01/01: gnu: ruby-minitar: Update to 0.5.4-1.e25205ec.

[Ben Woodcroft]

benwoodcroft pushed a commit to branch master
in repository guix.

commit bfaf8efd74e88d99f743845357e3f1ff191e23c2
Author: Ben Woodcroft 
Date:   Thu Jan 26 08:11:17 2017 +1000

gnu: ruby-minitar: Update to 0.5.4-1.e25205ec.

Fixes the security-related issue reported at
http://seclists.org/oss-sec/2017/q1/178.

* gnu/packages/ruby.scm (ruby-minitar): Update to 0.5.4-1.e25205ec.
[source]: Use GitHub URL.
---
 gnu/packages/ruby.scm |   42 --
 1 file changed, 24 insertions(+), 18 deletions(-)

diff --git a/gnu/packages/ruby.scm b/gnu/packages/ruby.scm
index 0f1ecd2..819e8e5 100644
--- a/gnu/packages/ruby.scm
+++ b/gnu/packages/ruby.scm
@@ -1859,25 +1859,31 @@ generation of complex SQL queries and is compatible 
with various RDBMSes.")
 (license license:expat)))
 
 (define-public ruby-minitar
-  (package
-(name "ruby-minitar")
-(version "0.5.4")
-(source
- (origin
-   (method url-fetch)
-   (uri (rubygems-uri "minitar" version))
-   (sha256
-(base32
- "1vpdjfmdq1yc4i620frfp9af02ia435dnpj8ybsd7dc3rypkvbka"
-(build-system ruby-build-system)
-(arguments
- '(#:tests? #f)) ; missing a gemspec
-(synopsis "Ruby library and utility for handling tar archives")
-(description
- "Archive::Tar::Minitar is a pure-Ruby library and command-line utility
+  ;; We package from the GitHub source to fix the security issue reported at
+  ;; https://github.com/halostatue/minitar/issues/16.
+  (let ((commit "e25205ecbb6277ae8a3df1e6a306d7ed4458b6e4"))
+(package
+  (name "ruby-minitar")
+  (version (string-append "0.5.4-1." (string-take commit 8)))
+  (source
+   (origin
+ (method git-fetch)
+ (uri (git-reference
+   (url "https://github.com/halostatue/minitar.git";)
+   (commit commit)))
+ (file-name (string-append name "-" version "-checkout"))
+ (sha256
+  (base32
+   "1iywfx07jgjqcmixzkxk9zdwfmij1fyg1z2jlwzj15cj7s99qlfv"
+  (build-system ruby-build-system)
+  (arguments
+   '(#:tests? #f)) ; missing a gemspec
+  (synopsis "Ruby library and utility for handling tar archives")
+  (description
+   "Archive::Tar::Minitar is a pure-Ruby library and command-line utility
 that provides the ability to deal with POSIX tar archive files.")
-(home-page "http://www.github.com/atoulme/minitar";)
-(license (list license:gpl2+ license:ruby
+  (home-page "http://www.github.com/atoulme/minitar";)
+  (license (list license:gpl2+ license:ruby)
 
 (define-public ruby-mini-portile
   (package

01/01: gnu: r-ggplot2: Add r-svglite to propagated-inputs.

[Ben Woodcroft]

benwoodcroft pushed a commit to branch master
in repository guix.

commit e4b6c565beef27a1ce2203a9bc119e84a126e5e0
Author: Ben Woodcroft 
Date:   Mon Jan 23 21:23:33 2017 +1000

gnu: r-ggplot2: Add r-svglite to propagated-inputs.

* gnu/packages/statistics.scm (r-ggplot2)[propagated-inputs]: Add
r-svglite.
---
 gnu/packages/statistics.scm |3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index f27cb57..596c2ba 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -727,7 +727,8 @@ legends.")
("r-lazyeval" ,r-lazyeval)
("r-tibble" ,r-tibble)
("r-reshape2" ,r-reshape2)
-   ("r-scales" ,r-scales)))
+   ("r-scales" ,r-scales)
+   ("r-svglite" ,r-svglite))) ; Needed for 'ggsave'
 (home-page "http://ggplot2.org";)
 (synopsis "An implementation of the grammar of graphics")
 (description

branch master updated (843f255 -> e4b6c56)

[Ben Woodcroft]

benwoodcroft pushed a change to branch master
in repository guix.

  from  843f255   gnu: bundler: Update to 1.14.2.
   new  e4b6c56   gnu: r-ggplot2: Add r-svglite to propagated-inputs.

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/statistics.scm |3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

branch master updated (4e58e9d -> 843f255)

[Ben Woodcroft]

benwoodcroft pushed a change to branch master
in repository guix.

  from  4e58e9d   gnu: Add libtorrent-rasterbar.
   new  843f255   gnu: bundler: Update to 1.14.2.

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

01/01: gnu: bundler: Update to 1.14.2.

[Ben Woodcroft]

benwoodcroft pushed a commit to branch master
in repository guix.

commit 843f25538840bd21e4db11f452332176068060ba
Author: Ben Woodcroft 
Date:   Mon Jan 23 20:49:00 2017 +1000

gnu: bundler: Update to 1.14.2.

* gnu/packages/ruby.scm (bundler): Update to 1.14.2.
---
 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 fb89238..0f1ecd2 100644
--- a/gnu/packages/ruby.scm
+++ b/gnu/packages/ruby.scm
@@ -426,13 +426,13 @@ expectations and mocks frameworks.")
 (define-public bundler
   (package
 (name "bundler")
-(version "1.13.6")
+(version "1.14.2")
 (source (origin
   (method url-fetch)
   (uri (rubygems-uri "bundler" version))
   (sha256
(base32
-"1xyhy9cn8w9passp64p6hb3df2fpiqbds6rj7xha1335xpgj5zgs"
+"1sfcmqmimssjmh4gjq6ls6a33l2hc353hb13g628kjh15qmddar7"
 (build-system ruby-build-system)
 (arguments
  '(#:tests? #f)) ; avoid dependency cycles

01/02: gnu: diamond: Update to 0.8.34.

[Ben Woodcroft]

benwoodcroft pushed a commit to branch master
in repository guix.

commit cda0f9a4a91e69c0d3468138ba2bf16f12dd471e
Author: Ben Woodcroft 
Date:   Sat Jan 21 17:28:11 2017 +1000

gnu: diamond: Update to 0.8.34.

* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.34.
---
 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 64c40c7..1209eaf 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -2047,7 +2047,7 @@ identify enrichments with functional annotations of the 
genome.")
 (define-public diamond
   (package
 (name "diamond")
-(version "0.8.31")
+(version "0.8.34")
 (source (origin
   (method url-fetch)
   (uri (string-append
@@ -2056,7 +2056,7 @@ identify enrichments with functional annotations of the 
genome.")
   (file-name (string-append name "-" version ".tar.gz"))
   (sha256
(base32
-"0nh79f4rpgq8vmlga743r7vd0z0ik6spy34f7vfq0v9lcmvfr7xq"
+"0jvr34g346gbz7z1zb9bs0vplivm9p4cxk0lbzklvdpa7g236p39"
 (build-system cmake-build-system)
 (arguments
  '(#:tests? #f ; no "check" target

branch master updated (5aa0932 -> c0dee46)

[Ben Woodcroft]

benwoodcroft pushed a change to branch master
in repository guix.

  from  5aa0932   gnu: linux-libre: Update to 4.9.5.
   new  cda0f9a   gnu: diamond: Update to 0.8.34.
   new  c0dee46   gnu: r-vegan: Update to 2.4-2.

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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been added to this reference.


Summary of changes:
 gnu/packages/bioinformatics.scm |8 
 1 file changed, 4 insertions(+), 4 deletions(-)

02/02: gnu: r-vegan: Update to 2.4-2.

[Ben Woodcroft]

benwoodcroft pushed a commit to branch master
in repository guix.

commit c0dee46c85c9ae9f9b40f83f693f666fdd3e5d28
Author: Ben Woodcroft 
Date:   Sat Jan 21 18:17:16 2017 +1000

gnu: r-vegan: Update to 2.4-2.

* gnu/packages/bioinformatics.scm (r-vegan): Update to 2.4-2.
---
 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 1209eaf..3bf3521 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -5290,14 +5290,14 @@ information as possible.")
 (define-public r-vegan
   (package
 (name "r-vegan")
-(version "2.4-1")
+(version "2.4-2")
 (source
  (origin
(method url-fetch)
(uri (cran-uri "vegan" version))
(sha256
 (base32
- "0i0c7rc0nzgbysd1nlxzxd2rvy75qcnw3yc7nggzqjzzj5d7yzsd"
+ "12wf64izrpq9z3ix7mgm5421mq0xsm8dw5qblvcrz452nfhjf5w9"
 (build-system r-build-system)
 (arguments
  `(#:phases

branch master updated (d33f889 -> cba53c6)

[Ben Woodcroft]

benwoodcroft pushed a change to branch master
in repository guix.

  from  d33f889   gnu: linux-libre: Update to 4.9.2.
   new  cba53c6   gnu: ruby-sqlite3: Update to 1.3.13.

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/ruby.scm |6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

01/01: gnu: ruby-sqlite3: Update to 1.3.13.

[Ben Woodcroft]

benwoodcroft pushed a commit to branch master
in repository guix.

commit cba53c60d59c9eac6fefabc799834b13ccacc314
Author: Ben Woodcroft 
Date:   Tue Jan 10 18:38:32 2017 +1000

gnu: ruby-sqlite3: Update to 1.3.13.

* gnu/packages/ruby.scm (ruby-sqlite3): Update to 1.3.13.
---
 gnu/packages/ruby.scm |6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/ruby.scm b/gnu/packages/ruby.scm
index 1c947cc..8fb22d0 100644
--- a/gnu/packages/ruby.scm
+++ b/gnu/packages/ruby.scm
@@ -4,7 +4,7 @@
 ;;; Copyright © 2014, 2015 Mark H Weaver 
 ;;; Copyright © 2014, 2015 David Thompson 
 ;;; Copyright © 2015 Ricardo Wurmus 
-;;; Copyright © 2015, 2016 Ben Woodcroft 
+;;; Copyright © 2015, 2016, 2017 Ben Woodcroft 
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -3300,14 +3300,14 @@ neither too verbose nor too minimal.")
 (define-public ruby-sqlite3
   (package
 (name "ruby-sqlite3")
-(version "1.3.12")
+(version "1.3.13")
 (source
  (origin
(method url-fetch)
(uri (rubygems-uri "sqlite3" version))
(sha256
 (base32
- "0hld87rvwyy31xsxzhicv2lj3g3kmvmwfxj09kw13g6lacdjz4bx"
+ "01ifzp8nwzqppda419c9wcvr8n82ysmisrs0hph9pdmv1lpa4f5i"
 (build-system ruby-build-system)
 (arguments
  `(#:phases

01/01: gnu: ruby-yard: Update to 0.9.6.

[Ben Woodcroft]

benwoodcroft pushed a commit to branch master
in repository guix.

commit 6499893ef82b85e9ba67b9e086e82644b94a55bb
Author: Ben Woodcroft 
Date:   Sun Jan 8 10:18:41 2017 +1000

gnu: ruby-yard: Update to 0.9.6.

* gnu/packages/ruby.scm (ruby-yard): Update to 0.9.6.
[source]: Use 'GitHub' source.
[arguments]: Run tests without 'Rakefile'.
[native-inputs]: Replace 'ruby-rspec-2' with ruby-rspec'.
* gnu/packages/patches/ruby-yard-fix-skip-of-markdown-tests.patch: Delete
file.
* gnu/local.mk (dist_patch_DATA): Remove it.
---
 gnu/local.mk   |1 -
 .../ruby-yard-fix-skip-of-markdown-tests.patch |   17 -
 gnu/packages/ruby.scm  |   66 +---
 3 files changed, 31 insertions(+), 53 deletions(-)

diff --git a/gnu/local.mk b/gnu/local.mk
index 0c95279..49d9554 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -844,7 +844,6 @@ dist_patch_DATA =   
\
   %D%/packages/patches/ruby-puma-ignore-broken-test.patch   \
   %D%/packages/patches/ruby-rack-ignore-failing-test.patch  \
   %D%/packages/patches/ruby-tzinfo-data-ignore-broken-test.patch\
-  %D%/packages/patches/ruby-yard-fix-skip-of-markdown-tests.patch \
   %D%/packages/patches/sed-hurd-path-max.patch \
   %D%/packages/patches/scheme48-tests.patch\
   %D%/packages/patches/scotch-test-threading.patch \
diff --git a/gnu/packages/patches/ruby-yard-fix-skip-of-markdown-tests.patch 
b/gnu/packages/patches/ruby-yard-fix-skip-of-markdown-tests.patch
deleted file mode 100644
index f592f5c..000
--- a/gnu/packages/patches/ruby-yard-fix-skip-of-markdown-tests.patch
+++ /dev/null
@@ -1,17 +0,0 @@
-The tests currently fail due to use of 'skip' rather than 'pending' to skip a
-test usually not skipped by upstream.  This patch has been proposed upstream
-at https://github.com/lsegal/yard/pull/1033
-
-diff --git a/spec/templates/helpers/html_helper_spec.rb 
b/spec/templates/helpers/html_helper_spec.rb
-index 84624c3..9c4fc2b 100644
 a/spec/templates/helpers/html_helper_spec.rb
-+++ b/spec/templates/helpers/html_helper_spec.rb
-@@ -184,7 +184,7 @@ describe YARD::Templates::Helpers::HtmlHelper do
- it "creates tables (markdown specific)" do
-   log.enter_level(Logger::FATAL) do
- unless markup_class(:markdown).to_s == "RedcarpetCompat"
--  skip "This test depends on a markdown engine that supports tables"
-+  pending "This test depends on a markdown engine that supports 
tables"
- end
-   end
- 
diff --git a/gnu/packages/ruby.scm b/gnu/packages/ruby.scm
index 50dde3f..4a2a3c1 100644
--- a/gnu/packages/ruby.scm
+++ b/gnu/packages/ruby.scm
@@ -3049,44 +3049,40 @@ features such as filtering and fine grained logging.")
 (license license:expat)))
 
 (define-public ruby-yard
-  ;; Use git reference because gem is >100 commits out of date and the tests
-  ;; do not pass with the released gem.
-  (let ((commit "d816482a0d4850506c3b9434550c536c28c6"))
-(package
-  (name "ruby-yard")
-  (version (string-append "0.9.5-1." (string-take commit 8)))
-  (source
-   (origin
- (method git-fetch)
- (uri (git-reference
-   (url "https://github.com/lsegal/yard.git";)
-   (commit commit)))
- (file-name (string-append name "-" version "-checkout"))
- (sha256
-  (base32
-   "1j16c85x22if7y0fzi3c900p9wzkx2riq1y7vsj92a0zvwsxai4i"))
- (patches (search-patches 
"ruby-yard-fix-skip-of-markdown-tests.patch"
-  (build-system ruby-build-system)
-  (arguments
-   `(#:test-target "spec"
- #:phases
- (modify-phases %standard-phases
-   (add-before 'check 'set-HOME-and-disable-failing-test
- (lambda _
-   ;; $HOME needs to be set to somewhere writeable for tests to run
-   (setenv "HOME" "/tmp")
-   #t)
-  (native-inputs
-   `(("ruby-rspec" ,ruby-rspec-2)
- ("ruby-rack" ,ruby-rack)))
-  (synopsis "Documentation generation tool for Ruby")
-  (description
-   "YARD is a documentation generation tool for the Ruby programming
+  (package
+(name "ruby-yard")
+(version "0.9.6")
+(source
+ (origin
+   (method url-fetch)
+   ;; Tests do not pass if we build from the distributed gem.
+   (uri (string-append "https://github.com/lsegal/yard/archive/v";
+   version "tar.gz"))
+   (file-name (string-append name "-" version ".tar.gz"))
+   (sha256
+

branch master updated (57fe28a -> 6499893)

[Ben Woodcroft]

benwoodcroft pushed a change to branch master
in repository guix.

  from  57fe28a   gnu: linux-libre: Update to 4.9.1.
   new  6499893   gnu: ruby-yard: Update to 0.9.6.

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/local.mk   |1 -
 .../ruby-yard-fix-skip-of-markdown-tests.patch |   17 -
 gnu/packages/ruby.scm  |   66 +---
 3 files changed, 31 insertions(+), 53 deletions(-)
 delete mode 100644 
gnu/packages/patches/ruby-yard-fix-skip-of-markdown-tests.patch

01/02: gnu: cd-hit: Update to 4.6.6.

[Ben Woodcroft]

benwoodcroft pushed a commit to branch master
in repository guix.

commit 0c37e2a3d2d6871572cb74e10aa9a897b5c4ed93
Author: Ben J Woodcroft 
Date:   Fri Jan 6 11:03:37 2017 +1000

gnu: cd-hit: Update to 4.6.6.

* gnu/packages/bioinformatics.scm (cd-hit): Update to 4.6.6.
---
 gnu/packages/bioinformatics.scm |6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 6b363af..d180f2a 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -1478,15 +1478,15 @@ high-throughput sequencing data – with an emphasis on 
simplicity.")
 (define-public cd-hit
   (package
 (name "cd-hit")
-(version "4.6.5")
+(version "4.6.6")
 (source (origin
   (method url-fetch)
   (uri (string-append "https://github.com/weizhongli/cdhit";
   "/releases/download/V" version
-  "/cd-hit-v" version "-2016-0304.tar.gz"))
+  "/cd-hit-v" version "-2016-0711.tar.gz"))
   (sha256
(base32
-"15db0hq38yyifwqx9b6l34z14jcq576dmjavhj8a426c18lvnhp3"
+"1w8hd4fszgg29nqiz569fldwy012la77nljcmlhglgicws56z54p"
 (build-system gnu-build-system)
 (arguments
  `(#:tests? #f ; there are no tests

branch master updated (e50d5b8 -> dbf9d37)

[Ben Woodcroft]

benwoodcroft pushed a change to branch master
in repository guix.

  from  e50d5b8   gnu: khal: Disable failing tests.
   new  0c37e2a   gnu: cd-hit: Update to 4.6.6.
   new  dbf9d37   gnu: bioruby: Update to 1.5.1.

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


Summary of changes:
 gnu/packages/bioinformatics.scm |   10 +-
 1 file changed, 5 insertions(+), 5 deletions(-)

02/02: gnu: bioruby: Update to 1.5.1.

[Ben Woodcroft]

benwoodcroft pushed a commit to branch master
in repository guix.

commit dbf9d371148e4d7b57b600b8ee74cecac9d0abed
Author: Ben J Woodcroft 
Date:   Fri Jan 6 16:17:42 2017 +1000

gnu: bioruby: Update to 1.5.1.

* gnu/packages/bioinformatics.scm (bioruby): Update to 1.5.1.
---
 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 d180f2a..f8d7304 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -5808,14 +5808,14 @@ generate FASTA, JSON, YAML, RDF, JSON-LD, HTML, CSV, 
tabular output etc.")
 (define-public bioruby
   (package
 (name "bioruby")
-(version "1.5.0")
+(version "1.5.1")
 (source
  (origin
(method url-fetch)
(uri (rubygems-uri "bio" version))
(sha256
 (base32
- "01k2fyjl5fpx4zn8g6gqiqvsg2j1fgixrs9p03vzxckynxdq3wmc"
+ "0hdl0789c9n4mprnx5pgd46bfwl8d000rqpamj5h6kkjgspijv49"
 (build-system ruby-build-system)
 (propagated-inputs
  `(("ruby-libxml" ,ruby-libxml)))

02/02: gnu: ruby-nokogiri: Update to 1.7.0.1.

[Ben Woodcroft]

benwoodcroft pushed a commit to branch master
in repository guix.

commit 19e5fb6030a9e901c5e9b6474c25a26e3696643c
Author: Ben Woodcroft 
Date:   Thu Jan 5 21:00:51 2017 +1000

gnu: ruby-nokogiri: Update to 1.7.0.1.

* gnu/packages/ruby.scm (ruby-nokogiri): Update to 1.7.0.1.
---
 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 b3bc882..50dde3f 100644
--- a/gnu/packages/ruby.scm
+++ b/gnu/packages/ruby.scm
@@ -1912,13 +1912,13 @@ to reproduce user environments.")
 (define-public ruby-nokogiri
   (package
 (name "ruby-nokogiri")
-(version "1.6.8")
+(version "1.7.0.1")
 (source (origin
   (method url-fetch)
   (uri (rubygems-uri "nokogiri" version))
   (sha256
(base32
-"17pjhvm4yigriizxbbpx266nnh6nckdm33m3j4ws9dcg99daz91p"
+"10xahg0fwydh27psm8bv429mdja2ks6x83vxizq26ib8wvs05mv3"
 (build-system ruby-build-system)
 (arguments
  ;; Tests fail because Nokogiri can only test with an installed extension,

01/02: gnu: ruby-hoe: Update to 3.16.0.

[Ben Woodcroft]

benwoodcroft pushed a commit to branch master
in repository guix.

commit 8e941f2068e18923256964418370206edd934619
Author: Ben Woodcroft 
Date:   Thu Jan 5 20:49:45 2017 +1000

gnu: ruby-hoe: Update to 3.16.0.

* gnu/packages/ruby.scm (ruby-hoe): Update to 3.16.0.
---
 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 c09e511..b3bc882 100644
--- a/gnu/packages/ruby.scm
+++ b/gnu/packages/ruby.scm
@@ -180,13 +180,13 @@ a focus on simplicity and productivity.")
 (define-public ruby-hoe
   (package
 (name "ruby-hoe")
-(version "3.15.2")
+(version "3.16.0")
 (source (origin
   (method url-fetch)
   (uri (rubygems-uri "hoe" version))
   (sha256
(base32
-"1riyf9j9vp7dzgpw5xj9xx1vqkdmg6lr7qiprmn91hcdp81kaszp"))) )
+"03r8nsw4n4mnia9iqiqk9kqhvrl96m2i81j4yg8cpnppd8vk7vlb"
 (build-system ruby-build-system)
 (synopsis "Ruby project management helper")
 (description

branch master updated (69355e1 -> 19e5fb6)

[Ben Woodcroft]

benwoodcroft pushed a change to branch master
in repository guix.

  from  69355e1   doc: Add a Git hook that verifies signatures before 
pushing.
   new  8e941f2   gnu: ruby-hoe: Update to 3.16.0.
   new  19e5fb6   gnu: ruby-nokogiri: Update to 1.7.0.1.

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


Summary of changes:
 gnu/packages/ruby.scm |8 
 1 file changed, 4 insertions(+), 4 deletions(-)

branch master updated (7fc2d37 -> 25d84d3)

[Ben Woodcroft]

benwoodcroft pushed a change to branch master
in repository guix.

  from  7fc2d37   gnu: nagios: Update to 4.2.4 [fixes CVE-2016-{9565,9566}].
   new  322a583   gnu: diamond: Update to 0.8.31.
   new  25d84d3   gnu: python-dendropy: Update to 4.2.0.

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/bioinformatics.scm|   22 
 .../python-dendropy-exclude-failing-tests.patch|   21 ---
 3 files changed, 4 insertions(+), 40 deletions(-)
 delete mode 100644 
gnu/packages/patches/python-dendropy-exclude-failing-tests.patch

02/02: gnu: python-dendropy: Update to 4.2.0.

[Ben Woodcroft]

benwoodcroft pushed a commit to branch master
in repository guix.

commit 25d84d3122b8de29a67d69e8ff5de6660b8d44c5
Author: Ben Woodcroft 
Date:   Sun Jan 1 16:37:08 2017 +1000

gnu: python-dendropy: Update to 4.2.0.

* gnu/packages/bioinformatics.scm (python-dendropy): Update to 4.2.0.
[source]: Remove patch.
(python2-dendropy)[source]: Use the same source as python-dendropy.
* gnu/packages/patches/python-dendropy-exclude-failing-tests.patch: Remove
file.
* gnu/local.mk (dist_patch_DATA): Remove it.
---
 gnu/local.mk   |1 -
 gnu/packages/bioinformatics.scm|   18 ++---
 .../python-dendropy-exclude-failing-tests.patch|   21 
 3 files changed, 2 insertions(+), 38 deletions(-)

diff --git a/gnu/local.mk b/gnu/local.mk
index 6963313..6ab1c1c 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -814,7 +814,6 @@ dist_patch_DATA =   
\
   %D%/packages/patches/python-3-search-paths.patch \
   %D%/packages/patches/python-3.4-fix-tests.patch  \
   %D%/packages/patches/python-3.5-fix-tests.patch  \
-  %D%/packages/patches/python-dendropy-exclude-failing-tests.patch \
   %D%/packages/patches/python-file-double-encoding-bug.patch   \
   %D%/packages/patches/python-fix-tests.patch  \
   %D%/packages/patches/python-parse-too-many-fields.patch  \
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index b1d0c38..7a61de2 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -1930,19 +1930,14 @@ accessing bigWig files.")
 (define-public python-dendropy
   (package
 (name "python-dendropy")
-(version "4.1.0")
+(version "4.2.0")
 (source
  (origin
(method url-fetch)
(uri (pypi-uri "DendroPy" version))
(sha256
 (base32
- "1jfz7gp18wph311w1yygbvjanb3n5mdqal439bb6myw41dwb5m63"))
-   ;; There are two known test failures that will be fixed in the next
-   ;; release after 4.1.0.
-   ;; https://github.com/jeetsukumaran/DendroPy/issues/48
-   (patches (search-patches
- "python-dendropy-exclude-failing-tests.patch"
+ "15c7s3d5gf19ljsxvq5advaa752wfi7pwrdjyhzmg85hccyvp47p"
 (build-system python-build-system)
 (home-page "http://packages.python.org/DendroPy/";)
 (synopsis "Library for phylogenetics and phylogenetic computing")
@@ -1957,15 +1952,6 @@ trees (phylogenies) and characters.")
   (let ((base (package-with-python2 (strip-python2-variant python-dendropy
 (package
   (inherit base)
-  ;; Do not use same source as 'python-dendropy' because the patched
-  ;; failing tests do not occur on Python 2.
-  (source
-   (origin
- (method url-fetch)
- (uri (pypi-uri "DendroPy" (package-version base)))
- (sha256
-  (base32
-   "1jfz7gp18wph311w1yygbvjanb3n5mdqal439bb6myw41dwb5m63"
   (arguments
`(#:python ,python-2
  #:phases
diff --git a/gnu/packages/patches/python-dendropy-exclude-failing-tests.patch 
b/gnu/packages/patches/python-dendropy-exclude-failing-tests.patch
deleted file mode 100644
index 288a58b..000
--- a/gnu/packages/patches/python-dendropy-exclude-failing-tests.patch
+++ /dev/null
@@ -1,21 +0,0 @@
-diff --git a/dendropy/test/test_phylogenetic_distance_matrix.py 
b/dendropy/test/test_phylogenetic_distance_matrix.py
-index 10c05f5..a18ba52 100644
 a/dendropy/test/test_phylogenetic_distance_matrix.py
-+++ b/dendropy/test/test_phylogenetic_distance_matrix.py
-@@ -793,7 +793,7 @@ class PdmUpgmaTree(PdmTreeChecker, unittest.TestCase):
- expected_tree=expected_tree)
- 
- class NodeToNodeDistancesTest(unittest.TestCase):
--
-+@unittest.expectedFailure
- def test_distances(self):
- ## get distances from ape
- # library(ape)
-@@ -825,6 +825,7 @@ class NodeToNodeDistancesTest(unittest.TestCase):
- e = reference_table[nd1.label, nd2.label]
- self.assertAlmostEqual(d, e)
- 
-+@unittest.expectedFailure
- def test_mrca(self):
- test_runs = [
- "hiv1.newick",

01/02: gnu: diamond: Update to 0.8.31.

[Ben Woodcroft]

benwoodcroft pushed a commit to branch master
in repository guix.

commit 322a583fcfff9f5173ad388ee876aa29d9f8edcc
Author: Ben Woodcroft 
Date:   Sun Jan 1 16:29:11 2017 +1000

gnu: diamond: Update to 0.8.31.

* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.31.
---
 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 54c8ce0..b1d0c38 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -2020,7 +2020,7 @@ identify enrichments with functional annotations of the 
genome.")
 (define-public diamond
   (package
 (name "diamond")
-(version "0.8.30")
+(version "0.8.31")
 (source (origin
   (method url-fetch)
   (uri (string-append
@@ -2029,7 +2029,7 @@ identify enrichments with functional annotations of the 
genome.")
   (file-name (string-append name "-" version ".tar.gz"))
   (sha256
(base32
-"1fqzbrh5kxxbw805nwanddfa8lic65s58y37x5n2swf28518w4zf"
+"0nh79f4rpgq8vmlga743r7vd0z0ik6spy34f7vfq0v9lcmvfr7xq"
 (build-system cmake-build-system)
 (arguments
  '(#:tests? #f ; no "check" target

01/01: gnu: multiqc: Update to 0.9.

[Ben Woodcroft]

benwoodcroft pushed a commit to branch master
in repository guix.

commit a29929b32caf9e437d18bdb0cd4d1b22bc096fed
Author: Ben Woodcroft 
Date:   Fri Dec 30 17:21:37 2016 +1000

gnu: multiqc: Update to 0.9.

Suggested by Raoul Bonnal .

* gnu/packages/bioinformatics.scm (multiqc): Update to 0.9.
[origin]: Add patch.
* gnu/packages/patches/multiqc-fix-git-subprocess-error.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
---
 gnu/local.mk   |1 +
 gnu/packages/bioinformatics.scm|9 +++--
 .../patches/multiqc-fix-git-subprocess-error.patch |   16 
 3 files changed, 24 insertions(+), 2 deletions(-)

diff --git a/gnu/local.mk b/gnu/local.mk
index 38c1b0b..b7c182f 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -730,6 +730,7 @@ dist_patch_DATA =   
\
   %D%/packages/patches/mpc123-initialize-ao.patch  \
   %D%/packages/patches/mplayer2-theora-fix.patch   \
   %D%/packages/patches/module-init-tools-moduledir.patch   \
+  %D%/packages/patches/multiqc-fix-git-subprocess-error.patch  \
   %D%/packages/patches/mumps-build-parallelism.patch   \
   %D%/packages/patches/mupdf-build-with-openjpeg-2.1.patch \
   %D%/packages/patches/mupen64plus-ui-console-notice.patch \
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 07c4a0a..54c8ce0 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7855,15 +7855,20 @@ replacement for strverscmp.")
 (define-public multiqc
   (package
 (name "multiqc")
-(version "0.6")
+(version "0.9")
 (source
  (origin
(method url-fetch)
(uri (pypi-uri "multiqc" version))
(sha256
 (base32
- "0avw11h63ldpxy5pizc3wl1wa01ha7q10wb240nggsjz3jaqvyiy"
+ "12gs1jw2jrxrij529rnl5kaqxfcqn15yzcsggxkfhdx634ml0cny"))
+   (patches (search-patches "multiqc-fix-git-subprocess-error.patch"
 (build-system python-build-system)
+(arguments
+ ;; Tests are to be introduced in the next version, see
+ ;; https://github.com/ewels/MultiQC/issues/376
+ `(#:tests? #f))
 (propagated-inputs
  `(("python-jinja2" ,python-jinja2)
("python-simplejson" ,python-simplejson)
diff --git a/gnu/packages/patches/multiqc-fix-git-subprocess-error.patch 
b/gnu/packages/patches/multiqc-fix-git-subprocess-error.patch
new file mode 100644
index 000..87be614
--- /dev/null
+++ b/gnu/packages/patches/multiqc-fix-git-subprocess-error.patch
@@ -0,0 +1,16 @@
+Without this patch, the incorrect exception is caught when 'git' is not in
+PATH.  See https://github.com/ewels/MultiQC/pull/377.
+
+diff --git a/multiqc/utils/config.py b/multiqc/utils/config.py
+index 01fa554..4a11793 100755
+--- a/multiqc/utils/config.py
 b/multiqc/utils/config.py
+@@ -28,7 +28,7 @@ try:
+ git_hash = subprocess.check_output(['git', 'rev-parse', 'HEAD'], 
stderr=subprocess.STDOUT)
+ git_hash_short = git_hash[:7]
+ version = '{} ({})'.format(version, git_hash_short)
+-except subprocess.CalledProcessError:
++except (subprocess.CalledProcessError, FileNotFoundError):
+ pass
+ os.chdir(cwd)
+ 

branch master updated (95d7d0c -> a29929b)

[Ben Woodcroft]

benwoodcroft pushed a change to branch master
in repository guix.

  from  95d7d0c   gnu: elogind: Enable ACL support.
   new  a29929b   gnu: multiqc: Update to 0.9.

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/local.mk   |1 +
 gnu/packages/bioinformatics.scm|9 +++--
 .../patches/multiqc-fix-git-subprocess-error.patch |   16 
 3 files changed, 24 insertions(+), 2 deletions(-)
 create mode 100644 gnu/packages/patches/multiqc-fix-git-subprocess-error.patch

branch master updated (c976b31 -> 9916ef8)

[Ben Woodcroft]

benwoodcroft pushed a change to branch master
in repository guix.

  from  c976b31   gnu: python-stem: Update to 1.5.3.
   new  9916ef8   gnu: diamond: Update to 0.8.30.

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 |4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

01/01: gnu: diamond: Update to 0.8.30.

[Ben Woodcroft]

benwoodcroft pushed a commit to branch master
in repository guix.

commit 9916ef8bb6e83855c2a7a4e972747610b410a3ed
Author: Ben Woodcroft 
Date:   Tue Dec 27 09:18:05 2016 +1000

gnu: diamond: Update to 0.8.30.

* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.30.
---
 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 912941e..d423f08 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -2020,7 +2020,7 @@ identify enrichments with functional annotations of the 
genome.")
 (define-public diamond
   (package
 (name "diamond")
-(version "0.8.29")
+(version "0.8.30")
 (source (origin
   (method url-fetch)
   (uri (string-append
@@ -2029,7 +2029,7 @@ identify enrichments with functional annotations of the 
genome.")
   (file-name (string-append name "-" version ".tar.gz"))
   (sha256
(base32
-"1mnhj7y13pk2bhfichjma5aw8ssdiqyria61ip1kps6facqlal3z"
+"1fqzbrh5kxxbw805nwanddfa8lic65s58y37x5n2swf28518w4zf"
 (build-system cmake-build-system)
 (arguments
  '(#:tests? #f ; no "check" target

01/01: gnu: ruby-minitest: Update to 5.10.1.

[Ben Woodcroft]

benwoodcroft pushed a commit to branch master
in repository guix.

commit f1775db66089d6b69b8061c00432ef04eb970840
Author: Ben Woodcroft 
Date:   Mon Dec 26 22:43:59 2016 +1000

gnu: ruby-minitest: Update to 5.10.1.

* gnu/packages/ruby.scm (ruby-minitest): Update to 5.10.1.
---
 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 c87f8b3..c09e511 100644
--- a/gnu/packages/ruby.scm
+++ b/gnu/packages/ruby.scm
@@ -1479,13 +1479,13 @@ with processes on remote servers, via SSH2.")
 (define-public ruby-minitest
   (package
 (name "ruby-minitest")
-(version "5.7.0")
+(version "5.10.1")
 (source (origin
   (method url-fetch)
   (uri (rubygems-uri "minitest" version))
   (sha256
(base32
-"0rxqfakp629mp3vwda7zpgb57lcns5znkskikbfd0kriwv8i1vq8"
+"1yk2m8sp0p5m1niawa3ncg157a4i0594cg7z91rzjxv963rzrwab"
 (build-system ruby-build-system)
 (native-inputs
  `(("ruby-hoe" ,ruby-hoe)))

branch master updated (328398e -> f1775db)

[Ben Woodcroft]

benwoodcroft pushed a change to branch master
in repository guix.

  from  328398e   gnu: Add ripit.
   new  f1775db   gnu: ruby-minitest: Update to 5.10.1.

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

02/02: gnu: r: Update to 3.3.2.

[Ben Woodcroft]

benwoodcroft pushed a commit to branch master
in repository guix.

commit a1814e4a27aa2e99283d381ec7e090706fa1031d
Author: Raoul Bonnal 
Date:   Sat Dec 17 23:26:02 2016 +1000

gnu: r: Update to 3.3.2.

* gnu/packages/statistics.scm (r): Update to 3.3.2.
---
 gnu/packages/statistics.scm |5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 6cdd694..f868da2 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -6,6 +6,7 @@
 ;;; Copyright © 2016 Pjotr Prins 
 ;;; Copyright © 2016 Roel Janssen 
 ;;; Copyright © 2016 Ben Woodcroft 
+;;; Copyright © 2016 Raoul Bonnal 
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -101,7 +102,7 @@ be output in text, PostScript, PDF or HTML.")
 (define-public r
   (package
 (name "r")
-(version "3.3.1")
+(version "3.3.2")
 (source (origin
   (method url-fetch)
   (uri (string-append "mirror://cran/src/base/R-"
@@ -109,7 +110,7 @@ be output in text, PostScript, PDF or HTML.")
   version ".tar.gz"))
   (sha256
(base32
-"1qm9znh8akfy9fkzzi6f1vz2w1dd0chsr6qn7kw80lqzhgjrmi9x"
+"0k2i9qdd83g09fcpls2198q4ykxkii5skczb514gnx7mx4hsv56j"
 (build-system gnu-build-system)
 (arguments
  `(#:make-flags

branch master updated (a32d0c8 -> a1814e4)

[Ben Woodcroft]

benwoodcroft pushed a change to branch master
in repository guix.

  from  a32d0c8   gnu: sane-backends: Remove timestamps from the output.
   new  3fffabc   gnu: Add attribution line for Raoul Bonnal.
   new  a1814e4   gnu: r: Update to 3.3.2.

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/bioinformatics.scm |1 +
 gnu/packages/statistics.scm |5 +++--
 2 files changed, 4 insertions(+), 2 deletions(-)

01/02: gnu: Add attribution line for Raoul Bonnal.

[Ben Woodcroft]

benwoodcroft pushed a commit to branch master
in repository guix.

commit 3fffabce2a0e7013379d090a72199df703d5e66d
Author: Ben Woodcroft 
Date:   Sun Dec 18 09:57:32 2016 +1000

gnu: Add attribution line for Raoul Bonnal.

This is a follow-up commit to c9e9154e993f055a438e2e43518bbd0740aaaf24.

* gnu/packages/bioinformatics.scm: Add attribution.
---
 gnu/packages/bioinformatics.scm |1 +
 1 file changed, 1 insertion(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 9ce4e3a..122205f 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -6,6 +6,7 @@
 ;;; Copyright © 2016 Roel Janssen 
 ;;; Copyright © 2016 Efraim Flashner 
 ;;; Copyright © 2016 Marius Bakke 
+;;; Copyright © 2016 Raoul Bonnal 
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;

01/01: gnu: star: Update to 2.5.2b.

[Ben Woodcroft]

benwoodcroft pushed a commit to branch master
in repository guix.

commit c9e9154e993f055a438e2e43518bbd0740aaaf24
Author: Raoul Bonnal 
Date:   Sat Dec 17 23:17:34 2016 +1000

gnu: star: Update to 2.5.2b.

* gnu/packages/bioinformatics (star): Update to 2.5.2b.
[source]: Delete precompiled binary.

Co-authored-by: Ben Woodcroft 
---
 gnu/packages/bioinformatics.scm |5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 3e9c82f..9ce4e3a 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -4924,7 +4924,7 @@ application of SortMeRNA is filtering rRNA from 
metatranscriptomic data.")
 (define-public star
   (package
 (name "star")
-(version "2.5.2a")
+(version "2.5.2b")
 (source (origin
   (method url-fetch)
   (uri (string-append "https://github.com/alexdobin/STAR/archive/";
@@ -4932,7 +4932,7 @@ application of SortMeRNA is filtering rRNA from 
metatranscriptomic data.")
   (file-name (string-append name "-" version ".tar.gz"))
   (sha256
(base32
-"0xjlsm4p9flln111hv4xx7xy94c2nl53zvdvbk9winmiradjsdra"))
+"1na6np880r1zaamiy00hy8bid5anpy0kgf63587v2yl080krk2zq"))
   (modules '((guix build utils)))
   (snippet
'(begin
@@ -4941,6 +4941,7 @@ application of SortMeRNA is filtering rRNA from 
metatranscriptomic data.")
   ;; Remove pre-built binaries and bundled htslib sources.
   (delete-file-recursively "bin/MacOSX_x86_64")
   (delete-file-recursively "bin/Linux_x86_64")
+  (delete-file-recursively "bin/Linux_x86_64_static")
   (delete-file-recursively "source/htslib")
   #t
 (build-system gnu-build-system)

branch master updated (51ad11a -> c9e9154)

[Ben Woodcroft]

benwoodcroft pushed a change to branch master
in repository guix.

  from  51ad11a   gnu: Add fatfsck-static.
   new  c9e9154   gnu: star: Update to 2.5.2b.

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 |5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

01/02: gnu: Add r-bit.

[Ben Woodcroft]

benwoodcroft pushed a commit to branch master
in repository guix.

commit 42066e6b4aa3670c6cb07558d391fdba07c83b46
Author: Ben Woodcroft 
Date:   Mon Dec 12 20:59:43 2016 +1000

gnu: Add r-bit.

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

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 36f1889..fdf7745 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -205,6 +205,27 @@ publication-quality data plots.  A large amount of 
3rd-party packages are
 available, greatly increasing its breadth and scope.")
 (license license:gpl3+)))
 
+(define-public r-bit
+  (package
+(name "r-bit")
+(version "1.1-12")
+(source
+ (origin
+   (method url-fetch)
+   (uri (cran-uri "bit" version))
+   (sha256
+(base32
+ "0a6ig6nnjzq80r2ll4hc74za3xwzbzig6wlyb4dby0knzf3iqa6f"
+(build-system r-build-system)
+(home-page "http://ff.r-forge.r-project.org";)
+(synopsis "Class for vectors of 1-bit booleans")
+(description
+ "This package provides bitmapped vectors of booleans (no @code{NA}s),
+coercion from and to logicals, integers and integer subscripts, fast boolean
+operators and fast summary statistics.  With @code{bit} class vectors of true
+binary booleans, @code{TRUE} and @code{FALSE} can be stored with 1 bit only.")
+(license license:gpl2)))
+
 (define-public r-colorspace
   (package
 (name "r-colorspace")

branch master updated (5a38494 -> ce3f92e)

[Ben Woodcroft]

benwoodcroft pushed a change to branch master
in repository guix.

  from  5a38494   gnu: linux-libre: Update to 4.9.
   new  42066e6   gnu: Add r-bit.
   new  ce3f92e   gnu: Add r-bit64.

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/statistics.scm |   47 +++
 1 file changed, 47 insertions(+)

02/02: gnu: Add r-bit64.

[Ben Woodcroft]

benwoodcroft pushed a commit to branch master
in repository guix.

commit ce3f92e7018e140f5e6b7333a604f26506de6c2a
Author: Ben Woodcroft 
Date:   Mon Dec 12 21:11:48 2016 +1000

gnu: Add r-bit64.

* gnu/packages/statistics.scm (r-bit64): New variable.
---
 gnu/packages/statistics.scm |   26 ++
 1 file changed, 26 insertions(+)

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index fdf7745..6cdd694 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -226,6 +226,32 @@ operators and fast summary statistics.  With @code{bit} 
class vectors of true
 binary booleans, @code{TRUE} and @code{FALSE} can be stored with 1 bit only.")
 (license license:gpl2)))
 
+(define-public r-bit64
+  (package
+(name "r-bit64")
+(version "0.9-5")
+(source
+ (origin
+   (method url-fetch)
+   (uri (cran-uri "bit64" version))
+   (sha256
+(base32
+ "0fz5m3fhvxgwjl76maag7yn0zdw24rx34gy6v77378fajag9yllg"
+(build-system r-build-system)
+(propagated-inputs
+ `(("r-bit" ,r-bit)))
+(home-page "http://ff.r-forge.r-project.org/";)
+(synopsis "S3 class for vectors of 64 bit integers")
+(description
+ "The bit64 package provides serializable S3 atomic 64 bit (signed)
+integers that can be used in vectors, matrices, arrays and @code{data.frames}.
+Methods are available for coercion from and to logicals, integers, doubles,
+characters and factors as well as many elementwise and summary functions.
+Many fast algorithmic operations such as @code{match} and @code{order} support
+interactive data exploration and manipulation and optionally leverage
+caching.")
+(license license:gpl2)))
+
 (define-public r-colorspace
   (package
 (name "r-colorspace")

01/02: gnu: orfm: Update to 0.6.1.

[Ben Woodcroft]

benwoodcroft pushed a commit to branch master
in repository guix.

commit ced1c496aa16d9c4c9a7c512c6763e09896c36fb
Author: Ben Woodcroft 
Date:   Tue Dec 13 20:00:50 2016 +1000

gnu: orfm: Update to 0.6.1.

* gnu/packages/bioinformatics.scm (orfm): Update to 0.6.1.
---
 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 fc22d8a..ccf75d3 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -3478,7 +3478,7 @@ trimming, pruning, condensing, drawing (ASCII graphics or 
SVG).")
 (define-public orfm
   (package
 (name "orfm")
-(version "0.6.0")
+(version "0.6.1")
 (source (origin
   (method url-fetch)
   (uri (string-append
@@ -3486,7 +3486,7 @@ trimming, pruning, condensing, drawing (ASCII graphics or 
SVG).")
 version "/orfm-" version ".tar.gz"))
   (sha256
(base32
-"0kp5p0a8wh1shxlj9arv47qyhv23s1inbvmiv7k2i5mrwx2izh79"
+"19hwp13n82isdvk16710l9m35cmzf0q3fsrcn3r8c5r67biiz39s"
 (build-system gnu-build-system)
 (inputs `(("zlib" ,zlib)))
 (native-inputs

branch master updated (310248c -> 991e143)

[Ben Woodcroft]

benwoodcroft pushed a change to branch master
in repository guix.

  from  310248c   gnu: libsrtp: Fix building on mips.
   new  ced1c49   gnu: orfm: Update to 0.6.1.
   new  991e143   gnu: diamond: Update to 0.8.29.

The 2 revisions listed above as "new" are entirely new to this
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been added to this reference.


Summary of changes:
 gnu/packages/bioinformatics.scm |8 
 1 file changed, 4 insertions(+), 4 deletions(-)

02/02: gnu: diamond: Update to 0.8.29.

[Ben Woodcroft]

benwoodcroft pushed a commit to branch master
in repository guix.

commit 991e143d25e590af5c1b3c81ffd253c7b1de1d5c
Author: Ben Woodcroft 
Date:   Tue Dec 13 20:01:56 2016 +1000

gnu: diamond: Update to 0.8.29.

* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.29.
---
 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 ccf75d3..3d84a44 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -2016,7 +2016,7 @@ identify enrichments with functional annotations of the 
genome.")
 (define-public diamond
   (package
 (name "diamond")
-(version "0.8.27")
+(version "0.8.29")
 (source (origin
   (method url-fetch)
   (uri (string-append
@@ -2025,7 +2025,7 @@ identify enrichments with functional annotations of the 
genome.")
   (file-name (string-append name "-" version ".tar.gz"))
   (sha256
(base32
-"0g0zdyfnri9v7nfbh8f7zqs4af1xydqkiw8m0cx4jc2ql4chpf6a"
+"1mnhj7y13pk2bhfichjma5aw8ssdiqyria61ip1kps6facqlal3z"
 (build-system cmake-build-system)
 (arguments
  '(#:tests? #f ; no "check" target

01/01: gnu: orfm: Update to 0.6.0.

[Ben Woodcroft]

benwoodcroft pushed a commit to branch master
in repository guix.

commit 2df3d147efcbe040d50f104479856fe9033c1716
Author: Ben Woodcroft 
Date:   Mon Dec 12 20:49:03 2016 +1000

gnu: orfm: Update to 0.6.0.

* gnu/packages/bioinformatics.scm (orfm): Update to 0.6.0.
---
 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 9ab55fb..fc22d8a 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -3478,7 +3478,7 @@ trimming, pruning, condensing, drawing (ASCII graphics or 
SVG).")
 (define-public orfm
   (package
 (name "orfm")
-(version "0.5.3")
+(version "0.6.0")
 (source (origin
   (method url-fetch)
   (uri (string-append
@@ -3486,7 +3486,7 @@ trimming, pruning, condensing, drawing (ASCII graphics or 
SVG).")
 version "/orfm-" version ".tar.gz"))
   (sha256
(base32
-"0vb6d771gl4mix8bwx919x5ayy9pkj44n7ki336nz3rz2rx4c7gk"
+"0kp5p0a8wh1shxlj9arv47qyhv23s1inbvmiv7k2i5mrwx2izh79"
 (build-system gnu-build-system)
 (inputs `(("zlib" ,zlib)))
 (native-inputs

branch master updated (23b40c6 -> 2df3d14)

[Ben Woodcroft]

benwoodcroft pushed a change to branch master
in repository guix.

  from  23b40c6   gnu: direnv: Update to 2.10.0.
   new  2df3d14   gnu: orfm: Update to 0.6.0.

The 1 revisions listed above as "new" are entirely new to this
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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/bioinformatics.scm |4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

01/02: gnu: pardre: Update to 1.1.5-1.

[Ben Woodcroft]

benwoodcroft pushed a commit to branch master
in repository guix.

commit 7922ab8fe87154f3ccaa7daf9304632f974fbe5d
Author: Ben Woodcroft 
Date:   Sat Dec 10 10:31:15 2016 +1000

gnu: pardre: Update to 1.1.5-1.

* gnu/packages/bioinformatics.scm (pardre): update to 1.1.5-1.
[source]: Update source hash.
---
 gnu/packages/bioinformatics.scm |7 ---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 625935d..2b00e86 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -5699,15 +5699,16 @@ Needleman-Wunsch).")
 (define-public pardre
   (package
 (name "pardre")
-(version "1.1.5")
+;; The source of 1.1.5 changed in place, so we append "-1" to the version.
+(version "1.1.5-1")
 (source
  (origin
(method url-fetch)
(uri (string-append "mirror://sourceforge/pardre/ParDRe-rel"
-   version ".tar.gz"))
+   "1.1.5" ".tar.gz"))
(sha256
 (base32
- "0zkyjzv4s8q2h5npalhirbk17r5b1h0n2a42mh7njzlf047h9bhy"
+ "17j73nc0viq4f6qj50nrndsrif5d6b71q8fl87m54psiv0ilns2b"
 (build-system gnu-build-system)
 (arguments
  `(#:tests? #f ; no tests included

02/02: gnu: vsearch: Update to 2.3.4.

[Ben Woodcroft]

benwoodcroft pushed a commit to branch master
in repository guix.

commit a225db529337035b159b2b75714ee18753c26d21
Author: Ben Woodcroft 
Date:   Sat Dec 10 10:45:08 2016 +1000

gnu: vsearch: Update to 2.3.4.

* gnu/packages/bioinformatics.scm (vsearch): Update to 2.3.4.
---
 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 2b00e86..9ab55fb 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -5629,7 +5629,7 @@ track.  The database is exposed as a @code{TxDb} object.")
 (define-public vsearch
   (package
 (name "vsearch")
-(version "2.3.3")
+(version "2.3.4")
 (source
  (origin
(method url-fetch)
@@ -5639,7 +5639,7 @@ track.  The database is exposed as a @code{TxDb} object.")
(file-name (string-append name "-" version ".tar.gz"))
(sha256
 (base32
- "1d3670apjy15c9l40fpq71lifxga6j9z2gisdirycwk18s4mvcp2"))
+ "1xyraxmhyx62mxx8z7c8waygvcijwkh48ms1ar60w2cv2y2sn4al"))
(modules '((guix build utils)))
(snippet
 '(begin

branch master updated (6b2921c -> a225db5)

[Ben Woodcroft]

benwoodcroft pushed a change to branch master
in repository guix.

  from  6b2921c   gnu: linux-libre: Add fixes for CVE-2016-8655 et al.
   new  7922ab8   gnu: pardre: Update to 1.1.5-1.
   new  a225db5   gnu: vsearch: Update to 2.3.4.

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 |   11 ++-
 1 file changed, 6 insertions(+), 5 deletions(-)

01/02: gnu: Adjust gemspec modifications for ruby-2.3.2.

[Ben Woodcroft]

benwoodcroft pushed a commit to branch staging
in repository guix.

commit 71596c3ce66ef9269c21d85f815e2f473ab6c7a1
Author: Ben Woodcroft 
Date:   Sat Dec 10 07:40:47 2016 +1000

gnu: Adjust gemspec modifications for ruby-2.3.2.

* gnu/packages/ruby.scm (ruby-mocha)[arguments]: Adjust 'substitute*' of
gemspec.
(ruby-domain-name)[arguments]: Likewise.
---
 gnu/packages/ruby.scm |6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/ruby.scm b/gnu/packages/ruby.scm
index 276aa5b..eb554c4 100644
--- a/gnu/packages/ruby.scm
+++ b/gnu/packages/ruby.scm
@@ -1426,8 +1426,8 @@ conversion to (X)HTML.")
  (add-before 'check 'use-latest-redcarpet
   (lambda _
 (substitute* "mocha.gemspec"
-  ((", \\[\"~> 1\"\\]")
-   ", [\">= 3\"]"))
+  ((".freeze, \\[\"~> 1\"\\]")
+   ".freeze, [\">= 3\"]"))
 #t))
  (add-before 'check 'hardcode-version
   (lambda _
@@ -3493,7 +3493,7 @@ support to both Ruby and JRuby.  It uses @code{unf_ext} 
on CRuby and
 "Bundler::GemHelper.gemspec.version"))
  ;; Loosen unnecessarily strict test-unit version specification.
  (substitute* "domain_name.gemspec"
-   ((", \\[\\\"~> 2.5.5") ", [\">0"))
+   ((".freeze, \\[\\\"~> 2.5.5") ", [\">0"))
  #t)
 (propagated-inputs
  `(("ruby-unf" ,ruby-unf)))

branch staging updated (f80b4d2 -> fdf3a68)

[Ben Woodcroft]

benwoodcroft pushed a change to branch staging
in repository guix.

  from  f80b4d2   Merge remote-tracking branch 'origin/master' into staging
   new  71596c3   gnu: Adjust gemspec modifications for ruby-2.3.2.
   new  fdf3a68   gnu: ruby-sdoc: Update to 0.4.2.

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/ruby.scm |   19 +--
 1 file changed, 9 insertions(+), 10 deletions(-)

02/02: gnu: ruby-sdoc: Update to 0.4.2.

[Ben Woodcroft]

benwoodcroft pushed a commit to branch staging
in repository guix.

commit fdf3a68d9e95ed1b70cc9751b9a2ce26babfce33
Author: Ben Woodcroft 
Date:   Fri Dec 9 19:27:12 2016 +1000

gnu: ruby-sdoc: Update to 0.4.2.

* gnu/packages/ruby.scm (ruby-sdoc): Update to 0.4.2.
[arguments]: Remove 'relax-minitest-requirement' phase, Add 'set-rubylib'
phase.
[native-inputs]: Add ruby-hoe.
---
 gnu/packages/ruby.scm |   13 ++---
 1 file changed, 6 insertions(+), 7 deletions(-)

diff --git a/gnu/packages/ruby.scm b/gnu/packages/ruby.scm
index eb554c4..c87f8b3 100644
--- a/gnu/packages/ruby.scm
+++ b/gnu/packages/ruby.scm
@@ -2204,28 +2204,27 @@ current line in an external editor.")
 (define-public ruby-sdoc
   (package
 (name "ruby-sdoc")
-(version "0.4.1")
+(version "0.4.2")
 (source (origin
   (method url-fetch)
   (uri (rubygems-uri "sdoc" version))
   (sha256
(base32
-"16xyfair1j4irfkd6sxvmdcak957z71lwkvhglrznfpkalfnqyqp"
+"0qhvy10vnmrqcgh8494m13kd5ag9c3sczzhfasv8j0294ylk679n"
 (build-system ruby-build-system)
 (arguments
  `(#:phases
(modify-phases %standard-phases
- (add-after 'build 'relax-minitest-requirement
+ (add-before 'check 'set-rubylib
   (lambda _
-(substitute* "sdoc.gemspec"
-  (("\\.freeze, \\[\"~> 4\\.0\"\\]")
-   ".freeze, [\">= 4.0\"]"))
+(setenv "RUBYLIB" "lib")
 #t)
 (propagated-inputs
  `(("ruby-json" ,ruby-json)))
 (native-inputs
  `(("bundler" ,bundler)
-   ("ruby-minitest" ,ruby-minitest)))
+   ("ruby-minitest" ,ruby-minitest)
+   ("ruby-hoe" ,ruby-hoe)))
 (synopsis "Generate searchable RDoc documentation")
 (description
  "SDoc is an RDoc documentation generator to build searchable HTML

branch master updated (cb72d34 -> 1b7f17e)

[Ben Woodcroft]

benwoodcroft pushed a change to branch master
in repository guix.

  from  cb72d34   gnu: libreoffice: Add 'libreoffice' symlink.
   new  1b7f17e   gnu: vsearch: Update to 2.3.3.

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

01/01: gnu: vsearch: Update to 2.3.3.

[Ben Woodcroft]

benwoodcroft pushed a commit to branch master
in repository guix.

commit 1b7f17ef90bcd8fc83cc985cc94ac984dcc2a07a
Author: Ben Woodcroft 
Date:   Thu Dec 8 22:39:10 2016 +1000

gnu: vsearch: Update to 2.3.3.

* gnu/packages/bioinformatics.scm (vsearch): Update to 2.3.3.
---
 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 4fac8e1..625935d 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -5629,7 +5629,7 @@ track.  The database is exposed as a @code{TxDb} object.")
 (define-public vsearch
   (package
 (name "vsearch")
-(version "2.3.0")
+(version "2.3.3")
 (source
  (origin
(method url-fetch)
@@ -5639,7 +5639,7 @@ track.  The database is exposed as a @code{TxDb} object.")
(file-name (string-append name "-" version ".tar.gz"))
(sha256
 (base32
- "1r8fk3whkil348y5hfsd4r56qjmchhq4nxm6s7ra5rlisw0mf9fy"))
+ "1d3670apjy15c9l40fpq71lifxga6j9z2gisdirycwk18s4mvcp2"))
(modules '((guix build utils)))
(snippet
 '(begin

01/01: gnu: Add newick-utils.

[Ben Woodcroft]

benwoodcroft pushed a commit to branch master
in repository guix.

commit 9926875572cf2936b7f23fb291328bfa68c038c6
Author: Ben Woodcroft 
Date:   Sun Nov 27 13:11:46 2016 +1000

gnu: Add newick-utils.

* gnu/packages/bioinformatics.scm (newick-utils): New variable.
---
 gnu/packages/bioinformatics.scm |   40 +++
 1 file changed, 40 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 8d2cb93..f04acc0 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -50,6 +50,7 @@
   #:use-module (gnu packages documentation)
   #:use-module (gnu packages datastructures)
   #:use-module (gnu packages file)
+  #:use-module (gnu packages flex)
   #:use-module (gnu packages gawk)
   #:use-module (gnu packages gcc)
   #:use-module (gnu packages gd)
@@ -3472,6 +3473,45 @@ program for nucleotide and protein sequences.")
 ;; License information found in 'muscle -h' and usage.cpp.
 (license license:public-domain)))
 
+(define-public newick-utils
+  ;; There are no recent releases so we package from git.
+  (let ((commit "da121155a977197cab9fbb15953ca1b40b11eb87"))
+(package
+  (name "newick-utils")
+  (version (string-append "1.6-1." (string-take commit 8)))
+  (source (origin
+(method git-fetch)
+(uri (git-reference
+  (url "https://github.com/tjunier/newick_utils.git";)
+  (commit commit)))
+(file-name (string-append name "-" version "-checkout"))
+(sha256
+ (base32
+  "1hkw21rq1mwf7xp0rmbb2gqc0i6p11108m69i7mr7xcjl268pxnb"
+(build-system gnu-build-system)
+(arguments
+ `(#:phases
+   (modify-phases %standard-phases
+ (add-after 'unpack 'autoconf
+   (lambda _ (zero? (system* "autoreconf" "-vif")))
+(inputs
+ ;; XXX: TODO: Enable Lua and Guile bindings.
+ ;; https://github.com/tjunier/newick_utils/issues/13
+ `(("libxml2" ,libxml2)
+   ("flex" ,flex)
+   ("bison" ,bison)))
+(native-inputs
+ `(("autoconf" ,autoconf)
+   ("automake" ,automake)
+   ("libtool" ,libtool)))
+(synopsis "Programs for working with newick format phylogenetic trees")
+(description
+ "Newick-utils is a suite of utilities for processing phylogenetic trees
+in Newick format.  Functions include re-rooting, extracting subtrees,
+trimming, pruning, condensing, drawing (ASCII graphics or SVG).")
+(home-page "https://github.com/tjunier/newick_utils";)
+(license license:bsd-3
+
 (define-public orfm
   (package
 (name "orfm")

branch master updated (aa28ecc -> 9926875)

[Ben Woodcroft]

benwoodcroft pushed a change to branch master
in repository guix.

  from  aa28ecc   pull: Hack to allow compilation with older Guile-SSH 
packages.
   new  9926875   gnu: Add newick-utils.

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 |   40 +++
 1 file changed, 40 insertions(+)

01/02: gnu: Add proteinortho.

[Ben Woodcroft]

benwoodcroft pushed a commit to branch master
in repository guix.

commit 31a9d653ad37c9f00b601cfe4a95d90c35c09223
Author: Ben Woodcroft 
Date:   Sat Nov 26 14:59:30 2016 +1000

gnu: Add proteinortho.

* gnu/packages/bioinformatics.scm (proteinortho): New variable.
---
 gnu/packages/bioinformatics.scm |   52 +++
 1 file changed, 52 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 773b590..308931f 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -3693,6 +3693,58 @@ for sequences to be aligned and then, simultaneously 
with the alignment,
 predicts the locations of structural units in the sequences.")
 (license license:gpl2+)))
 
+(define-public proteinortho
+  (package
+(name "proteinortho")
+(version "5.15")
+(source
+ (origin
+  (method url-fetch)
+  (uri
+   (string-append
+"http://www.bioinf.uni-leipzig.de/Software/proteinortho/proteinortho_v";
+version "_src.tar.gz"))
+  (sha256
+   (base32
+"05wacnnbx56avpcwhzlcf6b7s77swcpv3qnwz5sh1z54i51gg2ki"
+(build-system gnu-build-system)
+(arguments
+ `(#:test-target "test"
+   #:phases
+   (modify-phases %standard-phases
+ (replace 'configure
+   ;; There is no configure script, so we modify the Makefile directly.
+   (lambda* (#:key outputs #:allow-other-keys)
+ (substitute* "Makefile"
+   (("INSTALLDIR=.*")
+(string-append
+ "INSTALLDIR=" (assoc-ref outputs "out") "/bin\n")))
+ #t))
+ (add-before 'install 'make-install-directory
+   ;; The install directory is not created during 'make install'.
+   (lambda* (#:key outputs #:allow-other-keys)
+ (mkdir-p (string-append (assoc-ref outputs "out") "/bin"))
+ #t))
+ (add-after 'install 'wrap-programs
+   (lambda* (#:key inputs outputs #:allow-other-keys)
+ (let* ((path (getenv "PATH"))
+(out (assoc-ref outputs "out"))
+(binary (string-append out "/bin/proteinortho5.pl")))
+   (wrap-program binary `("PATH" ":" prefix (,path
+ #t)
+(inputs
+ `(("perl" ,perl)
+   ("python" ,python-2)
+   ("blast+" ,blast+)))
+(home-page "http://www.bioinf.uni-leipzig.de/Software/proteinortho";)
+(synopsis "Detect orthologous genes across species")
+(description
+ "Proteinortho is a tool to detect orthologous genes across different
+species.  For doing so, it compares similarities of given gene sequences and
+clusters them to find significant groups.  The algorithm was designed to handle
+large-scale data and can be applied to hundreds of species at once.")
+(license license:gpl2+)))
+
 (define-public pyicoteo
   (package
 (name "pyicoteo")

02/02: gnu: roary: Update to 3.7.0.

[Ben Woodcroft]

benwoodcroft pushed a commit to branch master
in repository guix.

commit 5e0a0f4226b1f146fe74c8347fc983ef9ac0d271
Author: Ben Woodcroft 
Date:   Sat Nov 26 19:00:17 2016 +1000

gnu: roary: Update to 3.7.0.

* gnu/packages/bioinformatics.scm (roary): Update to 3.7.0.
---
 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 308931f..8d2cb93 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -3817,7 +3817,7 @@ partial genes, and identifies translation initiation 
sites.")
 (define-public roary
   (package
 (name "roary")
-(version "3.6.8")
+(version "3.7.0")
 (source
  (origin
(method url-fetch)
@@ -3826,7 +3826,7 @@ partial genes, and identifies translation initiation 
sites.")
  version ".tar.gz"))
(sha256
 (base32
- "0g0pzcv8y7n2w8q7c9q0a7s2ghkwci6w8smg9mjw4agad5cd7yaw"
+ "0x2hpb3nfsc6x2nq1788w0fhqfzc7cn2dp4xwyva9m3k6xlz0m43"
 (build-system perl-build-system)
 (arguments
  `(#:phases

branch master updated (d3eff97 -> 5e0a0f4)

[Ben Woodcroft]

benwoodcroft pushed a change to branch master
in repository guix.

  from  d3eff97   gnu: Add python-polib.
   new  31a9d65   gnu: Add proteinortho.
   new  5e0a0f4   gnu: roary: Update to 3.7.0.

The 2 revisions listed above as "new" are entirely new to this
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Summary of changes:
 gnu/packages/bioinformatics.scm |   56 +--
 1 file changed, 54 insertions(+), 2 deletions(-)

branch master updated (8e5f8c9 -> ee7518a)

[Ben Woodcroft]

benwoodcroft pushed a change to branch master
in repository guix.

  from  8e5f8c9   gnu: diamond: Update to 0.8.27.
   new  ee7518a   gnu: ruby: Update replacement to 2.3.3.

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Summary of changes:
 gnu/packages/ruby.scm |8 
 1 file changed, 4 insertions(+), 4 deletions(-)

01/01: gnu: ruby: Update replacement to 2.3.3.

[Ben Woodcroft]

benwoodcroft pushed a commit to branch master
in repository guix.

commit ee7518a009f2595879bb7e0275fa1f7ba8740819
Author: Ben Woodcroft 
Date:   Tue Nov 22 21:39:18 2016 +1000

gnu: ruby: Update replacement to 2.3.3.

* gnu/packages/ruby.scm (ruby)[replacement]: Update to 2.3.3.
(ruby-2.3.2): Replace this ...
(ruby-2.3.3): ... with this.
---
 gnu/packages/ruby.scm |8 
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/gnu/packages/ruby.scm b/gnu/packages/ruby.scm
index 1abea02..baae553 100644
--- a/gnu/packages/ruby.scm
+++ b/gnu/packages/ruby.scm
@@ -47,7 +47,7 @@
 (define-public ruby
   (package
 (name "ruby")
-(replacement ruby-2.3.2)
+(replacement ruby-2.3.3)
 (version "2.3.1")
 (source
  (origin
@@ -102,10 +102,10 @@ a focus on simplicity and productivity.")
 (home-page "https://ruby-lang.org";)
 (license license:ruby)))
 
-(define ruby-2.3.2
+(define ruby-2.3.3
   (package
 (inherit ruby)
-(version "2.3.2")
+(version "2.3.3")
 (source
  (origin
(method url-fetch)
@@ -114,7 +114,7 @@ a focus on simplicity and productivity.")
"/ruby-" version ".tar.xz"))
(sha256
 (base32
- "031g76zxb2wp6988dmrpbqd98i17xi6l8q1115h83r2w0h8z6y2w"))
+ "1p0rfk0blrbfjcnv0vb0ha4hxflgkfhv9zbzp4vvld2pi31ahkqs"))
(modules '((guix build utils)))
(snippet `(begin
;; Remove bundled libffi

branch staging updated (856f30b -> f4a8081)

[Ben Woodcroft]

benwoodcroft pushed a change to branch staging
in repository guix.

  from  856f30b   gnu: shared-mime-info: Update to 1.7
   new  f4a8081   gnu: ruby: Update to 2.3.3.

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

01/01: gnu: ruby: Update to 2.3.3.

[Ben Woodcroft]

benwoodcroft pushed a commit to branch staging
in repository guix.

commit f4a8081d2485944fd6fe6dc412e8b25f7de709d3
Author: Ben Woodcroft 
Date:   Tue Nov 22 21:35:58 2016 +1000

gnu: ruby: Update to 2.3.3.

* gnu/packages/ruby.scm (ruby): Update to 2.3.3.
---
 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 0f9b0d2..31eb8df 100644
--- a/gnu/packages/ruby.scm
+++ b/gnu/packages/ruby.scm
@@ -47,7 +47,7 @@
 (define-public ruby
   (package
 (name "ruby")
-(version "2.3.2")
+(version "2.3.3")
 (source
  (origin
(method url-fetch)
@@ -56,7 +56,7 @@
"/ruby-" version ".tar.xz"))
(sha256
 (base32
- "031g76zxb2wp6988dmrpbqd98i17xi6l8q1115h83r2w0h8z6y2w"))
+ "1p0rfk0blrbfjcnv0vb0ha4hxflgkfhv9zbzp4vvld2pi31ahkqs"))
(modules '((guix build utils)))
(snippet `(begin
;; Remove bundled libffi

branch master updated (1ea7969 -> 8e5f8c9)

[Ben Woodcroft]

benwoodcroft pushed a change to branch master
in repository guix.

  from  1ea7969   gnu: zynaddsubfx: Update to 3.0.0.
   new  8e5f8c9   gnu: diamond: Update to 0.8.27.

The 1 revisions listed above as "new" are entirely new to this
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Summary of changes:
 gnu/packages/bioinformatics.scm |4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

01/01: gnu: diamond: Update to 0.8.27.

[Ben Woodcroft]

benwoodcroft pushed a commit to branch master
in repository guix.

commit 8e5f8c98e21932cc6bc58c0f976d650b2323c087
Author: Ben Woodcroft 
Date:   Tue Nov 22 20:47:56 2016 +1000

gnu: diamond: Update to 0.8.27.

* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.27.
---
 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 97d3e48..773b590 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -2045,7 +2045,7 @@ identify enrichments with functional annotations of the 
genome.")
 (define-public diamond
   (package
 (name "diamond")
-(version "0.8.26")
+(version "0.8.27")
 (source (origin
   (method url-fetch)
   (uri (string-append
@@ -2054,7 +2054,7 @@ identify enrichments with functional annotations of the 
genome.")
   (file-name (string-append name "-" version ".tar.gz"))
   (sha256
(base32
-"17s38pgjih6yc2z81040pircbv60c9wr33mbcyki2rfpv8rbxlh0"
+"0g0zdyfnri9v7nfbh8f7zqs4af1xydqkiw8m0cx4jc2ql4chpf6a"
 (build-system cmake-build-system)
 (arguments
  '(#:tests? #f ; no "check" target

branch staging updated (caa9b83 -> 66b1bac)

[Ben Woodcroft]

benwoodcroft pushed a change to branch staging
in repository guix.

  from  caa9b83   guxi: cmake-build-system: Enable output for failing 
test-cases.
   new  66b1bac   gnu: ruby: Update to 2.3.2.

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Summary of changes:
 gnu/local.mk   |1 -
 gnu/packages/patches/ruby-symlinkfix.patch |   53 
 gnu/packages/ruby.scm  |5 ++-
 3 files changed, 2 insertions(+), 57 deletions(-)
 delete mode 100644 gnu/packages/patches/ruby-symlinkfix.patch

01/01: gnu: ruby: Update to 2.3.2.

[Ben Woodcroft]

benwoodcroft pushed a commit to branch staging
in repository guix.

commit 66b1bac355dbe57625891e08c82056b567e42e65
Author: Ben J Woodcroft 
Date:   Sat Nov 19 07:35:21 2016 +1000

gnu: ruby: Update to 2.3.2.

* gnu/packages/ruby.scm (ruby): Update to 2.3.2.
[replacement]: Remove field.
[origin]: Remove patch.
* gnu/packages/patches/ruby-symlinkfix.patch: Remove file.
* gnu/local.mk (dist_patch_DATA): Remove it.
---
 gnu/local.mk   |1 -
 gnu/packages/patches/ruby-symlinkfix.patch |   53 
 gnu/packages/ruby.scm  |5 ++-
 3 files changed, 2 insertions(+), 57 deletions(-)

diff --git a/gnu/local.mk b/gnu/local.mk
index 08f99c4..9a455e5 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -834,7 +834,6 @@ dist_patch_DATA =   
\
   %D%/packages/patches/ruby-concurrent-ignore-broken-test.patch\
   %D%/packages/patches/ruby-puma-ignore-broken-test.patch   \
   %D%/packages/patches/ruby-rack-ignore-failing-test.patch  \
-  %D%/packages/patches/ruby-symlinkfix.patch\
   %D%/packages/patches/ruby-tzinfo-data-ignore-broken-test.patch\
   %D%/packages/patches/ruby-yard-fix-skip-of-markdown-tests.patch \
   %D%/packages/patches/sed-hurd-path-max.patch \
diff --git a/gnu/packages/patches/ruby-symlinkfix.patch 
b/gnu/packages/patches/ruby-symlinkfix.patch
deleted file mode 100644
index 16beecc..000
--- a/gnu/packages/patches/ruby-symlinkfix.patch
+++ /dev/null
@@ -1,53 +0,0 @@
-Fix symlinks to '..' to fix rubygems improperly expanding symlinked
-paths. Without this fix, some gems fail to install. This patch is applied in
-rubygems 2.5.2, but ruby version 2.3.1 bundles an older version of rubygems
-(2.5.1).
-
 a/lib/rubygems/package.rb
-+++ b/lib/rubygems/package.rb
-@@ -383,7 +383,7 @@ def extract_tar_gz io, destination_dir, pattern = "*" # 
:nodoc:
-   FileUtils.chmod entry.header.mode, destination
- end if entry.file?
-
--File.symlink(install_location(entry.header.linkname, 
destination_dir), destination) if entry.symlink?
-+File.symlink(entry.header.linkname, destination) if entry.symlink?
-
- verbose destination
-   end
-diff --git a/test/rubygems/test_gem_package.rb 
b/test/rubygems/test_gem_package.rb
-index 7848bc2..f287bd3 100644
 a/test/rubygems/test_gem_package.rb
-+++ b/test/rubygems/test_gem_package.rb
-@@ -428,19 +428,25 @@ def test_extract_tar_gz_absolute
-  "#{@destination} is not allowed", e.message)
-   end
-
--  def test_extract_tar_gz_symlink_absolute
-+  def test_extract_tar_gz_symlink_relative_path
-+skip 'symlink not supported' if Gem.win_platform?
-+
- package = Gem::Package.new @gem
-
- tgz_io = util_tar_gz do |tar|
--  tar.add_symlink 'code.rb', '/absolute.rb', 0644
-+  tar.add_file'relative.rb', 0644 do |io| io.write 'hi' end
-+  tar.mkdir   'lib', 0755
-+  tar.add_symlink 'lib/foo.rb', '../relative.rb', 0644
- end
-
--e = assert_raises Gem::Package::PathError do
--  package.extract_tar_gz tgz_io, @destination
--end
-+package.extract_tar_gz tgz_io, @destination
-
--assert_equal("installing into parent path /absolute.rb of " +
-- "#{@destination} is not allowed", e.message)
-+extracted = File.join @destination, 'lib/foo.rb'
-+assert_path_exists extracted
-+assert_equal '../relative.rb',
-+ File.readlink(extracted)
-+assert_equal 'hi',
-+ File.read(extracted)
-   end
-
-   def test_extract_tar_gz_directory
diff --git a/gnu/packages/ruby.scm b/gnu/packages/ruby.scm
index 42beda3..0f9b0d2 100644
--- a/gnu/packages/ruby.scm
+++ b/gnu/packages/ruby.scm
@@ -47,7 +47,7 @@
 (define-public ruby
   (package
 (name "ruby")
-(version "2.3.1")
+(version "2.3.2")
 (source
  (origin
(method url-fetch)
@@ -56,9 +56,8 @@
"/ruby-" version ".tar.xz"))
(sha256
 (base32
- "0f3395q7pd2hrl2gv26bib80038sjawxgmhl9zn22fjs9m9va9b7"))
+ "031g76zxb2wp6988dmrpbqd98i17xi6l8q1115h83r2w0h8z6y2w"))
(modules '((guix build utils)))
-   (patches (search-patches "ruby-symlinkfix.patch"))
(snippet `(begin
;; Remove bundled libffi
(delete-file-recursively "ext/fiddle/libffi-3.2.1")

branch master updated (966a543 -> 9b62c5a)

[Ben Woodcroft]

benwoodcroft pushed a change to branch master
in repository guix.

  from  966a543   gnu: Use 'mirror://' URLs in several places.
   new  9b62c5a   gnu: ruby: Replace with ruby-2.3.2 [fixes CVE-2015-3900].

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Summary of changes:
 gnu/packages/ruby.scm |   20 
 1 file changed, 20 insertions(+)

01/01: gnu: ruby: Replace with ruby-2.3.2 [fixes CVE-2015-3900].

[Ben Woodcroft]

benwoodcroft pushed a commit to branch master
in repository guix.

commit 9b62c5a8fb588aac5002b899e3b1a3b0ac1bb428
Author: Ben Woodcroft 
Date:   Sat Nov 19 09:00:22 2016 +1000

gnu: ruby: Replace with ruby-2.3.2 [fixes CVE-2015-3900].

* gnu/packages/ruby.scm (ruby)[replacement]: New field.
(ruby-2.3.2): New variable.
---
 gnu/packages/ruby.scm |   20 
 1 file changed, 20 insertions(+)

diff --git a/gnu/packages/ruby.scm b/gnu/packages/ruby.scm
index b6cb0a2..1abea02 100644
--- a/gnu/packages/ruby.scm
+++ b/gnu/packages/ruby.scm
@@ -47,6 +47,7 @@
 (define-public ruby
   (package
 (name "ruby")
+(replacement ruby-2.3.2)
 (version "2.3.1")
 (source
  (origin
@@ -101,6 +102,25 @@ a focus on simplicity and productivity.")
 (home-page "https://ruby-lang.org";)
 (license license:ruby)))
 
+(define ruby-2.3.2
+  (package
+(inherit ruby)
+(version "2.3.2")
+(source
+ (origin
+   (method url-fetch)
+   (uri (string-append "http://cache.ruby-lang.org/pub/ruby/";
+   (version-major+minor version)
+   "/ruby-" version ".tar.xz"))
+   (sha256
+(base32
+ "031g76zxb2wp6988dmrpbqd98i17xi6l8q1115h83r2w0h8z6y2w"))
+   (modules '((guix build utils)))
+   (snippet `(begin
+   ;; Remove bundled libffi
+   (delete-file-recursively "ext/fiddle/libffi-3.2.1")
+   #t))
+
 (define-public ruby-2.2
   (package (inherit ruby)
 (version "2.2.6")

branch master updated (4af8027 -> 6689c63)

[Ben Woodcroft]

benwoodcroft pushed a change to branch master
in repository guix.

  from  4af8027   gnu: ruby-2.2: Update to 2.2.6.
   new  6689c63   gnu: Add ruby-net-http-digest-auth.

The 1 revisions listed above as "new" are entirely new to this
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listed as "adds" were already present in the repository and have only
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Summary of changes:
 gnu/packages/ruby.scm |   22 ++
 1 file changed, 22 insertions(+)

01/01: gnu: Add ruby-net-http-digest-auth.

[Ben Woodcroft]

benwoodcroft pushed a commit to branch master
in repository guix.

commit 6689c636d039ce5bf160c1858b99f4329427fd15
Author: Muriithi Frederick Muriuki 
Date:   Thu Nov 17 17:33:01 2016 +1000

gnu: Add ruby-net-http-digest-auth.

* gnu/packages/ruby.scm (ruby-net-http-digest-auth): New variable.
---
 gnu/packages/ruby.scm |   22 ++
 1 file changed, 22 insertions(+)

diff --git a/gnu/packages/ruby.scm b/gnu/packages/ruby.scm
index e4c1ef0..b6cb0a2 100644
--- a/gnu/packages/ruby.scm
+++ b/gnu/packages/ruby.scm
@@ -4179,3 +4179,25 @@ patterns.")
 libraries for compiling Ruby native extensions.")
 (home-page "https://github.com/ruby-gnome2/pkg-config";)
 (license license:lgpl2.0+)))
+
+(define-public ruby-net-http-digest-auth
+  (package
+(name "ruby-net-http-digest-auth")
+(version "1.4")
+(source
+ (origin
+   (method url-fetch)
+   (uri (rubygems-uri "net-http-digest_auth" version))
+   (sha256
+(base32
+ "14801gr34g0rmqz9pv4rkfa3crfdbyfk6r48vpg5a5407v0sixqi"
+(build-system ruby-build-system)
+(native-inputs
+ `(("ruby-hoe" ,ruby-hoe)))
+(synopsis "RFC 2617 HTTP digest authentication library")
+(description
+ "This library implements HTTP's digest authentication scheme based on
+RFC 2617.  This enables the use of the digest authentication scheme instead
+of the more insecure basic authentication scheme.")
+(home-page "http://github.com/drbrain/net-http-digest_auth";)
+(license license:expat)))

01/01: gnu: ruby-2.2: Update to 2.2.6.

[Ben Woodcroft]

benwoodcroft pushed a commit to branch master
in repository guix.

commit 4af80275a87fceeb2dcc7cf5198bb7f12d911d0f
Author: Ben J Woodcroft 
Date:   Fri Nov 18 15:42:44 2016 +1000

gnu: ruby-2.2: Update to 2.2.6.

* gnu/packages/ruby.scm (ruby-2.2): Update to 2.2.6.
---
 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 42beda3..e4c1ef0 100644
--- a/gnu/packages/ruby.scm
+++ b/gnu/packages/ruby.scm
@@ -103,7 +103,7 @@ a focus on simplicity and productivity.")
 
 (define-public ruby-2.2
   (package (inherit ruby)
-(version "2.2.5")
+(version "2.2.6")
 (source
  (origin
(method url-fetch)
@@ -112,7 +112,7 @@ a focus on simplicity and productivity.")
"/ruby-" version ".tar.xz"))
(sha256
 (base32
- "1mw7bzw76g5w37cwhb57r6gxcl2vn9lfrlyf4h4xms3qlnhflvzq"))
+ "0fbk2pyjphynj4kxn27vb5rsq6brr3y85p784jd1rxwws30fq54l"))
 
 (define-public ruby-2.1
   (package (inherit ruby)

branch master updated (175d626 -> 4af8027)

[Ben Woodcroft]

benwoodcroft pushed a change to branch master
in repository guix.

  from  175d626   gnu: mps-youtube: Disable tests.
   new  4af8027   gnu: ruby-2.2: Update to 2.2.6.

The 1 revisions listed above as "new" are entirely new to this
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Summary of changes:
 gnu/packages/ruby.scm |4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

branch master updated (e2bb2e1 -> 8be62d3)

[Ben Woodcroft]

benwoodcroft pushed a change to branch master
in repository guix.

  from  e2bb2e1   gnu: ruby-yard: Update to 0.9.5-1.d816482a.
   new  bb4bcb0   gnu: bundler: Update to 1.13.6.
   new  c594911   gnu: ruby-rspec-core: Update to 3.5.4.
   new  81d0bd2   gnu: ruby-hoe: Update to 3.15.2.
   new  16d8d8b   gnu: ruby-rake-compiler: Update to 1.0.1.
   new  e87dfde   gnu: ruby-arel: Update to 7.1.4.
   new  8be62d3   gnu: ruby-lumberjack: Update to 1.0.10.

The 6 revisions listed above as "new" are entirely new to this
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listed as "adds" were already present in the repository and have only
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Summary of changes:
 gnu/packages/ruby.scm |   27 ++-
 1 file changed, 14 insertions(+), 13 deletions(-)

05/06: gnu: ruby-arel: Update to 7.1.4.

[Ben Woodcroft]

benwoodcroft pushed a commit to branch master
in repository guix.

commit e87dfdee865c6d73e272d734a6f4cf0e019c91aa
Author: Ben Woodcroft 
Date:   Fri Nov 11 22:48:22 2016 +1000

gnu: ruby-arel: Update to 7.1.4.

* gnu/packages/ruby.scm (ruby-arel): Update to 7.1.4.
---
 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 d6493a0..61f6ab8 100644
--- a/gnu/packages/ruby.scm
+++ b/gnu/packages/ruby.scm
@@ -1839,13 +1839,13 @@ net/http library.")
 (define-public ruby-arel
   (package
 (name "ruby-arel")
-(version "7.1.1")
+(version "7.1.4")
 (source (origin
   (method url-fetch)
   (uri (rubygems-uri "arel" version))
   (sha256
(base32
-"0d6kfsh7qf5gls0n1nrppxv89zyli27kw8nklpq2by3z7cxjcvjg"
+"0l757dkkaxk5fq3368l79jpyzq9a9driricjamhiwhwvh0h7xcyx"
 (build-system ruby-build-system)
 (arguments '(#:tests? #f)) ; no tests
 (home-page "https://github.com/rails/arel";)

03/06: gnu: ruby-hoe: Update to 3.15.2.

[Ben Woodcroft]

benwoodcroft pushed a commit to branch master
in repository guix.

commit 81d0bd2f443049e50be3927c24b7cdb3bf445b83
Author: Ben Woodcroft 
Date:   Fri Nov 11 22:44:03 2016 +1000

gnu: ruby-hoe: Update to 3.15.2.

* gnu/packages/ruby.scm (ruby-hoe): Update to 3.15.2.
---
 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 14fb7c9..0246093 100644
--- a/gnu/packages/ruby.scm
+++ b/gnu/packages/ruby.scm
@@ -178,13 +178,13 @@ a focus on simplicity and productivity.")
 (define-public ruby-hoe
   (package
 (name "ruby-hoe")
-(version "3.13.1")
+(version "3.15.2")
 (source (origin
   (method url-fetch)
   (uri (rubygems-uri "hoe" version))
   (sha256
(base32
-"1mac13krdrasn9819dd65xj27kklfy0xdbj3p6s2ij4vlcb46h8q"))) )
+"1riyf9j9vp7dzgpw5xj9xx1vqkdmg6lr7qiprmn91hcdp81kaszp"))) )
 (build-system ruby-build-system)
 (synopsis "Ruby project management helper")
 (description

04/06: gnu: ruby-rake-compiler: Update to 1.0.1.

[Ben Woodcroft]

benwoodcroft pushed a commit to branch master
in repository guix.

commit 16d8d8b289feccb5aacc18437177a05fa0f46df6
Author: Ben Woodcroft 
Date:   Fri Nov 11 22:45:38 2016 +1000

gnu: ruby-rake-compiler: Update to 1.0.1.

* gnu/packages/ruby.scm (ruby-rake-compiler): Update to 1.0.1.
---
 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 0246093..d6493a0 100644
--- a/gnu/packages/ruby.scm
+++ b/gnu/packages/ruby.scm
@@ -199,13 +199,13 @@ announcement.")
 (define-public ruby-rake-compiler
   (package
 (name "ruby-rake-compiler")
-(version "0.9.5")
+(version "1.0.1")
 (source (origin
   (method url-fetch)
   (uri (rubygems-uri "rake-compiler" version))
   (sha256
(base32
-"1k8im2vzj849xdgjk6wafspkiwwapqwm738majchb4dnhnsk64cx"
+"1lf91nf1fcnmsh54mxz06wyfmjkwh58vljr35zns5cwbg8fwmi20"
 (build-system ruby-build-system)
 (arguments
  '(#:tests? #f)) ; needs cucumber

06/06: gnu: ruby-lumberjack: Update to 1.0.10.

[Ben Woodcroft]

benwoodcroft pushed a commit to branch master
in repository guix.

commit 8be62d3f2031a1c0b046b8840948359dac104ac3
Author: Ben Woodcroft 
Date:   Fri Nov 11 22:49:19 2016 +1000

gnu: ruby-lumberjack: Update to 1.0.10.

* gnu/packages/ruby.scm (ruby-lumberjack): Update to 1.0.10.
[native-inputs]: Add 'ruby-timecop'.
---
 gnu/packages/ruby.scm |7 ---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/ruby.scm b/gnu/packages/ruby.scm
index 61f6ab8..42beda3 100644
--- a/gnu/packages/ruby.scm
+++ b/gnu/packages/ruby.scm
@@ -710,16 +710,17 @@ interfaces.")
 (define-public ruby-lumberjack
   (package
 (name "ruby-lumberjack")
-(version "1.0.9")
+(version "1.0.10")
 (source (origin
   (method url-fetch)
   (uri (rubygems-uri "lumberjack" version))
   (sha256
(base32
-"162frm2bwy58pj8ccsdqa4a6i0csrhb9h5l3inhkl1ivgfc8814l"
+"0ily8j83q959w19zb7qm6m7y53sdj9afxj4x6mn2adl4i7vpdsv4"
 (build-system ruby-build-system)
 (native-inputs
- `(("ruby-rspec" ,ruby-rspec)))
+ `(("ruby-rspec" ,ruby-rspec)
+   ("ruby-timecop" ,ruby-timecop)))
 (synopsis "Logging utility library for Ruby")
 (description "Lumberjack is a simple logging utility that can be a drop in
 replacement for Logger or ActiveSupport::BufferedLogger.  It provides support

02/06: gnu: ruby-rspec-core: Update to 3.5.4.

[Ben Woodcroft]

benwoodcroft pushed a commit to branch master
in repository guix.

commit c59491183a3eff24da52d46dabe99ef1c29df8f5
Author: Ben Woodcroft 
Date:   Fri Nov 11 22:40:39 2016 +1000

gnu: ruby-rspec-core: Update to 3.5.4.

* gnu/packages/ruby.scm (ruby-rspec-core): Update to 3.5.4.
---
 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 ec1b935..14fb7c9 100644
--- a/gnu/packages/ruby.scm
+++ b/gnu/packages/ruby.scm
@@ -262,13 +262,13 @@ an extensible architecture with a swappable backend.")
 (define-public ruby-rspec-core
   (package
 (name "ruby-rspec-core")
-(version "3.5.1")
+(version "3.5.4")
 (source (origin
   (method url-fetch)
   (uri (rubygems-uri "rspec-core" version))
   (sha256
(base32
-"0brfq51fwkkh5g6vw7smky5fvip46pryi243jmin0nzn7iwh9j5g"
+"1nacs062qbr98fx6czf1vwppn1js956nv2c8vfwj6i65axdfs46i"
 (build-system ruby-build-system)
 (arguments
  '(#:tests? #f)) ; avoid dependency cycles

01/06: gnu: bundler: Update to 1.13.6.

[Ben Woodcroft]

benwoodcroft pushed a commit to branch master
in repository guix.

commit bb4bcb02c269b9de72bbe1a3de9af5cbbea88451
Author: Ben Woodcroft 
Date:   Fri Nov 11 22:38:13 2016 +1000

gnu: bundler: Update to 1.13.6.

* gnu/packages/ruby.scm (bundler): Update to 1.13.6.
---
 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 dd9984f..ec1b935 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 "1.13.5")
+(version "1.13.6")
 (source (origin
   (method url-fetch)
   (uri (rubygems-uri "bundler" version))
   (sha256
(base32
-"0fxr7aq7qhlga423mygy7q96cwxmvqlcy676v2x5swlw8rlha2in"
+"1xyhy9cn8w9passp64p6hb3df2fpiqbds6rj7xha1335xpgj5zgs"
 (build-system ruby-build-system)
 (arguments
  '(#:tests? #f)) ; avoid dependency cycles

01/01: gnu: ruby-yard: Update to 0.9.5-1.d816482a.

[Ben Woodcroft]

benwoodcroft pushed a commit to branch master
in repository guix.

commit e2bb2e1780ce875cc03cd5cc559f1dbc528d6f8e
Author: Ben Woodcroft 
Date:   Tue Nov 8 09:39:47 2016 +1000

gnu: ruby-yard: Update to 0.9.5-1.d816482a.

* gnu/packages/ruby.scm (ruby-yard): Update to 0.9.5-1.d816482a.
[source]: Update source URL.
[arguments]: Remove unneeded substitutions.  Change test target.
* gnu/packages/patches/ruby-yard-fix-skip-of-markdown-tests.patch (New
file)
* gnu/local.mk (dist_patch_DATA): Add it.
---
 gnu/local.mk   |2 +
 .../ruby-yard-fix-skip-of-markdown-tests.patch |   17 +
 gnu/packages/ruby.scm  |   69 ++--
 3 files changed, 54 insertions(+), 34 deletions(-)

diff --git a/gnu/local.mk b/gnu/local.mk
index b3a4cd5..b8c597e 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -7,6 +7,7 @@
 # Copyright © 2016 Kei Kebreau 
 # Copyright © 2016 Adonay "adfeno" Felipe Nogueira 
<https://libreplanet.org/wiki/User:Adfeno> 
 # Copyright © 2016 Ricardo Wurmus 
+# Copyright © 2016 Ben Woodcroft 
 #
 # This file is part of GNU Guix.
 #
@@ -841,6 +842,7 @@ dist_patch_DATA =   
\
   %D%/packages/patches/ruby-rack-ignore-failing-test.patch  \
   %D%/packages/patches/ruby-symlinkfix.patch\
   %D%/packages/patches/ruby-tzinfo-data-ignore-broken-test.patch\
+  %D%/packages/patches/ruby-yard-fix-skip-of-markdown-tests.patch \
   %D%/packages/patches/sed-hurd-path-max.patch \
   %D%/packages/patches/scheme48-tests.patch\
   %D%/packages/patches/scotch-test-threading.patch \
diff --git a/gnu/packages/patches/ruby-yard-fix-skip-of-markdown-tests.patch 
b/gnu/packages/patches/ruby-yard-fix-skip-of-markdown-tests.patch
new file mode 100644
index 000..f592f5c
--- /dev/null
+++ b/gnu/packages/patches/ruby-yard-fix-skip-of-markdown-tests.patch
@@ -0,0 +1,17 @@
+The tests currently fail due to use of 'skip' rather than 'pending' to skip a
+test usually not skipped by upstream.  This patch has been proposed upstream
+at https://github.com/lsegal/yard/pull/1033
+
+diff --git a/spec/templates/helpers/html_helper_spec.rb 
b/spec/templates/helpers/html_helper_spec.rb
+index 84624c3..9c4fc2b 100644
+--- a/spec/templates/helpers/html_helper_spec.rb
 b/spec/templates/helpers/html_helper_spec.rb
+@@ -184,7 +184,7 @@ describe YARD::Templates::Helpers::HtmlHelper do
+ it "creates tables (markdown specific)" do
+   log.enter_level(Logger::FATAL) do
+ unless markup_class(:markdown).to_s == "RedcarpetCompat"
+-  skip "This test depends on a markdown engine that supports tables"
++  pending "This test depends on a markdown engine that supports 
tables"
+ end
+   end
+ 
diff --git a/gnu/packages/ruby.scm b/gnu/packages/ruby.scm
index a770486..dd9984f 100644
--- a/gnu/packages/ruby.scm
+++ b/gnu/packages/ruby.scm
@@ -3047,43 +3047,44 @@ features such as filtering and fine grained logging.")
 (license license:expat)))
 
 (define-public ruby-yard
-  (package
-(name "ruby-yard")
-(version "0.8.7.6")
-(source
- (origin
-   (method url-fetch)
-   (uri (rubygems-uri "yard" version))
-   (sha256
-(base32
- "1dj6ibc0qqvmb5a5r5kk0vhr04mnrz9b26gnfrs5p8jgp620i89x"
-(build-system ruby-build-system)
-(arguments
- `(#:test-target "specs"
-   #:phases
-   (modify-phases %standard-phases
- (add-before 'check 'set-HOME-and-disable-failing-test
-   (lambda _
- ;; $HOME needs to be set to somewhere writeable for tests to run
- (setenv "HOME" "/tmp")
- ;; Disable tests which fails on Ruby 2.3.  See
- ;; https://github.com/lsegal/yard/issues/927
- (substitute* "spec/parser/ruby/ruby_parser_spec.rb"
-   (("comment.type.should == :comment") "")
-   (("comment.docstring_hash_flag.should be_true") "")
-   (("comment.docstring.strip.should == .*") ""))
- #t)
-(native-inputs
- `(("ruby-rspec" ,ruby-rspec-2)
-   ("ruby-rack" ,ruby-rack)))
-(synopsis "Documentation generation tool for Ruby")
-(description
- "YARD is a documentation generation tool for the Ruby programming
+  ;; Use git reference because gem is >100 commits out of date and the tests
+  ;; do not pass with the released gem.
+  (let ((commit "d816482a0d4850506c3b9434550c536c28c6"))
+(package
+  (name "ruby-yard")
+  (version (string-append "0.9.5-1." (string-take 

branch master updated (7c45670 -> e2bb2e1)

[Ben Woodcroft]

benwoodcroft pushed a change to branch master
in repository guix.

  from  7c45670   gnu: r-org-mm-eg-db: Update to 3.4.0.
   new  e2bb2e1   gnu: ruby-yard: Update to 0.9.5-1.d816482a.

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 +
 .../ruby-yard-fix-skip-of-markdown-tests.patch |   17 +
 gnu/packages/ruby.scm  |   69 ++--
 3 files changed, 54 insertions(+), 34 deletions(-)
 create mode 100644 
gnu/packages/patches/ruby-yard-fix-skip-of-markdown-tests.patch

05/07: gnu: ruby-shoulda-context: Update to 1.2.2.

[Ben Woodcroft]

benwoodcroft pushed a commit to branch master
in repository guix.

commit e7d1d472cdd05f3de048e33c6a9b88212a0b059a
Author: Ben Woodcroft 
Date:   Mon Nov 7 21:35:07 2016 +1000

gnu: ruby-shoulda-context: Update to 1.2.2.

* gnu/packages/ruby.scm (ruby-shoulda-context): Update to 1.2.2.
---
 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 de186ff..99556df 100644
--- a/gnu/packages/ruby.scm
+++ b/gnu/packages/ruby.scm
@@ -,14 +,14 @@ engine.")
 (define-public ruby-shoulda-context
   (package
 (name "ruby-shoulda-context")
-(version "1.2.1")
+(version "1.2.2")
 (source
  (origin
(method url-fetch)
(uri (rubygems-uri "shoulda-context" version))
(sha256
 (base32
- "06wv2ika5zrbxn0m3qxwk0zkbspxids3zmlq3xxays5qmvl1qb55"
+ "1l0ncsxycb4s8n47dml97kdnixw4mizljbkwqc3rh05r70csq9bc"
 (build-system ruby-build-system)
 (arguments
  `(#:phases

03/07: gnu: ruby-http-cookie: Update to 1.0.3.

[Ben Woodcroft]

benwoodcroft pushed a commit to branch master
in repository guix.

commit 2a2eb07d87e8c1e1947b3cfb02071d37e3c6db20
Author: Ben Woodcroft 
Date:   Mon Nov 7 21:33:41 2016 +1000

gnu: ruby-http-cookie: Update to 1.0.3.

* gnu/packages/ruby.scm (ruby-http-cookie): Update to 1.0.3.
---
 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 8bd114c..54f9499 100644
--- a/gnu/packages/ruby.scm
+++ b/gnu/packages/ruby.scm
@@ -3509,14 +3509,14 @@ Suffix List.")
 (define-public ruby-http-cookie
   (package
 (name "ruby-http-cookie")
-(version "1.0.2")
+(version "1.0.3")
 (source
  (origin
(method url-fetch)
(uri (rubygems-uri "http-cookie" version))
(sha256
 (base32
- "0cz2fdkngs3jc5w32a6xcl511hy03a7zdiy988jk1sf3bf5v3hdw"
+ "004cgs4xg5n6byjs7qld0xhsjq3n6ydfh897myr2mibvh6fjc49g"
 (build-system ruby-build-system)
 (arguments
  `(#:phases

07/07: gnu: ruby-tzinfo-data: Update to 1.2016.9.

[Ben Woodcroft]

benwoodcroft pushed a commit to branch master
in repository guix.

commit 06028aed7c4faab5d3442feff49d117027116a30
Author: Ben Woodcroft 
Date:   Mon Nov 7 21:36:24 2016 +1000

gnu: ruby-tzinfo-data: Update to 1.2016.9.

* gnu/packages/ruby.scm (ruby-tzinfo-data): Update to 1.2016.9.
---
 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 7dec0fb..a770486 100644
--- a/gnu/packages/ruby.scm
+++ b/gnu/packages/ruby.scm
@@ -2115,7 +2115,7 @@ aware transformations between times in different time 
zones.")
 (define-public ruby-tzinfo-data
   (package
 (name "ruby-tzinfo-data")
-(version "1.2016.7")
+(version "1.2016.9")
 (source
  (origin
(method url-fetch)
@@ -2128,7 +2128,7 @@ aware transformations between times in different time 
zones.")
(file-name (string-append name "-" version ".tar.gz"))
(sha256
 (base32
- "0vh75hkfmqk4hdjv6nm7acw64izwpnv7slkmh2kj7qlfz133yh9l"))
+ "0i8vz2j7wmcpr4pd066qvlg4if5blscjrgxk2imavfa49nq5lp06"))
;; Remove the known test failure.
;; https://github.com/tzinfo/tzinfo-data/issues/10
;; https://bugs.launchpad.net/ubuntu/+source/glibc/+bug/1587128

04/07: gnu: ruby-domain-name: Update to 0.5.20161021.

[Ben Woodcroft]

benwoodcroft pushed a commit to branch master
in repository guix.

commit ca0839142e827e3d4b930f9b9e6eea7097f9b977
Author: Ben Woodcroft 
Date:   Mon Nov 7 21:34:15 2016 +1000

gnu: ruby-domain-name: Update to 0.5.20161021.

* gnu/packages/ruby.scm (ruby-domain-name): Update to 0.5.20161021.
---
 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 54f9499..de186ff 100644
--- a/gnu/packages/ruby.scm
+++ b/gnu/packages/ruby.scm
@@ -3469,14 +3469,14 @@ support to both Ruby and JRuby.  It uses @code{unf_ext} 
on CRuby and
 (define-public ruby-domain-name
   (package
 (name "ruby-domain-name")
-(version "0.5.20160826")
+(version "0.5.20161021")
 (source
  (origin
(method url-fetch)
(uri (rubygems-uri "domain_name" version))
(sha256
 (base32
- "0rg7gvp45xmb5qz8ydp7ivw05hhplh6k7mbawrpvkysl2c77w5xx"
+ "1y5c96gzyh6z4nrnkisljqngfvljdba36dww657ka0x7khzvx7jl"
 (build-system ruby-build-system)
 (arguments
  `(#:phases

branch master updated (bd91748 -> 06028ae)

[Ben Woodcroft]

benwoodcroft pushed a change to branch master
in repository guix.

  from  bd91748   gnu: texmaker: Use modular qt and qtwebkit.
   new  3cf7c31   gnu: diamond: Update to 0.8.26.
   new  420fdfe   gnu: ruby-sequel: Update to 4.40.0.
   new  2a2eb07   gnu: ruby-http-cookie: Update to 1.0.3.
   new  ca08391   gnu: ruby-domain-name: Update to 0.5.20161021.
   new  e7d1d47   gnu: ruby-shoulda-context: Update to 1.2.2.
   new  17ba688   gnu: ruby-sqlite3: Update to 1.3.12.
   new  06028ae   gnu: ruby-tzinfo-data: Update to 1.2016.9.

The 7 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 |4 ++--
 gnu/packages/ruby.scm   |   24 
 2 files changed, 14 insertions(+), 14 deletions(-)

01/07: gnu: diamond: Update to 0.8.26.

[Ben Woodcroft]

benwoodcroft pushed a commit to branch master
in repository guix.

commit 3cf7c3172080d5a7f442058c4145949b71e1201c
Author: Ben Woodcroft 
Date:   Mon Nov 7 21:31:09 2016 +1000

gnu: diamond: Update to 0.8.26.

* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.26.
---
 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 4dfac15..299275c 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -2048,7 +2048,7 @@ identify enrichments with functional annotations of the 
genome.")
 (define-public diamond
   (package
 (name "diamond")
-(version "0.8.23")
+(version "0.8.26")
 (source (origin
   (method url-fetch)
   (uri (string-append
@@ -2057,7 +2057,7 @@ identify enrichments with functional annotations of the 
genome.")
   (file-name (string-append name "-" version ".tar.gz"))
   (sha256
(base32
-"0xpcq3fbk4c52xbpgyk5brl58rljvl83bg8nkxy8vs00pxanm7i2"
+"17s38pgjih6yc2z81040pircbv60c9wr33mbcyki2rfpv8rbxlh0"
 (build-system cmake-build-system)
 (arguments
  '(#:tests? #f ; no "check" target

02/07: gnu: ruby-sequel: Update to 4.40.0.

[Ben Woodcroft]

benwoodcroft pushed a commit to branch master
in repository guix.

commit 420fdfef9a386f49c3cda0eabf9747c866a07007
Author: Ben Woodcroft 
Date:   Mon Nov 7 21:32:32 2016 +1000

gnu: ruby-sequel: Update to 4.40.0.

* gnu/packages/ruby.scm (ruby-sequel): Update to 4.40.0.
---
 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 60f1992..8bd114c 100644
--- a/gnu/packages/ruby.scm
+++ b/gnu/packages/ruby.scm
@@ -4043,14 +4043,14 @@ generation.")
 (define-public ruby-sequel
   (package
 (name "ruby-sequel")
-(version "4.39.0")
+(version "4.40.0")
 (source
  (origin
(method url-fetch)
(uri (rubygems-uri "sequel" version))
(sha256
 (base32
- "01zqd6mi9wvhbg76b91k35jppha0c944ar9f816gi400cf9817bg"
+ "0r39dv3yprai0cy7hslfxswjr4fg783xwxskmbih8ry24f18lbk0"
 (build-system ruby-build-system)
 (arguments
  '(#:tests? #f)) ; Avoid dependency loop with ruby-minitest-hooks.

06/07: gnu: ruby-sqlite3: Update to 1.3.12.

[Ben Woodcroft]

benwoodcroft pushed a commit to branch master
in repository guix.

commit 17ba688c4900d147fb404ab52d74facae9fef9aa
Author: Ben Woodcroft 
Date:   Mon Nov 7 21:35:31 2016 +1000

gnu: ruby-sqlite3: Update to 1.3.12.

* gnu/packages/ruby.scm (ruby-sqlite3): Update to 1.3.12.
---
 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 99556df..7dec0fb 100644
--- a/gnu/packages/ruby.scm
+++ b/gnu/packages/ruby.scm
@@ -3301,14 +3301,14 @@ neither too verbose nor too minimal.")
 (define-public ruby-sqlite3
   (package
 (name "ruby-sqlite3")
-(version "1.3.11")
+(version "1.3.12")
 (source
  (origin
(method url-fetch)
(uri (rubygems-uri "sqlite3" version))
(sha256
 (base32
- "19r06wglnm6479ffj9dl0fa4p5j2wi6dj7k6k3d0rbx7036cv3ny"
+ "0hld87rvwyy31xsxzhicv2lj3g3kmvmwfxj09kw13g6lacdjz4bx"
 (build-system ruby-build-system)
 (arguments
  `(#:phases

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

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)

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


Summary of changes:
 gnu/packages/ruby.scm |6 --
 1 file changed, 4 insertions(+), 2 deletions(-)

01/01: gnu: vsearch: Update to 2.3.0.

[Ben Woodcroft]

benwoodcroft pushed a commit to branch master
in repository guix.

commit 3dd50d974b63cb9c2d934164ac8d8d1b86fa3dc1
Author: Ben Woodcroft 
Date:   Tue Oct 11 22:29:48 2016 +1000

gnu: vsearch: Update to 2.3.0.

* gnu/packages/bioinformatics.scm (vsearch): Update to 2.3.0.
---
 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 e313721..5fbfdf0 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -5594,7 +5594,7 @@ track.  The database is exposed as a @code{TxDb} object.")
 (define-public vsearch
   (package
 (name "vsearch")
-(version "2.1.2")
+(version "2.3.0")
 (source
  (origin
(method url-fetch)
@@ -5604,7 +5604,7 @@ track.  The database is exposed as a @code{TxDb} object.")
(file-name (string-append name "-" version ".tar.gz"))
(sha256
 (base32
- "1zzfj6ydsfzljyswlwqknpp8s2cf31vimi1aqf9ljsbagjyizc58"))
+ "1r8fk3whkil348y5hfsd4r56qjmchhq4nxm6s7ra5rlisw0mf9fy"))
(modules '((guix build utils)))
(snippet
 '(begin

branch master updated (99c9056 -> 3dd50d9)

[Ben Woodcroft]

benwoodcroft pushed a change to branch master
in repository guix.

  from  99c9056   gnu: diamond: Update to 0.8.23.
   new  3dd50d9   gnu: vsearch: Update to 2.3.0.

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


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

01/01: gnu: diamond: Update to 0.8.23.

[Ben Woodcroft]

benwoodcroft pushed a commit to branch master
in repository guix.

commit 99c90561418bc572b096d0961d4e5dc0d6658d45
Author: Ben Woodcroft 
Date:   Tue Oct 11 19:51:49 2016 +1000

gnu: diamond: Update to 0.8.23.

* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.23.
---
 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 02ed8da..e313721 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -2037,7 +2037,7 @@ identify enrichments with functional annotations of the 
genome.")
 (define-public diamond
   (package
 (name "diamond")
-(version "0.8.22")
+(version "0.8.23")
 (source (origin
   (method url-fetch)
   (uri (string-append
@@ -2046,7 +2046,7 @@ identify enrichments with functional annotations of the 
genome.")
   (file-name (string-append name "-" version ".tar.gz"))
   (sha256
(base32
-"0lbqa07c5z8pr4dvdrc14rqc4311kq69j1ldry9glfc8hg3x1kd1"
+"0xpcq3fbk4c52xbpgyk5brl58rljvl83bg8nkxy8vs00pxanm7i2"
 (build-system cmake-build-system)
 (arguments
  '(#:tests? #f ; no "check" target

branch master updated (75fa191 -> 99c9056)

[Ben Woodcroft]

benwoodcroft pushed a change to branch master
in repository guix.

  from  75fa191   Update e-mail address for ng0.
   new  99c9056   gnu: diamond: Update to 0.8.23.

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 |4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

branch master updated (7fd30d1 -> 53aec09)

[Ben Woodcroft]

benwoodcroft pushed a change to branch master
in repository guix.

  from  7fd30d1   gnu: yoshimi: Update to 1.4.1.
   new  d91cb67   gnu: ruby-sequel: Update to 4.39.0.
   new  a751afb   gnu: r-mgcv: Update to 1.8-15.
   new  5ed00e1   gnu: ruby-domain-name: Update to 0.5.20160826.
   new  d034c77   gnu: ruby-tzinfo-data: Update to 1.2016.7.
   new  f49511d   gnu: ruby-mime-types-data: Update to 3.2016.0521.
   new  c2ad4d7   gnu: python-xlrd: Update to 1.0.0.
   new  53aec09   gnu: bundler: Update to 1.13.2.

The 7 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 |6 +++---
 gnu/packages/ruby.scm   |   20 ++--
 gnu/packages/statistics.scm |4 ++--
 3 files changed, 15 insertions(+), 15 deletions(-)

05/07: gnu: ruby-mime-types-data: Update to 3.2016.0521.

[Ben Woodcroft]

benwoodcroft pushed a commit to branch master
in repository guix.

commit f49511dbff6e9041381b98562257f9e9651ccae4
Author: Ben Woodcroft 
Date:   Fri Sep 23 23:22:14 2016 +1000

gnu: ruby-mime-types-data: Update to 3.2016.0521.

* gnu/packages/ruby.scm (ruby-mime-types-data): Update to 3.2016.0521.
---
 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 a1cd86c..28ea70a 100644
--- a/gnu/packages/ruby.scm
+++ b/gnu/packages/ruby.scm
@@ -3223,14 +3223,14 @@ that TURN is no longer being maintained.")
 (define-public ruby-mime-types-data
   (package
 (name "ruby-mime-types-data")
-(version "3.2016.0221")
+(version "3.2016.0521")
 (source
  (origin
(method url-fetch)
(uri (rubygems-uri "mime-types-data" version))
(sha256
 (base32
- "05ygjn0nnfh6yp1wsi574jckk95wqg9a6g598wk4svvrkmkrzkpn"
+ "04my3746hwa4yvbx1ranhfaqkgf6vavi1kyijjnw8w3dy37vqhkm"
 (build-system ruby-build-system)
 (native-inputs
  `(("ruby-hoe" ,ruby-hoe)))

04/07: gnu: ruby-tzinfo-data: Update to 1.2016.7.

[Ben Woodcroft]

benwoodcroft pushed a commit to branch master
in repository guix.

commit d034c779eb8b6b1b873a3bbbd1726cecad394c4e
Author: Ben Woodcroft 
Date:   Fri Sep 23 23:21:11 2016 +1000

gnu: ruby-tzinfo-data: Update to 1.2016.7.

* gnu/packages/ruby.scm (ruby-tzinfo-data): Update to 1.2016.7.
---
 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 ab2dc3b..a1cd86c 100644
--- a/gnu/packages/ruby.scm
+++ b/gnu/packages/ruby.scm
@@ -2115,7 +2115,7 @@ aware transformations between times in different time 
zones.")
 (define-public ruby-tzinfo-data
   (package
 (name "ruby-tzinfo-data")
-(version "1.2016.4")
+(version "1.2016.7")
 (source
  (origin
(method url-fetch)
@@ -2128,7 +2128,7 @@ aware transformations between times in different time 
zones.")
(file-name (string-append name "-" version ".tar.gz"))
(sha256
 (base32
- "0jnm8i379hn48cq5n39j7wzm08i0mw73kqzx3cqbxpiwlb1hnz80"))
+ "0vh75hkfmqk4hdjv6nm7acw64izwpnv7slkmh2kj7qlfz133yh9l"))
;; Remove the known test failure.
;; https://github.com/tzinfo/tzinfo-data/issues/10
;; https://bugs.launchpad.net/ubuntu/+source/glibc/+bug/1587128

06/07: gnu: python-xlrd: Update to 1.0.0.

[Ben Woodcroft]

benwoodcroft pushed a commit to branch master
in repository guix.

commit c2ad4d701e43250f745b914ba8d00accd9463f26
Author: Ben Woodcroft 
Date:   Fri Sep 23 23:37:02 2016 +1000

gnu: python-xlrd: Update to 1.0.0.

* gnu/packages/python.scm (python-xlrd, python2-xlrd): Update to 1.0.0.
---
 gnu/packages/python.scm |6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index cf86c71..742b246 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -5868,19 +5868,19 @@ object to help create WSGI responses.")
 (define-public python-xlrd
   (package
 (name "python-xlrd")
-(version "0.9.4")
+(version "1.0.0")
 (source (origin
   (method url-fetch)
   (uri (string-append "https://pypi.python.org/packages/source/x/";
   "xlrd/xlrd-" version ".tar.gz"))
   (sha256
(base32
-"0wpa55nvidmm5m2qr622dsh3cj46akdk0h3zjgzschcmydck73cf"
+"0s8hjiz01vbhy85xalrz0qlsmd9ypf36zjqrf97hh984spapvy0g"
 (build-system python-build-system)
 (arguments
  `(#:phases
(modify-phases %standard-phases
- ;; Current test in setup.py does not work as of 0.9.4, so use nose to
+ ;; Current test in setup.py does not work as of 1.0.0, so use nose to
  ;; run tests instead for now.
  (replace 'check (lambda _ (zero? (system* "nosetests")))
 (native-inputs `(("python-nose"   ,python-nose)

02/07: gnu: r-mgcv: Update to 1.8-15.

[Ben Woodcroft]

benwoodcroft pushed a commit to branch master
in repository guix.

commit a751afb21753a6039574db04522719edd81c1056
Author: Ben Woodcroft 
Date:   Fri Sep 23 23:15:19 2016 +1000

gnu: r-mgcv: Update to 1.8-15.

* gnu/packages/statistics.scm (r-mgcv): Update to 1.8-15.
---
 gnu/packages/statistics.scm |4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index cbaf026..959251d 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -430,14 +430,14 @@ and operations on them using LAPACK and SuiteSparse.")
 (define-public r-mgcv
   (package
(name "r-mgcv")
-   (version "1.8-14")
+   (version "1.8-15")
(source
 (origin
  (method url-fetch)
  (uri (cran-uri "mgcv" version))
  (sha256
   (base32
-   "0ly9x23q6kd7aqrsb8qjsj8jc597h3068iaqjmkkdv56r5dln29f"
+   "05xzmsx51y92c0r0yihac8m9d3v1sqnn8ahcgm3q75j8z6zybsjs"
(build-system r-build-system)
(home-page "http://cran.r-project.org/web/packages/mgcv";)
(synopsis "Mixed generalised additive model computation")

01/07: gnu: ruby-sequel: Update to 4.39.0.

[Ben Woodcroft]

benwoodcroft pushed a commit to branch master
in repository guix.

commit d91cb67dd721793676d23d1aed7f26522d41164e
Author: Ben Woodcroft 
Date:   Fri Sep 23 23:13:08 2016 +1000

gnu: ruby-sequel: Update to 4.39.0.

* gnu/packages/ruby.scm (ruby-sequel): Update to 4.39.0.
---
 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 a80b8f7..df21349 100644
--- a/gnu/packages/ruby.scm
+++ b/gnu/packages/ruby.scm
@@ -4041,14 +4041,14 @@ generation.")
 (define-public ruby-sequel
   (package
 (name "ruby-sequel")
-(version "4.34.0")
+(version "4.39.0")
 (source
  (origin
(method url-fetch)
(uri (rubygems-uri "sequel" version))
(sha256
 (base32
- "0qscddpfwcajggxvbm4a4jv8kkpn6q056bgdg03km34bz8bis1x1"
+ "01zqd6mi9wvhbg76b91k35jppha0c944ar9f816gi400cf9817bg"
 (build-system ruby-build-system)
 (arguments
  '(#:tests? #f)) ; Avoid dependency loop with ruby-minitest-hooks.

07/07: gnu: bundler: Update to 1.13.2.

[Ben Woodcroft]

benwoodcroft pushed a commit to branch master
in repository guix.

commit 53aec0999f5f5e2183d439c356dc1d7df6202a50
Author: Ben Woodcroft 
Date:   Sat Oct 8 22:13:47 2016 +1000

gnu: bundler: Update to 1.13.2.

* gnu/packages/ruby.scm (bundler): Update to 1.13.2.
---
 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 28ea70a..23d22a3 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 "1.12.5")
+(version "1.13.2")
 (source (origin
   (method url-fetch)
   (uri (rubygems-uri "bundler" version))
   (sha256
(base32
-"1q84xiwm9j771lpmiply0ls9l2bpvl5axn3jblxjvrldh8di2pkc"
+"05gwyhfn103vrmrw13r3n78bcl75mrj82ipsbazcl08wg1bql7x6"
 (build-system ruby-build-system)
 (arguments
  '(#:tests? #f)) ; avoid dependency cycles

03/07: gnu: ruby-domain-name: Update to 0.5.20160826.

[Ben Woodcroft]

benwoodcroft pushed a commit to branch master
in repository guix.

commit 5ed00e13d26db380a422c8ae6b7601be49430962
Author: Ben Woodcroft 
Date:   Fri Sep 23 23:19:29 2016 +1000

gnu: ruby-domain-name: Update to 0.5.20160826.

* gnu/packages/ruby.scm (ruby-domain-name): Update to 0.5.20160826.
---
 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 df21349..ab2dc3b 100644
--- a/gnu/packages/ruby.scm
+++ b/gnu/packages/ruby.scm
@@ -3467,14 +3467,14 @@ support to both Ruby and JRuby.  It uses @code{unf_ext} 
on CRuby and
 (define-public ruby-domain-name
   (package
 (name "ruby-domain-name")
-(version "0.5.20160310")
+(version "0.5.20160826")
 (source
  (origin
(method url-fetch)
(uri (rubygems-uri "domain_name" version))
(sha256
 (base32
- "0g1175zspkqhlvl9s11g7p2nbmqpvpxxv02q8csd0ryc81laapys"
+ "0rg7gvp45xmb5qz8ydp7ivw05hhplh6k7mbawrpvkysl2c77w5xx"
 (build-system ruby-build-system)
 (arguments
  `(#:phases

01/01: gnu: python2-dendropy: Fix tests.

[Ben Woodcroft]

benwoodcroft pushed a commit to branch master
in repository guix.

commit 9602e3cce95264d563804d372f44a0d88bad3e9f
Author: Ben Woodcroft 
Date:   Sat Oct 8 21:33:43 2016 +1000

gnu: python2-dendropy: Fix tests.

* gnu/packages/bioinformatics.scm (python2-dendropy)[source]: Use unpatched
source.
[arguments]: Use nose to run tests.
[native-inputs]: Add python2-nose.
---
 gnu/packages/bioinformatics.scm |   18 ++
 1 file changed, 18 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 76e6c31..02ed8da 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -1972,7 +1972,25 @@ trees (phylogenies) and characters.")
   (let ((base (package-with-python2 (strip-python2-variant python-dendropy
 (package
   (inherit base)
+  ;; Do not use same source as 'python-dendropy' because the patched
+  ;; failing tests do not occur on Python 2.
+  (source
+   (origin
+ (method url-fetch)
+ (uri (pypi-uri "DendroPy" (package-version base)))
+ (sha256
+  (base32
+   "1jfz7gp18wph311w1yygbvjanb3n5mdqal439bb6myw41dwb5m63"
+  (arguments
+   `(#:python ,python-2
+ #:phases
+   (modify-phases %standard-phases
+ (replace 'check
+   ;; There is currently a test failure that only happens on some
+   ;; systems, and only using "setup.py test"
+   (lambda _ (zero? (system* "nosetests")))
   (native-inputs `(("python2-setuptools" ,python2-setuptools)
+   ("python2-nose" ,python2-nose)
,@(package-native-inputs base))