From 8b1c8e4e27e3973ea97ecf7d774540a43886b90e Mon Sep 17 00:00:00 2001
From: Mark H Weaver <mhw@netris.org>
Date: Thu, 11 Jun 2015 10:07:34 -0400
Subject: gnu: inetutils: Update to 1.9.4.

* gnu/packages/admin.scm (inetutils): Update to 1.9.4.
---
 gnu/packages/admin.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/admin.scm b/gnu/packages/admin.scm
index a96ce9cdfb..960264bc2d 100644
--- a/gnu/packages/admin.scm
+++ b/gnu/packages/admin.scm
@@ -152,14 +152,14 @@ (define-public pies
 (define-public inetutils
   (package
     (name "inetutils")
-    (version "1.9.3")
+    (version "1.9.4")
     (source (origin
              (method url-fetch)
              (uri (string-append "mirror://gnu/inetutils/inetutils-"
                                  version ".tar.gz"))
              (sha256
               (base32
-               "06dshajjpyi9sxi7qfki9gnp5r3nxvyvf81r81gx0x2qkqzqcxlj"))))
+               "05n65k4ixl85dc6rxc51b1b732gnmm8xnqi424dy9f1nz7ppb3xy"))))
     (build-system gnu-build-system)
     (arguments `(;; FIXME: `tftp.sh' relies on `netstat' from utils-linux,
                  ;; which is currently missing.
-- 
cgit v1.2.3


From 4510b2da3e496f22495ecf9196e8f81dd1806b6d Mon Sep 17 00:00:00 2001
From: 宋文武 <iyzsong@gmail.com>
Date: Thu, 11 Jun 2015 23:29:19 +0800
Subject: gnu: Add librest.

* gnu/packages/gnome.scm (librest): New variable.
---
 gnu/packages/gnome.scm | 34 ++++++++++++++++++++++++++++++++++
 1 file changed, 34 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/gnome.scm b/gnu/packages/gnome.scm
index 4af1d13495..4599f4d234 100644
--- a/gnu/packages/gnome.scm
+++ b/gnu/packages/gnome.scm
@@ -1854,6 +1854,40 @@ (define-public glib-networking
 library.")
     (license license:lgpl2.0+)))
 
+(define-public librest
+  (package
+    (name "librest")
+    (version "0.7.93")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "mirror://gnome/sources/rest/"
+                                  (version-major+minor version)  "/"
+                                  "rest-" version ".tar.xz"))
+              (sha256
+               (base32
+                "05mj10hhiik23ai8w4wkk5vhsp7hcv24bih5q3fl82ilam268467"))))
+    (build-system gnu-build-system)
+    (arguments
+     '(#:tests? #f ; tests require internet connection
+       #:configure-flags
+       '("--with-ca-certificates=/etc/ssl/certs/ca-certificates.crt")))
+    (native-inputs
+     `(("glib-mkenums" ,glib "bin")
+       ("gobject-introspection" ,gobject-introspection)
+       ("pkg-config" ,pkg-config)))
+    (propagated-inputs
+     ;; rest-0.7.pc refers to all these.
+     `(("glib"    ,glib)
+       ("libsoup" ,libsoup)
+       ("libxml2" ,libxml2)))
+    (home-page "http://www.gtk.org/")
+    (synopsis "RESTful web api query library")
+    (description
+     "This library was designed to make it easier to access web services that
+claim to be \"RESTful\".  It includes convenience wrappers for libsoup and
+libxml to ease remote use of the RESTful API.")
+    (license license:lgpl2.1+)))
+
 (define-public libsoup
   (package
     (name "libsoup")
-- 
cgit v1.2.3


From b45ce07a8a338590cb45d70cf8cf9c08d59744f8 Mon Sep 17 00:00:00 2001
From: Mark H Weaver <mhw@netris.org>
Date: Thu, 11 Jun 2015 14:37:18 -0400
Subject: gnu: gnupg: Update to 2.1.5.

* gnu/packages/gnupg.scm (gnupg): Update to 2.1.5.
---
 gnu/packages/gnupg.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/gnupg.scm b/gnu/packages/gnupg.scm
index 5724bc8348..2044ef0501 100644
--- a/gnu/packages/gnupg.scm
+++ b/gnu/packages/gnupg.scm
@@ -190,14 +190,14 @@ (define-public npth
 (define-public gnupg
   (package
     (name "gnupg")
-    (version "2.1.4")
+    (version "2.1.5")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://gnupg/gnupg/gnupg-" version
                                   ".tar.bz2"))
               (sha256
                (base32
-                "1c3c89b7ziknz6h1dnwmfjhgyy28g982rcncrhmhylb8v3npw4k4"))))
+                "0k5818r847zplbrwjp6i48s6xb5zy44rny2kmbisd6y3c1qml45m"))))
     (build-system gnu-build-system)
     (inputs
      `(("bzip2" ,bzip2)
-- 
cgit v1.2.3


From 0004c5904c2e69a89005eac8b6322d18a8e9f611 Mon Sep 17 00:00:00 2001
From: Ludovic Courtès <ludo@gnu.org>
Date: Thu, 11 Jun 2015 23:06:06 +0200
Subject: packages: Make 'location' field innate.

* guix/packages.scm (<package>)[location]: Add 'innate' property.
* guix/build-system/gnu.scm (static-package): Remove 'loc' parameter and
  'location' field.
* gnu/packages/autotools.scm (autoconf-wrapper): Remove 'location' field.
* gnu/packages/commencement.scm (gnu-make-boot0, diffutils-boot0, gcc-final):
  Likewise.
* gnu/packages/cross-base.scm (cross): Likewise.
* gnu/packages/emacs.scm (emacs-no-x, emacs-no-x-toolkit): Likewise.
* gnu/packages/make-bootstrap.scm (tarball-package): Likewise.
* gnu/packages/maths.scm (petsc-complex): Likewise.
---
 gnu/packages/autotools.scm      | 1 -
 gnu/packages/commencement.scm   | 3 ---
 gnu/packages/cross-base.scm     | 1 -
 gnu/packages/emacs.scm          | 2 --
 gnu/packages/make-bootstrap.scm | 3 +--
 gnu/packages/maths.scm          | 1 -
 guix/build-system/gnu.scm       | 4 +---
 guix/packages.scm               | 3 ++-
 8 files changed, 4 insertions(+), 14 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/autotools.scm b/gnu/packages/autotools.scm
index 24ff90cc5c..f2b4d95b95 100644
--- a/gnu/packages/autotools.scm
+++ b/gnu/packages/autotools.scm
@@ -95,7 +95,6 @@ (define* (autoconf-wrapper #:optional (autoconf autoconf))
 only be used internally---users should not end up distributing `configure'
 files with a system-specific shebang."
   (package (inherit autoconf)
-    (location (source-properties->location (current-source-location)))
     (name (string-append (package-name autoconf) "-wrapper"))
     (build-system trivial-build-system)
     (inputs `(("guile"
diff --git a/gnu/packages/commencement.scm b/gnu/packages/commencement.scm
index 9611ff2620..a5402f0556 100644
--- a/gnu/packages/commencement.scm
+++ b/gnu/packages/commencement.scm
@@ -65,7 +65,6 @@ (define gnu-make-boot0
   (package-with-bootstrap-guile
    (package (inherit gnu-make)
      (name "make-boot0")
-     (location (source-properties->location (current-source-location)))
      (arguments
       `(#:guile ,%bootstrap-guile
         #:implicit-inputs? #f
@@ -93,7 +92,6 @@ (define diffutils-boot0
                                             ,@%bootstrap-inputs)
                                           #:guile %bootstrap-guile)))
      (package (inherit p)
-       (location (source-properties->location (current-source-location)))
        (arguments `(#:tests? #f         ; the test suite needs diffutils
                     ,@(package-arguments p)))))))
 
@@ -531,7 +529,6 @@ (define-public gcc-final
   ;; The final GCC.
   (package (inherit gcc-boot0)
     (name "gcc")
-    (location (source-properties->location (current-source-location)))
     (arguments
      `(#:guile ,%bootstrap-guile
        #:implicit-inputs? #f
diff --git a/gnu/packages/cross-base.scm b/gnu/packages/cross-base.scm
index 9a459400e8..f1aca505d8 100644
--- a/gnu/packages/cross-base.scm
+++ b/gnu/packages/cross-base.scm
@@ -38,7 +38,6 @@ (define-module (gnu packages cross-base)
 
 (define (cross p target)
   (package (inherit p)
-    (location (source-properties->location (current-source-location)))
     (name (string-append (package-name p) "-cross-" target))
     (arguments
      (substitute-keyword-arguments (package-arguments p)
diff --git a/gnu/packages/emacs.scm b/gnu/packages/emacs.scm
index fbddff1cf6..0f71c77bf2 100644
--- a/gnu/packages/emacs.scm
+++ b/gnu/packages/emacs.scm
@@ -123,7 +123,6 @@ (define-public emacs-no-x
   ;; This is the version that you should use as an input to packages that just
   ;; need to byte-compile .el files.
   (package (inherit emacs)
-    (location (source-properties->location (current-source-location)))
     (name "emacs-no-x")
     (synopsis "The extensible, customizable, self-documenting text
 editor (console only)")
@@ -138,7 +137,6 @@ (define-public emacs-no-x
 
 (define-public emacs-no-x-toolkit
   (package (inherit emacs)
-    (location (source-properties->location (current-source-location)))
     (name "emacs-no-x-toolkit")
     (synopsis "The extensible, customizable, self-documenting text
 editor (without an X toolkit)" )
diff --git a/gnu/packages/make-bootstrap.scm b/gnu/packages/make-bootstrap.scm
index 88fad0e604..7f1b6d50b0 100644
--- a/gnu/packages/make-bootstrap.scm
+++ b/gnu/packages/make-bootstrap.scm
@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2012, 2013, 2014 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2012, 2013, 2014, 2015 Ludovic Courtès <ludo@gnu.org>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -605,7 +605,6 @@ (define %guile-static-stripped
 (define (tarball-package pkg)
   "Return a package containing a tarball of PKG."
   (package (inherit pkg)
-    (location (source-properties->location (current-source-location)))
     (name (string-append (package-name pkg) "-tarball"))
     (build-system trivial-build-system)
     (native-inputs `(("tar" ,tar)
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 4d837c85e2..6fbe6fd27d 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -560,7 +560,6 @@ (define-public petsc
 
 (define-public petsc-complex
   (package (inherit petsc)
-    (location (source-properties->location (current-source-location)))
     (name "petsc-complex")
     (arguments
      (substitute-keyword-arguments (package-arguments petsc)
diff --git a/guix/build-system/gnu.scm b/guix/build-system/gnu.scm
index da664e5422..05b6e6f680 100644
--- a/guix/build-system/gnu.scm
+++ b/guix/build-system/gnu.scm
@@ -160,12 +160,10 @@ (define (static-libgcc-package p)
   "A version of P linked with `-static-gcc'."
   (package-with-extra-configure-variable p "LDFLAGS" "-static-libgcc"))
 
-(define* (static-package p #:optional (loc (current-source-location))
-                         #:key (strip-all? #t))
+(define* (static-package p #:key (strip-all? #t))
   "Return a statically-linked version of package P.  If STRIP-ALL? is true,
 use `--strip-all' as the arguments to `strip'."
   (package (inherit p)
-    (location (source-properties->location loc))
     (arguments
      (let ((a (default-keyword-arguments (package-arguments p)
                 '(#:configure-flags '()
diff --git a/guix/packages.scm b/guix/packages.scm
index c955b35155..c900541e53 100644
--- a/guix/packages.scm
+++ b/guix/packages.scm
@@ -240,7 +240,8 @@ (define-record-type* <package>
 
   (location package-location
             (default (and=> (current-source-location)
-                            source-properties->location))))
+                            source-properties->location))
+            (innate)))
 
 (set-record-type-printer! <package>
                           (lambda (package port)
-- 
cgit v1.2.3


From e21adc768e7e40362a26b60e73ecc30e988d79e0 Mon Sep 17 00:00:00 2001
From: Ludovic Courtès <ludo@gnu.org>
Date: Thu, 11 Jun 2015 23:10:26 +0200
Subject: gnu: guix: Update snapshot.

* gnu/packages/package-management.scm (guix-devel): Update to a43b55f.
  [source]: Add 'file-name' field.
  [native-inputs]: Add HELP2MAN.
---
 gnu/packages/package-management.scm | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/package-management.scm b/gnu/packages/package-management.scm
index db05969139..a2c74c2fe6 100644
--- a/gnu/packages/package-management.scm
+++ b/gnu/packages/package-management.scm
@@ -38,6 +38,7 @@ (define-module (gnu packages package-management)
   #:use-module (gnu packages perl)
   #:use-module (gnu packages curl)
   #:use-module (gnu packages web)
+  #:use-module (gnu packages man)
   #:use-module (gnu packages emacs)
   #:use-module (gnu packages openssl)
   #:use-module (gnu packages bdw-gc))
@@ -150,7 +151,7 @@ (define guix-devel
   ;;
   ;; Note: use a short commit id; when using the long one, the limit on socket
   ;; file names is exceeded while running the tests.
-  (let ((commit "c2ee19e"))
+  (let ((commit "a43b55f"))
     (package (inherit guix-0.8.2)
       (version (string-append "0.8.2." commit))
       (source (origin
@@ -160,7 +161,8 @@ (define guix-devel
                       (commit commit)))
                 (sha256
                  (base32
-                  "1gwc1gypgscxg2m3n2vd0mw4dmxr7vsisqgh3y0lr05q9z5742sj"))))
+                  "1r0l8gfh5nxc1j0sqj8ywkg280k9qbj7zsk33z84rvl7l0nwnk88"))
+                (file-name (string-append "guix-" version "-checkout"))))
       (arguments
        (substitute-keyword-arguments (package-arguments guix-0.8.2)
          ((#:phases phases)
@@ -180,6 +182,7 @@ (define guix-devel
          ("gettext" ,gnu-gettext)
          ("texinfo" ,texinfo)
          ("graphviz" ,graphviz)
+         ("help2man" ,help2man)
          ,@(package-native-inputs guix-0.8.2))))))
 
 (define-public guix guix-devel)
-- 
cgit v1.2.3


From 4f467e33de0b64b1afd935d14ec6a4839e03bdfc Mon Sep 17 00:00:00 2001
From: Mark H Weaver <mhw@netris.org>
Date: Fri, 12 Jun 2015 01:24:58 -0400
Subject: gnu: openssl: Update to 1.0.2b.

* gnu/packages/openssl.scm (openssl): Update to 1.0.2b.
---
 gnu/packages/openssl.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/openssl.scm b/gnu/packages/openssl.scm
index 1ed7a7a1f2..f55e54465c 100644
--- a/gnu/packages/openssl.scm
+++ b/gnu/packages/openssl.scm
@@ -29,14 +29,14 @@ (define-module (gnu packages openssl)
 (define-public openssl
   (package
    (name "openssl")
-   (version "1.0.2a")
+   (version "1.0.2b")
    (source (origin
             (method url-fetch)
             (uri (string-append "ftp://ftp.openssl.org/source/openssl-" version
                                 ".tar.gz"))
             (sha256
              (base32
-              "0jijgzf72659pikms2bc5w31h78xrd1h5zp2r01an2h340y3kdhm"))
+              "0gwf4fy1yqmai6wph0g9lh09iarwxaa70hm7jm0rf1qakz68im6m"))
             (patches (list (search-patch "openssl-runpath.patch")))))
    (build-system gnu-build-system)
    (native-inputs `(("perl" ,perl)))
-- 
cgit v1.2.3


From dc7b1817f6f75fa7e69b7675c313095cc1fddc63 Mon Sep 17 00:00:00 2001
From: Mark H Weaver <mhw@netris.org>
Date: Fri, 12 Jun 2015 01:46:03 -0400
Subject: Revert "gnu: openssl: Update to 1.0.2b."

This reverts commit 4f467e33de0b64b1afd935d14ec6a4839e03bdfc.
---
 gnu/packages/openssl.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/openssl.scm b/gnu/packages/openssl.scm
index f55e54465c..1ed7a7a1f2 100644
--- a/gnu/packages/openssl.scm
+++ b/gnu/packages/openssl.scm
@@ -29,14 +29,14 @@ (define-module (gnu packages openssl)
 (define-public openssl
   (package
    (name "openssl")
-   (version "1.0.2b")
+   (version "1.0.2a")
    (source (origin
             (method url-fetch)
             (uri (string-append "ftp://ftp.openssl.org/source/openssl-" version
                                 ".tar.gz"))
             (sha256
              (base32
-              "0gwf4fy1yqmai6wph0g9lh09iarwxaa70hm7jm0rf1qakz68im6m"))
+              "0jijgzf72659pikms2bc5w31h78xrd1h5zp2r01an2h340y3kdhm"))
             (patches (list (search-patch "openssl-runpath.patch")))))
    (build-system gnu-build-system)
    (native-inputs `(("perl" ,perl)))
-- 
cgit v1.2.3


From 48d21d6cd600cabc147cfec243518931bbc3169a Mon Sep 17 00:00:00 2001
From: Eric Bavier <bavier@member.fsf.org>
Date: Thu, 11 Jun 2015 17:51:47 -0500
Subject: gnu: ghc: Patch runtime references to /bin/sh.

* gnu/packages/haskell.scm (ghc)[arguments]: Rename
  'unpack-and-fix-testsuite' phase to 'unpack-testsuite-and-fix-bins'.
  Patch source files that reference /bin/sh.
---
 gnu/packages/haskell.scm | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index ac87de540e..75bbb24479 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -144,7 +144,7 @@ (define-public ghc
               (ghc-bootstrap-prefix
                (string-append ghc-bootstrap-path "/usr" )))
          (alist-cons-after
-          'unpack-bin 'unpack-and-fix-testsuite
+          'unpack-bin 'unpack-testsuite-and-fix-bins
           (lambda* (#:key inputs outputs #:allow-other-keys)
             (with-directory-excursion ".."
               (copy-file (assoc-ref inputs "ghc-testsuite")
@@ -155,7 +155,9 @@ (define-public ghc
                       "testsuite/timeout/timeout.py"
                       "testsuite/timeout/timeout.hs"
                       "testsuite/tests/rename/prog006/Setup.lhs"
-                      "testsuite/tests/programs/life_space_leak/life.test")
+                      "testsuite/tests/programs/life_space_leak/life.test"
+                      "libraries/process/System/Process/Internals.hs"
+                      "libraries/unix/cbits/execvpe.c")
               (("/bin/sh") (which "sh"))
               (("/bin/rm") "rm"))
             #t)
-- 
cgit v1.2.3


From e0a02cb21f7758f5e60f518f9ee115b64aac74da Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Mon, 1 Jun 2015 12:09:44 +0200
Subject: gnu: ngs-sdk: Update to version 1.1.1.

* gnu/packages/bioinformatics.scm (ngs-sdk): Update to version 1.1.1.
---
 gnu/packages/bioinformatics.scm | 18 ++----------------
 1 file changed, 2 insertions(+), 16 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index c7836f173e..1334600af6 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -1331,7 +1331,7 @@ (define-public samtools-0.1
 (define-public ngs-sdk
   (package
     (name "ngs-sdk")
-    (version "1.1.0")
+    (version "1.1.1")
     (source
      (origin
        (method url-fetch)
@@ -1341,7 +1341,7 @@ (define-public ngs-sdk
        (file-name (string-append name "-" version ".tar.gz"))
        (sha256
         (base32
-         "09fakv9w87lfg9g70kwzmnryqdjj1sz2c7kw01i6drjf787gkjhw"))))
+         "1x58gpm574n0xmk2a98gmikbgycq78ia0bvnb42k5ck34fmd5v8y"))))
     (build-system gnu-build-system)
     (arguments
      `(#:parallel-build? #f ; not supported
@@ -1351,20 +1351,6 @@ (define-public ngs-sdk
         'configure
         (lambda* (#:key outputs #:allow-other-keys)
           (let ((out (assoc-ref outputs "out")))
-            ;; Only replace the version suffix, not the version number in the
-            ;; directory name; fixed in commit 46d4509fa8 (no release yet).
-            (substitute* "setup/konfigure.perl"
-              (((string-append "\\$\\(subst "
-                               "(\\$\\(VERSION[^\\)]*\\)),"
-                               "(\\$\\([^\\)]+\\)),"
-                               "(\\$\\([^\\)]+\\)|\\$\\@)"
-                               "\\)")
-                _ pattern replacement target)
-               (string-append "$(patsubst "
-                              "%" pattern ","
-                              "%" replacement ","
-                              target ")")))
-
             ;; The 'configure' script doesn't recognize things like
             ;; '--enable-fast-install'.
             (zero? (system* "./configure"
-- 
cgit v1.2.3


From 741115b6490c111f9db7b86964b13bdb22fd6dd0 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Thu, 28 May 2015 15:53:14 +0200
Subject: gnu: Add libsvm.

* gnu/packages/machine-learning.scm: New file.
* gnu-system.am (GNU_SYSTEM_MODULES): Add it.
---
 gnu-system.am                     |  1 +
 gnu/packages/machine-learning.scm | 65 +++++++++++++++++++++++++++++++++++++++
 2 files changed, 66 insertions(+)
 create mode 100644 gnu/packages/machine-learning.scm

(limited to 'gnu/packages')

diff --git a/gnu-system.am b/gnu-system.am
index 978e839bfa..d79c2c7917 100644
--- a/gnu-system.am
+++ b/gnu-system.am
@@ -196,6 +196,7 @@ GNU_SYSTEM_MODULES =				\
   gnu/packages/lxqt.scm				\
   gnu/packages/lynx.scm				\
   gnu/packages/m4.scm				\
+  gnu/packages/machine-learning.scm		\
   gnu/packages/man.scm				\
   gnu/packages/mail.scm				\
   gnu/packages/make-bootstrap.scm		\
diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm
new file mode 100644
index 0000000000..78d7e649a9
--- /dev/null
+++ b/gnu/packages/machine-learning.scm
@@ -0,0 +1,65 @@
+;;; GNU Guix --- Functional package management for GNU
+;;; Copyright © 2015 Ricardo Wurmus <rekado@elephly.net>
+;;;
+;;; 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 machine-learning)
+  #:use-module ((guix licenses) #:prefix license:)
+  #:use-module (guix packages)
+  #:use-module (guix utils)
+  #:use-module (guix download)
+  #:use-module (guix build-system gnu)
+  #:use-module (gnu packages))
+
+(define-public libsvm
+  (package
+    (name "libsvm")
+    (version "3.20")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append
+             "https://github.com/cjlin1/libsvm/archive/v"
+             (string-delete #\. version) ".tar.gz"))
+       (file-name (string-append name "-" version ".tar.gz"))
+       (sha256
+        (base32
+         "1jpjlql3frjza7zxzrqqr2firh44fjb8fqsdmvz6bjz7sb47zgp4"))))
+    (build-system gnu-build-system)
+    (arguments
+     `(#:tests? #f ;no "check" target
+       #:phases (modify-phases %standard-phases
+                  (delete 'configure)
+                  (replace
+                   'install
+                   (lambda* (#:key outputs #:allow-other-keys)
+                     (let* ((out (assoc-ref outputs "out"))
+                            (bin (string-append out "/bin/")))
+                       (mkdir-p bin)
+                       (for-each (lambda (file)
+                                   (copy-file file (string-append bin file)))
+                                 '("svm-train"
+                                   "svm-predict"
+                                   "svm-scale")))
+                     #t)))))
+    (home-page "http://www.csie.ntu.edu.tw/~cjlin/libsvm/")
+    (synopsis "Library for Support Vector Machines")
+    (description
+     "LIBSVM is a machine learning library for support vector
+classification, (C-SVC, nu-SVC), regression (epsilon-SVR, nu-SVR) and
+distribution estimation (one-class SVM).  It supports multi-class
+classification.")
+    (license license:bsd-3)))
-- 
cgit v1.2.3


From 71f80f548741fa61fa3bc2039c296feb1a25d4de Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Tue, 2 Jun 2015 15:10:37 +0200
Subject: gnu: Add python-libsvm.

* gnu/packages/machine-learning.scm (python-libsvm): New variable.
---
 gnu/packages/machine-learning.scm | 35 ++++++++++++++++++++++++++++++++++-
 1 file changed, 34 insertions(+), 1 deletion(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm
index 78d7e649a9..b35e9b72c6 100644
--- a/gnu/packages/machine-learning.scm
+++ b/gnu/packages/machine-learning.scm
@@ -22,7 +22,8 @@ (define-module (gnu packages machine-learning)
   #:use-module (guix utils)
   #:use-module (guix download)
   #:use-module (guix build-system gnu)
-  #:use-module (gnu packages))
+  #:use-module (gnu packages)
+  #:use-module (gnu packages python))
 
 (define-public libsvm
   (package
@@ -63,3 +64,35 @@ (define-public libsvm
 distribution estimation (one-class SVM).  It supports multi-class
 classification.")
     (license license:bsd-3)))
+
+(define-public python-libsvm
+  (package (inherit libsvm)
+    (name "python-libsvm")
+    (build-system gnu-build-system)
+    (arguments
+     `(#:tests? #f ;no "check" target
+       #:make-flags '("-C" "python")
+       #:phases
+       (modify-phases %standard-phases
+         (delete 'configure)
+         (replace
+          'install
+          (lambda* (#:key inputs outputs #:allow-other-keys)
+            (let ((site (string-append (assoc-ref outputs "out")
+                                       "/lib/python"
+                                       (string-take
+                                        (string-take-right
+                                         (assoc-ref inputs "python") 5) 3)
+                                       "/site-packages/")))
+              (substitute* "python/svm.py"
+                (("../libsvm.so.2") "libsvm.so.2"))
+              (mkdir-p site)
+              (for-each (lambda (file)
+                          (copy-file file (string-append site (basename file))))
+                        (find-files "python" "\\.py"))
+              (copy-file "libsvm.so.2"
+                         (string-append site "libsvm.so.2")))
+            #t)))))
+    (inputs
+     `(("python" ,python)))
+    (synopsis "Python bindings of libSVM")))
-- 
cgit v1.2.3


From 0931c6091ccf028b9556c0c3d7e1e3157034b97d Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Tue, 2 Jun 2015 15:47:22 +0200
Subject: gnu: Add randomjungle.

* gnu/packages/machine-learning.scm (randomjungle): New variable.
---
 gnu/packages/machine-learning.scm | 50 ++++++++++++++++++++++++++++++++++++++-
 1 file changed, 49 insertions(+), 1 deletion(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm
index b35e9b72c6..cfeb1daf63 100644
--- a/gnu/packages/machine-learning.scm
+++ b/gnu/packages/machine-learning.scm
@@ -23,7 +23,12 @@ (define-module (gnu packages machine-learning)
   #:use-module (guix download)
   #:use-module (guix build-system gnu)
   #:use-module (gnu packages)
-  #:use-module (gnu packages python))
+  #:use-module (gnu packages boost)
+  #:use-module (gnu packages compression)
+  #:use-module (gnu packages gcc)
+  #:use-module (gnu packages maths)
+  #:use-module (gnu packages python)
+  #:use-module (gnu packages xml))
 
 (define-public libsvm
   (package
@@ -96,3 +101,46 @@ (define-public python-libsvm
     (inputs
      `(("python" ,python)))
     (synopsis "Python bindings of libSVM")))
+
+(define-public randomjungle
+  (package
+    (name "randomjungle")
+    (version "2.1.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append
+             "http://www.imbs-luebeck.de/imbs/sites/default/files/u59/"
+             "randomjungle-" version ".tar_.gz"))
+       (sha256
+        (base32
+         "12c8rf30cla71swx2mf4ww9mfd8jbdw5lnxd7dxhyw1ygrvg6y4w"))))
+    (build-system gnu-build-system)
+    (arguments
+     `(#:configure-flags
+       (list (string-append "--with-boost="
+                            (assoc-ref %build-inputs "boost")))
+       #:phases
+       (modify-phases %standard-phases
+         (add-before
+          'configure 'set-CXXFLAGS
+          (lambda _
+            (setenv "CXXFLAGS" "-fpermissive ")
+            #t)))))
+    (inputs
+     `(("boost" ,boost)
+       ("gsl" ,gsl)
+       ("libxml2" ,libxml2)
+       ("zlib" ,zlib)))
+    (native-inputs
+     `(("gfortran" ,gfortran-4.8)))
+    (home-page "http://www.imbs-luebeck.de/imbs/de/node/227/")
+    (synopsis "Implementation of the Random Forests machine learning method")
+    (description
+     "Random Jungle is an implementation of Random Forests.  It is supposed to
+analyse high dimensional data.  In genetics, it can be used for analysing big
+Genome Wide Association (GWA) data.  Random Forests is a powerful machine
+learning method.  Most interesting features are variable selection, missing
+value imputation, classifier creation, generalization error estimation and
+sample proximities between pairs of cases.")
+    (license license:gpl3+)))
-- 
cgit v1.2.3


From 36742f438939fc30c8ebd71400218e31540e8acb Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Wed, 3 Jun 2015 12:56:16 +0200
Subject: gnu: Add Couger.

* gnu/packages/bioinformatics.scm (couger): New variable.
---
 gnu/packages/bioinformatics.scm | 71 +++++++++++++++++++++++++++++++++++++++++
 1 file changed, 71 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 1334600af6..df627fbe48 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -34,6 +34,7 @@ (define-module (gnu packages bioinformatics)
   #:use-module (gnu packages file)
   #:use-module (gnu packages java)
   #:use-module (gnu packages linux)
+  #:use-module (gnu packages machine-learning)
   #:use-module (gnu packages maths)
   #:use-module (gnu packages ncurses)
   #:use-module (gnu packages perl)
@@ -438,6 +439,76 @@ (define-public clipper
      "CLIPper is a tool to define peaks in CLIP-seq datasets.")
     (license license:gpl2)))
 
+(define-public couger
+  (package
+    (name "couger")
+    (version "1.8.2")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append
+                    "http://couger.oit.duke.edu/static/assets/COUGER"
+                    version ".zip"))
+              (sha256
+               (base32
+                "04p2b14nmhzxw5h72mpzdhalv21bx4w9b87z0wpw0xzxpysyncmq"))))
+    (build-system gnu-build-system)
+    (arguments
+     `(#:tests? #f
+       #:phases
+       (modify-phases %standard-phases
+         (delete 'configure)
+         (delete 'build)
+         (replace
+          'install
+          (lambda* (#:key outputs #:allow-other-keys)
+            (let ((out (assoc-ref outputs "out")))
+              (copy-recursively "src" (string-append out "/src"))
+              (mkdir (string-append out "/bin"))
+              ;; Add "src" directory to module lookup path.
+              (substitute* "couger"
+                (("from argparse")
+                 (string-append "import sys\nsys.path.append(\""
+                                out "\")\nfrom argparse")))
+              (copy-file "couger" (string-append out "/bin/couger")))
+            #t))
+         (add-after
+          'install 'wrap-program
+          (lambda* (#:key inputs outputs #:allow-other-keys)
+            ;; Make sure 'couger' runs with the correct PYTHONPATH.
+            (let* ((out (assoc-ref outputs "out"))
+                   (path (getenv "PYTHONPATH")))
+              (wrap-program (string-append out "/bin/couger")
+                `("PYTHONPATH" ":" prefix (,path))))
+            #t)))))
+    (inputs
+     `(("python" ,python-2)
+       ("python2-pillow" ,python2-pillow)
+       ("python2-numpy" ,python2-numpy)
+       ("python2-scipy" ,python2-scipy)
+       ("python2-matplotlib" ,python2-matplotlib)))
+    (propagated-inputs
+     `(("r" ,r)
+       ("libsvm" ,libsvm)
+       ("randomjungle" ,randomjungle)))
+    (native-inputs
+     `(("unzip" ,unzip)))
+    (home-page "http://couger.oit.duke.edu")
+    (synopsis "Identify co-factors in sets of genomic regions")
+    (description
+     "COUGER can be applied to any two sets of genomic regions bound by
+paralogous TFs (e.g., regions derived from ChIP-seq experiments) to identify
+putative co-factors that provide specificity to each TF.  The framework
+determines the genomic targets uniquely-bound by each TF, and identifies a
+small set of co-factors that best explain the in vivo binding differences
+between the two TFs.
+
+COUGER uses classification algorithms (support vector machines and random
+forests) with features that reflect the DNA binding specificities of putative
+co-factors.  The features are generated either from high-throughput TF-DNA
+binding data (from protein binding microarray experiments), or from large
+collections of DNA motifs.")
+    (license license:gpl3+)))
+
 (define-public clustal-omega
   (package
     (name "clustal-omega")
-- 
cgit v1.2.3


From 47da6268c45796d858eccff601e17ce11a7aeb62 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Tue, 9 Jun 2015 12:53:23 +0200
Subject: gnu: icedtea7: Bootstrap with GCJ.

* gnu/packages/java.scm (icedtea7): Bootstrap with GCJ rather than compile
  with IcedTea6.
---
 gnu/packages/java.scm | 71 ++++++++++++++++++++++++++-------------------------
 1 file changed, 36 insertions(+), 35 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/java.scm b/gnu/packages/java.scm
index ea8de9e2cf..aa8cd2cf51 100644
--- a/gnu/packages/java.scm
+++ b/gnu/packages/java.scm
@@ -610,6 +610,9 @@ (define-public icedtea7
                 (modules '((guix build utils)))
                 (snippet
                  '(substitute* "Makefile.in"
+                    ;; link against libgcj to avoid linker error
+                    (("-o native-ecj")
+                     "-lgcj -o native-ecj")
                     ;; do not leak information about the build host
                     (("DISTRIBUTION_ID=\"\\$\\(DIST_ID\\)\"")
                      "DISTRIBUTION_ID=\"\\\"guix\\\"\"")))))
@@ -627,15 +630,7 @@ (define-public icedtea7
          #:locale "C"
          ,@(substitute-keyword-arguments (package-arguments icedtea6)
              ((#:configure-flags flags)
-              `(let ((jdk (assoc-ref %build-inputs "icedtea6"))
-                     (ant (assoc-ref %build-inputs "ant")))
-                 `("--disable-bootstrap"
-                   "--without-rhino"
-                   "--enable-nss"
-                   "--enable-system-lcms"
-                   "--disable-downloading"
-                   ,(string-append "--with-ant-home=" ant)
-                   ,(string-append "--with-jdk-home=" jdk))))
+              `(delete "--with-openjdk-src-dir=./openjdk" ,flags))
              ((#:phases phases)
               `(modify-phases ,phases
                  (replace
@@ -677,30 +672,37 @@ (define-public icedtea7
                  (replace
                   'set-additional-paths
                   (lambda* (#:key inputs #:allow-other-keys)
-                    (substitute* "openjdk/jdk/make/common/shared/Sanity.gmk"
-                      (("ALSA_INCLUDE=/usr/include/alsa/version.h")
-                       (string-append "ALSA_INCLUDE="
-                                      (assoc-ref inputs "alsa-lib")
-                                      "/include/alsa/version.h")))
-                    (setenv "CC" "gcc")
-                    (setenv "CPATH"
-                            (string-append (assoc-ref inputs "libxrender")
-                                           "/include/X11/extensions" ":"
-                                           (assoc-ref inputs "libxtst")
-                                           "/include/X11/extensions" ":"
-                                           (assoc-ref inputs "libxinerama")
-                                           "/include/X11/extensions" ":"
-                                           (or (getenv "CPATH") "")))
-                    (setenv "ALT_OBJCOPY" (which "objcopy"))
-                    (setenv "ALT_CUPS_HEADERS_PATH"
-                            (string-append (assoc-ref inputs "cups")
-                                           "/include"))
-                    (setenv "ALT_FREETYPE_HEADERS_PATH"
-                            (string-append (assoc-ref inputs "freetype")
-                                           "/include"))
-                    (setenv "ALT_FREETYPE_LIB_PATH"
-                            (string-append (assoc-ref inputs "freetype")
-                                           "/lib"))))
+                    (let (;; Get target-specific include directory so that
+                          ;; libgcj-config.h is found when compiling hotspot.
+                          (gcjinclude (let* ((port (open-input-pipe "gcj -print-file-name=include"))
+                                             (str  (read-line port)))
+                                        (close-pipe port)
+                                        str)))
+                      (substitute* "openjdk/jdk/make/common/shared/Sanity.gmk"
+                        (("ALSA_INCLUDE=/usr/include/alsa/version.h")
+                         (string-append "ALSA_INCLUDE="
+                                        (assoc-ref inputs "alsa-lib")
+                                        "/include/alsa/version.h")))
+                      (setenv "CC" "gcc")
+                      (setenv "CPATH"
+                              (string-append gcjinclude ":"
+                                             (assoc-ref inputs "libxrender")
+                                             "/include/X11/extensions" ":"
+                                             (assoc-ref inputs "libxtst")
+                                             "/include/X11/extensions" ":"
+                                             (assoc-ref inputs "libxinerama")
+                                             "/include/X11/extensions" ":"
+                                             (or (getenv "CPATH") "")))
+                      (setenv "ALT_OBJCOPY" (which "objcopy"))
+                      (setenv "ALT_CUPS_HEADERS_PATH"
+                              (string-append (assoc-ref inputs "cups")
+                                             "/include"))
+                      (setenv "ALT_FREETYPE_HEADERS_PATH"
+                              (string-append (assoc-ref inputs "freetype")
+                                             "/include"))
+                      (setenv "ALT_FREETYPE_LIB_PATH"
+                              (string-append (assoc-ref inputs "freetype")
+                                             "/lib")))))
                  (add-after
                   'unpack 'fix-x11-extension-include-path
                   (lambda* (#:key inputs #:allow-other-keys)
@@ -733,7 +735,6 @@ (define-public icedtea7
                  (delete 'patch-patches))))))
       (native-inputs
        `(("ant" ,ant)
-         ("icedtea6" ,icedtea6 "jdk")
          ("openjdk-drop"
           ,(drop "openjdk"
                  "03gxqn17cxwl1nspnwigacaqd28p02d45f396j5f4kkbzfnbl0ak"))
@@ -756,4 +757,4 @@ (define-public icedtea7
           ,(drop "hotspot"
                  "1yqxfd2jwbm5y41wscyfx8h0fr3h8ny2g2mda5iwd8sikxsaj96p"))
          ,@(fold alist-delete (package-native-inputs icedtea6)
-                 '("openjdk6-src" "ant-bootstrap" "gcj")))))))
+                 '("openjdk6-src" "ant-bootstrap")))))))
-- 
cgit v1.2.3


From 1e44cf8b0ffe88f2675718c0a0f5119c87a8bf6a Mon Sep 17 00:00:00 2001
From: Ben Woodcroft <b.woodcroft@uq.edu.au>
Date: Tue, 9 Jun 2015 16:10:51 +0200
Subject: gnu: Add OrfM.

* gnu/packages/bioinformatics.scm (orfm): New variable.

Signed-off-by: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
---
 gnu/packages/bioinformatics.scm | 21 +++++++++++++++++++++
 1 file changed, 21 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index df627fbe48..7175ecf41d 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -1101,6 +1101,27 @@ (define-public miso
 that a read originated from a particular isoform.")
     (license license:gpl2)))
 
+(define-public orfm
+  (package
+    (name "orfm")
+    (version "0.3.2")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append
+                    "https://github.com/wwood/OrfM/releases/download/v"
+                    version "/orfm-" version ".tar.gz"))
+              (sha256
+               (base32
+                "00jqvlspj9662ni9r4n1snxfnwkzc02i46g5nk1kwjshi6v3vgg3"))))
+    (build-system gnu-build-system)
+    (inputs `(("zlib" ,zlib)))
+    (synopsis "Simple and not slow open reading frame (ORF) caller")
+    (description
+     "An ORF caller finds stretches of DNA that when translated are not
+interrupted by stop codons.  OrfM finds and prints these ORFs.")
+    (home-page "https://github.com/wwood/OrfM")
+    (license license:lgpl3+)))
+
 (define-public python2-pbcore
   (package
     (name "python2-pbcore")
-- 
cgit v1.2.3


From 76e146384c3465beb5cdbfad05c31bd79808a668 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 25 May 2015 22:13:27 +0200
Subject: gnu: Add withershins.

* gnu/packages/code.scm (withershins): New variable.
---
 gnu/packages/code.scm | 64 +++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 64 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/code.scm b/gnu/packages/code.scm
index 9d2bde829d..97261d6c79 100644
--- a/gnu/packages/code.scm
+++ b/gnu/packages/code.scm
@@ -1,6 +1,7 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2013, 2015 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2015 Andreas Enge <andreas@enge.fr>
+;;; Copyright © 2015 Ricardo Wurmus <rekado@elephly.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -22,9 +23,12 @@ (define-module (gnu packages code)
   #:use-module (guix download)
   #:use-module ((guix licenses) #:prefix license:)
   #:use-module (guix build-system gnu)
+  #:use-module (guix build-system cmake)
+  #:use-module (gnu packages base)
   #:use-module (gnu packages compression)
   #:use-module (gnu packages databases)
   #:use-module (gnu packages emacs)
+  #:use-module (gnu packages gcc)
   #:use-module (gnu packages pcre)
   #:use-module (gnu packages pkg-config)
   #:use-module (gnu packages perl)
@@ -225,3 +229,63 @@ (define-public the-silver-searcher
 files, but compared to grep is much faster and respects files like .gitignore,
 .hgignore, etc.")
     (license license:asl2.0)))
+
+(define-public withershins
+  (package
+    (name "withershins")
+    (version "0.1")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append
+                    "https://github.com/cameronwhite/withershins/archive/v"
+                    version ".tar.gz"))
+              (file-name (string-append name "-" version ".tar.gz"))
+              (sha256
+               (base32
+                "08z3lyvswx7sad10637vfpwglbcbgzzcpfihw0x8lzr74f3b70bh"))))
+    (build-system cmake-build-system)
+    (arguments
+     `(#:out-of-source? #f
+       #:modules ((guix build utils)
+                  (guix build cmake-build-system)
+                  (ice-9 popen)
+                  (ice-9 rdelim))
+       #:phases
+       (modify-phases %standard-phases
+         (add-after
+          'unpack 'find-libiberty
+          (lambda _
+            (let ((plugin (let* ((port (open-input-pipe
+                                        "gcc -print-file-name=plugin"))
+                                 (str  (read-line port)))
+                            (close-pipe port)
+                            str)))
+              (substitute* "cmake/FindIberty.cmake"
+                (("/usr/include") (string-append plugin "/include"))
+                (("libiberty.a iberty") (string-append "NAMES libiberty.a iberty\nPATHS \""
+                                                       (assoc-ref %build-inputs "gcc")
+                                                       "/lib" "\"")))
+              #t)))
+         (replace
+          'install
+          (lambda* (#:key outputs #:allow-other-keys)
+            (let ((out (assoc-ref outputs "out")))
+              (mkdir-p (string-append out "/lib"))
+              (mkdir (string-append out "/include"))
+              (copy-file "src/withershins.hpp"
+                         (string-append out "/include/withershins.hpp"))
+              (copy-file "src/libwithershins.a"
+                         (string-append out "/lib/libwithershins.a")))
+            #t)))))
+    (home-page "https://github.com/cameronwhite/withershins")
+    (inputs
+     `(("gcc" ,gcc-4.8 "lib") ;for libiberty.a
+       ("binutils" ,binutils) ;for libbfd
+       ("zlib" ,zlib)))
+    (synopsis "C++11 library for generating stack traces")
+    (description
+     "Withershins is a simple cross-platform C++11 library for generating
+stack traces.")
+    ;; Sources are released under Expat license, but since BFD is licensed
+    ;; under the GPLv3+ the combined work is GPLv3+ as well.
+    (license license:gpl3+)))
-- 
cgit v1.2.3


From ccb8da2654ed4dc570c385331fafb9673d5ae452 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 25 May 2015 22:14:39 +0200
Subject: gnu: Add RapidJSON.

* gnu/packages/web.scm (rapidjson): New variable.
---
 gnu/packages/web.scm | 21 +++++++++++++++++++++
 1 file changed, 21 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm
index e77bad76d6..6660c3fe8e 100644
--- a/gnu/packages/web.scm
+++ b/gnu/packages/web.scm
@@ -259,6 +259,27 @@ (define-public json-c
 parse JSON formatted strings back into the C representation of JSON objects.")
     (license l:x11)))
 
+(define-public rapidjson
+  (package
+    (name "rapidjson")
+    (version "1.0.2")
+    (source (origin
+             (method url-fetch)
+             (uri (string-append
+                   "https://github.com/miloyip/rapidjson/archive/v"
+                   version ".tar.gz"))
+             (file-name (string-append name "-" version ".tar.gz"))
+             (sha256
+              (base32
+               "0rl6s0vg5y1dhh9vfl1lqay3sxf69sxjh0czxrjmasn7ng91wwf3"))))
+    (build-system cmake-build-system)
+    (home-page "https://github.com/miloyip/rapidjson")
+    (synopsis "JSON parser/generator for C++ with both SAX/DOM style API")
+    (description
+     "RapidJSON is a fast JSON parser/generator for C++ with both SAX/DOM
+style API.")
+    (license l:expat)))
+
 (define-public libwebsockets
   (package
     (name "libwebsockets")
-- 
cgit v1.2.3


From 6ce212b8686487355dd5797917faf819ab80dc3e Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 28 May 2015 09:43:53 +0200
Subject: gnu: Add pugixml.

* gnu/packages/xml.scm (pugixml): New variable.
---
 gnu/packages/xml.scm | 37 +++++++++++++++++++++++++++++++++++++
 1 file changed, 37 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/xml.scm b/gnu/packages/xml.scm
index 8a4d2fbb5b..a7925d9aa6 100644
--- a/gnu/packages/xml.scm
+++ b/gnu/packages/xml.scm
@@ -2,6 +2,7 @@
 ;;; Copyright © 2013, 2014, 2015 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2013, 2015 Andreas Enge <andreas@enge.fr>
 ;;; Copyright © 2015 Eric Bavier <bavier@member.fsf.org>
+;;; Copyright © 2015 Ricardo Wurmus <rekado@elephly.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -30,6 +31,7 @@ (define-module (gnu packages xml)
   #:use-module ((guix licenses) #:prefix license:)
   #:use-module (guix packages)
   #:use-module (guix download)
+  #:use-module (guix build-system cmake)
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system perl)
   #:use-module (gnu packages linux))
@@ -358,6 +360,41 @@ (define-public perl-xml-dom
 that conforms to the API of the Document Object Model.")
     (home-page "http://search.cpan.org/~tjmather/XML-DOM-1.44/lib/XML/DOM.pm")))
 
+(define-public pugixml
+  (package
+    (name "pugixml")
+    (version "1.6")
+    (source
+     (origin
+      (method url-fetch)
+      (uri (string-append "https://github.com/zeux/pugixml/archive/v"
+                          version ".tar.gz"))
+      (file-name (string-append name "-" version ".tar.gz"))
+      (sha256
+       (base32
+        "0czbcv9aqf2rw3s9cljz2wb1f4zbhd07wnj7ykklklccl0ipfnwi"))))
+    (build-system cmake-build-system)
+    (arguments
+     `(#:tests? #f
+       #:out-of-source? #f
+       #:phases (modify-phases %standard-phases
+                  (add-before
+                   'configure 'chdir
+                   (lambda _
+                     (chdir "scripts")
+                     #t)))))
+    (home-page "http://pugixml.org")
+    (synopsis "Light-weight, simple and fast XML parser for C++ with XPath support")
+    (description
+     "pugixml is a C++ XML processing library, which consists of a DOM-like
+interface with rich traversal/modification capabilities, a fast XML parser
+which constructs the DOM tree from an XML file/buffer, and an XPath 1.0
+implementation for complex data-driven tree queries.  Full Unicode support is
+also available, with Unicode interface variants and conversions between
+different Unicode encodings which happen automatically during
+parsing/saving.")
+    (license license:expat)))
+
 (define-public xmlto
   (package
     (name "xmlto")
-- 
cgit v1.2.3


From cc45cff83aaf190e7cefed957db20214b3586754 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 28 May 2015 09:44:30 +0200
Subject: gnu: Add rtmidi.

* gnu/packages/audio.scm (rtmidi): New variable.
---
 gnu/packages/audio.scm | 51 ++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 51 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm
index fdc783a455..3b2d4e1022 100644
--- a/gnu/packages/audio.scm
+++ b/gnu/packages/audio.scm
@@ -1031,6 +1031,57 @@ (define-public rubberband
 tempo and pitch of an audio recording independently of one another.")
     (license license:gpl2+)))
 
+(define-public rtmidi
+  (package
+    (name "rtmidi")
+    (version "2.1.0")
+    (source (origin
+              (method url-fetch)
+              (uri
+               (string-append "https://github.com/powertab/rtmidi/archive/"
+                              version ".tar.gz"))
+              (file-name (string-append name "-" version ".tar.gz"))
+              (sha256
+               (base32
+                "0d49lapnmdgmjxh4vw57h6xk74nn5r0zwysv7jbd7m8kqhpq5rjj"))))
+    (build-system gnu-build-system)
+    (arguments
+     `(#:tests? #f ;no "check" target
+       #:phases (modify-phases %standard-phases
+                  (add-before
+                   'configure 'autoconf
+                   (lambda _ (zero? (system* "autoreconf" "-vfi"))))
+                  (add-before
+                   'build 'fix-makefile
+                   (lambda _
+                     (substitute* "Makefile"
+                       (("/bin/ln") "ln")
+                       (("RtMidi.h RtError.h") "RtMidi.h"))
+                     #t))
+                  (add-before
+                   'install 'make-target-dirs
+                   (lambda _
+                     (let ((out (assoc-ref %outputs "out")))
+                       (mkdir-p (string-append out "/bin"))
+                       (mkdir (string-append out "/lib"))
+                       (mkdir (string-append out "/include")))
+                     #t)))))
+    (inputs
+     `(("jack" ,jack-1)
+       ("alsa-lib" ,alsa-lib)))
+    (native-inputs
+     `(("autoconf" ,autoconf)
+       ("automake" ,automake)
+       ("libtool" ,libtool)
+       ("pkg-config" ,pkg-config)))
+    (home-page "https://github.com/powertab/rtmidi")
+    (synopsis "Cross-platform MIDI library for C++")
+    (description
+     "RtMidi is a set of C++ classes (RtMidiIn, RtMidiOut, and API specific
+classes) that provide a common cross-platform API for realtime MIDI
+input/output.")
+    (license license:expat)))
+
 (define-public sratom
   (package
     (name "sratom")
-- 
cgit v1.2.3


From 14a17ef6f4e416c9b1f888679961e7ffe04166c6 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 3 Jun 2015 22:53:56 +0200
Subject: gnu: catch-framework: Update to 1.1.3.

* gnu/packages/check.scm (catch-framework): Update to 1.1.3.
---
 gnu/packages/check.scm | 9 ++++-----
 1 file changed, 4 insertions(+), 5 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/check.scm b/gnu/packages/check.scm
index 5349ede0fa..e0ee7c4d4f 100644
--- a/gnu/packages/check.scm
+++ b/gnu/packages/check.scm
@@ -113,18 +113,17 @@ (define-public cppunit
 (define-public catch-framework
   (package
     (name "catch")
-    (version "1.0.53")                  ;Sub-minor is the build number
+    (version "1.1.3")                  ;Sub-minor is the build number
     (source (origin
               (method git-fetch)
               (uri (git-reference
                     (url "https://github.com/philsquared/Catch")
-                    ;; Semi-arbitrary.  Contains mostly documentation fixes
-                    ;; since build 53.
-                    (commit "b9ec8a1")))
+                    ;; Semi-arbitrary.
+                    (commit "c51e86819d")))
               (file-name (string-append name "-" version))
               (sha256
                (base32
-                "05iijiwjwcjbza7qamwd32d0jypi0lpywmilmmj2xh280mcl4dbd"))))
+                "0kgi7wxxysgjbpisqfj4dj0k19cyyai92f001zi8gzkybd4fkgv5"))))
     (build-system trivial-build-system)
     (arguments
      `(#:modules ((guix build utils))
-- 
cgit v1.2.3


From 8b9ec354edc4a4f50ce67e43f4f7121331c8f4e4 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 4 Jun 2015 10:01:11 +0200
Subject: gnu: Add powertabeditor.

* gnu/packages/music.scm (powertabeditor): New variable.
---
 gnu/packages/music.scm | 98 ++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 98 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/music.scm b/gnu/packages/music.scm
index 5795ecbb0d..a42d5c35c5 100644
--- a/gnu/packages/music.scm
+++ b/gnu/packages/music.scm
@@ -22,9 +22,15 @@ (define-module (gnu packages music)
   #:use-module (guix download)
   #:use-module ((guix licenses) #:prefix license:)
   #:use-module (guix build-system gnu)
+  #:use-module (guix build-system cmake)
   #:use-module (gnu packages)
   #:use-module (gnu packages audio)
+  #:use-module (gnu packages base) ;libbdf
+  #:use-module (gnu packages boost)
   #:use-module (gnu packages bison)
+  #:use-module (gnu packages code)
+  #:use-module (gnu packages check)
+  #:use-module (gnu packages compression)
   #:use-module (gnu packages docbook)
   #:use-module (gnu packages flex)
   #:use-module (gnu packages fonts)
@@ -45,9 +51,11 @@ (define-module (gnu packages music)
   #:use-module (gnu packages perl)
   #:use-module (gnu packages pkg-config)
   #:use-module (gnu packages python)
+  #:use-module (gnu packages qt)
   #:use-module (gnu packages rsync)
   #:use-module (gnu packages texinfo)
   #:use-module (gnu packages texlive)
+  #:use-module (gnu packages web)
   #:use-module (gnu packages xml)
   #:use-module (gnu packages xiph)
   #:use-module (gnu packages zip))
@@ -224,6 +232,96 @@ (define-public solfege
 your own lessons.")
     (license license:gpl3+)))
 
+(define-public powertabeditor
+  (package
+    (name "powertabeditor")
+    (version "2.0.0-alpha7")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append
+                    "https://github.com/powertab/powertabeditor/archive/"
+                    version ".tar.gz"))
+              (file-name (string-append name "-" version ".tar.gz"))
+              (sha256
+               (base32
+                "1yp6ck2r72c2pfq31z1kpw1j639rndrifj85l3cbj2kdf8rdzhkk"))
+              (modules '((guix build utils)))
+              (snippet
+               '(begin
+                  ;; Remove bundled sources for external libraries
+                  (delete-file-recursively "external")
+                  (substitute* "CMakeLists.txt"
+                    (("include_directories\\(\\$\\{PROJECT_SOURCE_DIR\\}/external/.*") "")
+                    ;; TODO: tests cannot be built:
+                    ;; test/test_main.cpp:28:12: error: ‘Session’ is not a member of ‘Catch’
+                    (("add_subdirectory\\(test\\)") "")
+                    (("add_subdirectory\\(external\\)") ""))
+                  (substitute* "test/CMakeLists.txt"
+                    (("include_directories\\(\\$\\{PROJECT_SOURCE_DIR\\}/external/.*") ""))
+
+                  ;; Add install target
+                  (substitute* "source/CMakeLists.txt"
+                    (("qt5_use_modules")
+                     (string-append
+                      "install(TARGETS powertabeditor "
+                      "RUNTIME DESTINATION ${CMAKE_INSTALL_PREFIX}/bin)\n"
+                      "install(FILES data/tunings.json DESTINATION "
+                      "${CMAKE_INSTALL_PREFIX}/share/powertabeditor/)\n"
+                      "qt5_use_modules")))
+                  #t))))
+    (build-system cmake-build-system)
+    (arguments
+     `(#:tests? #f ; no "check" target
+       #:modules ((guix build cmake-build-system)
+                  (guix build utils)
+                  (ice-9 match))
+       #:configure-flags
+       ;; CMake appears to lose the RUNPATH for some reason, so it has to be
+       ;; explicitly set with CMAKE_INSTALL_RPATH.
+       (list (string-append "-DCMAKE_INSTALL_RPATH="
+                            (string-join (map (match-lambda
+                                                ((name . directory)
+                                                 (string-append directory "/lib")))
+                                              %build-inputs) ";")))
+       #:phases
+       (modify-phases %standard-phases
+         (add-before
+          'configure 'remove-third-party-libs
+          (lambda* (#:key inputs #:allow-other-keys)
+            ;; Link with required static libraries, because we're not
+            ;; using the bundled version of withershins.
+            (substitute* '("source/CMakeLists.txt"
+                           "test/CMakeLists.txt")
+              (("target_link_libraries\\((powertabeditor)" _ target)
+               (string-append "target_link_libraries(" target " "
+                              (assoc-ref inputs "binutils")
+                              "/lib/libbfd.a "
+                              (assoc-ref inputs "gcc")
+                              "/lib/libiberty.a "
+                              "dl")))
+            #t)))))
+    (inputs
+     `(("boost" ,boost)
+       ("alsa-lib" ,alsa-lib)
+       ("qt" ,qt)
+       ("withershins" ,withershins)
+       ("gcc" ,gcc-4.8 "lib") ;for libiberty.a (for withershins)
+       ("binutils" ,binutils) ;for -lbfd and -liberty (for withershins)
+       ("timidity" ,timidity++)
+       ("pugixml" ,pugixml)
+       ("rtmidi" ,rtmidi)
+       ("rapidjson" ,rapidjson)
+       ("zlib" ,zlib)))
+    (native-inputs
+     `(("catch" ,catch-framework)
+       ("pkg-config" ,pkg-config)))
+    (home-page "http://powertabs.net")
+    (synopsis "Guitar tablature editor")
+    (description
+     "Power Tab Editor 2.0 is the successor to the famous original Power Tab
+Editor.  It is compatible with Power Tab Editor 1.7 and Guitar Pro.")
+    (license license:gpl3+)))
+
 (define-public tuxguitar
   (package
     (name "tuxguitar")
-- 
cgit v1.2.3


From 1937e38d06ac35c9d683a6943c7d988d1ffdf4f9 Mon Sep 17 00:00:00 2001
From: Eric Bavier <bavier@member.fsf.org>
Date: Sun, 19 Apr 2015 09:54:23 -0500
Subject: gnu: Add Set-Object.

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

(limited to 'gnu/packages')

diff --git a/gnu/packages/perl.scm b/gnu/packages/perl.scm
index e5ec25e418..ec6f89a626 100644
--- a/gnu/packages/perl.scm
+++ b/gnu/packages/perl.scm
@@ -4095,6 +4095,28 @@ (define-public perl-set-infinite
     (description "Set::Infinite is a set theory module for infinite sets.")
     (license (package-license perl))))
 
+(define-public perl-set-object
+  (package
+    (name "perl-set-object")
+    (version "1.35")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "mirror://cpan/authors/id/R/RU/RURBAN/"
+                           "Set-Object-" version ".tar.gz"))
+       (sha256
+        (base32
+         "1rqf11274s3h17jgbimmg47k4fmayifajqwaa6lgm0z5qdy4v6hq"))))
+    (build-system perl-build-system)
+    (propagated-inputs
+     `(("perl-moose" ,perl-moose)
+       ("perl-test-leaktrace" ,perl-test-leaktrace)))
+    (home-page "http://search.cpan.org/dist/Set-Object")
+    (synopsis "Unordered collections of Perl Objects")
+    (description "Set::Object provides efficient sets, unordered collections
+of Perl objects without duplicates for scalars and references.")
+    (license artistic2.0)))
+
 (define-public perl-set-scalar
   (package
     (name "perl-set-scalar")
-- 
cgit v1.2.3


From 514214cbe5909a21d965986aa552c83885a5ff6f Mon Sep 17 00:00:00 2001
From: Eric Bavier <bavier@member.fsf.org>
Date: Sun, 19 Apr 2015 09:55:28 -0500
Subject: gnu: Add Catalyst-Plugin-Authorization-Roles.

* gnu/packages/web.scm (perl-catalyst-plugin-authorization-roles): New
  variable.
---
 gnu/packages/web.scm | 29 +++++++++++++++++++++++++++++
 1 file changed, 29 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm
index 6660c3fe8e..6446959d2f 100644
--- a/gnu/packages/web.scm
+++ b/gnu/packages/web.scm
@@ -926,6 +926,35 @@ (define-public perl-catalyst-plugin-authentication
 system authorises them to do).")
     (license (package-license perl))))
 
+(define-public perl-catalyst-plugin-authorization-roles
+  (package
+    (name "perl-catalyst-plugin-authorization-roles")
+    (version "0.09")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "mirror://cpan/authors/id/B/BO/BOBTFISH/"
+                           "Catalyst-Plugin-Authorization-Roles-"
+                           version ".tar.gz"))
+       (sha256
+        (base32
+         "0l83lkwmq0lngwh8b1rv3r719pn8w1gdbyhjqm74rnd0wbjl8h7f"))))
+    (build-system perl-build-system)
+    (native-inputs
+     `(("perl-test-exception" ,perl-test-exception)))
+    (propagated-inputs
+     `(("perl-catalyst-plugin-authentication"
+        ,perl-catalyst-plugin-authentication)
+       ("perl-catalyst-runtime" ,perl-catalyst-runtime)
+       ("perl-set-object" ,perl-set-object)
+       ("perl-universal-isa" ,perl-universal-isa)))
+    (home-page
+     "http://search.cpan.org/dist/Catalyst-Plugin-Authorization-Roles")
+    (synopsis "Role-based authorization for Catalyst")
+    (description "Catalyst::Plugin::Authorization::Roles provides role-based
+authorization for Catalyst based on Catalyst::Plugin::Authentication.")
+    (license (package-license perl))))
+
 (define-public perl-catalyst-plugin-captcha
   (package
     (name "perl-catalyst-plugin-captcha")
-- 
cgit v1.2.3


From 6e545bbf5565b6273423ac50187e2c50f84399b0 Mon Sep 17 00:00:00 2001
From: Eric Bavier <bavier@member.fsf.org>
Date: Fri, 17 Apr 2015 23:20:51 -0500
Subject: gnu: Add Catalyst-Authentication-Store-DBIx-Class.

* gnu/packages/web.scm (perl-catalyst-authentication-store-dbix-class):
  New variable.
---
 gnu/packages/web.scm | 35 +++++++++++++++++++++++++++++++++++
 1 file changed, 35 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm
index 6446959d2f..94d9970ea6 100644
--- a/gnu/packages/web.scm
+++ b/gnu/packages/web.scm
@@ -725,6 +725,41 @@ (define-public perl-catalyst-action-rest
 regular method.")
     (license (package-license perl))))
 
+(define-public perl-catalyst-authentication-store-dbix-class
+  (package
+    (name "perl-catalyst-authentication-store-dbix-class")
+    (version "0.1506")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "mirror://cpan/authors/id/I/IL/ILMARI/"
+                           "Catalyst-Authentication-Store-DBIx-Class-"
+                           version ".tar.gz"))
+       (sha256
+        (base32
+         "0i5ja7690fs9nhxcij6lw51j804sm8s06m5mvk1n8pi8jljrymvw"))))
+    (build-system perl-build-system)
+    (native-inputs
+     `(("perl-catalyst-plugin-authorization-roles"
+        ,perl-catalyst-plugin-authorization-roles)
+       ("perl-catalyst-plugin-session-state-cookie"
+        ,perl-catalyst-plugin-session-state-cookie)
+       ("perl-dbd-sqlite" ,perl-dbd-sqlite)
+       ("perl-test-www-mechanize-catalyst" ,perl-test-www-mechanize-catalyst)))
+    (propagated-inputs
+     `(("perl-catalyst-runtime" ,perl-catalyst-runtime)
+       ("perl-catalyst-plugin-authentication"
+        ,perl-catalyst-plugin-authentication)
+       ("perl-dbix-class" ,perl-dbix-class)
+       ("perl-catalyst-model-dbic-schema" ,perl-catalyst-model-dbic-schema)))
+    (home-page
+     "http://search.cpan.org/dist/Catalyst-Authentication-Store-DBIx-Class")
+    (synopsis "Storage class for Catalyst authentication using DBIx::Class")
+    (description "The Catalyst::Authentication::Store::DBIx::Class class
+provides access to authentication information stored in a database via
+DBIx::Class.")
+    (license (package-license perl))))
+
 (define-public perl-catalyst-component-instancepercontext
   (package
     (name "perl-catalyst-component-instancepercontext")
-- 
cgit v1.2.3


From 0061079a19c9ac38a2d2a170bcfea17fd362d15e Mon Sep 17 00:00:00 2001
From: Eric Bavier <bavier@member.fsf.org>
Date: Sun, 19 Apr 2015 12:59:37 -0500
Subject: gnu: Add hydra.

* gnu/packages/ci.scm: New file.
* gnu/packages/patches/hydra-automake-1.15.patch,
  gnu/packages/patches/hydra-disable-darcs-test.patch: New files.
* gnu-system.am (GNU_SYSTEM_MODULES): Add file.
  (dist_patch_DATA): Add patches.
---
 gnu-system.am                                      |   3 +
 gnu/packages/ci.scm                                | 182 +++++++++++++++++++++
 gnu/packages/patches/hydra-automake-1.15.patch     |  63 +++++++
 .../patches/hydra-disable-darcs-test.patch         |  25 +++
 4 files changed, 273 insertions(+)
 create mode 100644 gnu/packages/ci.scm
 create mode 100644 gnu/packages/patches/hydra-automake-1.15.patch
 create mode 100644 gnu/packages/patches/hydra-disable-darcs-test.patch

(limited to 'gnu/packages')

diff --git a/gnu-system.am b/gnu-system.am
index d79c2c7917..7e0ee52875 100644
--- a/gnu-system.am
+++ b/gnu-system.am
@@ -59,6 +59,7 @@ GNU_SYSTEM_MODULES =				\
   gnu/packages/cdrom.scm			\
   gnu/packages/certs.scm			\
   gnu/packages/check.scm			\
+  gnu/packages/ci.scm				\
   gnu/packages/cmake.scm			\
   gnu/packages/code.scm				\
   gnu/packages/commencement.scm			\
@@ -454,6 +455,8 @@ dist_patch_DATA =						\
   gnu/packages/patches/gtkglext-disable-disable-deprecated.patch \
   gnu/packages/patches/hop-bigloo-4.0b.patch			\
   gnu/packages/patches/hop-linker-flags.patch			\
+  gnu/packages/patches/hydra-automake-1.15.patch		\
+  gnu/packages/patches/hydra-disable-darcs-test.patch		\
   gnu/packages/patches/irrlicht-mesa-10.patch			\
   gnu/packages/patches/jbig2dec-ignore-testtest.patch		\
   gnu/packages/patches/kmod-module-directory.patch		\
diff --git a/gnu/packages/ci.scm b/gnu/packages/ci.scm
new file mode 100644
index 0000000000..b68e0dce3b
--- /dev/null
+++ b/gnu/packages/ci.scm
@@ -0,0 +1,182 @@
+;;; GNU Guix --- Functional package management for GNU
+;;; Copyright © 2015 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 ci)
+  #:use-module ((guix licenses) #:prefix l:)
+  #:use-module (gnu packages)
+  #:use-module (guix packages)
+  #:use-module (guix git-download)
+  #:use-module (gnu packages autotools)
+  #:use-module (gnu packages base)
+  #:use-module (gnu packages docbook)
+  #:use-module (gnu packages compression)
+  #:use-module (gnu packages databases)
+  #:use-module (gnu packages guile)
+  #:use-module (gnu packages mail)
+  #:use-module (gnu packages openssl)
+  #:use-module (gnu packages package-management)
+  #:use-module (gnu packages perl)
+  #:use-module (gnu packages pkg-config)
+  #:use-module (gnu packages version-control)
+  #:use-module (gnu packages web)
+  #:use-module (gnu packages xml)
+  #:use-module (gnu packages zip)
+  #:use-module (guix build-system gnu))
+
+(define-public hydra
+  (let ((commit "4c0e3e4"))
+    (package
+      (name "hydra")
+      (version (string-append "20150407." commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://github.com/NixOS/hydra")
+                      (commit commit)))
+                (file-name (string-append name "-" version))
+                (sha256
+                 (base32
+                  "08vc76xb7f42hh65j7qvjf58hw36aki5ml343170pq94vk75b1nh"))
+                (patches (map search-patch
+                              '("hydra-automake-1.15.patch"
+                                ;; TODO: Remove once we have a darcs input
+                                "hydra-disable-darcs-test.patch")))))
+      (build-system gnu-build-system)
+      (native-inputs
+       `(("unzip" ,unzip)
+         ("pkg-config" ,pkg-config)
+         ;; For documentation
+         ("dblatex" ,dblatex)
+         ("xsltproc" ,libxslt)
+         ("docbook-xsl" ,docbook-xsl)
+         ;; For bootstrap
+         ("autoconf" ,autoconf)
+         ("automake" ,automake)
+         ("libtool" ,libtool)
+         ;; For tests
+         ("git" ,git)
+         ("subversion" ,subversion)
+         ("mercurial" ,mercurial)
+         ("bazaar" ,bazaar)))
+      (inputs
+       `(("perl" ,perl)
+         ("guile" ,guile-2.0)
+         ("openssl" ,openssl)
+         ("bzip2" ,bzip2)
+         ("gzip" ,gzip)
+         ("sed" ,sed)
+         ("starman" ,starman)
+         ("git" ,git)
+         ("subversion" ,subversion)
+         ("mercurial" ,mercurial)
+         ("bazaar" ,bazaar)
+         ("nix" ,nix)
+         ;; Lots o' perl modules...
+         ("perl-catalyst-action-rest" ,perl-catalyst-action-rest)
+         ("perl-catalyst-authentication-store-dbix-class"
+          ,perl-catalyst-authentication-store-dbix-class)
+         ("perl-catalyst-devel" ,perl-catalyst-devel)
+         ("perl-catalyst-dispatchtype-regex" ,perl-catalyst-dispatchtype-regex)
+         ("perl-catalyst-plugin-accesslog" ,perl-catalyst-plugin-accesslog)
+         ("perl-catalyst-plugin-authorization-roles"
+          ,perl-catalyst-plugin-authorization-roles)
+         ("perl-catalyst-plugin-captcha" ,perl-catalyst-plugin-captcha)
+         ("perl-catalyst-plugin-session-state-cookie"
+          ,perl-catalyst-plugin-session-state-cookie)
+         ("perl-catalyst-plugin-session-store-fastmmap"
+          ,perl-catalyst-plugin-session-store-fastmmap)
+         ("perl-catalyst-plugin-stacktrace" ,perl-catalyst-plugin-stacktrace)
+         ("perl-catalyst-traitfor-request-proxybase"
+          ,perl-catalyst-traitfor-request-proxybase)
+         ("perl-catalyst-view-download" ,perl-catalyst-view-download)
+         ("perl-catalyst-view-json" ,perl-catalyst-view-json)
+         ("perl-catalyst-view-tt" ,perl-catalyst-view-tt)
+         ("perl-catalystx-roleapplicator" ,perl-catalystx-roleapplicator)
+         ("perl-catalystx-script-server-starman"
+          ,perl-catalystx-script-server-starman)
+         ("perl-crypt-randpasswd" ,perl-crypt-randpasswd)
+         ("perl-data-dump" ,perl-data-dump)
+         ("perl-datetime" ,perl-datetime)
+         ("perl-dbd-pg" ,perl-dbd-pg)
+         ("perl-dbd-sqlite" ,perl-dbd-sqlite)
+         ("perl-digest-sha1" ,perl-digest-sha1)
+         ("perl-email-mime" ,perl-email-mime)
+         ("perl-email-sender" ,perl-email-sender)
+         ("perl-file-slurp" ,perl-file-slurp)
+         ("perl-io-compress" ,perl-io-compress)
+         ("perl-ipc-run" ,perl-ipc-run)
+         ("perl-json-any" ,perl-json-any)
+         ("perl-json-xs" ,perl-json-xs)
+         ("perl-libwww" ,perl-libwww)
+         ("perl-lwp-protocol-https" ,perl-lwp-protocol-https)
+         ("perl-net-amazon-s3" ,perl-net-amazon-s3)
+         ("perl-padwalker" ,perl-padwalker)
+         ("perl-readonly" ,perl-readonly)
+         ("perl-set-scalar" ,perl-set-scalar)
+         ("perl-sql-splitstatement" ,perl-sql-splitstatement)
+         ("perl-sys-hostname-long" ,perl-sys-hostname-long)
+         ("perl-text-diff" ,perl-text-diff)
+         ("perl-text-table" ,perl-text-table)
+         ("perl-xml-simple" ,perl-xml-simple)))
+      (arguments
+       `(#:configure-flags
+         (let ((docbook (assoc-ref %build-inputs "docbook-xsl")))
+           (list (string-append "--with-docbook-xsl="
+                                docbook "/xml/xsl/docbook-xsl-"
+                                ,(package-version docbook-xsl))
+                 (string-append "--docdir=" %output
+                                "/doc/hydra-" ,version)))
+         #:phases (modify-phases %standard-phases
+                    (add-after
+                     'unpack 'bootstrap
+                     (lambda _ (zero? (system* "autoreconf" "-vfi"))))
+                    (add-before
+                     'check 'check-setup
+                     (lambda _ (setenv "LOGNAME" "test.log")))
+                    (add-after
+                     'install 'wrap-program
+                     (lambda* (#:key inputs outputs #:allow-other-keys)
+                       (let ((out (assoc-ref outputs "out")))
+                         (for-each
+                          (lambda (file)
+                            (wrap-program file
+                              `("PATH" ":" prefix
+                                (,(string-append out "/bin")
+                                 ,@(map (lambda (i)
+                                          (string-append (assoc-ref inputs i)
+                                                         "/bin"))
+                                        '("subversion" "git" "bazaar"
+                                          "mercurial" "coreutils" "gzip"
+                                          "sed" "unzip" "nix"))))
+                              `("PERL5LIB" ":" prefix
+                                (,(string-append out "/libexec/hydra/lib")
+                                 ,@(search-path-as-string->list
+                                    (getenv "PERL5LIB"))))
+                              `("HYDRA_RELEASE" = (,,version))
+                              `("HYDRA_HOME" =
+                                (,(string-append out "/libexec/hydra")))
+                              `("NIX_RELEASE" = (,,(package-version nix)))))
+                          (find-files (string-append out "/bin")
+                                      ".*"))))))))
+      (home-page "https://nixos.org/hydra")
+      (synopsis "Continuous build system")
+      (description
+       "Hydra is a tool for continuous integration testing and software
+release that uses a purely functional language to describe build jobs and
+their dependencies.")
+      (license l:gpl3+))))
diff --git a/gnu/packages/patches/hydra-automake-1.15.patch b/gnu/packages/patches/hydra-automake-1.15.patch
new file mode 100644
index 0000000000..0d8fa98519
--- /dev/null
+++ b/gnu/packages/patches/hydra-automake-1.15.patch
@@ -0,0 +1,63 @@
+This patch takes a slightly different approach to solving the issue reported
+at https://github.com/NixOS/hydra/issues/200.  This fix allows us to use
+Automake's parallel test harness.
+
+--- source/configure.ac.orig	1969-12-31 18:00:01.000000000 -0600
++++ source/configure.ac	2015-04-15 10:58:15.974679278 -0500
+@@ -33,7 +33,7 @@
+ fi
+ ])
+ 
+-NEED_PROG(perl, perl)
++NEED_PROG([PERL], perl)
+ 
+ NEED_PROG([NIX_STORE_PROGRAM], [nix-store])
+ 
+--- source/tests/Makefile.am.orig	1969-12-31 18:00:01.000000000 -0600
++++ source/tests/Makefile.am	2015-04-15 11:00:35.846682904 -0500
+@@ -1,19 +1,20 @@
+-TESTS_ENVIRONMENT = \
+-  BZR_HOME="$(abs_builddir)/data"			\
+-  HYDRA_DBI="dbi:SQLite:db.sqlite"			\
+-  HYDRA_DATA="$(abs_builddir)/data"			\
+-  HYDRA_HOME="$(top_srcdir)/src"			\
+-  HYDRA_CONFIG=						\
+-  NIX_REMOTE=						\
+-  NIX_CONF_DIR="$(abs_builddir)/nix/etc/nix"		\
+-  NIX_STATE_DIR="$(abs_builddir)/nix/var/nix"		\
+-  NIX_MANIFESTS_DIR="$(abs_builddir)/nix/var/nix/manifests"	\
+-  NIX_STORE_DIR="$(abs_builddir)/nix/store"			\
+-  NIX_LOG_DIR="$(abs_builddir)/nix/var/log/nix"		\
+-  NIX_BUILD_HOOK=					\
+-  PERL5LIB="$(srcdir):$(top_srcdir)/src/lib:$$PERL5LIB"	\
+-  PATH=$(abs_top_srcdir)/src/script:$(abs_top_srcdir)/src/c:$$PATH \
+-  perl -w
++AM_TESTS_ENVIRONMENT = \
++  BZR_HOME="$(abs_builddir)/data"; export BZR_HOME;	\
++  HYDRA_DBI="dbi:SQLite:db.sqlite"; export HYDRA_DBI;	\
++  HYDRA_DATA="$(abs_builddir)/data"; export HYDRA_DATA;	\
++  HYDRA_HOME="$(top_srcdir)/src"; export HYDRA_HOME;	\
++  HYDRA_CONFIG=; export HYDRA_CONFIG;			\
++  NIX_REMOTE=; export NIX_REMOTE;			\
++  NIX_CONF_DIR="$(abs_builddir)/nix/etc/nix"; export NIX_CONF_DIR; \
++  NIX_STATE_DIR="$(abs_builddir)/nix/var/nix"; export NIX_STATE_DIR; \
++  NIX_MANIFESTS_DIR="$(abs_builddir)/nix/var/nix/manifests"; export NIX_MANIFESTS_DIR; \
++  NIX_STORE_DIR="$(abs_builddir)/nix/store"; export NIX_STORE_DIR; \
++  NIX_LOG_DIR="$(abs_builddir)/nix/var/log/nix"; export NIX_LOG_DIR; \
++  NIX_BUILD_HOOK=; export NIX_BUILD_HOOK;		\
++  PERL5LIB="$(srcdir):$(top_srcdir)/src/lib:$$PERL5LIB"; export PERL5LIB; \
++  PATH=$(abs_top_srcdir)/src/script:$(abs_top_srcdir)/src/c:$$PATH; export PATH;
++LOG_COMPILER = $(PERL)
++AM_LOG_FLAGS = -w
+ 
+ EXTRA_DIST = \
+   $(wildcard *.pm) \
+@@ -33,7 +34,7 @@
+ check_SCRIPTS = db.sqlite repos
+ 
+ db.sqlite: $(top_srcdir)/src/sql/hydra-sqlite.sql
+-	$(TESTS_ENVIRONMENT) $(top_srcdir)/src/script/hydra-init
++	$(AM_TESTS_ENVIRONMENT) $(TESTS_ENVIRONMENT) $(top_srcdir)/src/script/hydra-init
+ 
+ repos: dirs
+ 
diff --git a/gnu/packages/patches/hydra-disable-darcs-test.patch b/gnu/packages/patches/hydra-disable-darcs-test.patch
new file mode 100644
index 0000000000..5d8e015b08
--- /dev/null
+++ b/gnu/packages/patches/hydra-disable-darcs-test.patch
@@ -0,0 +1,25 @@
+--- hydra-20150407.4c0e3e4/tests/evaluation-tests.pl	2015-04-15 12:00:19.000000000 -0500
++++ hydra-20150407.4c0e3e4/tests/evaluation-tests.pl	2015-04-17 08:53:04.940301471 -0500
+@@ -7,7 +7,7 @@
+ 
+ my $db = Hydra::Model::DB->new;
+ 
+-use Test::Simple tests => 72;
++use Test::Simple tests => 68;
+ 
+ hydra_setup($db);
+ 
+@@ -103,13 +103,6 @@
+         uri => "$jobsBaseUri/hg-repo",
+         update => getcwd . "/jobs/hg-update.sh"
+     },
+-    {
+-        name => "darcs",
+-        nixexpr => "darcs-input.nix",
+-        type => "darcs",
+-        uri => "$jobsBaseUri/darcs-repo",
+-        update => getcwd . "/jobs/darcs-update.sh"
+-    }
+ );
+ 
+ foreach my $scm ( @scminputs ) {
-- 
cgit v1.2.3


From 02c2cf43ce53718f02376c438b87504a7a2e1c0a Mon Sep 17 00:00:00 2001
From: Ludovic Courtès <ludo@gnu.org>
Date: Sat, 13 Jun 2015 18:32:35 +0200
Subject: gnu: guix: Use 'modify-phases'.

* gnu/packages/package-management.scm (guix-0.8.2)[arguments]: Use
  'modify-phases' instead of 'alist-cons-before'.
---
 gnu/packages/package-management.scm | 46 ++++++++++++++++++-------------------
 1 file changed, 23 insertions(+), 23 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/package-management.scm b/gnu/packages/package-management.scm
index a2c74c2fe6..33dce5c809 100644
--- a/gnu/packages/package-management.scm
+++ b/gnu/packages/package-management.scm
@@ -75,31 +75,31 @@ (define-public guix-0.8.2
                           (string-append "--with-libgcrypt-prefix="
                                          (assoc-ref %build-inputs
                                                     "libgcrypt")))
-       #:phases (alist-cons-before
-                 'configure 'copy-bootstrap-guile
-                 (lambda* (#:key system inputs #:allow-other-keys)
-                   (define (boot-guile-version arch)
-                     (if (string=? "armhf" arch)
-                         "2.0.11"
-                         "2.0.9"))
+       #:phases (modify-phases %standard-phases
+                  (add-before
+                   'configure 'copy-bootstrap-guile
+                   (lambda* (#:key system inputs #:allow-other-keys)
+                     (define (boot-guile-version arch)
+                       (if (string=? "armhf" arch)
+                           "2.0.11"
+                           "2.0.9"))
 
-                   (define (copy arch)
-                     (let ((guile  (assoc-ref inputs
-                                              (string-append "boot-guile/"
-                                                             arch)))
-                           (target (string-append "gnu/packages/bootstrap/"
-                                                  arch "-linux/"
-                                                  "/guile-"
-                                                  (boot-guile-version arch)
-                                                  ".tar.xz")))
-                       (copy-file guile target)))
+                     (define (copy arch)
+                       (let ((guile  (assoc-ref inputs
+                                                (string-append "boot-guile/"
+                                                               arch)))
+                             (target (string-append "gnu/packages/bootstrap/"
+                                                    arch "-linux/"
+                                                    "/guile-"
+                                                    (boot-guile-version arch)
+                                                    ".tar.xz")))
+                         (copy-file guile target)))
 
-                   (copy "i686")
-                   (copy "x86_64")
-                   (copy "mips64el")
-                   (copy "armhf")
-                   #t)
-                 %standard-phases)))
+                     (copy "i686")
+                     (copy "x86_64")
+                     (copy "mips64el")
+                     (copy "armhf")
+                     #t)))))
     (native-inputs `(("pkg-config" ,pkg-config)
                      ("emacs" ,emacs-no-x)))      ;for guix.el
     (inputs
-- 
cgit v1.2.3


From 932e7204afbe6d56b8319f7c298ea43e12004a95 Mon Sep 17 00:00:00 2001
From: Ludovic Courtès <ludo@gnu.org>
Date: Sat, 13 Jun 2015 19:31:24 +0200
Subject: gnu: guix: Wrap 'guix' so GUILE_LOAD_PATH includes the dependencies.

* gnu/packages/package-management.scm (guix-0.8.2)[arguments]: Add
  'wrap-program' phase.
---
 gnu/packages/package-management.scm | 17 ++++++++++++++++-
 1 file changed, 16 insertions(+), 1 deletion(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/package-management.scm b/gnu/packages/package-management.scm
index 33dce5c809..7f6ec56151 100644
--- a/gnu/packages/package-management.scm
+++ b/gnu/packages/package-management.scm
@@ -99,7 +99,22 @@ (define (copy arch)
                      (copy "x86_64")
                      (copy "mips64el")
                      (copy "armhf")
-                     #t)))))
+                     #t))
+                  (add-after
+                   'install 'wrap-program
+                   (lambda* (#:key inputs outputs #:allow-other-keys)
+                     ;; Make sure the 'guix' command finds GnuTLS and
+                     ;; Guile-JSON automatically.
+                     (let* ((out    (assoc-ref outputs "out"))
+                            (json   (assoc-ref inputs "guile-json"))
+                            (gnutls (assoc-ref inputs "gnutls"))
+                            (path   (string-append
+                                     json "/share/guile/site/2.0:"
+                                     gnutls "/share/guile/site/2.0")))
+                       (wrap-program (string-append out "/bin/guix")
+                         `("GUILE_LOAD_PATH" ":" prefix (,path))
+                         `("GUILE_LOAD_COMPILED_PATH" ":" prefix (,path)))
+                       #t))))))
     (native-inputs `(("pkg-config" ,pkg-config)
                      ("emacs" ,emacs-no-x)))      ;for guix.el
     (inputs
-- 
cgit v1.2.3


From 4c50e5ab3a393c6d86fc6362c58f7ecf32dd9680 Mon Sep 17 00:00:00 2001
From: Mark H Weaver <mhw@netris.org>
Date: Fri, 12 Jun 2015 03:24:12 -0400
Subject: gnu: python: Disable ssl test that fails with openssl-1.0.2b.

* gnu/packages/patches/python-disable-ssl-test.patch: New file.
* gnu-system.am (dist_patch_DATA): Add it.
* gnu/packages/python.scm (python): Add patch.
---
 gnu-system.am                                      |  1 +
 gnu/packages/patches/python-disable-ssl-test.patch | 12 ++++++++++++
 gnu/packages/python.scm                            |  4 +++-
 3 files changed, 16 insertions(+), 1 deletion(-)
 create mode 100644 gnu/packages/patches/python-disable-ssl-test.patch

(limited to 'gnu/packages')

diff --git a/gnu-system.am b/gnu-system.am
index 7e0ee52875..fd7b1e5e86 100644
--- a/gnu-system.am
+++ b/gnu-system.am
@@ -526,6 +526,7 @@ dist_patch_DATA =						\
   gnu/packages/patches/pybugz-encode-error.patch		\
   gnu/packages/patches/pybugz-stty.patch			\
   gnu/packages/patches/pyqt-configure.patch			\
+  gnu/packages/patches/python-disable-ssl-test.patch		\
   gnu/packages/patches/python-fix-tests.patch			\
   gnu/packages/patches/python-libffi-mips-n32-fix.patch		\
   gnu/packages/patches/python2-rdflib-drop-sparqlwrapper.patch	\
diff --git a/gnu/packages/patches/python-disable-ssl-test.patch b/gnu/packages/patches/python-disable-ssl-test.patch
new file mode 100644
index 0000000000..e351c77505
--- /dev/null
+++ b/gnu/packages/patches/python-disable-ssl-test.patch
@@ -0,0 +1,12 @@
+Disable a test that fails with openssl-1.0.2b.
+
+--- Lib/test/test_ssl.py.orig	2015-02-25 06:27:45.000000000 -0500
++++ Lib/test/test_ssl.py	2015-06-12 03:14:09.395212502 -0400
+@@ -2718,6 +2718,7 @@
+                                        chatty=True, connectionchatty=True)
+             self.assertIs(stats['compression'], None)
+ 
++        @unittest.skipIf(True, "openssl 1.0.2b complains: dh key too small")
+         def test_dh_params(self):
+             # Check we can get a connection with ephemeral Diffie-Hellman
+             context = ssl.SSLContext(ssl.PROTOCOL_TLSv1)
diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 914c2dc23c..232a785778 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -207,7 +207,9 @@ (define-public python
               (method url-fetch)
               (uri (string-append "https://www.python.org/ftp/python/"
                                   version "/Python-" version ".tar.xz"))
-              (patches (list (search-patch "python-fix-tests.patch")))
+              (patches (list (search-patch "python-fix-tests.patch")
+                             ;; XXX Try removing this patch for python > 3.4.3
+                             (search-patch "python-disable-ssl-test.patch")))
               (patch-flags '("-p0"))
               (sha256
                (base32
-- 
cgit v1.2.3


From 0ad8f76f7ff3233533dbc0afb109946d5c459b1e Mon Sep 17 00:00:00 2001
From: Mark H Weaver <mhw@netris.org>
Date: Fri, 12 Jun 2015 03:40:12 -0400
Subject: gnu: perl-net-ssleay: Disable test that fails with openssl-1.0.2b.

* gnu/packages/patches/perl-net-ssleay-disable-ede-test.patch: New file.
* gnu-system.am (dist_patch_DATA): Add it.
* gnu/packages/openssl.scm (perl-net-ssleay): Add patch.
---
 gnu-system.am                                      |  1 +
 gnu/packages/openssl.scm                           |  5 ++++-
 .../patches/perl-net-ssleay-disable-ede-test.patch | 23 ++++++++++++++++++++++
 3 files changed, 28 insertions(+), 1 deletion(-)
 create mode 100644 gnu/packages/patches/perl-net-ssleay-disable-ede-test.patch

(limited to 'gnu/packages')

diff --git a/gnu-system.am b/gnu-system.am
index fd7b1e5e86..d551eb8ba2 100644
--- a/gnu-system.am
+++ b/gnu-system.am
@@ -512,6 +512,7 @@ dist_patch_DATA =						\
   gnu/packages/patches/perl-gd-options-passthrough-and-fontconfig.patch \
   gnu/packages/patches/perl-module-pluggable-search.patch	\
   gnu/packages/patches/perl-net-amazon-s3-moose-warning.patch	\
+  gnu/packages/patches/perl-net-ssleay-disable-ede-test.patch	\
   gnu/packages/patches/perl-no-sys-dirs.patch			\
   gnu/packages/patches/perl-tk-x11-discover.patch		\
   gnu/packages/patches/petsc-fix-threadcomm.patch		\
diff --git a/gnu/packages/openssl.scm b/gnu/packages/openssl.scm
index 1ed7a7a1f2..5ed0f63268 100644
--- a/gnu/packages/openssl.scm
+++ b/gnu/packages/openssl.scm
@@ -91,7 +91,10 @@ (define-public perl-net-ssleay
                                   "Net-SSLeay-" version ".tar.gz"))
               (sha256
                (base32
-                "1m2wwzhjwsg0drlhp9w12fl6bsgj69v8gdz72jqrqll3qr7f408p"))))
+                "1m2wwzhjwsg0drlhp9w12fl6bsgj69v8gdz72jqrqll3qr7f408p"))
+              (patches
+               ;; XXX Try removing this patch for perl-net-ssleay > 1.68
+               (list (search-patch "perl-net-ssleay-disable-ede-test.patch")))))
     (build-system perl-build-system)
     (inputs `(("openssl" ,openssl)))
     (arguments
diff --git a/gnu/packages/patches/perl-net-ssleay-disable-ede-test.patch b/gnu/packages/patches/perl-net-ssleay-disable-ede-test.patch
new file mode 100644
index 0000000000..16f136fb54
--- /dev/null
+++ b/gnu/packages/patches/perl-net-ssleay-disable-ede-test.patch
@@ -0,0 +1,23 @@
+Disable a test that fails with openssl-1.0.2b.
+
+--- Net-SSLeay-1.68/t/local/33_x509_create_cert.t.orig	2014-06-07 02:01:39.000000000 -0400
++++ Net-SSLeay-1.68/t/local/33_x509_create_cert.t	2015-06-12 03:38:57.620286888 -0400
+@@ -2,7 +2,7 @@
+ 
+ use strict;
+ use warnings;
+-use Test::More tests => 123;
++use Test::More tests => 122;
+ use Net::SSLeay qw/MBSTRING_ASC MBSTRING_UTF8 EVP_PK_RSA EVP_PKT_SIGN EVP_PKT_ENC/;
+ use File::Spec;
+ use utf8;
+@@ -101,7 +101,8 @@
+   like(my $key_pem3 = Net::SSLeay::PEM_get_string_PrivateKey($pk,"password",$alg1), qr/-----BEGIN (ENCRYPTED|RSA) PRIVATE KEY-----/, "PEM_get_string_PrivateKey+passwd+enc_alg");
+   
+   ok(my $alg2 = Net::SSLeay::EVP_get_cipherbyname("DES-EDE3-OFB"), "EVP_get_cipherbyname");
+-  like(my $key_pem4 = Net::SSLeay::PEM_get_string_PrivateKey($pk,"password",$alg2), qr/-----BEGIN (ENCRYPTED|RSA) PRIVATE KEY-----/, "PEM_get_string_PrivateKey+passwd+enc_alg");
++  # This test fails with openssl-1.0.2b
++  #like(my $key_pem4 = Net::SSLeay::PEM_get_string_PrivateKey($pk,"password",$alg2), qr/-----BEGIN (ENCRYPTED|RSA) PRIVATE KEY-----/, "PEM_get_string_PrivateKey+passwd+enc_alg");
+   
+   is(Net::SSLeay::X509_NAME_print_ex($name), "O=Company Name,C=UK,CN=Common name text X509", "X509_NAME_print_ex");  
+ 
-- 
cgit v1.2.3


From 7871724df7218428fac53133496c474bac8c5ea8 Mon Sep 17 00:00:00 2001
From: Mark H Weaver <mhw@netris.org>
Date: Fri, 12 Jun 2015 01:24:58 -0400
Subject: gnu: openssl: Update to 1.0.2b.

* gnu/packages/openssl.scm (openssl): Update to 1.0.2b.
---
 gnu/packages/openssl.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/openssl.scm b/gnu/packages/openssl.scm
index 5ed0f63268..dec51a1e04 100644
--- a/gnu/packages/openssl.scm
+++ b/gnu/packages/openssl.scm
@@ -29,14 +29,14 @@ (define-module (gnu packages openssl)
 (define-public openssl
   (package
    (name "openssl")
-   (version "1.0.2a")
+   (version "1.0.2b")
    (source (origin
             (method url-fetch)
             (uri (string-append "ftp://ftp.openssl.org/source/openssl-" version
                                 ".tar.gz"))
             (sha256
              (base32
-              "0jijgzf72659pikms2bc5w31h78xrd1h5zp2r01an2h340y3kdhm"))
+              "0gwf4fy1yqmai6wph0g9lh09iarwxaa70hm7jm0rf1qakz68im6m"))
             (patches (list (search-patch "openssl-runpath.patch")))))
    (build-system gnu-build-system)
    (native-inputs `(("perl" ,perl)))
-- 
cgit v1.2.3