01/01: gnu: libndp: Update to 1.6 [fixes CVE-2016-3698].

[Leo Famulari]

lfam pushed a commit to branch master
in repository guix.

commit ad42be83888f983d51d4560d158a729ebf1b
Author: Leo Famulari 
Date:   Tue May 17 14:31:09 2016 -0400

gnu: libndp: Update to 1.6 [fixes CVE-2016-3698].

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

diff --git a/gnu/packages/networking.scm b/gnu/packages/networking.scm
index 306a3a0..ffad1db 100644
--- a/gnu/packages/networking.scm
+++ b/gnu/packages/networking.scm
@@ -138,14 +138,14 @@ more.")
 (define-public libndp
   (package
 (name "libndp")
-(version "1.5")
+(version "1.6")
 (source (origin
   (method url-fetch)
   (uri (string-append "http://libndp.org/files/;
   name "-" version ".tar.gz"))
   (sha256
(base32
-"15f743hjc7yy2sv3hzvfc27s1gny4mh5aww59vn195fff2midwgs"
+"03mczwrxqbp54msafxzzyhaazkvjdwm2kipjkrb5xg8kw22glz8c"
 (build-system gnu-build-system)
 (home-page "http://libndp.org/;)
 (synopsis "Library for Neighbor Discovery Protocol")

branch master updated (9576cc7 -> ad42be8)

[Leo Famulari]

lfam pushed a change to branch master
in repository guix.

  from  9576cc7   gnu: Add emacs-zenburn-theme.
   new  ad42be8   gnu: libndp: Update to 1.6 [fixes CVE-2016-3698].

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/networking.scm |4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

branch master updated (ad42be8 -> f1876bf)

[Leo Famulari]

lfam pushed a change to branch master
in repository guix.

  from  ad42be8   gnu: libndp: Update to 1.6 [fixes CVE-2016-3698].
   new  f1876bf   gnu: Add signify.

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/crypto.scm |   42 ++
 1 file changed, 42 insertions(+)

01/01: gnu: Add signify.

[Leo Famulari]

lfam pushed a commit to branch master
in repository guix.

commit f1876bfc7a7dcb9516fff1b2c82f3c52b16c2ab5
Author: Leo Famulari 
Date:   Thu Mar 17 03:59:31 2016 -0400

gnu: Add signify.

* gnu/packages/crypto.scm (signify): New variable.
---
 gnu/packages/crypto.scm |   42 ++
 1 file changed, 42 insertions(+)

diff --git a/gnu/packages/crypto.scm b/gnu/packages/crypto.scm
index a8d675b..08eb146 100644
--- a/gnu/packages/crypto.scm
+++ b/gnu/packages/crypto.scm
@@ -1,6 +1,7 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2014 David Thompson 
 ;;; Copyright © 2015 Ricardo Wurmus 
+;;; Copyright © 2016 Leo Famulari 
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -19,6 +20,8 @@
 
 (define-module (gnu packages crypto)
   #:use-module (gnu packages)
+  #:use-module (gnu packages pkg-config)
+  #:use-module (gnu packages libbsd)
   #:use-module (guix licenses)
   #:use-module (guix packages)
   #:use-module (guix download)
@@ -46,3 +49,42 @@
 communication, encryption, decryption, signatures, etc.")
 (license isc)
 (home-page "http://libsodium.org;)))
+
+(define-public signify
+  (package
+(name "signify")
+(version "17")
+(source (origin
+  (method url-fetch)
+  (uri (string-append "https://github.com/aperezdc/signify/;
+  "archive/v" version ".tar.gz"))
+  (file-name (string-append name "-" version ".tar.gz"))
+  (sha256
+   (base32
+"0kfv2k1fqck31vwlnicavb0h541ilad9zd7j8zz8x2kx36wwqpr7"
+(build-system gnu-build-system)
+;; TODO Build with libwaive (described in README.md), to implement 
something
+;; like OpenBSD's pledge().
+(arguments
+ `(#:tests? #f ; no test suite
+   #:make-flags
+   (list "CC=gcc"
+ (string-append "PREFIX=" (assoc-ref %outputs "out")))
+   #:phases
+   (modify-phases %standard-phases
+ (delete 'configure
+(native-inputs
+ `(("pkg-config" ,pkg-config)))
+(inputs
+ `(("libbsd" ,libbsd)))
+(synopsis "Create and verify cryptographic signatures")
+(description "The signify utility creates and verifies cryptographic
+signatures using the elliptic curve Ed25519.  This is a Linux port of the
+OpenBSD tool of the same name.")
+(home-page "https://github.com/aperezdc/signify;)
+;; This package includes third-party code that was originally released 
under
+;; various non-copyleft licenses. See the source files for clarification.
+(license (list bsd-3 bsd-4 expat isc public-domain
+   (non-copyleft "file://base64.c"
+ "See base64.c in the distribution for
+ the license from IBM.")

branch master updated (fb2b0f5 -> 9576cc7)

[Alex Kost]

alezost pushed a change to branch master
in repository guix.

  from  fb2b0f5   gnu: gd: Fix-CVE-2016-3074.
   new  9576cc7   gnu: Add emacs-zenburn-theme.

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/emacs.scm |   24 
 1 file changed, 24 insertions(+)

01/01: gnu: Add emacs-zenburn-theme.

[Alex Kost]

alezost pushed a commit to branch master
in repository guix.

commit 9576cc72dc4f2973551c72951e64e5bf6240ff6b
Author: humanitiesNerd 
Date:   Tue May 17 10:54:13 2016 +0200

gnu: Add emacs-zenburn-theme.

* gnu/packages/emacs.scm (emacs-zenburn-theme): New variable.

Signed-off-by: Alex Kost 
---
 gnu/packages/emacs.scm |   24 
 1 file changed, 24 insertions(+)

diff --git a/gnu/packages/emacs.scm b/gnu/packages/emacs.scm
index 8ba645e..32ed722 100644
--- a/gnu/packages/emacs.scm
+++ b/gnu/packages/emacs.scm
@@ -8,6 +8,7 @@
 ;;; Copyright © 2016 Nils Gillmann 
 ;;; Copyright © 2016 Chris Marusich 
 ;;; Copyright © 2015, 2016 Christopher Allan Webber 
+;;; Copyright © 2016 humanitiesNerd 
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -1588,3 +1589,26 @@ to recognize a name like \"RFC 1234\".  This package 
enhances ffap so
 that it correctly finds RFCs even when a space appears before the
 number.")
 (license license:gpl3+)))
+
+(define-public emacs-zenburn-theme
+  (package
+(name "emacs-zenburn-theme")
+(version "2.4")
+(source (origin
+  (method url-fetch)
+  (uri (string-append
+"https://github.com/bbatsov/zenburn-emacs/archive/v;
+version ".tar.gz"))
+  (file-name (string-append name "-" version ".tar.gz"))
+  (sha256
+   (base32
+"0lyi84bm8sa7vj40n6zg6rlbsmi53mi1y9xn6gkjj29s5zbcnlg7"
+(build-system emacs-build-system)
+(home-page "http://github.com/bbatsov/zenburn-emacs;)
+(synopsis "Low contrast color theme for Emacs")
+(description
+ "Zenburn theme is a port of the popular Vim Zenburn theme for Emacs.
+It is built on top of the custom theme support in Emacs 24 or later.")
+(license license:gpl3+)))
+
+

branch master updated (bbb5d8a -> fb2b0f5)

[Leo Famulari]

lfam pushed a change to branch master
in repository guix.

  from  bbb5d8a   gnu: gd: Specify 'cpe-name'.
   new  fb2b0f5   gnu: gd: Fix-CVE-2016-3074.

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|1 +
 gnu/packages/gd.scm |4 ++-
 gnu/packages/patches/gd-CVE-2016-3074.patch |   36 +++
 3 files changed, 40 insertions(+), 1 deletion(-)
 create mode 100644 gnu/packages/patches/gd-CVE-2016-3074.patch

01/01: gnu: gd: Fix-CVE-2016-3074.

[Leo Famulari]

lfam pushed a commit to branch master
in repository guix.

commit fb2b0f5c87321f5aab0dc13130ef92a76040fbe3
Author: Leo Famulari 
Date:   Tue May 17 00:20:17 2016 -0400

gnu: gd: Fix-CVE-2016-3074.

* gnu/packages/patches/gd-CVE-2016-3074.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/gd.scm (gd)[source]: Use it.
---
 gnu/local.mk|1 +
 gnu/packages/gd.scm |4 ++-
 gnu/packages/patches/gd-CVE-2016-3074.patch |   36 +++
 3 files changed, 40 insertions(+), 1 deletion(-)

diff --git a/gnu/local.mk b/gnu/local.mk
index 4bbded9..0e461b3 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -494,6 +494,7 @@ dist_patch_DATA =   
\
   gnu/packages/patches/gcc-cross-environment-variables.patch   \
   gnu/packages/patches/gcc-libvtv-runpath.patch\
   gnu/packages/patches/gcc-5.0-libvtv-runpath.patch\
+  gnu/packages/patches/gd-CVE-2016-3074.patch  \
   gnu/packages/patches/geoclue-config.patch\
   gnu/packages/patches/ghostscript-CVE-2015-3228.patch \
   gnu/packages/patches/ghostscript-runpath.patch   \
diff --git a/gnu/packages/gd.scm b/gnu/packages/gd.scm
index 769e7ce..e52a030 100644
--- a/gnu/packages/gd.scm
+++ b/gnu/packages/gd.scm
@@ -2,6 +2,7 @@
 ;;; Copyright © 2013, 2016 Ludovic Courtès 
 ;;; Copyright © 2015 Mark H Weaver 
 ;;; Copyright © 2015 Eric Bavier 
+;;; Copyright © 2016 Leo Famulari 
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -48,7 +49,8 @@
"libgd-" version ".tar.xz"))
  (sha256
   (base32
-   "11djy9flzxczphigqgp7fbbblbq35gqwwhn9xfcckawlapa1xnls"
+   "11djy9flzxczphigqgp7fbbblbq35gqwwhn9xfcckawlapa1xnls"))
+ (patches (search-patches "gd-CVE-2016-3074.patch"
 (build-system gnu-build-system)
 (native-inputs
  `(("pkg-config" ,pkg-config)))
diff --git a/gnu/packages/patches/gd-CVE-2016-3074.patch 
b/gnu/packages/patches/gd-CVE-2016-3074.patch
new file mode 100644
index 000..a90c51d
--- /dev/null
+++ b/gnu/packages/patches/gd-CVE-2016-3074.patch
@@ -0,0 +1,36 @@
+Adapted from upstream commit 2bb97f407c1145c850416a3bfbcc8cf124e68a19
+(gd2: handle corrupt images better (CVE-2016-3074)).
+
+This patch omits the upstream changes to '.gitignore', and the test
+added in files 'tests/Makefile.am', 'tests/gd2/gd2_read_corrupt.c', and
+'tests/gd2/invalid_neg_size.gd2'.
+
+We omit the test because its input data,
+'tests/gd2/invalid_neg_size.gd2', is provided as a binary Git diff,
+which is not supported by `patch`.
+
+https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2016-3074
+https://github.com/libgd/libgd/commit/2bb97f407c1145c850416a3bfbcc8cf124e68a19
+---
+ .gitignore |   1 +
+ src/gd_gd2.c   |   2 ++
+ tests/Makefile.am  |   3 ++-
+ tests/gd2/gd2_read_corrupt.c   |  25 +
+ tests/gd2/invalid_neg_size.gd2 | Bin 0 -> 1676 bytes
+ 5 files changed, 30 insertions(+), 1 deletion(-)
+ create mode 100644 tests/gd2/gd2_read_corrupt.c
+ create mode 100644 tests/gd2/invalid_neg_size.gd2
+
+diff --git a/src/gd_gd2.c b/src/gd_gd2.c
+index 6f28461..a50b33d 100644
+--- a/src/gd_gd2.c
 b/src/gd_gd2.c
+@@ -165,6 +165,8 @@ _gd2GetHeader (gdIOCtxPtr in, int *sx, int *sy,
+   if (gdGetInt ([i].size, in) != 1) {
+   goto fail2;
+   };
++  if (cidx[i].offset < 0 || cidx[i].size < 0)
++  goto fail2;
+   };
+   *chunkIdx = cidx;
+   };

02/02: gnu: gd: Specify 'cpe-name'.

[Ludovic Court�s]

civodul pushed a commit to branch master
in repository guix.

commit bbb5d8aeea213f32e51ae18407aa8941f18a010b
Author: Ludovic Courtès 
Date:   Tue May 17 18:07:08 2016 +0200

gnu: gd: Specify 'cpe-name'.

* gnu/packages/gd.scm (gd)[properties]: New field.
---
 gnu/packages/gd.scm |5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/gd.scm b/gnu/packages/gd.scm
index 6ae5579..769e7ce 100644
--- a/gnu/packages/gd.scm
+++ b/gnu/packages/gd.scm
@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2013 Ludovic Courtès 
+;;; Copyright © 2013, 2016 Ludovic Courtès 
 ;;; Copyright © 2015 Mark H Weaver 
 ;;; Copyright © 2015 Eric Bavier 
 ;;;
@@ -69,7 +69,8 @@ formats.  GD is commonly used to generate charts, graphics, 
thumbnails, and
 most anything else, on the fly.  While not restricted to use on the web, the
 most common applications of GD involve website development.")
 (license (non-copyleft "file://COPYING"
-"See COPYING file in the distribution."
+   "See COPYING file in the distribution."))
+(properties '((cpe-name . "libgd")
 
 (define-public perl-gd
   (package

branch master updated (1c29f3e -> bbb5d8a)

[Ludovic Court�s]

civodul pushed a change to branch master
in repository guix.

  from  1c29f3e   gnu: emacs-constants: Remove old patch.
   new  99effc8   lint: Honor 'cpe-name' and 'cpe-version' package 
properties.
   new  bbb5d8a   gnu: gd: Specify 'cpe-name'.

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:
 doc/guix.texi |   13 +
 gnu/packages/gd.scm   |5 +++--
 gnu/packages/gnuzilla.scm |6 +-
 gnu/packages/grub.scm |5 +++--
 guix/scripts/lint.scm |   21 +
 5 files changed, 33 insertions(+), 17 deletions(-)

01/02: lint: Honor 'cpe-name' and 'cpe-version' package properties.

[Ludovic Court�s]

civodul pushed a commit to branch master
in repository guix.

commit 99effc8faa43d478371eb06aee5df8ae1383c51a
Author: Ludovic Courtès 
Date:   Tue May 17 18:04:13 2016 +0200

lint: Honor 'cpe-name' and 'cpe-version' package properties.

* guix/scripts/lint.scm (package-name->cpe-name): Remove.
(package-vulnerabilities): Honor 'cpe-name' and 'cpe-version'
properties.
* gnu/packages/grub.scm (grub)[properties]: New field.
* gnu/packages/gnuzilla.scm (icecat)[properties]: Add 'cpe-name' and
'cpe-version'.
* doc/guix.texi (Invoking guix lint): Mention 'cpe-name'.
---
 doc/guix.texi |   13 +
 gnu/packages/gnuzilla.scm |6 +-
 gnu/packages/grub.scm |5 +++--
 guix/scripts/lint.scm |   21 +
 4 files changed, 30 insertions(+), 15 deletions(-)

diff --git a/doc/guix.texi b/doc/guix.texi
index 0e63eca..3f0106b 100644
--- a/doc/guix.texi
+++ b/doc/guix.texi
@@ -4961,6 +4961,19 @@ To view information about a particular vulnerability, 
visit pages such as:
 where @code{CVE--ABCD} is the CVE identifier---e.g.,
 @code{CVE-2015-7554}.
 
+Package developers can specify in package recipes the
+@uref{https://nvd.nist.gov/cpe.cfm,Common Platform Enumeration (CPE)}
+name and version of the package when they differ from the name that Guix
+uses, as in this example:
+
+@example
+(package
+  (name "grub")
+  ;; @dots{}
+  ;; CPE calls this package "grub2".
+  (properties '((cpe-name . "grub2"
+@end example
+
 @item formatting
 Warn about obvious source code formatting issues: trailing white space,
 use of tabulations, etc.
diff --git a/gnu/packages/gnuzilla.scm b/gnu/packages/gnuzilla.scm
index df1075c..7e52534 100644
--- a/gnu/packages/gnuzilla.scm
+++ b/gnu/packages/gnuzilla.scm
@@ -517,4 +517,8 @@ standards.")
 software, which does not recommend non-free plugins and addons.  It also
 features built-in privacy-protecting features.")
 (license license:mpl2.0) ;and others, see toolkit/content/license.html
-(properties '((ftp-directory . "/gnu/gnuzilla")
+(properties
+ `((ftp-directory . "/gnu/gnuzilla")
+   (cpe-name . "firefox_esr")
+   (cpe-version . ,(string-drop-right version
+  (string-length "-gnu1")))
diff --git a/gnu/packages/grub.scm b/gnu/packages/grub.scm
index 5fc7ee8..ec2feeb 100644
--- a/gnu/packages/grub.scm
+++ b/gnu/packages/grub.scm
@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2013, 2014, 2015 Ludovic Courtès 
+;;; Copyright © 2013, 2014, 2015, 2016 Ludovic Courtès 
 ;;; Copyright © 2015 Mark H Weaver 
 ;;; Copyright © 2015 Leo Famulari 
 ;;;
@@ -132,4 +132,5 @@ then goes on to load the rest of the operating system.  As 
a multiboot
 bootloader, GRUB handles the presence of multiple operating systems installed
 on the same computer; upon booting the computer, the user is presented with a
 menu to select one of the installed operating systems.")
-(license gpl3+)))
+(license gpl3+)
+(properties '((cpe-name . "grub2")
diff --git a/guix/scripts/lint.scm b/guix/scripts/lint.scm
index 06001d3..b4fdb6f 100644
--- a/guix/scripts/lint.scm
+++ b/guix/scripts/lint.scm
@@ -600,15 +600,6 @@ be determined."
 ((? origin?)
  (and=> (origin-actual-file-name patch) basename
 
-(define (package-name->cpe-name name)
-  "Do a basic conversion of NAME, a Guix package name, to the corresponding
-Common Platform Enumeration (CPE) name."
-  (match name
-("icecat"   "firefox");or "firefox_esr"
-("grub" "grub2")
-;; TODO: Add more.
-(_  name)))
-
 (define (current-vulnerabilities*)
   "Like 'current-vulnerabilities', but return the empty list upon networking
 or HTTP errors.  This allows network-less operation and makes problems with
@@ -635,9 +626,15 @@ from ~s: ~a (~s)~%")
 (current-vulnerabilities*)
 (lambda (package)
   "Return a list of vulnerabilities affecting PACKAGE."
-  ((force lookup)
-   (package-name->cpe-name (package-name package))
-   (package-version package)
+  ;; First we retrieve the Common Platform Enumeration (CPE) name and
+  ;; version for PACKAGE, then we can pass them to LOOKUP.
+  (let ((name(or (assoc-ref (package-properties package)
+'cpe-name)
+ (package-name package)))
+(version (or (assoc-ref (package-properties package)
+'cpe-version)
+ (package-version package
+((force lookup) name version)
 
 (define (check-vulnerabilities package)
   "Check for known vulnerabilities for PACKAGE."

01/02: gnu: gnutls: Update to 3.5.0.

[Efraim Flashner]

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

commit c19700c396f66426d7ec4cea01ef19614775ce88
Author: Efraim Flashner 
Date:   Tue May 17 17:06:29 2016 +0300

gnu: gnutls: Update to 3.5.0.

* gnu/packages/tls.scm (gnutls): Update to 3.5.0.
---
 gnu/packages/tls.scm |6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/tls.scm b/gnu/packages/tls.scm
index 8ec8e60..4305404 100644
--- a/gnu/packages/tls.scm
+++ b/gnu/packages/tls.scm
@@ -108,7 +108,7 @@ living in the same process.")
 (define-public gnutls
   (package
 (name "gnutls")
-(version "3.4.9")
+(version "3.5.0")
 (source (origin
  (method url-fetch)
  (uri
@@ -119,7 +119,7 @@ living in the same process.")
  "/gnutls-" version ".tar.xz"))
  (sha256
   (base32
-   "0gvwyl0kdp1qpzbzp46wqfdzzrmwy9n54sgcjvvm1m1kpanlyna8"
+   "09dfb0fn4spmdja6hs2yl470fn85fx0pa5nn9njnq7j19ma3nszw"
 (build-system gnu-build-system)
 (arguments
  '(#:configure-flags
@@ -169,7 +169,7 @@ living in the same process.")
("libidn" ,libidn)
("nettle" ,nettle)
("zlib" ,zlib)))
-(home-page "http://www.gnu.org/software/gnutls/;)
+(home-page "https://www.gnu.org/software/gnutls/;)
 (synopsis "Transport layer security library")
 (description
  "GnuTLS is a secure communications library implementing the SSL, TLS

branch core-updates updated (74d6373 -> 45ff4b5)

[Efraim Flashner]

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

  from  74d6373   gnu: tar: Update to 1.29.
   new  c19700c   gnu: gnutls: Update to 3.5.0.
   new  45ff4b5   gnu: sqlite: Update to 3.12.2.

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/packages/databases.scm |4 ++--
 gnu/packages/tls.scm   |6 +++---
 2 files changed, 5 insertions(+), 5 deletions(-)

02/02: gnu: sqlite: Update to 3.12.2.

[Efraim Flashner]

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

commit 45ff4b568d5adac1ba0185055844517af3c9b318
Author: Efraim Flashner 
Date:   Tue May 17 17:07:47 2016 +0300

gnu: sqlite: Update to 3.12.2.

* gnu/packages/databases.scm (sqlite): Update to 3.12.2.
---
 gnu/packages/databases.scm |4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm
index a7f3837..6bf829f 100644
--- a/gnu/packages/databases.scm
+++ b/gnu/packages/databases.scm
@@ -408,7 +408,7 @@ types are supported, as is encryption.")
 (define-public sqlite
   (package
(name "sqlite")
-   (version "3.11.1")
+   (version "3.12.2")
(source (origin
 (method url-fetch)
 ;; TODO: Download from sqlite.org once this bug :
@@ -439,7 +439,7 @@ types are supported, as is encryption.")
))
 (sha256
  (base32
-  "0xs3gl3kbxqfx2ahrymgcf2n8c8sy37724jr05pncbhw4z8g2gsk"
+  "1fwss0i2lixv39b27gkqiibdd2syym90wh3qbiaxnfgxk867f07x"
(build-system gnu-build-system)
(inputs `(("readline" ,readline)))
(arguments

01/01: gnu: emacs-constants: Remove old patch.

[Federico Beffa]

beffa pushed a commit to branch master
in repository guix.

commit 1c29f3ef8452860c4301d7ae57c89ac5956d1663
Author: Federico Beffa 
Date:   Tue May 17 14:13:56 2016 +0200

gnu: emacs-constants: Remove old patch.

* gnu/packages/patches/emacs-constants-lisp-like.patch: Remove it.
* gnu/local.mk (dist_patch_DATA): Remove entry for above patch.
---
 gnu/local.mk   |1 -
 .../patches/emacs-constants-lisp-like.patch|   81 
 2 files changed, 82 deletions(-)

diff --git a/gnu/local.mk b/gnu/local.mk
index f64adeb..4bbded9 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -466,7 +466,6 @@ dist_patch_DATA =   
\
   gnu/packages/patches/duplicity-test_selection-tmp.patch  \
   gnu/packages/patches/elfutils-tests-ptrace.patch \
   gnu/packages/patches/einstein-build.patch\
-  gnu/packages/patches/emacs-constants-lisp-like.patch \
   gnu/packages/patches/emacs-exec-path.patch   \
   gnu/packages/patches/emacs-scheme-complete-scheme-r5rs-info.patch\
   gnu/packages/patches/emacs-source-date-epoch.patch   \
diff --git a/gnu/packages/patches/emacs-constants-lisp-like.patch 
b/gnu/packages/patches/emacs-constants-lisp-like.patch
deleted file mode 100644
index 5ec37f3..000
--- a/gnu/packages/patches/emacs-constants-lisp-like.patch
+++ /dev/null
@@ -1,81 +0,0 @@
-Add Scheme support
-
 constants/constants.el.orig2015-12-26 17:44:31.734520833 +0100
-+++ constants/constants.el 2015-12-30 17:41:28.402871263 +0100
-@@ -684,6 +684,33 @@
- 
- (eval-when-compile (defvar ctable))
- 
-+(defun constants-is-lisp-like (mode)
-+  (save-match-data
-+(string-match "\\(lisp\\|scheme\\)" (symbol-name mode
-+
-+(defun constants-is-set-like ()
-+  (save-excursion
-+(condition-case nil
-+(save-match-data
-+  (progn (up-list -1)
-+ (or (looking-at "(set[qf!]?\\>") (looking-at "(define\\>"
-+  (error nil ; return value nil means use default
-+
-+;;;###autoload
-+(defun constants-lisp-like-function ()
-+  "Check context for constants insertion."
-+  (if (constants-is-set-like)
-+  '(emacs-lisp-mode "%n %v%t; %d %u" "e" "(* %p %v)")
-+'(emacs-lisp-mode "(%n %v)%t; %d %u" "e" "(* %p %v)")))
-+
-+;;;###autoload
-+(mapc (lambda (mode-hook)
-+(add-hook mode-hook
-+  (lambda ()
-+(setq constants-language-function
-+  'constants-lisp-like-function
-+  '(scheme-mode-hook emacs-lisp-mode-hook lisp-mode-hook))
-+
- ;;;###autoload
- (defun constants-insert ( unit-system names)
-   "Insert one or more natural constant definitions in source code.
-@@ -826,8 +853,9 @@
- (funcall process-func ins))
- ;; Here comes the insertion stuff for source code editing modes.
- ;; First make sure we start a new line
--(if (string-match
-- "\\S-" (buffer-substring (point-at-bol) (point-at-eol)))
-+(if (and (string-match
-+  "\\S-" (buffer-substring (point-at-bol) (point-at-eol)))
-+ (not (constants-is-lisp-like mode)))
- ;; non-empty line, insert after this line
- (progn 
-   (end-of-line 1) 
-@@ -841,13 +869,24 @@
-   (if (string-match "\\(.*\\)%t\\(.*\\)" line)
-   (let ((comment-column 42))
- (insert (match-string 1 line))
--(indent-to comment-column)
--(insert (match-string 2 line)))
-+(if (and (constants-is-lisp-like mode)
-+ (or (constants-is-set-like)
-+ (null clist)))
-+(save-excursion
-+  (progn
-+(move-to-column comment-column t)
-+(insert (match-string 2 line))
-+;; insert a newline such that paredit's M-) can mode
-+;; the closing parentheses to the next line.
-+(newline-and-indent)))
-+  (progn
-+(indent-to comment-column)
-+(insert (match-string 2 line)
- (insert line)))
--(if constants-indent-code
--(newline-and-indent)
--  (newline))
--
-+(unless (and (constants-is-lisp-like mode) (null clist))
-+  (if constants-indent-code
-+  (newline-and-indent)
-+(newline)))
- ;;;###autoload
- (defun constants-get ( const message)
-   "Return the value of CONST as defined in the constants package.

branch master updated (aa8fff0 -> 1c29f3e)

[Federico Beffa]

beffa pushed a change to branch master
in repository guix.

  from  aa8fff0   store: Clarify 'query-path-hash' docstring.
   new  1c29f3e   gnu: emacs-constants: Remove old patch.

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   |1 -
 .../patches/emacs-constants-lisp-like.patch|   81 
 2 files changed, 82 deletions(-)
 delete mode 100644 gnu/packages/patches/emacs-constants-lisp-like.patch

03/03: store: Clarify 'query-path-hash' docstring.

[Ludovic Court�s]

civodul pushed a commit to branch master
in repository guix.

commit aa8fff0cebd8390c2faf733da79d9a1499458261
Author: Ludovic Courtès 
Date:   Tue May 17 13:50:10 2016 +0200

store: Clarify 'query-path-hash' docstring.

* guix/store.scm (query-path-hash): Clarify docstring.
---
 guix/store.scm |2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/guix/store.scm b/guix/store.scm
index f352a99..4d89f4a 100644
--- a/guix/store.scm
+++ b/guix/store.scm
@@ -615,7 +615,7 @@ store directory (/gnu/store)."
   boolean)
 
 (define-operation (query-path-hash (store-path path))
-  "Return the SHA256 hash of PATH as a bytevector."
+  "Return the SHA256 hash of the nar serialization of PATH as a bytevector."
   base16)
 
 (define hash-part->path

01/03: import: Exit with non-zero when an unknown importer is asked.

[Ludovic Court�s]

civodul pushed a commit to branch master
in repository guix.

commit 787afdd0f1ce1d4aa7500d858f2635462b444699
Author: Ludovic Courtès 
Date:   Tue May 17 13:36:44 2016 +0200

import: Exit with non-zero when an unknown importer is asked.

* guix/scripts/import.scm (guix-import): Use 'leave' instead of 'format'
when IMPORTER is unknown.
---
 guix/scripts/import.scm |3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/guix/scripts/import.scm b/guix/scripts/import.scm
index 7b29794..cf8fc07 100644
--- a/guix/scripts/import.scm
+++ b/guix/scripts/import.scm
@@ -109,5 +109,4 @@ Run IMPORTER with ARGS.\n"))
  (if (member importer importers)
  (let ((expr (apply (resolve-importer importer) args)))
(pretty-print expr (newline-rewriting-port (current-output-port
- (format (current-error-port)
- (_ "guix import: invalid importer~%"))
+ (leave (_ "~a: invalid importer~%") importer)

branch master updated (f99f3f2 -> aa8fff0)

[Ludovic Court�s]

civodul pushed a change to branch master
in repository guix.

  from  f99f3f2   gnu: emacs-constants: Update to 2.6.
   new  787afdd   import: Exit with non-zero when an unknown importer is 
asked.
   new  1495903   import: Gracefully report import failures.
   new  aa8fff0   store: Clarify 'query-path-hash' docstring.

The 3 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:
 guix/import/gnu.scm |   48 +--
 guix/scripts/import.scm |   11 +++
 guix/store.scm  |2 +-
 guix/upstream.scm   |5 +++--
 4 files changed, 37 insertions(+), 29 deletions(-)

02/03: import: Gracefully report import failures.

[Ludovic Court�s]

civodul pushed a commit to branch master
in repository guix.

commit 149590380adb240e0993931b4f72e6f285b24483
Author: Ludovic Courtès 
Date:   Tue May 17 13:41:07 2016 +0200

import: Gracefully report import failures.

Previously, something like 'guix import gnu which' would spit out a
backtrace if, say, the 'which' tarball could not be authenticated.

* guix/upstream.scm (download-tarball): Mention failure modes in
docstring.
* guix/import/gnu.scm (gnu-package->sexp): Return #f when
'download-tarball' returns #f.
* guix/scripts/import.scm (guix-import): Call 'leave' when IMPORTER does
not return a (package ...) sexp.
---
 guix/import/gnu.scm |   48 +--
 guix/scripts/import.scm |8 ++--
 guix/upstream.scm   |5 +++--
 3 files changed, 35 insertions(+), 26 deletions(-)

diff --git a/guix/import/gnu.scm b/guix/import/gnu.scm
index 834f0ae..2cfb46b 100644
--- a/guix/import/gnu.scm
+++ b/guix/import/gnu.scm
@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2014, 2015 Ludovic Courtès 
+;;; Copyright © 2014, 2015, 2016 Ludovic Courtès 
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -55,8 +55,8 @@
 (define* (gnu-package->sexp package release
 #:key (key-download 'interactive))
   "Return the 'package' sexp for the RELEASE (a ) of PACKAGE (a
-).  Use KEY-DOWNLOAD as the OpenPGP key download policy (see
-'download-tarball' for details.)"
+), or #f upon failure.  Use KEY-DOWNLOAD as the OpenPGP key
+download policy (see 'download-tarball' for details.)"
   (define name
 (gnu-package-name package))
 
@@ -79,25 +79,29 @@
 (find (cute string-suffix? (string-append archive-type ".sig") <>)
   (upstream-source-signature-urls release)))
 
-  (let ((tarball (with-store store
-   (download-tarball store url sig-url
- #:key-download key-download
-`(package
-   (name ,name)
-   (version ,(upstream-source-version release))
-   (source (origin
- (method url-fetch)
- (uri (string-append ,url-base version
- ,(string-append ".tar." archive-type)))
- (sha256
-  (base32
-   ,(bytevector->nix-base32-string (file-sha256 tarball))
-   (build-system gnu-build-system)
-   (synopsis ,(gnu-package-doc-summary package))
-   (description ,(gnu-package-doc-description package))
-   (home-page ,(match (gnu-package-doc-urls package)
- ((head . tail) (qualified-url head
-   (license find-by-yourself!
+  (with-store store
+(match (download-tarball store url sig-url
+ #:key-download key-download)
+  ((? string? tarball)
+   `(package
+  (name ,name)
+  (version ,(upstream-source-version release))
+  (source (origin
+(method url-fetch)
+(uri (string-append ,url-base version
+,(string-append ".tar." archive-type)))
+(sha256
+ (base32
+  ,(bytevector->nix-base32-string
+(file-sha256 tarball))
+  (build-system gnu-build-system)
+  (synopsis ,(gnu-package-doc-summary package))
+  (description ,(gnu-package-doc-description package))
+  (home-page ,(match (gnu-package-doc-urls package)
+((head . tail) (qualified-url head
+  (license find-by-yourself!)))
+  (#f ;failure to download or authenticate the tarball
+   #f
 
 (define* (gnu->guix-package name
 #:key (key-download 'interactive))
diff --git a/guix/scripts/import.scm b/guix/scripts/import.scm
index cf8fc07..e54744f 100644
--- a/guix/scripts/import.scm
+++ b/guix/scripts/import.scm
@@ -107,6 +107,10 @@ Run IMPORTER with ARGS.\n"))
  (show-version-and-exit "guix import"))
 ((importer args ...)
  (if (member importer importers)
- (let ((expr (apply (resolve-importer importer) args)))
-   (pretty-print expr (newline-rewriting-port (current-output-port
+ (match (apply (resolve-importer importer) args)
+   ((and expr ('package _ ...))
+(pretty-print expr (newline-rewriting-port
+(current-output-port
+   (x
+(leave (_ "'~a' import failed~%") importer)))
  (leave (_ "~a: invalid importer~%") importer)
diff --git a/guix/upstream.scm b/guix/upstream.scm
index 167c9ff..1815737 100644
--- a/guix/upstream.scm
+++ b/guix/upstream.scm
@@ -143,8 +143,9 @@ no update is needed or known."
#:key (key-download 'interactive))
   "Download the tarball 

branch master updated (849485f -> f99f3f2)

[Federico Beffa]

beffa pushed a change to branch master
in repository guix.

  from  849485f   gnu: sortmerna: Update to 2.1b.
   new  f99f3f2   gnu: emacs-constants: Update to 2.6.

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/emacs.scm |   10 +-
 1 file changed, 5 insertions(+), 5 deletions(-)

01/01: gnu: emacs-constants: Update to 2.6.

[Federico Beffa]

beffa pushed a commit to branch master
in repository guix.

commit f99f3f24ef604f44023379da4b375c80e6844be1
Author: Federico Beffa 
Date:   Tue May 17 13:51:34 2016 +0200

gnu: emacs-constants: Update to 2.6.

* gnu/packages/emacs.scm (emacs-constants): Change to versioned repository 
and
  update to 2.6.
---
 gnu/packages/emacs.scm |   10 +-
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/gnu/packages/emacs.scm b/gnu/packages/emacs.scm
index 5fbbc03..8ba645e 100644
--- a/gnu/packages/emacs.scm
+++ b/gnu/packages/emacs.scm
@@ -1409,17 +1409,17 @@ identifiers in the MIT-Scheme documentation.")
 (define-public emacs-constants
   (package
 (name "emacs-constants")
-(version "2.2")
+(version "2.6")
 (home-page "https://staff.fnwi.uva.nl/c.dominik/Tools/constants;)
 (source
  (origin
(file-name (string-append name "-" version ".el"))
-   (method uncompressed-file-fetch)
-   (uri (string-append home-page "/constants.el")) ;FIXME: unversioned URI
-   (patches (search-patches "emacs-constants-lisp-like.patch"))
+   (method url-fetch)
+   (uri (string-append "https://github.com/fedeinthemix/emacs-constants;
+   "/archive/v" version ".tar.gz"))
(sha256
 (base32
- "14q094aphsjhq8gklv7i5a7byl0ygz63cv3n6b5p8ji2jy0mnnw3"
+ "0pnrpmmxq8mh5h2hbrp5vcym0j0fh6dv3s7c5ccn18wllhzg9g7n"
 (build-system emacs-build-system)
 (synopsis "Enter definition of constants into an Emacs buffer")
 (description

branch master updated (122395f -> 849485f)

[Ben Woodcroft]

benwoodcroft pushed a change to branch master
in repository guix.

  from  122395f   gnu: diamond: Update to 0.8.1.
   new  daaeed7   gnu: vsearch: Update to 1.11.1.
   new  849485f   gnu: sortmerna: Update to 2.1b.

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/packages/bioinformatics.scm |   10 ++
 1 file changed, 6 insertions(+), 4 deletions(-)

02/02: gnu: sortmerna: Update to 2.1b.

[Ben Woodcroft]

benwoodcroft pushed a commit to branch master
in repository guix.

commit 849485f5a05badf502e28c673e546b4660c4ca46
Author: Ben Woodcroft 
Date:   Tue May 17 21:45:49 2016 +1000

gnu: sortmerna: Update to 2.1b.

* gnu/packages/bioinformatics.scm (sortmerna): Update to 2.1b.
[inputs]: New field.
---
 gnu/packages/bioinformatics.scm |6 --
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 7aa1853..60cf6b7 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -3549,7 +3549,7 @@ of these reads to align data quickly through a hash-based 
indexing scheme.")
 (define-public sortmerna
   (package
 (name "sortmerna")
-(version "2.1")
+(version "2.1b")
 (source
  (origin
(method url-fetch)
@@ -3559,7 +3559,7 @@ of these reads to align data quickly through a hash-based 
indexing scheme.")
(file-name (string-append name "-" version ".tar.gz"))
(sha256
 (base32
- "1mc5cf1c7xh0h7xb11vh7gqgzx0qvrfa606cb8ixlfg3f2av58s4"
+ "1ghaghvd82af9j5adavxh77g7hm247d1r69m3fbi6f1jdivj5ldk"
 (build-system gnu-build-system)
 (outputs '("out"  ;for binaries
"db")) ;for sequence databases
@@ -3579,6 +3579,8 @@ of these reads to align data quickly through a hash-based 
indexing scheme.")
(install-file file share))
  (find-files "rRNA_databases" ".*fasta"))
#t))
+(inputs
+ `(("zlib" ,zlib)))
 (home-page "http://bioinfo.lifl.fr/RNA/sortmerna;)
 (synopsis "Biological sequence analysis tool for NGS reads")
 (description

01/02: gnu: vsearch: Update to 1.11.1.

[Ben Woodcroft]

benwoodcroft pushed a commit to branch master
in repository guix.

commit daaeed765aebae138b4af1d3861eace0368fe2a6
Author: Ben Woodcroft 
Date:   Tue May 17 21:36:46 2016 +1000

gnu: vsearch: Update to 1.11.1.

* gnu/packages/bioinformatics.scm (vsearch): Update to 1.11.1.
---
 gnu/packages/bioinformatics.scm |4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index f882185..7aa1853 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -3810,7 +3810,7 @@ data in the form of VCF files.")
 (define-public vsearch
   (package
 (name "vsearch")
-(version "1.10.0")
+(version "1.11.1")
 (source
  (origin
(method url-fetch)
@@ -3820,7 +3820,7 @@ data in the form of VCF files.")
(file-name (string-append name "-" version ".tar.gz"))
(sha256
 (base32
- "1i3bad7gnn2y3a1yfixzshd99xdkjc8w5bxzgifpysc6jiljwvb5"))
+ "1pdvm3znjgq3zryy240yj9gc0bf1z31k6vf9jxrxgdgkvzgw85c7"))
(modules '((guix build utils)))
(snippet
 '(begin

branch master updated (a9e41d2 -> 122395f)

[Ben Woodcroft]

benwoodcroft pushed a change to branch master
in repository guix.

  from  a9e41d2   gnu: emacs-constants: Factorize home-page in source URL.
   new  122395f   gnu: diamond: Update to 0.8.1.

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 |   31 +--
 1 file changed, 5 insertions(+), 26 deletions(-)

01/01: gnu: diamond: Update to 0.8.1.

[Ben Woodcroft]

benwoodcroft pushed a commit to branch master
in repository guix.

commit 122395f9fc42de7dbe2643b437ca4e484adb8ba0
Author: Ben Woodcroft 
Date:   Tue May 17 21:07:00 2016 +1000

gnu: diamond: Update to 0.8.1.

* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.1.
[source]: Remove 'snippet'.
[build-system]: Use cmake-build-system.
[arguments]: Remove modifications to phases.
[native-inputs]: Remove field.
[inputs]: Remove 'boost'.
---
 gnu/packages/bioinformatics.scm |   31 +--
 1 file changed, 5 insertions(+), 26 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index aa16d39..f882185 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -1482,7 +1482,7 @@ identify enrichments with functional annotations of the 
genome.")
 (define-public diamond
   (package
 (name "diamond")
-(version "0.7.9")
+(version "0.8.1")
 (source (origin
   (method url-fetch)
   (uri (string-append
@@ -1491,33 +1491,12 @@ identify enrichments with functional annotations of the 
genome.")
   (file-name (string-append name "-" version ".tar.gz"))
   (sha256
(base32
-"0hfkcfv9f76h5brbyw9fyvmc0l9cmbsxrcdqk0fa9xv82zj47p15"))
-  (snippet '(begin
-  (delete-file "bin/diamond")
-  #t
-(build-system gnu-build-system)
+"1dqancz32c2l7w1b2vkvh5zqa2jnf99j1c41djnx1l8pxn044zdc"
+(build-system cmake-build-system)
 (arguments
- '(#:tests? #f  ;no "check" target
-   #:phases
-   (modify-phases %standard-phases
- (add-after 'unpack 'enter-source-dir
-(lambda _
-  (chdir "src")
-  #t))
- (delete 'configure)
- (replace 'install
-  (lambda* (#:key outputs #:allow-other-keys)
-(let ((bin (string-append (assoc-ref outputs "out")
-  "/bin")))
-  (mkdir-p bin)
-  (copy-file "../bin/diamond"
- (string-append bin "/diamond"))
-  #t))
-(native-inputs
- `(("bc" ,bc)))
+ '(#:tests? #f)) ; no "check" target
 (inputs
- `(("boost" ,boost)
-   ("zlib" ,zlib)))
+ `(("zlib" ,zlib)))
 (home-page "https://github.com/bbuchfink/diamond;)
 (synopsis "Accelerated BLAST compatible local sequence aligner")
 (description

02/02: gnu: tar: Update to 1.29.

[Ludovic Court�s]

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

commit 74d637397b44a90d2dbc2ac100b38591dd4f81eb
Author: Ludovic Courtès 
Date:   Tue May 17 10:46:26 2016 +0200

gnu: tar: Update to 1.29.

* gnu/packages/base.scm (tar): Update to 1.29.
[source]: Remove 'tar-d_ino_in_dirent-fix.patch'.
[arguments]: New field.
* gnu/packages/patches/tar-d_ino_in_dirent-fix.patch: Remove.
* gnu/local.mk (dist_patch_DATA): Adjust accordingly.
---
 gnu/local.mk   |1 -
 gnu/packages/base.scm  |   18 ---
 gnu/packages/patches/tar-d_ino_in_dirent-fix.patch |   33 
 3 files changed, 14 insertions(+), 38 deletions(-)

diff --git a/gnu/local.mk b/gnu/local.mk
index 8cf5ef5..a1700a5 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -721,7 +721,6 @@ dist_patch_DATA =   
\
   gnu/packages/patches/sudo-CVE-2015-5602.patch\
   gnu/packages/patches/superlu-dist-scotchmetis.patch  \
   gnu/packages/patches/synfig-build-fix.patch  \
-  gnu/packages/patches/tar-d_ino_in_dirent-fix.patch   \
   gnu/packages/patches/tar-skip-unreliable-tests.patch \
   gnu/packages/patches/tcl-mkindex-deterministic.patch \
   gnu/packages/patches/tclxml-3.2-install.patch\
diff --git a/gnu/packages/base.scm b/gnu/packages/base.scm
index 0d12376..f5da787 100644
--- a/gnu/packages/base.scm
+++ b/gnu/packages/base.scm
@@ -137,17 +137,27 @@ implementation offers several extensions over the 
standard utility.")
 (define-public tar
   (package
(name "tar")
-   (version "1.28")
+   (version "1.29")
(source (origin
 (method url-fetch)
 (uri (string-append "mirror://gnu/tar/tar-"
 version ".tar.xz"))
 (sha256
  (base32
-  "1wi2zwm4c9r3h3b8y4w0nm0qq897kn8kyj9k22ba0iqvxj48vvk4"))
-(patches (search-patches "tar-d_ino_in_dirent-fix.patch"
- "tar-skip-unreliable-tests.patch"
+  "097hx7sbzp8qirl4m930lw84kn0wmxhmq7v1qpra3mrg0b8cyba0"))
+(patches (search-patches "tar-skip-unreliable-tests.patch"
(build-system gnu-build-system)
+   ;; Note: test suite requires ~1GiB of disk space.
+   (arguments
+'(#:phases (modify-phases %standard-phases
+ (add-before 'build 'set-shell-file-name
+   (lambda* (#:key inputs #:allow-other-keys)
+ ;; Do not use "/bin/sh" to run programs.
+ (let ((bash (assoc-ref inputs "bash")))
+   (substitute* "src/system.c"
+ (("/bin/sh")
+  (string-append bash "/bin/sh")))
+   #t))
(synopsis "Managing tar archives")
(description
 "Tar provides the ability to create tar archives, as well as the
diff --git a/gnu/packages/patches/tar-d_ino_in_dirent-fix.patch 
b/gnu/packages/patches/tar-d_ino_in_dirent-fix.patch
deleted file mode 100644
index 39d8e2b..000
--- a/gnu/packages/patches/tar-d_ino_in_dirent-fix.patch
+++ /dev/null
@@ -1,33 +0,0 @@
-commit e9ddc08da0982f36581ae5a8c7763453ff41cfe8
-Author: Sergey Poznyakoff 
-Date:   Thu Sep 25 00:22:16 2014 +0300
-
-Bugfixes.
-
-* doc/tar.1: Fix typo in font spec.
-* src/tar.c (sort_mode_arg, sort_mode_flag): Protect "inode"
-(SAVEDIR_SORT_INODE) with D_INO_IN_DIRENT
-
-diff --git a/src/tar.c b/src/tar.c
-index 225c624..f8102e0 100644
 a/src/tar.c
-+++ b/src/tar.c
-@@ -1341,14 +1341,18 @@ static char filename_terminator;
- static char const *const sort_mode_arg[] = {
-   "none",
-   "name",
-+#if D_INO_IN_DIRENT
-   "inode",
-+#endif
-   NULL
- };
- 
- static int sort_mode_flag[] = {
- SAVEDIR_SORT_NONE,
- SAVEDIR_SORT_NAME,
-+#if D_INO_IN_DIRENT
- SAVEDIR_SORT_INODE
-+#endif
- };
- 
- ARGMATCH_VERIFY (sort_mode_arg, sort_mode_flag);
\ No newline at end of file

branch core-updates updated (ec0ea24 -> 74d6373)

[Ludovic Court�s]

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

  from  ec0ea24   gnu: openldap: Update to 2.4.44.
   new  2135d1e   gnu: gdbm: Update to 1.12.
   new  74d6373   gnu: tar: Update to 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/base.scm  |   18 ---
 gnu/packages/databases.scm |4 +--
 gnu/packages/patches/tar-d_ino_in_dirent-fix.patch |   33 
 4 files changed, 16 insertions(+), 40 deletions(-)
 delete mode 100644 gnu/packages/patches/tar-d_ino_in_dirent-fix.patch

01/02: gnu: gdbm: Update to 1.12.

[Ludovic Court�s]

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

commit 2135d1eb3faa061bcdceaf174bba4334770d44d4
Author: Ludovic Courtès 
Date:   Tue May 17 09:45:06 2016 +0200

gnu: gdbm: Update to 1.12.

* gnu/packages/databases.scm (gdbm): Update to 1.12.
---
 gnu/packages/databases.scm |4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm
index 1606721..a7f3837 100644
--- a/gnu/packages/databases.scm
+++ b/gnu/packages/databases.scm
@@ -114,14 +114,14 @@ either single machines or networked clusters.")
 (define-public gdbm
   (package
 (name "gdbm")
-(version "1.11")
+(version "1.12")
 (source (origin
   (method url-fetch)
   (uri (string-append "mirror://gnu/gdbm/gdbm-"
   version ".tar.gz"))
   (sha256
(base32
-"1hz3jgh3pd4qzp6jy0l8pd8x01g9abw7csnrlnj1a2sxy122z4cd"
+"1smwz4x5qa4js0zf1w3asq6z7mh20zlgwbh2bk5dczw6xrk22yyr"
 (arguments `(#:configure-flags '("--enable-libgdbm-compat")))
 (build-system gnu-build-system)
 (home-page "http://www.gnu.org/software/gdbm/;)

01/02: gnu: 'uncompressed-file-fetch' no longer depends on gzip.

[Ludovic Court�s]

civodul pushed a commit to branch master
in repository guix.

commit 4f04243405706a52b73c1acca883abfc030ce4d4
Author: Ludovic Courtès 
Date:   Mon May 16 22:45:37 2016 +0200

gnu: 'uncompressed-file-fetch' no longer depends on gzip.

* gnu/packages/emacs.scm (uncompressed-file-fetch): Remove dependency on
GZIP.
---
 gnu/packages/emacs.scm |2 --
 1 file changed, 2 deletions(-)

diff --git a/gnu/packages/emacs.scm b/gnu/packages/emacs.scm
index f0c1555..860ef11 100644
--- a/gnu/packages/emacs.scm
+++ b/gnu/packages/emacs.scm
@@ -1403,8 +1403,6 @@ identifiers in the MIT-Scheme documentation.")
 (gexp->derivation (or name (basename url))
   #~(begin
   (mkdir #$output)
-  (setenv "PATH"
-  (string-append #$gzip "/bin"))
   (chdir #$output)
   (copy-file #$drv (basename #$url))
 

branch master updated (cb307c0 -> a9e41d2)

[Ludovic Court�s]

civodul pushed a change to branch master
in repository guix.

  from  cb307c0   gnu: cflow: Update to 1.5.
   new  4f04243   gnu: 'uncompressed-file-fetch' no longer depends on gzip.
   new  a9e41d2   gnu: emacs-constants: Factorize home-page in source URL.

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/packages/emacs.scm |6 ++
 1 file changed, 2 insertions(+), 4 deletions(-)

branch master updated (11e4c1f -> cb307c0)

[Efraim Flashner]

efraim pushed a change to branch master
in repository guix.

  from  11e4c1f   gnu: Add geiser-next.
   new  cb307c0   gnu: cflow: Update to 1.5.

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/code.scm |4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

01/01: gnu: cflow: Update to 1.5.

[Efraim Flashner]

efraim pushed a commit to branch master
in repository guix.

commit cb307c0833742299f28abc236b5a9530f7349493
Author: Efraim Flashner 
Date:   Tue May 17 09:03:39 2016 +0300

gnu: cflow: Update to 1.5.

* gnu/packages/code.scm (cflow): Update to 1.5.
---
 gnu/packages/code.scm |4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/code.scm b/gnu/packages/code.scm
index af671d5..7e8a361 100644
--- a/gnu/packages/code.scm
+++ b/gnu/packages/code.scm
@@ -43,14 +43,14 @@
 (define-public cflow
   (package
 (name "cflow")
-(version "1.4")
+(version "1.5")
 (source (origin
   (method url-fetch)
   (uri (string-append "mirror://gnu/cflow/cflow-"
   version ".tar.bz2"))
   (sha256
(base32
-"1jkbq97ajcf834z68hbn3xfhiz921zhn39gklml1racf0kb3jzh3"
+"0yq33k5ap1zpnja64n89iai4zh018ffr72wki5a6mzczd880mr3g"
 (build-system gnu-build-system)
 
 ;; Needed to have cflow-mode.el installed.