branch master updated (4fb5f83 -> cb0866c)

[Hartmut Goebel]

htgoebel pushed a change to branch master
in repository guix.

  from  4fb5f83   gnu: Add sslh.
   new  cb0866c   gnu: Add geierlein.

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
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Summary of changes:
 gnu/packages/finance.scm |   54 +-
 1 file changed, 53 insertions(+), 1 deletion(-)

01/01: gnu: Add geierlein.

[Hartmut Goebel]

htgoebel pushed a commit to branch master
in repository guix.

commit cb0866c325f25e5b54493426fc83345133674c66
Author: Hartmut Goebel 
Date:   Mon Oct 17 10:39:21 2016 +0200

gnu: Add geierlein.

* gnu/packages/finance.scm (geierlein): New variable.
---
 gnu/packages/finance.scm |   54 +-
 1 file changed, 53 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/finance.scm b/gnu/packages/finance.scm
index 57c9f60..7924827 100644
--- a/gnu/packages/finance.scm
+++ b/gnu/packages/finance.scm
@@ -2,6 +2,7 @@
 ;;; Copyright © 2015, 2016 Andreas Enge 
 ;;; Copyright © 2016 Efraim Flashner 
 ;;; Copyright © 2016 Alex Griffin 
+;;; Copyright © 2016 Hartmut Goebel 
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -41,7 +42,8 @@
  #:use-module (gnu packages texinfo)
  #:use-module (gnu packages textutils)
  #:use-module (gnu packages tls)
- #:use-module (gnu packages upnp))
+ #:use-module (gnu packages upnp)
+ #:use-module (gnu packages gnuzilla))
 
 (define-public bitcoin-core
   (package
@@ -188,3 +190,53 @@ in ability, and easy to use.")
 "file://src/wcwidth.cc"
 "See src/wcwidth.cc in the distribution.")
license:gpl2+  ; lisp/*
+
+(define-public geierlein
+  (package
+(name "geierlein")
+(version "0.9.5")
+(source
+ (origin
+   (method url-fetch)
+   (uri (string-append "https://github.com/stesie/geierlein";
+   "/archive/V" version ".tar.gz"))
+   (file-name (string-append name "-" version ".tar.gz"))
+   (sha256
+(base32
+ "0b11fq8v5w8nxjb20jl4dsfhv76xky6n3sq3k3fbb0m2sq9ikikw"
+(build-system gnu-build-system)
+(arguments
+ `(#:tests? #f ; would require npm, python and a lot more
+   #:phases
+(modify-phases %standard-phases
+  (delete 'configure)
+  (add-after 'unpack 'override-target-directory-and-tool-paths
+(lambda* (#:key inputs outputs #:allow-other-keys)
+  (substitute* "Makefile"
+(("prefix := .*")
+ (string-append "prefix := " (assoc-ref outputs "out") "\n"))
+;; Required for tests, unused for now:
+;;(("PYTHON := .*")
+;; (string-append (which "python") "\n")))
+(("INSTALL := .*")
+ (string-append "INSTALL := " (which "install") "\n")))
+  (substitute* "bin/xgeierlein.in"
+;; Use icecat as XULRUNNER
+(("^for search ")
+ (string-append "XULRUNNER=" (which "icecat") "\n"
+"for search ")))
+  #t)
+(inputs
+ `(("icecat" ,icecat)))
+(home-page "http://stesie.github.io/geierlein/";)
+(synopsis "Free Elster client, for sending Germany VAT declarations")
+(description
+ "Geierlein is a free Elster client, i.e. an application that
+allows to send VAT declarations to Germany's fiscal authorities.
+
+Currently it is *not* possible to send returns that are due annually
+(especially the income tax return) since the fiscal authority doesn't
+allow to do that off the ERiC library (which is proprietary however).
+It's not clear at the moment whether one day it will be possible to
+do so.")
+(license license:agpl3+)))

branch master updated (cb0866c -> a8de0d1)

[Ben Woodcroft]

benwoodcroft pushed a change to branch master
in repository guix.

  from  cb0866c   gnu: Add geierlein.
   new  b8004a7   gnu: bundler: Update to 1.13.5.
   new  a8de0d1   gnu: ruby-json-pure: Fix tests.

The 2 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
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Summary of changes:
 gnu/packages/ruby.scm |6 --
 1 file changed, 4 insertions(+), 2 deletions(-)

02/02: gnu: ruby-json-pure: Fix tests.

[Ben Woodcroft]

benwoodcroft pushed a commit to branch master
in repository guix.

commit a8de0d1ec411aa1ecb744cb93c6188baa93c2b76
Author: Ben Woodcroft 
Date:   Mon Oct 17 19:13:38 2016 +1000

gnu: ruby-json-pure: Fix tests.

* gnu/packages/ruby.scm (ruby-json-pure)[arguments]: Remove unneeded
reference to 'json-java.gemspec' in 'Gemfile'.
---
 gnu/packages/ruby.scm |2 ++
 1 file changed, 2 insertions(+)

diff --git a/gnu/packages/ruby.scm b/gnu/packages/ruby.scm
index d400710..60f1992 100644
--- a/gnu/packages/ruby.scm
+++ b/gnu/packages/ruby.scm
@@ -2477,6 +2477,8 @@ a native C extension.")
(substitute* "Rakefile"
  (("FileList\\[`git ls-files`\\.split\\(/n/\\)\\]")
   (string-append "FileList" files
+ (substitute* "Gemfile"
+   ((".*json-java.*") "\n"))
  #t)
 (native-inputs
  `(("ruby-permutation" ,ruby-permutation)

01/02: gnu: bundler: Update to 1.13.5.

[Ben Woodcroft]

benwoodcroft pushed a commit to branch master
in repository guix.

commit b8004a7b797fda093fdf6675437cbdc1dd8a103a
Author: Ben Woodcroft 
Date:   Mon Oct 17 18:27:27 2016 +1000

gnu: bundler: Update to 1.13.5.

* gnu/packages/ruby.scm (bundler): Update to 1.13.5.
---
 gnu/packages/ruby.scm |4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/ruby.scm b/gnu/packages/ruby.scm
index 23d22a3..d400710 100644
--- a/gnu/packages/ruby.scm
+++ b/gnu/packages/ruby.scm
@@ -423,13 +423,13 @@ expectations and mocks frameworks.")
 (define-public bundler
   (package
 (name "bundler")
-(version "1.13.2")
+(version "1.13.5")
 (source (origin
   (method url-fetch)
   (uri (rubygems-uri "bundler" version))
   (sha256
(base32
-"05gwyhfn103vrmrw13r3n78bcl75mrj82ipsbazcl08wg1bql7x6"
+"0fxr7aq7qhlga423mygy7q96cwxmvqlcy676v2x5swlw8rlha2in"
 (build-system ruby-build-system)
 (arguments
  '(#:tests? #f)) ; avoid dependency cycles

01/01: gnu: node: Update to 6.8.0.

[Ludovic Court�s]

civodul pushed a commit to branch master
in repository guix.

commit dd04f56a2b25f6d32891bccd22a1315504257718
Author: Al McElrath 
Date:   Fri Oct 14 16:39:44 2016 -0700

gnu: node: Update to 6.8.0.

Remove  and
 workaround.

* gnu/packages/node.scm (node): Update to 6.8.0.
  (node)[arguments]: Disabled more tests. Remove custom 'patch-shebangs'
  phase. Manually patch npm script shebang in new 'patch-npm-shebang'
  phase.
* gnu/packages/patches/node-9077.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add patches.

Signed-off-by: Ludovic Courtès 
---
 gnu/local.mk |1 +
 gnu/packages/node.scm|   34 +++---
 gnu/packages/patches/node-9077.patch |   30 ++
 3 files changed, 46 insertions(+), 19 deletions(-)

diff --git a/gnu/local.mk b/gnu/local.mk
index 19dd9ae..27872ce 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -725,6 +725,7 @@ dist_patch_DATA =   
\
   %D%/packages/patches/ngircd-no-dns-in-tests.patch\
   %D%/packages/patches/ninja-tests.patch   \
   %D%/packages/patches/ninja-zero-mtime.patch  \
+  %D%/packages/patches/node-9077.patch \
   %D%/packages/patches/nss-pkgconfig.patch \
   %D%/packages/patches/nvi-assume-preserve-path.patch  \
   %D%/packages/patches/nvi-dbpagesize-binpower.patch   \
diff --git a/gnu/packages/node.scm b/gnu/packages/node.scm
index 887ef93..617dffc 100644
--- a/gnu/packages/node.scm
+++ b/gnu/packages/node.scm
@@ -25,6 +25,7 @@
   #:use-module (guix derivations)
   #:use-module (guix download)
   #:use-module (guix build-system gnu)
+  #:use-module (gnu packages)
   #:use-module (gnu packages base)
   #:use-module (gnu packages compression)
   #:use-module (gnu packages gcc)
@@ -37,14 +38,16 @@
 (define-public node
   (package
 (name "node")
-(version "6.0.0")
+(version "6.8.0")
 (source (origin
   (method url-fetch)
   (uri (string-append "http://nodejs.org/dist/v"; version
   "/node-v" version ".tar.gz"))
   (sha256
(base32
-"0cpw7ng193jgfbw2g1fd0kcglmjjkbj4xb89g00z8zz0lj0nvdbd"
+"0lj3250hglz4w5ic4svd7wlg2r3qc49hnasvbva1v69l8yvx98m8"))
+  ;; https://github.com/nodejs/node/pull/9077
+  (patches (search-patches "node-9077.patch"
 (build-system gnu-build-system)
 (arguments
  ;; TODO: Package http_parser and add --shared-http-parser.
@@ -78,10 +81,10 @@
  ;; FIXME: These tests fail in the build container, but they don't
  ;; seem to be indicative of real problems in practice.
  (for-each delete-file
-   '("test/parallel/test-cluster-master-error.js"
+   '("test/parallel/test-dgram-membership.js"
+ "test/parallel/test-cluster-master-error.js"
  "test/parallel/test-cluster-master-kill.js"
  "test/parallel/test-npm-install.js"
- "test/parallel/test-stdout-close-unref.js"
  "test/sequential/test-child-process-emfile.js"))
  #t))
  (replace 'configure
@@ -101,22 +104,15 @@
  (string-append (assoc-ref inputs "python")
 "/bin/python")
  "configure" flags)
- (replace 'patch-shebangs
-   (lambda* (#:key outputs #:allow-other-keys #:rest all)
- ;; Work around .
- (let* ((patch  (assoc-ref %standard-phases 'patch-shebangs))
-(npm(string-append (assoc-ref outputs "out")
-   "/bin/npm"))
+ (add-after 'patch-shebangs 'patch-npm-shebang
+   (lambda* (#:key outputs #:allow-other-keys)
+ (let* ((bindir (string-append (assoc-ref outputs "out")
+   "/bin"))
+(npm(string-append bindir "/npm"))
 (target (readlink npm)))
-   (and (apply patch all)
-(with-directory-excursion (dirname npm)
-  ;; Turn NPM into a symlink to TARGET again, which 'npm'
-  ;; relies on for the resolution of relative file names
-  ;; in JS files.
-  (delete-file target)
-  (rename-file npm target)
-  (symlink target npm)
-  #t
+   (with-directory-excursion bindir
+ (patch-shebang target (list bindir))
+ #t)))
 

branch master updated (a8de0d1 -> dd04f56)

[Ludovic Court�s]

civodul pushed a change to branch master
in repository guix.

  from  a8de0d1   gnu: ruby-json-pure: Fix tests.
   new  dd04f56   gnu: node: Update to 6.8.0.

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/local.mk |1 +
 gnu/packages/node.scm|   34 +++---
 gnu/packages/patches/node-9077.patch |   30 ++
 3 files changed, 46 insertions(+), 19 deletions(-)
 create mode 100644 gnu/packages/patches/node-9077.patch

01/01: gnu: wrap-python3: Use a bash wrapper for 'python3-config'.

[???]

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

commit 3969ca548c3230815242e95d07eee05d45b2947d
Author: 宋文武 
Date:   Sun Oct 16 10:44:29 2016 +0800

gnu: wrap-python3:  Use a bash wrapper for 'python3-config'.

See 
for details.

* gnu/packages/python.scm (wrap-python3)[arguments]: Use a bash wrapper
instead of a symlink for python3-config.
---
 gnu/packages/python.scm |   18 --
 1 file changed, 16 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 032530c..e49d336 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -52,6 +52,7 @@
   #:use-module (gnu packages adns)
   #:use-module (gnu packages attr)
   #:use-module (gnu packages backup)
+  #:use-module (gnu packages bash)
   #:use-module (gnu packages compression)
   #:use-module (gnu packages databases)
   #:use-module (gnu packages django)
@@ -379,6 +380,7 @@ data types.")
 (source #f)
 (build-system trivial-build-system)
 (outputs '("out"))
+(inputs `(("bash" ,bash)))
 (propagated-inputs `(("python" ,python)))
 (arguments
  `(#:modules ((guix build utils))
@@ -392,8 +394,20 @@ data types.")
   (lambda (old new)
 (symlink (string-append python old)
  (string-append bin "/" new)))
-  `("python3" ,"pydoc3" ,"idle3" ,"pip3" ,"python3-config")
-  `("python"  ,"pydoc"  ,"idle"  ,"pip"  ,"python-config"))
+  `("python3" ,"pydoc3" ,"idle3" ,"pip3")
+  `("python"  ,"pydoc"  ,"idle"  ,"pip"))
+;; python-config outputs search paths based upon its location,
+;; use a bash wrapper to avoid changing its outputs.
+(let ((bash (string-append (assoc-ref %build-inputs "bash")
+   "/bin/bash"))
+  (old  (string-append python "python3-config"))
+  (new  (string-append bin "/python-config")))
+  (with-output-to-file new
+(lambda ()
+  (format #t "#!~a~%" bash)
+  (format #t "exec \"~a\" \"$@\"~%" old)
+  (chmod new #o755)
+  #t)))
 (synopsis "Wrapper for the Python 3 commands")
 (description
  "This package provides wrappers for the commands of Python@tie{}3.x such

branch core-updates updated (964fc66 -> 3969ca5)

[???]

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

  from  964fc66   gnu: python-requests-mock: Fix build failure with Python 
3.5.
   new  3969ca5   gnu: wrap-python3:  Use a bash wrapper for 
'python3-config'.

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listed as "adds" were already present in the repository and have only
been added to this reference.


Summary of changes:
 gnu/packages/python.scm |   18 --
 1 file changed, 16 insertions(+), 2 deletions(-)

01/01: gnu: artanis: Remove implied $(DESTDIR) usage.

[Marius Bakke]

mbakke pushed a commit to branch master
in repository guix.

commit 8a666bc5cb3c50b4b881290c7776c3f681a734bc
Author: Adonay Felipe Nogueira 
Date:   Mon Oct 17 10:47:21 2016 -0200

gnu: artanis: Remove implied $(DESTDIR) usage.

* gnu/packages/patches/artanis-fix-Makefile.in.patch: New file.
* gnu/local.mk (dist_patch_DATA): Register patch.
* gnu/packages/guile.scm (artanis)[source]: Use patch.
[arguments]: Remove DESTDIR from #:make-flags.

Signed-off-by: Marius Bakke 
---
 gnu/local.mk   |2 +
 gnu/packages/guile.scm |7 +-
 gnu/packages/patches/artanis-fix-Makefile.in.patch |   70 
 3 files changed, 76 insertions(+), 3 deletions(-)

diff --git a/gnu/local.mk b/gnu/local.mk
index 27872ce..9079b42 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -5,6 +5,7 @@
 # Copyright © 2013, 2014, 2015, 2016 Mark H Weaver 
 # Copyright © 2016 Chris Marusich 
 # Copyright © 2016 Kei Kebreau 
+# Copyright © 2016 Adonay "adfeno" Felipe Nogueira 
 
 #
 # This file is part of GNU Guix.
 #
@@ -454,6 +455,7 @@ dist_patch_DATA =   
\
   %D%/packages/patches/antiword-CVE-2014-8123.patch\
   %D%/packages/patches/apr-skip-getservbyname-test.patch   \
   %D%/packages/patches/arb-ldconfig.patch  \
+  %D%/packages/patches/artanis-fix-Makefile.in.patch   \
   %D%/packages/patches/ath9k-htc-firmware-binutils.patch   \
   %D%/packages/patches/ath9k-htc-firmware-gcc.patch\
   %D%/packages/patches/ath9k-htc-firmware-objcopy.patch\
diff --git a/gnu/packages/guile.scm b/gnu/packages/guile.scm
index 7361f1f..43071e6 100644
--- a/gnu/packages/guile.scm
+++ b/gnu/packages/guile.scm
@@ -7,6 +7,7 @@
 ;;; Copyright © 2016 Erik Edrosa 
 ;;; Copyright © 2016 Eraim Flashner 
 ;;; Copyright © 2016 Alex Kost 
+;;; Copyright © 2016 Adonay "adfeno" Felipe Nogueira 
 
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -305,7 +306,8 @@ applicable."
   version ".tar.gz"))
   (sha256
(base32
-"19m3ak12cqk8js9d2mdg11kh4fjsq8frfpd10qw75h0zpr5cywpp"
+"19m3ak12cqk8js9d2mdg11kh4fjsq8frfpd10qw75h0zpr5cywpp"))
+  (patches (search-patches "artanis-fix-Makefile.in.patch"
 (build-system gnu-build-system)
 ;; TODO: Add guile-dbi and guile-dbd optional dependencies.
 (inputs `(("guile" ,guile-2.0)))
@@ -319,8 +321,7 @@ applicable."
   (dir (string-append out "/share/guile/site/2.0")))
  ;; Don't use (%site-dir) for site paths.
  (list (string-append "MOD_PATH=" dir)
-   (string-append "MOD_COMPILED_PATH=" dir)
-   (string-append "DESTDIR=" out)))
+   (string-append "MOD_COMPILED_PATH=" dir)))
#:test-target "test"
#:phases
(modify-phases %standard-phases
diff --git a/gnu/packages/patches/artanis-fix-Makefile.in.patch 
b/gnu/packages/patches/artanis-fix-Makefile.in.patch
new file mode 100644
index 000..7e4800d
--- /dev/null
+++ b/gnu/packages/patches/artanis-fix-Makefile.in.patch
@@ -0,0 +1,70 @@
+Applies until an Artanis release comes with the following patches
+applied:
+* 
+* 
+diff -ru artanis-0.1.2/Makefile.in artanis-0.1.2.1/Makefile.in
+--- artanis-0.1.2/Makefile.in  2016-02-10 12:35:18.800490571 -0200
 artanis-0.1.2.1/Makefile.in2016-10-15 19:44:35.140907367 -0300
+@@ -19,9 +19,18 @@
+ MOD_OBJ := $(OBJ)/artanis
+ BIN := bin
+ TEMP_LIB_PATH := $(OBJ)
+-MOD_PATH := $(shell guile -c "(display (%site-dir))")
+ MOD_COMPILED_PATH := $(shell guile -c "(display (%site-ccache-dir))")
++
++ifdef DESTDIR
++INFO_DIR := $(DESTDIR)/share/info/
++MOD_PATH := $(DESTDIR)/$(shell guile -c "(display (%site-dir))")
+ MOD_TARGET_PATH := $(DESTDIR)/$(MOD_COMPILED_PATH)
++else
++INFO_DIR := $(PREFIX)/share/info/
++MOD_PATH := $(shell guile -c "(display (%site-dir))")
++MOD_TARGET_PATH := $(MOD_COMPILED_PATH)
++endif
++
+ GUILE_CFLAGS := -Wunsupported-warning -Wunbound-variable -Warity-mismatch 
-Wduplicate-case-datum -Wbad-case-datum -Wformat
+ GUILEC := GUILE_LOAD_COMPILED_PATH=$(TEMP_LIB_PATH) guild compile 
$(GUILE_CFLAGS)
+ ARTANIS_ETC := $(SRC)/etc/artanis
+@@ -36,7 +45,6 @@
+ GENDOCS :=$(BUILD_AUX)/gendocs.sh
+ CHK_TEXINFO := $(BUILD_AUX)/check_texinfo.scm
+ CP := cp -frd -P
+-INFO_DIR := $(PREFIX)/share/info/
+ TARBALL_NAME := artanis-$(VERSION)
+ TMP_DIR := $(shell mktemp -d)
+ ANN_GEN := $(BUILD_AUX)/announce-gen
+@@ -124,18 +132,29 @@
+   -rm -f config.{h,log}
+ 
+ install: $(ALL_TARGETS)
+-  mkdir -p $(DESTDIR)/$(MOD_PATH)
+-  $(CP) $(MOD) $(DESTDIR)/$(MOD_PATH)/
++  mkdir -p $(MOD_PATH)
++ 

branch master updated (dd04f56 -> 8a666bc)

[Marius Bakke]

mbakke pushed a change to branch master
in repository guix.

  from  dd04f56   gnu: node: Update to 6.8.0.
   new  8a666bc   gnu: artanis: Remove implied $(DESTDIR) usage.

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 +
 gnu/packages/guile.scm |7 +-
 gnu/packages/patches/artanis-fix-Makefile.in.patch |   70 
 3 files changed, 76 insertions(+), 3 deletions(-)
 create mode 100644 gnu/packages/patches/artanis-fix-Makefile.in.patch

05/05: gnu: Add rcas-web.

[Ricardo Wurmus]

rekado pushed a commit to branch master
in repository guix.

commit 509372970408584d769d0152bdaececccba753e4
Author: Ricardo Wurmus 
Date:   Wed Oct 12 17:12:45 2016 +0200

gnu: Add rcas-web.

* gnu/packages/bioinformatics.scm (rcas-web): New variable.
---
 gnu/packages/bioinformatics.scm |   45 +++
 1 file changed, 45 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 49d8ca9..43faaa0 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -56,6 +56,7 @@
   #:use-module (gnu packages gtk)
   #:use-module (gnu packages glib)
   #:use-module (gnu packages groff)
+  #:use-module (gnu packages guile)
   #:use-module (gnu packages haskell)
   #:use-module (gnu packages image)
   #:use-module (gnu packages imagemagick)
@@ -7184,6 +7185,50 @@ library implementing most of the pipeline's features.")
 (home-page "https://github.com/BIMSBbioinfo/RCAS";)
 (license license:expat)))
 
+(define-public rcas-web
+  (package
+(name "rcas-web")
+(version "0.0.3")
+(source
+ (origin
+   (method url-fetch)
+   (uri (string-append "https://github.com/BIMSBbioinfo/rcas-web/";
+   "releases/download/v" version
+   "/rcas-web-" version ".tar.gz"))
+   (sha256
+(base32
+ "0d3my0g8i7js59n184zzzjdki7hgmhpi4rhfvk7i6jsw01ba04qq"
+(build-system gnu-build-system)
+(arguments
+ `(#:phases
+   (modify-phases %standard-phases
+ (add-after 'install 'wrap-executable
+   (lambda* (#:key inputs outputs #:allow-other-keys)
+ (let* ((out (assoc-ref outputs "out"))
+(json   (assoc-ref inputs "guile-json"))
+(redis  (assoc-ref inputs "guile-redis"))
+(path   (string-append
+ json  "/share/guile/site/2.2:"
+ redis "/share/guile/site/2.2")))
+   (wrap-program (string-append out "/bin/rcas-web")
+ `("GUILE_LOAD_PATH" ":" = (,path))
+ `("GUILE_LOAD_COMPILED_PATH" ":" = (,path))
+ `("R_LIBS_SITE" ":" = (,(getenv "R_LIBS_SITE")
+ #t)
+(inputs
+ `(("r" ,r)
+   ("r-rcas" ,r-rcas)
+   ("guile-next" ,guile-next)
+   ("guile-json" ,guile2.2-json)
+   ("guile-redis" ,guile2.2-redis)))
+(native-inputs
+ `(("pkg-config" ,pkg-config)))
+(home-page "https://github.com/BIMSBbioinfo/rcas-web";)
+(synopsis "Web interface for RNA-centric annotation system (RCAS)")
+(description "This package provides a simple web interface for the
+@dfn{RNA-centric annotation system} (RCAS).")
+(license license:agpl3+)))
+
 (define-public emboss
   (package
 (name "emboss")

01/05: gnu: sfml: Install pkgconfig files.

[Ricardo Wurmus]

rekado pushed a commit to branch master
in repository guix.

commit a6e25a50f9b560291889e87401d5c9ec598a89fa
Author: Ricardo Wurmus 
Date:   Sun Oct 16 20:07:09 2016 +0200

gnu: sfml: Install pkgconfig files.

* gnu/packages/game-development.scm (sfml)[arguments]: Add configure
flag to install pkgconfig files.
---
 gnu/packages/game-development.scm |4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/game-development.scm 
b/gnu/packages/game-development.scm
index 5e6cf0b..de0b842 100644
--- a/gnu/packages/game-development.scm
+++ b/gnu/packages/game-development.scm
@@ -183,7 +183,9 @@ clone.")
 "0k2fl5xk3ni2q8bsxl0551inx26ww3w6cp6hssvww0wfjdjcirsm"
 (build-system cmake-build-system)
 (arguments
- '(#:tests? #f)) ; no tests
+ '(#:configure-flags
+   (list "-DSFML_INSTALL_PKGCONFIG_FILES=TRUE")
+   #:tests? #f)) ; no tests
 (inputs
  `(("mesa" ,mesa)
("glew" ,glew)

branch master updated (8a666bc -> 5093729)

[Ricardo Wurmus]

rekado pushed a change to branch master
in repository guix.

  from  8a666bc   gnu: artanis: Remove implied $(DESTDIR) usage.
   new  a6e25a5   gnu: sfml: Install pkgconfig files.
   new  b8a35cc   gnu: extremetuxracer: Update to 0.7.3.
   new  f90b2db   gnu: irrlicht: Update to 1.8.4.
   new  89984be   gnu: Add r-rcas.
   new  5093729   gnu: Add rcas-web.

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/local.mk|1 -
 gnu/packages/bioinformatics.scm |   92 +++
 gnu/packages/game-development.scm   |4 +-
 gnu/packages/games.scm  |   50 ---
 gnu/packages/patches/irrlicht-mesa-10.patch |   46 --
 5 files changed, 106 insertions(+), 87 deletions(-)
 delete mode 100644 gnu/packages/patches/irrlicht-mesa-10.patch

04/05: gnu: Add r-rcas.

[Ricardo Wurmus]

rekado pushed a commit to branch master
in repository guix.

commit 89984be46e7714bc1b29fe04035964dfef3dec7e
Author: Ricardo Wurmus 
Date:   Wed Oct 12 17:12:44 2016 +0200

gnu: Add r-rcas.

* gnu/packages/bioinformatics.scm (r-rcas): New variable.
---
 gnu/packages/bioinformatics.scm |   47 +++
 1 file changed, 47 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 5fbfdf0..49d8ca9 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -56,6 +56,7 @@
   #:use-module (gnu packages gtk)
   #:use-module (gnu packages glib)
   #:use-module (gnu packages groff)
+  #:use-module (gnu packages haskell)
   #:use-module (gnu packages image)
   #:use-module (gnu packages imagemagick)
   #:use-module (gnu packages java)
@@ -7137,6 +7138,52 @@ ranges and it computes reads profiles and coverage 
profiles.  It also handles
 paired-end data.")
 (license license:gpl2+)))
 
+(define-public r-rcas
+  (package
+(name "r-rcas")
+(version "0.99.6")
+(source (origin
+  (method url-fetch)
+  (uri (string-append 
"https://github.com/BIMSBbioinfo/RCAS/archive/v";
+  version ".tar.gz"))
+  (file-name (string-append name "-" version ".tar.gz"))
+  (sha256
+   (base32
+"1ljgl2b4r6w2n0i9i04d9xaphajsvhfkjdj2i2z830nha4m3w8f0"
+(build-system r-build-system)
+(native-inputs
+ `(("r-knitr" ,r-knitr)
+   ("r-testthat" ,r-testthat)
+   ;; During vignette building knitr checks that "pandoc-citeproc"
+   ;; is in the PATH.
+   ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc)))
+(propagated-inputs
+ `(("r-data-table" ,r-data-table)
+   ("r-biomart" ,r-biomart)
+   ("r-org-hs-eg-db" ,r-org-hs-eg-db)
+   ("r-org-ce-eg-db" ,r-org-ce-eg-db)
+   ("r-org-dm-eg-db" ,r-org-dm-eg-db)
+   ("r-org-mm-eg-db" ,r-org-mm-eg-db)
+   ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
+   ("r-bsgenome-mmusculus-ucsc-mm9" ,r-bsgenome-mmusculus-ucsc-mm9)
+   ("r-bsgenome-celegans-ucsc-ce10" ,r-bsgenome-celegans-ucsc-ce10)
+   ("r-bsgenome-dmelanogaster-ucsc-dm3" ,r-bsgenome-dmelanogaster-ucsc-dm3)
+   ("r-topgo" ,r-topgo)
+   ("r-dt" ,r-dt)
+   ("r-plotly" ,r-plotly)
+   ("r-motifrg" ,r-motifrg)
+   ("r-genomation" ,r-genomation)
+   ("r-genomicfeatures" ,r-genomicfeatures)
+   ("r-rtracklayer" ,r-rtracklayer)
+   ("r-rmarkdown" ,r-rmarkdown)))
+(synopsis "RNA-centric annotation system")
+(description
+ "RCAS aims to be a standalone RNA-centric annotation system that provides
+intuitive reports and publication-ready graphics.  This package provides the R
+library implementing most of the pipeline's features.")
+(home-page "https://github.com/BIMSBbioinfo/RCAS";)
+(license license:expat)))
+
 (define-public emboss
   (package
 (name "emboss")

02/05: gnu: extremetuxracer: Update to 0.7.3.

[Ricardo Wurmus]

rekado pushed a commit to branch master
in repository guix.

commit b8a35ccea6c179c2ea259e8fe761007c7f94be1b
Author: Ricardo Wurmus 
Date:   Sun Oct 16 20:16:19 2016 +0200

gnu: extremetuxracer: Update to 0.7.3.

* gnu/packages/games.scm (extremetuxracer): Update to 0.7.3.
[inputs]: Remove freetype, mesa, libice, libpng, sdl, sdl-mixer,
sdl-image, libsm, libunwind, libx11, libext, libxi, libxmu, libxt, tcl,
zlib; add sfml.
[arguments]: Remove field.
---
 gnu/packages/games.scm |   30 --
 1 file changed, 4 insertions(+), 26 deletions(-)

diff --git a/gnu/packages/games.scm b/gnu/packages/games.scm
index 2bb53e0..edd3651 100644
--- a/gnu/packages/games.scm
+++ b/gnu/packages/games.scm
@@ -946,7 +946,7 @@ Protocol).")
 (define-public extremetuxracer
   (package
 (name "extremetuxracer")
-(version "0.6.0")
+(version "0.7.3")
 (source (origin
   (method url-fetch)
   (uri (string-append
@@ -954,35 +954,13 @@ Protocol).")
 version "/etr-" version ".tar.xz"))
   (sha256
(base32
-"0fl9pwkywqnsmgr6plfj9zb05xrdnl5xb2hcmbjk7ap9l4cjfca4"
+"1lg3z7jhzmsjym53qss8mbydny8hafwjnfsc7x91hrr9zrkwblly"
 (build-system gnu-build-system)
 (native-inputs
  `(("pkg-config" ,pkg-config)))
 (inputs
- `(("freetype" ,freetype)
-   ("mesa" ,mesa)
-   ("glu" ,glu)
-   ("libice" ,libice)
-   ("libpng" ,libpng)
-   ("sdl" ,sdl)
-   ("sdl-mixer" ,sdl-mixer)
-   ("sdl-image" ,sdl-image)
-   ("libsm" ,libsm)
-   ("libunwind" ,libunwind)
-   ("libx11" ,libx11)
-   ("libxext" ,libxext)
-   ("libxi" ,libxi)
-   ("libxmu" ,libxmu)
-   ("libxt" ,libxt)
-   ("tcl" ,tcl)
-   ("zlib" ,zlib)))
-(arguments
- '(#:phases
-   (modify-phases %standard-phases
- (add-after 'configure 'patch-makefile
-   (lambda _
- (substitute* "Makefile"
-   (("CXXFLAGS =") "CXXFLAGS = ${CFLAGS}")))
+ `(("glu" ,glu)
+   ("sfml" ,sfml)))
 (synopsis "High speed arctic racing game based on Tux Racer")
 ;; Snarfed straight from Debian
 (description "Extreme Tux Racer, or etracer as it is called for short, is

03/05: gnu: irrlicht: Update to 1.8.4.

[Ricardo Wurmus]

rekado pushed a commit to branch master
in repository guix.

commit f90b2dbdb715b4eb255b32f7843b1e830a285bda
Author: Ricardo Wurmus 
Date:   Mon Oct 17 08:48:06 2016 +0200

gnu: irrlicht: Update to 1.8.4.

* gnu/packages/games.scm (irrlicht): Update to 1.8.4.
[arguments]: Delete phase "apply-patch/mesa-10-fix".
[native-inputs]: Remove "patch/mesa-10-fix".
* gnu/packages/patches/irrlicht-mesa-10.patch: Delete file.
* gnu/local.mk (dist_path_DATA): Remove irrlicht patch.
---
 gnu/local.mk|1 -
 gnu/packages/games.scm  |   20 
 gnu/packages/patches/irrlicht-mesa-10.patch |   46 ---
 3 files changed, 7 insertions(+), 60 deletions(-)

diff --git a/gnu/local.mk b/gnu/local.mk
index 9079b42..c80b213 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -604,7 +604,6 @@ dist_patch_DATA =   
\
   %D%/packages/patches/id3lib-CVE-2007-4460.patch  \
   %D%/packages/patches/ilmbase-fix-tests.patch \
   %D%/packages/patches/inkscape-drop-wait-for-targets.patch\
-  %D%/packages/patches/irrlicht-mesa-10.patch  \
   %D%/packages/patches/jansson-CVE-2016-4425.patch \
   %D%/packages/patches/jasper-CVE-2007-2721.patch  \
   %D%/packages/patches/jasper-CVE-2008-3520.patch  \
diff --git a/gnu/packages/games.scm b/gnu/packages/games.scm
index edd3651..17ca12b 100644
--- a/gnu/packages/games.scm
+++ b/gnu/packages/games.scm
@@ -545,7 +545,7 @@ are primarily in English, however some in other languages 
are provided.")
 (define-public irrlicht
   (package
 (name "irrlicht")
-(version "1.8.1")
+(version "1.8.4")
 (source (origin
   (method url-fetch)
   (uri (string-append
@@ -554,10 +554,10 @@ are primarily in English, however some in other languages 
are provided.")
 "/" version "/irrlicht-" version ".zip"))
   (sha256
(base32
-"0yz9lvsc8aqk8wj4rnpanxrw90gqpwn9w5hxp94r8hnm2q0vjjw1"
+"0cz4z4dwrv5ypl19ll67wl6jjpy5k6ly4vr042w4br88qq5jhazl"
 (build-system gnu-build-system)
 (arguments
- '(#:phases (alist-cons-after
+ `(#:phases (alist-cons-after
  'unpack 'fix-build-env
  (lambda* (#:key outputs #:allow-other-keys)
(let ((out (assoc-ref outputs "out")))
@@ -572,19 +572,13 @@ are primarily in English, however some in other languages 
are provided.")
   (lambda* (#:key source #:allow-other-keys)
 (and (zero? (system* "unzip" source))
  ;; The actual source is buried a few directories deep.
- (chdir "irrlicht-1.8.1/source/Irrlicht/")))
-  (alist-cons-after
-   'unpack 'apply-patch/mesa-10-fix
-   (lambda* (#:key inputs #:allow-other-keys)
- (zero? (system* "patch" "--force" "-p3" "-i"
- (assoc-ref inputs "patch/mesa-10-fix"
-   ;; No configure script
-   (alist-delete 'configure %standard-phases
+ (chdir (string-append "irrlicht-" ,version 
"/source/Irrlicht/"
+  ;; No configure script
+  (alist-delete 'configure %standard-phases)))
#:tests? #f ; no check target
#:make-flags '("CC=gcc" "sharedlib")))
 (native-inputs
- `(("patch/mesa-10-fix" ,(search-patch "irrlicht-mesa-10.patch"))
-   ("unzip" ,unzip)))
+ `(("unzip" ,unzip)))
 (inputs
  `(("mesa" ,mesa)
("glu" ,glu)))
diff --git a/gnu/packages/patches/irrlicht-mesa-10.patch 
b/gnu/packages/patches/irrlicht-mesa-10.patch
deleted file mode 100644
index b567c38..000
--- a/gnu/packages/patches/irrlicht-mesa-10.patch
+++ /dev/null
@@ -1,46 +0,0 @@
-Patch to work around incompatibility between irrlicht-1.8.1 and mesa-10.x.
-Upstream bug (fixed in trunk): http://sourceforge.net/p/irrlicht/bugs/429/
-Upstream fix: http://sourceforge.net/p/irrlicht/code/4810
-This patch copied from:
-http://sources.gentoo.org/cgi-bin/viewvc.cgi/gentoo-x86/dev-games/irrlicht/files/irrlicht-1.8.1-mesa-10.x.patch?view=markup
-
-From 244d00280c1b082ca164f92337773e9e4e1a3898 Mon Sep 17 00:00:00 2001
-From: hiker 
-Date: Wed, 26 Feb 2014 11:13:03 +1100
-Subject: [PATCH] Applied patch from jpirie for fixing mesa 10 compilation
- problems.
-
 irrlicht-1.8.1/source/Irrlicht/COpenGLExtensionHandler.h
-+++ irrlicht-1.8.1/source/Irrlicht/COpenGLExtensionHandler.h
-@@ -21,6 +21,7 @@
-   #endif
-   #include 
-   #if defined(_IRR_OPENGL_USE_EXTPOINTER_)
-+  typedef void (APIENTRYP PFNGLBLENDEQUATIONPROC) (GLenum mode);
-   #include "glext.h"
-   #endif
-   #include "wglext.h"
-@@ -35,6 +36,7 @@
-   #endif
-  

03/04: gnu: Add python-betamax.

[Leo Famulari]

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

commit 66d3f50a76df00fffb6f241960c9bab48f91173d
Author: Leo Famulari 
Date:   Sun Oct 16 13:15:46 2016 -0400

gnu: Add python-betamax.

* gnu/packages/python.scm (python-betamax, python2-betamax): New variables.
---
 gnu/packages/python.scm |   32 
 1 file changed, 32 insertions(+)

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 7938f74..85330f8 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -11082,3 +11082,35 @@ with an associated set of resolve methods that know 
how to fetch data.")
 provide extendible implementations of common aspects of a cloud so that you can
 focus on building massively scalable web applications.")
 (license license:expat)))
+
+(define-public python-betamax
+  (package
+(name "python-betamax")
+(version "0.8.0")
+(source
+  (origin
+(method url-fetch)
+(uri (pypi-uri "betamax" version))
+(sha256
+ (base32
+  "18f8v5gng3j773jlbbzx4rg1i4y2zw3m2l1zpmbvp8bh5a2q1i42"
+(build-system python-build-system)
+(arguments
+ '(;; Many tests fail because they require networking.
+   #:tests? #f))
+(inputs
+ `(("python-requests" ,python-requests)))
+(home-page "https://github.com/sigmavirus24/betamax";)
+(synopsis "Record HTTP interactions with python-requests")
+(description "Betamax will record your test suite's HTTP interactions and
+replay them during future tests.  It is designed to work with 
python-requests.")
+(license license:expat)
+(properties `((python2-variant . ,(delay python2-betamax))
+
+(define-public python2-betamax
+  (let ((base (package-with-python2 (strip-python2-variant python-betamax
+(package
+  (inherit base)
+  (native-inputs
+   `(("python2-setuptools" ,python2-setuptools)
+ ,@(package-native-inputs base))

01/04: gnu: python-wsgi-intercept: Fix build failure with Python 3.5.

[Leo Famulari]

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

commit 8757f05046dfc2423edc0345c6da21d2e0a6257e
Author: Leo Famulari 
Date:   Sun Oct 16 12:53:18 2016 -0400

gnu: python-wsgi-intercept: Fix build failure with Python 3.5.

* gnu/packages/python.scm (python-wsgi-intercept)[native-inputs]:
Add python-urllib3.
---
 gnu/packages/python.scm |3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index e49d336..8d2195c 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -7439,7 +7439,8 @@ framework which enables you to test server connections 
locally.")
 (build-system python-build-system)
 (native-inputs
  `(("python-pytest" ,python-pytest)
-   ("python-six" ,python-six)))
+   ("python-six" ,python-six)
+   ("python-urllib3" ,python-urllib3)))
 (propagated-inputs
  `(("python-httplib2" ,python-httplib2)
("python-requests" ,python-requests)))

02/04: gnu: python-vobject: Disable the test suite.

[Leo Famulari]

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

commit a9871b7b523eefba58645b20c88a2499119ca48e
Author: Leo Famulari 
Date:   Sun Oct 16 13:05:30 2016 -0400

gnu: python-vobject: Disable the test suite.

The tests were silently skipped with Python 3.4. With Python 3.5, this 
caused
the python-vobject build to fail.

* gnu/packages/python.scm (python-vobject, python2-vobject)[arguments]: 
Disable
the tests.
---
 gnu/packages/python.scm |3 +++
 1 file changed, 3 insertions(+)

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 8d2195c..7938f74 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -8742,6 +8742,9 @@ introspection of @code{zope.interface} instances in 
code.")
(base32
 "1qfnwlx8qwkgr6nf5wvl6ff1r3kll53dh3z6nyp173nmlhhhqccb"
 (build-system python-build-system)
+(arguments
+ '(;; The test suite relies on some non-portable Windows interfaces.
+   #:tests? #f))
 (inputs
  `(("python-dateutil-2" ,python-dateutil-2)
("python-pyicu" ,python-pyicu)))

branch core-updates updated (3969ca5 -> 759aadd)

[Leo Famulari]

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

  from  3969ca5   gnu: wrap-python3:  Use a bash wrapper for 
'python3-config'.
   new  8757f050  gnu: python-wsgi-intercept: Fix build failure with Python 
3.5.
   new  a9871b7   gnu: python-vobject: Disable the test suite.
   new  66d3f50   gnu: Add python-betamax.
   new  759aadd   gnu: python-requests-toolbelt: Fix build failure by 
adding missing dependencies.

The 4 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 |   42 +-
 1 file changed, 41 insertions(+), 1 deletion(-)

04/04: gnu: python-requests-toolbelt: Fix build failure by adding missing dependencies.

[Leo Famulari]

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

commit 759aadd46fdc8b9816c33667129d4e9bae310ba7
Author: Leo Famulari 
Date:   Sun Oct 16 13:18:12 2016 -0400

gnu: python-requests-toolbelt: Fix build failure by adding missing 
dependencies.

* gnu/packages/python.scm (python-requests-toolbelt)[native-inputs]: Add
python-betamax, python-mock and python-pytest.
---
 gnu/packages/python.scm |4 
 1 file changed, 4 insertions(+)

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 85330f8..e0ead50 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -7240,6 +7240,10 @@ for atomic file system operations.")
   (base32
"15q9nrgp85nqlr4kdz1zvj8z2npafi2sr12y7fqgxbkq28j1aci6"
 (build-system python-build-system)
+(native-inputs
+ `(("python-betamax" ,python-betamax)
+   ("python-mock" ,python-mock)
+   ("python-pytest" ,python-pytest)))
 (propagated-inputs
  `(("python-requests" ,python-requests)))
 (synopsis "Extensions to python-requests")

branch master updated (5093729 -> 0bd6975)

[Kei Kebreau]

kkebreau pushed a change to branch master
in repository guix.

  from  5093729   gnu: Add rcas-web.
   new  0bd6975   gnu: Add xpad.

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 |   28 
 1 file changed, 28 insertions(+)

01/01: gnu: Add xpad.

[Kei Kebreau]

kkebreau pushed a commit to branch master
in repository guix.

commit 0bd697591bd5f020032cc2650fa6f0f43377ff67
Author: Rene Saavedra 
Date:   Sat Oct 15 21:51:25 2016 -0500

gnu: Add xpad.

* gnu/packages/gnome.scm (xpad): New variable.

Signed-off-by: Kei Kebreau 
---
 gnu/packages/gnome.scm |   28 
 1 file changed, 28 insertions(+)

diff --git a/gnu/packages/gnome.scm b/gnu/packages/gnome.scm
index 2b75781..52d6cd4 100644
--- a/gnu/packages/gnome.scm
+++ b/gnu/packages/gnome.scm
@@ -5544,3 +5544,31 @@ handling the startup notification side.")
  "Calculator is an application that solves mathematical equations and
 is suitable as a default application in a Desktop environment.")
 (license license:gpl3)))
+
+(define-public xpad
+  (package
+(name "xpad")
+(version "4.8.0")
+(source
+ (origin
+   (method url-fetch)
+   (uri (string-append "https://launchpad.net/xpad/trunk/4.8.0/+download/";
+   name "-" version ".tar.bz2"))
+   (sha256
+(base32
+ "17f915yyvfa2fsavq6wh0q0dfhib28b4k1gc0292b9xdlrvy7f22"
+(build-system gnu-build-system)
+(native-inputs
+ `(("intltool" ,intltool)
+   ("pkg-config" ,pkg-config)))
+(inputs
+ `(("gtk+" ,gtk+)
+   ("gtksourceview" ,gtksourceview)
+   ("libsm" ,libsm)))
+(home-page "https://wiki.gnome.org/Apps/Xpad";)
+(synopsis "Virtual sticky note")
+(description
+ "Xpad is a sticky note that strives to be simple, fault tolerant,
+and customizable.  Xpad consists of independent pad windows, each is
+basically a text box in which notes can be written.")
+(license license:gpl3+)))

01/02: gnu: linux-libre@4.4: Update to 4.4.25.

[Mark H. Weaver]

mhw pushed a commit to branch master
in repository guix.

commit 43f1d02ddcd12ac4a92b127bc724cd41d679ecfc
Author: Mark H Weaver 
Date:   Mon Oct 17 15:22:33 2016 -0400

gnu: linux-libre@4.4: Update to 4.4.25.

* gnu/packages/linux.scm (linux-libre-4.4): Update to 4.4.25.
---
 gnu/packages/linux.scm |4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm
index 293ff3f..993903e 100644
--- a/gnu/packages/linux.scm
+++ b/gnu/packages/linux.scm
@@ -329,8 +329,8 @@ It has been modified to remove all non-free binary blobs.")
 #:configuration-file kernel-config))
 
 (define-public linux-libre-4.4
-  (make-linux-libre "4.4.24"
-"1wg1d9rq29612psr5v4krabx7nv1y1gzfshq7wpx6i1lpqf3lill"
+  (make-linux-libre "4.4.25"
+"1a677h8vvjkbzqwnklqnjvhq33lwig5z453dwi125zzzvawgr463"
 %intel-compatible-systems
 #:configuration-file kernel-config))
 

02/02: gnu: linux-libre: Update to 4.8.2.

[Mark H. Weaver]

mhw pushed a commit to branch master
in repository guix.

commit cd829fe306e471a8f8941c720f622b83fdd05d71
Author: Mark H Weaver 
Date:   Mon Oct 17 15:23:46 2016 -0400

gnu: linux-libre: Update to 4.8.2.

* gnu/packages/linux.scm (%linux-libre-version, %linux-libre-hash)
(linux-libre): Update to 4.8.2.
---
 gnu/packages/linux.scm |8 
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm
index 993903e..08fd7ac 100644
--- a/gnu/packages/linux.scm
+++ b/gnu/packages/linux.scm
@@ -323,8 +323,8 @@ It has been modified to remove all non-free binary blobs.")
 (define %intel-compatible-systems '("x86_64-linux" "i686-linux"))
 
 (define-public linux-libre
-  (make-linux-libre "4.8.1"
-"0l57ab8v52nvx4d898qfvkl7c6zlrm7qd080z6jg0bg0adn4w5lf"
+  (make-linux-libre "4.8.2"
+"111v014j9b2zgyhv8f0aka5lmyc3imdc5yag7azw6hv3vjqqkn67"
 %intel-compatible-systems
 #:configuration-file kernel-config))
 
@@ -341,8 +341,8 @@ It has been modified to remove all non-free binary blobs.")
 #:configuration-file kernel-config))
 
 ;; Avoid rebuilding kernel variants when there is a minor version bump.
-(define %linux-libre-version "4.8.1")
-(define %linux-libre-hash 
"0l57ab8v52nvx4d898qfvkl7c6zlrm7qd080z6jg0bg0adn4w5lf")
+(define %linux-libre-version "4.8.2")
+(define %linux-libre-hash 
"111v014j9b2zgyhv8f0aka5lmyc3imdc5yag7azw6hv3vjqqkn67")
 
 (define-public linux-libre-arm-generic
   (make-linux-libre %linux-libre-version

branch master updated (0bd6975 -> cd829fe)

[Mark H. Weaver]

mhw pushed a change to branch master
in repository guix.

  from  0bd6975   gnu: Add xpad.
   new  43f1d02   gnu: linux-libre@4.4: Update to 4.4.25.
   new  cd829fe   gnu: linux-libre: Update to 4.8.2.

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/linux.scm |   12 ++--
 1 file changed, 6 insertions(+), 6 deletions(-)

branch core-updates updated (759aadd -> bf62b8f)

[Ludovic Court�s]

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

  from  759aadd   gnu: python-requests-toolbelt: Fix build failure by 
adding missing dependencies.
   new  c21af65   gnu: recutils: Adjust to Bash 4.4.
   new  9d356c9   gnu: guile-lib: Use 'modify-phases'.
   new  bf62b8f   gnu: guile-lib: Update to 0.2.3.

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:
 gnu/packages/databases.scm |   19 ++-
 gnu/packages/guile.scm |   28 +++-
 2 files changed, 37 insertions(+), 10 deletions(-)

01/01: gnu: openssh: Enable kerberos features.

[John Darrington]

jmd pushed a commit to branch master
in repository guix.

commit 040b6299d505c034b4960c335434a500ae2f8187
Author: John Darrington 
Date:   Sun Oct 16 08:31:55 2016 +0200

gnu: openssh: Enable kerberos features.

* gnu/packages/ssh.scm (openssh) [arguments]: Add flag --with-kerberos5.
[inputs]: Add mit-krb5.
---
 gnu/packages/ssh.scm |   11 +--
 1 file changed, 9 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/ssh.scm b/gnu/packages/ssh.scm
index c551f18..9fd1506 100644
--- a/gnu/packages/ssh.scm
+++ b/gnu/packages/ssh.scm
@@ -37,6 +37,7 @@
   #:use-module (gnu packages multiprecision)
   #:use-module (gnu packages ncurses)
   #:use-module (gnu packages nettle)
+  #:use-module (gnu packages mit-krb5)
   #:use-module (gnu packages perl)
   #:use-module (gnu packages pkg-config)
   #:autoload   (gnu packages protobuf) (protobuf)
@@ -126,15 +127,21 @@ a server that supports the SSH-2 protocol.")
(inputs `(("groff" ,groff)
  ("openssl" ,openssl)
  ("pam" ,linux-pam)
+ ("mit-krb5" ,mit-krb5)
  ("zlib" ,zlib)
  ("xauth" ,xauth)))   ;for 'ssh -X' and 'ssh -Y'
(arguments
 `(#:test-target "tests"
-  #:configure-flags '("--sysconfdir=/etc/ssh"
+  #:configure-flags  `("--sysconfdir=/etc/ssh"
 
-  ;; Default value of 'PATH' used by sshd.
+   ;; Default value of 'PATH' used by sshd.
   "--with-default-path=/run/current-system/profile/bin"
 
+  ;; configure needs to find krb5-config
+  ,(string-append "--with-kerberos5="
+  (assoc-ref %build-inputs "mit-krb5")
+  "/bin")
+
   ;; Enable PAM support in sshd.
   "--with-pam")
 

branch master updated (cd829fe -> 040b629)

[John Darrington]

jmd pushed a change to branch master
in repository guix.

  from  cd829fe   gnu: linux-libre: Update to 4.8.2.
   new  040b629   gnu: openssh: Enable kerberos features.

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/ssh.scm |   11 +--
 1 file changed, 9 insertions(+), 2 deletions(-)

02/03: gnu: guile-lib: Use 'modify-phases'.

[Ludovic Court�s]

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

commit 9d356c9c925451634d2d39e3e1b87efa91e8446b
Author: Ludovic Courtès 
Date:   Mon Oct 17 21:48:08 2016 +0200

gnu: guile-lib: Use 'modify-phases'.

* gnu/packages/guile.scm (guile-lib)[arguments]: Use 'modify-phases'.
---
 gnu/packages/guile.scm |   13 ++---
 1 file changed, 6 insertions(+), 7 deletions(-)

diff --git a/gnu/packages/guile.scm b/gnu/packages/guile.scm
index 28a52fc..0325e63 100644
--- a/gnu/packages/guile.scm
+++ b/gnu/packages/guile.scm
@@ -520,13 +520,12 @@ format is also supported.")
"1f9n2b5b5r75lzjinyk6zp6g20g60msa0jpfrk5hhg4j8cy0ih4b"
 (build-system gnu-build-system)
 (arguments
- '(#:phases (alist-cons-before
- 'configure 'patch-module-dir
- (lambda _
-   (substitute* "src/Makefile.in"
- (("^moddir[[:blank:]]*=[[:blank:]]*([[:graph:]]+)" _ rhs)
-  (string-append "moddir = " rhs "/2.0\n"
- %standard-phases)))
+ '(#:phases (modify-phases %standard-phases
+  (add-before 'configure 'patch-module-dir
+(lambda _
+  (substitute* "src/Makefile.in"
+(("^moddir[[:blank:]]*=[[:blank:]]*([[:graph:]]+)" _ 
rhs)
+ (string-append "moddir = " rhs "/2.0\n"
 (inputs `(("guile" ,guile-2.0)))
 (home-page "http://www.nongnu.org/guile-lib/";)
 (synopsis "Collection of useful Guile Scheme modules")

01/03: gnu: recutils: Adjust to Bash 4.4.

[Ludovic Court�s]

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

commit c21af659b4e6871b9576278cd5745881c696fd70
Author: Ludovic Courtès 
Date:   Mon Oct 17 21:36:25 2016 +0200

gnu: recutils: Adjust to Bash 4.4.

* gnu/packages/databases.scm (recutils)[arguments]: Add
'set-bash4.4-header-location' phase.
---
 gnu/packages/databases.scm |   19 ++-
 1 file changed, 18 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm
index b7bd1f0..5219766 100644
--- a/gnu/packages/databases.scm
+++ b/gnu/packages/databases.scm
@@ -405,7 +405,24 @@ pictures, sounds, or video.")
  #:configure-flags
  (list (string-append "--with-bash-headers="
   (assoc-ref %build-inputs "bash:include")
-  "/include/bash"
+  "/include/bash"))
+
+ #:phases (modify-phases %standard-phases
+(add-before 'build 'set-bash4.4-header-location
+  (lambda _
+(substitute* "bash/Makefile.in"
+  ;; Adjust the header search path for Bash
+  ;; 4.4 in accordance with 'bash.pc'.
+  (("AM_CPPFLAGS = (.*)$" _ rest)
+   (string-append "AM_CPPFLAGS = "
+  "-I$(BASH_HEADERS)/include "
+  rest))
+
+  ;; Install to PREFIX/lib/bash to match Bash
+  ;; 4.4's search path.
+  (("^libdir = .*$")
+   "libdir = @libdir@/bash\n"))
+#t)
 
 (native-inputs `(("emacs" ,emacs-minimal)
  ("bc" ,bc)

03/03: gnu: guile-lib: Update to 0.2.3.

[Ludovic Court�s]

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

commit bf62b8ff79f9d60136996b8251b6475965cf4994
Author: Ludovic Courtès 
Date:   Mon Oct 17 22:04:27 2016 +0200

gnu: guile-lib: Update to 0.2.3.

* gnu/packages/guile.scm (guile-lib): Update to 0.2.3.
[arguments]: Adjust 'patch-module-dir' to change both 'moddir' and
'godir'; use '@GUILE_EFFECTIVE_VERSION@' instead of a hard-coded
"2.0".  Add 'check' phase.
[native-inputs]: New field.
---
 gnu/packages/guile.scm |   19 +++
 1 file changed, 15 insertions(+), 4 deletions(-)

diff --git a/gnu/packages/guile.scm b/gnu/packages/guile.scm
index 0325e63..aa2cdb1 100644
--- a/gnu/packages/guile.scm
+++ b/gnu/packages/guile.scm
@@ -510,22 +510,33 @@ format is also supported.")
 (define-public guile-lib
   (package
 (name "guile-lib")
-(version "0.2.2")
+(version "0.2.3")
 (source (origin
  (method url-fetch)
  (uri (string-append "mirror://savannah/guile-lib/guile-lib-"
  version ".tar.gz"))
  (sha256
   (base32
-   "1f9n2b5b5r75lzjinyk6zp6g20g60msa0jpfrk5hhg4j8cy0ih4b"
+   "0pwdd52vakni1fabaiav8v0ad7xp3bx8x3brijbr1mpgamm9dxqc"
 (build-system gnu-build-system)
 (arguments
  '(#:phases (modify-phases %standard-phases
   (add-before 'configure 'patch-module-dir
 (lambda _
   (substitute* "src/Makefile.in"
-(("^moddir[[:blank:]]*=[[:blank:]]*([[:graph:]]+)" _ 
rhs)
- (string-append "moddir = " rhs "/2.0\n"
+(("^moddir = ([[:graph:]]+)")
+ "moddir = 
$(datadir)/guile/site/@GUILE_EFFECTIVE_VERSION@\n")
+(("^godir = ([[:graph:]]+)")
+ "godir = \
+$(libdir)/guile/@GUILE_EFFECTIVE_VERSION@/site-ccache\n"))
+  #t))
+  (replace 'check
+(lambda _
+  ;; Work around a harmless test failure involving
+  ;; two-spaces-after-period rendering.
+  (zero? (system* "make" "check" ;"-C" "unit-tests"
+  
"XFAIL_TESTS=texinfo.serialize.scm")))
+(native-inputs `(("pkg-config" ,pkg-config)))
 (inputs `(("guile" ,guile-2.0)))
 (home-page "http://www.nongnu.org/guile-lib/";)
 (synopsis "Collection of useful Guile Scheme modules")

01/01: gnu: diffoscope: Update to 61.

[Leo Famulari]

lfam pushed a commit to branch master
in repository guix.

commit 6ace9f80f15f7d5fc35e76b0dad7c0d298ad04ad
Author: Leo Famulari 
Date:   Mon Oct 17 16:38:21 2016 -0400

gnu: diffoscope: Update to 61.

* gnu/packages/package-management.scm (diffoscope): Update to 61.
---
 gnu/packages/package-management.scm |4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/package-management.scm 
b/gnu/packages/package-management.scm
index 70a6a49..b437599 100644
--- a/gnu/packages/package-management.scm
+++ b/gnu/packages/package-management.scm
@@ -476,13 +476,13 @@ transactions from C or Python.")
 (define-public diffoscope
   (package
 (name "diffoscope")
-(version "60")
+(version "61")
 (source (origin
   (method url-fetch)
   (uri (pypi-uri name version))
   (sha256
(base32
-"0qwsnh7sldjlwi4qydn1ljzh3322k2ga45d867ml49xr2wnsivcc"
+"1qpk2l6p9z58s61jfx6adm96f5r21ns128db0876zd6b6h34411p"
 (build-system python-build-system)
 (arguments
  `(#:phases (modify-phases %standard-phases

branch master updated (040b629 -> 6ace9f8)

[Leo Famulari]

lfam pushed a change to branch master
in repository guix.

  from  040b629   gnu: openssh: Enable kerberos features.
   new  6ace9f8   gnu: diffoscope: Update to 61.

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

01/01: Merge branch 'master' into core-updates

[Mark H. Weaver]

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

commit dcaf70897a0bad38a4638a2905aaa3c46b1f1402
Merge: bf62b8f 040b629
Author: Mark H Weaver 
Date:   Mon Oct 17 16:47:12 2016 -0400

Merge branch 'master' into core-updates

 doc/guix.texi  |   14 +
 gnu/local.mk   |8 +-
 gnu/packages/audio.scm |4 +-
 gnu/packages/bioinformatics.scm|   92 
 gnu/packages/cdrom.scm |   13 +-
 gnu/packages/emacs.scm |   71 ++-
 gnu/packages/embedded.scm  |   60 ++
 gnu/packages/finance.scm   |   54 +-
 gnu/packages/game-development.scm  |4 +-
 gnu/packages/games.scm |   50 +-
 gnu/packages/gd.scm|1 +
 gnu/packages/glib.scm  |1 +
 gnu/packages/gnome.scm |   28 +
 gnu/packages/graphics.scm  |   10 +-
 gnu/packages/guile.scm |7 +-
 gnu/packages/image.scm |   21 +-
 gnu/packages/linux.scm |   16 +-
 gnu/packages/mail.scm  |   48 ++
 gnu/packages/music.scm |  388 +
 gnu/packages/networking.scm|   76 ++-
 gnu/packages/node.scm  |   34 +-
 gnu/packages/patches/artanis-fix-Makefile.in.patch |   70 +++
 gnu/packages/patches/freeimage-CVE-2016-5684.patch |   34 ++
 .../patches/gcc-6-arm-none-eabi-multilib.patch |  206 +++
 .../gcc-6-cross-environment-variables.patch|   65 +++
 gnu/packages/patches/gd-CVE-2016-8670.patch|   38 ++
 gnu/packages/patches/hdf4-architectures.patch  |  579 
 gnu/packages/patches/irrlicht-mesa-10.patch|   46 --
 gnu/packages/patches/node-9077.patch   |   30 +
 gnu/packages/pdf.scm   |   54 ++
 gnu/packages/photo.scm |4 +-
 gnu/packages/python.scm|   87 ++-
 gnu/packages/qt.scm|6 +-
 gnu/packages/ruby.scm  |6 +-
 gnu/packages/serialization.scm |9 +-
 gnu/packages/ssh.scm   |   11 +-
 gnu/packages/terminals.scm |   14 +-
 gnu/packages/tls.scm   |   18 +-
 gnu/packages/version-control.scm   |6 +-
 gnu/packages/webkit.scm|4 +-
 gnu/services/sddm.scm  |2 +-
 guix/grafts.scm|   32 +-
 guix/import/utils.scm  |1 -
 guix/packages.scm  |6 +-
 guix/scripts/graph.scm |   53 +-
 tests/grafts.scm   |   62 +++
 tests/graph.scm|   22 +
 tests/packages.scm |  106 +++-
 48 files changed, 2324 insertions(+), 247 deletions(-)

diff --cc gnu/local.mk
index 59d424a,c80b213..1c91e79
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@@ -5,7 -5,7 +5,8 @@@
  # Copyright © 2013, 2014, 2015, 2016 Mark H Weaver 
  # Copyright © 2016 Chris Marusich 
  # Copyright © 2016 Kei Kebreau 
 +# Copyright © 2016 Rene Saavedra 
+ # Copyright © 2016 Adonay "adfeno" Felipe Nogueira 
 
  #
  # This file is part of GNU Guix.
  #
@@@ -525,10 -526,12 +527,11 @@@ dist_patch_DATA =   

%D%/packages/patches/flint-ldconfig.patch   \
%D%/packages/patches/fltk-shared-lib-defines.patch  \
%D%/packages/patches/fltk-xfont-on-demand.patch \
 -  %D%/packages/patches/fontconfig-CVE-2016-5384.patch \
%D%/packages/patches/fontforge-svg-modtime.patch\
%D%/packages/patches/freeimage-CVE-2015-0852.patch  \
+   %D%/packages/patches/freeimage-CVE-2016-5684.patch  \
 -  %D%/packages/patches/gawk-fts-test.patch\
%D%/packages/patches/gawk-shell.patch   \
 +  %D%/packages/patches/gcc-arm-bug-71399.patch\
%D%/packages/patches/gcc-arm-link-spec-fix.patch\
%D%/packages/patches/gcc-cross-environment-variables.patch  \
%D%/packages/patches/gcc-libvtv-runpath.patch   \
@@@ -597,8 -604,6 +603,7 @@@
%D%/packages/patches/id3lib-CVE-2007-4460.patch \
%D%/packages/patches/ilmbase-fix-tests.patch\
%D%/packages/patches/inkscape-drop-wait-for-targets.patch   \
-   %D%/packages/patches/irrlicht-mesa-10.patc

branch core-updates updated (bf62b8f -> dcaf708)

[Mark H. Weaver]

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

  from  bf62b8f   gnu: guile-lib: Update to 0.2.3.
  adds  b23ece1   gnu: linux-libre@4.1: Update to 4.1.34.
  adds  c8ed730   git: webkitgtk: Update to 2.14.1.
  adds  32d0456   gnu: python2-pytest-runner, python2-msgpack: Remove 
duplicate definitions.
  adds  de585a7   gnu: python-pytest-xdist: Remove python byte-code files 
from source.
  adds  b02f7a2   gnu: python-zope-testing: Strip byte-code and 
backup-files from source.
  adds  6a8f26a   gnu: python-pylockfile: Update home-page url.
  adds  190ba6c   gnu: python-keyring: Update home-page url.
  adds  7a8894e   gnu: python-pathlib: Update description.
  adds  635a7af   guix: python-build-system: Fix an outdated comment.
  adds  4193567   Revert "guix: python-build-system: Fix an outdated 
comment."
  adds  ce74e52   gnu: Add emacs-goto-chg.
  adds  2edbfbf   gnu: Add emacs-evil.
  adds  71d3ee1   gnu: Add emacs-nginx-mode.
  adds  4960468   gnu: Add gx-guvnor-lv2.
  adds  85ae347   gnu: Add gx-vbass-preamp-lv2.
  adds  cdc7a02   gnu: Add gx-overdriver-lv2.
  adds  4d95cd3   gnu: Add gx-tone-mender-lv2.
  adds  4d4bfdc   gnu: Add gx-push-pull-lv2.
  adds  3eb1a96   gnu: Add gx-suppa-tone-bender-lv2.
  adds  664f677   gnu: Add gx-saturator-lv2.
  adds  8941223   gnu: Add gx-hyperion-lv2.
  adds  32536f0   gnu: Add gx-voodoo-fuzz-lv2.
  adds  29f6322   gnu: Add gx-super-fuzz-lv2.
  adds  40bffdf   gnu: Add gx-vintage-fuzz-master-lv2.
  adds  631f817   gnu: Add gx-slow-gear-lv2.
  adds  d75e8f5   gnu: Add gx-switchless-wah-lv2.
  adds  a9f55bf   gnu: Add jack-keyboard.
  adds  34f9582   gnu: dbus: Replace with 1.10.12 [security fix].
  adds  0350a8b   gnu: mail: Add notifymuch.
  adds  76e8566   gnu: freeimage: Fix CVE-2016-5684.
  adds  4a2798e   gnu: freeimage: Use 'modify-phases' syntax.
  adds  b280e67   gnu: libraw: Update to 0.17.2 [fixes 
CVE-2015-{8366,8367}].
  adds  d0025d0   packages: 'package-grafts' applies grafts on replacement.
  adds  b013c33   grafts: 'graft-derivation' does now introduce grafts that 
shadow other grafts.
  adds  9d54b12   gnu: gx-saturator-lv2: Fix SSE detection.
  adds  b9ac372   gnu: gx-hyperion-lv2: Fix SSE detection.
  adds  2dedc16   gnu: gx-voodoo-fuzz-lv2: Fix SSE detection.
  adds  c6e45a9   gnu: gx-super-fuzz-lv2: Fix SSE detection.
  adds  3497537   gnu: gx-vintage-fuzz-master-lv2: Fix SSE detection.
  adds  759318f   gnu: gx-slow-gear-lv2: Fix SSE detection.
  adds  b74d79d   gnu: gx-switchless-wah-lv2: Fix SSE detection.
  adds  7bc2f3a   gnu: guitarix: Update to 0.35.2.
  adds  6f30a55   gnu: services sddm  Fix typo.
  adds  e1376e2   gnu: gd: Fix CVE-2016-8670.
  adds  2e36f7e   gnu: qt: Update to 5.6.2.
  adds  c2a3b23   gnu: abcde: Update to 2.7.2.
  adds  9bf160a   gnu: libgit2: Update to 0.24.2.
  adds  ebe3515   gnu: termite: Update to 12.
  adds  66bb5db   gnu: termite: Use 'modify-phases' syntax.
  adds  d0cddec   gnu: picocom: Update to 2.2.
  adds  43593f5   gnu: cereal: Update to 1.2.1.
  adds  608bf1d   gnu: jsoncpp: Update to 1.7.7.
  adds  5f01e1b   gnu: assimp: Update to 3.3.1.
  adds  783ae21   grafts: Remove unused variables and confusing monad use.
  adds  7f8fec0   graph: Add '%referrer-node-type'.
  adds  fcb9b93   gnu: dbus-1.10.12: Fix search paths.
  adds  f4a4b85   gnu: youtube-dl: Update to 2016-10-16.
  adds  dbc3c34   gnu: Add arm-none-eabi-gcc-6.
  adds  569f601   gnu: Add arm-none-eabi-toolchain variants.
  adds  b7afd01   gnu: Add python-whoosh.
  adds  caa0edb   gnu: python-pyasn1: Update to 0.1.9.
  adds  eb68d26   gnu: python-pyopenssl: Update to 16.1.0.
  adds  0580e38   gnu: python-werkzeug: Update to 0.11.11.
  adds  6c51412   gnu: python-dnspython: Update to 0.15.0.
  adds  f349d36   gnu: certbot, python-acme: Update to 0.9.3.
  adds  60da9fb   gnu: hdf4: Fix non-x86 architectures.
  adds  b37e1e6   import: utils: Remove dependency on (json) module.
  adds  f3e2221   gnu: Add fbida.
  adds  2f96872   gnu: httping: Update to 2.5.
  adds  4fb5f83   gnu: Add sslh.
  adds  cb0866c   gnu: Add geierlein.
  adds  b8004a7   gnu: bundler: Update to 1.13.5.
  adds  a8de0d1   gnu: ruby-json-pure: Fix tests.
  adds  dd04f56   gnu: node: Update to 6.8.0.
  adds  8a666bc   gnu: artanis: Remove implied $(DESTDIR) usage.
  adds  a6e25a5   gnu: sfml: Install pkgconfig files.
  adds  b8a35cc   gnu: extremetuxracer: Update to 0.7.3.
  adds  f90b2db   gnu: irrlicht: Update to 1.8.4.
  adds  89984be   gnu: Add r-rcas.
  adds  5093729   gnu: Add rcas-web.
  adds  0bd6975   gnu: Add xpad.
  adds  43f1d02   gnu: linux-libre@4.4: Update to 4.4.25.
  adds  cd829fe   gnu: linux-libre: Update to 4.8.2.

branch master updated (6ace9f8 -> a31ac11)

[Efraim Flashner]

efraim pushed a change to branch master
in repository guix.

  from  6ace9f8   gnu: diffoscope: Update to 61.
   new  b333d00   gnu: jasper: Update to 1.900.5.
   new  8ee0462   gnu: zimg: Update to 2.3.
   new  a31ac11   gnu: vapoursynth: Update to 34.

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:
 gnu/local.mk   |   13 -
 gnu/packages/image.scm |   28 +-
 gnu/packages/patches/jasper-CVE-2007-2721.patch|   20 -
 gnu/packages/patches/jasper-CVE-2008-3520.patch|  931 
 gnu/packages/patches/jasper-CVE-2008-3522.patch|   14 -
 .../jasper-CVE-2011-4516-and-CVE-2011-4517.patch   |   31 -
 gnu/packages/patches/jasper-CVE-2014-8137.patch|   64 --
 gnu/packages/patches/jasper-CVE-2014-8138.patch|   21 -
 gnu/packages/patches/jasper-CVE-2014-8157.patch|   19 -
 gnu/packages/patches/jasper-CVE-2014-8158.patch|  336 ---
 gnu/packages/patches/jasper-CVE-2014-9029.patch|   36 -
 gnu/packages/patches/jasper-CVE-2016-1577.patch|   19 -
 gnu/packages/patches/jasper-CVE-2016-1867.patch|   18 -
 gnu/packages/patches/jasper-CVE-2016-2089.patch|   90 --
 gnu/packages/patches/jasper-CVE-2016-2116.patch|   19 -
 gnu/packages/video.scm |4 +-
 16 files changed, 8 insertions(+), 1655 deletions(-)
 delete mode 100644 gnu/packages/patches/jasper-CVE-2007-2721.patch
 delete mode 100644 gnu/packages/patches/jasper-CVE-2008-3520.patch
 delete mode 100644 gnu/packages/patches/jasper-CVE-2008-3522.patch
 delete mode 100644 
gnu/packages/patches/jasper-CVE-2011-4516-and-CVE-2011-4517.patch
 delete mode 100644 gnu/packages/patches/jasper-CVE-2014-8137.patch
 delete mode 100644 gnu/packages/patches/jasper-CVE-2014-8138.patch
 delete mode 100644 gnu/packages/patches/jasper-CVE-2014-8157.patch
 delete mode 100644 gnu/packages/patches/jasper-CVE-2014-8158.patch
 delete mode 100644 gnu/packages/patches/jasper-CVE-2014-9029.patch
 delete mode 100644 gnu/packages/patches/jasper-CVE-2016-1577.patch
 delete mode 100644 gnu/packages/patches/jasper-CVE-2016-1867.patch
 delete mode 100644 gnu/packages/patches/jasper-CVE-2016-2089.patch
 delete mode 100644 gnu/packages/patches/jasper-CVE-2016-2116.patch

01/03: gnu: jasper: Update to 1.900.5.

[Efraim Flashner]

efraim pushed a commit to branch master
in repository guix.

commit b333d00c3566a8a6b058a35426da96200ebf2c6d
Author: Efraim Flashner 
Date:   Mon Oct 17 23:47:14 2016 +0300

gnu: jasper: Update to 1.900.5.

* gnu/packages/image.scm (jasper): Update to 1.900.5.
[source]: Remove patches.
[native-inputs]: Remove unzip.
* gnu/packages/patches/jasper-CVE-2007-2721.patch,
gnu/packages/patches/jasper-CVE-2008-3520.patch,
gnu/packages/patches/jasper-CVE-2008-3522.patch,
gnu/packages/patches/jasper-CVE-2011-4516-and-CVE-2011-4517.patch,
gnu/packages/patches/jasper-CVE-2014-8137.patch,
gnu/packages/patches/jasper-CVE-2014-8138.patch,
gnu/packages/patches/jasper-CVE-2014-8157.patch,
gnu/packages/patches/jasper-CVE-2014-8158.patch,
gnu/packages/patches/jasper-CVE-2014-9029.patch,
gnu/packages/patches/jasper-CVE-2016-1577.patch,
gnu/packages/patches/jasper-CVE-2016-1867.patch,
gnu/packages/patches/jasper-CVE-2016-2089.patch,
gnu/packages/patches/jasper-CVE-2016-2116.patch: Delete files.
* gnu/local.mk (dist_patch_DATA): Remove them.
---
 gnu/local.mk   |   13 -
 gnu/packages/image.scm |   22 +-
 gnu/packages/patches/jasper-CVE-2007-2721.patch|   20 -
 gnu/packages/patches/jasper-CVE-2008-3520.patch|  931 
 gnu/packages/patches/jasper-CVE-2008-3522.patch|   14 -
 .../jasper-CVE-2011-4516-and-CVE-2011-4517.patch   |   31 -
 gnu/packages/patches/jasper-CVE-2014-8137.patch|   64 --
 gnu/packages/patches/jasper-CVE-2014-8138.patch|   21 -
 gnu/packages/patches/jasper-CVE-2014-8157.patch|   19 -
 gnu/packages/patches/jasper-CVE-2014-8158.patch|  336 ---
 gnu/packages/patches/jasper-CVE-2014-9029.patch|   36 -
 gnu/packages/patches/jasper-CVE-2016-1577.patch|   19 -
 gnu/packages/patches/jasper-CVE-2016-1867.patch|   18 -
 gnu/packages/patches/jasper-CVE-2016-2089.patch|   90 --
 gnu/packages/patches/jasper-CVE-2016-2116.patch|   19 -
 15 files changed, 3 insertions(+), 1650 deletions(-)

diff --git a/gnu/local.mk b/gnu/local.mk
index c80b213..5226b49 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -605,19 +605,6 @@ dist_patch_DATA =  
\
   %D%/packages/patches/ilmbase-fix-tests.patch \
   %D%/packages/patches/inkscape-drop-wait-for-targets.patch\
   %D%/packages/patches/jansson-CVE-2016-4425.patch \
-  %D%/packages/patches/jasper-CVE-2007-2721.patch  \
-  %D%/packages/patches/jasper-CVE-2008-3520.patch  \
-  %D%/packages/patches/jasper-CVE-2008-3522.patch  \
-  %D%/packages/patches/jasper-CVE-2011-4516-and-CVE-2011-4517.patch \
-  %D%/packages/patches/jasper-CVE-2014-8137.patch  \
-  %D%/packages/patches/jasper-CVE-2014-8138.patch  \
-  %D%/packages/patches/jasper-CVE-2014-8157.patch  \
-  %D%/packages/patches/jasper-CVE-2014-8158.patch  \
-  %D%/packages/patches/jasper-CVE-2014-9029.patch  \
-  %D%/packages/patches/jasper-CVE-2016-1577.patch  \
-  %D%/packages/patches/jasper-CVE-2016-1867.patch  \
-  %D%/packages/patches/jasper-CVE-2016-2089.patch  \
-  %D%/packages/patches/jasper-CVE-2016-2116.patch  \
   %D%/packages/patches/jbig2dec-ignore-testtest.patch  \
   %D%/packages/patches/jq-CVE-2015-8863.patch  \
   %D%/packages/patches/khmer-use-libraries.patch\
diff --git a/gnu/packages/image.scm b/gnu/packages/image.scm
index 7455bb8..ed14e83 100644
--- a/gnu/packages/image.scm
+++ b/gnu/packages/image.scm
@@ -781,31 +781,15 @@ convert, manipulate, filter and display a wide variety of 
image formats.")
 (define-public jasper
   (package
 (name "jasper")
-(version "1.900.1")
+(version "1.900.5")
 (source (origin
   (method url-fetch)
   (uri (string-append "https://www.ece.uvic.ca/~frodo/jasper";
-  "/software/jasper-" version ".zip"))
+  "/software/jasper-" version ".tar.gz"))
   (sha256
(base32
-"154l7zk7yh3v8l2l6zm5s2alvd2fzkp6c9i18iajfbna5af5m43b"))
-  (patches (search-patches
-"jasper-CVE-2007-2721.patch"
-"jasper-CVE-2008-3520.patch"
-"jasper-CVE-2008-3522.patch"
-"jasper-CVE-2011-4516-and-CVE-2011-4517.patch"
-"jasper-CVE-2014-8137.patch"
-"jasper-CVE-2014-8138.patch"
-"jasper-CVE-2014-8157.patch"
-"jasper-CVE-2014-8158.patch"
-"jasper-CVE-2014-9029.patch"
-"jasper-CVE-2016-1577.patch"
-"jasper-CVE-2016-1867.patch"
-"jas

02/03: gnu: zimg: Update to 2.3.

[Efraim Flashner]

efraim pushed a commit to branch master
in repository guix.

commit 8ee04627d8f88cf446ae503c80aef6907d834636
Author: Efraim Flashner 
Date:   Tue Oct 18 00:07:20 2016 +0300

gnu: zimg: Update to 2.3.

* gnu/packages/image.scm (zimg): Update to 2.3.
---
 gnu/packages/image.scm |6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/image.scm b/gnu/packages/image.scm
index ed14e83..4b064bb 100644
--- a/gnu/packages/image.scm
+++ b/gnu/packages/image.scm
@@ -800,7 +800,7 @@ ISO/IEC 15444-1).")
 (define-public zimg
   (package
 (name "zimg")
-(version "2.2.1")
+(version "2.3")
 (source
   (origin
 (method url-fetch)
@@ -809,7 +809,7 @@ ISO/IEC 15444-1).")
 (file-name (string-append name "-" version ".tar.gz"))
 (sha256
  (base32
-  "0m2gjpkb0dlg4j77nr41z284zvyfq9qg3ahsv8p1xy8jfr7h1hqa"
+  "1yh6kkq8596a9cxcmcxzqvwbwmxwqapwsq31xpccznw6z62j75h9"
 (build-system gnu-build-system)
 (native-inputs
  `(("autoconf" ,autoconf)
@@ -827,7 +827,7 @@ of scaling, colorspace conversion, and depth conversion.  A 
simple API enables
 conversion between any supported formats to operate with minimal knowledge from
 the programmer.")
 (home-page "https://github.com/sekrit-twc/zimg";)
-;; test/extra/ contains musl-libm, 
+;; test/extra/ contains musl-libm,
 ;; which is MIT/expat licensed, but only used for tests
 (license (license:fsf-free "file://COPYING" ;WTFPL version 2
 

03/03: gnu: vapoursynth: Update to 34.

[Efraim Flashner]

efraim pushed a commit to branch master
in repository guix.

commit a31ac113856f392118123b233c07b95f1c65334b
Author: Efraim Flashner 
Date:   Tue Oct 18 00:08:09 2016 +0300

gnu: vapoursynth: Update to 34.

* gnu/packages/video.scm (vapoursynth): Update to 34.
---
 gnu/packages/video.scm |4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/video.scm b/gnu/packages/video.scm
index 3ddf858..f56b1ca 100644
--- a/gnu/packages/video.scm
+++ b/gnu/packages/video.scm
@@ -1252,7 +1252,7 @@ capabilities.")
 (define-public vapoursynth
   (package
 (name "vapoursynth")
-(version "33.1")
+(version "34")
 (source (origin
   (method url-fetch)
   (uri (string-append
@@ -1261,7 +1261,7 @@ capabilities.")
   (file-name (string-append name "-" version))
   (sha256
(base32
-"1504jaw4yqdlyls0bz9f90rvqq7cy1jvmrnhdvwnmdfbpikqwi4c"
+"0rfldphg4gy3sdfffi5yzklqz93vsj2j6nny8snjbavnf161blyi"
 (build-system gnu-build-system)
 (native-inputs
  `(("autoconf" ,autoconf)

branch master updated (a31ac11 -> 00bfd49)

[Efraim Flashner]

efraim pushed a change to branch master
in repository guix.

  from  a31ac11   gnu: vapoursynth: Update to 34.
   new  00bfd49   gnu: tor: Update to 0.2.8.9.

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

01/01: gnu: tor: Update to 0.2.8.9.

[Efraim Flashner]

efraim pushed a commit to branch master
in repository guix.

commit 00bfd498f93570cf0ce7b6de17fb3155306b8950
Author: Efraim Flashner 
Date:   Tue Oct 18 00:25:30 2016 +0300

gnu: tor: Update to 0.2.8.9.

* gnu/packages/tor.scm (tor): Update to 0.2.8.9.
---
 gnu/packages/tor.scm |4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/tor.scm b/gnu/packages/tor.scm
index 42d882e..0812b57 100644
--- a/gnu/packages/tor.scm
+++ b/gnu/packages/tor.scm
@@ -40,14 +40,14 @@
 (define-public tor
   (package
 (name "tor")
-(version "0.2.8.8")
+(version "0.2.8.9")
 (source (origin
  (method url-fetch)
  (uri (string-append "https://dist.torproject.org/tor-";
  version ".tar.gz"))
  (sha256
   (base32
-   "1pp3h0a1cl25fv04b3j6wp8aw1sfpbd2lmag397dpp2k2b305bxi"
+   "05jkvhbgyq81fcmk1xpl3yw97ljj5sg9pngl27zlmgl7p0xjfp1z"
 (build-system gnu-build-system)
 (native-inputs
  `(("python" ,python-2)))  ; for tests

03/05: guix build: Add '--with-graft'.

[Ludovic Court�s]

civodul pushed a commit to branch master
in repository guix.

commit 645b9df858683dc05ffa04c9eb2fdc45ccef4a65
Author: Ludovic Courtès 
Date:   Mon Oct 17 23:40:03 2016 +0200

guix build: Add '--with-graft'.

* guix/scripts/build.scm (transform-package-inputs/graft): New procedure.
(%transformations): Add 'with-graft'.
(%transformation-options): Likewise.
(show-transformation-options-help): Document it.
* tests/scripts-build.scm ("options->transformation, with-graft"): New
test.
* doc/guix.texi (Package Transformation Options): Document it.
---
 doc/guix.texi   |   24 
 guix/scripts/build.scm  |   29 ++---
 tests/scripts-build.scm |   19 +++
 3 files changed, 69 insertions(+), 3 deletions(-)

diff --git a/doc/guix.texi b/doc/guix.texi
index 47fc199..0c5d641 100644
--- a/doc/guix.texi
+++ b/doc/guix.texi
@@ -4513,6 +4513,30 @@ This is a recursive, deep replacement.  So in this 
example, both
 
 This is implemented using the @code{package-input-rewriting} Scheme
 procedure (@pxref{Defining Packages, @code{package-input-rewriting}}).
+
+@item --with-graft=@var{package}=@var{replacement}
+This is similar to @code{--with-input} but with an important difference:
+instead of rebuilding all the dependency chain, @var{replacement} is
+built and then @dfn{grafted} onto the binaries that were initially
+referring to @var{package}.  @xref{Security Updates}, for more
+information on grafts.
+
+For example, the command below grafts version 3.5.4 of GnuTLS onto Wget
+and all its dependencies, replacing references to the version of GnuTLS
+they currently refer to:
+
+@example
+guix build --with-graft=gnutls=gnutls@@3.5.4 wget
+@end example
+
+This has the advantage of being much faster than rebuilding everything.
+But there is a caveat: it works if and only if @var{package} and
+@var{replacement} are strictly compatible---for example, if they provide
+a library, the application binary interface (ABI) of those libraries
+must be compatible.  If @var{replacement} is somehow incompatible with
+@var{package}, then the resulting package may be unusable.  Use with
+care!
+
 @end table
 
 @node Additional Build Options
diff --git a/guix/scripts/build.scm b/guix/scripts/build.scm
index bd97d56..8c2c490 100644
--- a/guix/scripts/build.scm
+++ b/guix/scripts/build.scm
@@ -209,13 +209,31 @@ called \"guile\" must be replaced with a dependency on a 
version 2.1 of
   (rewrite obj)
   obj
 
+(define (transform-package-inputs/graft replacement-specs)
+  "Return a procedure that, when passed a package, replaces its direct
+dependencies according to REPLACEMENT-SPECS.  REPLACEMENT-SPECS is a list of
+strings like \"gnutls=gnutls@3.5.4\" meaning that packages are built using the
+current 'gnutls' package, after which version 3.5.4 is grafted onto them."
+  (define (replacement-pair old new)
+(cons old
+  (package (inherit old) (replacement new
+
+  (let* ((replacements (evaluate-replacement-specs replacement-specs
+   replacement-pair))
+ (rewrite  (package-input-rewriting replacements)))
+(lambda (store obj)
+  (if (package? obj)
+  (rewrite obj)
+  obj
+
 (define %transformations
   ;; Transformations that can be applied to things to build.  The car is the
   ;; key used in the option alist, and the cdr is the transformation
   ;; procedure; it is called with two arguments: the store, and a list of
   ;; things to build.
   `((with-source . ,transform-package-source)
-(with-input  . ,transform-package-inputs)))
+(with-input  . ,transform-package-inputs)
+(with-graft  . ,transform-package-inputs/graft)))
 
 (define %transformation-options
   ;; The command-line interface to the above transformations.
@@ -227,7 +245,9 @@ called \"guile\" must be replaced with a dependency on a 
version 2.1 of
 (list (option '("with-source") #t #f
   (parser 'with-source))
   (option '("with-input") #t #f
-  (parser 'with-input)
+  (parser 'with-input))
+  (option '("with-graft") #t #f
+  (parser 'with-graft)
 
 (define (show-transformation-options-help)
   (display (_ "
@@ -235,7 +255,10 @@ called \"guile\" must be replaced with a dependency on a 
version 2.1 of
  use SOURCE when building the corresponding package"))
   (display (_ "
   --with-input=PACKAGE=REPLACEMENT
- replace dependency PACKAGE by REPLACEMENT")))
+ replace dependency PACKAGE by REPLACEMENT"))
+  (display (_ "
+  --with-graft=PACKAGE=REPLACEMENT
+ graft REPLACEMENT on packages that refer to 
PACKAGE")))
 
 
 (define (options->transformation opts)
diff --git a/tests/scripts-build.scm b/tests/scripts-build.scm
index e48c8da..e261090 100644
--- a/tests/script

02/05: guix build: Factorize transformation option parsing.

[Ludovic Court�s]

civodul pushed a commit to branch master
in repository guix.

commit 31c2fd1e01d5f95cd1fb873c44f5fa4ac1164e69
Author: Ludovic Courtès 
Date:   Mon Oct 17 22:51:38 2016 +0200

guix build: Factorize transformation option parsing.

* guix/scripts/build.scm (%transformation-options): Introduce 'parser'
procedure and use it.
---
 guix/scripts/build.scm |   19 +--
 1 file changed, 9 insertions(+), 10 deletions(-)

diff --git a/guix/scripts/build.scm b/guix/scripts/build.scm
index 6449931..bd97d56 100644
--- a/guix/scripts/build.scm
+++ b/guix/scripts/build.scm
@@ -219,16 +219,15 @@ called \"guile\" must be replaced with a dependency on a 
version 2.1 of
 
 (define %transformation-options
   ;; The command-line interface to the above transformations.
-  (list (option '("with-source") #t #f
-(lambda (opt name arg result . rest)
-  (apply values
- (cons (alist-cons 'with-source arg result)
-   rest
-(option '("with-input") #t #f
-(lambda (opt name arg result . rest)
-  (apply values
- (cons (alist-cons 'with-input arg result)
-   rest))
+  (let ((parser (lambda (symbol)
+  (lambda (opt name arg result . rest)
+(apply values
+   (alist-cons symbol arg result)
+   rest)
+(list (option '("with-source") #t #f
+  (parser 'with-source))
+  (option '("with-input") #t #f
+  (parser 'with-input)
 
 (define (show-transformation-options-help)
   (display (_ "

01/05: guix build: Extract '--with-input' replacement spec parsing.

[Ludovic Court�s]

civodul pushed a commit to branch master
in repository guix.

commit 5cf01aa53f67a226198cba63fd952a9c9e5aa842
Author: Ludovic Courtès 
Date:   Mon Oct 17 22:43:49 2016 +0200

guix build: Extract '--with-input' replacement spec parsing.

* guix/scripts/build.scm (evaluate-replacement-specs): New procedure.
(transform-package-inputs)[not-equal]: Remove.
[replacements]: Define in terms of 'evaluate-replacement-specs'.
---
 guix/scripts/build.scm |   40 ++--
 1 file changed, 22 insertions(+), 18 deletions(-)

diff --git a/guix/scripts/build.scm b/guix/scripts/build.scm
index b64138e..6449931 100644
--- a/guix/scripts/build.scm
+++ b/guix/scripts/build.scm
@@ -179,27 +179,31 @@ matching URIs given in SOURCES."
 (_
  obj)
 
-(define (transform-package-inputs replacement-specs)
-  "Return a procedure that, when passed a package, replaces its direct
-dependencies according to REPLACEMENT-SPECS.  REPLACEMENT-SPECS is a list of
-strings like \"guile=guile@2.1\" meaning that, any direct dependency on a
-package called \"guile\" must be replaced with a dependency on a version 2.1
-of \"guile\"."
+(define (evaluate-replacement-specs specs proc)
+  "Parse SPECS, a list of strings like \"guile=guile@2.1\", and invoke PROC on
+each package pair specified by SPECS.  Return the resulting list.  Raise an
+error if an element of SPECS uses invalid syntax, or if a package it refers to
+could not be found."
   (define not-equal
 (char-set-complement (char-set #\=)))
 
-  (define replacements
-;; List of name/package pairs.
-(map (lambda (spec)
-   (match (string-tokenize spec not-equal)
- ((old new)
-  (cons (specification->package old)
-(specification->package new)))
- (x
-  (leave (_ "invalid replacement specification: ~s~%") spec
- replacement-specs))
-
-  (let ((rewrite (package-input-rewriting replacements)))
+  (map (lambda (spec)
+ (match (string-tokenize spec not-equal)
+   ((old new)
+(proc (specification->package old)
+  (specification->package new)))
+   (x
+(leave (_ "invalid replacement specification: ~s~%") spec
+   specs))
+
+(define (transform-package-inputs replacement-specs)
+  "Return a procedure that, when passed a package, replaces its direct
+dependencies according to REPLACEMENT-SPECS.  REPLACEMENT-SPECS is a list of
+strings like \"guile=guile@2.1\" meaning that, any dependency on a package
+called \"guile\" must be replaced with a dependency on a version 2.1 of
+\"guile\"."
+  (let* ((replacements (evaluate-replacement-specs replacement-specs cons))
+ (rewrite  (package-input-rewriting replacements)))
 (lambda (store obj)
   (if (package? obj)
   (rewrite obj)

04/05: grafts: Apply the right grafts in the presence of multiple outputs.

[Ludovic Court�s]

civodul pushed a commit to branch master
in repository guix.

commit 3d47aa81ba4c19b45ce9a9ff0ece0252777ea8ed
Author: Ludovic Courtès 
Date:   Mon Oct 17 23:43:33 2016 +0200

grafts: Apply the right grafts in the presence of multiple outputs.

Fixes .

* guix/grafts.scm (cumulative-grafts): Add grafts for all the outputs of
DRV.
* tests/grafts.scm ("graft-derivation, replaced derivation has multiple
outputs"): New test.
---
 guix/grafts.scm  |   15 +--
 tests/grafts.scm |   48 
 2 files changed, 61 insertions(+), 2 deletions(-)

diff --git a/guix/grafts.scm b/guix/grafts.scm
index 80ae27e..dda7c1d 100644
--- a/guix/grafts.scm
+++ b/guix/grafts.scm
@@ -280,8 +280,19 @@ derivations to the corresponding set of grafts."
  (let* ((new(graft-derivation/shallow store drv applicable
   #:guile guile
   #:system system))
-(grafts (cons (graft (origin drv) (replacement new))
-  grafts)))
+
+;; Replace references to any of the outputs of DRV,
+;; even if that's more than needed.  This is so that
+;; the result refers only to the outputs of NEW and
+;; not to those of DRV.
+(grafts (append (map (lambda (output)
+   (graft
+ (origin drv)
+ (origin-output output)
+ (replacement new)
+ (replacement-output output)))
+ (derivation-output-names drv))
+grafts)))
(return/cache cache grafts
 
 (define* (graft-derivation store drv grafts
diff --git a/tests/grafts.scm b/tests/grafts.scm
index 4eff06b..6454a03 100644
--- a/tests/grafts.scm
+++ b/tests/grafts.scm
@@ -201,6 +201,54 @@
(and (string=? (readlink one) repl)
 (string=? (readlink two) one))
 
+(test-assert "graft-derivation, replaced derivation has multiple outputs"
+  ;; Here we have a replacement just for output "one" of P1 and not for the
+  ;; other output.  Make sure the graft for P1:one correctly applies to the
+  ;; dependents of P1.  See .
+  (let* ((p1  (build-expression->derivation
+   %store "p1"
+   `(let ((one (assoc-ref %outputs "one"))
+  (two (assoc-ref %outputs "two")))
+  (mkdir one)
+  (mkdir two))
+   #:outputs '("one" "two")))
+ (p1r (build-expression->derivation
+   %store "P1"
+   `(let ((other (assoc-ref %outputs "ONE")))
+  (mkdir other)
+  (call-with-output-file (string-append other "/replacement")
+(const #t)))
+   #:outputs '("ONE")))
+ (p2  (build-expression->derivation
+   %store "p2"
+   `(let ((out (assoc-ref %outputs "aaa")))
+  (mkdir (assoc-ref %outputs "zzz"))
+  (mkdir out) (chdir out)
+  (symlink (assoc-ref %build-inputs "p1:one") "one")
+  (symlink (assoc-ref %build-inputs "p1:two") "two"))
+   #:outputs '("aaa" "zzz")
+   #:inputs `(("p1:one" ,p1 "one")
+  ("p1:two" ,p1 "two"
+ (p3  (build-expression->derivation
+   %store "p3"
+   `(symlink (assoc-ref %build-inputs "p2:aaa")
+ (assoc-ref %outputs "out"))
+   #:inputs `(("p2:aaa" ,p2 "aaa")
+  ("p2:zzz" ,p2 "zzz"
+ (p1g (graft
+(origin p1)
+(origin-output "one")
+(replacement p1r)
+(replacement-output "ONE")))
+ (p3d (graft-derivation %store p3 (list p1g
+(and (build-derivations %store (list p3d))
+ (let ((out (derivation->output-path (pk 'p2d p3d
+   (and (not (string=? (readlink out)
+   (derivation->output-path p2 "aaa")))
+(string=? (derivation->output-path p1 "two")
+  (readlink (string-append out "/two")))
+(file-exists? (string-append out "/one/replacement")))
+
 (test-assert "graft-derivation, renaming" ;
   (let* ((build `(begin
(use-modules (guix build utils))

branch master updated (00bfd49 -> fb3af75)

[Ludovic Court�s]

civodul pushed a change to branch master
in repository guix.

  from  00bfd49   gnu: tor: Update to 0.2.8.9.
   new  5cf01aa   guix build: Extract '--with-input' replacement spec 
parsing.
   new  31c2fd1   guix build: Factorize transformation option parsing.
   new  645b9df   guix build: Add '--with-graft'.
   new  3d47aa8   grafts: Apply the right grafts in the presence of 
multiple outputs.
   new  fb3af75   grafts: Remove unnecessary 'umask' call.

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:
 doc/guix.texi   |   24 ++
 guix/build/graft.scm|5 ---
 guix/grafts.scm |   15 +++--
 guix/scripts/build.scm  |   84 +++
 tests/grafts.scm|   48 +++
 tests/scripts-build.scm |   19 +++
 6 files changed, 159 insertions(+), 36 deletions(-)

05/05: grafts: Remove unnecessary 'umask' call.

[Ludovic Court�s]

civodul pushed a commit to branch master
in repository guix.

commit fb3af759ee284fb1cb14c5514ed0432d9cbbfdbf
Author: Ludovic Courtès 
Date:   Mon Oct 17 23:55:28 2016 +0200

grafts: Remove unnecessary 'umask' call.

This is a followup to d72267863382041b84a9712eea354882be72ef55.

* guix/build/graft.scm (rewrite-directory): Remove 'umask' call.
---
 guix/build/graft.scm |5 -
 1 file changed, 5 deletions(-)

diff --git a/guix/build/graft.scm b/guix/build/graft.scm
index 7025b72..16df169 100644
--- a/guix/build/graft.scm
+++ b/guix/build/graft.scm
@@ -307,11 +307,6 @@ file name pairs."
 (else
  (error "unsupported file type" stat)
 
-  ;; XXX: Work around occasional "suspicious ownership or permission" daemon
-  ;; errors that arise when we create the top-level /gnu/store/… directory as
-  ;; #o777.
-  (umask #o022)
-
   ;; Use 'exit-on-exception' to force an exit upon I/O errors, given that
   ;; 'n-par-for-each' silently swallows exceptions.
   ;; See .

01/01: gnu: dbus: Fix bad 'origin' form in dbus-1.10.12.

[Mark H. Weaver]

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

commit c9a71c6fdab6914dd648b76c349c3af9018cad35
Author: Mark H Weaver 
Date:   Mon Oct 17 21:04:57 2016 -0400

gnu: dbus: Fix bad 'origin' form in dbus-1.10.12.

This is a followup to commit dcaf70897a0bad38a4638a2905aaa3c46b1f1402.

* gnu/packages/glib.scm (dbus-1.10.12)[source]: Remove unneeded 'method'
field, so that 'inherit' comes first.
---
 gnu/packages/glib.scm |1 -
 1 file changed, 1 deletion(-)

diff --git a/gnu/packages/glib.scm b/gnu/packages/glib.scm
index 9a1459a..2b57f85 100644
--- a/gnu/packages/glib.scm
+++ b/gnu/packages/glib.scm
@@ -139,7 +139,6 @@ shared NFS home directories.")
 (source
   (let ((version "1.10.12"))
 (origin
-  (method url-fetch)
   (inherit (package-source dbus))
   (uri (string-append
 "https://dbus.freedesktop.org/releases/dbus/dbus-";

branch core-updates updated (dcaf708 -> c9a71c6)

[Mark H. Weaver]

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

  from  dcaf708   Merge branch 'master' into core-updates
   new  c9a71c6   gnu: dbus: Fix bad 'origin' form in dbus-1.10.12.

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/glib.scm |1 -
 1 file changed, 1 deletion(-)

branch master updated (fb3af75 -> 1dc30f9)

[Efraim Flashner]

efraim pushed a change to branch master
in repository guix.

  from  fb3af75   grafts: Remove unnecessary 'umask' call.
   new  1dc30f9   gnu: enlightenment: Update to 0.21.3.

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

01/01: gnu: enlightenment: Update to 0.21.3.

[Efraim Flashner]

efraim pushed a commit to branch master
in repository guix.

commit 1dc30f92320c5e1b528a7eec2b0a4ce529f70c56
Author: Efraim Flashner 
Date:   Tue Oct 18 08:57:23 2016 +0300

gnu: enlightenment: Update to 0.21.3.

* gnu/packages/enlightenment.scm (enlightenment): Update to 0.21.3.
---
 gnu/packages/enlightenment.scm |4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/enlightenment.scm b/gnu/packages/enlightenment.scm
index e8bd387..99c5b39 100644
--- a/gnu/packages/enlightenment.scm
+++ b/gnu/packages/enlightenment.scm
@@ -196,7 +196,7 @@ Libraries with some extra bells and whistles.")
 (define-public enlightenment
   (package
 (name "enlightenment")
-(version "0.21.2")
+(version "0.21.3")
 (source (origin
   (method url-fetch)
   (uri
@@ -204,7 +204,7 @@ Libraries with some extra bells and whistles.")
   name "/" name "-" version ".tar.xz"))
   (sha256
(base32
-"0fi5dxrprnvhnn2y51gnfpsjj44snriqi20k20a73vhaqxfn8xx8"
+"1ljzcq775njhbcaj8vdnypf2rgc6yqqdwfkf7c22603qvv9if1dr"
 (build-system gnu-build-system)
 (arguments
  `(#:configure-flags '("--enable-mount-eeze")))