branch master updated (e4a44a6 -> 32ac717)

[David Thompson]

davexunit pushed a change to branch master
in repository guix.

  from  e4a44a6   gnu: Add ruby-bio-kseq.
   new  32ac717   gnu: Add gnome-shell-extensions.

The 1 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.


Summary of changes:
 gnu/packages/gnome.scm |   27 +++
 1 file changed, 27 insertions(+)

01/01: gnu: Add gnome-shell-extensions.

[David Thompson]

davexunit pushed a commit to branch master
in repository guix.

commit 32ac717c5f38192b8bf832e2aba4e83e38a201c3
Author: David Thompson 
Date:   Sat Jun 11 21:21:02 2016 -0400

gnu: Add gnome-shell-extensions.

* gnu/packages/gnome.scm (gnome-shell-extensions): New variable.
---
 gnu/packages/gnome.scm |   27 +++
 1 file changed, 27 insertions(+)

diff --git a/gnu/packages/gnome.scm b/gnu/packages/gnome.scm
index c87c371..0b80ebb 100644
--- a/gnu/packages/gnome.scm
+++ b/gnu/packages/gnome.scm
@@ -5183,6 +5183,33 @@ alternative user interface themes, changes in window 
management behavior,
 GNOME Shell appearance and extension, etc.")
 (license license:gpl3+)))
 
+(define-public gnome-shell-extensions
+  (package
+(name "gnome-shell-extensions")
+(version "3.20.1")
+(source (origin
+  (method url-fetch)
+  (uri (string-append "mirror://gnome/sources/" name "/"
+  (version-major+minor version)  "/"
+  name "-" version ".tar.xz"))
+  (sha256
+   (base32
+"18rr55krnqx1nzrzlj6kfzh4n67f3crakmwh28rr95y7cg0jwhxw"
+(build-system gnu-build-system)
+(arguments
+ '(#:configure-flags '("--enable-extensions=all")))
+(native-inputs
+ `(("intltool" ,intltool)
+   ("pkg-config" ,pkg-config)))
+(propagated-inputs
+ `(("glib" ,glib)
+   ("glib" ,glib "bin")))
+(synopsis "Extensions for GNOME Shell")
+(description "GNOME Shell extensions modify and extend GNOME Shell
+functionality and behavior.")
+(home-page "https://extensions.gnome.org/;)
+(license license:gpl3+)))
+
 (define-public arc-theme
   (package
 (name "arc-theme")

branch master updated (d3ef652 -> e4a44a6)

[Ben Woodcroft]

benwoodcroft pushed a change to branch master
in repository guix.

  from  d3ef652   gnu: wget: Update to 1.18.
   new  e4a44a6   gnu: Add ruby-bio-kseq.

The 1 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.


Summary of changes:
 gnu/packages/bioinformatics.scm |   28 
 1 file changed, 28 insertions(+)

01/01: gnu: Add ruby-bio-kseq.

[Ben Woodcroft]

benwoodcroft pushed a commit to branch master
in repository guix.

commit e4a44a6aa5b6dcda39ab8c347d1dc68a4cc7e4f9
Author: Ben Woodcroft 
Date:   Fri Jun 10 19:45:14 2016 +1000

gnu: Add ruby-bio-kseq.

* gnu/packages/bioinformatics.scm (ruby-bio-kseq): New variable.
---
 gnu/packages/bioinformatics.scm |   28 
 1 file changed, 28 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 98b0034..58877f7 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -3926,6 +3926,34 @@ clusters.")
 (home-page "https://sourceforge.net/projects/pardre/;)
 (license license:gpl3+)))
 
+(define-public ruby-bio-kseq
+  (package
+(name "ruby-bio-kseq")
+(version "0.0.2")
+(source
+ (origin
+   (method url-fetch)
+   (uri (rubygems-uri "bio-kseq" version))
+   (sha256
+(base32
+ "1xyaha46khb5jc6wzkbf7040jagac49jbimn0vcrzid0j8jdikrz"
+(build-system ruby-build-system)
+(arguments
+ `(#:test-target "spec"))
+(native-inputs
+ `(("bundler" ,bundler)
+   ("ruby-rspec" ,ruby-rspec)
+   ("ruby-rake-compiler" ,ruby-rake-compiler)))
+(inputs
+ `(("zlib" ,zlib)))
+(synopsis "Ruby bindings for the kseq.h FASTA/Q parser")
+(description
+ "@code{Bio::Kseq} provides ruby bindings to the @code{kseq.h} FASTA and
+FASTQ parsing code.  It provides a fast iterator over sequences and their
+quality scores.")
+(home-page "https://github.com/gusevfe/bio-kseq;)
+(license license:expat)))
+
 (define-public bio-locus
   (package
 (name "bio-locus")

01/01: gnu: wget: Update to 1.18.

[Ludovic Court�s]

civodul pushed a commit to branch master
in repository guix.

commit d3ef652aa15b899084613dd1d41ac7722dc582b3
Author: Ludovic Courtès 
Date:   Mon Jun 13 23:13:16 2016 +0200

gnu: wget: Update to 1.18.

* gnu/packages/wget.scm (wget): Update to 1.18.
---
 gnu/packages/wget.scm |4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/wget.scm b/gnu/packages/wget.scm
index d8a7bea..80da332 100644
--- a/gnu/packages/wget.scm
+++ b/gnu/packages/wget.scm
@@ -32,7 +32,7 @@
 (define-public wget
   (package
 (name "wget")
-(version "1.17.1")
+(version "1.18")
 (source
  (origin
   (method url-fetch)
@@ -40,7 +40,7 @@
   version ".tar.xz"))
   (sha256
(base32
-"1jcpvl5sxb2ag8yahpy370c5jlfb097a21k2mhsidh4wxdhrnmgy"
+"1hcwx8ww3sxzdskkx3l7q70a7wd6569yrnjkw9pw013cf9smpddm"
 (build-system gnu-build-system)
 (inputs
  `(("gnutls" ,gnutls)

branch master updated (6508921 -> d3ef652)

[Ludovic Court�s]

civodul pushed a change to branch master
in repository guix.

  from  6508921   gnu: wayland: Update to 1.11.0.
   new  d3ef652   gnu: wget: Update to 1.18.

The 1 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.


Summary of changes:
 gnu/packages/wget.scm |4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

01/01: gnu: wayland: Update to 1.11.0.

[Efraim Flashner]

efraim pushed a commit to branch master
in repository guix.

commit 65089213c8dd26f6fc6e2be52d04823c91f32763
Author: Efraim Flashner 
Date:   Mon Jun 13 22:37:35 2016 +0300

gnu: wayland: Update to 1.11.0.

* gnu/packages/freedesktop.scm (wayland): Update to 1.11.0.
---
 gnu/packages/freedesktop.scm |4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/freedesktop.scm b/gnu/packages/freedesktop.scm
index 9bd080c..53bd757 100644
--- a/gnu/packages/freedesktop.scm
+++ b/gnu/packages/freedesktop.scm
@@ -253,14 +253,14 @@ Python.")
 (define-public wayland
   (package
 (name "wayland")
-(version "1.10.0")
+(version "1.11.0")
 (source (origin
   (method url-fetch)
   (uri (string-append "https://wayland.freedesktop.org/releases/;
   name "-" version ".tar.xz"))
   (sha256
(base32
-"1p307ly1yyqjnzn9dbv78yffql2qszn84qk74lwanl3gma8fgxjb"
+"1c0d5ivy9n44hykvw2ggrvqrnn7naw3wg11vbvgwzgi8g5gr4h4m"
 (build-system gnu-build-system)
 (arguments `(#:parallel-tests? #f))
 (native-inputs

branch master updated (c6bccf7 -> 6508921)

[Efraim Flashner]

efraim pushed a change to branch master
in repository guix.

  from  c6bccf7   gnu: python-pykafka: Change uri.
   new  6508921   gnu: wayland: Update to 1.11.0.

The 1 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.


Summary of changes:
 gnu/packages/freedesktop.scm |4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

01/01: gnu: python-pykafka: Change uri.

[Efraim Flashner]

efraim pushed a commit to branch master
in repository guix.

commit c6bccf713bf2e2bbd072df2d60b17a661db919d7
Author: Efraim Flashner 
Date:   Mon Jun 13 21:31:13 2016 +0300

gnu: python-pykafka: Change uri.

* gnu/packages/python.scm (python-pykafka)[source]: Update pypi uri.
---
 gnu/packages/python.scm |5 -
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 2645b8e..fa06a12 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -9160,7 +9160,10 @@ programming errors.")
 (version "2.4.0")
 (source (origin
   (method url-fetch)
-  (uri (pypi-uri "pykafka" version))
+  (uri (string-append
+ "https://pypi.python.org/packages/8b/3e/;
+ 
"384eeff406b06315738b62483fd2126c6e4f544167116b17cc04ea7d2a59/"
+ "pykafka-" version ".tar.gz"))
   (sha256
(base32
 "1id6sr159p6aa13bxcqyr9gln8sqg1l0ddzns5iws8kk5q1p5cfv"

branch master updated (2fb3ddd -> c6bccf7)

[Efraim Flashner]

efraim pushed a change to branch master
in repository guix.

  from  2fb3ddd   gnu: giac-xcas: Update to 1.2.2-59
   new  c6bccf7   gnu: python-pykafka: Change uri.

The 1 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.


Summary of changes:
 gnu/packages/python.scm |5 -
 1 file changed, 4 insertions(+), 1 deletion(-)

01/02: packages: Use '--no-backup-if-mismatch' for patching.

[Leo Famulari]

lfam pushed a commit to branch core-updates-next
in repository guix.

commit 98e8dc61736f48a9a0be54281d63e03a77b601f3
Author: Alex Kost 
Date:   Thu May 19 19:11:58 2016 +0300

packages: Use '--no-backup-if-mismatch' for patching.

Suggested-by: Ludovic Courtès 

* guix/packages.scm (patch-and-repack)[build]: Use
  '--no-backup-if-mismatch' patch flag to avoid making *.orig files.
---
 guix/packages.scm |7 +--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/guix/packages.scm b/guix/packages.scm
index d62d1f3..7178674 100644
--- a/guix/packages.scm
+++ b/guix/packages.scm
@@ -2,6 +2,7 @@
 ;;; Copyright © 2012, 2013, 2014, 2015, 2016 Ludovic Courtès 
 ;;; Copyright © 2014, 2015 Mark H Weaver 
 ;;; Copyright © 2015 Eric Bavier 
+;;; Copyright © 2016 Alex Kost 
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -464,9 +465,11 @@ IMPORTED-MODULES specify modules to use/import for use by 
SNIPPET."
 (format (current-error-port) "applying '~a'...~%" patch)
 
 ;; Use '--force' so that patches that do not apply perfectly are
-;; rejected.
+;; rejected.  Use '--no-backup-if-mismatch' to prevent making
+;; "*.orig" file if a patch is applied with offset.
 (zero? (system* (string-append #+patch "/bin/patch")
-"--force" #+@flags "--input" patch)))
+"--force" "--no-backup-if-mismatch"
+#+@flags "--input" patch)))
 
   (define (first-file directory)
 ;; Return the name of the first file in DIRECTORY.

branch core-updates-next created (now d35bc36)

[Leo Famulari]

lfam pushed a change to branch core-updates-next
in repository guix.

at  d35bc36   gnu: curl: Update to 7.49.1.

This branch includes the following new commits:

   new  98e8dc6   packages: Use '--no-backup-if-mismatch' for patching.
   new  d35bc36   gnu: curl: Update to 7.49.1.

The 2 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.

02/02: gnu: curl: Update to 7.49.1.

[Leo Famulari]

lfam pushed a commit to branch core-updates-next
in repository guix.

commit d35bc362161150c79ab2632feb01a33d1f637a50
Author: Leo Famulari 
Date:   Mon Jun 13 11:54:06 2016 -0400

gnu: curl: Update to 7.49.1.

* gnu/packages/curl.scm (curl): Update to 7.49.1.
[arguments]: Re-enable test.
---
 gnu/packages/curl.scm |8 ++--
 1 file changed, 2 insertions(+), 6 deletions(-)

diff --git a/gnu/packages/curl.scm b/gnu/packages/curl.scm
index 222910b..4fe27c0 100644
--- a/gnu/packages/curl.scm
+++ b/gnu/packages/curl.scm
@@ -40,14 +40,14 @@
 (define-public curl
   (package
(name "curl")
-   (version "7.47.0")
+   (version "7.49.1")
(source (origin
 (method url-fetch)
 (uri (string-append "https://curl.haxx.se/download/curl-;
 version ".tar.lzma"))
 (sha256
  (base32
-  "1n284wdqzwb4bkmv0fnh36zl6lhlzy3clw2b7pn28kpgdy09ly7p"
+  "033w3wyawali0rc5s15ywxpjnf476671m595r49sr4vj07idf3al"
(build-system gnu-build-system)
(outputs '("out"
   "doc")) ;1.2 MiB of man3 pages
@@ -83,10 +83,6 @@
  (lambda _
(substitute* "tests/runtests.pl"
  (("/bin/sh") (which "sh")))
-   ;; Test #1135 requires extern-scan.pl, which is not part of the
-   ;; tarball due to a mistake.  It has been fixed upstream.  We can
-   ;; simply disable the test as it is specific to VMS and OS/400.
-   (delete-file "tests/data/test1135")
 
;; XXX FIXME: Test #1510 seems to work on some machines and not
;; others, possibly based on the kernel version.  It works on GuixSD

branch core-updates-next deleted (was 659494e)

[Leo Famulari]

lfam pushed a change to branch core-updates-next
in repository guix.

   was  659494e   Revert "gnu: libxslt: Update to 1.1.29."

This change permanently discards the following revisions:

  discards  659494e   Revert "gnu: libxslt: Update to 1.1.29."
  discards  5f39448   Revert "gnu: expat: Remove replacement."
  discards  32a8eb0   gnu: curl: Update to 7.49.1.
  discards  aee7f2e   gnu: libxslt: Update to 1.1.29.
  discards  b0bbf24   gnu: expat: Remove replacement.
  discards  98e8dc6   packages: Use '--no-backup-if-mismatch' for patching.

branch core-updates-next updated (32a8eb0 -> 659494e)

[Leo Famulari]

lfam pushed a change to branch core-updates-next
in repository guix.

  from  32a8eb0   gnu: curl: Update to 7.49.1.
   new  5f39448   Revert "gnu: expat: Remove replacement."
   new  659494e   Revert "gnu: libxslt: Update to 1.1.29."

The 2 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.


Summary of changes:
 gnu/local.mk |1 +
 gnu/packages/patches/libxslt-CVE-2015-7995.patch |   29 ++
 gnu/packages/xml.scm |   19 ++
 3 files changed, 44 insertions(+), 5 deletions(-)
 create mode 100644 gnu/packages/patches/libxslt-CVE-2015-7995.patch

02/02: Revert "gnu: libxslt: Update to 1.1.29."

[Leo Famulari]

lfam pushed a commit to branch core-updates-next
in repository guix.

commit 659494ef1809ecc7492ccb3d83a852c9632bc1e7
Author: Leo Famulari 
Date:   Mon Jun 13 12:15:42 2016 -0400

Revert "gnu: libxslt: Update to 1.1.29."

This reverts commit aee7f2e98ae2cbbd0cd765beda6c0a4279929c94.

This commit has already been applied to another branch.
---
 gnu/local.mk |1 +
 gnu/packages/patches/libxslt-CVE-2015-7995.patch |   29 ++
 gnu/packages/xml.scm |5 ++--
 3 files changed, 33 insertions(+), 2 deletions(-)

diff --git a/gnu/local.mk b/gnu/local.mk
index 0beadfc..c130901 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -606,6 +606,7 @@ dist_patch_DATA =   
\
   gnu/packages/patches/libwmf-CVE-2015-0848+CVE-2015-4588.patch\
   gnu/packages/patches/libwmf-CVE-2015-4695.patch  \
   gnu/packages/patches/libwmf-CVE-2015-4696.patch  \
+  gnu/packages/patches/libxslt-CVE-2015-7995.patch \
   gnu/packages/patches/lirc-localstatedir.patch\
   gnu/packages/patches/libpthread-glibc-preparation.patch  \
   gnu/packages/patches/lm-sensors-hwmon-attrs.patch\
diff --git a/gnu/packages/patches/libxslt-CVE-2015-7995.patch 
b/gnu/packages/patches/libxslt-CVE-2015-7995.patch
new file mode 100644
index 000..f291d5b
--- /dev/null
+++ b/gnu/packages/patches/libxslt-CVE-2015-7995.patch
@@ -0,0 +1,29 @@
+From 7ca19df892ca22d9314e95d59ce2abdeff46b617 Mon Sep 17 00:00:00 2001
+From: Daniel Veillard 
+Date: Thu, 29 Oct 2015 19:33:23 +0800
+Subject: [PATCH] Fix for type confusion in preprocessing attributes
+
+CVE-2015-7995 http://www.openwall.com/lists/oss-security/2015/10/27/10
+We need to check that the parent node is an element before dereferencing
+its namespace
+---
+ libxslt/preproc.c | 3 ++-
+ 1 file changed, 2 insertions(+), 1 deletion(-)
+
+diff --git a/libxslt/preproc.c b/libxslt/preproc.c
+index 0eb80a0..7f69325 100644
+--- a/libxslt/preproc.c
 b/libxslt/preproc.c
+@@ -2249,7 +2249,8 @@ xsltStylePreCompute(xsltStylesheetPtr style, xmlNodePtr 
inst) {
+   } else if (IS_XSLT_NAME(inst, "attribute")) {
+   xmlNodePtr parent = inst->parent;
+ 
+-  if ((parent == NULL) || (parent->ns == NULL) ||
++  if ((parent == NULL) ||
++  (parent->type != XML_ELEMENT_NODE) || (parent->ns == NULL) ||
+   ((parent->ns != inst->ns) &&
+(!xmlStrEqual(parent->ns->href, inst->ns->href))) ||
+   (!xmlStrEqual(parent->name, BAD_CAST "attribute-set"))) {
+-- 
+2.6.3
+
diff --git a/gnu/packages/xml.scm b/gnu/packages/xml.scm
index 5ae14d5..9eaf71a 100644
--- a/gnu/packages/xml.scm
+++ b/gnu/packages/xml.scm
@@ -135,14 +135,15 @@ project (but it is usable outside of the Gnome 
platform).")
 (define-public libxslt
   (package
 (name "libxslt")
-(version "1.1.29")
+(version "1.1.28")
 (source (origin
  (method url-fetch)
  (uri (string-append "ftp://xmlsoft.org/libxslt/libxslt-;
  version ".tar.gz"))
  (sha256
   (base32
-   "1klh81xbm9ppzgqk339097i39b7fnpmlj8lzn8bpczl3aww6x5xm"
+   "13029baw9kkyjgr7q3jccw2mz38amq7mmpr5p3bh775qawd1bisz"))
+ (patches (search-patches "libxslt-CVE-2015-7995.patch"
 (build-system gnu-build-system)
 (home-page "http://xmlsoft.org/XSLT/index.html;)
 (synopsis "C library for applying XSLT stylesheets to XML documents")

02/05: syscalls: Use 'syscall->procedure' everywhere.

[Ludovic Court�s]

civodul pushed a commit to branch master
in repository guix.

commit d1f33ba44b60526d20da04d384f3af5437f8a3ae
Author: Ludovic Courtès 
Date:   Mon Jun 13 17:57:25 2016 +0200

syscalls: Use 'syscall->procedure' everywhere.

* guix/build/syscalls.scm (mkdtemp!, setns, %ioctl, network-interfaces):
(free-ifaddrs): Use 'syscall->procedure'.
---
 guix/build/syscalls.scm |   16 +---
 1 file changed, 5 insertions(+), 11 deletions(-)

diff --git a/guix/build/syscalls.scm b/guix/build/syscalls.scm
index ed0eb06..c663899 100644
--- a/guix/build/syscalls.scm
+++ b/guix/build/syscalls.scm
@@ -494,8 +494,7 @@ user-land process."
 <))
 
 (define mkdtemp!
-  (let* ((ptr  (dynamic-func "mkdtemp" (dynamic-link)))
- (proc (pointer->procedure '* ptr '(*
+  (let ((proc (syscall->procedure '* "mkdtemp" '(*
 (lambda (tmpl)
   "Create a new unique directory in the file system using the template
 string TMPL and return its file name.  TMPL must end with 'XX'."
@@ -626,8 +625,7 @@ are shared between the parent and child processes."
   ;; Some systems may be using an old (pre-2.14) version of glibc where there
   ;; is no 'setns' function available.
   (false-if-exception
-   (let* ((ptr  (dynamic-func "setns" (dynamic-link)))
-  (proc (pointer->procedure int ptr (list int int
+   (let ((proc (syscall->procedure int "setns" (list int int
  (lambda (fdes nstype)
"Reassociate the current process with the namespace specified by FDES, a
 file descriptor obtained by opening a /proc/PID/ns/* file.  NSTYPE specifies
@@ -833,9 +831,7 @@ bytevector BV at INDEX."
 
 (define %ioctl
   ;; The most terrible interface, live from Scheme.
-  (pointer->procedure int
-  (dynamic-func "ioctl" (dynamic-link))
-  (list int unsigned-long '*)))
+  (syscall->procedure int "ioctl" (list int unsigned-long '*)))
 
 (define (bytevector->string-list bv stride len)
   "Return the null-terminated strings found in BV every STRIDE bytes.  Read at
@@ -1075,8 +1071,7 @@ return the list of resulting  objects."
(loop ptr (cons ifaddr result)))
 
 (define network-interfaces
-  (let* ((ptr  (dynamic-func "getifaddrs" (dynamic-link)))
- (proc (pointer->procedure int ptr (list '*
+  (let ((proc (syscall->procedure int "getifaddrs" (list '*
 (lambda ()
   "Return a list of  objects, each denoting a configured
 network interface.  This is implemented using the 'getifaddrs' libc function."
@@ -1093,8 +1088,7 @@ network interface.  This is implemented using the 
'getifaddrs' libc function."
(list err)))
 
 (define free-ifaddrs
-  (let ((ptr (dynamic-func "freeifaddrs" (dynamic-link
-(pointer->procedure void ptr '(*
+  (syscall->procedure void "freeifaddrs" '(*)))
 
 
 ;;;

01/02: Revert "gnu: expat: Remove replacement."

[Leo Famulari]

lfam pushed a commit to branch core-updates-next
in repository guix.

commit 5f39448378dad95e3a46b82e90e5ac52ff4ab323
Author: Leo Famulari 
Date:   Mon Jun 13 12:15:27 2016 -0400

Revert "gnu: expat: Remove replacement."

This reverts commit b0bbf2491e346a355c1ec5584c16de7fbfa14f5e.

This change has already been made on another branch.
---
 gnu/packages/xml.scm |   14 +++---
 1 file changed, 11 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/xml.scm b/gnu/packages/xml.scm
index e7b0599..5ae14d5 100644
--- a/gnu/packages/xml.scm
+++ b/gnu/packages/xml.scm
@@ -45,6 +45,7 @@
 (define-public expat
   (package
 (name "expat")
+(replacement expat/fixed)
 (version "2.1.0")
 (source (origin
  (method url-fetch)
@@ -53,9 +54,7 @@
  (sha256
   (base32
"11pblz61zyxh68s5pdcbhc30ha1b2vfjd83aiwfg4vc15x3hadw2"))
- (patches (search-patches "expat-CVE-2015-1283.patch"
-  "expat-CVE-2015-1283-refix.patch"
-  "expat-CVE-2016-0718.patch"
+ (patches (search-patches "expat-CVE-2015-1283.patch"
 (build-system gnu-build-system)
 (home-page "http://www.libexpat.org/;)
 (synopsis "Stream-oriented XML parser library written in C")
@@ -65,6 +64,15 @@ stream-oriented parser in which an application registers 
handlers for
 things the parser might find in the XML document (like start tags).")
 (license license:expat)))
 
+(define expat/fixed
+  (package
+(inherit expat)
+(source (origin
+  (inherit (package-source expat))
+  (patches (search-patches "expat-CVE-2015-1283.patch"
+   "expat-CVE-2015-1283-refix.patch"
+   "expat-CVE-2016-0718.patch"))
+
 (define-public libxml2
   (package
 (name "libxml2")

01/01: gnu: curl: Update to 7.49.1.

[Leo Famulari]

lfam pushed a commit to branch core-updates-next
in repository guix.

commit 32a8eb01e9d312670929a619a5dd6363d6f133d2
Author: Leo Famulari 
Date:   Mon Jun 13 11:54:06 2016 -0400

gnu: curl: Update to 7.49.1.

* gnu/packages/curl.scm (curl): Update to 7.49.1.
[arguments]: Re-enable test.
---
 gnu/packages/curl.scm |8 ++--
 1 file changed, 2 insertions(+), 6 deletions(-)

diff --git a/gnu/packages/curl.scm b/gnu/packages/curl.scm
index 222910b..4fe27c0 100644
--- a/gnu/packages/curl.scm
+++ b/gnu/packages/curl.scm
@@ -40,14 +40,14 @@
 (define-public curl
   (package
(name "curl")
-   (version "7.47.0")
+   (version "7.49.1")
(source (origin
 (method url-fetch)
 (uri (string-append "https://curl.haxx.se/download/curl-;
 version ".tar.lzma"))
 (sha256
  (base32
-  "1n284wdqzwb4bkmv0fnh36zl6lhlzy3clw2b7pn28kpgdy09ly7p"
+  "033w3wyawali0rc5s15ywxpjnf476671m595r49sr4vj07idf3al"
(build-system gnu-build-system)
(outputs '("out"
   "doc")) ;1.2 MiB of man3 pages
@@ -83,10 +83,6 @@
  (lambda _
(substitute* "tests/runtests.pl"
  (("/bin/sh") (which "sh")))
-   ;; Test #1135 requires extern-scan.pl, which is not part of the
-   ;; tarball due to a mistake.  It has been fixed upstream.  We can
-   ;; simply disable the test as it is specific to VMS and OS/400.
-   (delete-file "tests/data/test1135")
 
;; XXX FIXME: Test #1510 seems to work on some machines and not
;; others, possibly based on the kernel version.  It works on GuixSD

05/05: gnu: giac-xcas: Update to 1.2.2-59

[Ludovic Court�s]

civodul pushed a commit to branch master
in repository guix.

commit 2fb3dddabfc06c9454cfaa9fb6aba427f393b04e
Author: Nicolas Goaziou 
Date:   Sun Jun 12 17:02:18 2016 +0200

gnu: giac-xcas: Update to 1.2.2-59

* gnu/packages/algebra.scm (giac-xcas): Update to 1.2.2-59.

Signed-off-by: Ludovic Courtès 
---
 gnu/packages/algebra.scm |4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/algebra.scm b/gnu/packages/algebra.scm
index 9518e65..12691da 100644
--- a/gnu/packages/algebra.scm
+++ b/gnu/packages/algebra.scm
@@ -202,7 +202,7 @@ GP2C, the GP to C compiler, translates GP scripts to PARI 
programs.")
 (define-public giac-xcas
   (package
 (name "giac-xcas")
-(version "1.2.2-41")
+(version "1.2.2-59")
 (source (origin
   (method url-fetch)
   ;; "~parisse/giac" is not used because the maintainer regularly
@@ -214,7 +214,7 @@ GP2C, the GP to C compiler, translates GP scripts to PARI 
programs.")
   "source/giac_" version ".tar.gz"))
   (sha256
(base32
-"061a0p5l1qlb9iqk7n7yznhv2f3hvll1hrzjbhn81bf31f2wj6sq"
+"02s774v2zg2ya43rm8s7bcwzrmp4wlmn8h2rlg4816zpfrjkrdn4"
 (build-system gnu-build-system)
 (arguments
  `(#:phases

branch master updated (883302d -> 9f8ee3f)

[Ricardo Wurmus]

rekado pushed a change to branch master
in repository guix.

  from  883302d   gnu: piranha: Update to 1.2.1.
   new  9f8ee3f   gnu: Add python-tables.

The 1 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.


Summary of changes:
 gnu/packages/python.scm |   57 +++
 1 file changed, 57 insertions(+)

03/05: utils: 'with-atomic-file-output' closes the port upon exception.

[Ludovic Court�s]

civodul pushed a commit to branch master
in repository guix.

commit c25637dfe8aaf2aa7550c9196fb7e18820552ca6
Author: Ludovic Courtès 
Date:   Mon Jun 13 18:00:29 2016 +0200

utils: 'with-atomic-file-output' closes the port upon exception.

Previously it could have left the file descriptor open.

* guix/utils.scm (with-atomic-file-output): Call 'close-port' in handler.
---
 guix/utils.scm |3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/guix/utils.scm b/guix/utils.scm
index 18d913c..2d8bfd8 100644
--- a/guix/utils.scm
+++ b/guix/utils.scm
@@ -630,7 +630,8 @@ output port, and PROC's result is returned."
   (rename-file template file)
   result))
   (lambda (key . args)
-(false-if-exception (delete-file template))
+(false-if-exception (delete-file template))
+(close-port out)
 
 (define (cache-directory)
   "Return the cache directory for Guix, by default ~/.cache/guix."

01/01: gnu: Add python-tables.

[Ricardo Wurmus]

rekado pushed a commit to branch master
in repository guix.

commit 9f8ee3fe0ed615a89520618c4df66647845b15b3
Author: Ricardo Wurmus 
Date:   Thu Apr 21 17:27:42 2016 +0200

gnu: Add python-tables.

* gnu/packages/python.scm (python-tables, python2-tables): New
  variables.
---
 gnu/packages/python.scm |   57 +++
 1 file changed, 57 insertions(+)

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index b2d27ef..2645b8e 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -5716,6 +5716,63 @@ printing of sub-tables by specifying a row range.")
 (define-public python2-prettytable
   (package-with-python2 python-prettytable))
 
+(define-public python-tables
+  (package
+(name "python-tables")
+(version "3.2.2")
+(source
+ (origin
+   (method url-fetch)
+   (uri (pypi-uri "tables" version))
+   (sha256
+(base32
+ "117s6w7s3yxafpmf3zz3svana7xfrsviw01va1xp7h8ylx8v6r1m"
+(build-system python-build-system)
+(arguments
+ `(;; FIXME: python-build-system does not pass configure-flags to "build"
+   ;; or "check", so we must override the build and check phases.
+   #:phases
+   (modify-phases %standard-phases
+ (add-after 'unpack 'use-gcc
+   (lambda _
+ (substitute* "setup.py"
+   (("compiler = new_compiler\\(\\)" line)
+(string-append line
+   "\ncompiler.set_executables(compiler='gcc',"
+   "compiler_so='gcc',"
+   "linker_exe='gcc',"
+   "linker_so='gcc -shared')")))
+ #t))
+ (replace 'build
+   (lambda* (#:key inputs #:allow-other-keys)
+ (zero? (system* "python" "setup.py" "build"
+ (string-append "--hdf5="
+(assoc-ref inputs "hdf5"))
+ (replace 'check
+   (lambda* (#:key inputs #:allow-other-keys)
+ (zero? (system* "python" "setup.py" "check"
+ (string-append "--hdf5="
+(assoc-ref inputs "hdf5")
+(propagated-inputs
+ `(("python-numexpr" ,python-numexpr)
+   ("python-numpy" ,python-numpy)))
+(native-inputs
+ `(("python-setuptools" ,python-setuptools)
+   ("python-cython" ,python-cython)
+   ("pkg-config" ,pkg-config)))
+(inputs
+ `(("hdf5" ,hdf5)
+   ("bzip2" ,bzip2)
+   ("zlib" ,zlib)))
+(home-page "http://www.pytables.org/;)
+(synopsis "Hierarchical datasets for Python")
+(description "PyTables is a package for managing hierarchical datasets and
+designed to efficently cope with extremely large amounts of data.")
+(license bsd-3)))
+
+(define-public python2-tables
+  (package-with-python2 python-tables))
+
 (define-public python-pyasn1
   (package
 (name "python-pyasn1")

branch master updated (9f8ee3f -> 2fb3ddd)

[Ludovic Court�s]

civodul pushed a change to branch master
in repository guix.

  from  9f8ee3f   gnu: Add python-tables.
   new  1752a17   utils: 'with-atomic-file-output' calls 'fdatasync'.
   new  d1f33ba   syscalls: Use 'syscall->procedure' everywhere.
   new  c25637d   utils: 'with-atomic-file-output' closes the port upon 
exception.
   new  2e2c6e9   gnu: asymptote: Update to 2.38
   new  2fb3ddd   gnu: giac-xcas: Update to 1.2.2-59

The 5 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.


Summary of changes:
 gnu/packages/algebra.scm   |4 ++--
 gnu/packages/plotutils.scm |4 ++--
 guix/build/syscalls.scm|   31 ---
 guix/utils.scm |8 +---
 4 files changed, 29 insertions(+), 18 deletions(-)

04/05: gnu: asymptote: Update to 2.38

[Ludovic Court�s]

civodul pushed a commit to branch master
in repository guix.

commit 2e2c6e965573e91b5e9455c5009e61adfbaae7ec
Author: Nicolas Goaziou 
Date:   Sun Jun 12 13:52:45 2016 +0200

gnu: asymptote: Update to 2.38

* gnu/packages/plotutils.scm (asymptote): Update to 2.38.

Signed-off-by: Ludovic Courtès 
---
 gnu/packages/plotutils.scm |4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/plotutils.scm b/gnu/packages/plotutils.scm
index 3edb25a..74d2091 100644
--- a/gnu/packages/plotutils.scm
+++ b/gnu/packages/plotutils.scm
@@ -173,14 +173,14 @@ colors, styles, options and details.")
 (define-public asymptote
   (package
 (name "asymptote")
-(version "2.37")
+(version "2.38")
 (source (origin
   (method url-fetch)
   (uri (string-append "mirror://sourceforge/asymptote/"
   version "/asymptote-" version ".src.tgz"))
   (sha256
(base32
-"16nh02m52mk9a53i8wc6l9vg710gnzr3lfbypcbvamghvaj0458i"
+"1dxwvq0xighqckkjkjva8s0igxfgy1j25z81pbwvlz6jzsrxpip9"
 (build-system gnu-build-system)
 ;; Note: The 'asy' binary retains a reference to docdir for use with its
 ;; "help" command in interactive mode, so adding a "doc" output is not

branch core-updates-next updated (aee7f2e -> 32a8eb0)

[Leo Famulari]

lfam pushed a change to branch core-updates-next
in repository guix.

  from  aee7f2e   gnu: libxslt: Update to 1.1.29.
   new  32a8eb0   gnu: curl: Update to 7.49.1.

The 1 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.


Summary of changes:
 gnu/packages/curl.scm |8 ++--
 1 file changed, 2 insertions(+), 6 deletions(-)

branch core-updates updated (809f176 -> 9f44dfc)

[Ludovic Court�s]

civodul pushed a change to branch core-updates
in repository guix.

  from  809f176   gnu: swig: Adjust to pcre output split.
   new  9f44dfc   build: Update list of libxslt patches.

The 1 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.


Summary of changes:
 gnu/local.mk |2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

01/01: build: Update list of libxslt patches.

[Ludovic Court�s]

civodul pushed a commit to branch core-updates
in repository guix.

commit 9f44dfc077e68308d80c4ddc684015edf4d9aa5f
Author: Ludovic Courtès 
Date:   Mon Jun 13 13:11:51 2016 +0200

build: Update list of libxslt patches.

* gnu/local.mk (dist_patch_DATA): Remove libxslt-CVE-2015-7995.patch,
unneeded since 28b33172c9d67795e3ac641f9230b99905c90664.
Re-add libxslt-generated-ids.patch.
---
 gnu/local.mk |2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/gnu/local.mk b/gnu/local.mk
index 15c5138..b734576 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -626,7 +626,7 @@ dist_patch_DATA =   
\
   %D%/packages/patches/libwmf-CVE-2015-0848+CVE-2015-4588.patch\
   %D%/packages/patches/libwmf-CVE-2015-4695.patch  \
   %D%/packages/patches/libwmf-CVE-2015-4696.patch  \
-  %D%/packages/patches/libxslt-CVE-2015-7995.patch \
+  %D%/packages/patches/libxslt-generated-ids.patch \
   %D%/packages/patches/lirc-localstatedir.patch\
   %D%/packages/patches/lm-sensors-hwmon-attrs.patch\
   %D%/packages/patches/lua-CVE-2014-5461.patch  \

branch master updated (fe585be -> 883302d)

[Ricardo Wurmus]

rekado pushed a change to branch master
in repository guix.

  from  fe585be   serialization: Add #:select? parameter to 'write-file'.
   new  883302d   gnu: piranha: Update to 1.2.1.

The 1 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.


Summary of changes:
 gnu/packages/bioinformatics.scm |  119 ---
 1 file changed, 61 insertions(+), 58 deletions(-)

branch core-updates updated (28b3317 -> 809f176)

[Ludovic Court�s]

civodul pushed a change to branch core-updates
in repository guix.

  from  28b3317   gnu: libxslt: Update to 1.1.29.
   new  809f176   gnu: swig: Adjust to pcre output split.

The 1 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.


Summary of changes:
 gnu/packages/swig.scm |9 -
 1 file changed, 4 insertions(+), 5 deletions(-)

01/01: gnu: swig: Adjust to pcre output split.

[Ludovic Court�s]

civodul pushed a commit to branch core-updates
in repository guix.

commit 809f17628ffcac04bf7b194c6ee5ef0c872db73d
Author: Ludovic Courtès 
Date:   Mon Jun 13 09:41:48 2016 +0200

gnu: swig: Adjust to pcre output split.

This fixes a regression introduced in
commit 6d49ca3bad613700b539c30272e164207455735b.

* gnu/packages/swig.scm (swig)[native-inputs]: Add pcre:bin.
[inputs]: Remove pcre.
---
 gnu/packages/swig.scm |9 -
 1 file changed, 4 insertions(+), 5 deletions(-)

diff --git a/gnu/packages/swig.scm b/gnu/packages/swig.scm
index 273d0c4..6a66a71 100644
--- a/gnu/packages/swig.scm
+++ b/gnu/packages/swig.scm
@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2013, 2015 Ludovic Courtès 
+;;; Copyright © 2013, 2015, 2016 Ludovic Courtès 
 ;;; Copyright © 2015 Mark H Weaver 
 ;;;
 ;;; This file is part of GNU Guix.
@@ -41,10 +41,9 @@
   (base32
"0g1a69vrqxgsnr1wkx851ljn73a2x3jqzxa66s2l3w0kyblbjk4z"
 (build-system gnu-build-system)
-(native-inputs `(("boost" ,boost)))
-(inputs `(("pcre" ,pcre)
-
-  ;; Provide these to run the corresponding tests.
+(native-inputs `(("boost" ,boost)
+ ("pcre" ,pcre "bin")))   ;for 'pcre-config'
+(inputs `(;; Provide these to run the corresponding tests.
   ("guile" ,guile-2.0)
   ("perl" ,perl)))
   ;; FIXME: reactivate input python as soon as the test failures