.")
                            "Compress-Raw-Bzip2-" version ".tar.gz"))
        (sha256
         (base32
-         "16hl58xppckldz05zdyid1l5gpaykzwvkq682h3rc3nilbhgjqqg"))))
+         "0b5jwqf15zr787acnx8sfyy2zavdd7gfkd98n1dgy8fs6r8yb8a4"))))
     (build-system perl-build-system)
     ;; TODO: Use our bzip2 package.
     (home-page "http://search.cpan.org/dist/Compress-Raw-Bzip2")
-- 
cgit v1.2.3


From c70b50efb95a4b0fa0391fb7557a0c6862493163 Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Wed, 22 Mar 2017 12:50:36 +0200
Subject: gnu: perl-io-compress: Update to 2.074.

* gnu/packages/compression.scm (perl-io-compress): Update to 2.074.
[propagated-inputs]: Update minimum versions to 2.074.
---
 gnu/packages/compression.scm | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

(limited to 'gnu')

diff --git a/gnu/packages/compression.scm b/gnu/packages/compression.scm
index 479daf89a7..6cdddb99a5 100644
--- a/gnu/packages/compression.scm
+++ b/gnu/packages/compression.scm
@@ -651,7 +651,7 @@ compression library.")
 (define-public perl-io-compress
   (package
     (name "perl-io-compress")
-    (version "2.068")
+    (version "2.074")
     (source
      (origin
        (method url-fetch)
@@ -659,11 +659,11 @@ compression library.")
                            "IO-Compress-" version ".tar.gz"))
        (sha256
         (base32
-         "0dy0apjp7j9dfkzfjspjd3z9gh26srx5vac72g59bkkz1jf8s1gs"))))
+         "1wlpy2026djfmq0bjync531yq6s695jf7bcnpvjphrasi776igdl"))))
     (build-system perl-build-system)
     (propagated-inputs
-     `(("perl-compress-raw-zlib" ,perl-compress-raw-zlib)     ; >=2.068
-       ("perl-compress-raw-bzip2" ,perl-compress-raw-bzip2))) ; >=2.068
+     `(("perl-compress-raw-zlib" ,perl-compress-raw-zlib)     ; >=2.074
+       ("perl-compress-raw-bzip2" ,perl-compress-raw-bzip2))) ; >=2.074
     (home-page "http://search.cpan.org/dist/IO-Compress")
     (synopsis "IO Interface to compressed files/buffers")
     (description "IO-Compress provides a Perl interface to allow reading and
-- 
cgit v1.2.3


From 0e7c3ba1c0566daffd9627aebf6b6df28fcb7f35 Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Wed, 22 Mar 2017 12:56:23 +0200
Subject: gnu: perl-mojolicious: Update to 7.29.

* gnu/packages/perl-web.scm (perl-mojolicious): Update to 7.29.
---
 gnu/packages/perl-web.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu')

diff --git a/gnu/packages/perl-web.scm b/gnu/packages/perl-web.scm
index 9c92a95dad..75637e6545 100644
--- a/gnu/packages/perl-web.scm
+++ b/gnu/packages/perl-web.scm
@@ -26,7 +26,7 @@
 (define-public perl-mojolicious
   (package
     (name "perl-mojolicious")
-    (version "7.10")
+    (version "7.29")
     (source
      (origin
        (method url-fetch)
@@ -34,7 +34,7 @@
                            version ".tar.gz"))
        (sha256
         (base32
-         "0811f3wajgf71y02dr2khqnaswjh582pcvhv93k101qpg61syihn"))))
+         "1kmyb9axqbklyvr3l4d6mxnb0r97s9hzn7jpzksgckklp1ic8sqh"))))
     (build-system perl-build-system)
     (home-page "http://mojolicious.org/")
     (synopsis "Real-time web framework")
-- 
cgit v1.2.3


From 879b521cd051325255f03444d024c30106b4e9a1 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 22 Mar 2017 12:18:23 +0100
Subject: gnu: python-pysam: Update to 0.10.0.

* gnu/packages/bioinformatics.scm (python-pysam): Update to 0.10.0.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu')

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 90092ddf70..8f0cd0ae77 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -1413,7 +1413,7 @@ multiple sequence alignments.")
 (define-public python-pysam
   (package
     (name "python-pysam")
-    (version "0.9.1.4")
+    (version "0.10.0")
     (source (origin
               (method url-fetch)
               ;; Test data is missing on PyPi.
@@ -1423,7 +1423,7 @@ multiple sequence alignments.")
               (file-name (string-append name "-" version ".tar.gz"))
               (sha256
                (base32
-                "0y41ssbg6nvn2jgcbnrvkzblpjcwszaiv1rgyd8dwzjkrbfsgsmc"))
+                "1mmvn91agr238kwz7226xq0i7k84lg2nxywn9712mzj7gvgqhfy8"))
               (modules '((guix build utils)))
               (snippet
                ;; Drop bundled htslib. TODO: Also remove samtools and bcftools.
-- 
cgit v1.2.3


From 71dbf592c49e31b2f5e235278942b98f4ba99e72 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 22 Mar 2017 12:18:59 +0100
Subject: gnu: python-pysam: Run tests before installation.

* gnu/packages/bioinformatics.scm (python-pysam)[arguments]: Adjust check
phase to be run before installation.
---
 gnu/packages/bioinformatics.scm | 28 +++++++++++++++-------------
 1 file changed, 15 insertions(+), 13 deletions(-)

(limited to 'gnu')

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 8f0cd0ae77..51f0e0c0b0 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -1430,7 +1430,11 @@ multiple sequence alignments.")
                '(delete-file-recursively "htslib"))))
     (build-system python-build-system)
     (arguments
-     `(#:phases
+     `(#:modules ((ice-9 ftw)
+                  (srfi srfi-26)
+                  (guix build python-build-system)
+                  (guix build utils))
+       #:phases
        (modify-phases %standard-phases
          (add-before 'build 'set-flags
            (lambda* (#:key inputs #:allow-other-keys)
@@ -1442,23 +1446,21 @@ multiple sequence alignments.")
              (setenv "LDFLAGS" "-lncurses")
              (setenv "CFLAGS" "-D_CURSES_LIB=1")
              #t))
-         (delete 'check)
-         (add-after 'install 'check
+         (replace 'check
            (lambda* (#:key inputs outputs #:allow-other-keys)
+             ;; Add first subdirectory of "build" directory to PYTHONPATH.
              (setenv "PYTHONPATH"
                      (string-append
                       (getenv "PYTHONPATH")
-                      ":" (assoc-ref outputs "out")
-                      "/lib/python"
-                      (string-take (string-take-right
-                                    (assoc-ref inputs "python") 5) 3)
-                      "/site-packages"))
+                      ":" (getcwd) "/build/"
+                      (car (scandir "build"
+                                    (compose not (cut string-prefix? "." <>))))))
              ;; Step out of source dir so python does not import from CWD.
-             (chdir "tests")
-             (setenv "HOME" "/tmp")
-             (and (zero? (system* "make" "-C" "pysam_data"))
-                  (zero? (system* "make" "-C" "cbcf_data"))
-                  (zero? (system* "nosetests" "-v"))))))))
+             (with-directory-excursion "tests"
+               (setenv "HOME" "/tmp")
+               (and (zero? (system* "make" "-C" "pysam_data"))
+                    (zero? (system* "make" "-C" "cbcf_data"))
+                    (zero? (system* "nosetests" "-v")))))))))
     (propagated-inputs
      `(("htslib"            ,htslib))) ; Included from installed header files.
     (inputs
-- 
cgit v1.2.3


From 54262c543553a023c8835d706c2c1063cf20c079 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 22 Mar 2017 12:20:18 +0100
Subject: gnu: python-pysam: Run tests in parallel.

* gnu/packages/bioinformatics.scm (python-pysam)[arguments]: Run nose tests in
parallel.
---
 gnu/packages/bioinformatics.scm | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

(limited to 'gnu')

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 51f0e0c0b0..97380fc032 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -1460,7 +1460,9 @@ multiple sequence alignments.")
                (setenv "HOME" "/tmp")
                (and (zero? (system* "make" "-C" "pysam_data"))
                     (zero? (system* "make" "-C" "cbcf_data"))
-                    (zero? (system* "nosetests" "-v")))))))))
+                    (zero? (system* "nosetests" "-v"
+                                    "--processes"
+                                    (number->string (parallel-job-count)))))))))))
     (propagated-inputs
      `(("htslib"            ,htslib))) ; Included from installed header files.
     (inputs
-- 
cgit v1.2.3


From 326249bab8e525b8c71f862fb1f2569d703a3e84 Mon Sep 17 00:00:00 2001
From: Danny Milosavljevic <dannym@scratchpost.org>
Date: Wed, 22 Mar 2017 12:45:48 +0100
Subject: gnu: rustc: End resultless phases in #t.

* gnu/packages/rust.scm (rustc): End resultless phases in #t.
---
 gnu/packages/rust.scm | 9 ++++++---
 1 file changed, 6 insertions(+), 3 deletions(-)

(limited to 'gnu')

diff --git a/gnu/packages/rust.scm b/gnu/packages/rust.scm
index 2dedef8373..b72a206e6a 100644
--- a/gnu/packages/rust.scm
+++ b/gnu/packages/rust.scm
@@ -229,11 +229,13 @@ rustc-bootstrap and cargo-bootstrap packages.")
                (("/usr/bin/env") (which "env")))
              ;; Avoid curl as a build dependency.
              (substitute* "configure"
-               (("probe_need CFG_CURL curl") ""))))
+               (("probe_need CFG_CURL curl") ""))
+             #t))
          (add-after 'unpack 'set-env
            (lambda _
              (setenv "SHELL" (which "sh"))
-             (setenv "CONFIG_SHELL" (which "sh"))))
+             (setenv "CONFIG_SHELL" (which "sh"))
+             #t))
          (add-after 'unpack 'patch-tests
            (lambda* (#:key inputs #:allow-other-keys)
              (substitute* "src/tools/tidy/src/main.rs"
@@ -275,7 +277,8 @@ rustc-bootstrap and cargo-bootstrap packages.")
                ;; Let gcc find ld and libc startup files.
                (wrap-program (string-append out "/bin/rustc")
                  `("PATH" ":" prefix (,(string-append ld-wrapper "/bin")))
-                 `("LIBRARY_PATH" ":" suffix (,(string-append libc "/lib"))))))))))
+                 `("LIBRARY_PATH" ":" suffix (,(string-append libc "/lib"))))
+               #t))))))
     ;; rustc invokes gcc, so we need to set its search paths accordingly.
     (native-search-paths (package-native-search-paths gcc))
     (synopsis "Compiler for the Rust progamming language")
-- 
cgit v1.2.3


From 5cd074ea32debac844ce3761f6baa3f63e3d61b2 Mon Sep 17 00:00:00 2001
From: Ludovic Courtès <ludo@gnu.org>
Date: Wed, 22 Mar 2017 09:47:42 +0100
Subject: gnu: guile: Add 'guile-next' as a deprecated alias.

This is a followup to f6396d862f9f8ce0c0e6894ce30599773167af0c.

* gnu/packages/guile.scm (guile-next): New variable.
---
 gnu/packages/guile.scm | 3 +++
 1 file changed, 3 insertions(+)

(limited to 'gnu')

diff --git a/gnu/packages/guile.scm b/gnu/packages/guile.scm
index df1f17201e..abb4fe9884 100644
--- a/gnu/packages/guile.scm
+++ b/gnu/packages/guile.scm
@@ -261,6 +261,9 @@ without requiring the source code to be rewritten.")
             (files '("lib/guile/2.2/site-ccache"
                      "share/guile/site/2.2")))))))
 
+(define-public guile-next
+  (deprecated-package "guile-next" guile-2.2))
+
 (define (guile-variant-package-name prefix)
   (lambda (name)
     "Return NAME with PREFIX instead of \"guile-\", when applicable."
-- 
cgit v1.2.3


From aeb6fe5fa0891c1b825a8f403dd1c42bbfd6e952 Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Wed, 22 Mar 2017 15:01:03 +0200
Subject: gnu: autoconf-archive: Update to 2017.03.21.

* gnu/packages/autotools.scm (autoconf-archive): Update to 2017.03.21.
---
 gnu/packages/autotools.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu')

diff --git a/gnu/packages/autotools.scm b/gnu/packages/autotools.scm
index 72492e70eb..72d84b51b1 100644
--- a/gnu/packages/autotools.scm
+++ b/gnu/packages/autotools.scm
@@ -163,7 +163,7 @@ exec ~a --no-auto-compile \"$0\" \"$@\"
 (define-public autoconf-archive
   (package
     (name "autoconf-archive")
-    (version "2016.09.16")
+    (version "2017.03.21")
     (source
      (origin
       (method url-fetch)
@@ -171,7 +171,7 @@ exec ~a --no-auto-compile \"$0\" \"$@\"
                           version ".tar.xz"))
       (sha256
        (base32
-        "10mxz9hfnfz66m1l9s28sbyfb9a04akz92wkyv9blhpq6p9fzwp8"))))
+        "0rfpapadka2023qhy8294ca5awxpb8d4904js6kv7piby5ax8siq"))))
     (build-system gnu-build-system)
     (home-page "https://www.gnu.org/software/autoconf-archive")
     (synopsis "Collection of freely reusable Autoconf macros")
-- 
cgit v1.2.3


From 493ae57ecad7313cf4820bf50cda80804653c6b8 Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Wed, 22 Mar 2017 16:08:36 +0200
Subject: gnu: binutils-vc4: Set source file-name.

* gnu/packages/embedded.scm (binutils-vc4)[source]: Add file-name field.
---
 gnu/packages/embedded.scm | 1 +
 1 file changed, 1 insertion(+)

(limited to 'gnu')

diff --git a/gnu/packages/embedded.scm b/gnu/packages/embedded.scm
index 3e1f87d749..fbbafc6a3b 100644
--- a/gnu/packages/embedded.scm
+++ b/gnu/packages/embedded.scm
@@ -732,6 +732,7 @@ simulator.")
                 (uri (git-reference
                        (url "https://github.com/puppeh/binutils-vc4.git")
                        (commit commit)))
+                (file-name (string-append name "-" version "-checkout"))
                 (sha256
                  (base32
                   "1kdrz6fki55lm15rwwamn74fnqpy0zlafsida2zymk76n3656c63"))))
-- 
cgit v1.2.3


From 61a3137bdd72b87aa4a4d4ce9b764fac05e835bb Mon Sep 17 00:00:00 2001
From: Ludovic Courtès <ludo@gnu.org>
Date: Wed, 22 Mar 2017 16:03:23 +0100
Subject: gnu: guix: Update development snapshot.

* gnu/packages/package-management.scm (guix-devel): Update to 73a4645.
---
 gnu/packages/package-management.scm | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

(limited to 'gnu')

diff --git a/gnu/packages/package-management.scm b/gnu/packages/package-management.scm
index f675e22ad9..cabfc862ac 100644
--- a/gnu/packages/package-management.scm
+++ b/gnu/packages/package-management.scm
@@ -214,9 +214,9 @@ the Nix package manager.")
   ;;
   ;; Note: use a very short commit id; with a longer one, the limit on
   ;; hash-bang lines would be exceeded while running the tests.
-  (let ((commit "1162418ee88f155f6b14fd8926479c2176e40e76"))
+  (let ((commit "73a46451af333c77d2e79aa8764f51be8c34d1ae"))
     (package (inherit guix-0.12.0)
-      (version (string-append "0.12.0-5." (string-take commit 4)))
+      (version (string-append "0.12.0-6." (string-take commit 4)))
       (source (origin
                 (method git-fetch)
                 (uri (git-reference
@@ -226,7 +226,7 @@ the Nix package manager.")
                       (commit commit)))
                 (sha256
                  (base32
-                  "16pxqbywhayazdgg9l19frigncmyq20j5fvaq4zgvm0iidndhfja"))
+                  "1zfa6c1vf52rg7ba1nrz4hzgdwl16brc4iylcdnhl9mnkjg2fbr5"))
                 (file-name (string-append "guix-" version "-checkout"))))
       (arguments
        (substitute-keyword-arguments (package-arguments guix-0.12.0)
-- 
cgit v1.2.3


From 9b7a9580d46e7c2840e7cbd9bb0bfa2fb9dd654f Mon Sep 17 00:00:00 2001
From: Danny Milosavljevic <dannym@scratchpost.org>
Date: Wed, 22 Mar 2017 17:40:06 +0100
Subject: gnu: rustc: Honor max line length.

* gnu/packages/rust.scm (rustc)[arguments]: patch-tests: Honor max line
length.
---
 gnu/packages/rust.scm | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

(limited to 'gnu')

diff --git a/gnu/packages/rust.scm b/gnu/packages/rust.scm
index b72a206e6a..af4d322a73 100644
--- a/gnu/packages/rust.scm
+++ b/gnu/packages/rust.scm
@@ -238,11 +238,12 @@ rustc-bootstrap and cargo-bootstrap packages.")
              #t))
          (add-after 'unpack 'patch-tests
            (lambda* (#:key inputs #:allow-other-keys)
-             (substitute* "src/tools/tidy/src/main.rs"
-               (("^.*cargo.*::check.*$") ""))
-             (substitute* "src/libstd/process.rs"
-               (("\"/bin/sh\"") (string-append "\"" (assoc-ref inputs "bash") "/bin/sh\"")))
-             #t))
+             (let ((bash (assoc-ref inputs "bash")))
+               (substitute* "src/tools/tidy/src/main.rs"
+                 (("^.*cargo.*::check.*$") ""))
+               (substitute* "src/libstd/process.rs"
+                 (("\"/bin/sh\"") (string-append "\"" bash "/bin/sh\"")))
+               #t)))
          (replace 'configure
            (lambda* (#:key inputs outputs #:allow-other-keys)
              (let* ((out (assoc-ref outputs "out"))
-- 
cgit v1.2.3


From 112d645ffa5f4ce210d84a9c4c9d917da937e3b3 Mon Sep 17 00:00:00 2001
From: Leo Famulari <leo@famulari.name>
Date: Wed, 22 Mar 2017 13:04:07 -0400
Subject: gnu: dovecot: Update to 2.2.28.

* gnu/packages/mail.scm (dovecot): Update to 2.2.28.
---
 gnu/packages/mail.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu')

diff --git a/gnu/packages/mail.scm b/gnu/packages/mail.scm
index aaf9fce609..2ae1277ae1 100644
--- a/gnu/packages/mail.scm
+++ b/gnu/packages/mail.scm
@@ -1080,7 +1080,7 @@ facilities for checking incoming mail.")
 (define-public dovecot
   (package
     (name "dovecot")
-    (version "2.2.27")
+    (version "2.2.28")
     (source
      (origin
        (method url-fetch)
@@ -1088,7 +1088,7 @@ facilities for checking incoming mail.")
                            (version-major+minor version) "/"
                            name "-" version ".tar.gz"))
        (sha256 (base32
-                "1s8qvr6fa9d0n179kdwgpsi72zkvpbh9q57q8fr2fjysgjl94zw9"))))
+                "098zpkmkk93372qnv6drgbfg8hp5mynspzc1735qgar6wdcqya70"))))
     (build-system gnu-build-system)
     (native-inputs
      `(("pkg-config" ,pkg-config)))
-- 
cgit v1.2.3


From 359e9c4215c624a3fa7235096b49902238ce7864 Mon Sep 17 00:00:00 2001
From: Kei Kebreau <kei@openmailbox.org>
Date: Tue, 21 Mar 2017 14:54:04 -0400
Subject: gnu: chicken: Update to 4.12.0.

* gnu/packages/scheme.scm (chicken): Update to 4.12.0.
---
 gnu/local.mk                                       |   2 +-
 .../chicken-CVE-2016-6830+CVE-2016-6831.patch      |  81 -------------
 gnu/packages/patches/chicken-CVE-2017-6949.patch   | 132 +++++++++++++++++++++
 gnu/packages/scheme.scm                            |  16 +--
 4 files changed, 137 insertions(+), 94 deletions(-)
 delete mode 100644 gnu/packages/patches/chicken-CVE-2016-6830+CVE-2016-6831.patch
 create mode 100644 gnu/packages/patches/chicken-CVE-2017-6949.patch

(limited to 'gnu')

diff --git a/gnu/local.mk b/gnu/local.mk
index 97ca3eb720..0eb18f26c1 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -505,7 +505,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/calibre-drop-unrar.patch			\
   %D%/packages/patches/calibre-no-updates-dialog.patch		\
   %D%/packages/patches/cdparanoia-fpic.patch			\
-  %D%/packages/patches/chicken-CVE-2016-6830+CVE-2016-6831.patch	\
+  %D%/packages/patches/chicken-CVE-2017-6949.patch		\
   %D%/packages/patches/chmlib-inttypes.patch			\
   %D%/packages/patches/clang-libc-search-path.patch		\
   %D%/packages/patches/clang-3.8-libc-search-path.patch		\
diff --git a/gnu/packages/patches/chicken-CVE-2016-6830+CVE-2016-6831.patch b/gnu/packages/patches/chicken-CVE-2016-6830+CVE-2016-6831.patch
deleted file mode 100644
index 59decde0e9..0000000000
--- a/gnu/packages/patches/chicken-CVE-2016-6830+CVE-2016-6831.patch
+++ /dev/null
@@ -1,81 +0,0 @@
-diff -ur a/irregex-core.scm b/irregex-core.scm
---- a/irregex-core.scm	2016-09-11 19:03:00.000000000 -0400
-+++ b/irregex-core.scm	2017-01-01 22:24:08.000000000 -0500
-@@ -30,6 +30,8 @@
- 
- ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
- ;;;; History
-+;; 0.9.6: 2016/12/05 - fixed exponential memory use of + in compilation
-+;;                     of backtracking matcher.
- ;; 0.9.5: 2016/09/10 - fixed a bug in irregex-fold handling of bow
- ;; 0.9.4: 2015/12/14 - performance improvement for {n,m} matches
- ;; 0.9.3: 2014/07/01 - R7RS library
-@@ -3170,16 +3172,7 @@
-               ((sre-empty? (sre-sequence (cdr sre)))
-                (error "invalid sre: empty *" sre))
-               (else
--               (letrec
--                   ((body
--                     (lp (sre-sequence (cdr sre))
--                         n
--                         flags
--                         (lambda (cnk init src str i end matches fail)
--                           (body cnk init src str i end matches
--                                 (lambda ()
--                                   (next cnk init src str i end matches fail)
--                                   ))))))
-+               (let ((body (rec (list '+ (sre-sequence (cdr sre))))))
-                  (lambda (cnk init src str i end matches fail)
-                    (body cnk init src str i end matches
-                          (lambda ()
-@@ -3204,10 +3197,21 @@
-                          (lambda ()
-                            (body cnk init src str i end matches fail))))))))
-             ((+)
--             (lp (sre-sequence (cdr sre))
--                 n
--                 flags
--                 (rec (list '* (sre-sequence (cdr sre))))))
-+             (cond
-+              ((sre-empty? (sre-sequence (cdr sre)))
-+               (error "invalid sre: empty +" sre))
-+              (else
-+               (letrec
-+                   ((body
-+                     (lp (sre-sequence (cdr sre))
-+                         n
-+                         flags
-+                         (lambda (cnk init src str i end matches fail)
-+                           (body cnk init src str i end matches
-+                                 (lambda ()
-+                                   (next cnk init src str i end matches fail)
-+                                   ))))))
-+                 body))))
-             ((=)
-              (rec `(** ,(cadr sre) ,(cadr sre) ,@(cddr sre))))
-             ((>=)
-diff -ur a/irregex-utils.scm b/irregex-utils.scm
---- a/irregex-utils.scm	2016-09-11 19:03:00.000000000 -0400
-+++ b/irregex-utils.scm	2017-01-01 22:25:25.000000000 -0500
-@@ -89,7 +89,7 @@
-         (case (car x)
-           ((: seq)
-            (cond
--            ((and (pair? (cddr x)) (pair? (cddr x)) (not (eq? x obj)))
-+            ((and (pair? (cdr x)) (pair? (cddr x)) (not (eq? x obj)))
-              (display "(?:" out) (for-each lp (cdr x)) (display ")" out))
-             (else (for-each lp (cdr x)))))
-           ((submatch)
-diff -ur "a/manual-html/Unit irregex.html" "b/manual-html/Unit irregex.html"
---- "a/manual-html/Unit irregex.html"	2016-09-11 19:10:47.000000000 -0400
-+++ "b/manual-html/Unit irregex.html"	2017-01-01 22:26:05.000000000 -0500
-@@ -353,6 +353,6 @@
- <dd class="defsig"><p>Returns an optimized SRE matching any of the literal strings in the list, like Emacs' <tt>regexp-opt</tt>.  Note this optimization doesn't help when irregex is able to build a DFA.</p></dd>
- </dl>
- <h5 id="sec:sre-.3estring"><a href="#sec:sre-.3estring">sre-&gt;string</a></h5><dl class="defsig"><dt class="defsig" id="def:sre-.3estring"><span class="sig"><tt>(sre-&gt;string &lt;sre&gt;)</tt></span> <span class="type">procedure</span></dt>
--<dd class="defsig"><p>Convert an SRE to a POSIX-style regular expression string, if possible.</p></dd>
-+<dd class="defsig"><p>Convert an SRE to a PCRE-style regular expression string, if possible.</p></dd>
- </dl>
--<hr /><p>Previous: <a href="Unit%20extras.html">Unit extras</a></p><p>Next: <a href="Unit%20srfi-1.html">Unit srfi-1</a></p></div></div></body>
-\ No newline at end of file
-+<hr /><p>Previous: <a href="Unit%20extras.html">Unit extras</a></p><p>Next: <a href="Unit%20srfi-1.html">Unit srfi-1</a></p></div></div></body>
diff --git a/gnu/packages/patches/chicken-CVE-2017-6949.patch b/gnu/packages/patches/chicken-CVE-2017-6949.patch
new file mode 100644
index 0000000000..00552eec76
--- /dev/null
+++ b/gnu/packages/patches/chicken-CVE-2017-6949.patch
@@ -0,0 +1,132 @@
+From: LemonBoy <thatlemon@gmail.com>
+Date: Fri, 10 Mar 2017 16:29:47 +0100
+Subject: [PATCH] Add bound checking to all srfi-4 vector allocations.
+
+Do what C_allocate_vector already does and prevent the creation of a
+vector that's too big or too small.
+We should be very careful to avoid the latter case because the
+allocation size is directly fed into `malloc' as 'x + sizeof(C_header)'
+thus making possible to successfully allocate a vector smaller than the
+C_header structure and get C_block_header_init to write over
+uninitialized memory.
+
+To reduce code duplication, type checking is moved from each of the
+make-*vector procedures to the common "alloc" helper procedure.
+
+Signed-off-by: Peter Bex <peter@more-magic.net>
+Signed-off-by: Kooda <kooda@upyum.com>
+---
+ srfi-4.scm | 34 +++++++++++++++-------------------
+ 1 file changed, 15 insertions(+), 19 deletions(-)
+
+diff --git a/srfi-4.scm b/srfi-4.scm
+index 7f5412b..69f58ba 100644
+--- a/srfi-4.scm
++++ b/srfi-4.scm
+@@ -255,24 +255,28 @@ EOF
+ 
+ ;;; Basic constructors:
+ 
+-(let* ([ext-alloc
+-	(foreign-lambda* scheme-object ([int bytes])
+-	  "C_word *buf = (C_word *)C_malloc(bytes + sizeof(C_header));"
++(let* ((ext-alloc
++	(foreign-lambda* scheme-object ((size_t bytes))
++	  "C_word *buf;"
++	  "if (bytes > C_HEADER_SIZE_MASK) C_return(C_SCHEME_FALSE);"
++	  "buf = (C_word *)C_malloc(bytes + sizeof(C_header));"
+ 	  "if(buf == NULL) C_return(C_SCHEME_FALSE);"
+ 	  "C_block_header_init(buf, C_make_header(C_BYTEVECTOR_TYPE, bytes));"
+-	  "C_return(buf);") ]
+-       [ext-free
+-	(foreign-lambda* void ([scheme-object bv])
+-	  "C_free((void *)C_block_item(bv, 1));") ]
+-       [alloc
++	  "C_return(buf);") )
++       (ext-free
++	(foreign-lambda* void ((scheme-object bv))
++	  "C_free((void *)C_block_item(bv, 1));") )
++       (alloc
+ 	(lambda (loc len ext?)
++	  (##sys#check-exact len loc)
++	  (when (fx< len 0) (##sys#error loc "size is negative" len))
+ 	  (if ext?
+-	      (let ([bv (ext-alloc len)])
++	      (let ((bv (ext-alloc len)))
+ 		(or bv
+ 		    (##sys#error loc "not enough memory - cannot allocate external number vector" len)) )
+-	      (let ([bv (##sys#allocate-vector len #t #f #t)]) ; this could be made better...
++	      (let ((bv (##sys#allocate-vector len #t #f #t))) ; this could be made better...
+ 		(##core#inline "C_string_to_bytevector" bv)
+-		bv) ) ) ] )
++		bv) ) ) ) )
+ 
+   (set! release-number-vector
+     (lambda (v)
+@@ -282,7 +286,6 @@ EOF
+ 
+   (set! make-u8vector
+     (lambda (len #!optional (init #f)  (ext? #f) (fin? #t))
+-      (##sys#check-exact len 'make-u8vector)
+       (let ((v (##sys#make-structure 'u8vector (alloc 'make-u8vector len ext?))))
+ 	(when (and ext? fin?) (set-finalizer! v ext-free))
+ 	(if (not init)
+@@ -295,7 +298,6 @@ EOF
+ 
+   (set! make-s8vector
+     (lambda (len #!optional (init #f)  (ext? #f) (fin? #t))
+-      (##sys#check-exact len 'make-s8vector)
+       (let ((v (##sys#make-structure 's8vector (alloc 'make-s8vector len ext?))))
+ 	(when (and ext? fin?) (set-finalizer! v ext-free))
+ 	(if (not init)
+@@ -308,7 +310,6 @@ EOF
+ 
+   (set! make-u16vector
+     (lambda (len #!optional (init #f)  (ext? #f) (fin? #t))
+-      (##sys#check-exact len 'make-u16vector)
+       (let ((v (##sys#make-structure 'u16vector (alloc 'make-u16vector (##core#inline "C_fixnum_shift_left" len 1) ext?))))
+ 	(when (and ext? fin?) (set-finalizer! v ext-free))
+ 	(if (not init)
+@@ -321,7 +322,6 @@ EOF
+ 
+   (set! make-s16vector
+     (lambda (len #!optional (init #f)  (ext? #f) (fin? #t))
+-      (##sys#check-exact len 'make-s16vector)
+       (let ((v (##sys#make-structure 's16vector (alloc 'make-s16vector (##core#inline "C_fixnum_shift_left" len 1) ext?))))
+ 	(when (and ext? fin?) (set-finalizer! v ext-free))
+ 	(if (not init)
+@@ -334,7 +334,6 @@ EOF
+ 
+   (set! make-u32vector
+     (lambda (len #!optional (init #f)  (ext? #f) (fin? #t))
+-      (##sys#check-exact len 'make-u32vector)
+       (let ((v (##sys#make-structure 'u32vector (alloc 'make-u32vector (##core#inline "C_fixnum_shift_left" len 2) ext?))))
+ 	(when (and ext? fin?) (set-finalizer! v ext-free))
+ 	(if (not init)
+@@ -347,7 +346,6 @@ EOF
+ 
+   (set! make-s32vector
+     (lambda (len #!optional (init #f)  (ext? #f) (fin? #t))
+-      (##sys#check-exact len 'make-s32vector)
+       (let ((v (##sys#make-structure 's32vector (alloc 'make-s32vector (##core#inline "C_fixnum_shift_left" len 2) ext?))))
+ 	(when (and ext? fin?) (set-finalizer! v ext-free))
+ 	(if (not init)
+@@ -360,7 +358,6 @@ EOF
+ 
+   (set! make-f32vector
+     (lambda (len #!optional (init #f)  (ext? #f) (fin? #t))
+-      (##sys#check-exact len 'make-f32vector)
+       (let ((v (##sys#make-structure 'f32vector (alloc 'make-f32vector (##core#inline "C_fixnum_shift_left" len 2) ext?))))
+ 	(when (and ext? fin?) (set-finalizer! v ext-free))
+ 	(if (not init)
+@@ -375,7 +372,6 @@ EOF
+ 
+   (set! make-f64vector
+     (lambda (len #!optional (init #f)  (ext? #f) (fin? #t))
+-      (##sys#check-exact len 'make-f64vector)
+       (let ((v (##sys#make-structure
+ 		'f64vector
+ 		(alloc 'make-f64vector (##core#inline "C_fixnum_shift_left" len 3) ext?))))
+--
+2.1.4
+
diff --git a/gnu/packages/scheme.scm b/gnu/packages/scheme.scm
index e1dba9bed7..fec872f5f9 100644
--- a/gnu/packages/scheme.scm
+++ b/gnu/packages/scheme.scm
@@ -325,18 +325,16 @@ mashups, office (web agendas, mail clients, ...), etc.")
 (define-public chicken
   (package
     (name "chicken")
-    (version "4.11.1")
+    (version "4.12.0")
     (source (origin
               (method url-fetch)
-              (uri (string-append "http://code.call-cc.org/releases/"
+              (uri (string-append "https://code.call-cc.org/releases/"
                                   version "/chicken-" version ".tar.gz"))
-              (uri (string-append "http://code.call-cc.org/dev-snapshots/"
-                                  "2016/09/12/chicken-" version ".tar.gz"))
               (sha256
                (base32
-                "1rwymbbmnwdyhdzilv9w75an989xw9kjf3x52iqdng3nphpflcga"))
+                "12b9gaa9lqh39lj1v4wm48f6z8ww3jdkvc5bh9gqqvn6kd2wwnk0"))
               (patches
-               (search-patches "chicken-CVE-2016-6830+CVE-2016-6831.patch"))))
+               (search-patches "chicken-CVE-2017-6949.patch"))))
     (build-system gnu-build-system)
     (arguments
      `(#:modules ((guix build gnu-build-system)
@@ -359,12 +357,6 @@ mashups, office (web agendas, mail clients, ...), etc.")
 
        ;; Parallel builds are not supported, as noted in README.
        #:parallel-build? #f))
-    ;; One of the tests ("testing direct invocation can detect calls of too
-    ;; many arguments...") times out when building with a more recent GCC.
-    ;; The problem was reported here:
-    ;; https://lists.gnu.org/archive/html/chicken-hackers/2015-04/msg00059.html
-    (native-inputs
-     `(("gcc" ,gcc-4.8)))
     (home-page "http://www.call-cc.org/")
     (synopsis "R5RS Scheme implementation that compiles native code via C")
     (description
-- 
cgit v1.2.3


From 283f04b053ce423a323fa4da000e21b4649b370a Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Wed, 22 Mar 2017 22:36:04 +0200
Subject: gnu: libffcall: Set source file-name.

* gnu/packages/libffcall.scm (libffcall)[source]: Add file-name field.
[home-page]: Use https.
---
 gnu/packages/libffcall.scm | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

(limited to 'gnu')

diff --git a/gnu/packages/libffcall.scm b/gnu/packages/libffcall.scm
index 74d6b6347f..aae5ac991b 100644
--- a/gnu/packages/libffcall.scm
+++ b/gnu/packages/libffcall.scm
@@ -36,6 +36,7 @@
               ":pserver:anonymous@cvs.savannah.gnu.org:/sources/libffcall")
              (module "ffcall")
              (revision "2015-01-15")))
+       (file-name (string-append name "-" version "-checkout"))
        (sha256
         (base32
          "1lwdskc2w4rr98x9flr2726lmj4190l16r0izg7gqxy50801wwgd"))))
@@ -45,5 +46,5 @@
     (description
      "GNU Libffcall is a collection of libraries that can be used to build
 foreign function call interfaces in embedded interpreters.")
-    (home-page "http://www.gnu.org/software/libffcall/")
+    (home-page "https://www.gnu.org/software/libffcall/")
     (license l:gpl2+)))
-- 
cgit v1.2.3


From 745d85b7dba7b81c7447b67b48c7a25c6db78cba Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Wed, 22 Mar 2017 20:48:55 +0100
Subject: gnu: python-pafy: Update to 0.5.3.1.

* gnu/packages/python.scm (python-pafy): Update to 0.5.3.1.
---
 gnu/packages/python.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu')

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 764512eb08..9786033d06 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -1735,14 +1735,14 @@ standard library.")
 (define-public python-pafy
   (package
     (name "python-pafy")
-    (version "0.5.2")
+    (version "0.5.3.1")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "pafy" version))
        (sha256
         (base32
-         "1ckvrypyvb7jbqlgwdz0y337ajagjv7dgxyns326nqwypn1wpq0i"))))
+         "1a7dxi95m1043rxx1r5x3ngb66nwlq6aqcasyqqjzmmmjps4zrim"))))
     (build-system python-build-system)
     (arguments
      `(#:tests? #f)) ; Currently pafy can not find itself in the tests
-- 
cgit v1.2.3


From fd2662e950d29e1f31a664adbd56c9f225794a32 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Wed, 22 Mar 2017 20:49:35 +0100
Subject: gnu: python-sqlalchemy-utils: Update to 0.32.13.

* gnu/packages/python.scm (python-sqlalchemy-utils): Update to 0.32.13.
---
 gnu/packages/python.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu')

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 9786033d06..b156214ac5 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -4382,14 +4382,14 @@ both of which are installed automatically if you install this library.")
 (define-public python-sqlalchemy-utils
   (package
     (name "python-sqlalchemy-utils")
-    (version "0.32.11")
+    (version "0.32.13")
     (source
       (origin
         (method url-fetch)
         (uri (pypi-uri "SQLAlchemy-Utils" version))
         (sha256
          (base32
-          "1wghyvk73cmq3iqyg3fczw128fv2pan2v76m0xg1bw05h8fhvnk3"))))
+          "0vsib7gidjamzsz6w4s5pdhxzxsrkghjnm4sqwk94igjrl3i5ixj"))))
     (build-system python-build-system)
     (arguments
      '(#:tests? #f)) ; FIXME: Many tests require a running database server.
-- 
cgit v1.2.3


From 7c4279322eaa800fae0e7197ec4757764a162f6c Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Wed, 22 Mar 2017 20:50:16 +0100
Subject: gnu: python-drmaa: Update to 0.7.7.

* gnu/packages/python.scm (python-drmaa): Update to 0.7.7.
---
 gnu/packages/python.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu')

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index b156214ac5..1e04639aa3 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -4805,7 +4805,7 @@ etc.  The core of this module is a decorator factory.")
 (define-public python-drmaa
   (package
     (name "python-drmaa")
-    (version "0.7.6")
+    (version "0.7.7")
     (source
      (origin
        (method url-fetch)
@@ -4813,7 +4813,7 @@ etc.  The core of this module is a decorator factory.")
              "https://pypi.python.org/packages/source/d/drmaa/drmaa-"
              version ".tar.gz"))
        (sha256
-        (base32 "0bzl9f9g34dlhwf09i3fdv7dqqzf2iq0w7d6c2bafx1nlap8qfbh"))))
+        (base32 "0xzqriqyvk5b8hszbavsyxd29wm3sxirm8zvvdm73rs2iq7w4hkx"))))
     (build-system python-build-system)
     ;; The test suite requires libdrmaa which is provided by the cluster
     ;; environment.  At runtime the environment variable DRMAA_LIBRARY_PATH
-- 
cgit v1.2.3


From 80e8d8517af92e2335f0bdcd9fbb38e621d2454a Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Wed, 22 Mar 2017 20:51:04 +0100
Subject: gnu: python-beautifulsoup4: Update to 4.5.3.

* gnu/packages/python.scm (python-beautifulsoup4): Update to 4.5.3.
---
 gnu/packages/python.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu')

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 1e04639aa3..98189c1d49 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -5675,14 +5675,14 @@ libxml2 and libxslt.")
 (define-public python-beautifulsoup4
   (package
     (name "python-beautifulsoup4")
-    (version "4.5.1")
+    (version "4.5.3")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "beautifulsoup4" version))
        (sha256
         (base32
-         "1qgmhw65ncsgccjhslgkkszif47q6gvxwqv4mim17agxd81p951w"))))
+         "0glaw1vyxnbp03fni7h5496n6iib0n5iim4gax1n0ngscs9s075j"))))
     (build-system python-build-system)
     (arguments
      `(#:phases
-- 
cgit v1.2.3


From 543782e1ff1e296d61ca528debe3fc6420f5e45a Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Wed, 22 Mar 2017 20:51:45 +0100
Subject: gnu: python-appdirs: Update to 1.4.3.

* gnu/packages/python.scm (python-appdirs): Update to 1.4.3.
---
 gnu/packages/python.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu')

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 98189c1d49..abf4ec6b7d 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -6751,7 +6751,7 @@ provided that can be used to do various manipulations with LilyPond files.")
 (define-public python-appdirs
   (package
     (name "python-appdirs")
-    (version "1.4.0")
+    (version "1.4.3")
     (source
       (origin
         (method url-fetch)
@@ -6761,7 +6761,7 @@ provided that can be used to do various manipulations with LilyPond files.")
                ".tar.gz"))
         (sha256
           (base32
-            "1iddva7v3fq0aqzsahkazxr7vpw28mqcrsy818z4wyiqnkplbhlg"))))
+            "14id6wxi12lgyw0mg3bcfnf888ad07jz9yj46gfzhn186z8rcn4y"))))
     (build-system python-build-system)
     (home-page "http://github.com/ActiveState/appdirs")
     (synopsis
-- 
cgit v1.2.3


From 36e0d9db90abe2d6e28994858cd0e74edb873112 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Wed, 22 Mar 2017 20:52:21 +0100
Subject: gnu: python-ipaddress: Update to 1.0.18.

* gnu/packages/python.scm (python-ipaddress): Update to 1.0.18.
---
 gnu/packages/python.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu')

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index abf4ec6b7d..1730d5d44c 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -7135,13 +7135,13 @@ implementations of ASN.1-based codecs and protocols.")
 (define-public python-ipaddress
   (package
     (name "python-ipaddress")
-    (version "1.0.16")
+    (version "1.0.18")
     (source (origin
               (method url-fetch)
               (uri (pypi-uri "ipaddress" version))
               (sha256
                (base32
-                "1c3imabdrw8nfksgjjflzg7h4ynjckqacb188rf541m74arq4cas"))))
+                "1q8klj9d84cmxgz66073x1j35cplr3r77vx1znhxiwl5w74391ax"))))
     (build-system python-build-system)
     (home-page "https://github.com/phihag/ipaddress")
     (synopsis "IP address manipulation library")
-- 
cgit v1.2.3


From 06fe79f263a70cf6f368406e23147a3e87eb1551 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Wed, 22 Mar 2017 20:53:14 +0100
Subject: gnu: python-rauth: Update to 0.7.3.

* gnu/packages/python.scm (python-rauth): Update to 0.7.3.
---
 gnu/packages/python.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu')

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 1730d5d44c..2b9b6cad16 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -9003,14 +9003,14 @@ Python at your fingertips, in Lisp form.")
 (define-public python-rauth
   (package
     (name "python-rauth")
-    (version "0.7.2")
+    (version "0.7.3")
     (source
       (origin
         (method url-fetch)
         (uri (pypi-uri "rauth" version))
         (sha256
          (base32
-          "00pq7zw429hhza9c0qzxiqp77m653jv09z92nralnmzwdf6pzicf"))))
+          "02kv8w8l98ky223avyq7vw7x1f2ya9chrm59r77ylq45qb0xnk2j"))))
     (build-system python-build-system)
     (arguments
      `(#:test-target "check"))
-- 
cgit v1.2.3


From e17a12482b7e125d4f07d33402647e615b7d4d1e Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Wed, 22 Mar 2017 20:53:51 +0100
Subject: gnu: python2-futures: Update to 3.0.5.

* gnu/packages/python.scm (python2-futures): Update to 3.0.5.
---
 gnu/packages/python.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu')

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 2b9b6cad16..c33d28213b 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -9099,14 +9099,14 @@ otherwise matches 3.2’s API.")
 (define-public python2-futures
   (package
     (name "python2-futures")
-    (version "3.0.3")
+    (version "3.0.5")
     (source
       (origin
         (method url-fetch)
         (uri (pypi-uri "futures" version))
         (sha256
          (base32
-          "1vcb34dqhzkhbq1957vdjszhhm5y3j9ba88dgwhqx2zynhmk9qig"))))
+          "1pw1z4329xvlabdpwqa6b7v2fxf7hl64m4cgr22ckbym8m8m4hh5"))))
     (build-system python-build-system)
     (arguments `(#:python ,python-2))
     (home-page "https://github.com/agronholm/pythonfutures")
-- 
cgit v1.2.3


From a06cd95ab0eea223eb44a6ac2b6d8996b49243b2 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Wed, 22 Mar 2017 20:54:21 +0100
Subject: gnu: python-natsort: Update to 5.0.2.

* gnu/packages/python.scm (python-natsort): Update to 5.0.2.
---
 gnu/packages/python.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu')

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index c33d28213b..d423ecde58 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -12303,13 +12303,13 @@ failures.")
 (define-public python-natsort
   (package
     (name "python-natsort")
-    (version "5.0.1")
+    (version "5.0.2")
     (source (origin
               (method url-fetch)
               (uri (pypi-uri "natsort" version))
               (sha256
                (base32
-                "1abld5p4a6n5zjnyw5mi2pv37gqalcybv2brjr2y6l9l2p8v9mja"))))
+                "0bh6j0l8iapjnsgg3bs6q075cnzjl6zw1vlgqyv3qrygm2cxypkn"))))
     (build-system python-build-system)
     (arguments
      `(#:phases
-- 
cgit v1.2.3


From b27bd0b05764e442f54d56e5398ed6cfc3dc4901 Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Wed, 22 Mar 2017 21:15:17 +0100
Subject: gnu: youtube-dl: Update to 2017.03.22.

* gnu/packages/video.scm (youtube-dl): Update to 2017.03.22.
---
 gnu/packages/video.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu')

diff --git a/gnu/packages/video.scm b/gnu/packages/video.scm
index 3af1e5282f..201d755a9a 100644
--- a/gnu/packages/video.scm
+++ b/gnu/packages/video.scm
@@ -975,7 +975,7 @@ access to mpv's powerful playback capabilities.")
 (define-public youtube-dl
   (package
     (name "youtube-dl")
-    (version "2017.03.16")
+    (version "2017.03.22")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://yt-dl.org/downloads/"
@@ -983,7 +983,7 @@ access to mpv's powerful playback capabilities.")
                                   version ".tar.gz"))
               (sha256
                (base32
-                "14nlgl0kh4mwl7sx58vd7nxr5iklxi00612lmydy91ngm6ykrpsm"))))
+                "1zz97g23diggcnqg2hjq9grijskly8ag727f1i509hl7z0lxkh69"))))
     (build-system python-build-system)
     (arguments
      ;; The problem here is that the directory for the man page and completion
-- 
cgit v1.2.3


From 939b6b113bcd94c80fe50acdd634a2c0338b343c Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 23 Mar 2017 11:20:13 +0100
Subject: gnu: star: Update to 2.5.3a.

* gnu/packages/bioinformatics.scm (star): Update to 2.5.3a.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu')

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 97380fc032..232c7db838 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -5051,7 +5051,7 @@ application of SortMeRNA is filtering rRNA from metatranscriptomic data.")
 (define-public star
   (package
     (name "star")
-    (version "2.5.2b")
+    (version "2.5.3a")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://github.com/alexdobin/STAR/archive/"
@@ -5059,7 +5059,7 @@ application of SortMeRNA is filtering rRNA from metatranscriptomic data.")
               (file-name (string-append name "-" version ".tar.gz"))
               (sha256
                (base32
-                "1na6np880r1zaamiy00hy8bid5anpy0kgf63587v2yl080krk2zq"))
+                "013wirlz8lllgjyagl48l75n1isxyabqb3sj7qlsl0x1rmvqw99a"))
               (modules '((guix build utils)))
               (snippet
                '(begin
-- 
cgit v1.2.3


From df7309fc6ed7ac15e50de22396e761ec0815c5e9 Mon Sep 17 00:00:00 2001
From: Peter Mikkelsen <petermikkelsen10@gmail.com>
Date: Mon, 20 Mar 2017 20:17:09 +0100
Subject: gnu: Add ghc-code-page.
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

* gnu/packages/haskell.scm (ghc-code-page): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
---
 gnu/packages/haskell.scm | 22 ++++++++++++++++++++++
 1 file changed, 22 insertions(+)

(limited to 'gnu')

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index 2415881e8e..d48983a81a 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -9,6 +9,7 @@
 ;;; Copyright © 2015, 2016, 2017 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2016, 2017 David Craven <david@craven.ch>
 ;;; Copyright © 2017 Danny Milosavljevic <dannym@scratchpost.org>
+;;; Copyright © 2017 Peter Mikkelsen <petermikkelsen10@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -562,6 +563,27 @@ package.")
 package.")
     (license license:bsd-3)))
 
+(define-public ghc-code-page
+  (package
+  (name "ghc-code-page")
+  (version "0.1.3")
+  (source
+   (origin
+     (method url-fetch)
+     (uri (string-append
+           "https://hackage.haskell.org/package/code-page/code-page-"
+           version ".tar.gz"))
+      (sha256
+       (base32
+        "1491frk4jx6dlhifky9dvcxbsbcfssrz979a5hp5zn061rh8cp76"))))
+  (build-system haskell-build-system)
+  (home-page "https://github.com/RyanGlScott/code-page")
+  (synopsis "Windows code page library for Haskell")
+  (description "A cross-platform library with functions for adjusting
+code pages on Windows.  On all other operating systems, the library does
+nothing.")
+  (license license:bsd-3)))
+
 (define-public ghc-haddock-library
   (package
     (name "ghc-haddock-library")
-- 
cgit v1.2.3


From c53af0016e283ef642ac43ccc2ee5d650f06a888 Mon Sep 17 00:00:00 2001
From: Peter Mikkelsen <petermikkelsen10@gmail.com>
Date: Mon, 20 Mar 2017 20:17:10 +0100
Subject: gnu: idris: Update to 0.99.1.
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

* gnu/packages/idris.scm (idris): Update to 0.99.1.
[inputs]: Add ghc-code-page.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
---
 gnu/packages/idris.scm | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

(limited to 'gnu')

diff --git a/gnu/packages/idris.scm b/gnu/packages/idris.scm
index 02198a5a7d..2b7f4cc9dd 100644
--- a/gnu/packages/idris.scm
+++ b/gnu/packages/idris.scm
@@ -31,7 +31,7 @@
 (define-public idris
   (package
     (name "idris")
-    (version "0.99")
+    (version "0.99.1")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -39,7 +39,7 @@
                     "idris-" version "/idris-" version ".tar.gz"))
               (sha256
                (base32
-                "1sd4vy5rx0mp32xj99qijhknkgw4d2rxvz6wiy3pym6kaqmc497i"))))
+                "12kw452arnl5ldip2x749j5np3l40bv7asqdv9w0f60j45hii40r"))))
     (build-system haskell-build-system)
     (inputs
      `(("gmp" ,gmp)
@@ -53,6 +53,7 @@
        ("ghc-blaze-html" ,ghc-blaze-html)
        ("ghc-blaze-markup" ,ghc-blaze-markup)
        ("ghc-cheapskate" ,ghc-cheapskate)
+       ("ghc-code-page" ,ghc-code-page)
        ("ghc-fingertree" ,ghc-fingertree)
        ("ghc-fsnotify" ,ghc-fsnotify)
        ("ghc-ieee754" ,ghc-ieee754)
-- 
cgit v1.2.3