01/03: gnu: Add python-xenon.

[Ludovic Court�s]

civodul pushed a commit to branch master
in repository guix.

commit 2038a48f4d68fd0a15922abb86a4402419d0e20c
Author: Muriithi Frederick Muriuki 
Date:   Sat Jun 24 06:56:13 2017 +0300

gnu: Add python-xenon.

* gnu/packages/python.scm (python-xenon, python2-xenon) New variables.

Signed-off-by: Ludovic Courtès 
---
 gnu/packages/python.scm | 45 +
 1 file changed, 45 insertions(+)

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 30d67b1..346faf4 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -16057,6 +16057,51 @@ pure Python module.")
 (define-public python2-rencode
   (package-with-python2 python-rencode))
 
+(define-public python-xenon
+  (package
+(name "python-xenon")
+(version "0.5.1")
+(source
+ (origin
+   (method url-fetch)
+   (uri (pypi-uri "xenon" version))
+   (sha256
+(base32
+ "14kby2y48vp3sgwxqlm5d5789yibqwb1qli5fwcmdqg3iayrbklc"
+(build-system python-build-system)
+(native-inputs
+ `(("python-pyyaml" ,python-pyyaml)
+   ("python-radon" ,python-radon)
+   ("python-requests" ,python-requests)
+   ("python-flake8" ,python-flake8)
+   ("python-tox" ,python-tox)))
+(arguments
+ `(#:phases
+   (modify-phases %standard-phases
+ (add-before 'build 'patch-test-requirements
+   (lambda* (#:key inputs #:allow-other-keys)
+ ;; Update requirements from dependency==version to
+ ;; dependency>=version.
+ (substitute* "requirements.txt"
+   (("==") ">=")
+   ((",<1.5.0") ""))
+ ;; Remove httpretty dependency for tests.
+ (substitute* "setup.py"
+   (("httpretty") ""))
+ #t)
+(home-page "https://xenon.readthedocs.org/;)
+(synopsis "Monitor code metrics for Python on your CI server")
+(description
+ "Xenon is a monitoring tool based on Radon.  It monitors code complexity.
+Ideally, @code{xenon} is run every time code is committed.  Through command
+line options, various thresholds can be set for the complexity of code.  It
+will fail (i.e.  it will exit with a non-zero exit code) when any of these
+requirements is not met.")
+(license license:expat)))
+
+(define-public python2-xenon
+  (package-with-python2 python-xenon))
+
 (define-public python-flask-principal
   (package
 (name "python-flask-principal")

branch master updated (6106d19 -> 7bd65a6)

[Ludovic Court�s]

civodul pushed a change to branch master
in repository guix.

  from  6106d19   gnu: perl-html-tree: Update to 5.07.
   new  2038a48   gnu: Add python-xenon.
   new  75f2395   nls: Update 'fr' translation.
   new  7bd65a6   gnu: swish-e: Work around compilation error and test 
failures.

The 3 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.


Summary of changes:
 gnu/packages/python.scm |45 +
 gnu/packages/search.scm |10 +-
 po/packages/fr.po   | 17387 +++---
 3 files changed, 16318 insertions(+), 1124 deletions(-)

03/03: gnu: swish-e: Work around compilation error and test failures.

[Ludovic Court�s]

civodul pushed a commit to branch master
in repository guix.

commit 7bd65a6304b6639554b625db32a1e887deab9158
Author: Ethan R. Jones 
Date:   Sun May 14 13:01:53 2017 -0400

gnu: swish-e: Work around compilation error and test failures.

* gnu/packages/search.scm (swish-e)[inputs]: Remove ZLIB and LIBXML2.
[arguments]: Add #:configure-flags.

Co-authored-by: Ludovic Courtès 
---
 gnu/packages/search.scm | 10 ++
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/gnu/packages/search.scm b/gnu/packages/search.scm
index cc8c063..62da3be 100644
--- a/gnu/packages/search.scm
+++ b/gnu/packages/search.scm
@@ -264,15 +264,17 @@ conflict with slocate compatibility.")
 ;; building: xpdf, catdoc, MP3::Tag, Spreadsheet::ParseExcel,
 ;; HTML::Entities.
 (inputs
- `(("libxml" ,libxml2)
-   ("zlib" ,zlib)
-   ("perl" ,perl)
+ `(("perl" ,perl)
("perl-uri" ,perl-uri)
("perl-html-parser" ,perl-html-parser)
("perl-html-tagset" ,perl-html-tagset)
("perl-mime-types" ,perl-mime-types)))
 (arguments
- `(#:phases (modify-phases %standard-phases
+ `(;; XXX: This fails to build with zlib (API mismatch) and tests fail
+   ;; with libxml2, so disable both.
+   #:configure-flags (list (string-append "--without-zlib")
+   (string-append "--without-libxml2"))
+   #:phases (modify-phases %standard-phases
   (add-after 'install 'wrap-programs
 (lambda* (#:key inputs outputs #:allow-other-keys)
   (let* ((out (assoc-ref outputs "out")))

05/06: gnu: youtube-dl: Update to 2017.09.02.

[Tobias Geerinckx-Rice]

nckx pushed a commit to branch master
in repository guix.

commit 33fd32c285e88f2f2eb3491306390774b6cd96e2
Author: Tobias Geerinckx-Rice 
Date:   Fri Sep 1 22:34:33 2017 +0200

gnu: youtube-dl: Update to 2017.09.02.

* gnu/packages/video.scm (youtube-dl): Update to 2017.09.02.
---
 gnu/packages/video.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/video.scm b/gnu/packages/video.scm
index 068c2ac..581e21c 100644
--- a/gnu/packages/video.scm
+++ b/gnu/packages/video.scm
@@ -,7 +,7 @@ access to mpv's powerful playback capabilities.")
 (define-public youtube-dl
   (package
 (name "youtube-dl")
-(version "2017.08.27.1")
+(version "2017.09.02")
 (source (origin
   (method url-fetch)
   (uri (string-append "https://yt-dl.org/downloads/;
@@ -1119,7 +1119,7 @@ access to mpv's powerful playback capabilities.")
   version ".tar.gz"))
   (sha256
(base32
-"1b0ad0fkayj6l0cd2rkycn6lbms8ps0y887r407c850pmaw27n1j"
+"1sfra8rfb7hkbgmw2n2s42fpkh0y7j9lyars7qda3rj34ai7r6k9"
 (build-system python-build-system)
 (arguments
  ;; The problem here is that the directory for the man page and completion

branch master updated (81fe131 -> 6106d19)

[Tobias Geerinckx-Rice]

nckx pushed a change to branch master
in repository guix.

  from  81fe131   build: emacs-build-system: Make the install phase more 
helpful.
   new  d5909be   gnu: gparted: Update home page.
   new  0c3a167   gnu: python-ruamel.yaml: Update to 0.15.33.
   new  def056d   gnu: perl-context-preserve: Update source URL.
   new  bbfc523   gnu: dub: Update to 1.5.0.
   new  33fd32c   gnu: youtube-dl: Update to 2017.09.02.
   new  6106d19   gnu: perl-html-tree: Update to 5.07.

The 6 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/disk.scm  | 2 +-
 gnu/packages/ldc.scm   | 4 ++--
 gnu/packages/perl.scm  | 2 +-
 gnu/packages/serialization.scm | 4 ++--
 gnu/packages/video.scm | 4 ++--
 gnu/packages/web.scm   | 4 ++--
 6 files changed, 10 insertions(+), 10 deletions(-)

04/06: gnu: dub: Update to 1.5.0.

[Tobias Geerinckx-Rice]

nckx pushed a commit to branch master
in repository guix.

commit bbfc523d95589553a9e1ecf49ab05d7318837859
Author: Tobias Geerinckx-Rice 
Date:   Fri Sep 1 21:05:31 2017 +0200

gnu: dub: Update to 1.5.0.

* gnu/packages/ldc.scm (dub): Update to 1.5.0.
---
 gnu/packages/ldc.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/ldc.scm b/gnu/packages/ldc.scm
index 25fcb51..d2aee9c 100644
--- a/gnu/packages/ldc.scm
+++ b/gnu/packages/ldc.scm
@@ -279,7 +279,7 @@ latest DMD frontend and uses LLVM as backend.")
 (define-public dub
   (package
 (name "dub")
-(version "1.4.1")
+(version "1.5.0")
 (source (origin
   (method url-fetch)
   (uri (string-append "https://github.com/dlang/dub/archive/;
@@ -287,7 +287,7 @@ latest DMD frontend and uses LLVM as backend.")
   (file-name (string-append name "-" version ".tar.gz"))
   (sha256
(base32
-"0hpl5srbrzwzv8abc96j4cgbmvm1zhr109ljbl7hrphzzc39zyan"
+"1p9pmzjsmd7v3jpilv0z0c8ar1ykvri6nn5fv95f8d2vriczj29m"
(build-system gnu-build-system)
 (arguments
  `(#:tests? #f ; it would have tested itself by installing some packages 
(vibe etc)

02/06: gnu: python-ruamel.yaml: Update to 0.15.33.

[Tobias Geerinckx-Rice]

nckx pushed a commit to branch master
in repository guix.

commit 0c3a1674e4997754c02016d4ce3e4b6185ef5313
Author: Tobias Geerinckx-Rice 
Date:   Fri Sep 1 03:14:03 2017 +0200

gnu: python-ruamel.yaml: Update to 0.15.33.

* gnu/packages/serialization.scm (python-ruamel.yaml): Update to 0.15.33.
---
 gnu/packages/serialization.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/serialization.scm b/gnu/packages/serialization.scm
index d5fdbf3..54ccbf7 100644
--- a/gnu/packages/serialization.scm
+++ b/gnu/packages/serialization.scm
@@ -359,14 +359,14 @@ However, “Memory efficiency” and “Speed” have not been 
primary goals.")
 (define-public python-ruamel.yaml
   (package
 (name "python-ruamel.yaml")
-(version "0.15.19")
+(version "0.15.33")
 (source
  (origin
(method url-fetch)
(uri (pypi-uri "ruamel.yaml" version))
(sha256
 (base32
- "0qx779avw8d1vsjqyi7z21h1g5ykp8paqavgj0lzbp8h7bw9vpgv"
+ "1s4b0zwn9pkk4xxjhx77giyfddc738drd6vgraw6n2syvj03s31d"
 (build-system python-build-system)
 (native-inputs
  `(("python-pytest" ,python-pytest)))

06/06: gnu: perl-html-tree: Update to 5.07.

[Tobias Geerinckx-Rice]

nckx pushed a commit to branch master
in repository guix.

commit 6106d195a2cb8d3a8dc7aea4f06a0e4bfc02be05
Author: Tobias Geerinckx-Rice 
Date:   Fri Sep 1 23:06:09 2017 +0200

gnu: perl-html-tree: Update to 5.07.

* gnu/packages/web.scm (perl-html-tree): Update to 5.07.
---
 gnu/packages/web.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm
index 87ca2fd..ee009bc 100644
--- a/gnu/packages/web.scm
+++ b/gnu/packages/web.scm
@@ -2233,7 +2233,7 @@ in tables within an HTML document, either as text or 
encoded element trees.")
 (define-public perl-html-tree
   (package
 (name "perl-html-tree")
-(version "5.06")
+(version "5.07")
 (source
  (origin
(method url-fetch)
@@ -2241,7 +2241,7 @@ in tables within an HTML document, either as text or 
encoded element trees.")
"HTML-Tree-" version ".tar.gz"))
(sha256
 (base32
- "0vjk4xrybjqs511qrh9cymhpbg9m3jjqr52qr035k6nzrccyndlw"
+ "1gyvm4qlwm9y6hczkpnrdfl303ggbybr0nqxdjw09hii8yw4sdzh"
 (build-system perl-build-system)
 (native-inputs
  `(("perl-module-build" ,perl-module-build)

01/06: gnu: gparted: Update home page.

[Tobias Geerinckx-Rice]

nckx pushed a commit to branch master
in repository guix.

commit d5909be93b1f7bc4689884d159d570e8470e054d
Author: Tobias Geerinckx-Rice 
Date:   Thu Aug 31 15:05:53 2017 +0200

gnu: gparted: Update home page.

* gnu/packages/disk.scm (gparted)[home-page]: Use now-HTTPS gparted.org.
---
 gnu/packages/disk.scm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/gnu/packages/disk.scm b/gnu/packages/disk.scm
index 030fabf..49bbbfa 100644
--- a/gnu/packages/disk.scm
+++ b/gnu/packages/disk.scm
@@ -344,7 +344,7 @@ and can dramatically shorten the lifespan of the drive if 
left unchecked.")
 (native-inputs
  `(("intltool" ,intltool)
("pkg-config" ,pkg-config)))
-(home-page "https://sourceforge.net/projects/gparted/;)
+(home-page "https://gparted.org/;)
 (synopsis "Partition editor to graphically manage disk partitions")
 (description "GParted is a GNOME partition editor for creating,
 reorganizing, and deleting disk partitions.  It uses libparted from the parted

03/06: gnu: perl-context-preserve: Update source URL.

[Tobias Geerinckx-Rice]

nckx pushed a commit to branch master
in repository guix.

commit def056d13842f7cd799970844f79d071c6b82739
Author: Tobias Geerinckx-Rice 
Date:   Fri Sep 1 20:48:13 2017 +0200

gnu: perl-context-preserve: Update source URL.

* gnu/packages/perl.scm (perl-context-preserve)[source]: Update CPAN author.
---
 gnu/packages/perl.scm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/gnu/packages/perl.scm b/gnu/packages/perl.scm
index 3967ef8..249f478 100644
--- a/gnu/packages/perl.scm
+++ b/gnu/packages/perl.scm
@@ -1295,7 +1295,7 @@ and writing of @code{.ini}-style configuration files.")
 (source
  (origin
(method url-fetch)
-   (uri (string-append "mirror://cpan/authors/id/J/JR/JROCKWAY/"
+   (uri (string-append "mirror://cpan/authors/id/E/ET/ETHER/"
"Context-Preserve-" version ".tar.gz"))
(sha256
 (base32

branch master updated (ebbb630 -> 81fe131)

[Christopher Baines]

cbaines pushed a change to branch master
in repository guix.

  from  ebbb630   gnu: r-minimal: Update to 3.4.1.
   new  81fe131   build: emacs-build-system: Make the install phase more 
helpful.

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:
 guix/build/emacs-build-system.scm | 45 ---
 1 file changed, 32 insertions(+), 13 deletions(-)

01/01: build: emacs-build-system: Make the install phase more helpful.

[Christopher Baines]

cbaines pushed a commit to branch master
in repository guix.

commit 81fe131e0fc3c1fcfa29c140071c8cc4cff7cd2f
Author: Christopher Baines 
Date:   Tue Aug 22 18:11:35 2017 +0100

build: emacs-build-system: Make the install phase more helpful.

Modify the install phase to detect when nothing has been installed, and 
error
if this happens. This is preferable to continuing, and allowing the next 
phase
to fail.

Also, when nothing can be found to be installed, print out each file that 
was
considered, along with the regular expressions that were used to include and
exclude it.

* gnu/build/emacs-build-system.scm (install-file?): Add additional error
  checking and logging.
---
 guix/build/emacs-build-system.scm | 45 ---
 1 file changed, 32 insertions(+), 13 deletions(-)

diff --git a/guix/build/emacs-build-system.scm 
b/guix/build/emacs-build-system.scm
index bda699d..202ce53 100644
--- a/guix/build/emacs-build-system.scm
+++ b/guix/build/emacs-build-system.scm
@@ -110,22 +110,41 @@ store in '.el' files."
 
   (define source (getcwd))
 
-  (define (install-file? file stat)
-(let ((stripped-file (string-trim (string-drop file (string-length 
source)) #\/)))
-  (and (any (cut string-match <> stripped-file) include)
-   (not (any (cut string-match <> stripped-file) exclude)
+  (define* (install-file? file stat #:key verbose?)
+(let* ((stripped-file (string-trim
+   (string-drop file (string-length source)) #\/)))
+  (define (match-stripped-file action regex)
+(let ((result (string-match regex stripped-file)))
+  (when (and result verbose?)
+(format #t "info: ~A ~A as it matches \"~A\"\n"
+stripped-file action regex))
+  result))
+
+  (when verbose?
+(format #t "info: considering installing ~A\n" stripped-file))
+
+  (and (any (cut match-stripped-file "included" <>) include)
+   (not (any (cut match-stripped-file "excluded" <>) exclude)
 
   (let* ((out (assoc-ref outputs "out"))
  (elpa-name-ver (store-directory->elpa-name-version out))
- (target-directory (string-append out %install-suffix "/" 
elpa-name-ver)))
-(for-each
- (lambda (file)
-   (let* ((stripped-file (string-drop file (string-length source)))
-  (target-file (string-append target-directory stripped-file)))
- (format #t "`~a' -> `~a'~%" file target-file)
- (install-file file (dirname target-file
- (find-files source install-file?)))
-  #t)
+ (target-directory (string-append out %install-suffix "/" 
elpa-name-ver))
+ (files-to-install (find-files source install-file?)))
+(cond
+ (files-to-install
+  (for-each
+   (lambda (file)
+ (let* ((stripped-file (string-drop file (string-length source)))
+(target-file (string-append target-directory stripped-file)))
+   (format #t "`~a' -> `~a'~%" file target-file)
+   (install-file file (dirname target-file
+   files-to-install)
+  #t)
+ (else
+  (format #t "error: No files found to install.\n")
+  (find-files source (lambda (file stat)
+   (install-file? file stat #:verbose? #t)))
+  #f
 
 (define* (move-doc #:key outputs #:allow-other-keys)
   "Move info files from the ELPA package directory to the info directory."

branch master updated (3bf0245 -> ebbb630)

[Ricardo Wurmus]

rekado pushed a change to branch master
in repository guix.

  from  3bf0245   gnu: vdirsyncer: Update to 0.16.2.
   new  ebbb630   gnu: r-minimal: Update to 3.4.1.

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

01/01: gnu: r-minimal: Update to 3.4.1.

[Ricardo Wurmus]

rekado pushed a commit to branch master
in repository guix.

commit ebbb6301a34716dd8047d2105d668e192060342d
Author: Ricardo Wurmus 
Date:   Fri Sep 1 22:05:01 2017 +0200

gnu: r-minimal: Update to 3.4.1.

* gnu/packages/statistics.scm (r-minimal): Update to 3.4.1.
---
 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 05ab1c2..df2d562 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -106,7 +106,7 @@ be output in text, PostScript, PDF or HTML.")
 (define-public r-minimal
   (package
 (name "r-minimal")
-(version "3.4.0")
+(version "3.4.1")
 (source (origin
   (method url-fetch)
   (uri (string-append "mirror://cran/src/base/R-"
@@ -114,7 +114,7 @@ be output in text, PostScript, PDF or HTML.")
   version ".tar.gz"))
   (sha256
(base32
-"14cb8bwi3akvdb6934kqic2862f2qgav6cq4g0h7gi2p4ka9x3i8"
+"0y7wlfk3cn1dxn2mpnxwvsk31s0599crbsyah8srm5pa2mfi7c82"
 (build-system gnu-build-system)
 (arguments
  `(#:disallowed-references (,tzdata-2017a)

01/03: gnu: python-click-threading: Update to 0.4.3.

[Leo Famulari]

lfam pushed a commit to branch master
in repository guix.

commit 19ecdbedd3e39dfecbc834d2f70dbbea64f7ca84
Author: Leo Famulari 
Date:   Fri Sep 1 13:47:49 2017 -0400

gnu: python-click-threading: Update to 0.4.3.

* gnu/packages/python.scm (python-click-threading): Update to 0.4.3.
[source]: Use pypi-uri.
---
 gnu/packages/python.scm | 9 +++--
 1 file changed, 3 insertions(+), 6 deletions(-)

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index e2d96c9..a062356 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -9198,16 +9198,13 @@ with python-requests.")
 (define-public python-click-threading
   (package
 (name "python-click-threading")
-(version "0.2.0")
+(version "0.4.3")
 (source (origin
  (method url-fetch)
- (uri (string-append
-"https://pypi.python.org/packages/;
-
"fe/b7/e7f609d18a2a351cb71616adcf54df1acd82f83cb9b5936935a4d20e2c23/"
-"click-threading-" version ".tar.gz"))
+ (uri (pypi-uri "click-threading" version))
  (sha256
   (base32
-   "18bcqikxwb3drb8rf60cclxkxw52521b38ax3byah6j8cn8y9p4j"
+   "0xs4bg2ws0zgyiplk312l049hi23c2zqf1g771rjhh5vr2msk4cg"
 (build-system python-build-system)
 (propagated-inputs
  `(("python-click" ,python-click)))

02/03: gnu: python-click-log: Update to 0.2.0.

[Leo Famulari]

lfam pushed a commit to branch master
in repository guix.

commit 3a91ac837877de32e393fe804b03547f324ffabf
Author: Leo Famulari 
Date:   Fri Sep 1 13:48:22 2017 -0400

gnu: python-click-log: Update to 0.2.0.

* gnu/packages/python.scm (python-click-log): Update to 0.2.0.
---
 gnu/packages/python.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index a062356..30d67b1 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -9217,13 +9217,13 @@ applications.")
 (define-public python-click-log
   (package
 (name "python-click-log")
-(version "0.1.8")
+(version "0.2.0")
 (source (origin
  (method url-fetch)
  (uri (pypi-uri "click-log" version))
  (sha256
   (base32
-   "14ikfjfgnzf21mjniq9lfk2igzykgzfvwwrk85nw2b9fq44109sp"
+   "1bjrfxji1yv4fj0g78ri2yfgn2wbivn8g69fxfinxvxpmighhshp"
 (build-system python-build-system)
 (propagated-inputs
  `(("python-click" ,python-click)))

03/03: gnu: vdirsyncer: Update to 0.16.2.

[Leo Famulari]

lfam pushed a commit to branch master
in repository guix.

commit 3bf0245bb8af7a3cd9c840dd87958100b706e3b3
Author: Leo Famulari 
Date:   Fri Sep 1 13:29:39 2017 -0400

gnu: vdirsyncer: Update to 0.16.2.

* gnu/packages/dav.scm (vdirsyncer): Update to 0.16.2.
---
 gnu/packages/dav.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/dav.scm b/gnu/packages/dav.scm
index 86cfaa6..6c46697 100644
--- a/gnu/packages/dav.scm
+++ b/gnu/packages/dav.scm
@@ -55,13 +55,13 @@ clients.")
 (define-public vdirsyncer
   (package
 (name "vdirsyncer")
-(version "0.16.1")
+(version "0.16.2")
 (source (origin
  (method url-fetch)
  (uri (pypi-uri name version))
  (sha256
   (base32
-   "0pnsb9h4r0hhmqhzx9nbrd7jawir9ysrh3wrrkhzi0ssarmxyp67"
+   "19xqzxcgmpm2z56l2d4a1n4sqmhrnzfwx3d9avfzgldwyhlrz0da"
 (build-system python-build-system)
 (arguments
   `(#:phases (modify-phases %standard-phases

branch master updated (2da21e4 -> 3bf0245)

[Leo Famulari]

lfam pushed a change to branch master
in repository guix.

  from  2da21e4   gnu: python-icalendar: Update to 3.11.7.
   new  19ecdbe   gnu: python-click-threading: Update to 0.4.3.
   new  3a91ac8   gnu: python-click-log: Update to 0.2.0.
   new  3bf0245   gnu: vdirsyncer: Update to 0.16.2.

The 3 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.


Summary of changes:
 gnu/packages/dav.scm|  4 ++--
 gnu/packages/python.scm | 13 +
 2 files changed, 7 insertions(+), 10 deletions(-)

branch master updated (81195d1 -> 2da21e4)

[Leo Famulari]

lfam pushed a change to branch master
in repository guix.

  from  81195d1   gnu: r-genomicalignments: Update to 1.12.2.
   new  2da21e4   gnu: python-icalendar: Update to 3.11.7.

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


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

01/01: gnu: python-icalendar: Update to 3.11.7.

[Leo Famulari]

lfam pushed a commit to branch master
in repository guix.

commit 2da21e48a810308e880bd8b06a42d5312f774e8f
Author: Leo Famulari 
Date:   Fri Sep 1 13:29:01 2017 -0400

gnu: python-icalendar: Update to 3.11.7.

* gnu/packages/python.scm (python-icalendar): Update to 3.11.7.
---
 gnu/packages/python.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 874ad82..e2d96c9 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -9431,13 +9431,13 @@ processes across test runs.")
 (define-public python-icalendar
   (package
 (name "python-icalendar")
-(version "3.11.6")
+(version "3.11.7")
 (source (origin
  (method url-fetch)
  (uri (pypi-uri "icalendar" version))
  (sha256
   (base32
-   "1ny9mbm9zgghl612b8wc4ap52bz3kgl486d7f307gxjmlqgz3i64"
+   "0ahf1i98wjizhld2qd7v2vmvzsmdw08mmins82bf3fpbnp2sxbgc"
 (build-system python-build-system)
 (propagated-inputs
  `(("python-dateutil" ,python-dateutil)

07/14: gpce-2017: Deanonymize.

[Ludovic Court�s]

civodul pushed a commit to branch master
in repository maintenance.

commit 6b7a859524a2716075ec96a10da2edf0e2b8b69a
Author: Ludovic Courtès 
Date:   Wed Aug 30 16:05:18 2017 +0200

gpce-2017: Deanonymize.
---
 doc/gpce-2017/gpce.skb | 21 +++--
 1 file changed, 19 insertions(+), 2 deletions(-)

diff --git a/doc/gpce-2017/gpce.skb b/doc/gpce-2017/gpce.skb
index 1cc9ba4..114e161 100644
--- a/doc/gpce-2017/gpce.skb
+++ b/doc/gpce-2017/gpce.skb
@@ -96,10 +96,24 @@
 
 (let ((latex (find-engine 'latex)))
(engine-custom-set! latex 'documentclass
-  "\\documentclass[sigplan, anonymous, review]{acmart}")
+  "\\documentclass[sigplan]{acmart}")
 
(engine-custom-set! latex 'maketitle #f)
-   
+
+   (markup-writer ' latex
+  :action (lambda (n e)
+(let ((body (markup-body n)))
+   (for-each (lambda (a)
+(display "\\author{")
+(output (markup-option a :name) e)
+(display "}\n\\affiliation{\n")
+(display "  \\institution{")
+(output (markup-option a :affiliation) e)
+(display "}\n  \\streetaddress{")
+(output (markup-option a :address) e)
+(display "}}\n"))
+ (if (pair? body) body (list body))
+
(markup-writer ' latex
   :options '(:index :section :subsection)
   :action (lambda (n e)
@@ -151,6 +165,9 @@
 
 
 (document :title [Code Staging in GNU Guix]
+   :author (list (author :name "Ludovic Courtès"
+   :affiliation "Inria"
+   :address (list "Bordeaux, France")))

(acmart-abstract

03/14: gpce-2017: Write some more.

[Ludovic Court�s]

civodul pushed a commit to branch master
in repository maintenance.

commit 8e152a0e188549c0091620ab53b4620498a3b62d
Author: Ludovic Courtès 
Date:   Thu Jul 6 18:56:20 2017 +0200

gpce-2017: Write some more.
---
 doc/gpce-2017/categories.tex  |  23 +++
 doc/gpce-2017/code/gexp-expansion.scm |  65 ---
 doc/gpce-2017/code/system-test.scm|  19 ++
 doc/gpce-2017/gpce.skb| 350 --
 doc/gpce-2017/staging.sbib|  35 +++-
 5 files changed, 355 insertions(+), 137 deletions(-)

diff --git a/doc/gpce-2017/categories.tex b/doc/gpce-2017/categories.tex
new file mode 100644
index 000..5988a97
--- /dev/null
+++ b/doc/gpce-2017/categories.tex
@@ -0,0 +1,23 @@
+\begin{CCSXML}
+
+
+10011007.10011006.10011041.10011047
+Software and its engineering~Source code 
generation
+500
+
+
+10011007.10011006.10011008.10011009.10011012
+Software and its engineering~Functional languages
+300
+
+
+10011007.10011074.1001.10011697
+Software and its engineering~System administration
+300
+
+
+\end{CCSXML}
+
+\ccsdesc[500]{Software and its engineering~Source code generation}
+\ccsdesc[300]{Software and its engineering~Functional languages}
+\ccsdesc[300]{Software and its engineering~System administration}
diff --git a/doc/gpce-2017/code/gexp-expansion.scm 
b/doc/gpce-2017/code/gexp-expansion.scm
index 003b767..111fa81 100644
--- a/doc/gpce-2017/code/gexp-expansion.scm
+++ b/doc/gpce-2017/code/gexp-expansion.scm
@@ -1,33 +1,40 @@
 (use-modules (guix))
 
-;;!begin-condensed
+;;!begin-gexp-expansion
 #~(list (string-append #$imagemagick "/bin/convert")
 (string-append #$emacs "/bin/emacs"))
-;;!end-condensed
-
-;;!begin-gexp-without-reader-macro
-(gexp (list (string-append (ungexp imagemagick)
-   "/bin/convert")
-(string-append (ungexp emacs)
-   "/bin/emacs")))
-;;!end-gexp-without-reader-macro
-
-;;!begin-expansion
-(let ((references
-   (list (gexp-input imagemagick)
- (gexp-input emacs)))
-  (proc (lambda (a b)
-  (list 'list
-(list 'string-append a
-  "/bin/convert")
-(list 'string-append b
-  "/bin/emacs")
-  (make-gexp references proc))
-;;!end-expansion
-
-;;!begin-staged-sexp
-(list (string-append "/gnu/store/65qrc…-imagemagick-6.9"
- "/bin/convert")
-  (string-append "/gnu/store/825n3…-emacs-25.2"
- "/bin/emacs"))
-;;!end-staged-sexp
+
+
+⇒ (gexp (list (string-append (ungexp imagemagick)
+ "/bin/convert")
+  (string-append (ungexp emacs)
+ "/bin/emacs")))
+
+⇒ (let ((references
+ (list (gexp-input imagemagick)
+   (gexp-input emacs)))
+(proc (lambda (a b)
+(list 'list
+  (list 'string-append a
+"/bin/convert")
+  (list 'string-append b
+"/bin/emacs")
+(make-gexp references proc))
+
+⇝ (list (string-append "/gnu/store/65qrc…-imagemagick-6.9"
+   "/bin/convert")
+(string-append "/gnu/store/825n3…-emacs-25.2"
+   "/bin/emacs"))
+;;!end-gexp-expansion
+
+;;!begin-gexp-hygiene
+(let ((gen-body (lambda (x)
+  #~(let ((x 40))
+  (+ x #$x)
+  #~(let ((x 2))
+  #$(gen-body #~x))
+
+⇒ (let ((x0 2))
+(let ((x1 40)) (+ x1 x0)))
+;;!end-gexp-hygiene
+
diff --git a/doc/gpce-2017/code/system-test.scm 
b/doc/gpce-2017/code/system-test.scm
new file mode 100644
index 000..6a086b7
--- /dev/null
+++ b/doc/gpce-2017/code/system-test.scm
@@ -0,0 +1,19 @@
+#~(begin
+(use-modules (gnu build marionette)
+ (srfi srfi-64) (ice-9 match))
+
+;; Spawn the VM that runs the declared OS.
+(define marionette (make-marionette (list #$run)))
+
+(test-begin "basic")
+(test-assert "uname"
+  (match (marionette-eval '(uname) marionette)
+(#("Linux" host-name version _ architecture)
+ (and (string=? host-name
+#$(operating-system-host-name os))
+  (string-prefix? #$(package-version
+ (operating-system-kernel os))
+  version)
+  (string-prefix? architecture %host-type)
+(test-end)
+(exit (= (test-runner-fail-count (test-runner-current)) 0
diff --git a/doc/gpce-2017/gpce.skb b/doc/gpce-2017/gpce.skb
index 48b2733..8101a93 100644
--- a/doc/gpce-2017/gpce.skb
+++ b/doc/gpce-2017/gpce.skb
@@ -79,14 +79,37 @@
"\\usepackage{microtype}\n"
;; "\\usepackage[hypcap]{caption}\n"
;; "\\DeclareCaptionType{copyrightbox}\n"
-   

10/14: gpce-2017: Adjust as suggested by the reviewers.

[Ludovic Court�s]

civodul pushed a commit to branch master
in repository maintenance.

commit 832e95ad0012cd09e5713268fe1dca98bda95fe2
Author: Ludovic Courtès 
Date:   Fri Sep 1 14:02:21 2017 +0200

gpce-2017: Adjust as suggested by the reviewers.
---
 doc/gpce-2017/gpce.skb | 22 +++---
 doc/gpce-2017/staging.sbib | 29 +
 2 files changed, 44 insertions(+), 7 deletions(-)

diff --git a/doc/gpce-2017/gpce.skb b/doc/gpce-2017/gpce.skb
index b58eafc..8a98b27 100644
--- a/doc/gpce-2017/gpce.skb
+++ b/doc/gpce-2017/gpce.skb
@@ -79,7 +79,7 @@
"\\usepackage{microtype}\n"
;; "\\usepackage[hypcap]{caption}\n"
;; "\\DeclareCaptionType{copyrightbox}\n"
-   ;; "\\usepackage{balance}\n"
+   "\\usepackage{balance}\n"

;; Recognize ‘⇒’ and ‘⇝’ in LaTeX input.

"\\DeclareUnicodeCharacter{21D2}{$\\Rightarrow$}\n"
@@ -245,8 +245,8 @@ rollback “for free.”  While Guix and Nix are package 
managers, the
 Guix System Distribution (or GuixSD) as well as NixOS extend the
 functional paradigm to whole operating system deployments ,(ref :bib
 'dolstra2010:nixos).])
-  (p [While Guix implements this functional deployment paradigm
-pioneered by Nix, we explained in previous work that its
+  (p [Guix implements this functional deployment paradigm
+pioneered by Nix but, as explained in previous work, its
 implementation departs from Nix in interesting ways ,(ref :bib
 'courtes2013:functional).  First, while Nix relies on a custom
 domain-specific language (DSL), the Nix language, Guix instead
@@ -325,7 +325,7 @@ concludes.]))
   :ident "origins"
   
   (p [Scheme is a dialect of Lisp, and Lisp is famous for its
-homoiconicity—the fact that code has a direct representation as a data
+its direct representation of code as a data
 structure using the same syntax.  “S-expressions” or “sexps”, Lisp’s
 parenthecal expressions, thus look like they lend themselves to code
 staging.
@@ -420,7 +420,9 @@ cases.])
  :start ";!begin-imagemagick-gexp"
  :stop ";!end-imagemagick-gexp")))
 
-(p [G-expressions ,(emph [bind software deployment to staging]).
+(p [G-expressions ,(emph [bind software deployment to
+staging]): when a gexp is staged, the software and artifacts it refers
+to are guaranteed to be deployed as well.
 A gexp bundles an sexp and its inputs
 and outputs, and it can be serialized with ,(tt [/gnu/store]) file
 names substituted as needed.  We first define two operators:
@@ -689,7 +691,7 @@ Guix.])
 the history of Guix.  Package definitions like that of Figure ,(ref
 :figure "fig-package-def") rely on the previous ad-hoc staging
 mechanism, as can be seen in the use of labels in the ,(tt
-[inputs]) field of definitions.  Guix today includes more than 5,500
+[inputs]) field of definitions.  Guix today includes more than 6,000
 packages, which still use this old, pre-gexp style.  We are
 considering a migration to a new style but given the size of the
 repository, this is a challenging task and we must make sure every use
@@ -711,7 +713,7 @@ flexibility.]))
 (p [GuixSD, the Guix-based GNU/Linux distribution, was one of
 the main motivations behind gexps.  The principle behind GuixSD is
 that, given a high-level ,(tt [operating-system]) declaration that
-specifies user accounts, system services, and other OS settings, the
+specifies user accounts, system services, and other settings, the
 complete system is instantiated to the store.  To achieve that, a lot
 of files must be generated: start/stop script for all the system
 services (daemons, operations such as file system mounts, etc.),
@@ -890,6 +892,11 @@ escaping syntax.  The “code-as-string” paradigm also has 
other side
 effects: comments and whitespace in those strings is preserved, and
 changing those triggers a rebuild of the derivation, which is
 inconvenient.])
+  (p [There are similarities between GuixSD and MirageOS, which both
+aim to unify configuration and deployment into a single high-level
+language framework ,(ref :bib 'madhavapeddy2013:unikernels).  Mirage
+uses code staging through MetaOCaml, though that is limited to the
+implementation of its data storage layer.])
   (p [Code staging is often studied in the context of optimized code
 generation ,(ref :bib '(rompf2012:lms wang2002:s2 aktemur2013:shonan)),
 or that of hygienic macros ,(ref :bib '(kohlbecker1986:hygienic
@@ -955,6 +962,7 @@ the assembly of operating system components in GuixSD.  
Using a
 single-language framework with staging has proved to enable new ways
 of code reuse and composition.]))

+   (!latex "\n\\newpage\n\\balance\n")
(references))

 ;;; Local Variables:
diff --git 

11/14: gpce-2017: Enable hyphenation at hyphens.

[Ludovic Court�s]

civodul pushed a commit to branch master
in repository maintenance.

commit 05b0731d26b154cf6c61e4e965fcdcf2bd0d3cdb
Author: Ludovic Courtès 
Date:   Fri Sep 1 15:18:21 2017 +0200

gpce-2017: Enable hyphenation at hyphens.
---
 doc/gpce-2017/gpce.skb | 5 +
 1 file changed, 5 insertions(+)

diff --git a/doc/gpce-2017/gpce.skb b/doc/gpce-2017/gpce.skb
index 8a98b27..f311865 100644
--- a/doc/gpce-2017/gpce.skb
+++ b/doc/gpce-2017/gpce.skb
@@ -42,6 +42,11 @@
 (define (=>)
   (symbol "=>"))
   
+;; XXX: Terrible hack to turn hyphens into hyphenation points in 'tt'.
+(set! (@@ (skribilo engine latex) latex-tt-encoding)
+  `((#\- "-\\-")
+,@(@@ (skribilo engine latex) latex-tt-encoding)))
+
 (define %guix-keywords
   (append (map (lambda (x) (cons x '))
  '(set! if let let* letrec quote cond case else begin do lambda

04/14: gpce-2017: Fixlets.

[Ludovic Court�s]

civodul pushed a commit to branch master
in repository maintenance.

commit 5ffdfc4afd03ec251eec2e7bd1a31186d9c54a14
Author: Ludovic Courtès 
Date:   Thu Jul 6 23:52:34 2017 +0200

gpce-2017: Fixlets.
---
 doc/gpce-2017/code/gexp-expansion.scm |   4 +-
 doc/gpce-2017/gpce.skb| 227 +++---
 doc/gpce-2017/staging.sbib|   4 +-
 3 files changed, 128 insertions(+), 107 deletions(-)

diff --git a/doc/gpce-2017/code/gexp-expansion.scm 
b/doc/gpce-2017/code/gexp-expansion.scm
index 111fa81..ecd5637 100644
--- a/doc/gpce-2017/code/gexp-expansion.scm
+++ b/doc/gpce-2017/code/gexp-expansion.scm
@@ -34,7 +34,7 @@
   #~(let ((x 2))
   #$(gen-body #~x))
 
-⇒ (let ((x0 2))
-(let ((x1 40)) (+ x1 x0)))
+⇝ (let ((x-1bd8-0 2))
+(let ((x-4f05-0 40)) (+ x-4f05-0 x-1bd8-0)))
 ;;!end-gexp-hygiene
 
diff --git a/doc/gpce-2017/gpce.skb b/doc/gpce-2017/gpce.skb
index 8101a93..29afd69 100644
--- a/doc/gpce-2017/gpce.skb
+++ b/doc/gpce-2017/gpce.skb
@@ -157,21 +157,21 @@
  (p [GNU Guix is a “functional” package manager that builds upon
 earlier work on Nix.  Guix implements high-level abstractions such as
 packages and operating system services as domain-specific languages
-(DSL) embedded in Scheme, and it also implements build actions and
+(DSLs) embedded in Scheme.  It also implements build actions and
 operating system orchestration in Scheme.  This leads to a multi-tier
 programming environment where embedded code snippets are staged for
 eventual execution.])
 
- (p [In this paper we present ,(emph [G-expressions]) or “,(emph
+ (p [This paper presents ,(emph [G-expressions]) or “,(emph
 [gexps])”, the staging mechanism we devised for Guix.  We explain our
 journey from traditional Lisp S-expressions to G-expressions, which
 augment the former with contextual information and ensure hygienic code 
staging.
 We discuss the
 implementation of gexps and report on our experience using them in a
 variety of operating system use cases—from package build processes
-to system services.  To our knowledge, gexps
-provide a unique way to cover many aspects of OS configuration in a
-single, multi-tier language, and to facilitate code reuse and code
+to system services.  Gexps
+provide a novel way to cover many aspects of OS configuration in a
+single, multi-tier language, while facilitating code reuse and code
 sharing.]))

;; See .
@@ -194,7 +194,7 @@ that software build processes are considered as pure 
functions: given
 a set of inputs (compiler, libraries, build scripts, and so on), a
 package’s build function is assumed to always produce the same result.
 Build results are stored in an immutable persistent data structure,
-the store, implemented as a single directory, ,(tt [/gnu/store]).
+the ,(emph [store]), implemented as a single directory, ,(tt [/gnu/store]).
 Each entry in ,(tt [/gnu/store]) has a file name composed of the hash
 of all the build inputs used to produce it, followed by a symbolic
 name.  For example, ,(tt [/gnu/store/yr9rk90jf…-gcc-7.1.0]) identifies
@@ -202,21 +202,21 @@ a specific build of GCC 7.1.  A variant of GCC 7.1, for 
instance one
 using different build options or different dependencies, would get a
 different hash.  Thus, each store file name uniquely identifies build
 results, and build processes are ,(emph [referentially transparent]).
-This simplifies the reasoning on complex package compositions, but it
+This simplifies reasoning on complex package compositions, and
 also has nice properties such as supporting transactional upgrades and
 rollback “for free.”  While Guix and Nix are package managers, the
-Guix System Distribution (or GuixSD) as well as NixOS extends the
+Guix System Distribution (or GuixSD) as well as NixOS extend the
 functional paradigm to whole operating system deployments ,(ref :bib
 'dolstra2010:nixos).])
   (p [While Guix implements this functional deployment paradigm
 pioneered by Nix, we explained in previous work that its
 implementation departs from Nix in interesting ways ,(ref :bib
 'courtes2013:functional).  First, while Nix relies on a custom
-domain-specific language (DSL), the Nix language, Guix instead chooses
-to devise a set of DSLs and data structures embedded in the
-general-purpose language Scheme.  The rationale was that this approach
-would ease the development of user interfaces and tools dealing with
-packages, and would allow users to benefit from everything a
+domain-specific language (DSL), the Nix language, Guix instead
+implements a set of DSLs and data structures embedded in the
+general-purpose language Scheme.  This simplifies
+the development of user interfaces and tools dealing with
+packages, and allows users to benefit from everything a
 general-purpose language brings: compiler, debugger, REPL, editor
 support, libraries, and so on.  Four years later, Guix has indeed
 gained rich tooling that would have 

09/14: gpce-2017: Fix typo.

[Ludovic Court�s]

civodul pushed a commit to branch master
in repository maintenance.

commit cbcd16f03608afdc46bfc14e0deabad152554d4b
Author: Ludovic Courtès 
Date:   Fri Sep 1 14:01:56 2017 +0200

gpce-2017: Fix typo.
---
 doc/gpce-2017/gpce.skb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/doc/gpce-2017/gpce.skb b/doc/gpce-2017/gpce.skb
index 6aef32b..b58eafc 100644
--- a/doc/gpce-2017/gpce.skb
+++ b/doc/gpce-2017/gpce.skb
@@ -303,7 +303,7 @@ definitions in Nix can embed Bash or Perl snippets to 
refine build
 steps, Guix package definitions instead embed Scheme code.
 Consequently, we have two strata of Scheme code: the ,(emph [host code]),
 which provides the package definition, and the ,(emph [build code]), which is
-staged for later execution by the build daemon.)
+staged for later execution by the build daemon.])
   (p [This paper focuses on code staging in Guix.  Our contribution
 is twofold: we present G-expressions (or “gexps”), a new code staging
 mechanism implemented through mere syntactic extensions of the Scheme

13/14: gpce-2017: Shrink to 7 pages (10pt font).

[Ludovic Court�s]

civodul pushed a commit to branch master
in repository maintenance.

commit 0ef6b13eed6872662105d011e9d7d3d42e9e4a8d
Author: Ludovic Courtès 
Date:   Fri Sep 1 15:27:49 2017 +0200

gpce-2017: Shrink to 7 pages (10pt font).

acmart v1.46 (required for the camera-ready version) uses a 10pt font,
whereas acmart v1.09 (part of TeX Live 2016, which I used for the
submission) uses 9pt.
---
 doc/gpce-2017/gpce.skb | 52 +-
 1 file changed, 22 insertions(+), 30 deletions(-)

diff --git a/doc/gpce-2017/gpce.skb b/doc/gpce-2017/gpce.skb
index f311865..c334c0e 100644
--- a/doc/gpce-2017/gpce.skb
+++ b/doc/gpce-2017/gpce.skb
@@ -30,12 +30,6 @@
 (! "{-}{-}")
 "--"
 
-(define (corresponding)
-  (resolve (lambda (n e env)
- (if (engine-format? "latex" e)
-(! "co\\-rres\\-pon\\-ding")
-"corresponding"
-
 (define (url url)
   (ref :text (tt url) :url url))
 
@@ -155,9 +149,9 @@
(let ((ident (markup-ident n))
  (legend (markup-option n :legend))
  (mc (markup-option n :multicolumns)))
-  (display "\\begin{figure}[ht]\n\\begin{footnotesize}\n")
+  (display "\\begin{figure}[ht]\n\\begin{scriptsize}\n")
   (output (markup-body n) e)
-  (display "\n\\end{footnotesize}\n")
+  (display "\n\\end{scriptsize}\n")
   (format #t "\\caption{\\label{~a}"
   (string-canonicalize ident))
   (output legend e)
@@ -219,7 +213,7 @@ sharing.]))
;; See .
(!latex "\\input{categories.tex}\n")
 
-   (acm-keywords [Code staging, Scheme, Functional package management])
+   (acm-keywords [Code staging, Scheme, Software deployment])
 
(!latex "\\maketitle\n")
 
@@ -246,8 +240,8 @@ different hash.  Thus, each store file name uniquely 
identifies build
 results, and build processes are ,(emph [referentially transparent]).
 This simplifies reasoning on complex package compositions, and
 also has nice properties such as supporting transactional upgrades and
-rollback “for free.”  While Guix and Nix are package managers, the
-Guix System Distribution (or GuixSD) as well as NixOS extend the
+rollback “for free.”  The
+Guix System Distribution (or GuixSD) and NixOS extend the
 functional paradigm to whole operating system deployments ,(ref :bib
 'dolstra2010:nixos).])
   (p [Guix implements this functional deployment paradigm
@@ -257,8 +251,8 @@ implementation departs from Nix in interesting ways ,(ref 
:bib
 domain-specific language (DSL), the Nix language, Guix instead
 implements a set of DSLs and data structures embedded in the
 general-purpose language Scheme.  This simplifies
-the development of user interfaces and tools dealing with
-packages, and allows users to benefit from everything a
+the development of user interfaces and tools,
+and allows users to benefit from everything a
 general-purpose language brings: compiler, debugger, REPL, editor
 support, libraries, and so on.])
 
@@ -286,8 +280,8 @@ interface.]
   (assoc-ref %build-inputs "gawk")
 (inputs `(("gawk" ,gawk)));!inputs
 (synopsis "GNU Hello")
-(description "An illustration of GNU's engineering practices.")
-(home-page "http://www.gnu.org/software/hello/;)
+(description "Example of a GNU package.")
+(home-page "https://gnu.org/software/hello/;)
 (license gpl3+)))
 ])))
 
@@ -364,9 +358,9 @@ add the file ,(tt [GuixSD.png]) to ,(tt [/gnu/store]).  The 
variable
 ,(tt [build]) contains our build program as an sexp (the
 apostrophe is equivalent to ,(tt [quote]); it introduces unevaluated
 code).  Finally, ,(tt
-[build,(!latex "\\")-expression->derivation]) takes the build program and 
computes
+[build-expression->derivation]) takes the build program and computes
 the corresponding derivation without building it.  The user can then
-make an RPC to the build daemon asking it to build this derivation;
+make an RPC to the daemon asking it to build this derivation;
 only then will the daemon create an isolated environment and run our
 build program.])
 (p [,(tt [build-expression->derivation]) arranges so that the
@@ -615,13 +609,13 @@ seen earlier.  We defined a ,(tt [file-append]) function 
that returns
 objects with a custom expander: one that performs string concatenation
 when generating the sexp.  We can now write gexps like:]
 
-  (!latex "[0.3cm]\n")
+  (!latex "[0.3cm]\n\\begin{scriptsize}\n")
   (prog :line #f
 (source :language guix [
 #~(execl #$(file-append emacs "/bin/emacs"))
 
 ⇝ (execl "/gnu/store/…-emacs-25.2/bin/emacs")]))
-  (!latex "[0.3cm]\n")
+  (!latex "\\end{scriptsize}\n[0.3cm]\n")
 
 [This is convenient in situations where we do not want or cannot impose
 a ,(tt 

12/14: gpce-2017: Use acmart v1.47.

[Ludovic Court�s]

civodul pushed a commit to branch master
in repository maintenance.

commit a6b3c0245c8328e1ca3f6b7c2fc9f983e609c56d
Author: Ludovic Courtès 
Date:   Fri Sep 1 15:33:02 2017 +0200

gpce-2017: Use acmart v1.47.

Taken from ,
commit 257e068be2f5919d3b0d003356f747eb2b3076c7.
---
 doc/gpce-2017/GNUmakefile |2 +-
 doc/gpce-2017/acmart.cls  | 2544 +
 2 files changed, 2545 insertions(+), 1 deletion(-)

diff --git a/doc/gpce-2017/GNUmakefile b/doc/gpce-2017/GNUmakefile
index 361691a..18df321 100644
--- a/doc/gpce-2017/GNUmakefile
+++ b/doc/gpce-2017/GNUmakefile
@@ -5,7 +5,7 @@ RUBBER   := rubber
 .DEFAULT_GOAL := gpce.pdf
 
 %.pdf: %.tex
-   $(RUBBER) --pdf "$<"
+   $(RUBBER) --pdf -I $$PWD "$<"
 
 %.tex: %.skb
$(SKRIBILO)  -t latex -o "$@" "$<"
diff --git a/doc/gpce-2017/acmart.cls b/doc/gpce-2017/acmart.cls
new file mode 100644
index 000..cf83c8a
--- /dev/null
+++ b/doc/gpce-2017/acmart.cls
@@ -0,0 +1,2544 @@
+%%
+%% This is file `acmart.cls',
+%% generated with the docstrip utility.
+%%
+%% The original source files were:
+%%
+%% acmart.dtx  (with options: `class')
+%% 
+%% IMPORTANT NOTICE:
+%% 
+%% For the copyright see the source file.
+%% 
+%% Any modified versions of this file must be renamed
+%% with new filenames distinct from acmart.cls.
+%% 
+%% For distribution of the original source see the terms
+%% for copying and modification in the file acmart.dtx.
+%% 
+%% This generated file may be distributed as long as the
+%% original source files, as listed above, are part of the
+%% same distribution. (The sources need not necessarily be
+%% in the same archive or directory.)
+%% \CharacterTable
+%%  {Upper-case\A\B\C\D\E\F\G\H\I\J\K\L\M\N\O\P\Q\R\S\T\U\V\W\X\Y\Z
+%%   Lower-case\a\b\c\d\e\f\g\h\i\j\k\l\m\n\o\p\q\r\s\t\u\v\w\x\y\z
+%%   Digits\0\1\2\3\4\5\6\7\8\9
+%%   Exclamation   \! Double quote  \" Hash (number) \#
+%%   Dollar\$ Percent   \% Ampersand \&
+%%   Acute accent  \' Left paren\( Right paren   \)
+%%   Asterisk  \* Plus  \+ Comma \,
+%%   Minus \- Point \. Solidus   \/
+%%   Colon \: Semicolon \; Less than \<
+%%   Equals\= Greater than  \> Question mark \?
+%%   Commercial at \@ Left bracket  \[ Backslash \\
+%%   Right bracket \] Circumflex\^ Underscore\_
+%%   Grave accent  \` Left brace\{ Vertical bar  \|
+%%   Right brace   \} Tilde \~}
+\NeedsTeXFormat{LaTeX2e}
+\ProvidesClass{acmart}
+[2017/08/31 v1.47 Typesetting articles for Association of
+Computing Machinery]
+\def\@classname{acmart}
+\InputIfFileExists{acmart-preload-hook.tex}{%
+  \ClassWarning{\@classname}{%
+I am loading acmart-preload-hook.tex. You are fully responsible
+for any problems from now on.}}{}
+\RequirePackage{xkeyval}
+\RequirePackage{xstring}
+\define@choicekey*+{acmart.cls}{format}[\ACM@format\ACM@format@nr]{%
+  manuscript, acmsmall, acmlarge, acmtog, sigconf, siggraph,
+  sigplan, sigchi, sigchi-a}[manuscript]{}{%
+  \ClassError{\@classname}{The option format must be manuscript,
+acmsmall, acmlarge, acmtog, sigconf, siggraph,
+sigplan, sigchi or sigchi-a}}
+\def\@DeclareACMFormat#1{\DeclareOptionX{#1}{\setkeys{acmart.cls}{format=#1}}}
+\@DeclareACMFormat{manuscript}
+\@DeclareACMFormat{acmsmall}
+\@DeclareACMFormat{acmlarge}
+\@DeclareACMFormat{acmtog}
+\@DeclareACMFormat{sigconf}
+\@DeclareACMFormat{siggraph}
+\@DeclareACMFormat{sigplan}
+\@DeclareACMFormat{sigchi}
+\@DeclareACMFormat{sigchi-a}
+\ExecuteOptionsX{format}
+\define@boolkey+{acmart.cls}[@ACM@]{screen}[true]{%
+  \if@ACM@screen
+\PackageInfo{\@classname}{Using screen mode}%
+  \else
+\PackageInfo{\@classname}{Not using screen mode}%
+  \fi}{\PackageError{\@classname}{Option screen can be either true or
+false}}
+\ExecuteOptionsX{screen=false}
+\define@boolkey+{acmart.cls}[@ACM@]{acmthm}[true]{%
+  \if@ACM@acmthm
+\PackageInfo{\@classname}{Requiring acmthm}%
+  \else
+\PackageInfo{\@classname}{Suppressing acmthm}%
+  \fi}{\PackageError{\@classname}{Option acmthm can be either true or
+false}}
+\ExecuteOptionsX{acmthm=true}
+\define@boolkey+{acmart.cls}[@ACM@]{review}[true]{%
+  \if@ACM@review
+\PackageInfo{\@classname}{Using review mode}%
+  \else
+\PackageInfo{\@classname}{Not using review mode}%
+  \fi}{\PackageError{\@classname}{Option review can be either true or
+false}}
+\ExecuteOptionsX{review=false}
+\define@boolkey+{acmart.cls}[@ACM@]{authorversion}[true]{%
+  \if@ACM@authorversion
+\PackageInfo{\@classname}{Using authorversion mode}%
+  \else
+\PackageInfo{\@classname}{Not using authorversion mode}%
+  \fi}{\PackageError{\@classname}{Option authorversion can be either true or
+false}}
+\ExecuteOptionsX{authorversion=false}

05/14: gpce-2017: Shrink.

[Ludovic Court�s]

civodul pushed a commit to branch master
in repository maintenance.

commit 995bb0914536322e9802babbcc8cca3015d96d2d
Author: Ludovic Courtès 
Date:   Fri Jul 7 00:35:54 2017 +0200

gpce-2017: Shrink.
---
 doc/gpce-2017/gpce.skb | 28 ++--
 1 file changed, 6 insertions(+), 22 deletions(-)

diff --git a/doc/gpce-2017/gpce.skb b/doc/gpce-2017/gpce.skb
index 29afd69..b14 100644
--- a/doc/gpce-2017/gpce.skb
+++ b/doc/gpce-2017/gpce.skb
@@ -218,14 +218,7 @@ general-purpose language Scheme.  This simplifies
 the development of user interfaces and tools dealing with
 packages, and allows users to benefit from everything a
 general-purpose language brings: compiler, debugger, REPL, editor
-support, libraries, and so on.  Four years later, Guix has indeed
-gained rich tooling that would have been harder to develop for an
-external DSL like Nix: ,(tt [guix lint]) checks style conformance and
-mistakes in package definition, ,(tt [guix refresh]) updates package
-definitions to the latest version of a package, user interfaces in
-Emacs and in Web browsers have been developed, tools to rewrite a
-package’s dependency graph are available from the command line and
-through the API, and so on.])
+support, libraries, and so on.])
 
  (figure :legend [A package definition using the high-level
 interface.]
@@ -273,12 +266,7 @@ definitions in Nix can embed Bash or Perl snippets to 
refine build
 steps, Guix package definitions instead embed Scheme code.
 Consequently, we have two strata of Scheme code: the ,(emph [host code]),
 which provides the package definition, and the ,(emph [build code]), which is
-staged for later execution by the build daemon.  Our thesis is that
-this single-language, “multi-tier” approach facilitates code reuse and
-code sharing among the several tiers, and that it can avoid a whole
-class of errors in the staged code—as opposed to generation of code in
-a “foreign” language, which is treated a mere strings where syntactic
-and semantic errors cannot be detected by the host code.])
+staged for later execution by the build daemon.)
   (p [This paper focuses on code staging in Guix.  Our contribution
 is twofold: we present G-expressions (or “gexps”), a new code staging
 mechanism implemented through mere syntactic extensions of the Scheme
@@ -334,7 +322,7 @@ add the file ,(tt [GuixSD.png]) to ,(tt [/gnu/store]).  The 
variable
 ,(tt [build]) contains our build program as an sexp (the
 apostrophe is equivalent to ,(tt [quote]); it introduces unevaluated
 code).  Finally, ,(tt
-[build-expression->derivation]) takes the build program and computes
+[build,(!latex "\\")-expression->derivation]) takes the build program and 
computes
 the corresponding derivation without building it.  The user can then
 make an RPC to the build daemon asking it to build this derivation;
 only then will the daemon create an isolated environment and run our
@@ -881,9 +869,7 @@ of user-defined binding constructs (macros).  This strategy 
is
 appropriate in a macro-less language with a fixed set of binding
 constructs like OCaml, but we have seen that languages such as Scheme
 that support user-defined binding constructs create additional
-challenges.  MetaScheme supports cross-stage persistence (CSP) but the
-implementation provided assumes that an array of cross-stage values is
-shared among stages, which is hard to transpose to concrete settings.
+challenges.
 Rhiger’s work ,(ref :bib 'rhiger2012:hygienic) follows a similar
 approach but chooses to redefine Scheme’s quasiquotation rather than
 introduce new constructs.])
@@ -891,10 +877,8 @@ introduce new constructs.])
 quasiquotations by providing bracket, escape, and lift forms separate
 from ,(tt [quasiquote]) and ,(tt [unquote]) ,(ref :bib 'wang2002:s2).
 Therefore, as with ,(tt [syntax-case]) and gexps, quoted code has a
-disjoint type as opposed to being a list.  S,(sup [2]) supports CSP,
-whereby staged code can seemlessly refer to variables of the previous
-stage that are in scope; the article does not explain the
-implementation strategy.  S,(sup [2])’s focus is on programs with
+disjoint type as opposed to being a list.
+S,(sup [2])’s focus is on programs with
 possibly more than two stages, whereas gexp are, in practice, used for
 two-stage programs.  The article discusses ,(emph [code regeneration])
 at run time; gexps have a similar requirement here: at run time a

06/14: gpce-2017: Tweak some more.

[Ludovic Court�s]

civodul pushed a commit to branch master
in repository maintenance.

commit ee3a74c6e2a25956342157d555826626c00de3b0
Author: Ludovic Courtès 
Date:   Fri Jul 7 11:48:54 2017 +0200

gpce-2017: Tweak some more.
---
 doc/gpce-2017/code/system-test.scm |   2 +-
 doc/gpce-2017/gpce.skb | 154 ++---
 doc/gpce-2017/staging.sbib |  36 +
 3 files changed, 113 insertions(+), 79 deletions(-)

diff --git a/doc/gpce-2017/code/system-test.scm 
b/doc/gpce-2017/code/system-test.scm
index 6a086b7..4ea879b 100644
--- a/doc/gpce-2017/code/system-test.scm
+++ b/doc/gpce-2017/code/system-test.scm
@@ -3,7 +3,7 @@
  (srfi srfi-64) (ice-9 match))
 
 ;; Spawn the VM that runs the declared OS.
-(define marionette (make-marionette (list #$run)))
+(define marionette (make-marionette (list #$vm)))
 
 (test-begin "basic")
 (test-assert "uname"
diff --git a/doc/gpce-2017/gpce.skb b/doc/gpce-2017/gpce.skb
index b14..1cc9ba4 100644
--- a/doc/gpce-2017/gpce.skb
+++ b/doc/gpce-2017/gpce.skb
@@ -292,7 +292,7 @@ homoiconicity—the fact that code has a direct 
representation as a data
 structure using the same syntax.  “S-expressions” or “sexps”, Lisp’s
 parenthecal expressions, thus look like they lend themselves to code
 staging.
-In this section we show how we this early experience made it clear that
+In this section we show how our early experience made it clear that
 we needed an ,(emph [augmented]) version of sexps.])
 
   (section :title [Staging Build Expressions]
@@ -312,7 +312,7 @@ which relied solely on Lisp quotation ,(ref :bib
 'bawden1999:quasiquotation).  Figure ,(ref :figure "fig-build-sexp")
 shows an example that creates a derivation that, when built, converts
 the input image to JPEG, using the ,(tt [convert]) program from the
-ImageMagick package—this is equivalent to a three-line makefile, but
+ImageMagick package—this is equivalent to a three-line makefile rule, but
 referentially transparent.  In this example, variable ,(tt [store])
 represents the connection to the build daemon.  The ,(tt
 [package-derivation]) function takes the ,(tt [imagemagick]) package
@@ -367,7 +367,7 @@ file name.])))
(chapter :title [G-Expressions]
   :ident "gexps"

-  (p [We devised “G-expressions” as a mechanism to address
+  (p [We devised “G-expressions” to address
 these shortcomings.  This section describes the design and implementation of
 G-expressions, as well as extensions we added to address new use
 cases.])
@@ -383,7 +383,8 @@ cases.])
  :start ";!begin-imagemagick-gexp"
  :stop ";!end-imagemagick-gexp")))
 
-(p [In essence, a gexp bundles an sexp and its inputs
+(p [G-expressions ,(emph [bind software deployment to staging]).
+A gexp bundles an sexp and its inputs
 and outputs, and it can be serialized with ,(tt [/gnu/store]) file
 names substituted as needed.  We first define two operators:
 
@@ -513,17 +514,7 @@ as illustrated by Figure ,(ref :figure 
"fig-gexp-hygiene").  The
 implementation is similar to MetaScheme ,(ref :bib
 'kiselyov2008:metascheme) and to that described by Rhiger ,(ref :bib
 'rhiger2012:hygienic), with caveats discussed in ,(numref :text
-[Section] :ident "limitations").  Unlike the examples usually given in
-the literature, identifiers must be generated in a ,(emph
-[deterministic]) fashion: if they were not, we would produce different
-derivations at each run, which in turn would trigger full rebuilds of
-the package graph.  Thus, instead of relying on ,(tt [gensym]) and
-,(tt [generate-temporaries]), we generate identifiers as a function of
-the hash of
-the input expression and of the lexical nesting level of
-the identifier—these are the two components we can see in the generated
-identifiers of Figure ,(ref
-:figure "fig-gexp-hygiene").])
+[Section] :ident "limitations").])
 (item [The second pass ,(emph [collects the escape forms]) (,(tt
 [ungexp]) variants) in the input source.  The list of escape forms is
 needed to construct the list of inputs stored in the gexp
@@ -533,7 +524,19 @@ generation function shown in Figure ,(ref :figure
 (item [The third pass ,(emph [substitutes escape forms]) with
 references to the corresponding formal arguments of the code
 generation function.  This leads to the sexp-construction expression
-shown in Figure ,(ref :figure "fig-gexp-expansion").]))])
+shown in Figure ,(ref :figure "fig-gexp-expansion").]))
+
+Unlike the examples usually given in
+the literature, our renaming pass must generate identifiers in a ,(emph
+[deterministic]) fashion: if they were not, we would produce different
+derivations at each run, which in turn would trigger full rebuilds of
+the package graph.  Thus, instead of relying on ,(tt [gensym]) and
+,(tt [generate-temporaries]), we generate identifiers as a function of
+the hash of
+the input expression and of the lexical nesting level of
+the 

02/14: gpce-2017: Write, write, write.

[Ludovic Court�s]

civodul pushed a commit to branch master
in repository maintenance.

commit ba736f621a54af89390c92304b2ca1de9c0979bf
Author: Ludovic Courtès 
Date:   Tue Jul 4 18:19:36 2017 +0200

gpce-2017: Write, write, write.
---
 .gitignore|   1 +
 doc/gpce-2017/code/gexp-compilers.scm |  14 +
 doc/gpce-2017/code/gexp-expansion.scm |  19 +-
 doc/gpce-2017/code/gexp-modules.scm   |   8 +
 doc/gpce-2017/code/initrd.scm |  11 +
 doc/gpce-2017/gpce.skb| 500 +-
 doc/gpce-2017/staging.sbib|  67 +
 7 files changed, 549 insertions(+), 71 deletions(-)

diff --git a/.gitignore b/.gitignore
index 948e1f9..a80c8ec 100644
--- a/.gitignore
+++ b/.gitignore
@@ -126,3 +126,4 @@
 /doc/gpce-2017/gpce.log
 /doc/gpce-2017/gpce.out
 /doc/gpce-2017/gpce.pdf
+/doc/gpce-2017/gpce.tex
diff --git a/doc/gpce-2017/code/gexp-compilers.scm 
b/doc/gpce-2017/code/gexp-compilers.scm
new file mode 100644
index 000..3989c73
--- /dev/null
+++ b/doc/gpce-2017/code/gexp-compilers.scm
@@ -0,0 +1,14 @@
+(define-gexp-compiler (package-compiler (package )
+system target)
+  ;; Compile PACKAGE to a derivation for SYSTEM, optionally
+  ;; cross-compiled for TARGET.
+  (if target
+  (package->cross-derivation package target system)
+  (package->derivation package system)))
+
+(define-gexp-compiler (local-file-compiler (file )
+   system target)
+  ;; "Compile" FILE by adding it to the store.
+  (match file
+(($  file name)
+ (interned-file file name
diff --git a/doc/gpce-2017/code/gexp-expansion.scm 
b/doc/gpce-2017/code/gexp-expansion.scm
index aab1365..003b767 100644
--- a/doc/gpce-2017/code/gexp-expansion.scm
+++ b/doc/gpce-2017/code/gexp-expansion.scm
@@ -1,18 +1,18 @@
 (use-modules (guix))
 
-;!begin-condensed
+;;!begin-condensed
 #~(list (string-append #$imagemagick "/bin/convert")
 (string-append #$emacs "/bin/emacs"))
-;!end-condensed
+;;!end-condensed
 
-;!begin-gexp-without-reader-macro
+;;!begin-gexp-without-reader-macro
 (gexp (list (string-append (ungexp imagemagick)
"/bin/convert")
 (string-append (ungexp emacs)
"/bin/emacs")))
-;!end-gexp-without-reader-macro
+;;!end-gexp-without-reader-macro
 
-;!begin-expansion
+;;!begin-expansion
 (let ((references
(list (gexp-input imagemagick)
  (gexp-input emacs)))
@@ -23,4 +23,11 @@
 (list 'string-append b
   "/bin/emacs")
   (make-gexp references proc))
-;!end-expansion
+;;!end-expansion
+
+;;!begin-staged-sexp
+(list (string-append "/gnu/store/65qrc…-imagemagick-6.9"
+ "/bin/convert")
+  (string-append "/gnu/store/825n3…-emacs-25.2"
+ "/bin/emacs"))
+;;!end-staged-sexp
diff --git a/doc/gpce-2017/code/gexp-modules.scm 
b/doc/gpce-2017/code/gexp-modules.scm
new file mode 100644
index 000..75cdf5a
--- /dev/null
+++ b/doc/gpce-2017/code/gexp-modules.scm
@@ -0,0 +1,8 @@
+(with-imported-modules (source-module-closure
+'((guix build utils)))
+  #~(begin
+  ;; Import the module in scope.
+  (use-modules (guix build utils))
+
+  ;; Use a function from (guix build utils).
+  (mkdir-p #$output)))
diff --git a/doc/gpce-2017/code/initrd.scm b/doc/gpce-2017/code/initrd.scm
new file mode 100644
index 000..f88bd4c
--- /dev/null
+++ b/doc/gpce-2017/code/initrd.scm
@@ -0,0 +1,11 @@
+;;!begin-initrd
+(expression->initrd
+ (with-imported-modules (source-module-closure
+ '((gnu build linux-boot)))
+   #~(begin
+   (use-modules (gnu build linux-boot))
+
+   (boot-system #:mounts '#$file-systems
+#:linux-modules '#$linux-modules
+#:linux-module-directory '#$kodir)))
+;;!end-initrd
diff --git a/doc/gpce-2017/gpce.skb b/doc/gpce-2017/gpce.skb
index 7c8aae6..48b2733 100644
--- a/doc/gpce-2017/gpce.skb
+++ b/doc/gpce-2017/gpce.skb
@@ -3,9 +3,14 @@
 (skribilo engine latex)
 (skribilo ast)
 (skribilo writer)
+(skribilo output)
+(skribilo utils strings)
+(skribilo lib)
 (skribilo evaluator)
 (skribilo biblio author)
-(skribilo source lisp))
+(skribilo source)
+(skribilo source lisp)
+(skribilo source parameters))
 
 (define (---) ; emdash
   (resolve (lambda (n e env)
@@ -37,6 +42,28 @@
 (define (=>)
   (symbol "=>"))
   
+(define %guix-keywords
+  (append (map (lambda (x) (cons x '))
+ '(set! if let let* letrec quote cond case else begin do lambda
+   gexp ungexp match))
+   (map (lambda (x) (cons x '))
+   '(define define-syntax define-gexp-compiler
+ with-imported-modules use-modules
+
+(define 

01/14: doc: Add GPCE paper.

[Ludovic Court�s]

civodul pushed a commit to branch master
in repository maintenance.

commit 6727f8e6b262d8071a45362f7e3c12eb101ce8ba
Author: Ludovic Courtès 
Date:   Fri Jun 30 18:40:03 2017 +0200

doc: Add GPCE paper.
---
 .gitignore|   4 +
 doc/gpce-2017/GNUmakefile |  11 +
 doc/gpce-2017/abstract.md |  20 ++
 doc/gpce-2017/code/GuixSD.png | Bin 0 -> 14332 bytes
 doc/gpce-2017/code/build-sexp.scm |  39 
 doc/gpce-2017/code/gexp-expansion.scm |  26 +++
 doc/gpce-2017/gpce.org|  48 
 doc/gpce-2017/gpce.skb| 417 ++
 doc/gpce-2017/staging.sbib|  22 ++
 9 files changed, 587 insertions(+)

diff --git a/.gitignore b/.gitignore
index 98201c3..948e1f9 100644
--- a/.gitignore
+++ b/.gitignore
@@ -122,3 +122,7 @@
 /talks/ghm-2017/update/talk.snm
 /talks/ghm-2017/update/talk.toc
 /talks/ghm-2017/update/talk.vrb
+/doc/gpce-2017/gpce.aux
+/doc/gpce-2017/gpce.log
+/doc/gpce-2017/gpce.out
+/doc/gpce-2017/gpce.pdf
diff --git a/doc/gpce-2017/GNUmakefile b/doc/gpce-2017/GNUmakefile
new file mode 100644
index 000..361691a
--- /dev/null
+++ b/doc/gpce-2017/GNUmakefile
@@ -0,0 +1,11 @@
+SKRIBILO := skribilo
+PDFLATEX := pdflatex
+RUBBER   := rubber
+
+.DEFAULT_GOAL := gpce.pdf
+
+%.pdf: %.tex
+   $(RUBBER) --pdf "$<"
+
+%.tex: %.skb
+   $(SKRIBILO)  -t latex -o "$@" "$<"
diff --git a/doc/gpce-2017/abstract.md b/doc/gpce-2017/abstract.md
new file mode 100644
index 000..54bbab9
--- /dev/null
+++ b/doc/gpce-2017/abstract.md
@@ -0,0 +1,20 @@
+Staging in GNU Guix
+=
+
+GNU Guix is a “functional” package manager that borrows from earlier
+work on Nix by Dolstra _et al._.  Guix implements high-level
+abstractions such as packages and operating system services as
+domain-specific languages (DSL) embedded in Scheme, and it also
+implements build actions and operating system orchestration in Scheme.
+This leads to a multi-tier programming environment where embedded code
+snippets are _staged_ for eventual execution.
+
+In this paper we present _G-expressions_ or “_gexps_”.  We explain our
+journey from traditional Lisp S-expressions to G-expressions, which
+augment the former with contextual information, and we discuss the
+implementation of gexps.  We report on our experience using gexps in a
+variety of operating system use cases—from package build processes, to
+initial RAM disk code, to system services.  To our knowledge, gexps
+provide a unique way to cover many aspects of OS configuration in a
+single, multi-tier language, and to facilitate code reuse and code
+sharing.  Finally we compare to related work on staging.
diff --git a/doc/gpce-2017/code/GuixSD.png b/doc/gpce-2017/code/GuixSD.png
new file mode 100644
index 000..eab9c59
Binary files /dev/null and b/doc/gpce-2017/code/GuixSD.png differ
diff --git a/doc/gpce-2017/code/build-sexp.scm 
b/doc/gpce-2017/code/build-sexp.scm
new file mode 100644
index 000..44f7a2e
--- /dev/null
+++ b/doc/gpce-2017/code/build-sexp.scm
@@ -0,0 +1,39 @@
+(use-modules (guix) (gnu))
+
+(define imagemagick
+  (specification->package "imagemagick"))
+
+(with-store store
+  (%guile-for-build (package-derivation store
+(specification->package "guile"
+
+;!begin-build-sexp
+(let* ((store (open-connection))
+   (drv   (package-derivation store imagemagick))
+   (image (add-to-store store "image.png" #t "sha256"
+"./GuixSD.png"))
+   (build
+'(let ((imagemagick (assoc-ref %build-inputs
+   "imagemagick"))
+   (image (assoc-ref %build-inputs "image")))
+   (mkdir %output)
+   (system* (string-append imagemagick "/bin/convert")
+"-quality" "75%"
+image
+(string-append %output "/image.jpg")
+  (build-expression->derivation store "example" build
+#:inputs `(("imagemagick" ,drv)
+   ("image" ,image
+;!end-build-sexp
+
+;!begin-imagemagick-gexp
+(let* ((image (local-file "./GuixSD.png" "image.png"))
+   (build #~(begin
+  (mkdir #$output)
+  (system* (string-append #$imagemagick
+  "/bin/convert")
+   "-quality" "75%"
+   #$image
+   (string-append #$output "/image.jpg")
+  (gexp->derivation "example" build))
+;!end-imagemagick-gexp
diff --git a/doc/gpce-2017/code/gexp-expansion.scm 
b/doc/gpce-2017/code/gexp-expansion.scm
new file mode 100644
index 000..aab1365
--- /dev/null
+++ b/doc/gpce-2017/code/gexp-expansion.scm
@@ -0,0 +1,26 @@
+(use-modules (guix))
+
+;!begin-condensed
+#~(list (string-append #$imagemagick "/bin/convert")
+(string-append #$emacs "/bin/emacs"))

08/14: gpce-2017: Add an explicit license.

[Ludovic Court�s]

civodul pushed a commit to branch master
in repository maintenance.

commit ce3cfaae1c6dcd86b0c099c3de42e51f5282fc8f
Author: Ludovic Courtès 
Date:   Thu Aug 31 11:35:09 2017 +0200

gpce-2017: Add an explicit license.
---
 doc/gpce-2017/gpce.skb | 22 +-
 1 file changed, 21 insertions(+), 1 deletion(-)

diff --git a/doc/gpce-2017/gpce.skb b/doc/gpce-2017/gpce.skb
index 114e161..6aef32b 100644
--- a/doc/gpce-2017/gpce.skb
+++ b/doc/gpce-2017/gpce.skb
@@ -92,7 +92,27 @@
"\
 \\acmConference[GPCE'17]{International Conference on Generative Programming: 
Concepts \\& Experience}{October 2017}{Vancouver, Canada}
 \\acmYear{2017}
-\\copyrightyear{2017}\n")))
+\\copyrightyear{2017}
+
+\\let\\oldthing\\footnotetextcopyrightpermission
+\\renewcommand\\footnotetextcopyrightpermission[1]{\\oldthing{
+  % Per
+  % 
,
+  % the copyright holder is me personally, not Inria.
+  Copyright \\copyright 2017 Ludovic Courtès.\\
+
+  Permission is granted to copy, distribute and/or modify this document
+  under the terms of the GNU Free Documentation License, Version 1.3
+  or any later version published by the Free Software Foundation;
+  with no Invariant Sections, no Front-Cover Texts, and no Back-Cover Texts.
+  A copy of the license is
+  available at \\url{https://www.gnu.org/licenses/gfdl.html}.
+
+  % Give a link to the 'Transparent Copy', as per Section 3 of the GFDL.
+  The source of this document is available from
+  \\url{https://git.sv.gnu.org/cgit/guix/maintenance.git}.
+}}
+")))
 
 (let ((latex (find-engine 'latex)))
(engine-custom-set! latex 'documentclass

14/14: gpce-2017: Adjust ACM boilerplate.

[Ludovic Court�s]

civodul pushed a commit to branch master
in repository maintenance.

commit fb91f645dc5526b45ff400f533bbaf89a7e7dadd
Author: Ludovic Courtès 
Date:   Fri Sep 1 15:51:18 2017 +0200

gpce-2017: Adjust ACM boilerplate.
---
 doc/gpce-2017/gpce.skb | 8 ++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/doc/gpce-2017/gpce.skb b/doc/gpce-2017/gpce.skb
index c334c0e..5e0869b 100644
--- a/doc/gpce-2017/gpce.skb
+++ b/doc/gpce-2017/gpce.skb
@@ -89,9 +89,13 @@

"\\DeclareUnicodeCharacter{2026}{\\textrm{\\ldots}}\n"
 
"\
-\\acmConference[GPCE'17]{International Conference on Generative Programming: 
Concepts \\& Experience}{October 2017}{Vancouver, Canada}
+% \\setcopyright{ACMUNKNOWN}
+% \\acmPrice{15.00}
+\\acmDOI{10.1145/3136040.3136045}
 \\acmYear{2017}
 \\copyrightyear{2017}
+% \acmISBN{978-1-4503-5524-7/17/10}
+\\acmConference[GPCE'17]{16th ACM SIGPLAN International Conference on 
Generative Programming: Concepts and Experiences}{October 23--24, 
2017}{Vancouver, Canada}
 
 \\let\\oldthing\\footnotetextcopyrightpermission
 \\renewcommand\\footnotetextcopyrightpermission[1]{\\oldthing{
@@ -128,7 +132,7 @@
 (display "}\n\\affiliation{\n")
 (display "  \\institution{")
 (output (markup-option a :affiliation) e)
-(display "}\n  \\streetaddress{")
+(display "}\n  \\city{")
 (output (markup-option a :address) e)
 (display "}}\n"))
  (if (pair? body) body (list body))

branch master updated (036cd84 -> fb91f64)

[Ludovic Court�s]

civodul pushed a change to branch master
in repository maintenance.

  from  036cd84   hydra: bayfront: Use nginx-service-type.
   new  6727f8e   doc: Add GPCE paper.
   new  ba736f6   gpce-2017: Write, write, write.
   new  8e152a0   gpce-2017: Write some more.
   new  5ffdfc4   gpce-2017: Fixlets.
   new  995bb09   gpce-2017: Shrink.
   new  ee3a74c   gpce-2017: Tweak some more.
   new  6b7a859   gpce-2017: Deanonymize.
   new  ce3cfaa   gpce-2017: Add an explicit license.
   new  cbcd16f   gpce-2017: Fix typo.
   new  832e95a   gpce-2017: Adjust as suggested by the reviewers.
   new  05b0731   gpce-2017: Enable hyphenation at hyphens.
   new  a6b3c02   gpce-2017: Use acmart v1.47.
   new  0ef6b13   gpce-2017: Shrink to 7 pages (10pt font).
   new  fb91f64   gpce-2017: Adjust ACM boilerplate.

The 14 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:
 .gitignore|5 +
 doc/gpce-2017/GNUmakefile |   11 +
 doc/gpce-2017/abstract.md |   20 +
 doc/gpce-2017/acmart.cls  | 2544 +
 doc/gpce-2017/categories.tex  |   23 +
 doc/gpce-2017/code/GuixSD.png |  Bin 0 -> 14332 bytes
 doc/gpce-2017/code/build-sexp.scm |   39 +
 doc/gpce-2017/code/gexp-compilers.scm |   14 +
 doc/gpce-2017/code/gexp-expansion.scm |   40 +
 doc/gpce-2017/code/gexp-modules.scm   |8 +
 doc/gpce-2017/code/initrd.scm |   11 +
 doc/gpce-2017/code/system-test.scm|   19 +
 doc/gpce-2017/gpce.org|   48 +
 doc/gpce-2017/gpce.skb|  974 +
 doc/gpce-2017/staging.sbib|  185 +++
 15 files changed, 3941 insertions(+)
 create mode 100644 doc/gpce-2017/GNUmakefile
 create mode 100644 doc/gpce-2017/abstract.md
 create mode 100644 doc/gpce-2017/acmart.cls
 create mode 100644 doc/gpce-2017/categories.tex
 create mode 100644 doc/gpce-2017/code/GuixSD.png
 create mode 100644 doc/gpce-2017/code/build-sexp.scm
 create mode 100644 doc/gpce-2017/code/gexp-compilers.scm
 create mode 100644 doc/gpce-2017/code/gexp-expansion.scm
 create mode 100644 doc/gpce-2017/code/gexp-modules.scm
 create mode 100644 doc/gpce-2017/code/initrd.scm
 create mode 100644 doc/gpce-2017/code/system-test.scm
 create mode 100644 doc/gpce-2017/gpce.org
 create mode 100644 doc/gpce-2017/gpce.skb
 create mode 100644 doc/gpce-2017/staging.sbib

09/29: gnu: r-ade4: Update to 1.7-8.

[Ricardo Wurmus]

rekado pushed a commit to branch master
in repository guix.

commit 5d84369bdafbccb8a2b7de14abad2c9c229016cb
Author: Ricardo Wurmus 
Date:   Fri Sep 1 14:30:56 2017 +0200

gnu: r-ade4: Update to 1.7-8.

* gnu/packages/statistics.scm (r-ade4): Update to 1.7-8.
---
 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 5cf4c98..e0f6ddb 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -1884,14 +1884,14 @@ chain.")
 (define-public r-ade4
   (package
 (name "r-ade4")
-(version "1.7-6")
+(version "1.7-8")
 (source
   (origin
 (method url-fetch)
 (uri (cran-uri "ade4" version))
 (sha256
   (base32
-"0lnc37d6waajmagy8qvw206pyc4vgrpzl3hk3j9frh6wa0b8x140"
+"1a5p3wf8l9cp1bjp57b1pc5bqs39kw1v21i4waj9j18wawzlmpb6"
 (build-system r-build-system)
 (home-page "http://pbil.univ-lyon1.fr/ADE-4;)
 (synopsis "Multivariate data analysis and graphical display")

11/29: gnu: r-httr: Update to 1.3.1.

[Ricardo Wurmus]

rekado pushed a commit to branch master
in repository guix.

commit 7d60652ebedc004047cc88cc850263f6b057d78b
Author: Ricardo Wurmus 
Date:   Fri Sep 1 14:32:21 2017 +0200

gnu: r-httr: Update to 1.3.1.

* gnu/packages/statistics.scm (r-httr): Update to 1.3.1.
[propagated-inputs]: Remove r-digest and r-stringr.
---
 gnu/packages/statistics.scm | 8 +++-
 1 file changed, 3 insertions(+), 5 deletions(-)

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index bf52d66..3700667 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -2237,22 +2237,20 @@ integers.")
 (define-public r-httr
   (package
 (name "r-httr")
-(version "1.2.1")
+(version "1.3.1")
 (source (origin
   (method url-fetch)
   (uri (cran-uri "httr" version))
   (sha256
(base32
-"03kkjlhyvvi5znwaxfm6cmdsg3q7ivwsvkzgabhjdj2jxs80pfg7"
+"0n7jz2digbgv48rbr9vmzv4vmf4rahl9jjy31izs7sxj4rs4s4r2"
 (build-system r-build-system)
 (propagated-inputs
  `(("r-curl" ,r-curl)
-   ("r-digest" ,r-digest)
("r-jsonlite" ,r-jsonlite)
("r-openssl" ,r-openssl)
("r-mime" ,r-mime)
-   ("r-r6" ,r-r6)
-   ("r-stringr" ,r-stringr)))
+   ("r-r6" ,r-r6)))
 (home-page "https://github.com/hadley/httr;)
 (synopsis "Tools for working with URLs and HTTP")
 (description

06/29: gnu: r-knitr: Update to 1.17.

[Ricardo Wurmus]

rekado pushed a commit to branch master
in repository guix.

commit 5a00ef095013aadbfe7856ed37ec98b3f7df2951
Author: Ricardo Wurmus 
Date:   Fri Sep 1 14:30:02 2017 +0200

gnu: r-knitr: Update to 1.17.

* gnu/packages/statistics.scm (r-knitr): Update to 1.17.
---
 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 95fdc97..c67e4f5 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -1310,13 +1310,13 @@ emitter (http://pyyaml.org/wiki/LibYAML) for R.")
 (define-public r-knitr
   (package
 (name "r-knitr")
-(version "1.16")
+(version "1.17")
 (source (origin
   (method url-fetch)
   (uri (cran-uri "knitr" version))
   (sha256
(base32
-"02balmhvc955rkqv4v0wkxbw4vjphydajgcpy4ml0s3b4sziyj0h"
+"00gljbz57n9lkvbd6az4n37gpbs8vg3fxx5p9biamhmhqyra514l"
 (build-system r-build-system)
 (propagated-inputs
  `(("r-evaluate" ,r-evaluate)

07/29: gnu: r-rlang: Update to 0.1.2.

[Ricardo Wurmus]

rekado pushed a commit to branch master
in repository guix.

commit edd5fd720855a1b4b20a36fcd377e937311b6cbb
Author: Ricardo Wurmus 
Date:   Fri Sep 1 14:30:20 2017 +0200

gnu: r-rlang: Update to 0.1.2.

* gnu/packages/statistics.scm (r-rlang): Update to 0.1.2.
---
 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 c67e4f5..fb7a781 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -1512,13 +1512,13 @@ defined in different packages.")
 (define-public r-rlang
   (package
 (name "r-rlang")
-(version "0.1.1")
+(version "0.1.2")
 (source (origin
   (method url-fetch)
   (uri (cran-uri "rlang" version))
   (sha256
(base32
-"0grwqy3zkvz96mvpwfbfyqid4jkfrqh3ldy2n6dpv2kjd1fzj0ar"
+"1yc5qyq6h0nrya7m2fqnfv19zh5xwsl28jx6zi2g1zz6ra4cvkwh"
 (build-system r-build-system)
 (home-page "http://rlang.tidyverse.org;)
 (synopsis "Functions for base types, core R and Tidyverse features")

08/29: gnu: r-tibble: Update to 1.3.4.

[Ricardo Wurmus]

rekado pushed a commit to branch master
in repository guix.

commit fb10c923b37c1d5b919d78237a4211963dbaf8f9
Author: Ricardo Wurmus 
Date:   Fri Sep 1 14:30:38 2017 +0200

gnu: r-tibble: Update to 1.3.4.

* gnu/packages/statistics.scm (r-tibble): Update to 1.3.4.
---
 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 fb7a781..5cf4c98 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -1530,14 +1530,14 @@ like tidy evaluation.")
 (define-public r-tibble
   (package
 (name "r-tibble")
-(version "1.3.3")
+(version "1.3.4")
 (source
  (origin
(method url-fetch)
(uri (cran-uri "tibble" version))
(sha256
 (base32
- "1bhq4pm56l7l6s1k44ajrcr7hz56h37m9ck4zji9f8xfdqschbl0"
+ "02vn6yqzcvmazy5jaqar3wwbrmh83a1bfgsqgk0hgz38i80zgvm7"
 (build-system r-build-system)
 (propagated-inputs
  `(("r-rlang" ,r-rlang)

02/29: gnu: r-matrix: Update to 1.2-11.

[Ricardo Wurmus]

rekado pushed a commit to branch master
in repository guix.

commit fefe9f47533d99dff83c8cf79572425933e3029e
Author: Ricardo Wurmus 
Date:   Fri Sep 1 14:26:02 2017 +0200

gnu: r-matrix: Update to 1.2-11.

* gnu/packages/statistics.scm (r-matrix): Update to 1.2-11.
---
 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 5d47a00..d406ebc 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -455,14 +455,14 @@ also flexible enough to handle most nonstandard 
requirements.")
 (define-public r-matrix
   (package
 (name "r-matrix")
-(version "1.2-10")
+(version "1.2-11")
 (source
  (origin
(method url-fetch)
(uri (cran-uri "Matrix" version))
(sha256
 (base32
- "0r3qjcz92xwgdzrfz444mqzwnja5sv9abaf252fh6k48qbyahahh"
+ "1yvd6fx3n99j4gvzrng43ji38pr5h8y03kijccgjdalym2hcp36g"
 (properties `((upstream-name . "Matrix")))
 (build-system r-build-system)
 (propagated-inputs

18/29: gnu: r-powerlaw: Update to 0.70.1.

[Ricardo Wurmus]

rekado pushed a commit to branch master
in repository guix.

commit eeb54328029463f930da07244b494f47bcc01151
Author: Ricardo Wurmus 
Date:   Fri Sep 1 14:35:25 2017 +0200

gnu: r-powerlaw: Update to 0.70.1.

* gnu/packages/cran.scm (r-powerlaw): Update to 0.70.1.
---
 gnu/packages/cran.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 2843de4..196b7e2 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -271,14 +271,14 @@ patterns behind multiple dimensional data.")
 (define-public r-powerlaw
   (package
 (name "r-powerlaw")
-(version "0.70.0")
+(version "0.70.1")
 (source
  (origin
(method url-fetch)
(uri (cran-uri "poweRlaw" version))
(sha256
 (base32
- "1p2la3hslxq2xa8jkwvci6zcpn47cvyr9xqd5agp1riwwp2xw5gh"
+ "04sr0nhdd1v915m0zf5gasznzgi08ykcy20kkwdw0l5mvvdbic8m"
 (properties `((upstream-name . "poweRlaw")))
 (build-system r-build-system)
 (propagated-inputs

21/29: gnu: r-sp: Update to 1.2-5.

[Ricardo Wurmus]

rekado pushed a commit to branch master
in repository guix.

commit f7b172187a06934b218367bcebc4026a8bc98cd6
Author: Ricardo Wurmus 
Date:   Fri Sep 1 14:36:22 2017 +0200

gnu: r-sp: Update to 1.2-5.

* gnu/packages/cran.scm (r-sp): Update to 1.2-5.
---
 gnu/packages/cran.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index ce46dcc..1d30ebd 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -556,14 +556,14 @@ most popular ones.")
 (define-public r-sp
   (package
 (name "r-sp")
-(version "1.2-4")
+(version "1.2-5")
 (source
  (origin
(method url-fetch)
(uri (cran-uri "sp" version))
(sha256
 (base32
- "0crba3j00mb2xv2yk60rpa57gn97xq4ql3a6p9cjzqjxzv2cknk2"
+ "09yydnacp33yx0kn537k96fjlbf75fjafqfknpa5gvci4l888bqd"
 (build-system r-build-system)
 (propagated-inputs
  `(("r-lattice" ,r-lattice)))

22/29: gnu: r-distillery: Update to 1.0-4.

[Ricardo Wurmus]

rekado pushed a commit to branch master
in repository guix.

commit 28f2f8939158a3a2d3203c08c106fe7349af026a
Author: Ricardo Wurmus 
Date:   Fri Sep 1 14:36:43 2017 +0200

gnu: r-distillery: Update to 1.0-4.

* gnu/packages/cran.scm (r-distillery): Update to 1.0-4.
---
 gnu/packages/cran.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 1d30ebd..d07d6b6 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -623,14 +623,14 @@ quantile mixture from L-moments and trimmed L-moments.")
 (define-public r-distillery
   (package
 (name "r-distillery")
-(version "1.0-2")
+(version "1.0-4")
 (source
  (origin
(method url-fetch)
(uri (cran-uri "distillery" version))
(sha256
 (base32
- "12m4cacvc18fd3aayc8iih5q6bwsmvf29b55fwp7vs8wp1h8nd8c"
+ "1m0pgmlvk7bsb6q3kxagnq422babk61sf73naavac68v8x2q8fix"
 (build-system r-build-system)
 (home-page "http://www.ral.ucar.edu/staff/ericg;)
 (synopsis "Functions for confidence intervals and object information")

25/29: gnu: r-maldiquant: Update to 1.16.4.

[Ricardo Wurmus]

rekado pushed a commit to branch master
in repository guix.

commit 7b92acdf52481325e3c0c0be7419dd513c028df0
Author: Ricardo Wurmus 
Date:   Fri Sep 1 14:37:50 2017 +0200

gnu: r-maldiquant: Update to 1.16.4.

* gnu/packages/bioinformatics.scm (r-maldiquant): Update to 1.16.4.
---
 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 5c770fa..c617ce6 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -8841,14 +8841,14 @@ trait.")
 (define-public r-maldiquant
   (package
 (name "r-maldiquant")
-(version "1.16.2")
+(version "1.16.4")
 (source
  (origin
(method url-fetch)
(uri (cran-uri "MALDIquant" version))
(sha256
 (base32
- "0z5srzsfgsgi4bssr4chls4ry6d18y2g9143znqmraylppwrrqzr"
+ "1pmhsfvd45a44xdiml4zx3zd5fhygqyziqvygahkk9yibnyhv4cv"
 (properties `((upstream-name . "MALDIquant")))
 (build-system r-build-system)
 (home-page "http://cran.r-project.org/web/packages/MALDIquant;)

12/29: gnu: r-plotrix: Update to 3.6-6.

[Ricardo Wurmus]

rekado pushed a commit to branch master
in repository guix.

commit 2dda8fca6f4cb6adb9a94bc4d7fe800bdc20968b
Author: Ricardo Wurmus 
Date:   Fri Sep 1 14:32:58 2017 +0200

gnu: r-plotrix: Update to 3.6-6.

* gnu/packages/statistics.scm (r-plotrix): Update to 3.6-6.
---
 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 3700667..31afb1c 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -2395,13 +2395,13 @@ disk (or a connection).")
 (define-public r-plotrix
   (package
 (name "r-plotrix")
-(version "3.6-5")
+(version "3.6-6")
 (source (origin
   (method url-fetch)
   (uri (cran-uri "plotrix" version))
   (sha256
(base32
-"01655y3qzy0283ppc85bi0g42g20zrqzcl0qb30cl6rcbflhymlb"
+"07hywp3ym0gbpqdj3f4vhr0bhmynhby8vh6p1b9cm2hv26pzs9q4"
 (build-system r-build-system)
 (home-page "http://cran.r-project.org/web/packages/plotrix;)
 (synopsis "Various plotting functions")

29/29: gnu: r-genomicalignments: Update to 1.12.2.

[Ricardo Wurmus]

rekado pushed a commit to branch master
in repository guix.

commit 81195d139fca664811f199de248f91a72d6938f7
Author: Ricardo Wurmus 
Date:   Fri Sep 1 14:54:51 2017 +0200

gnu: r-genomicalignments: Update to 1.12.2.

* gnu/packages/bioinformatics.scm (r-genomicalignments): Update to 1.12.2.
---
 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 e2dd982..1f1b686 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7120,13 +7120,13 @@ samples.")
 (define-public r-genomicalignments
   (package
 (name "r-genomicalignments")
-(version "1.12.1")
+(version "1.12.2")
 (source (origin
   (method url-fetch)
   (uri (bioconductor-uri "GenomicAlignments" version))
   (sha256
(base32
-"127690sys4i5q3l4vxnjg4xg8q19qlw2258vgs5d1156w9ypp04h"
+"03ysxi9fdd3bcfj05iaysya9knn2aa2irwpypb5srg0xwv92bdb9"
 (properties
  `((upstream-name . "GenomicAlignments")))
 (build-system r-build-system)

28/29: gnu: r-tidyr: Update to 0.7.0.

[Ricardo Wurmus]

rekado pushed a commit to branch master
in repository guix.

commit 89b620e7eee1d7649e7c782e315a12d77a98c0b2
Author: Ricardo Wurmus 
Date:   Fri Sep 1 14:39:30 2017 +0200

gnu: r-tidyr: Update to 0.7.0.

* gnu/packages/statistics.scm (r-tidyr): Update to 0.7.0.
[propagated-inputs]: Remove r-lazyeval; add r-glue, r-purrr, r-rlang, and
r-tidyselect.
---
 gnu/packages/statistics.scm | 9 ++---
 1 file changed, 6 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 100dcbd..05ab1c2 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -3586,19 +3586,22 @@ selection.")
 (define-public r-tidyr
   (package
 (name "r-tidyr")
-(version "0.6.3")
+(version "0.7.0")
 (source
  (origin
(method url-fetch)
(uri (cran-uri "tidyr" version))
(sha256
 (base32
- "14s57zrjm2phiy600z9ivq4az71z0ggmp6nj0js7yrybxf0dlah6"
+ "1lg0amx5hs37ajwjxz7ya50q4s28jcdj51kzl10s1x4l1akp7xls"
 (build-system r-build-system)
 (propagated-inputs
  `(("r-dplyr" ,r-dplyr)
-   ("r-lazyeval" ,r-lazyeval)
("r-magrittr" ,r-magrittr)
+   ("r-glue" ,r-glue)
+   ("r-purrr" ,r-purrr)
+   ("r-rlang" ,r-rlang)
+   ("r-tidyselect" ,r-tidyselect)
("r-rcpp" ,r-rcpp)
("r-stringi" ,r-stringi)
("r-tibble" ,r-tibble)))

04/29: gnu: r-scales: Update to 0.5.0.

[Ricardo Wurmus]

rekado pushed a commit to branch master
in repository guix.

commit b93881b9c5c2c609bf23824a41287ea4a2a5
Author: Ricardo Wurmus 
Date:   Fri Sep 1 14:26:47 2017 +0200

gnu: r-scales: Update to 0.5.0.

* gnu/packages/statistics.scm (r-scales): Update to 0.5.0.
[propagated-inputs]: Add r-r6 and r-viridislite.
---
 gnu/packages/statistics.scm | 8 +---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 8226fad..01d667a 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -1000,13 +1000,13 @@ using just two functions: melt and dcast (or acast).")
 (define-public r-scales
   (package
 (name "r-scales")
-(version "0.4.1")
+(version "0.5.0")
 (source
  (origin
(method url-fetch)
(uri (cran-uri "scales" version))
(sha256
-(base32 "1lqccfmqdwrw0cjyqvw2zvgpk2jvnqrfb303l1raqyyf3zxqhav4"
+(base32 "0zg9wfzmsdjxpbld0nzv7hcpq5r0wazqxmn7grvvif2agj0w1z6v"
 (build-system r-build-system)
 (propagated-inputs
  `(("r-dichromat" ,r-dichromat)
@@ -1014,7 +1014,9 @@ using just two functions: melt and dcast (or acast).")
("r-munsell" ,r-munsell)
("r-plyr" ,r-plyr)
("r-rcolorbrewer" ,r-rcolorbrewer)
-   ("r-rcpp" ,r-rcpp)))
+   ("r-rcpp" ,r-rcpp)
+   ("r-r6" ,r-r6)
+   ("r-viridislite" ,r-viridislite)))
 (home-page "https://github.com/hadley/scales;)
 (synopsis "Scale functions for visualization")
 (description

05/29: gnu: r-bh: Update to 1.65.0-1.

[Ricardo Wurmus]

rekado pushed a commit to branch master
in repository guix.

commit 3949aef60111a6e738158eb826203eca0d9b3d98
Author: Ricardo Wurmus 
Date:   Fri Sep 1 14:29:41 2017 +0200

gnu: r-bh: Update to 1.65.0-1.

* gnu/packages/statistics.scm (r-bh): Update to 1.65.0-1.
---
 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 01d667a..95fdc97 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -1169,13 +1169,13 @@ R/DBMS implementations.")
 (define-public r-bh
   (package
 (name "r-bh")
-(version "1.62.0-1")
+(version "1.65.0-1")
 (source (origin
   (method url-fetch)
   (uri (cran-uri "BH" version))
   (sha256
(base32
-"01vfdpfznd4ynqql33z238xr262mvy3i80lyi8l3a3p3hi0a262p"
+"0n6byzrvl1w4hjdxz479q4a7w1118f9ckqc4gqydq7lgzs5agfl2"
 (build-system r-build-system)
 (home-page "https://github.com/eddelbuettel/bh;)
 (synopsis "R package providing subset of Boost headers")

branch master updated (1cf3066 -> 81195d1)

[Ricardo Wurmus]

rekado pushed a change to branch master
in repository guix.

  from  1cf3066   gnu: php: Update to 7.1.9.
   new  3c2a5bf   gnu: r-servr: Update to 0.7.
   new  fefe9f4   gnu: r-matrix: Update to 1.2-11.
   new  2d99a31   gnu: r-mgcv: Update to 1.8-19.
   new  b93881b   gnu: r-scales: Update to 0.5.0.
   new  3949aef   gnu: r-bh: Update to 1.65.0-1.
   new  5a00ef0   gnu: r-knitr: Update to 1.17.
   new  edd5fd7   gnu: r-rlang: Update to 0.1.2.
   new  fb10c92   gnu: r-tibble: Update to 1.3.4.
   new  5d84369   gnu: r-ade4: Update to 1.7-8.
   new  e3323e0   gnu: r-commonmark: Update to 1.4.
   new  7d60652   gnu: r-httr: Update to 1.3.1.
   new  2dda8fc   gnu: r-plotrix: Update to 3.6-6.
   new  d574d6b   gnu: r-rcpparmadillo: Update to 0.7.960.1.2.
   new  347cab6   gnu: r-fastcluster: Update to 1.1.24.
   new  9077f6d   gnu: r-tclust: Update to 1.3-1.
   new  ea4d4f7   gnu: r-shape: Update to 1.4.3.
   new  a5c2980   gnu: r-circlize: Update to 0.4.1.
   new  eeb5432   gnu: r-powerlaw: Update to 0.70.1.
   new  38ea6cf   gnu: r-reshape: Update to 0.8.7.
   new  bf958fc   gnu: r-ggally: Update to 1.3.2.
   new  f7b1721   gnu: r-sp: Update to 1.2-5.
   new  28f2f89   gnu: r-distillery: Update to 1.0-4.
   new  c62276b   gnu: r-ksamples: Update to 1.2-7.
   new  6bd2798   gnu: r-bookdown: Update to 0.5.
   new  7b92acd   gnu: r-maldiquant: Update to 1.16.4.
   new  db2e438   gnu: r-vegan: Update to 2.4-4.
   new  c4a4ef3   gnu: Add r-tidyselect.
   new  89b620e   gnu: r-tidyr: Update to 0.7.0.
   new  81195d1   gnu: r-genomicalignments: Update to 1.12.2.

The 29 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 |  19 
 gnu/packages/cran.scm   |  32 ++---
 gnu/packages/statistics.scm | 100 +---
 gnu/packages/web.scm|   4 +-
 4 files changed, 91 insertions(+), 64 deletions(-)

27/29: gnu: Add r-tidyselect.

[Ricardo Wurmus]

rekado pushed a commit to branch master
in repository guix.

commit c4a4ef39edee3105c35a667dd02efa524fadf798
Author: Ricardo Wurmus 
Date:   Fri Sep 1 14:39:14 2017 +0200

gnu: Add r-tidyselect.

* gnu/packages/statistics.scm (r-tidyselect): 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 f800e1c..100dcbd 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -3557,6 +3557,32 @@ perceived by readers with the most common form of color 
blindness.  This is
 the 'lite' version of the more complete @code{viridis} package.")
 (license license:expat)))
 
+(define-public r-tidyselect
+  (package
+(name "r-tidyselect")
+(version "0.2.0")
+(source
+ (origin
+   (method url-fetch)
+   (uri (cran-uri "tidyselect" version))
+   (sha256
+(base32
+ "1h10qc5bxk5v0zhmip3gwnzy50fs2gbdvcg2163is0k9a8rifq9r"
+(build-system r-build-system)
+(propagated-inputs
+ `(("r-glue" ,r-glue)
+   ("r-purrr" ,r-purrr)
+   ("r-rcpp" ,r-rcpp)
+   ("r-rlang" ,r-rlang)))
+(home-page "http://cran.r-project.org/web/packages/tidyselect;)
+(synopsis "Select from a set of strings")
+(description
+ "This package provides a backend for the selecting functions of the
+tidyverse.  It makes it easy to implement select-like functions in your own
+packages in a way that is consistent with other tidyverse interfaces for
+selection.")
+(license license:gpl3)))
+
 (define-public r-tidyr
   (package
 (name "r-tidyr")

01/29: gnu: r-servr: Update to 0.7.

[Ricardo Wurmus]

rekado pushed a commit to branch master
in repository guix.

commit 3c2a5bf299d9dc750446ed2f2c4e1d45c8e688ce
Author: Ricardo Wurmus 
Date:   Fri Sep 1 14:25:19 2017 +0200

gnu: r-servr: Update to 0.7.

* gnu/packages/web.scm (r-servr): Update to 0.7.
---
 gnu/packages/web.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm
index 0e0058b..87ca2fd 100644
--- a/gnu/packages/web.scm
+++ b/gnu/packages/web.scm
@@ -3507,13 +3507,13 @@ in systems and applications.")
 (define-public r-servr
   (package
 (name "r-servr")
-(version "0.6")
+(version "0.7")
 (source (origin
   (method url-fetch)
   (uri (cran-uri "servr" version))
   (sha256
(base32
-"0sqz3wssxa19g9mpmf9s4gx2a5rvzl8nrd11qkgpz5v3iqsc6ysr"
+"0rxh89csqlpyf9wv5wlymya9kbddj79mlmxz2x0xmls12gbrxaaa"
 (build-system r-build-system)
 (propagated-inputs
  `(("r-httpuv" ,r-httpuv)

20/29: gnu: r-ggally: Update to 1.3.2.

[Ricardo Wurmus]

rekado pushed a commit to branch master
in repository guix.

commit bf958fcd63e820c19b1e0083b03baab764f1408a
Author: Ricardo Wurmus 
Date:   Fri Sep 1 14:36:04 2017 +0200

gnu: r-ggally: Update to 1.3.2.

* gnu/packages/cran.scm (r-ggally): Update to 1.3.2.
---
 gnu/packages/cran.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 2243a44..ce46dcc 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -505,14 +505,14 @@ package also provides a C++ API, that works with or 
without Rcpp.")
 (define-public r-ggally
   (package
 (name "r-ggally")
-(version "1.3.0")
+(version "1.3.2")
 (source
  (origin
(method url-fetch)
(uri (cran-uri "GGally" version))
(sha256
 (base32
- "12ddab0nd0f9c7bb6cx3c22mliyvc8xsxv26aqz3cvfbla8crp3b"
+ "02px7j28wzbhcgcwm2m0pxb6g7s5zvphl64ix55pkvag4m2ky57l"
 (properties `((upstream-name . "GGally")))
 (build-system r-build-system)
 (propagated-inputs

16/29: gnu: r-shape: Update to 1.4.3.

[Ricardo Wurmus]

rekado pushed a commit to branch master
in repository guix.

commit ea4d4f761635017a8cd87dac84685b526ba7e36b
Author: Ricardo Wurmus 
Date:   Fri Sep 1 14:34:44 2017 +0200

gnu: r-shape: Update to 1.4.3.

* gnu/packages/cran.scm (r-shape): Update to 1.4.3.
---
 gnu/packages/cran.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index bb75763..ff1ad8d 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -202,14 +202,14 @@ on (non-orthogonal) variable vectors in scatterplots and 
biplots.")
 (define-public r-shape
   (package
 (name "r-shape")
-(version "1.4.2")
+(version "1.4.3")
 (source
  (origin
(method url-fetch)
(uri (cran-uri "shape" version))
(sha256
 (base32
- "0yk3cmsa57svcvbnm21pyr0s0qbhnllka8nmsg4yb41frjlqph66"
+ "1v9xp60p813rnx41vchkh32qmcb4z2zp9l7r1a8a6f8aqylnq3vj"
 (build-system r-build-system)
 (home-page "http://cran.r-project.org/web/packages/shape;)
 (synopsis "Functions for plotting graphical shapes")

24/29: gnu: r-bookdown: Update to 0.5.

[Ricardo Wurmus]

rekado pushed a commit to branch master
in repository guix.

commit 6bd27981f6a1c5c8eaf6a45aada31c0cabecfad3
Author: Ricardo Wurmus 
Date:   Fri Sep 1 14:37:31 2017 +0200

gnu: r-bookdown: Update to 0.5.

* gnu/packages/bioinformatics.scm (r-bookdown): Update to 0.5.
---
 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 57db745..5c770fa 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -6445,13 +6445,13 @@ also known as views, in a controlled vocabulary.")
 (define-public r-bookdown
   (package
   (name "r-bookdown")
-  (version "0.4")
+  (version "0.5")
   (source (origin
 (method url-fetch)
 (uri (cran-uri "bookdown" version))
 (sha256
  (base32
-  "1fp1k7hivrb7s2dwgrsqy9s7xg6pk9hczhrc149y1dwh901j6qvv"
+  "0zm63kr4f4kja4qpwkzl119zzyciqj7ihajfqgfjpgb4dzaiycxp"
   (build-system r-build-system)
   (propagated-inputs
`(("r-htmltools" ,r-htmltools)

15/29: gnu: r-tclust: Update to 1.3-1.

[Ricardo Wurmus]

rekado pushed a commit to branch master
in repository guix.

commit 9077f6d9aae0587490fb71ff638d5303ddb9cbc4
Author: Ricardo Wurmus 
Date:   Fri Sep 1 14:34:18 2017 +0200

gnu: r-tclust: Update to 1.3-1.

* gnu/packages/statistics.scm (r-tclust): Update to 1.3-1.
---
 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 cb878af..f800e1c 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -5231,14 +5231,14 @@ multivariate case.")
 (define-public r-tclust
   (package
 (name "r-tclust")
-(version "1.2-7")
+(version "1.3-1")
 (source
  (origin
(method url-fetch)
(uri (cran-uri "tclust" version))
(sha256
 (base32
- "1mvqr280c6kwpg98byd0r1y0qf238xn2x15y8npqch6lpcszlb3x"
+ "1li62wynv81kb17fx7nk63a26qlb78l8fdf63in8yzcl7fkpji7y"
 (build-system r-build-system)
 (propagated-inputs
  `(("r-cluster" ,r-cluster)

19/29: gnu: r-reshape: Update to 0.8.7.

[Ricardo Wurmus]

rekado pushed a commit to branch master
in repository guix.

commit 38ea6cfab4067807769f40a74901f2a90134aee8
Author: Ricardo Wurmus 
Date:   Fri Sep 1 14:35:43 2017 +0200

gnu: r-reshape: Update to 0.8.7.

* gnu/packages/cran.scm (r-reshape): Update to 0.8.7.
---
 gnu/packages/cran.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 196b7e2..2243a44 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -459,14 +459,14 @@ quantities.")
 (define-public r-reshape
   (package
 (name "r-reshape")
-(version "0.8.6")
+(version "0.8.7")
 (source
  (origin
(method url-fetch)
(uri (cran-uri "reshape" version))
(sha256
 (base32
- "1f1ngalc22knhdm9djv1m6abnjqpv1frdzxfkpakhph2l67bk7fq"
+ "14ir3w4bb3bsz8jsak27nj7kpn227pdgr9653gjq5wc93rywi9ig"
 (build-system r-build-system)
 (propagated-inputs
  `(("r-plyr" ,r-plyr)

23/29: gnu: r-ksamples: Update to 1.2-7.

[Ricardo Wurmus]

rekado pushed a commit to branch master
in repository guix.

commit c62276b2faa4d74df30428f48fe942d8797f7f53
Author: Ricardo Wurmus 
Date:   Fri Sep 1 14:37:03 2017 +0200

gnu: r-ksamples: Update to 1.2-7.

* gnu/packages/cran.scm (r-ksamples): Update to 1.2-7.
---
 gnu/packages/cran.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index d07d6b6..80335c468 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -904,14 +904,14 @@ George Marsaglia are included.")
 (define-public r-ksamples
   (package
 (name "r-ksamples")
-(version "1.2-6")
+(version "1.2-7")
 (source
  (origin
(method url-fetch)
(uri (cran-uri "kSamples" version))
(sha256
 (base32
- "1pbam0zqq44slpxdgl2s2fsfdgl7i0pgm8bzlvnm0fy0na24bgdj"
+ "0f19rjngk0lg6s8c6h5l55qpxp8sl4vxj3kpi05cizzncny9b9bj"
 (properties `((upstream-name . "kSamples")))
 (build-system r-build-system)
 (propagated-inputs

branch master updated (5fe2a13 -> 1cf3066)

[julien lepiller]

roptat pushed a change to branch master
in repository guix.

  from  5fe2a13   gnu: djvulibre: Remove timestamps from .svgz files.
   new  dcf7a8a   gnu: java-slf4j-api: Fix tests.
   new  1cf3066   gnu: php: Update to 7.1.9.

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/java.scm | 24 +++-
 gnu/packages/php.scm  |  4 ++--
 2 files changed, 21 insertions(+), 7 deletions(-)

02/02: gnu: php: Update to 7.1.9.

[julien lepiller]

roptat pushed a commit to branch master
in repository guix.

commit 1cf306639ce85b59446e9a9b5a1ee344754680a6
Author: Julien Lepiller 
Date:   Fri Sep 1 14:15:09 2017 +0200

gnu: php: Update to 7.1.9.

* gnu/packages/php.scm (php): Update to 7.1.9.
---
 gnu/packages/php.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/php.scm b/gnu/packages/php.scm
index 44fa78d..bcf1d00 100644
--- a/gnu/packages/php.scm
+++ b/gnu/packages/php.scm
@@ -52,7 +52,7 @@
 (define-public php
   (package
 (name "php")
-(version "7.1.8")
+(version "7.1.9")
 (home-page "https://secure.php.net/;)
 (source (origin
   (method url-fetch)
@@ -60,7 +60,7 @@
   name "-" version ".tar.xz"))
   (sha256
(base32
-"1aramb6dm57pr2iz61id9vzfy7h5qkb6bf7dxhrwnjk0723qahw9"))
+"130y50nawipd12nbs10661vzk8gvy7zsqcsxvj29mwaivm4a777c"))
   (modules '((guix build utils)))
   (snippet
'(with-directory-excursion "ext"

01/01: gnu: djvulibre: Remove timestamps from .svgz files.

[Ludovic Court�s]

civodul pushed a commit to branch master
in repository guix.

commit 5fe2a139dfdef058f544fc4b83742628e1fa04bc
Author: Z. Ren 
Date:   Tue Aug 8 14:22:18 2017 +0800

gnu: djvulibre: Remove timestamps from .svgz files.

* gnu/packages/djvu.scm (djvulibre)[arguments]: New field.

Signed-off-by: Ludovic Courtès 
---
 gnu/packages/djvu.scm | 8 
 1 file changed, 8 insertions(+)

diff --git a/gnu/packages/djvu.scm b/gnu/packages/djvu.scm
index e739df3..10cdbf3 100644
--- a/gnu/packages/djvu.scm
+++ b/gnu/packages/djvu.scm
@@ -34,6 +34,14 @@
(base32
 "0psh3zl9dj4n4r3lx25390nx34xz0bg0ql48zdskhq354ljni5p6"
 (build-system gnu-build-system)
+(arguments
+ `(#:phases (modify-phases %standard-phases
+  (add-after 'unpack 'reproducible
+(lambda _
+  ;; Ensure there are no timestamps in .svgz files.
+  (substitute* "desktopfiles/Makefile.in"
+(("gzip") "gzip -n"))
+  #t)
 (home-page "http://djvu.sourceforge.net/;)
 (synopsis "Implementation of DjVu, the document format")
 (description "DjVuLibre is an implementation of DjVu,

04/05: gnu: emacs-ebuild-mode: Update to 1.37.

[Ludovic Court�s]

civodul pushed a commit to branch master
in repository guix.

commit 4735393a767708de21c05f5beeec2ee4e244c123
Author: ng0 
Date:   Wed Aug 30 08:58:10 2017 +

gnu: emacs-ebuild-mode: Update to 1.37.

* gnu/packages/emacs.scm (emacs-ebuild-mode): Update to 1.37.

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

diff --git a/gnu/packages/emacs.scm b/gnu/packages/emacs.scm
index 9852265..612126e 100644
--- a/gnu/packages/emacs.scm
+++ b/gnu/packages/emacs.scm
@@ -3608,7 +3608,7 @@ Lua programing language}.")
 (define-public emacs-ebuild-mode
   (package
 (name "emacs-ebuild-mode")
-(version "1.30")
+(version "1.37")
 (source (origin
   (method url-fetch)
   (uri (string-append
@@ -3617,7 +3617,7 @@ Lua programing language}.")
   (file-name (string-append name "-" version ".tar.xz"))
   (sha256
(base32
-"0vp7lq1kvmh1b2bms2x1kf2k76dy9m02d7cirkxpiglwaxa0h9vz"
+"07dzrdjjczkxdfdgi60h4jjkvzi4p0k9rij2wpfp8s03ay3qldpp"
 (build-system emacs-build-system)
 (home-page "https://devmanual.gentoo.org;)
 (synopsis "Major modes for Gentoo package files")

02/05: packages: 'fold-packages' takes an optional 'modules' parameter.

[Ludovic Court�s]

civodul pushed a commit to branch master
in repository guix.

commit 5c5ae46c00fd553c6fd23aeba1961e201f6555c7
Author: Ludovic Courtès 
Date:   Fri Sep 1 10:26:27 2017 +0200

packages: 'fold-packages' takes an optional 'modules' parameter.

Suggested by Christopher Baines .

* gnu/packages.scm (fold-packages): Add optional 'modules' parameter and
honor it.
---
 gnu/packages.scm | 12 +++-
 1 file changed, 7 insertions(+), 5 deletions(-)

diff --git a/gnu/packages.scm b/gnu/packages.scm
index 5629061..b4ac666 100644
--- a/gnu/packages.scm
+++ b/gnu/packages.scm
@@ -140,17 +140,19 @@ for system '~a'")
   directory))
 %load-path)))
 
-(define (fold-packages proc init)
-  "Call (PROC PACKAGE RESULT) for each available package, using INIT as
-the initial value of RESULT.  It is guaranteed to never traverse the
-same package twice."
+(define* (fold-packages proc init
+#:optional
+(modules (all-modules (%package-module-path
+  "Call (PROC PACKAGE RESULT) for each available package defined in one of
+MODULES, using INIT as the initial value of RESULT.  It is guaranteed to never
+traverse the same package twice."
   (fold-module-public-variables (lambda (object result)
   (if (and (package? object)
(not (hidden-package? object)))
   (proc object result)
   result))
 init
-(all-modules (%package-module-path
+modules))
 
 (define find-packages-by-name
   (let ((packages (delay

branch master updated (75690c9 -> 833ade6)

[Ludovic Court�s]

civodul pushed a change to branch master
in repository guix.

  from  75690c9   gnu: r-rcas: Correct license.
   new  fe55199   scripts: Remove 'max-silent-time' from the default 
options.
   new  5c5ae46   packages: 'fold-packages' takes an optional 'modules' 
parameter.
   new  ab966b8   gnu: Add emacs-2048-game.
   new  4735393   gnu: emacs-ebuild-mode: Update to 1.37.
   new  833ade6   gnu: Add emacs-tuareg.

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


Summary of changes:
 gnu/packages.scm | 12 +++-
 gnu/packages/emacs.scm   | 27 ---
 gnu/packages/ocaml.scm   | 40 
 guix/scripts/archive.scm |  1 -
 guix/scripts/copy.scm|  1 -
 guix/scripts/environment.scm |  1 -
 guix/scripts/pack.scm|  1 -
 guix/scripts/package.scm |  3 +--
 guix/scripts/pull.scm|  1 -
 guix/scripts/system.scm  |  1 -
 10 files changed, 72 insertions(+), 16 deletions(-)

01/05: scripts: Remove 'max-silent-time' from the default options.

[Ludovic Court�s]

civodul pushed a commit to branch master
in repository guix.

commit fe55199542590d16aa6ca6a8bfa0fda27903db5c
Author: Maxim Cournoyer 
Date:   Wed Aug 30 23:12:12 2017 -0400

scripts: Remove 'max-silent-time' from the default options.

Fixes .

Having a finite default `max-silent-time' value for scripts such as 'guix
environment' could lead to timeouts when building subtitutes; this was
undesirable.

This change also fixes client behavior to match the documentation, which
is that by default the daemon's settings are honored.

* guix/scripts/archive.scm (%default-options): Remove max-silent-time entry.
* guix/scripts/copy.scm (%default-options): Likewise.
* guix/scripts/environment.scm (%default-options): Likewise.
* guix/scripts/pack.scm (%default-options): Likewise.
* guix/scripts/package.scm (%default-options): Likewise.
* guix/scripts/pull.scm (%default-options): Likewise.
* guix/scripts/system.scm (%default-options): Likewise.

Signed-off-by: Ludovic Courtès 
---
 guix/scripts/archive.scm | 1 -
 guix/scripts/copy.scm| 1 -
 guix/scripts/environment.scm | 1 -
 guix/scripts/pack.scm| 1 -
 guix/scripts/package.scm | 3 +--
 guix/scripts/pull.scm| 1 -
 guix/scripts/system.scm  | 1 -
 7 files changed, 1 insertion(+), 8 deletions(-)

diff --git a/guix/scripts/archive.scm b/guix/scripts/archive.scm
index 5ea1978..a569848 100644
--- a/guix/scripts/archive.scm
+++ b/guix/scripts/archive.scm
@@ -54,7 +54,6 @@
   `((system . ,(%current-system))
 (substitutes? . #t)
 (graft? . #t)
-(max-silent-time . 3600)
 (verbosity . 0)))
 
 (define (show-help)
diff --git a/guix/scripts/copy.scm b/guix/scripts/copy.scm
index 32438b9..9e8 100644
--- a/guix/scripts/copy.scm
+++ b/guix/scripts/copy.scm
@@ -151,7 +151,6 @@ Copy ITEMS to or from the specified host over SSH.\n"))
   `((system . ,(%current-system))
 (substitutes? . #t)
 (graft? . #t)
-(max-silent-time . 3600)
 (verbosity . 0)))
 
 
diff --git a/guix/scripts/environment.scm b/guix/scripts/environment.scm
index 95ba199..0d69218 100644
--- a/guix/scripts/environment.scm
+++ b/guix/scripts/environment.scm
@@ -179,7 +179,6 @@ COMMAND or an interactive shell in that environment.\n"))
   `((system . ,(%current-system))
 (substitutes? . #t)
 (graft? . #t)
-(max-silent-time . 3600)
 (verbosity . 0)))
 
 (define (tag-package-arg opts arg)
diff --git a/guix/scripts/pack.scm b/guix/scripts/pack.scm
index c269a1f..21fea44 100644
--- a/guix/scripts/pack.scm
+++ b/guix/scripts/pack.scm
@@ -263,7 +263,6 @@ the image."
 (system . ,(%current-system))
 (substitutes? . #t)
 (graft? . #t)
-(max-silent-time . 3600)
 (verbosity . 0)
 (symlinks . ())
 (compressor . ,(first %compressors
diff --git a/guix/scripts/package.scm b/guix/scripts/package.scm
index fa45bd4..9ec6950 100644
--- a/guix/scripts/package.scm
+++ b/guix/scripts/package.scm
@@ -377,8 +377,7 @@ ENTRIES, a list of manifest entries, in the context of 
PROFILE."
 
 (define %default-options
   ;; Alist of default option values.
-  `((max-silent-time . 3600)
-(verbosity . 0)
+  `((verbosity . 0)
 (graft? . #t)
 (substitutes? . #t)))
 
diff --git a/guix/scripts/pull.scm b/guix/scripts/pull.scm
index a1deec8..b1c87c8 100644
--- a/guix/scripts/pull.scm
+++ b/guix/scripts/pull.scm
@@ -96,7 +96,6 @@ Install it by running:
 (system . ,(%current-system))
 (substitutes? . #t)
 (graft? . #t)
-(max-silent-time . 3600)
 (verbosity . 0)))
 
 (define (show-help)
diff --git a/guix/scripts/system.scm b/guix/scripts/system.scm
index 8793c40..7737793 100644
--- a/guix/scripts/system.scm
+++ b/guix/scripts/system.scm
@@ -864,7 +864,6 @@ Some ACTIONS support additional ARGS.\n"))
 (substitutes? . #t)
 (graft? . #t)
 (build-hook? . #t)
-(max-silent-time . 3600)
 (verbosity . 0)
 (file-system-type . "ext4")
 (image-size . guess)

05/05: gnu: Add emacs-tuareg.

[Ludovic Court�s]

civodul pushed a commit to branch master
in repository guix.

commit 833ade67f18311f1e162088c14a989fad62d81bd
Author: Oleg Pykhalov 
Date:   Wed Aug 30 09:29:44 2017 +0300

gnu: Add emacs-tuareg.

* gnu/packages/ocaml.scm (emacs-tuareg): New variable.

Signed-off-by: Ludovic Courtès 
---
 gnu/packages/ocaml.scm | 40 
 1 file changed, 40 insertions(+)

diff --git a/gnu/packages/ocaml.scm b/gnu/packages/ocaml.scm
index 43bbdcd..2597775 100644
--- a/gnu/packages/ocaml.scm
+++ b/gnu/packages/ocaml.scm
@@ -575,6 +575,46 @@ assistant to write formal mathematical proofs using a 
variety of theorem
 provers.")
 (license license:gpl2+)))
 
+(define-public emacs-tuareg
+  (package
+(name "emacs-tuareg")
+(version "2.0.10")
+(source (origin
+  (method url-fetch)
+  (uri (string-append "https://github.com/ocaml/tuareg/archive/;
+  version ".tar.gz"))
+  (file-name (string-append name "-" version ".tar.gz"))
+  (sha256
+   (base32
+"1r2smclcs63n74lcyckbp90j09wyjdngn816cqzfkw54iwh3hd7q"
+(build-system gnu-build-system)
+(native-inputs `(("emacs" ,emacs-minimal)
+ ("opam" ,opam)))
+(arguments
+ `(#:phases
+   (modify-phases %standard-phases
+ (delete 'configure)
+ (add-before 'install 'fix-install-path
+   (lambda* (#:key outputs #:allow-other-keys)
+ (substitute* "Makefile"
+   (("/emacs/site-lisp")
+(string-append (assoc-ref %outputs "out")
+   "/share/emacs/site-lisp/")))
+ #t))
+ (add-after 'install 'post-install
+   (lambda* (#:key outputs #:allow-other-keys)
+ (symlink "tuareg.el"
+  (string-append (assoc-ref outputs "out")
+ "/share/emacs/site-lisp/"
+ "tuareg-autoloads.el"))
+ #t)
+(home-page "https://github.com/ocaml/tuareg;)
+(synopsis "OCaml programming mode, REPL, debugger for Emacs")
+(description "Tuareg helps editing OCaml code, to highlight important
+parts of the code, to run an OCaml REPL, and to run the OCaml debugger within
+Emacs.")
+(license license:gpl2+)))
+
 (define-public ocaml-menhir
   (package
 (name "ocaml-menhir")

branch master updated (7d099cb -> 75690c9)

[Ricardo Wurmus]

rekado pushed a change to branch master
in repository guix.

  from  7d099cb   gnu: mysql: Enable tests on aarch64.
   new  eda8f36   gnu: r-rcas: Update to 1.3.3.
   new  75690c9   gnu: r-rcas: Correct license.

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 | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

01/02: gnu: r-rcas: Update to 1.3.3.

[Ricardo Wurmus]

rekado pushed a commit to branch master
in repository guix.

commit eda8f36cd6be051b5c999ef92c01d872e5e9b96a
Author: Ricardo Wurmus 
Date:   Fri Sep 1 08:51:47 2017 +0200

gnu: r-rcas: Update to 1.3.3.

* gnu/packages/bioinformatics.scm (r-rcas): Update to 1.3.3.
---
 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 f785dec..eb1d458 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -8002,7 +8002,7 @@ paired-end data.")
 (define-public r-rcas
   (package
 (name "r-rcas")
-(version "1.1.1")
+(version "1.3.3")
 (source (origin
   (method url-fetch)
   (uri (string-append 
"https://github.com/BIMSBbioinfo/RCAS/archive/v;
@@ -8010,7 +8010,7 @@ paired-end data.")
   (file-name (string-append name "-" version ".tar.gz"))
   (sha256
(base32
-"1hd0r66556bxbdd82ksjklq7nfli36l4k6y88ic7kkg9873wa1nw"
+"19mk7vkbngmch54kzcxb52161ljfchhjsaanza8iwv5h98sjj66d"
 (build-system r-build-system)
 (native-inputs
  `(("r-knitr" ,r-knitr)

02/02: gnu: r-rcas: Correct license.

[Ricardo Wurmus]

rekado pushed a commit to branch master
in repository guix.

commit 75690c9f6bd7909868ae0f91ee7f3cf9e0be1942
Author: Ricardo Wurmus 
Date:   Fri Sep 1 08:52:51 2017 +0200

gnu: r-rcas: Correct license.

* gnu/packages/bioinformatics.scm (r-rcas)[license]: Use correct license.
---
 gnu/packages/bioinformatics.scm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index eb1d458..57db745 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -8044,7 +8044,7 @@ paired-end data.")
 intuitive reports and publication-ready graphics.  This package provides the R
 library implementing most of the pipeline's features.")
 (home-page "https://github.com/BIMSBbioinfo/RCAS;)
-(license license:expat)))
+(license license:artistic2.0)))
 
 (define-public rcas-web
   (package

01/01: gnu: mysql: Enable tests on aarch64.

[Efraim Flashner]

efraim pushed a commit to branch master
in repository guix.

commit 7d099cbe137a4d9af18957e4ae4d11ad3e888260
Author: Efraim Flashner 
Date:   Fri Sep 1 10:48:44 2017 +0300

gnu: mysql: Enable tests on aarch64.

* gnu/packages/databases.scm (mysql)[arguments]: Remove logic disabling
the tests on aarch64-linux.
---
 gnu/packages/databases.scm | 7 +--
 1 file changed, 1 insertion(+), 6 deletions(-)

diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm
index 19e51e9..93d5983 100644
--- a/gnu/packages/databases.scm
+++ b/gnu/packages/databases.scm
@@ -371,12 +371,7 @@ applications.")
(for-each delete-file
  (find-files (string-append out "/bin")
  "_embedded$"))
-   #t
-   ;; On aarch64 the test suite runs out of memory and fails.
-   ,@(if (string-prefix? "aarch64-linux"
- (or (%current-target-system) (%current-system)))
-   '(#:tests? #f)
-   '(
+   #t))
 (native-inputs
  `(("bison" ,bison)
("perl" ,perl)))

branch master updated (f4bf420 -> 7d099cb)

[Efraim Flashner]

efraim pushed a change to branch master
in repository guix.

  from  f4bf420   gnu: vsearch: Update to 2.4.4.
   new  7d099cb   gnu: mysql: Enable tests on aarch64.

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/databases.scm | 7 +--
 1 file changed, 1 insertion(+), 6 deletions(-)

01/02: gnu: metabat: Update to 2.12.1.

[Ben Woodcroft]

benwoodcroft pushed a commit to branch master
in repository guix.

commit 25bd1fc1c12ee2dfbcb12daf36f25285a4f7e55a
Author: Ben Woodcroft 
Date:   Fri Sep 1 13:59:28 2017 +0800

gnu: metabat: Update to 2.12.1.

* gnu/packages/patches/metabat-remove-compilation-date.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove it.
* gnu/packages/bioinformatics.scm (metabat): Update to 2.12.1.
[source]: Remove it.  Use url-fetch.
---
 gnu/local.mk |  1 -
 gnu/packages/bioinformatics.scm  | 16 +++-
 .../patches/metabat-remove-compilation-date.patch| 16 
 3 files changed, 7 insertions(+), 26 deletions(-)

diff --git a/gnu/local.mk b/gnu/local.mk
index 2e40026..8c683b8 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -846,7 +846,6 @@ dist_patch_DATA =   
\
   %D%/packages/patches/mcrypt-CVE-2012-4527.patch  \
   %D%/packages/patches/mesa-skip-disk-cache-test.patch \
   %D%/packages/patches/mesa-wayland-egl-symbols-check-mips.patch   \
-  %D%/packages/patches/metabat-remove-compilation-date.patch   \
   %D%/packages/patches/metabat-fix-compilation.patch   \
   %D%/packages/patches/mhash-keygen-test-segfault.patch\
   %D%/packages/patches/mingw-w64-5.0rc2-gcc-4.9.3.patch\
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 70418cd..37980f3 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -3475,19 +3475,17 @@ form of assemblies or reads.")
 (define-public metabat
   (package
 (name "metabat")
-(version "2.11.3")
+(version "2.12.1")
 (source
  (origin
-   (method git-fetch)
-   (uri (git-reference
- (url "https://bitbucket.org/berkeleylab/metabat.git;)
- (commit "d0ad65367ffc8e08d1a9dd1388d6170daa047e5c")))
-   (file-name (string-append name "-" version "-checkout"))
+   (method url-fetch)
+   (uri (string-append "https://bitbucket.org/berkeleylab/metabat/get/v;
+   version ".tar.gz"))
+   (file-name (string-append name "-" version ".tar.gz"))
(sha256
 (base32
- "1rlsrkz8iq8xah65222p055kzv5i3szz8bwysnvnh0pv72wvv6ww"))
-   (patches (search-patches "metabat-remove-compilation-date.patch"
-"metabat-fix-compilation.patch"
+ "1hmvdalz3zj5sqqklg0l4npjdv37cv2hsdi1al9iby2ndxjs1b73"))
+   (patches (search-patches "metabat-fix-compilation.patch"
 (build-system gnu-build-system)
 (arguments
  `(#:phases
diff --git a/gnu/packages/patches/metabat-remove-compilation-date.patch 
b/gnu/packages/patches/metabat-remove-compilation-date.patch
deleted file mode 100644
index 7672205..000
--- a/gnu/packages/patches/metabat-remove-compilation-date.patch
+++ /dev/null
@@ -1,16 +0,0 @@
-Remove the reference to the compilation date so that the build is
-reproducible.
-
-diff --git a/src/metabat.cpp b/src/metabat.cpp
-index 88e06de..c95cb1a 100644
 a/src/metabat.cpp
-+++ b/src/metabat.cpp
-@@ -49,7 +49,7 @@ int main(int ac, char* av[]) {
-   po::notify(vm);
- 
-   if (vm.count("help") || inFile.length() == 0 || outFile.length() == 0) {
--  cerr << "\nMetaBAT: Metagenome Binning based on Abundance and 
Tetranucleotide frequency (version " << version << "; " << __DATE__ << " " << 
__TIME__ << ")" << endl;
-+  cerr << "\nMetaBAT: Metagenome Binning based on Abundance and 
Tetranucleotide frequency (version " << version << "; unknown compilation 
date)" << endl;
-   cerr << "by Don Kang (ddk...@lbl.gov), Jeff Froula, Rob Egan, 
and Zhong Wang (zhongw...@lbl.gov) \n" << endl;
-   cerr << desc << endl << endl;
- 

02/02: gnu: vsearch: Update to 2.4.4.

[Ben Woodcroft]

benwoodcroft pushed a commit to branch master
in repository guix.

commit f4bf420c84f8d3b06eb448e0b3d80125203cc836
Author: Ben Woodcroft 
Date:   Fri Sep 1 14:45:38 2017 +0800

gnu: vsearch: Update to 2.4.4.

* gnu/packages/bioinformatics.scm (vsearch): Update to 2.4.4.
---
 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 37980f3..f785dec 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -6141,7 +6141,7 @@ track.  The database is exposed as a @code{TxDb} object.")
 (define-public vsearch
   (package
 (name "vsearch")
-(version "2.4.3")
+(version "2.4.4")
 (source
  (origin
(method url-fetch)
@@ -6151,7 +6151,7 @@ track.  The database is exposed as a @code{TxDb} object.")
(file-name (string-append name "-" version ".tar.gz"))
(sha256
 (base32
- "0hc110ycqpa54nr6x173qg7190hk08qp7yz7zzqxlsypqnpc5zzp"))
+ "1d8a4gjwaqdv57krlr80x18mg5py1bbdiqs5m0jdn38filc9z40k"))
(patches (search-patches "vsearch-unbundle-cityhash.patch"))
(snippet
 '(begin

branch master updated (a0596a2 -> 43d0167)

[Thomas Danckaert]

thomasd pushed a change to branch master
in repository guix.

  from  a0596a2   gnu: python2-larch: Enable tests.
   new  e3a1a1d   gnu: hdf5: Add output for fortran interface.
   new  fd0378a   gnu: hdf5: Avoid unneeded store references to compilers.
   new  e464b45   gnu: hdf4: Avoid unneeded store references to compilers.
   new  43d0167   gnu: netcdf: Fix reproducibility issue; remove unneeded 
references.

The 4 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.


Summary of changes:
 gnu/packages/maths.scm | 99 --
 1 file changed, 95 insertions(+), 4 deletions(-)

01/04: gnu: hdf5: Add output for fortran interface.

[Thomas Danckaert]

thomasd pushed a commit to branch master
in repository guix.

commit e3a1a1deda03e52fbdb38e9c7a92ce69f78c8eb3
Author: Thomas Danckaert 
Date:   Thu Aug 24 11:00:59 2017 +0200

gnu: hdf5: Add output for fortran interface.

* gnu/packages/maths.scm (hdf5) [native-inputs]: Add gfortran.
  [outputs]: Add "fortran".
  [arguments]: Enable Fortran compilation; add "/lib" directory of the 
fortran
  output to the runpath of the Fortran libs; add a 'split phase to move
  all Fortran-related files to the the Fortran output store location.
---
 gnu/packages/maths.scm | 53 +++---
 1 file changed, 50 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 7481636..b561531 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -648,16 +648,30 @@ incompatible with HDF5.")
 (build-system gnu-build-system)
 (inputs
  `(("zlib" ,zlib)))
+(native-inputs
+ `(("gfortran" ,gfortran)))
+(outputs '("out"   ; core library
+   "fortran")) ; fortran interface
 (arguments
  `(;; Some of the users, notably Flann, need the C++ interface.
-   #:configure-flags '("--enable-cxx")
+   #:configure-flags '("--enable-cxx"
+   "--enable-fortran"
+   "--enable-fortran2003")
 
#:phases
(modify-phases %standard-phases
  (add-before 'configure 'patch-configure
-   (lambda _
+   (lambda* (#:key outputs #:allow-other-keys)
  (substitute* "configure"
(("/bin/mv") "mv"))
+ (substitute* "fortran/src/Makefile.in"
+   (("libhdf5_fortran_la_LDFLAGS =")
+(string-append "libhdf5_fortran_la_LDFLAGS = -Wl-rpath="
+   (assoc-ref outputs "fortran") "/lib")))
+ (substitute* "hl/fortran/src/Makefile.in"
+   (("libhdf5hl_fortran_la_LDFLAGS =")
+(string-append "libhdf5hl_fortran_la_LDFLAGS = -Wl,-rpath="
+   (assoc-ref outputs "fortran") "/lib")))
  #t))
  (add-after 'install 'patch-references
(lambda* (#:key inputs outputs #:allow-other-keys)
@@ -666,7 +680,40 @@ incompatible with HDF5.")
(substitute* (find-files bin "h5p?cc")
  (("-lz" lib)
   (string-append "-L" zlib "/lib " lib)))
-   #t))
+   #t)))
+ (add-after 'install 'split
+(lambda* (#:key inputs outputs #:allow-other-keys)
+  ;; Move all fortran-related files
+  (let* ((out (assoc-ref outputs "out"))
+ (bin (string-append out "/bin"))
+ (lib (string-append out "/lib"))
+ (inc (string-append out "/include"))
+ (ex (string-append out "/share/hdf5_examples/fortran"))
+ (fort (assoc-ref outputs "fortran"))
+ (fbin (string-append fort "/bin"))
+ (flib (string-append fort "/lib"))
+ (finc (string-append fort "/include"))
+ (fex (string-append fort "/share/hdf5_examples/fortran")))
+(mkdir-p fbin)
+(mkdir-p flib)
+(mkdir-p finc)
+(mkdir-p fex)
+(rename-file (string-append bin "/h5fc")
+ (string-append fbin "/h5fc"))
+(for-each (lambda (file)
+(rename-file file
+ (string-append flib "/" (basename 
file
+  (find-files lib ".*fortran.*"))
+(for-each (lambda (file)
+(rename-file file
+ (string-append finc "/" (basename 
file
+  (find-files inc ".*mod"))
+(for-each (lambda (file)
+(rename-file file
+ (string-append fex "/" (basename 
file
+  (find-files ex ".*"))
+(delete-file-recursively ex))
+  #t)
 (home-page "http://www.hdfgroup.org;)
 (synopsis "Management suite for extremely large and complex data")
 (description "HDF5 is a suite that makes possible the management of

04/04: gnu: netcdf: Fix reproducibility issue; remove unneeded references.

[Thomas Danckaert]

thomasd pushed a commit to branch master
in repository guix.

commit 43d01672a11814ca4cdcc592544064d75d1653f0
Author: Thomas Danckaert 
Date:   Thu Aug 24 15:13:02 2017 +0200

gnu: netcdf: Fix reproducibility issue; remove unneeded references.

* gnu/packages/maths.scm (netcdf) [arguments]: Add phase to fix the embedded
  'Configured On' date; truncate reference to compiler store item.
---
 gnu/packages/maths.scm | 23 +++
 1 file changed, 23 insertions(+)

diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index a8c81a7..bebed14 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -918,6 +918,29 @@ similar to MATLAB, GNU Octave or SciPy.")
("libjpeg" ,libjpeg)))
 (arguments
  `(#:configure-flags '("--enable-doxygen" "--enable-dot" "--enable-hdf4")
+
+   #:phases (modify-phases %standard-phases
+ (add-before 'configure 'fix-source-date
+   (lambda _
+ ;; As we ${SOURCE_DATE_EPOCH} evaluates to "1" in the build
+ ;; environment, `date -u -d ${SOURCE_DATE_EPOCH}` will evaluate
+ ;; to '1st hour of the current day', and therefore makes the
+ ;; package not reproducible.
+ (substitute* "./configure"
+   (("date -u -d \"\\$\\{SOURCE_DATE_EPOCH\\}\"")
+"date --date='@0'"))
+ #t))
+ (add-after 'configure 'patch-settings
+   (lambda _
+ ;; libnetcdf.settings contains the full filename of the compilers
+ ;; used to build the library.  We truncate the hashes of those
+ ;; filenames to avoid unnecessary references to the corresponding
+ ;; store items.
+ (substitute* "libnetcdf.settings"
+   (("(/gnu/store/)([a-Z0-9]*)" all prefix hash)
+(string-append prefix (string-take hash 10) "...")))
+ #t)))
+
#:parallel-tests? #f))   ;various race conditions
 (home-page "http://www.unidata.ucar.edu/software/netcdf/;)
 (synopsis "Library for scientific data")

02/04: gnu: hdf5: Avoid unneeded store references to compilers.

[Thomas Danckaert]

thomasd pushed a commit to branch master
in repository guix.

commit fd0378a1475900bdbd1da43066811677ba41f3ea
Author: Thomas Danckaert 
Date:   Thu Aug 31 17:29:36 2017 +0200

gnu: hdf5: Avoid unneeded store references to compilers.

* gnu/packages/maths.scm (hdf5) [arguments]: Add phase to patch
  "libhdf5.settings", removing references to the C/C++/Fortran compilers.
---
 gnu/packages/maths.scm | 10 ++
 1 file changed, 10 insertions(+)

diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index b561531..47e7ba3 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -673,6 +673,16 @@ incompatible with HDF5.")
 (string-append "libhdf5hl_fortran_la_LDFLAGS = -Wl,-rpath="
(assoc-ref outputs "fortran") "/lib")))
  #t))
+ (add-after 'configure 'patch-settings
+   (lambda _
+ ;; libhdf5.settings contains the full path of the
+ ;; compilers used, and its contents are included in
+ ;; libhdf5.so.  We truncate the hashes to avoid
+ ;; unnecessary store references to those compilers:
+ (substitute* "src/libhdf5.settings"
+  (("(/gnu/store/)([a-Z0-9]*)" all prefix hash)
+   (string-append prefix (string-take hash 10) "...")))
+ #t))
  (add-after 'install 'patch-references
(lambda* (#:key inputs outputs #:allow-other-keys)
  (let ((bin (string-append (assoc-ref outputs "out") "/bin"))

03/03: gnu: python2-larch: Enable tests.

[Arun Isaac]

arunisaac pushed a commit to branch master
in repository guix.

commit a0596a2f27c339bcb4c5d3f2ffc8d6df38ff7947
Author: Arun Isaac 
Date:   Tue Aug 29 16:02:50 2017 +0530

gnu: python2-larch: Enable tests.

* gnu/packages/patches/python2-larch-coverage-4.0a6-compatibility.patch: New
file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/python.scm (python2-larch)[source]: Use it.
[arguments]: Move 'check' phase to before 'build' phase.
---
 gnu/local.mk   |  1 +
 ...ython2-larch-coverage-4.0a6-compatibility.patch | 29 ++
 gnu/packages/python.scm| 17 -
 3 files changed, 46 insertions(+), 1 deletion(-)

diff --git a/gnu/local.mk b/gnu/local.mk
index fbc6ff0..2e40026 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -962,6 +962,7 @@ dist_patch_DATA =   
\
   %D%/packages/patches/python-genshi-fix-tests-on-python-3.5.patch \
   %D%/packages/patches/python-genshi-isstring-helper.patch \
   %D%/packages/patches/python-genshi-stripping-of-unsafe-script-tags.patch 
\
+  %D%/packages/patches/python2-larch-coverage-4.0a6-compatibility.patch \
   %D%/packages/patches/python-parse-too-many-fields.patch  \
   %D%/packages/patches/python2-rdflib-drop-sparqlwrapper.patch \
   %D%/packages/patches/python-statsmodels-fix-tests.patch  \
diff --git 
a/gnu/packages/patches/python2-larch-coverage-4.0a6-compatibility.patch 
b/gnu/packages/patches/python2-larch-coverage-4.0a6-compatibility.patch
new file mode 100644
index 000..f1db5d7
--- /dev/null
+++ b/gnu/packages/patches/python2-larch-coverage-4.0a6-compatibility.patch
@@ -0,0 +1,29 @@
+From ca548da9ba78ddee90779051210e3e89185e4f7d Mon Sep 17 00:00:00 2001
+From: Michel Alexandre Salim 
+Date: Mon, 15 Feb 2016 23:03:42 +0700
+Subject: coverage-4.0a6 compatibility
+
+coverage 4.0a6 no longer generates .coverage file, so use -f when
+deleting .coverage to ensure deletion does not fail.
+---
+ Makefile | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+(limited to 'Makefile')
+
+diff --git a/Makefile b/Makefile
+index 7818f57..362c07f 100644
+--- a/Makefile
 b/Makefile
+@@ -23,7 +23,7 @@ fsck-larch.1: fsck-larch.1.in fsck-larch
+ 
+ check:
+   python -m CoverageTestRunner --ignore-missing-from=without-tests
+-  rm .coverage
++  rm -f .coverage
+   ./insert-remove-test tempdir 100
+   rm -r tempdir larch.log
+   cmdtest tests
+-- 
+cgit v1.1
+
diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 8bdd865..874ad82 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -68,6 +68,7 @@
   #:use-module (gnu packages attr)
   #:use-module (gnu packages backup)
   #:use-module (gnu packages bash)
+  #:use-module (gnu packages check)
   #:use-module (gnu packages compression)
   #:use-module (gnu packages crypto)
   #:use-module (gnu packages databases)
@@ -14193,12 +14194,26 @@ happens using the @code{logging} library.")
(uri (string-append
  "http://git.liw.fi/cgi-bin/cgit/cgit.cgi/larch/snapshot/larch-;
  version ".tar.gz"))
+   (patches (search-patches
+ "python2-larch-coverage-4.0a6-compatibility.patch"))
(sha256
 (base32
  "1p4knkkavlqymgciz2wbcnfrdgdbafhg14maplnk4vbw0q8xs663"
 (build-system python-build-system)
 (arguments
- `(#:python ,python-2))
+ `(#:python ,python-2
+   #:phases
+   (modify-phases %standard-phases
+ ;; check phase needs to be run before the build phase. If not,
+ ;; coverage-test-runner looks for tests for the built source files,
+ ;; and fails.
+ (delete 'check)
+ (add-before 'build 'check
+   (lambda _
+ (zero? (system* "make" "check")))
+(native-inputs
+ `(("cmdtest" ,cmdtest)
+   ("python2-coverage-test-runner" ,python2-coverage-test-runner)))
 (propagated-inputs
  `(("python2-tracing" ,python2-tracing)))
 (home-page "https://liw.fi/larch/;)

02/03: gnu: python2-ttystatus: Enable tests.

[Arun Isaac]

arunisaac pushed a commit to branch master
in repository guix.

commit f618086220106a15842fce9b4cbe1525a1473f42
Author: Arun Isaac 
Date:   Thu Aug 24 18:33:43 2017 +0530

gnu: python2-ttystatus: Enable tests.

* gnu/packages/python.scm (python2-ttystatus)[arguments]: Replace 'check'
phase with custom function.
---
 gnu/packages/python.scm | 14 +-
 1 file changed, 13 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 0687a23..8bdd865 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -14133,8 +14133,20 @@ iterating over input files.")
 (base32
  "0vivqbw7ddhsq1zj3g9cvvv4f0phl0pis2smsnwcr2szz2fk3hl6"
 (build-system python-build-system)
+(native-inputs
+ `(("python2-coverage-test-runner" ,python2-coverage-test-runner)
+   ("python2-pep8" ,python2-pep8)))
 (arguments
- `(#:python ,python-2))
+ `(#:python ,python-2
+   #:phases
+   (modify-phases %standard-phases
+ ;; check phase needs to be run before the build phase. If not,
+ ;; coverage-test-runner looks for tests for the built source files,
+ ;; and fails.
+ (delete 'check)
+ (add-before 'build 'check
+   (lambda _
+ (zero? (system* "make" "check")))
 (home-page "https://liw.fi/ttystatus/;)
 (synopsis "Python library for showing progress reporting and
 status updates on terminals")

branch master updated (fe36ecf -> a0596a2)

[Arun Isaac]

arunisaac pushed a change to branch master
in repository guix.

  from  fe36ecf   gnu: linux-libre: Update to 4.12.10.
   new  689042e   gnu: python2-cliapp: Enable tests.
   new  f618086   gnu: python2-ttystatus: Enable tests.
   new  a0596a2   gnu: python2-larch: Enable tests.

The 3 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.


Summary of changes:
 gnu/local.mk   |  1 +
 ...ython2-larch-coverage-4.0a6-compatibility.patch | 29 +
 gnu/packages/python.scm| 48 --
 3 files changed, 75 insertions(+), 3 deletions(-)
 create mode 100644 
gnu/packages/patches/python2-larch-coverage-4.0a6-compatibility.patch