branch master updated (3880537 -> 07b0662)

[Efraim Flashner]

efraim pushed a change to branch master
in repository guix.

  from  3880537   gnu: zstd: Don't use unstable tarball.
   new  07b0662   gnu: abiword: Remove wmf support.

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

01/01: gnu: abiword: Remove wmf support.

[Efraim Flashner]

efraim pushed a commit to branch master
in repository guix.

commit 07b0662754014f7ac8ab81ce6a8878d0cc206b19
Author: Efraim Flashner 
Date:   Tue Oct 9 09:56:02 2018 +0300

gnu: abiword: Remove wmf support.

* gnu/packages/abiword.scm (abiword)[arguments]: Remove 'wmf' from the
list of enabled plugins.
---
 gnu/packages/abiword.scm | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/abiword.scm b/gnu/packages/abiword.scm
index cf906c6..02f132f 100644
--- a/gnu/packages/abiword.scm
+++ b/gnu/packages/abiword.scm
@@ -1,6 +1,6 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2014 Marek Benc 
-;;; Copyright © 2016 Efraim Flashner 
+;;; Copyright © 2016, 2018 Efraim Flashner 
 ;;; Copyright © 2017 Ricardo Wurmus 
 ;;; Copyright © 2017 Leo Famulari 
 ;;;
@@ -62,7 +62,7 @@
 (build-system glib-or-gtk-build-system)
 (arguments   ;; NOTE: rsvg is disabled, since Abiword
   `(#:configure-flags;; supports it directly, and its BS is broken.
-(list
+(list;; wmf was removed from Guix for security.
   "--enable-clipart" ;; TODO: The following plugins have unresolved
   "--enable-templates"   ;; dependencies: aiksaurus, grammar, wpg, gda,
   (string-append ;; wordperfect, psion, mathview.
@@ -73,7 +73,7 @@
   "latex " "loadbindings " "mht " "mif " "mswrite " "opendocument "
   "openwriter " "openxml " "opml " "ots " "paint " "passepartout "
   "pdb " "pdf " "presentation " "s5 " "sdw " "t602 " "urldict "
-  "wikipedia " "wmf " "wml " "xslfo"))
+  "wikipedia " "wml " "xslfo"))
 ;; tests fail with: Gtk-CRITICAL **: gtk_settings_get_for_screen:
 ;;  assertion 'GDK_IS_SCREEN (screen)' failed
 ;;  GLib-GObject-CRITICAL **: g_object_get_qdata:

01/01: gnu: zstd: Don't use unstable tarball.

[Tobias Geerinckx-Rice]

nckx pushed a commit to branch master
in repository guix.

commit 3880537c7403c3677ec46e991da9d25ca542c64b
Author: Tobias Geerinckx-Rice 
Date:   Tue Oct 9 05:46:00 2018 +0200

gnu: zstd: Don't use unstable tarball.

* gnu/packages/compression.scm (zstd)[source]: Use release archive.
---
 gnu/packages/compression.scm | 15 +++
 1 file changed, 7 insertions(+), 8 deletions(-)

diff --git a/gnu/packages/compression.scm b/gnu/packages/compression.scm
index 38d72f1..8c940f3 100644
--- a/gnu/packages/compression.scm
+++ b/gnu/packages/compression.scm
@@ -1695,14 +1695,13 @@ or junctions, and always follows hard links.")
   (package
 (name "zstd")
 (version "1.3.6")
-(source (origin
-  (method url-fetch)
-  (uri (string-append "https://github.com/facebook/zstd/archive/v";
-  version ".tar.gz"))
-  (file-name (string-append name "-" version ".tar.gz"))
-  (sha256
-   (base32
-"1iwxcpxg51yskiwfw5nhsflvcm3pk4184kkfpm61hsxniwa1cmbz"
+(source
+ (origin
+   (method url-fetch)
+   (uri (string-append 
"https://github.com/facebook/zstd/releases/download/";
+   "v" version "/zstd-" version ".tar.gz"))
+   (sha256
+(base32 "1525b31jmbiczjj1n58nckdzky4cdnbwcsil3zgy4cx03v0a0cp8"
 (build-system gnu-build-system)
 (arguments
  `(#:phases

branch master updated (317e80c -> 3880537)

[Tobias Geerinckx-Rice]

nckx pushed a change to branch master
in repository guix.

  from  317e80c   gnu: unison: End all phases with #t.
   new  3880537   gnu: zstd: Don't use unstable tarball.

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/compression.scm | 15 +++
 1 file changed, 7 insertions(+), 8 deletions(-)

01/03: gnu: zstd: Update to 1.3.6.

[Tobias Geerinckx-Rice]

nckx pushed a commit to branch master
in repository guix.

commit de68ad095db7cdd06c45c53c47e7cbcb3fdf8bf6
Author: Tobias Geerinckx-Rice 
Date:   Tue Oct 9 05:32:35 2018 +0200

gnu: zstd: Update to 1.3.6.

* gnu/packages/compression.scm (zstd): Update to 1.3.6.
[source]: Remove merged patches.
* gnu/packages/patches/zstd-fix-stdin-list-test.patch,
gnu/packages/patches/zstd-fix-stdin-list-without-tty.patch: Delete files.
* gnu/local.mk (dist_patch_DATA): Remove them.
---
 gnu/local.mk   |  4 +-
 gnu/packages/compression.scm   |  8 +--
 .../patches/zstd-fix-stdin-list-test.patch | 30 --
 .../patches/zstd-fix-stdin-list-without-tty.patch  | 67 --
 4 files changed, 3 insertions(+), 106 deletions(-)

diff --git a/gnu/local.mk b/gnu/local.mk
index ea2d650..821e83a 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -1247,9 +1247,7 @@ dist_patch_DATA = 
\
   %D%/packages/patches/xinetd-CVE-2013-4342.patch  \
   %D%/packages/patches/xmodmap-asprintf.patch  \
   %D%/packages/patches/zathura-pdf-mupdf-link-to-jpeg-libraries.patch \
-  %D%/packages/patches/zathura-plugindir-environment-variable.patch\
-  %D%/packages/patches/zstd-fix-stdin-list-without-tty.patch   \
-  %D%/packages/patches/zstd-fix-stdin-list-test.patch
+  %D%/packages/patches/zathura-plugindir-environment-variable.patch
 
 MISC_DISTRO_FILES =\
   %D%/packages/ld-wrapper.in
diff --git a/gnu/packages/compression.scm b/gnu/packages/compression.scm
index 666c9bf..38d72f1 100644
--- a/gnu/packages/compression.scm
+++ b/gnu/packages/compression.scm
@@ -1694,7 +1694,7 @@ or junctions, and always follows hard links.")
 (define-public zstd
   (package
 (name "zstd")
-(version "1.3.5")
+(version "1.3.6")
 (source (origin
   (method url-fetch)
   (uri (string-append "https://github.com/facebook/zstd/archive/v";
@@ -1702,11 +1702,7 @@ or junctions, and always follows hard links.")
   (file-name (string-append name "-" version ".tar.gz"))
   (sha256
(base32
-"1sifbq18p0hc978g0pq8fymrlpzz1fcxqkbxfqk44z6v9jg5bqfn"))
-  ;; Fix a regression that causes the tests to fail.  Both patches
-  ;; have been merged upstream and will be part of the next 
release.
-  (patches (search-patches "zstd-fix-stdin-list-without-tty.patch"
-   "zstd-fix-stdin-list-test.patch"
+"1iwxcpxg51yskiwfw5nhsflvcm3pk4184kkfpm61hsxniwa1cmbz"
 (build-system gnu-build-system)
 (arguments
  `(#:phases
diff --git a/gnu/packages/patches/zstd-fix-stdin-list-test.patch 
b/gnu/packages/patches/zstd-fix-stdin-list-test.patch
deleted file mode 100644
index a103554..000
--- a/gnu/packages/patches/zstd-fix-stdin-list-test.patch
+++ /dev/null
@@ -1,30 +0,0 @@
-From 8e7bdc18d62632adcee029b2f8f5013d11549dd7 Mon Sep 17 00:00:00 2001
-From: "W. Felix Handte" 
-Date: Fri, 29 Jun 2018 16:31:22 -0400
-Subject: [PATCH] Fix Tests of `--list` Behavior with `stdin`
-

- tests/playTests.sh | 10 --
- 1 file changed, 8 insertions(+), 2 deletions(-)
-
-diff --git a/tests/playTests.sh b/tests/playTests.sh
-index 09a7377f2..aa5535d59 100755
 a/tests/playTests.sh
-+++ b/tests/playTests.sh
-@@ -731,8 +731,14 @@ $ECHO "\n===>  zstd --list/-l error detection tests "
- ! $ZSTD -lv tmp1*
- ! $ZSTD --list -v tmp2 tmp12.zst
- 
--$ECHO "\n===>  zstd --list/-l exits 1 when stdin is piped in"
--! echo "piped STDIN" | $ZSTD --list
-+$ECHO "\n===>  zstd --list/-l errors when presented with stdin / no files"
-+! $ZSTD -l
-+! $ZSTD -l -
-+! $ZSTD -l < tmp1.zst
-+! $ZSTD -l - < tmp1.zst
-+! $ZSTD -l - tmp1.zst
-+! $ZSTD -l - tmp1.zst < tmp1.zst
-+$ZSTD -l tmp1.zst < tmp1.zst # but doesn't error just because stdin is not a 
tty
- 
- $ECHO "\n===>  zstd --list/-l test with null files "
- ./datagen -g0 > tmp5
diff --git a/gnu/packages/patches/zstd-fix-stdin-list-without-tty.patch 
b/gnu/packages/patches/zstd-fix-stdin-list-without-tty.patch
deleted file mode 100644
index 47fa3e5..000
--- a/gnu/packages/patches/zstd-fix-stdin-list-without-tty.patch
+++ /dev/null
@@ -1,67 +0,0 @@
-From 712a9fd9721c314f4b0238577d803b012845f6d2 Mon Sep 17 00:00:00 2001
-From: "W. Felix Handte" 
-Date: Fri, 29 Jun 2018 15:33:44 -0400
-Subject: [PATCH] Allow Invoking `zstd --list` When `stdin` is not a `tty`
-
-Also now returns an error when no inputs are given.
-
-New proposed behavior:
-
-```
-felix@odin:~/prog/zstd (list-stdin-check)$ ./zstd -l; echo $?
-No files given
-1
-felix@odin:~/prog/zstd (list-stdin-check)$ ./zstd -l Makefile.zst; echo $?
-Frames  Skips  Compressed  Uncompressed  Ratio  Check  Filename
- 1  0 3.08 KB  10.92 KB  3.544  XXH64  Makefile.zst
-0
-felix@odin:~/prog/zstd (list-stdin-check)$ ./z

branch master updated (65b8d61 -> 317e80c)

[Tobias Geerinckx-Rice]

nckx pushed a change to branch master
in repository guix.

  from  65b8d61   gnu: Add gimp-resynthesizer.
   new  de68ad0   gnu: zstd: Update to 1.3.6.
   new  f6ccb95   gnu: docx2txt: End phases with #t.
   new  317e80c   gnu: unison: End all phases with #t.

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   |  4 +-
 gnu/packages/compression.scm   |  8 +--
 gnu/packages/ocaml.scm | 31 +-
 .../patches/zstd-fix-stdin-list-test.patch | 30 --
 .../patches/zstd-fix-stdin-list-without-tty.patch  | 67 --
 gnu/packages/textutils.scm |  3 +-
 6 files changed, 20 insertions(+), 123 deletions(-)
 delete mode 100644 gnu/packages/patches/zstd-fix-stdin-list-test.patch
 delete mode 100644 gnu/packages/patches/zstd-fix-stdin-list-without-tty.patch

02/03: gnu: docx2txt: End phases with #t.

[Tobias Geerinckx-Rice]

nckx pushed a commit to branch master
in repository guix.

commit f6ccb95a86ef22ae678e80b0e9a353e5b2404334
Author: Tobias Geerinckx-Rice 
Date:   Mon Oct 8 16:20:19 2018 +0200

gnu: docx2txt: End phases with #t.

* gnu/packages/textutils.scm (docx2txt)[arguments]: End 'fix-install'
phase with #t.
---
 gnu/packages/textutils.scm | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/textutils.scm b/gnu/packages/textutils.scm
index 7e26bdc..8780bb2 100644
--- a/gnu/packages/textutils.scm
+++ b/gnu/packages/textutils.scm
@@ -735,7 +735,8 @@ measuring and checking the width of strings, with support 
east asian text.")
  unzip
  "/bin/unzip',")))
;; Makefile is wrong.
-   (chmod config #o644)))
+   (chmod config #o644)
+   #t))
 (synopsis "Recover text from @file{.docx} files, with good formatting")
 (description
  "@command{docx2txt} is a Perl based command line utility to convert

03/03: gnu: unison: End all phases with #t.

[Tobias Geerinckx-Rice]

nckx pushed a commit to branch master
in repository guix.

commit 317e80cead5d8f78ed021069a3ef108d44824f76
Author: Tobias Geerinckx-Rice 
Date:   Mon Oct 8 16:38:27 2018 +0200

gnu: unison: End all phases with #t.

* gnu/packages/ocaml.scm (unison)[arguments]: End all phases with #t.
---
 gnu/packages/ocaml.scm | 31 +++
 1 file changed, 15 insertions(+), 16 deletions(-)

diff --git a/gnu/packages/ocaml.scm b/gnu/packages/ocaml.scm
index 0756aec..6b55e84 100644
--- a/gnu/packages/ocaml.scm
+++ b/gnu/packages/ocaml.scm
@@ -820,7 +820,8 @@ libpanel, librsvg and quartz.")
(let* ((out (assoc-ref outputs "out"))
   (bin (string-append out "/bin")))
  ;; 'unison-fsmonitor' is used in "unison -repeat watch" mode.
- (install-file "src/unison-fsmonitor" bin
+ (install-file "src/unison-fsmonitor" bin)
+ #t)))
(add-after 'install 'install-doc
  (lambda* (#:key outputs #:allow-other-keys)
(let ((doc (string-append (assoc-ref outputs "doc")
@@ -829,21 +830,19 @@ libpanel, librsvg and quartz.")
  ;; This file needs write-permissions, because it's
  ;; overwritten by 'docs' during documentation generation.
  (chmod "src/strings.ml" #o600)
- (and (zero? (system* "make" "docs"
-  "TEXDIRECTIVES=draftfalse"))
-  (begin
-(for-each (lambda (f)
-(install-file f doc))
-  (map (lambda (ext)
- (string-append
-  "doc/unison-manual." ext))
-   ;; Install only html documentation,
-   ;; since the build is currently
-   ;; non-reproducible with the ps, pdf,
-   ;; and dvi docs.
-   '(;;"ps" "pdf" "dvi"
- "html")))
-#t
+ (invoke "make" "docs"
+ "TEXDIRECTIVES=draftfalse")
+ (for-each (lambda (f)
+ (install-file f doc))
+   (map (lambda (ext)
+  (string-append "doc/unison-manual." ext))
+;; Install only html documentation,
+;; since the build is currently
+;; non-reproducible with the ps, pdf,
+;; and dvi docs.
+'(;; "ps" "pdf" "dvi"
+  "html")))
+ #t))
 (home-page "https://www.cis.upenn.edu/~bcpierce/unison/";)
 (synopsis "File synchronizer")
 (description

02/02: gnu: Add gimp-resynthesizer.

[Ludovic Court�]

civodul pushed a commit to branch master
in repository guix.

commit 65b8d610739065671af288836d74e5ffbf382c8f
Author: Thorsten Wilms 
Date:   Mon Oct 8 21:11:10 2018 +0200

gnu: Add gimp-resynthesizer.

* gnu/packages/gimp.scm (gimp-resynthesizer): New variable.

Signed-off-by: Ludovic Courtès 
---
 gnu/packages/gimp.scm | 65 +++
 1 file changed, 65 insertions(+)

diff --git a/gnu/packages/gimp.scm b/gnu/packages/gimp.scm
index df8f242..cd0deac 100644
--- a/gnu/packages/gimp.scm
+++ b/gnu/packages/gimp.scm
@@ -4,6 +4,7 @@
 ;;; Copyright © 2016, 2017, 2018 Efraim Flashner 
 ;;; Copyright © 2018 Tobias Geerinckx-Rice 
 ;;; Copyright © 2018 Leo Famulari 
+;;; Copyright © 2018 Thorsten Wilms 
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -305,3 +306,67 @@ brushstrokes which is used by MyPaint and GIMP.")
 MyPaint.")
 (home-page "https://github.com/Jehan/mypaint-brushes";)
 (license license:cc0)))
+
+(define-public gimp-resynthesizer
+  ;; GIMP does not respect any plugin search path environment variable, so 
after
+  ;; installation users have to edit their GIMP settings to include
+  ;; "$HOME/.guix-profile/lib/gimp/2.0/plug-ins/" in
+  ;; “Edit->Preferences->Folders->Plug Ins”.
+  (package
+(name "gimp-resynthesizer")
+(version "2.0.3")
+(source
+ (origin
+   (method url-fetch)
+   (uri (string-append "https://github.com/bootchk/resynthesizer/archive/v";
+  version ".tar.gz"))
+   (sha256
+(base32
+ "0l3404w6rqny7h3djskxf149gzx6x4qhndgbh3403c9lbh4pi1kr"))
+   (file-name (string-append name "-" version ".tar.gz"
+(build-system gnu-build-system)
+(arguments
+ `( ;; Turn off tests to avoid:
+   ;; make[1]: *** No rule to make target '../src/resynth-gui.c', needed 
by 'resynthesizer.pot'.  Stop.
+   #:tests? #f
+   #:phases
+   (modify-phases %standard-phases
+(add-after 'unpack 'set-env
+  (lambda _
+(setenv "CONFIG_SHELL" (which "sh"))
+#t))
+(add-after 'configure 'set-prefix
+   ;; Install plugin under $prefix, not under GIMP's libdir.
+   (lambda* (#:key outputs #:allow-other-keys)
+ (let ((target (string-append (assoc-ref outputs "out")
+  "/lib/gimp/"
+  ,(version-major
+(package-version gimp))
+  ".0")))
+   (substitute* (list "src/resynthesizer/Makefile"
+ "src/resynthesizer-gui/Makefile")
+(("GIMP_LIBDIR = .*")
+  (string-append "GIMP_LIBDIR = " target "\n")))
+   (mkdir-p target)
+   #t))
+(native-inputs
+ `(("autoconf" ,autoconf-wrapper)
+   ("automake" ,automake)
+   ("glib" ,glib "bin")   ; glib-gettextize
+   ("intltool" ,intltool)
+   ("pkg-config" ,pkg-config)))
+(inputs
+ `(("gimp" ,gimp)
+   ("gdk-pixbuf" ,gdk-pixbuf) ; needed by gimp-2.0.pc
+   ("cairo" ,cairo)
+   ("gegl" ,gegl)
+   ("gtk+" ,gtk+-2)   ; needed by gimpui-2.0.pc
+   ("glib" ,glib)))
+(home-page "https://github.com/bootchk/resynthesizer";)
+(synopsis "GIMP plugins for texture synthesis")
+(description
+ "This package provides resynthesizer plugins for GIMP, which encompasses
+tools for healing selections (content-aware fill), enlarging the canvas and
+healing the border, increasing the resolution while adding detail, and
+transfering the style of an image.")
+(license license:gpl3+)))

branch master updated (b6bd8b1 -> 65b8d61)

[Ludovic Court�]

civodul pushed a change to branch master
in repository guix.

  from  b6bd8b1   gnu: Add filtlong.
   new  df2d77c   gnu: Add emacs-colum-marker.
   new  65b8d61   gnu: Add gimp-resynthesizer.

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


Summary of changes:
 gnu/packages/emacs.scm | 22 +
 gnu/packages/gimp.scm  | 65 ++
 2 files changed, 87 insertions(+)

01/02: gnu: Add emacs-colum-marker.

[Ludovic Court�]

civodul pushed a commit to branch master
in repository guix.

commit df2d77c45ff357a25fee5f96478b1b65dc93f507
Author: Thorsten Wilms 
Date:   Mon Oct 8 21:12:54 2018 +0200

gnu: Add emacs-colum-marker.

* gnu/packages/emacs.scm (emacs-colum-marker): New variable.

Signed-off-by: Ludovic Courtès 
---
 gnu/packages/emacs.scm | 22 ++
 1 file changed, 22 insertions(+)

diff --git a/gnu/packages/emacs.scm b/gnu/packages/emacs.scm
index aad698d..c9493da 100644
--- a/gnu/packages/emacs.scm
+++ b/gnu/packages/emacs.scm
@@ -39,6 +39,7 @@
 ;;; Copyright © 2018 Jack Hill 
 ;;; Copyright © 2018 Pierre-Antoine Rouby 
 ;;; Copyright © 2018 Alex Branham 
+;;; Copyright © 2018 Thorsten Wilms 
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -12353,3 +12354,24 @@ with a handful of easy tweaks.
 scratch, and you think the Spacemacs theme looks good.
 @end itemize")
 (license license:gpl3+)))
+
+(define-public emacs-column-marker
+  (package
+(name "emacs-column-marker")
+(version "9")
+(source
+ (origin
+   (method url-fetch)
+   (uri "https://www.emacswiki.org/emacs/download/column-marker.el";)
+   (sha256 (base32 
"05bv198zhqw5hqq6cr11mhz02dpca74hhp1ycwq369m0yb2naxy9"
+(build-system emacs-build-system)
+(home-page "https://www.emacswiki.org/emacs/ColumnMarker";)
+(synopsis "Emacs mode for highlighting columns")
+(description
+ "With @code{column-marker.el} you can highlight any number of text 
columns.
+Three such highlight column markers are provided by default.  This is
+especially useful for languages like COBOL or Fortran where certain columns
+have special meaning.  It is also handy for aligning text across long vertical
+distances.  Multi-column characters, such as @kbd{TAB} are treated
+correctly.")
+(license license:gpl2+)))

02/04: gnu: Add font-sil-charis.

[Ludovic Court�]

civodul pushed a commit to branch master
in repository guix.

commit 46e78707a3d72d1fd08432cba8886415c79ebacc
Author: Ludovic Courtès 
Date:   Mon Oct 8 17:35:22 2018 +0200

gnu: Add font-sil-charis.

* gnu/packages/fonts.scm (font-sil-charis): New variable.
---
 gnu/packages/fonts.scm | 24 
 1 file changed, 24 insertions(+)

diff --git a/gnu/packages/fonts.scm b/gnu/packages/fonts.scm
index 7fdcda4..1195695 100644
--- a/gnu/packages/fonts.scm
+++ b/gnu/packages/fonts.scm
@@ -1328,3 +1328,27 @@ produce readable, high-quality publications.  The font 
comes with regular and
 italics shapes.  This package provides only TrueType files (TTF).")
 (home-page "https://software.sil.org/gentium/";)
 (license license:silofl1.1)))
+
+(define-public font-sil-charis
+  (package
+(name "font-sil-charis")
+(version "5.000")
+(source (origin
+  (method url-fetch)
+  (uri (string-append
+"https://software.sil.org/downloads/r/charis/CharisSIL-";
+version ".zip"))
+  (sha256
+   (base32
+"1zcvw37f1a7gkml3yfm6hxh93844llm7xj4w52600qq3ndrm8gjy"
+;; As for Gentium (see above), the TTF files are considered source.
+(build-system font-build-system)
+(synopsis "Serif font for the Cyrillic and Latin alphabets")
+(description
+ "Charis SIL is a Unicode-based font family that supports the wide range
+of languages that use the Latin and Cyrillic scripts.  It is specially
+designed to make long texts pleasant and easy to read, even in less than ideal
+reproduction and display environments.  This package provides only TrueType
+files (TTF).")
+(home-page "https://software.sil.org/charis/";)
+(license license:silofl1.1)))

01/04: gnu: Add font-sil-gentium.

[Ludovic Court�]

civodul pushed a commit to branch master
in repository guix.

commit 1d6417340d6c6a80e24b9cd7e9c357b87c8da309
Author: Ludovic Courtès 
Date:   Mon Oct 8 17:29:34 2018 +0200

gnu: Add font-sil-gentium.

* gnu/packages/fonts.scm (font-sil-gentium): New variable.
---
 gnu/packages/fonts.scm | 26 ++
 1 file changed, 26 insertions(+)

diff --git a/gnu/packages/fonts.scm b/gnu/packages/fonts.scm
index 6d4abc6..7fdcda4 100644
--- a/gnu/packages/fonts.scm
+++ b/gnu/packages/fonts.scm
@@ -1302,3 +1302,29 @@ Kannada, Malayalam, Manipuri, Oriya, Punjabi, Tamil and 
Telugu scripts.")
  "Inria Sans and Inria Serif are the two members of a type family designed
 for Inria, a public research institute in computer science and mathematics.")
 (license license:silofl1.1)))
+
+(define-public font-sil-gentium
+  (package
+(name "font-sil-gentium")
+(version "5.000")
+(source (origin
+  (method url-fetch)
+  (uri (string-append
+"https://software.sil.org/downloads/r/gentium/GentiumPlus-";
+version ".zip"))
+  (sha256
+   (base32
+"0m7189870hha217n1vgpmf89mwggrxkh679ffi1lxpnjggqi2n9k"
+;; Note: The zip file provides TTF files only, but the developer release,
+;; which contains additional files, has a 'SOURCES.txt' file that says
+;; that "the primary source files for the fonts are the fonts themselves".
+;; Thus it looks like the TTF can be considered source.
+(build-system font-build-system)
+(synopsis "Serif font for the Cyrillic, Greek, and Latin alphabets")
+(description
+ "Gentium is a typeface family designed to enable the diverse ethnic
+groups around the world who use the Latin, Cyrillic and Greek scripts to
+produce readable, high-quality publications.  The font comes with regular and
+italics shapes.  This package provides only TrueType files (TTF).")
+(home-page "https://software.sil.org/gentium/";)
+(license license:silofl1.1)))

branch master updated (f6e9976 -> b6bd8b1)

[Ludovic Court�]

civodul pushed a change to branch master
in repository guix.

  from  f6e9976   gnu: Add r-dnabarcodes.
   new  1d64173   gnu: Add font-sil-gentium.
   new  46e7870   gnu: Add font-sil-charis.
   new  f8e0d27   gnu: emacs-google-translate: Update to 0.11.15.
   new  b6bd8b1   gnu: Add filtlong.

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/bioinformatics.scm | 60 +
 gnu/packages/emacs.scm  | 38 +-
 gnu/packages/fonts.scm  | 50 ++
 3 files changed, 128 insertions(+), 20 deletions(-)

04/04: gnu: Add filtlong.

[Ludovic Court�]

civodul pushed a commit to branch master
in repository guix.

commit b6bd8b108a4ad53e89d6b83edc57df18935f131c
Author: pimi 
Date:   Mon Oct 8 11:17:41 2018 +0200

gnu: Add filtlong.

* gnu/packages/bioinformatics.scm (filtlong): New variable.

Co-authored-by: Ludovic Courtès 
---
 gnu/packages/bioinformatics.scm | 60 +
 1 file changed, 60 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index ab9dc18..ed713cd 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -14057,3 +14057,63 @@ absolute GSEA.")
 (description "Ngless is a domain-specific language for
 @dfn{next-generation sequencing} (NGS) data processing.")
 (license license:expat)))
+
+(define-public filtlong
+  ;; The recommended way to install is to clone the git repository
+  ;; https://github.com/rrwick/Filtlong#installation
+  ;; and the lastest release is more than nine months old
+  (let ((commit "d1bb46dfe8bc7efe6257b5ce222c04bfe8aedaab")
+(revision "1"))
+(package
+  (name "filtlong")
+  (version (git-version "0.2.0" revision commit))
+  (source
+   (origin
+ (method git-fetch)
+ (uri (git-reference
+   (url "https://github.com/rrwick/Filtlong.git";)
+   (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+  (base32 "1xr92r820x8qlkcr3b57iw223yq8vjgyi42jr79w2xgw47qzr575"
+  (build-system gnu-build-system)
+  (arguments
+   `(#:tests? #f; no check target
+ #:phases
+ (modify-phases %standard-phases
+   (delete 'configure)
+   (replace 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+   (let* ((out (assoc-ref outputs "out"))
+  (bin (string-append out "/bin"))
+  (scripts (string-append out "/share/filtlong/scripts")))
+ (install-file "bin/filtlong" bin)
+ (install-file "scripts/histogram.py" scripts)
+ (install-file "scripts/read_info_histograms.sh" scripts))
+   #t))
+   (add-after 'install 'wrap-program
+ (lambda* (#:key inputs outputs #:allow-other-keys)
+   (let* ((out (assoc-ref outputs "out"))
+  (path (getenv "PYTHONPATH")))
+ (wrap-program (string-append out
+  
"/share/filtlong/scripts/histogram.py")
+   `("PYTHONPATH" ":" prefix (,path
+   #t))
+   (add-before 'check 'patch-tests
+ (lambda _
+   (substitute* "scripts/read_info_histograms.sh"
+ (("awk") (which "gawk")))
+   #t)
+  (inputs
+   `(("gawk" ,gawk) ;for read_info_histograms.sh
+ ("python" ,python-2)   ;required for histogram.py
+ ("zlib" ,zlib)))
+  (home-page "https://github.com/rrwick/Filtlong/";)
+  (synopsis "Tool for quality filtering of Nanopore and PacBio data")
+  (description
+   "The Filtlong package is a tool for filtering long reads by quality.
+It can take a set of long reads and produce a smaller, better subset.  It uses
+both read length (longer is better) and read identity (higher is better) when
+choosing which reads pass the filter.")
+  (license (list license:gpl3   ;filtlong
+ license:asl2.0) ;histogram.py

03/04: gnu: emacs-google-translate: Update to 0.11.15.

[Ludovic Court�]

civodul pushed a commit to branch master
in repository guix.

commit f8e0d27c5c2f338012f00cd3c4620ca76751495c
Author: Mathieu Lirzin 
Date:   Sun Oct 7 17:53:04 2018 +0200

gnu: emacs-google-translate: Update to 0.11.15.

* gnu/packages/emacs.scm (emacs-google-translate): Update to 0.11.15.

Signed-off-by: Ludovic Courtès 
---
 gnu/packages/emacs.scm | 38 ++
 1 file changed, 18 insertions(+), 20 deletions(-)

diff --git a/gnu/packages/emacs.scm b/gnu/packages/emacs.scm
index 1df3456..aad698d 100644
--- a/gnu/packages/emacs.scm
+++ b/gnu/packages/emacs.scm
@@ -11344,27 +11344,25 @@ the GIF result.")
   (license license:gpl3+
 
 (define-public emacs-google-translate
-  (let ((commit "d8b84a8359fcc697114d1298840e9a45b111c974"))
-(package
-  (name "emacs-google-translate")
-  (version (git-version "0.11.14" "1" commit))
-  (source
-   (origin
- (method git-fetch)
- (uri (git-reference
-   (url "https://github.com/atykhonov/google-translate";)
-   (commit commit)))
- (file-name (string-append name "-" version "-checkout"))
- (sha256
-  (base32
-   "1qs4hcg1i2m487z50nnwgs0sa2xj4lpgizbrvi2yda0mf3m75fgc"
-  (build-system emacs-build-system)
-  (home-page "https://github.com/atykhonov/google-translate";)
-  (synopsis "Emacs interface to Google Translate")
-  (description
-   "This packages provides an Emacs interface to the Google Translate
+  (package
+(name "emacs-google-translate")
+(version "0.11.15")
+(source
+ (origin
+   (method url-fetch)
+   (uri (string-append "https://github.com/atykhonov/google-translate/";
+   "archive/v" version ".tar.gz"))
+   (file-name (string-append name "-" version ".tar.gz"))
+   (sha256
+(base32
+ "1zxvfagbaf5mxi528mz33c8vxdk86wj0xx5y2jfy97wi8dzrwn3g"
+(build-system emacs-build-system)
+(home-page "https://github.com/atykhonov/google-translate";)
+(synopsis "Emacs interface to Google Translate")
+(description
+ "This packages provides an Emacs interface to the Google Translate
 on-line service.")
-  (license license:gpl3+
+(license license:gpl3+)))
 
 (define-public emacs-helm-company
   (let ((commit "acc9c7901e094c1591327a0db1ec7a439f67a84d"))

[shepherd] 02/02: doc: Fix typos.

[Ludovic Court�]

civodul pushed a commit to branch master
in repository shepherd.

commit 8a406dc558bd3faa4fdf2a61c019038e069a2a23
Author: Ludovic Courtès 
Date:   Mon Oct 8 15:51:12 2018 +0200

doc: Fix typos.

Fixes .
Reported by Meiyo Peng .

* doc/shepherd.texi (The root and unknown services): Replace "safe" by
"save".
---
 doc/shepherd.texi | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/doc/shepherd.texi b/doc/shepherd.texi
index afefc77..8a5687a 100644
--- a/doc/shepherd.texi
+++ b/doc/shepherd.texi
@@ -1018,11 +1018,11 @@ respawnable services are started, as otherwise we would 
not get the
 @code{SIGCHLD} signals when they terminate.
 
 @item enable-persistency
-When terminating, safe the list of running services in a file.
+When terminating, save the list of running services in a file.
 @c FIXME-CRITICAL: How can we specify which one?
 
 @item disable-persistency
-Don't safe the list of running services when terminating.
+Don't save the list of running services when terminating.
 
 @end table
 

[shepherd] branch master updated (0dfc941 -> 8a406dc)

[Ludovic Court�]

civodul pushed a change to branch master
in repository shepherd.

  from  0dfc941   doc: Add missing @command markup.
   new  b1fdcb8   service: Simplify 'register-services'.
   new  8a406dc   doc: Fix typos.

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


Summary of changes:
 doc/shepherd.texi|  4 ++--
 modules/shepherd/service.scm | 22 ++
 2 files changed, 8 insertions(+), 18 deletions(-)

[shepherd] 01/02: service: Simplify 'register-services'.

[Ludovic Court�]

civodul pushed a commit to branch master
in repository shepherd.

commit b1fdcb823ca35b0d114112b5151d2d7f11229cb8
Author: Ludovic Courtès 
Date:   Fri Sep 28 22:43:32 2018 +0200

service: Simplify 'register-services'.

* modules/shepherd/service.scm (register-services)[register-single-service]:
Simplify by using 'assert'.
---
 modules/shepherd/service.scm | 22 ++
 1 file changed, 6 insertions(+), 16 deletions(-)

diff --git a/modules/shepherd/service.scm b/modules/shepherd/service.scm
index 43cf5a7..34a55a1 100644
--- a/modules/shepherd/service.scm
+++ b/modules/shepherd/service.scm
@@ -1102,22 +1102,12 @@ is currently stopped, replace it immediately."
   (let ((old (lookup-services name)))
 (hashq-set! %services name (cons new old
 (provided-by new)))
-  ((old) ;; one service registered, so it may be an old version of us
-   (cond
-((not (eq? (canonical-name new) (canonical-name old)))
- (local-output
-  "Cannot register service ~a: canonical name is not unique."
-  (canonical-name new))
- (throw 'non-canonical-name))
-((running? old)
- (slot-set! old 'replacement new))
-(else
- (replace-service old new
-  (_ ;; in any other case, there are too many services to register
-   (local-output
-"Cannot register service ~a: canonical name is not unique."
-(canonical-name new))
-   (throw 'non-canonical-name
+  ((old . rest) ;; one service registered, it may be an old version of us
+   (assert (null? rest))
+   (assert (eq? (canonical-name new) (canonical-name old)))
+   (if (running? old)
+   (slot-set! old 'replacement new)
+   (replace-service old new)
 
   (for-each register-single-service new-services))
 

[no subject]

[Ludovic Court�]

branch: master
commit be489a26c0e6a5f23a48142a87728a0ec8bc3c9c
Author: Ludovic Courtès 
Date:   Mon Oct 8 15:19:06 2018 +0200

base: Distinguish between 'failed' and 'failed-dependency'.

* src/cuirass/base.scm (update-build-statuses!): Call 'log-file' and use
that to distinguish between 'failed' and 'failed-dependency'.
---
 src/cuirass/base.scm | 6 +-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/src/cuirass/base.scm b/src/cuirass/base.scm
index deee05b..cd095e0 100644
--- a/src/cuirass/base.scm
+++ b/src/cuirass/base.scm
@@ -372,7 +372,11 @@ outputs are invalid, that they failed to build.)"
   (((_ . outputs) ...)
(if (any (cut valid-path? store <>) outputs)
(db-update-build-status! drv (build-status succeeded))
-   (db-update-build-status! drv (build-status failed))
+   (db-update-build-status! drv
+(if (log-file store
+  (derivation-file-name drv))
+(build-status failed)
+(build-status failed-dependency)))
 
   (for-each update! lst))
 

master updated (fe2b73c -> be489a2)

[Ludovic Court�]

civodul pushed a change to branch master.

  from  fe2b73c   database: Return #f when one row is expected and there is 
none.
   new  be489a2   base: Distinguish between 'failed' and 
'failed-dependency'.


Summary of changes:
 src/cuirass/base.scm | 6 +-
 1 file changed, 5 insertions(+), 1 deletion(-)

branch master updated (1deab8c -> f6e9976)

[Ricardo Wurmus]

rekado pushed a change to branch master
in repository guix.

  from  1deab8c   gnu: Add picard.
   new  f6e9976   gnu: Add r-dnabarcodes.

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/bioconductor.scm | 27 +++
 1 file changed, 27 insertions(+)

01/01: gnu: Add r-dnabarcodes.

[Ricardo Wurmus]

rekado pushed a commit to branch master
in repository guix.

commit f6e9976393c80d12b5f3235bf7fe593077cbc9d1
Author: Ricardo Wurmus 
Date:   Mon Oct 8 14:18:48 2018 +0200

gnu: Add r-dnabarcodes.

* gnu/packages/bioconductor.scm (r-dnabarcodes): New variable.
---
 gnu/packages/bioconductor.scm | 27 +++
 1 file changed, 27 insertions(+)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 108f3c3..1b77985 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -886,3 +886,30 @@ Time-Course experiments) analyses 4sU-seq and RNA-seq 
time-course data in
 order to evaluate synthesis, processing and degradation rates and assess via
 modeling the rates that determines changes in mature mRNA levels.")
 (license license:gpl2)))
+
+(define-public r-dnabarcodes
+  (package
+(name "r-dnabarcodes")
+(version "1.10.0")
+(source
+ (origin
+   (method url-fetch)
+   (uri (bioconductor-uri "DNABarcodes" version))
+   (sha256
+(base32
+ "0xhna7f0kr7pp2hqwara5i57m9mdr65shflfxiyw6yy3g90pgb5x"
+(properties `((upstream-name . "DNABarcodes")))
+(build-system r-build-system)
+(propagated-inputs
+ `(("r-bh" ,r-bh)
+   ("r-matrix" ,r-matrix)
+   ("r-rcpp" ,r-rcpp)))
+(home-page "https://bioconductor.org/packages/DNABarcodes";)
+(synopsis "Create and analyze DNA barcodes")
+(description
+ "This package offers tools to create DNA barcode sets capable of
+correcting insertion, deletion, and substitution errors.  Existing barcodes
+can be analyzed regarding their minimal, maximal and average distances between
+barcodes.  Finally, reads that start with a (possibly mutated) barcode can be
+demultiplexed, i.e. assigned to their original reference barcode.")
+(license license:gpl2)))