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authorEfraim Flashner <efraim@flashner.co.il>2017-03-13 23:08:49 +0200
committerEfraim Flashner <efraim@flashner.co.il>2017-03-13 23:08:49 +0200
commit3f9543aee1e49001d0f80542dd71ba73c44787c7 (patch)
tree50ee1bdd53b1e5ec69cb8655f23da79c332dde1e /gnu/packages
parent864a9590ad948df09f2ad6e9e929608a7587a5f7 (diff)
parenta71c863834448e2645518b31b60a96ef488dd761 (diff)
downloadguix-3f9543aee1e49001d0f80542dd71ba73c44787c7.tar
guix-3f9543aee1e49001d0f80542dd71ba73c44787c7.tar.gz
Merge remote-tracking branch 'origin/master' into core-updates
Diffstat (limited to 'gnu/packages')
-rw-r--r--gnu/packages/admin.scm5
-rw-r--r--gnu/packages/backup.scm33
-rw-r--r--gnu/packages/bioinformatics.scm143
-rw-r--r--gnu/packages/certs.scm62
-rw-r--r--gnu/packages/ci.scm6
-rw-r--r--gnu/packages/compression.scm27
-rw-r--r--gnu/packages/emacs.scm39
-rw-r--r--gnu/packages/fonts.scm64
-rw-r--r--gnu/packages/fpga.scm5
-rw-r--r--gnu/packages/games.scm8
-rw-r--r--gnu/packages/gnupg.scm4
-rw-r--r--gnu/packages/gnuzilla.scm95
-rw-r--r--gnu/packages/guile.scm5
-rw-r--r--gnu/packages/haskell.scm18
-rw-r--r--gnu/packages/ibus.scm8
-rw-r--r--gnu/packages/imagemagick.scm6
-rw-r--r--gnu/packages/irc.scm4
-rw-r--r--gnu/packages/kde-frameworks.scm50
-rw-r--r--gnu/packages/ldc.scm4
-rw-r--r--gnu/packages/linux.scm22
-rw-r--r--gnu/packages/lisp.scm14
-rw-r--r--gnu/packages/mail.scm21
-rw-r--r--gnu/packages/maths.scm5
-rw-r--r--gnu/packages/messaging.scm4
-rw-r--r--gnu/packages/package-management.scm4
-rw-r--r--gnu/packages/patches/hmmer-remove-cpu-specificity.patch22
-rw-r--r--gnu/packages/patches/python-pandas-skip-failing-tests.patch44
-rw-r--r--gnu/packages/patches/wget-CVE-2017-6508.patch45
-rw-r--r--gnu/packages/python.scm194
-rw-r--r--gnu/packages/regex.scm14
-rw-r--r--gnu/packages/statistics.scm677
-rw-r--r--gnu/packages/video.scm4
-rw-r--r--gnu/packages/web.scm7
-rw-r--r--gnu/packages/wget.scm2
-rw-r--r--gnu/packages/wine.scm9
-rw-r--r--gnu/packages/xorg.scm14
36 files changed, 1511 insertions, 177 deletions
diff --git a/gnu/packages/admin.scm b/gnu/packages/admin.scm
index 3d9226299b..34f6c222ce 100644
--- a/gnu/packages/admin.scm
+++ b/gnu/packages/admin.scm
@@ -257,7 +257,10 @@ re-executing them as necessary.")
"05n65k4ixl85dc6rxc51b1b732gnmm8xnqi424dy9f1nz7ppb3xy"))))
(build-system gnu-build-system)
(arguments
- '(#:configure-flags '("--localstatedir=/var")))
+ '(#:configure-flags '("--localstatedir=/var")
+ ;; On some systems, 'libls.sh' may fail with an error such as:
+ ;; "Failed to tell switch -a apart from -A".
+ #:parallel-tests? #f))
(inputs `(("ncurses" ,ncurses)
("readline" ,readline))) ;for 'ftp'
(native-inputs `(("netstat" ,net-tools))) ;for tests
diff --git a/gnu/packages/backup.scm b/gnu/packages/backup.scm
index 923b0ba9ed..9e20b9f033 100644
--- a/gnu/packages/backup.scm
+++ b/gnu/packages/backup.scm
@@ -4,6 +4,7 @@
;;; Copyright © 2015, 2016 Leo Famulari <leo@famulari.name>
;;; Copyright © 2017 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2017 Thomas Danckaert <post@thomasdanckaert.be>
+;;; Copyright © 2017 Arun Isaac <arunisaac@systemreboot.net>
;;;
;;; This file is part of GNU Guix.
;;;
@@ -622,3 +623,35 @@ NTFS volumes using @code{ntfs-3g}, preserving NTFS-specific attributes.")
(license (list license:gpl3+
license:lgpl3+
license:cc0))))
+
+(define-public obnam
+ (package
+ (name "obnam")
+ (version "1.21")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append
+ "http://code.liw.fi/debian/pool/main/o/obnam/obnam_"
+ version ".orig.tar.xz"))
+ (sha256
+ (base32
+ "0qlipsq50hca71zc0dp1mg9zs12qm0sbblw7qfzl0hj6mk2rv1by"))))
+ (build-system python-build-system)
+ (arguments
+ `(#:python ,python-2))
+ (inputs
+ `(("python2-cliapp" ,python2-cliapp)
+ ("python2-larch" ,python2-larch)
+ ("python2-paramiko" ,python2-paramiko)
+ ("python2-pyaml" ,python2-pyaml)
+ ("python2-tracing" ,python2-tracing)
+ ("python2-ttystatus" ,python2-ttystatus)))
+ (home-page "https://obnam.org/")
+ (synopsis "Easy and secure backup program")
+ (description "Obnam is an easy, secure backup program. Features
+include snapshot backups, data de-duplication and encrypted backups
+using GnuPG. Backups can be stored on local hard disks, or online via
+the SSH SFTP protocol. The backup server, if used, does not require
+any special software, on top of SSH.")
+ (license license:gpl3+)))
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 7bf39c6b03..770bea7e32 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -63,6 +63,7 @@
#:use-module (gnu packages image)
#:use-module (gnu packages imagemagick)
#:use-module (gnu packages java)
+ #:use-module (gnu packages ldc)
#:use-module (gnu packages linux)
#:use-module (gnu packages logging)
#:use-module (gnu packages machine-learning)
@@ -95,6 +96,28 @@
#:use-module (gnu packages zip)
#:use-module (srfi srfi-1))
+(define-public r-ape
+ (package
+ (name "r-ape")
+ (version "4.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "ape" version))
+ (sha256
+ (base32
+ "0959fiiy11rzfzrzaknmgrx64bhszj02l0ycz79k5a6bmpfzanlk"))))
+ (build-system r-build-system)
+ (home-page "http://ape-package.ird.fr/")
+ (synopsis "Analyses of phylogenetics and evolution")
+ (description
+ "This package provides functions for reading, writing, plotting, and
+manipulating phylogenetic trees, analyses of comparative data in a
+phylogenetic framework, ancestral character analyses, analyses of
+diversification and macroevolution, computing distances from DNA sequences,
+and several other tools.")
+ (license license:gpl2+)))
+
(define-public aragorn
(package
(name "aragorn")
@@ -2838,15 +2861,17 @@ indexing scheme is called a @dfn{Hierarchical Graph FM index} (HGFM).")
(package
(name "hmmer")
(version "3.1b2")
- (source (origin
- (method url-fetch)
- (uri (string-append
- "http://eddylab.org/software/hmmer"
- (version-prefix version 1) "/"
- version "/hmmer-" version ".tar.gz"))
- (sha256
- (base32
- "0djmgc0pfli0jilfx8hql1axhwhqxqb8rxg2r5rg07aw73sfs5nx"))))
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append
+ "http://eddylab.org/software/hmmer"
+ (version-prefix version 1) "/"
+ version "/hmmer-" version ".tar.gz"))
+ (sha256
+ (base32
+ "0djmgc0pfli0jilfx8hql1axhwhqxqb8rxg2r5rg07aw73sfs5nx"))
+ (patches (search-patches "hmmer-remove-cpu-specificity.patch"))))
(build-system gnu-build-system)
(native-inputs `(("perl" ,perl)))
(home-page "http://hmmer.org/")
@@ -5741,7 +5766,7 @@ track. The database is exposed as a @code{TxDb} object.")
(define-public vsearch
(package
(name "vsearch")
- (version "2.4.0")
+ (version "2.4.2")
(source
(origin
(method url-fetch)
@@ -5751,7 +5776,7 @@ track. The database is exposed as a @code{TxDb} object.")
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
- "007q9a50hdw4vs2iajabvbw7qccml4r8cbqzyi5ipkkf42jk3vnr"))
+ "15zy2d9xvgbgdjlxvrhj8s5ga42p13k7a3xv015ingn0bi1p3n6w"))
(patches (search-patches "vsearch-unbundle-cityhash.patch"))
(snippet
'(begin
@@ -8574,3 +8599,99 @@ identifications while not exceeding a specified false discovery rate. It also
contains a number of utilities to explore the MS/MS results and assess missed
and irregular enzymatic cleavages, mass measurement accuracy, etc.")
(license license:artistic2.0)))
+
+(define htslib-for-sambamba
+ (let ((commit "2f3c3ea7b301f9b45737a793c0b2dcf0240e5ee5"))
+ (package
+ (inherit htslib)
+ (name "htslib-for-sambamba")
+ (version (string-append "1.3.1-1." (string-take commit 9)))
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/lomereiter/htslib.git")
+ (commit commit)))
+ (file-name (string-append "htslib-" version "-checkout"))
+ (sha256
+ (base32
+ "0g38g8s3npr0gjm9fahlbhiskyfws9l5i0x1ml3rakzj7az5l9c9"))))
+ (arguments
+ (substitute-keyword-arguments (package-arguments htslib)
+ ((#:phases phases)
+ `(modify-phases ,phases
+ (add-before 'configure 'bootstrap
+ (lambda _
+ (zero? (system* "autoreconf" "-vif"))))))))
+ (native-inputs
+ `(("autoconf" ,autoconf)
+ ("automake" ,automake)
+ ,@(package-native-inputs htslib))))))
+
+(define-public sambamba
+ (package
+ (name "sambamba")
+ (version "0.6.5")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "https://github.com/lomereiter/sambamba/"
+ "archive/v" version ".tar.gz"))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "17076gijd65a3f07zns2gvbgahiz5lriwsa6dq353ss3jl85d8vy"))))
+ (build-system gnu-build-system)
+ (arguments
+ `(#:tests? #f ; there is no test target
+ #:make-flags
+ '("D_COMPILER=ldc2"
+ ;; Override "--compiler" flag only.
+ "D_FLAGS=--compiler=ldc2 -IBioD -g -d"
+ "sambamba-ldmd2-64")
+ #:phases
+ (modify-phases %standard-phases
+ (delete 'configure)
+ (add-after 'unpack 'place-biod
+ (lambda* (#:key inputs #:allow-other-keys)
+ (copy-recursively (assoc-ref inputs "biod") "BioD")
+ #t))
+ (add-after 'unpack 'unbundle-prerequisites
+ (lambda _
+ (substitute* "Makefile"
+ ((" htslib-static lz4-static") ""))
+ #t))
+ (replace 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let* ((out (assoc-ref outputs "out"))
+ (bin (string-append out "/bin")))
+ (mkdir-p bin)
+ (install-file "build/sambamba" bin)
+ #t))))))
+ (native-inputs
+ `(("ldc" ,ldc)
+ ("rdmd" ,rdmd)
+ ("biod"
+ ,(let ((commit "1248586b54af4bd4dfb28ebfebfc6bf012e7a587"))
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/biod/BioD.git")
+ (commit commit)))
+ (file-name (string-append "biod-"
+ (string-take commit 9)
+ "-checkout"))
+ (sha256
+ (base32
+ "1m8hi1n7x0ri4l6s9i0x6jg4z4v94xrfdzp7mbizdipfag0m17g3")))))))
+ (inputs
+ `(("lz4" ,lz4)
+ ("htslib" ,htslib-for-sambamba)))
+ (home-page "http://lomereiter.github.io/sambamba")
+ (synopsis "Tools for working with SAM/BAM data")
+ (description "Sambamba is a high performance modern robust and
+fast tool (and library), written in the D programming language, for
+working with SAM and BAM files. Current parallelised functionality is
+an important subset of samtools functionality, including view, index,
+sort, markdup, and depth.")
+ (license license:gpl2+)))
diff --git a/gnu/packages/certs.scm b/gnu/packages/certs.scm
index 246e5ca14a..7f5c5b793f 100644
--- a/gnu/packages/certs.scm
+++ b/gnu/packages/certs.scm
@@ -2,6 +2,7 @@
;;; Copyright © 2015 Andreas Enge <andreas@enge.fr>
;;; Copyright © 2015 Mark H Weaver <mhw@netris.org>
;;; Copyright © 2016 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2017 Leo Famulari <leo@famulari.name>
;;;
;;; This file is part of GNU Guix.
;;;
@@ -73,7 +74,7 @@
(define-public nss-certs
(package
(name "nss-certs")
- (version "3.29.2")
+ (version "3.29.3")
(source (origin
(method url-fetch)
(uri (let ((version-with-underscores
@@ -84,7 +85,7 @@
"nss-" version ".tar.gz")))
(sha256
(base32
- "149807rmzb76hnh48rw4m9jw83iw0168njzchz0hmbsgc8mk0i5w"))))
+ "1sz1r2iml9bhd4iqiqz75gii855a25895vpy9scjky0y4lqwrp9m"))))
(build-system gnu-build-system)
(outputs '("out"))
(native-inputs
@@ -139,3 +140,60 @@
taken from the NSS package and thus ultimately from the Mozilla project.")
(home-page "https://developer.mozilla.org/en-US/docs/Mozilla/Projects/NSS")
(license license:mpl2.0)))
+
+(define-public le-certs
+ (package
+ (name "le-certs")
+ (version "0")
+ (source #f)
+ (build-system trivial-build-system)
+ (arguments
+ '(#:modules ((guix build utils))
+ #:builder
+ (begin
+ (use-modules (guix build utils))
+ (let ((root (assoc-ref %build-inputs "isrgrootx1.pem"))
+ (intermediate (assoc-ref %build-inputs "letsencryptauthorityx3.pem"))
+ (backup (assoc-ref %build-inputs "letsencryptauthorityx4.pem"))
+ (out (string-append (assoc-ref %outputs "out") "/etc/ssl/certs")))
+ (mkdir-p out)
+ (for-each
+ (lambda (cert)
+ (copy-file cert (string-append out "/"
+ (strip-store-file-name cert))))
+ (list root intermediate backup))))))
+ (inputs
+ `(; The Let's Encrypt root certificate, "ISRG Root X1".
+ ("isrgrootx1.pem"
+ ,(origin
+ (method url-fetch)
+ (uri "https://letsencrypt.org/certs/isrgrootx1.pem")
+ (sha256
+ (base32
+ "0zhd1ps7sz4w1x52xk3v7ng6d0rcyi7y7rcrplwkmilnq5hzjv1y"))))
+ ;; "Let’s Encrypt Authority X3", the active Let's Encrypt intermediate
+ ;; certificate.
+ ("letsencryptauthorityx3.pem"
+ ,(origin
+ (method url-fetch)
+ (uri "https://letsencrypt.org/certs/letsencryptauthorityx3.pem")
+ (sha256
+ (base32
+ "0zbamj6c7zqw1j9mbqygc8k1ykgj6xiisp9svmlif5lkbnyjhnkk"))))
+ ;; "Let’s Encrypt Authority X4", the backup Let's Encrypt intermediate
+ ;; certificate. This will be used for disaster recovery and will only be
+ ;; used should Let's Encrypt lose the ability to issue with "Let’s
+ ;; Encrypt Authority X3".
+ ("letsencryptauthorityx4.pem"
+ ,(origin
+ (method url-fetch)
+ (uri "https://letsencrypt.org/certs/letsencryptauthorityx4.pem")
+ (sha256
+ (base32
+ "003dc94c8qwj634h0dq743x7hqv9rdcfaisdksprkmi2jd107xq4"))))))
+ (home-page "https://letsencrypt.org/certificates/")
+ (synopsis "Let's Encrypt root and intermediate certificates")
+ (description "This package provides a certificate store containing only the
+Let's Encrypt root and intermediate certificates. It is intended to be used
+within Guix.")
+ (license license:public-domain)))
diff --git a/gnu/packages/ci.scm b/gnu/packages/ci.scm
index c25bc389c0..ae91464a18 100644
--- a/gnu/packages/ci.scm
+++ b/gnu/packages/ci.scm
@@ -187,8 +187,8 @@ their dependencies.")
(license l:gpl3+))))
(define-public cuirass
- (let ((commit "f695c79eb3b93a0432901844c8ede16de39b8d07")
- (revision "4"))
+ (let ((commit "8c811abb3174b44601b8996a1fe1718f37d7bd14")
+ (revision "5"))
(package
(name "cuirass")
(version (string-append "0.0.1-" revision "." (string-take commit 7)))
@@ -200,7 +200,7 @@ their dependencies.")
(file-name (string-append name "-" version))
(sha256
(base32
- "1zsj3l85d8jq7h9a0zfb2w5pyvlwkirgvis4bv60syhbpblfvmri"))))
+ "0kz2ys01xlmxagsfr9qf3p212vm31wfl76rvxa7ii5804aidlz5n"))))
(build-system gnu-build-system)
(arguments
'(#:phases
diff --git a/gnu/packages/compression.scm b/gnu/packages/compression.scm
index 4e6a248e8e..dbc4795d02 100644
--- a/gnu/packages/compression.scm
+++ b/gnu/packages/compression.scm
@@ -97,6 +97,33 @@ independent of the input data and can be reduced, if necessary, at some cost
in compression.")
(license license:zlib)))
+(define-public minizip
+ (package
+ (name "minizip")
+ (version (package-version zlib))
+ (source (package-source zlib))
+ (build-system gnu-build-system)
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'enter-source
+ (lambda _ (chdir "contrib/minizip") #t))
+ (add-before 'configure 'autoreconf
+ (lambda _
+ (zero? (system* "autoreconf" "-vif")))))))
+ (native-inputs
+ `(("autoconf" ,autoconf)
+ ("automake" ,automake)
+ ("libtool" ,libtool)))
+ (propagated-inputs `(("zlib" ,zlib)))
+ (home-page (package-home-page zlib))
+ (synopsis "Zip Compression library")
+ (description
+ "Minizip is a minimalistic library that supports compressing,
+extracting and viewing ZIP archives. This version is extracted from
+the @code{zlib} source.")
+ (license (package-license zlib))))
+
(define-public fastjar
(package
(name "fastjar")
diff --git a/gnu/packages/emacs.scm b/gnu/packages/emacs.scm
index 1daf8e4e68..3db5527e60 100644
--- a/gnu/packages/emacs.scm
+++ b/gnu/packages/emacs.scm
@@ -16,7 +16,7 @@
;;; Copyright © 2016 Alex Griffin <a@ajgrf.com>
;;; Copyright © 2016, 2017 Nicolas Goaziou <mail@nicolasgoaziou.fr>
;;; Copyright © 2016 Alex Vong <alexvong1995@gmail.com>
-;;; Copyright © 2016 Arun Isaac <arunisaac@systemreboot.net>
+;;; Copyright © 2016, 2017 Arun Isaac <arunisaac@systemreboot.net>
;;; Copyright © 2017 Christopher Baines <mail@cbaines.net>
;;; Copyright © 2017 Mathieu Othacehe <m.othacehe@gmail.com>
;;; Copyright © 2017 Clément Lassieur <clement@lassieur.org>
@@ -366,7 +366,7 @@ when typing parentheses directly or commenting out code line by line.")
(define-public git-modes
(package
(name "git-modes")
- (version "1.2.2")
+ (version "1.2.4")
(source (origin
(method url-fetch)
(uri (string-append
@@ -375,7 +375,7 @@ when typing parentheses directly or commenting out code line by line.")
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
- "0gb9c18jib8rpm14vig9774104lwmd8353ps0259m861syf6664d"))))
+ "0xxrmf0jnyljxvllc22qa0v8lgi4k1ldnayjm5hf68m25jsr378l"))))
(build-system gnu-build-system)
(arguments
`(#:modules ((guix build gnu-build-system)
@@ -436,7 +436,7 @@ on stdout instead of using a socket as the Emacsclient does.")
(define-public magit
(package
(name "magit")
- (version "2.10.2")
+ (version "2.10.3")
(source (origin
(method url-fetch)
(uri (string-append
@@ -444,7 +444,7 @@ on stdout instead of using a socket as the Emacsclient does.")
version "/" name "-" version ".tar.gz"))
(sha256
(base32
- "09qcc3a61irxi89x7q82hdy8dk0liiwyz66632wzcd881mhrhx18"))))
+ "03ln65ss420gc3h4pi56dayd1p163xfxrxrd9fkb9xnkl8mjglqk"))))
(build-system gnu-build-system)
(native-inputs `(("texinfo" ,texinfo)
("emacs" ,emacs-minimal)))
@@ -3852,3 +3852,32 @@ mode-line.")
"YASnippet is a template system for Emacs. It allows you to type an
abbreviation and automatically expand it into function templates.")
(license license:gpl3+)))
+
+(define-public emacs-memoize
+ (package
+ (name "emacs-memoize")
+ (version "20130421.b55eab0")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/skeeto/emacs-memoize")
+ (commit "b55eab0cb6ab05d941e07b8c01f1655c0cf1dd75")))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "0fjwlrdm270qcrqffvarw5yhijk656q4lam79ybhaznzj0dq3xpw"))))
+ (build-system emacs-build-system)
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (add-before 'install 'check
+ (lambda _
+ (zero? (system* "emacs" "-batch" "-l" "memoize.el"
+ "-l" "memoize-test.el"
+ "-f" "ert-run-tests-batch-and-exit")))))))
+ (home-page "https://github.com/skeeto/emacs-memoize")
+ (synopsis "Emacs lisp memoization library")
+ (description "@code{emacs-memoize} is an Emacs library for
+memoizing functions.")
+ (license license:unlicense)))
diff --git a/gnu/packages/fonts.scm b/gnu/packages/fonts.scm
index ce07accbf2..1f01ad6ad0 100644
--- a/gnu/packages/fonts.scm
+++ b/gnu/packages/fonts.scm
@@ -1035,6 +1035,70 @@ designed to work well in user interface environments.")
vector graphics.")
(license license:silofl1.1)))
+(define-public font-tamzen
+ (package
+ (name "font-tamzen")
+ (version "1.11.4")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "https://github.com/sunaku/tamzen-font/archive/"
+ "Tamzen-" version ".tar.gz"))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "1ryd7gp6qiwaqw73jqbmh4kwlriyd8xykh4j7z90z8xp9fm7lrys"))))
+ (build-system trivial-build-system)
+ (arguments
+ `(#:modules ((guix build utils))
+ #:builder
+ (begin
+ (use-modules (guix build utils))
+
+ (let ((tar (string-append (assoc-ref %build-inputs "tar")
+ "/bin/tar"))
+ (PATH (string-append (assoc-ref %build-inputs "gzip")
+ "/bin"))
+ (font-dir (string-append %output "/share/fonts/misc"))
+ (psf-dir (string-append %output "/share/kbd/consolefonts"))
+ (src-pcf-dir (string-append "tamzen-font-Tamzen-"
+ ,version "/pcf")))
+ (setenv "PATH" PATH)
+ (system* tar "xvf" (assoc-ref %build-inputs "source"))
+ (mkdir-p font-dir)
+ (mkdir-p psf-dir)
+ (chdir src-pcf-dir)
+ (for-each (lambda (pcf)
+ (install-file pcf font-dir))
+ (find-files "." "\\.pcf$"))
+ (chdir "../psf")
+ (for-each (lambda (psf)
+ (install-file psf psf-dir))
+ (find-files "." "\\.psf$"))
+ #t))))
+ (native-inputs
+ `(("tar" ,tar)
+ ("gzip" ,gzip)))
+ (home-page "https://github.com/sunaku/tamzen-font")
+ (synopsis "Monospaced bitmap font for console and X11")
+ (description
+ "Tamzen is a fork of the @code{Tamsyn} font. It is programatically forked
+from @code{Tamsyn} version 1.11, backporting glyphs from older versions while
+deleting deliberately empty glyphs (which are marked as unimplemented) to
+allow secondary/fallback fonts to provide real glyphs at those codepoints.
+
+The @code{TamzenForPowerline} fonts provide additional @code{Powerline} symbols,
+which are programatically injected with @code{bitmap-font-patcher} and
+later hand-tweaked with the gbdfed(1) editor:
+
+@enumerate
+@item all icons are expanded to occupy the maximum available space
+@item the branch of the fork icon ( U+E0A0) was made larger than the trunk
+@item for the newline icon ( U+E0A1), the @emph{N} was made larger at the bottom
+@item the keyhole in the padlock icon ( U+E0A2) was replaced with @emph{//} lines.
+@end enumerate\n")
+ (license (license:non-copyleft "file://LICENSE"))))
+
(define-public font-comic-neue
(package
(name "font-comic-neue")
diff --git a/gnu/packages/fpga.scm b/gnu/packages/fpga.scm
index f65eae8673..0b98e2db0d 100644
--- a/gnu/packages/fpga.scm
+++ b/gnu/packages/fpga.scm
@@ -231,6 +231,11 @@ For synthesis, the compiler generates netlists in the desired format.")
(("-I/usr/local/include") "")
(("-L/usr/local/lib") ""))
#t))
+ (add-after 'remove-usr-local 'fix-usr-local
+ (lambda* (#:key outputs #:allow-other-keys)
+ (substitute* "icebox/icebox_vlog.py"
+ (("/usr/local/share") (string-append (assoc-ref outputs "out") "/share")))
+ #t))
(delete 'configure))))
(inputs
`(("libftdi" ,libftdi)))
diff --git a/gnu/packages/games.scm b/gnu/packages/games.scm
index 550652eefd..1ce18658d0 100644
--- a/gnu/packages/games.scm
+++ b/gnu/packages/games.scm
@@ -1349,7 +1349,7 @@ is programmed in Haskell.")
(define-public manaplus
(package
(name "manaplus")
- (version "1.7.1.21")
+ (version "1.7.3.4")
(source (origin
(method url-fetch)
(uri (string-append
@@ -1357,7 +1357,7 @@ is programmed in Haskell.")
version "/manaplus-" version ".tar.xz"))
(sha256
(base32
- "0q9hk9jgz5jja1mmba5iafxwavk6991kjpmdxdkgbam0hk15pqmz"))))
+ "0mbxzsgjg16pqa3jnxkd7wwvw1lrx455r7fvwjfhzp0yv7acrn10"))))
(build-system gnu-build-system)
(arguments
'(#:configure-flags
@@ -2880,8 +2880,8 @@ the GNU GPL.")
(version "2.01.2")
(source (origin
(method url-fetch)
- (uri (string-append "https://sourceforge.net/projects/tintin"
- "/files/TinTin++ Source Code/" version
+ (uri (string-append "mirror://sourceforge/tintin"
+ "/TinTin++ Source Code/" version
"/tintin" "-" version ".tar.gz"))
(sha256
(base32
diff --git a/gnu/packages/gnupg.scm b/gnu/packages/gnupg.scm
index 1b59cf7ecf..532dbf88f7 100644
--- a/gnu/packages/gnupg.scm
+++ b/gnu/packages/gnupg.scm
@@ -519,7 +519,7 @@ and signature functionality from Python programs.")
(define-public pius
(package
(name "pius")
- (version "2.2.3")
+ (version "2.2.4")
(source (origin
(method url-fetch)
(uri (string-append
@@ -527,7 +527,7 @@ and signature functionality from Python programs.")
version "/pius-" version ".tar.bz2"))
(sha256
(base32
- "0iy0gnms6lv9hpvk29313kc495a2f7pq2mg6ljxhy233vxsmjsk6"))))
+ "0lgc0ipwdfqbq16zax8kn17wbv8xyw4ygc09fawl2yp459z0ql4n"))))
(build-system python-build-system)
(inputs `(("perl" ,perl) ;for 'pius-party-worksheet'
("gpg" ,gnupg)))
diff --git a/gnu/packages/gnuzilla.scm b/gnu/packages/gnuzilla.scm
index e6e24f6650..55dfda4948 100644
--- a/gnu/packages/gnuzilla.scm
+++ b/gnu/packages/gnuzilla.scm
@@ -186,7 +186,7 @@ in the Mozilla clients.")
(define-public nss
(package
(name "nss")
- (version "3.29.2")
+ (version "3.29.3")
(source (origin
(method url-fetch)
(uri (let ((version-with-underscores
@@ -197,7 +197,7 @@ in the Mozilla clients.")
"nss-" version ".tar.gz")))
(sha256
(base32
- "149807rmzb76hnh48rw4m9jw83iw0168njzchz0hmbsgc8mk0i5w"))
+ "1sz1r2iml9bhd4iqiqz75gii855a25895vpy9scjky0y4lqwrp9m"))
;; Create nss.pc and nss-config.
(patches (search-patches "nss-pkgconfig.patch"))))
(build-system gnu-build-system)
@@ -221,55 +221,52 @@ in the Mozilla clients.")
(ice-9 match)
(srfi srfi-26))
#:phases
- (alist-replace
- 'configure
- (lambda* (#:key system inputs #:allow-other-keys)
- (setenv "CC" "gcc")
- ;; Tells NSS to build for the 64-bit ABI if we are 64-bit system.
- (when (string-prefix? "x86_64" system)
- (setenv "USE_64" "1"))
- #t)
- (alist-replace
- 'check
- (lambda _
- ;; Use 127.0.0.1 instead of $HOST.$DOMSUF as HOSTADDR for testing.
- ;; The later requires a working DNS or /etc/hosts.
- (setenv "DOMSUF" "(none)")
- (setenv "USE_IP" "TRUE")
- (setenv "IP_ADDRESS" "127.0.0.1")
- (zero? (system* "./nss/tests/all.sh")))
- (alist-replace
- 'install
- (lambda* (#:key outputs #:allow-other-keys)
- (let* ((out (assoc-ref outputs "out"))
- (bin (string-append (assoc-ref outputs "bin") "/bin"))
- (inc (string-append out "/include/nss"))
- (lib (string-append out "/lib/nss"))
- (obj (match (scandir "dist" (cut string-suffix? "OBJ" <>))
- ((obj) (string-append "dist/" obj)))))
- ;; Install nss-config to $out/bin.
- (install-file (string-append obj "/bin/nss-config")
- (string-append out "/bin"))
- (delete-file (string-append obj "/bin/nss-config"))
- ;; Install nss.pc to $out/lib/pkgconfig.
- (install-file (string-append obj "/lib/pkgconfig/nss.pc")
- (string-append out "/lib/pkgconfig"))
- (delete-file (string-append obj "/lib/pkgconfig/nss.pc"))
- (rmdir (string-append obj "/lib/pkgconfig"))
- ;; Install other files.
- (copy-recursively "dist/public/nss" inc)
- (copy-recursively (string-append obj "/bin") bin)
- (copy-recursively (string-append obj "/lib") lib)
+ (modify-phases %standard-phases
+ (replace 'configure
+ (lambda* (#:key system inputs #:allow-other-keys)
+ (setenv "CC" "gcc")
+ ;; Tells NSS to build for the 64-bit ABI if we are 64-bit system.
+ (when (string-prefix? "x86_64" system)
+ (setenv "USE_64" "1"))
+ #t))
+ (replace 'check
+ (lambda _
+ ;; Use 127.0.0.1 instead of $HOST.$DOMSUF as HOSTADDR for testing.
+ ;; The later requires a working DNS or /etc/hosts.
+ (setenv "DOMSUF" "(none)")
+ (setenv "USE_IP" "TRUE")
+ (setenv "IP_ADDRESS" "127.0.0.1")
+ (zero? (system* "./nss/tests/all.sh"))))
+ (replace 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let* ((out (assoc-ref outputs "out"))
+ (bin (string-append (assoc-ref outputs "bin") "/bin"))
+ (inc (string-append out "/include/nss"))
+ (lib (string-append out "/lib/nss"))
+ (obj (match (scandir "dist" (cut string-suffix? "OBJ" <>))
+ ((obj) (string-append "dist/" obj)))))
+ ;; Install nss-config to $out/bin.
+ (install-file (string-append obj "/bin/nss-config")
+ (string-append out "/bin"))
+ (delete-file (string-append obj "/bin/nss-config"))
+ ;; Install nss.pc to $out/lib/pkgconfig.
+ (install-file (string-append obj "/lib/pkgconfig/nss.pc")
+ (string-append out "/lib/pkgconfig"))
+ (delete-file (string-append obj "/lib/pkgconfig/nss.pc"))
+ (rmdir (string-append obj "/lib/pkgconfig"))
+ ;; Install other files.
+ (copy-recursively "dist/public/nss" inc)
+ (copy-recursively (string-append obj "/bin") bin)
+ (copy-recursively (string-append obj "/lib") lib)
- ;; FIXME: libgtest1.so is installed in the above step, and it's
- ;; (unnecessarily) linked with several NSS libraries, but
- ;; without the needed rpaths, causing the 'validate-runpath'
- ;; phase to fail. Here we simply delete libgtest1.so, since it
- ;; seems to be used only during the tests.
- (delete-file (string-append lib "/libgtest1.so"))
+ ;; FIXME: libgtest1.so is installed in the above step, and it's
+ ;; (unnecessarily) linked with several NSS libraries, but
+ ;; without the needed rpaths, causing the 'validate-runpath'
+ ;; phase to fail. Here we simply delete libgtest1.so, since it
+ ;; seems to be used only during the tests.
+ (delete-file (string-append lib "/libgtest1.so"))
- #t))
- %standard-phases)))))
+ #t))))))
(inputs
`(("sqlite" ,sqlite)
("zlib" ,zlib)))
diff --git a/gnu/packages/guile.scm b/gnu/packages/guile.scm
index 8fdd85add9..13ff0e069a 100644
--- a/gnu/packages/guile.scm
+++ b/gnu/packages/guile.scm
@@ -220,7 +220,7 @@ without requiring the source code to be rewritten.")
(define-public guile-next
(package (inherit guile-2.0)
(name "guile-next")
- (version "2.1.7")
+ (version "2.1.8")
(replacement #f)
(source (origin
(method url-fetch)
@@ -228,7 +228,7 @@ without requiring the source code to be rewritten.")
version ".tar.xz"))
(sha256
(base32
- "0qf2664bglv5rrj4c99cc7gry7v9x0sqdyzgfg8zi8gm5wbcmqda"))
+ "0rh9vahqqwbyj79p1lc9pljkgxg8rczczf074dr8wl13j5h0y27m"))
(modules '((guix build utils)))
;; Remove the pre-built object files. Instead, build everything
@@ -238,6 +238,7 @@ without requiring the source code to be rewritten.")
(find-files "prebuilt" "\\.go$")))))
(synopsis "Snapshot of what will become version 2.2 of GNU Guile")
(properties '((timeout . 72000) ;20 hours
+ (max-silent-time . 10800) ;3 hours (needed on ARM)
(upstream-name . "guile")
(ftp-server . "alpha.gnu.org")
(ftp-directory . "/gnu/guile")))
diff --git a/gnu/packages/haskell.scm b/gnu/packages/haskell.scm
index d0f659f6e3..2415881e8e 100644
--- a/gnu/packages/haskell.scm
+++ b/gnu/packages/haskell.scm
@@ -8194,4 +8194,22 @@ or filter messages based on the priority and source. It also has a syslog
handler built in.")
(license license:bsd-3)))
+(define-public ghc-unexceptionalio
+ (package
+ (name "ghc-unexceptionalio")
+ (version "0.3.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "https://hackage.haskell.org/package/"
+ "unexceptionalio-" version "/" "unexceptionalio-"
+ version ".tar.gz"))
+ (sha256 (base32 "1f7h7zwky4scdcyjspg4ksfh7x6yra0wjybxq70p7vcwpgk2nzlj"))))
+ (build-system haskell-build-system)
+ (home-page "https://github.com/singpolyma/unexceptionalio")
+ (synopsis "IO without any non-error, synchronous exceptions")
+ (description "When you've caught all the exceptions that can be
+handled safely, this is what you're left with.")
+ (license license:isc)))
+
;;; haskell.scm ends here
diff --git a/gnu/packages/ibus.scm b/gnu/packages/ibus.scm
index d441485296..6c5537579e 100644
--- a/gnu/packages/ibus.scm
+++ b/gnu/packages/ibus.scm
@@ -42,7 +42,7 @@
(define-public ibus
(package
(name "ibus")
- (version "1.5.14")
+ (version "1.5.15")
(source (origin
(method url-fetch)
(uri (string-append "https://github.com/ibus/ibus/"
@@ -50,7 +50,7 @@
version "/ibus-" version ".tar.gz"))
(sha256
(base32
- "0g4x02d7j5w1lfn4zvmzsq93h17lajgn9d7hlvr6pws28vz40ax4"))))
+ "11g3jf6dgvmszvpgpva0y587kr0sffl79xmymvghrb1sdynvmxs1"))))
(build-system glib-or-gtk-build-system)
(arguments
`(#:tests? #f ; tests fail because there's no connection to dbus
@@ -237,7 +237,7 @@ Chinese pinyin input methods.")
(define-public ibus-anthy
(package
(name "ibus-anthy")
- (version "1.5.8")
+ (version "1.5.9")
(source (origin
(method url-fetch)
(uri (string-append
@@ -245,7 +245,7 @@ Chinese pinyin input methods.")
version "/ibus-anthy-" version ".tar.gz"))
(sha256
(base32
- "1aj7vnfky7izl23xyjky78z3qas3q72l3kr8dnql2lnivsrb8q1y"))))
+ "1y8sf837rmp662bv6zakny0xcm7c9c5qda7f9kq9riv9ywpcbw6x"))))
(build-system gnu-build-system)
(arguments
'(#:configure-flags
diff --git a/gnu/packages/imagemagick.scm b/gnu/packages/imagemagick.scm
index 74483965dd..73496ccfc0 100644
--- a/gnu/packages/imagemagick.scm
+++ b/gnu/packages/imagemagick.scm
@@ -46,14 +46,14 @@
;; The 7 release series has an incompatible API, while the 6 series is still
;; maintained. Don't update to 7 until we've made sure that the ImageMagick
;; users are ready for the 7-series API.
- (version "6.9.7-9")
+ (version "6.9.7-10")
(source (origin
(method url-fetch)
(uri (string-append "mirror://imagemagick/ImageMagick-"
version ".tar.xz"))
(sha256
(base32
- "1fqvi6h96mfbyw292awiwsqs449sjmw6i9ib53c66nnq1zchw7l3"))))
+ "02gvxz1xap5nm1vrgjxhkx13q6ja06vf23n28nc6cfdpb4s2xyqb"))))
(build-system gnu-build-system)
(arguments
`(#:configure-flags '("--with-frozenpaths" "--without-gcc-arch")
@@ -187,6 +187,8 @@ script.")
(list "--with-frozenpaths"
"--enable-shared=yes"
"--with-x=yes"
+ "--with-quantum-depth=16" ; required by Octave
+ "--enable-quantum-library-names"
(string-append "--with-gs-font-dir="
(assoc-ref %build-inputs "gs-fonts")
"/share/fonts/type1/ghostscript"))))
diff --git a/gnu/packages/irc.scm b/gnu/packages/irc.scm
index 6ba950763b..3d06df9ed8 100644
--- a/gnu/packages/irc.scm
+++ b/gnu/packages/irc.scm
@@ -101,7 +101,7 @@ irssi, but graphical.")
(define-public irssi
(package
(name "irssi")
- (version "1.0.1")
+ (version "1.0.2")
(source (origin
(method url-fetch)
(uri (string-append "https://github.com/irssi/irssi/"
@@ -109,7 +109,7 @@ irssi, but graphical.")
version ".tar.xz"))
(sha256
(base32
- "1krw71n24mj4p3f5nhzj6kdi1kq9ssl53hrqyjpgz61m7wdcaa4l"))))
+ "1sgvfprgrncbxcyg99rkd10kpjzqw00b1ppsfg8al0zirb13q72w"))))
(build-system gnu-build-system)
(arguments
`(#:phases
diff --git a/gnu/packages/kde-frameworks.scm b/gnu/packages/kde-frameworks.scm
index 8bb05453da..7b90c1436b 100644
--- a/gnu/packages/kde-frameworks.scm
+++ b/gnu/packages/kde-frameworks.scm
@@ -3,6 +3,7 @@
;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il>
;;; Copyright © 2016 Hartmut Goebel <h.goebel@crazy-compilers.com>
;;; Copyright © 2016 David Craven <david@craven.ch>
+;;; Copyright © 2017 Thomas Danckaert <post@thomasdanckaert.be>
;;;
;;; This file is part of GNU Guix.
;;;
@@ -42,6 +43,7 @@
#:use-module (gnu packages glib)
#:use-module (gnu packages gnome)
#:use-module (gnu packages gnupg)
+ #:use-module (gnu packages gstreamer)
#:use-module (gnu packages linux)
#:use-module (gnu packages perl)
#:use-module (gnu packages pkg-config)
@@ -119,12 +121,58 @@ common build settings used in software produced by the KDE community.")
(arguments
`(#:configure-flags
'("-DCMAKE_CXX_FLAGS=-fPIC"
- "-DPHONON_BUILD_PHONON4QT5=ON")))
+ "-DPHONON_BUILD_PHONON4QT5=ON"
+ "-DPHONON_INSTALL_QT_EXTENSIONS_INTO_SYSTEM_QT=ON")
+ #:phases
+ (modify-phases %standard-phases
+ (add-before 'install 'patch-installdir
+ (lambda* (#:key inputs outputs #:allow-other-keys)
+ (let ((regex (string-append "(INSTALL DESTINATION \")"
+ (assoc-ref inputs "qtbase"))))
+ (substitute* "cmake_install.cmake"
+ ((regex all dest)
+ (string-append dest (assoc-ref outputs "out")))))
+ #t)))))
(home-page "https://phonon.kde.org")
(synopsis "KDE's multimedia library")
(description "KDE's multimedia library.")
(license license:lgpl2.1+)))
+(define-public phonon-backend-gstreamer
+ (package
+ (name "phonon-backend-gstreamer")
+ (version "4.9.0")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append
+ "mirror://kde/stable/phonon/"
+ name "/" version "/"
+ name "-" version ".tar.xz"))
+ (sha256
+ (base32
+ "1wc5p1rqglf0n1avp55s50k7fjdzdrhg0gind15k8796w7nfbhyf"))))
+ (build-system cmake-build-system)
+ (native-inputs
+ `(("extra-cmake-modules" ,extra-cmake-modules)
+ ("pkg-config" ,pkg-config)))
+ (inputs
+ `(("qtbase" ,qtbase)
+ ("phonon" ,phonon)
+ ("qtbase" ,qtbase)
+ ("qtx11extras" ,qtx11extras)
+ ("gstreamer" ,gstreamer)
+ ("gst-plugins-base" ,gst-plugins-base)
+ ("libxml2" ,libxml2)))
+ (arguments
+ `(#:configure-flags
+ '( "-DPHONON_BUILD_PHONON4QT5=ON")))
+ (home-page "https://phonon.kde.org")
+ (synopsis "Phonon backend which uses GStreamer")
+ (description "Phonon makes use of backend libraries to provide sound.
+Phonon-GStreamer is a backend based on the GStreamer multimedia library.")
+ ;; license: source files mention "either version 2.1 or 3"
+ (license (list license:lgpl2.1 license:lgpl3))))
+
(define-public gpgmepp
(package
(name "gpgmepp")
diff --git a/gnu/packages/ldc.scm b/gnu/packages/ldc.scm
index 614e2d6d0c..fd4d60e8b8 100644
--- a/gnu/packages/ldc.scm
+++ b/gnu/packages/ldc.scm
@@ -276,7 +276,7 @@ latest DMD frontend and uses LLVM as backend.")
(define-public dub
(package
(name "dub")
- (version "1.2.0")
+ (version "1.2.2")
(source (origin
(method url-fetch)
(uri (string-append "https://github.com/dlang/dub/archive/"
@@ -284,7 +284,7 @@ latest DMD frontend and uses LLVM as backend.")
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
- "1sd8i1rvxc7y7kk0y6km5zyvaladc5zh56r6afj74ndd63dssv43"))))
+ "02k11x34nck0lbv13ww103niiswnwnslbnswj3b5faszzadbi1v4"))))
(build-system gnu-build-system)
(arguments
`(#:tests? #f ; it would have tested itself by installing some packages (vibe etc)
diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm
index 53b0f2a678..cd6d32f0fd 100644
--- a/gnu/packages/linux.scm
+++ b/gnu/packages/linux.scm
@@ -348,8 +348,8 @@ It has been modified to remove all non-free binary blobs.")
(define %intel-compatible-systems '("x86_64-linux" "i686-linux"))
-(define %linux-libre-version "4.10.1")
-(define %linux-libre-hash "0mvwrjny1bjqyjqjxff9m97j48ybfdw8qpdazr5rwk12234v4k3d")
+(define %linux-libre-version "4.10.2")
+(define %linux-libre-hash "01kinnv40lqsk6fyz1k7hkx2diyg4mgp28bwraar5sii1gqmcw7k")
(define-public linux-libre
(make-linux-libre %linux-libre-version
@@ -358,14 +358,14 @@ It has been modified to remove all non-free binary blobs.")
#:configuration-file kernel-config))
(define-public linux-libre-4.9
- (make-linux-libre "4.9.13"
- "16miggwcwfpm7kx0yz256x887rky9wgmp1grg850lf8sdkiz0a1p"
+ (make-linux-libre "4.9.14"
+ "104715z772if18qi61jbyhvidfh6qnwkiy0m9aa8irxgzs1pk9mn"
%intel-compatible-systems
#:configuration-file kernel-config))
(define-public linux-libre-4.4
- (make-linux-libre "4.4.52"
- "1fzcq9bbsxiij2fh6kgwrp417sy2j5gnbzs0wwlmznj7mvysl7qg"
+ (make-linux-libre "4.4.53"
+ "07sfg4i506f3hmd9k4iimnq1w3x0980qxnh649d1sldqxbmhdgjs"
%intel-compatible-systems
#:configuration-file kernel-config))
@@ -2764,7 +2764,7 @@ and copy/paste text in the console and in xterm.")
(define-public btrfs-progs
(package
(name "btrfs-progs")
- (version "4.9.1")
+ (version "4.10")
(source (origin
(method url-fetch)
(uri (string-append "mirror://kernel.org/linux/kernel/"
@@ -2772,7 +2772,7 @@ and copy/paste text in the console and in xterm.")
"btrfs-progs-v" version ".tar.xz"))
(sha256
(base32
- "1ppy2y9vypxw9awchari21yd3s2d7w2a9q3f4jq7dnjy5gyrnjj6"))))
+ "1njw2nrm51380d8arvqfmspa3app9353yd7hiddas3gpkaiwrjs4"))))
(build-system gnu-build-system)
(outputs '("out"
"static")) ; static versions of binaries in "out" (~16MiB!)
@@ -2839,9 +2839,9 @@ easy administration.")
(remove-store-references target)
(chmod target #o555)))))
(home-page (package-home-page btrfs-progs))
- (synopsis "Statically-linked btrfs command from btrfsprogs")
- (description "This package provides statically-linked command of btrfs taken
-from the btrfsprogs package. It is meant to be used in initrds.")
+ (synopsis "Statically-linked btrfs command from btrfs-progs")
+ (description "This package provides the statically-linked @command{btrfs}
+from the btrfs-progs package. It is meant to be used in initrds.")
(license (package-license btrfs-progs))))
(define-public freefall
diff --git a/gnu/packages/lisp.scm b/gnu/packages/lisp.scm
index 647c64dcc7..425c273e0d 100644
--- a/gnu/packages/lisp.scm
+++ b/gnu/packages/lisp.scm
@@ -129,7 +129,7 @@ interface to the Tk widget system.")
(define-public ecl
(package
(name "ecl")
- (version "16.1.2")
+ (version "16.1.3")
(source
(origin
(method url-fetch)
@@ -137,7 +137,7 @@ interface to the Tk widget system.")
"https://common-lisp.net/project/ecl/static/files/release/"
name "-" version ".tgz"))
(sha256
- (base32 "16ab8qs3awvdxy8xs8jy82v8r04x4wr70l9l2j45vgag18d2nj1d"))
+ (base32 "0m0j24w5d5a9dwwqyrg0d35c0nys16ijb4r0nyk87yp82v38b9bn"))
(modules '((guix build utils)))
(snippet
;; Add ecl-bundle-systems to 'default-system-source-registry'.
@@ -152,9 +152,6 @@ interface to the Tk widget system.")
("libffi" ,libffi)))
(arguments
'(#:tests? #t
- #:make-flags `(,(string-append "ECL="
- (assoc-ref %outputs "out")
- "/bin/ecl"))
#:parallel-tests? #f
#:phases
(modify-phases %standard-phases
@@ -182,7 +179,12 @@ interface to the Tk widget system.")
`("kernel-headers" ,@libraries)))
`("LIBRARY_PATH" suffix ,library-directories)
`("LD_LIBRARY_PATH" suffix ,library-directories)))))
- (add-after 'wrap 'check (assoc-ref %standard-phases 'check)))))
+ (add-after 'wrap 'check (assoc-ref %standard-phases 'check))
+ (add-before 'check 'fix-path-to-ecl
+ (lambda _
+ (substitute* "build/tests/Makefile"
+ (("\\$\\{exec_prefix\\}/") ""))
+ #t)))))
(native-search-paths
(list (search-path-specification
(variable "XDG_DATA_DIRS")
diff --git a/gnu/packages/mail.scm b/gnu/packages/mail.scm
index b70597b84d..070d9ba093 100644
--- a/gnu/packages/mail.scm
+++ b/gnu/packages/mail.scm
@@ -254,7 +254,7 @@ operating systems.")
(package
(inherit mutt)
(name "neomutt")
- (version "20170225")
+ (version "20170306")
(source
(origin
(method url-fetch)
@@ -263,20 +263,20 @@ operating systems.")
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
- "00ll35g9pcanzrxsjp09vrmq6flml249dipcznrq2z4jy2zd386p"))))
+ "0qwcbjm9j1hgzmybw15w53pvfbqcdf47d4sw21s6r2yaj8kx1hag"))))
(inputs
`(("cyrus-sasl" ,cyrus-sasl)
("gdbm" ,gdbm)
- ("lmdb" ,lmdb)
- ("tokyocabinet" ,tokyocabinet)
("gpgme" ,gpgme)
("ncurses" ,ncurses)
("gnutls" ,gnutls)
("openssl" ,openssl) ;For smime
("perl" ,perl)
+ ("kyotocabinet" ,kyotocabinet)
("libxslt" ,libxslt)
("libidn" ,libidn)
("libxml2" ,libxml2)
+ ("lmdb" ,lmdb)
("docbook-xsl" ,docbook-xsl)
("notmuch" ,notmuch)))
(native-inputs
@@ -291,11 +291,12 @@ operating systems.")
"--enable-gpgme"
;; database, implies header caching
- ;; neomutt supports building multiple backends
- "--with-tokyocabinet"
+ "--without-tokyocabinet"
"--without-qdbm"
"--without-bdb"
"--with-lmdb"
+ (string-append "--with-kyotocabinet="
+ (assoc-ref %build-inputs "kyotocabinet"))
"--with-gdbm"
"--with-gnutls"
@@ -410,7 +411,7 @@ and corrections. It is based on a Bayesian filter.")
(define-public offlineimap
(package
(name "offlineimap")
- (version "7.0.13")
+ (version "7.0.14")
(source (origin
(method url-fetch)
(uri (string-append "https://github.com/OfflineIMAP/offlineimap/"
@@ -418,7 +419,7 @@ and corrections. It is based on a Bayesian filter.")
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
- "1kl72wcxnxb4y5lm2f7ymwjsisnnpwb4w971ajkxlsiwjhzq8i7p"))))
+ "0i5dvygps1ai2qwgamab8kngrp0c5m3bgaw0jk34l8ypsk54wj8r"))))
(build-system python-build-system)
(native-inputs
`(("asciidoc" ,asciidoc)
@@ -662,14 +663,14 @@ invoking @command{notifymuch} from the post-new hook.")
(define-public notmuch
(package
(name "notmuch")
- (version "0.23.7")
+ (version "0.24")
(source (origin
(method url-fetch)
(uri (string-append "https://notmuchmail.org/releases/notmuch-"
version ".tar.gz"))
(sha256
(base32
- "04w90c43zk23pys6prkqb14al408qypifcfj2qznqpwlf46v26zi"))))
+ "1z3m9knsdmchvfjzjhjf2cmdc9yahmvbvzn46wsrsrihfvv4rr7p"))))
(build-system gnu-build-system)
(arguments
'(#:make-flags (list "V=1") ; Verbose test output.
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 9533f5f0a8..d274d50bbc 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -72,6 +72,7 @@
#:use-module (gnu packages guile)
#:use-module (gnu packages xorg)
#:use-module (gnu packages gl)
+ #:use-module (gnu packages imagemagick)
#:use-module (gnu packages m4)
#:use-module (gnu packages mpi)
#:use-module (gnu packages multiprecision)
@@ -949,7 +950,9 @@ can solve two kinds of problems:
("libxft" ,libxft)
("mesa" ,mesa)
("glu" ,glu)
- ("zlib" ,zlib)))
+ ("zlib" ,zlib)
+ ("curl" ,curl)
+ ("graphicsmagick" ,graphicsmagick)))
(native-inputs
`(("lzip" ,lzip)
("gfortran" ,gfortran)
diff --git a/gnu/packages/messaging.scm b/gnu/packages/messaging.scm
index 0ffc031c85..f2f36ad876 100644
--- a/gnu/packages/messaging.scm
+++ b/gnu/packages/messaging.scm
@@ -265,7 +265,7 @@ supports IPv6, SSL-protected connections as well as PAM for authentication.")
(define-public pidgin
(package
(name "pidgin")
- (version "2.11.0")
+ (version "2.12.0")
(source
(origin
(method url-fetch)
@@ -273,7 +273,7 @@ supports IPv6, SSL-protected connections as well as PAM for authentication.")
version "/" name "-" version ".tar.bz2"))
(sha256
(base32
- "0crkggjj6y07v1kdwil9vw532b0vrs6p33nmlvdkpnl60m2169pp"))
+ "1y5p2mq3bfw35b66jsafmbva0w5gg1k99y9z8fyp3jfksqv3agcc"))
(patches (search-patches "pidgin-add-search-path.patch"))))
(build-system glib-or-gtk-build-system)
(native-inputs
diff --git a/gnu/packages/package-management.scm b/gnu/packages/package-management.scm
index c608f397dc..685636e8ba 100644
--- a/gnu/packages/package-management.scm
+++ b/gnu/packages/package-management.scm
@@ -445,13 +445,13 @@ transactions from C or Python.")
(define-public diffoscope
(package
(name "diffoscope")
- (version "77")
+ (version "78")
(source (origin
(method url-fetch)
(uri (pypi-uri name version))
(sha256
(base32
- "0wrb6pl88611frxj19kq3vikhbld40fy1ncrskb1iayxsmbfcbn9"))))
+ "1bx8i6sx2mcvm166nhw0i5442ld6wigkwav8dsnv22y7gnsl9d7n"))))
(build-system python-build-system)
(arguments
`(#:phases (modify-phases %standard-phases
diff --git a/gnu/packages/patches/hmmer-remove-cpu-specificity.patch b/gnu/packages/patches/hmmer-remove-cpu-specificity.patch
new file mode 100644
index 0000000000..ba98db4d0e
--- /dev/null
+++ b/gnu/packages/patches/hmmer-remove-cpu-specificity.patch
@@ -0,0 +1,22 @@
+This patch removes compilation flags which make the build for the machine
+where compilation takes place, rendering the build not reproducible.
+
+diff --git a/configure b/configure
+index 8b6aaef..49a6afc 100755
+--- a/configure
++++ b/configure
+@@ -6125,14 +6125,6 @@ fi # guess arch
+
+ if test "x$ax_gcc_arch" != x -a "x$ax_gcc_arch" != xno; then
+ for arch in $ax_gcc_arch; do
+- if test "x$acx_maxopt_portable" = xyes; then # if we require portable code
+- flags="-mtune=$arch"
+- # -mcpu=$arch and m$arch generate nonportable code on every arch except
+- # x86. And some other arches (e.g. Alpha) don't accept -mtune. Grrr.
+- case $host_cpu in i*86|x86_64*) flags="$flags -mcpu=$arch -m$arch";; esac
+- else
+- flags="-march=$arch -mcpu=$arch -m$arch"
+- fi
+ for flag in $flags; do
+ as_CACHEVAR=`$as_echo "ax_cv_check_cflags__$flag" | $as_tr_sh`
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking whether C compiler accepts $flag" >&5
diff --git a/gnu/packages/patches/python-pandas-skip-failing-tests.patch b/gnu/packages/patches/python-pandas-skip-failing-tests.patch
index 31fc912d00..8ac330c18f 100644
--- a/gnu/packages/patches/python-pandas-skip-failing-tests.patch
+++ b/gnu/packages/patches/python-pandas-skip-failing-tests.patch
@@ -2,39 +2,29 @@ These tests fail on 32bit architectures.
Upstream bug URL: https://github.com/pandas-dev/pandas/issues/14866
---- a/pandas/tests/test_base.py 2017-03-08 17:49:44.422282717 +0100
-+++ b/pandas/tests/test_base.py 2017-03-08 17:50:59.476701799 +0100
-@@ -363,30 +363,6 @@
- self.assertFalse(result.iat[0])
- self.assertFalse(result.iat[1])
+--- a/pandas/tests/indexes/common.py 2017-03-09 00:10:26.063996176 +0100
++++ b/pandas/tests/indexes/common.py 2017-03-09 00:10:53.152844191 +0100
+@@ -119,20 +119,6 @@
+ with tm.assertRaisesRegexp(ValueError, 'Invalid fill method'):
+ idx.get_indexer(idx, method='invalid')
- def test_ndarray_compat_properties(self):
-
-- for o in self.objs:
+- idx = self.create_index()
+- self.assertTrue(idx.T.equals(idx))
+- self.assertTrue(idx.transpose().equals(idx))
-
-- # check that we work
-- for p in ['shape', 'dtype', 'flags', 'T', 'strides', 'itemsize',
-- 'nbytes']:
-- self.assertIsNotNone(getattr(o, p, None))
-- self.assertTrue(hasattr(o, 'base'))
+- values = idx.values
+- for prop in self._compat_props:
+- self.assertEqual(getattr(idx, prop), getattr(values, prop))
-
-- # if we have a datetimelike dtype then needs a view to work
-- # but the user is responsible for that
-- try:
-- self.assertIsNotNone(o.data)
-- except ValueError:
-- pass
+- # test for validity
+- idx.nbytes
+- idx.values.nbytes
-
-- self.assertRaises(ValueError, o.item) # len > 1
-- self.assertEqual(o.ndim, 1)
-- self.assertEqual(o.size, len(o))
--
-- self.assertEqual(Index([1]).item(), 1)
-- self.assertEqual(Series([1]).item(), 1)
--
- def test_ops(self):
- for op in ['max', 'min']:
- for o in self.objs:
+ def test_repr_roundtrip(self):
+
+ idx = self.create_index()
--- a/pandas/tools/tests/test_tile.py 2017-03-08 17:47:39.762261841 +0100
+++ b/pandas/tools/tests/test_tile.py 2017-03-08 17:48:26.831780495 +0100
@@ -271,19 +271,6 @@
diff --git a/gnu/packages/patches/wget-CVE-2017-6508.patch b/gnu/packages/patches/wget-CVE-2017-6508.patch
new file mode 100644
index 0000000000..0218fceaad
--- /dev/null
+++ b/gnu/packages/patches/wget-CVE-2017-6508.patch
@@ -0,0 +1,45 @@
+Fix CVE-2017-6508:
+
+https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2017-6508
+
+Patch copied from upstream source repository:
+
+https://git.savannah.gnu.org/cgit/wget.git/commit/?id=4d729e322fae359a1aefaafec1144764a54e8ad4
+
+From 4d729e322fae359a1aefaafec1144764a54e8ad4 Mon Sep 17 00:00:00 2001
+From: =?UTF-8?q?Tim=20R=C3=BChsen?= <tim.ruehsen@gmx.de>
+Date: Mon, 6 Mar 2017 10:04:22 +0100
+Subject: [PATCH] Fix CRLF injection in Wget host part
+
+* src/url.c (url_parse): Reject control characters in host part of URL
+
+Reported-by: Orange Tsai
+---
+ src/url.c | 11 +++++++++++
+ 1 file changed, 11 insertions(+)
+
+diff --git a/src/url.c b/src/url.c
+index 8f8ff0b8..7d36b27d 100644
+--- a/src/url.c
++++ b/src/url.c
+@@ -925,6 +925,17 @@ url_parse (const char *url, int *error, struct iri *iri, bool percent_encode)
+ url_unescape (u->host);
+ host_modified = true;
+
++ /* check for invalid control characters in host name */
++ for (p = u->host; *p; p++)
++ {
++ if (c_iscntrl(*p))
++ {
++ url_free(u);
++ error_code = PE_INVALID_HOST_NAME;
++ goto error;
++ }
++ }
++
+ /* Apply IDNA regardless of iri->utf8_encode status */
+ if (opt.enable_iri && iri)
+ {
+--
+2.12.0
+
diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 60f0594453..5baf329995 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -30,12 +30,13 @@
;;; Copyright © 2016 Stefan Reichoer <stefan@xsteve.at>
;;; Copyright © 2016 Dylan Jeffers <sapientech@sapientech@openmailbox.org>
;;; Copyright © 2016 Alex Vong <alexvong1995@gmail.com>
-;;; Copyright © 2016 Arun Isaac <arunisaac@systemreboot.net>
+;;; Copyright © 2016, 2017 Arun Isaac <arunisaac@systemreboot.net>
;;; Copyright © 2016, 2017 Julien Lepiller <julien@lepiller.eu>
;;; Copyright © 2016, 2017 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2016, 2017 Thomas Danckaert <post@thomasdanckaert.be>
;;; Copyright © 2017 Carlo Zancanaro <carlo@zancanaro.id.au>
;;; Copyright © 2017 Frederick M. Muriithi <fredmanglis@gmail.com>
+;;; Copyright © 2017 humanitiesNerd <catonano@gmail.com>
;;;
;;; This file is part of GNU Guix.
;;;
@@ -3433,8 +3434,6 @@ producing implementations of dynamic languages, emphasizing a clean separation
between language specification and implementation aspects.")
(license license:expat)))
-;; This version of numpy is missing the documentation and is only used to
-;; build matplotlib which is required to build numpy's documentation.
(define-public python-numpy
(package
(name "python-numpy")
@@ -3581,10 +3580,10 @@ association studies (GWAS) on extremely large data sets.")
(method git-fetch)
(uri (git-reference
(url "https://github.com/scipy/scipy-sphinx-theme.git")
- (commit "c466764e22")))
+ (commit "c466764e2231ba132c09826b5b138fffa1cfcec3")))
(sha256
(base32
- "0q2y87clwlsgc7wvlsn9pzyssybcq10plwhq2w1ydykfsyyqbmkl"))))
+ "0q2y87clwlsgc7wvlsn9pzyssybcq10plwhq2w1ydykfsyyqbmkl"))))
,@(package-native-inputs python-numpy)))
(arguments
`(#:tests? #f ; we're only generating the documentation
@@ -13479,3 +13478,188 @@ specified to apply on the key before comparison (e.g. @code{string.lower})).")
Python. It is based on Parsing Expression Grammars, PEG. With pyPEG you can
parse many formal languages.")
(license license:gpl2)))
+
+(define-public python2-cliapp
+ (package
+ (name "python2-cliapp")
+ (version "1.20160724")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append
+ "http://git.liw.fi/cgi-bin/cgit/cgit.cgi/cliapp/snapshot/cliapp-"
+ version ".tar.gz"))
+ (sha256
+ (base32
+ "025cyi75vxyghbm4hav8dz4fzwksshddavy9g9fwr440awcvw74f"))))
+ (build-system python-build-system)
+ (arguments
+ `(#:python ,python-2))
+ (propagated-inputs
+ `(("python2-pyaml" ,python2-pyaml)))
+ (home-page "https://liw.fi/cliapp/")
+ (synopsis "Python framework for command line programs")
+ (description "@code{python2-cliapp} is a python framework for
+command line programs. It contains the typical stuff such programs
+need to do, such as parsing the command line for options, and
+iterating over input files.")
+ (license license:gpl2+)))
+
+(define-public python2-ttystatus
+ (package
+ (name "python2-ttystatus")
+ (version "0.32")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append
+ "http://git.liw.fi/cgi-bin/cgit/cgit.cgi/ttystatus/snapshot/ttystatus-"
+ version ".tar.gz"))
+ (sha256
+ (base32
+ "0b5g889jj23r2w1hi300cdldx6jvspanp0ybf5n1qvdvl150aamf"))))
+ (build-system python-build-system)
+ (arguments
+ `(#:python ,python-2))
+ (home-page "https://liw.fi/ttystatus/")
+ (synopsis "Python library for showing progress reporting and
+status updates on terminals")
+ (description "@code{python2-ttystatus} is a python library for
+showing progress reporting and status updates on terminals, for
+command line programs. Output is automatically adapted to the width
+of the terminal: truncated if it does not fit, and resized if the
+terminal size changes.")
+ (license license:gpl3+)))
+
+(define-public python2-tracing
+ (package
+ (name "python2-tracing")
+ (version "0.10")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append
+ "http://git.liw.fi/cgi-bin/cgit/cgit.cgi/python-tracing/snapshot/tracing-"
+ version ".tar.gz"))
+ (sha256
+ (base32
+ "06cw4zg42fsvqy372vi2whj26w56vzg5axhzwdjc2bgwf03garbw"))))
+ (build-system python-build-system)
+ (arguments
+ `(#:python ,python-2))
+ (home-page "https://liw.fi/tracing/")
+ (synopsis "Python debug logging helper")
+ (description "@code{python2-tracing} is a python library for
+logging debug messages. It provides a way to turn debugging messages
+on and off, based on the filename they occur in. It is much faster
+than using @code{logging.Filter} to accomplish the same thing, which
+matters when code is run in production mode. The actual logging still
+happens using the @code{logging} library.")
+ (license license:gpl3+)))
+
+(define-public python2-larch
+ (package
+ (name "python2-larch")
+ (version "1.20151025")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append
+ "http://git.liw.fi/cgi-bin/cgit/cgit.cgi/larch/snapshot/larch-"
+ version ".tar.gz"))
+ (sha256
+ (base32
+ "1p4knkkavlqymgciz2wbcnfrdgdbafhg14maplnk4vbw0q8xs663"))))
+ (build-system python-build-system)
+ (arguments
+ `(#:python ,python-2))
+ (propagated-inputs
+ `(("python2-tracing" ,python2-tracing)))
+ (home-page "https://liw.fi/larch/")
+ (synopsis "Python copy-on-write B-tree library")
+ (description "@code{python2-larch} is an implementation of
+particular kind of B-tree, based on research by Ohad Rodeh. See
+@url{http://liw.fi/larch/ohad-btrees-shadowing-clones.pdf} for details
+on the data structure.
+
+The distinctive feature of this B-tree is that a node is never
+(conceptually) modified. Instead, all updates are done by
+copy-on-write. This makes it easy to clone a tree, and modify only the
+clone, while other processes access the original tree.")
+ (license license:gpl3+)))
+
+(define-public python-htmlmin
+ (package
+ (name "python-htmlmin")
+ (version "0.1.10")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "htmlmin" version))
+ (sha256
+ (base32
+ "0qxa93j3p1ak32qh8d9kshqv8v3z0hkc13dwbhp5cn7sn3xmsp6a"))))
+ (arguments
+ `(#:tests? #f)) ;htmlmin has no tests
+ (build-system python-build-system)
+ (home-page "https://htmlmin.readthedocs.org/en/latest/")
+ (synopsis "HTML minifier")
+ (description "@code{htmlmin} is an HTML minifier that just works.
+It comes with safe defaults and easily configurable options.")
+ (license license:bsd-3)))
+
+(define-public python2-htmlmin
+ (package-with-python2 python-htmlmin))
+
+(define-public python-flask-htmlmin
+ (package
+ (name "python-flask-htmlmin")
+ (version "1.2")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "Flask-HTMLmin" version))
+ (sha256
+ (base32
+ "1n6zlq72kakkw0z2jpq6nh74lfsmxybm4g053pwhc14fbr809348"))))
+ (propagated-inputs
+ `(("python-flask" ,python-flask)
+ ("python-htmlmin" ,python-htmlmin)))
+ (build-system python-build-system)
+ (home-page "https://github.com/hamidfzm/Flask-HTMLmin")
+ (synopsis "HTML response minifier for Flask")
+ (description
+ "Minify @code{text/html} MIME type responses when using @code{Flask}.")
+ (license license:bsd-3)))
+
+(define-public python2-flask-htmlmin
+ (package-with-python2 python-flask-htmlmin))
+
+(define-public python-flask-login
+ (package
+ (name "python-flask-login")
+ (version "0.4.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "https://github.com/maxcountryman/flask-login/archive/"
+ version ".tar.gz"))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "1pdqp7a2gyb7k06xda004x0fi2w66s6kn2i0ndkqndmg12d83f9w"))))
+ (arguments
+ ;; Tests fail PEP8 compliance. See:
+ ;; https://github.com/maxcountryman/flask-login/issues/340
+ `(#:tests? #f))
+ (build-system python-build-system)
+ (home-page "https://github.com/maxcountryman/flask-login")
+ (synopsis "User session management for Flask")
+ (description
+ "@code{Flask-Login} provides user session management for Flask. It
+handles the common tasks of logging in, logging out, and remembering your
+users' sessions over extended periods of time.")
+ (license license:expat)))
+
+(define-public python2-flask-login
+ (package-with-python2 python-flask-login))
diff --git a/gnu/packages/regex.scm b/gnu/packages/regex.scm
index 11f4716033..f55faaf042 100644
--- a/gnu/packages/regex.scm
+++ b/gnu/packages/regex.scm
@@ -22,7 +22,8 @@
#:use-module ((guix licenses) #:prefix license:)
#:use-module (guix packages)
#:use-module (guix download)
- #:use-module (guix build-system gnu))
+ #:use-module (guix build-system gnu)
+ #:use-module (guix utils))
(define-public re2
(package
@@ -42,7 +43,16 @@
(arguments
`(#:test-target "test"
;; There is no configure step, but the Makefile respects a prefix.
- #:make-flags (list (string-append "prefix=" %output))
+ ;; As ./configure does not know anything about the target CXX
+ ;; we need to specify TARGET-g++ explicitly.
+ #:make-flags (list (string-append "prefix=" %output)
+ (string-append
+ "CXX=" ,(string-append
+ (if (%current-target-system)
+ (string-append
+ (%current-target-system) "-")
+ "")
+ "g++")))
#:phases
(modify-phases %standard-phases
(delete 'configure)
diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 64b0b0e940..49bb24e594 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -3227,14 +3227,17 @@ and tidyr provides no margins or aggregation.")
(define-public r-hexbin
(package
(name "r-hexbin")
- (version "1.27.1")
+ ;; The package tarball was updated in place, resulting in a change in the
+ ;; hash value. We decided to bump the version to 1.27.1-1 instead of
+ ;; keeping the version at upstream's 1.27.1.
+ (version "1.27.1-1")
(source
(origin
(method url-fetch)
- (uri (cran-uri "hexbin" version))
+ (uri (cran-uri "hexbin" "1.27.1"))
(sha256
(base32
- "0xi6fbf1fvyn2gffr052n3viibqzpr3603sgi4xaminbzja4syjh"))))
+ "025d609z1nyy684hwvp34b9mjzkgvild7fvfr95f941dmsikan87"))))
(build-system r-build-system)
(propagated-inputs
`(("r-lattice" ,r-lattice)))
@@ -4170,3 +4173,671 @@ perform @dfn{independent component analysis} (ICA) and projection pursuit.")
"This package provides the Breiman and Cutler's random forests algorithm, based on a
forest of trees using random inputs, for classification and regression.")
(license license:gpl2+)))
+
+(define-public r-diptest
+ (package
+ (name "r-diptest")
+ (version "0.75-7")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "diptest" version))
+ (sha256
+ (base32
+ "06xnc5gv1284ll0addxnxb6ljz6fn8dbyrp5vchyz6551h800aa6"))))
+ (build-system r-build-system)
+ (home-page "http://cran.r-project.org/web/packages/diptest")
+ (synopsis "Hartigan's dip test statistic for unimodality")
+ (description
+ "This package computes Hartigan's dip test statistic for unimodality,
+multimodality and provides a test with simulation based p-values, where the
+original public code has been corrected.")
+ (license license:gpl2+)))
+
+(define-public r-modeltools
+ (package
+ (name "r-modeltools")
+ (version "0.2-21")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "modeltools" version))
+ (sha256
+ (base32
+ "0ynds453xprxv0jqqzi3blnv5w6vrdww9pvd1sq4lrr5ar3k3cq7"))))
+ (build-system r-build-system)
+ (home-page "http://cran.r-project.org/web/packages/modeltools")
+ (synopsis "Tools and classes for statistical models")
+ (description
+ "This package provides a collection of tools to deal with statistical
+models. The functionality is experimental and the user interface is likely
+to change in the future.")
+ (license license:gpl2)))
+
+(define-public r-flexmix
+ (package
+ (name "r-flexmix")
+ (version "2.3-13")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "flexmix" version))
+ (sha256
+ (base32
+ "1i205yw3kkxs27gqcs6zx0c2mh16p332a2p06wq6fdzb20bazg3z"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-modeltools" ,r-modeltools)))
+ (home-page "http://cran.r-project.org/web/packages/flexmix")
+ (synopsis "Flexible mixture modeling")
+ (description
+ "This package implements a general framework for finite mixtures of
+regression models using the EM algorithm. FlexMix provides the E-step and
+all data handling, while the M-step can be supplied by the user to easily
+define new models. Existing drivers implement mixtures of standard linear
+models, generalized linear models and model-based clustering.")
+ (license license:gpl2+)))
+
+(define-public r-mclust
+ (package
+ (name "r-mclust")
+ (version "5.2.2")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "mclust" version))
+ (sha256
+ (base32
+ "19cbg7p5h2b6h9mvcx9rjppyd3awma18ymaljakbnclpvhwbqpwd"))))
+ (build-system r-build-system)
+ (native-inputs
+ `(("gfortran" ,gfortran)))
+ (home-page "http://www.stat.washington.edu/mclust/")
+ (synopsis "Gaussian mixture modelling for model-based clustering etc.")
+ (description
+ "This package provides Gaussian finite mixture models fitted via EM
+algorithm for model-based clustering, classification, and density estimation,
+including Bayesian regularization, dimension reduction for visualisation,
+and resampling-based inference.")
+ (license license:gpl2+)))
+
+(define-public r-prabclus
+ (package
+ (name "r-prabclus")
+ (version "2.2-6")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "prabclus" version))
+ (sha256
+ (base32
+ "0qjsxrx6yv338bxm4ki0w9h8hind1l98abdrz828588bwj02jya1"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-mclust" ,r-mclust)))
+ (home-page "https://cran.r-project.org/web/packages/prabclus")
+ (synopsis "Parametric bootstrap tests for spatial neighborhood clustering")
+ (description
+ "This package provides a distance-based parametric bootstrap tests
+for clustering with spatial neighborhood information. Some distance measures,
+clustering of presence-absence, abundance and multilocus genetical data for
+species delimitation, nearest neighbor based noise detection.")
+ (license license:gpl2+)))
+
+(define-public r-deoptimr
+ (package
+ (name "r-deoptimr")
+ (version "1.0-8")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "DEoptimR" version))
+ (sha256
+ (base32
+ "1vz546hyjyhly70z62h5n3mn62b8llhhmim8ffp9y6jnnb0i2sc4"))))
+ (properties `((upstream-name . "DEoptimR")))
+ (build-system r-build-system)
+ (home-page "http://cran.r-project.org/web/packages/DEoptimR")
+ (synopsis "Differential evolution optimization in pure R")
+ (description
+ "This package provides a differential evolution (DE) stochastic
+algorithms for global optimization of problems with and without constraints.
+The aim is to curate a collection of its state-of-the-art variants that (1) do
+not sacrifice simplicity of design, (2) are essentially tuning-free, and (3)
+can be efficiently implemented directly in the R language.")
+ (license license:gpl2+)))
+
+(define-public r-robustbase
+ (package
+ (name "r-robustbase")
+ (version "0.92-7")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "robustbase" version))
+ (sha256
+ (base32
+ "13xz4am7y0s0kl5bmbcw3dlhl7ji8h9sjx56wsgmj6r9n35nrggw"))))
+ (build-system r-build-system)
+ (inputs
+ `(("gfortran" ,gfortran)))
+ (propagated-inputs
+ `(("r-deoptimr" ,r-deoptimr)))
+ (home-page "http://robustbase.r-forge.r-project.org/")
+ (synopsis "Basic robust statistics")
+ (description
+ "This packages allows to analyze data with robust methods such as
+regression methodology including model selections and multivariate statistics.")
+ (license license:gpl2+)))
+
+(define-public r-trimcluster
+ (package
+ (name "r-trimcluster")
+ (version "0.1-2")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "trimcluster" version))
+ (sha256
+ (base32
+ "0lsgbg93hm0w1rdb813ry0ks2l0jfpyqzqkf3h3bj6fch0avcbv2"))))
+ (build-system r-build-system)
+ (home-page "http://cran.r-project.org/web/packages/trimcluster")
+ (synopsis "Cluster analysis with trimming")
+ (description
+ "The trimmed k-means clustering method by Cuesta-Albertos, Gordaliza and
+Matran (1997). This optimizes the k-means criterion under trimming a portion
+of the points.")
+ (license license:gpl2+)))
+
+(define-public r-fpc
+ (package
+ (name "r-fpc")
+ (version "2.1-10")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "fpc" version))
+ (sha256
+ (base32
+ "15m0p9l9w2v7sl0cnzyg81i2fmx3hrhvr3371544mwn3fpsca5sx"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-diptest" ,r-diptest)
+ ("r-flexmix" ,r-flexmix)
+ ("r-kernlab" ,r-kernlab)
+ ("r-mclust" ,r-mclust)
+ ("r-mvtnorm" ,r-mvtnorm)
+ ("r-prabclus" ,r-prabclus)
+ ("r-robustbase" ,r-robustbase)
+ ("r-trimcluster" ,r-trimcluster)))
+ (home-page "http://cran.r-project.org/web/packages/fpc")
+ (synopsis "Flexible procedures for clustering")
+ (description
+ "This package provides various methods for clustering and cluster validation.
+For example, it provides fixed point clustering, linear regression clustering,
+clustering by merging Gaussian mixture components, as well as symmetric and
+asymmetric discriminant projections for visualisation of the separation of
+groupings.")
+ (license license:gpl2+)))
+
+(define-public r-vgam
+ (package
+ (name "r-vgam")
+ (version "1.0-3")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "VGAM" version))
+ (sha256
+ (base32
+ "0wr6szcpj8r4a1rlzgd6iym7khin69fmvxcf37iyvs8mms86dfr3"))))
+ (properties `((upstream-name . "VGAM")))
+ (build-system r-build-system)
+ (inputs
+ `(("gfortran" ,gfortran)))
+ (home-page "https://www.stat.auckland.ac.nz/~yee/VGAM")
+ (synopsis "Vector generalized linear and additive models")
+ (description
+ "This package is an implementation of about 6 major classes of statistical
+regression models. Currently only fixed-effects models are implemented, i.e.,
+no random-effects models. Many (150+) models and distributions are estimated
+by maximum likelihood estimation (MLE) or penalized MLE, using Fisher scoring.
+VGLMs can be loosely thought of as multivariate generalised linear models.")
+ (license license:gpl2+)))
+
+(define-public r-pbapply
+ (package
+ (name "r-pbapply")
+ (version "1.3-2")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "pbapply" version))
+ (sha256
+ (base32
+ "1sdmjlnwxb99f95g5v8k8mirrkzw99yig377v0qi9lzwjgd6fqqr"))))
+ (build-system r-build-system)
+ (home-page "https://github.com/psolymos/pbapply")
+ (synopsis "Adding progress bar to apply functions")
+ (description
+ "This lightweight package that adds progress bar to vectorized R
+functions apply. The implementation can easily be added to functions where
+showing the progress is useful e.g. bootstrap.")
+ (license license:gpl2)))
+
+(define-public r-fnn
+ (package
+ (name "r-fnn")
+ (version "1.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "FNN" version))
+ (sha256
+ (base32
+ "1kncmiaraq1mrykb9fj3fsxswabk3l71fnp1vks0x9aay5xfk8mj"))))
+ (properties `((upstream-name . "FNN")))
+ (build-system r-build-system)
+ (home-page "http://cran.r-project.org/web/packages/FNN")
+ (synopsis "Fast nearest neighbor search algorithms and applications")
+ (description
+ "This package provides cover-tree and kd-tree fast k-nearest neighbor
+search algorithms and related applications including KNN classification,
+regression and information measures.")
+ (license license:gpl2+)))
+
+(define-public r-minqa
+ (package
+ (name "r-minqa")
+ (version "1.2.4")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "minqa" version))
+ (sha256
+ (base32
+ "036drja6xz7awja9iwb76x91415p26fb0jmg7y7v0p65m6j978fg"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-rcpp" ,r-rcpp)))
+ (inputs
+ `(("gfortran" ,gfortran)))
+ (home-page "http://optimizer.r-forge.r-project.org")
+ (synopsis "Derivative-free optimization algorithms by quadratic approximation")
+ (description
+ "This package provides a derivative-free optimization by quadratic approximation
+based on an interface to Fortran implementations by M. J. D. Powell.")
+ (license license:gpl2)))
+
+(define-public r-rcppeigen
+ (package
+ (name "r-rcppeigen")
+ (version "0.3.2.9.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "RcppEigen" version))
+ (sha256
+ (base32
+ "0fy9kr03160f1ywzff3p380s8a59jz7d2d0rggb14g2y0slzpbr5"))))
+ (properties `((upstream-name . "RcppEigen")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-rcpp" ,r-rcpp)))
+ (home-page "http://eigen.tuxfamily.org")
+ (synopsis "Rcpp integration for the Eigen templated linear algebra library")
+ (description
+ "This package provides an integration of Eigen in R using a C++ template
+library for linear algebra: matrices, vectors, numerical solvers and related algorithms.
+It supports dense and sparse matrices on integer, floating point and complex numbers,
+decompositions of such matrices, and solutions of linear systems.")
+ (license license:gpl2+)))
+
+(define-public r-modelmetrics
+ (package
+ (name "r-modelmetrics")
+ (version "1.1.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "ModelMetrics" version))
+ (sha256
+ (base32
+ "119xxmzb5biq7k1yxqsf0jmmarmfn6lds9x9hfgv593xlpym6za8"))))
+ (properties `((upstream-name . "ModelMetrics")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-rcpp" ,r-rcpp)))
+ (home-page "http://cran.r-project.org/web/packages/ModelMetrics")
+ (synopsis "Rapid calculation of model metrics")
+ (description
+ "Written in C++ using @code{Rcpp}, this package provides a collection of
+metrics for evaluating models.")
+ (license license:gpl2+)))
+
+(define-public r-matrixmodels
+ (package
+ (name "r-matrixmodels")
+ (version "0.4-1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "MatrixModels" version))
+ (sha256
+ (base32
+ "0cyfvhci2p1vr2x52ymkyqqs63x1qchn856dh2j94yb93r08x1zy"))))
+ (properties `((upstream-name . "MatrixModels")))
+ (build-system r-build-system)
+ (home-page "https://cran.r-project.org/web/packages/MatrixModels")
+ (synopsis "Modelling with sparse and dense matrices")
+ (description
+ "This package models with sparse and dense matrix matrices,
+using modular prediction and response module classes.")
+ (license license:gpl2+)))
+
+(define-public r-quantreg
+ (package
+ (name "r-quantreg")
+ (version "5.29")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "quantreg" version))
+ (sha256
+ (base32
+ "098gy8xv9kcl5y0cm93b8chr5sm6crrdxi20bkx9lmwmybl3himv"))))
+ (build-system r-build-system)
+ (native-inputs
+ `(("gfortran" ,gfortran)))
+ (propagated-inputs
+ `(("r-matrixmodels" ,r-matrixmodels)
+ ("r-sparsem" ,r-sparsem)))
+ (home-page "http://www.r-project.org")
+ (synopsis "Quantile regression")
+ (description
+ "This package provides an estimation and inference methods for models
+of conditional quantiles: linear and nonlinear parametric and non-parametric
+models for conditional quantiles of a univariate response and several methods
+for handling censored survival data. Portfolio selection methods based on
+expected shortfall risk are also included.")
+ (license license:gpl2+)))
+
+(define-public r-nloptr
+ (package
+ (name "r-nloptr")
+ (version "1.0.4")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "nloptr" version))
+ (sha256
+ (base32
+ "1cypz91z28vhvwq2rzqjrbdc6a2lvfr2g16vid2sax618q6ai089"))))
+ (build-system r-build-system)
+ (native-inputs
+ `(("pkg-config" ,pkg-config)))
+ (inputs
+ `(("nlopt" ,nlopt)))
+ (home-page "http://cran.r-project.org/web/packages/nloptr")
+ (synopsis "R interface to NLopt")
+ (description
+ "This package is interface to NLopt, a library for nonlinear
+optimization. NLopt is a library for nonlinear optimization, providing a
+common interface for a number of different free optimization routines
+available online as well as original implementations of various other
+algorithms.")
+ (license license:lgpl3)))
+
+(define-public r-lme4
+ (package
+ (name "r-lme4")
+ (version "1.1-12")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "lme4" version))
+ (sha256
+ (base32
+ "0j60l5kgx1wvw2wm3jwfqwi63hammaq8gfcxzwa4h552likvaxi9"))))
+ (build-system r-build-system)
+ (native-inputs
+ `(("r-rcpp" ,r-rcpp)
+ ("r-rcppeigen" ,r-rcppeigen)))
+ (propagated-inputs
+ `(("r-minqa" ,r-minqa)
+ ("r-nloptr" ,r-nloptr)))
+ (home-page "http://cran.r-project.org/web/packages/lme4")
+ (synopsis "Linear mixed-effects models using eigen and S4")
+ (description
+ "This package provides fit linear and generalized linear mixed-effects
+models. The models and their components are represented using S4 classes and
+methods. The core computational algorithms are implemented using the Eigen
+C++ library for numerical linear algebra and RcppEigen glue.")
+ (license license:gpl2+)))
+
+(define-public r-pbkrtest
+ (package
+ (name "r-pbkrtest")
+ (version "0.4-6")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "pbkrtest" version))
+ (sha256
+ (base32
+ "00cw18q7wvddzjrbxz917wkix6r7672vi2wmsp4gwgzady8vha4x"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-lme4" ,r-lme4)))
+ (home-page "http://people.math.aau.dk/~sorenh/software/pbkrtest/")
+ (synopsis "Methods for linear mixed model comparison")
+ (description
+ "This package implements a parametric bootstrap test and a Kenward Roger
+modification of F-tests for linear mixed effects models and a parametric
+bootstrap test for generalized linear mixed models.")
+ (license license:gpl2+)))
+
+(define-public r-car
+ (package
+ (name "r-car")
+ (version "2.1-4")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "car" version))
+ (sha256
+ (base32
+ "0a6v7rsd1xsdyapnfqy37m7c4kx9wslkzsizc9k0lmnba0bwyfgx"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-pbkrtest" ,r-pbkrtest)
+ ("r-quantreg" ,r-quantreg)))
+ (home-page "https://r-forge.r-project.org/projects/car/")
+ (synopsis "Companion to applied regression")
+ (description
+ "This package provides functions and datasets from book Companion
+to Applied regression, Second Edition, Sage, 2011.")
+ (license license:gpl2+)))
+
+(define-public r-caret
+ (package
+ (name "r-caret")
+ (version "6.0-73")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "caret" version))
+ (sha256
+ (base32
+ "1jzaqwv4glyqqnfbpalgajd0ag866247vvdh5i83ffqs1yhs984h"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-car" ,r-car)
+ ("r-foreach" ,r-foreach)
+ ("r-ggplot2" ,r-ggplot2)
+ ("r-modelmetrics" ,r-modelmetrics)
+ ("r-plyr" ,r-plyr)
+ ("r-reshape2" ,r-reshape2)))
+ (home-page "https://github.com/topepo/caret")
+ (synopsis "Classification and regression training")
+ (description
+ "This package provides misc functions for training and plotting
+classification and regression models.")
+ (license license:gpl2+)))
+
+(define-public r-rcppprogress
+ (package
+ (name "r-rcppprogress")
+ (version "0.3")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "RcppProgress" version))
+ (sha256
+ (base32
+ "0796g11w7iv3ix1wfm3fh09qq7jki4r4cp1mjagq77igri3xrr9x"))))
+ (properties `((upstream-name . "RcppProgress")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-rcpp" ,r-rcpp)))
+ (home-page "https://github.com/kforner/rcpp_progress")
+ (synopsis "Interruptible progress bar for C++ in R packages")
+ (description
+ "This package allows to display a progress bar in the R console for long running
+computations taking place in C++ code, and support for interrupting those computations
+even in multithreaded code, typically using OpenMP.")
+ (license license:gpl3+)))
+
+(define-public r-mnormt
+ (package
+ (name "r-mnormt")
+ (version "1.5-5")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "mnormt" version))
+ (sha256
+ (base32
+ "1b34xxrnf35khsx82mhvmk96sgfr2flyasaah7qkb2976pwxay7z"))))
+ (build-system r-build-system)
+ (native-inputs
+ `(("gfortran" ,gfortran)))
+ (home-page "http://azzalini.stat.unipd.it/SW/Pkg-mnormt")
+ (synopsis "Multivariate normal and \"t\" distributions")
+ (description
+ "This package provides functions for computing the density and the
+distribution function of multivariate normal and \"t\" random variables, and
+for generating random vectors sampled from these distributions. Probabilities
+are computed via non-Monte Carlo methods.")
+ (license license:gpl2+)))
+
+(define-public r-numderiv
+ (package
+ (name "r-numderiv")
+ (version "2016.8-1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "numDeriv" version))
+ (sha256
+ (base32
+ "07ni52rwiap4wilfz94w5mrqaxr59axxmgn57857ip4p6qkiss0v"))))
+ (properties `((upstream-name . "numDeriv")))
+ (build-system r-build-system)
+ (home-page "https://cran.r-project.org/web/packages/numDeriv")
+ (synopsis "Accurate numerical derivatives")
+ (description
+ "This package provides methods for calculating accurate numerical
+first and second order derivatives.")
+ (license license:gpl2)))
+
+(define-public r-sn
+ (package
+ (name "r-sn")
+ (version "1.5-0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "sn" version))
+ (sha256
+ (base32
+ "0fh7xjsfd2x8d9lbnss7raldh24b72b3pvcv7zqa1qprzg7zfr01"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-mnormt" ,r-mnormt)
+ ("r-numderiv" ,r-numderiv)))
+ (home-page "http://azzalini.stat.unipd.it/SN")
+ (synopsis "The skew-normal and skew-t distributions")
+ (description
+ "This packages provides functionalities to build and manipulate
+probability distributions of the skew-normal family and some related
+ones, notably the skew-t family, and provides related statistical
+methods for data fitting and diagnostics, in the univariate and the
+multivariate case.")
+ (license license:gpl2+)))
+
+(define-public r-tclust
+ (package
+ (name "r-tclust")
+ (version "1.2-3")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "tclust" version))
+ (sha256
+ (base32
+ "0a1b7yp4l9wf6ic5czizyl2cnxrc1virj0icr8i6m1vv23jd8jfp"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-mclust" ,r-mclust)
+ ("r-mvtnorm" ,r-mvtnorm)
+ ("r-sn" ,r-sn)))
+ (home-page "http://cran.r-project.org/web/packages/tclust")
+ (synopsis "Robust trimmed clustering")
+ (description
+ "This package implements different robust clustering
+algorithms (@code{tclust}) based on trimming and including some graphical
+diagnostic tools (@code{ctlcurves} and @code{DiscrFact}).")
+ (license license:gpl3)))
+
+(define-public r-ranger
+ (package
+ (name "r-ranger")
+ (version "0.6.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "ranger" version))
+ (sha256
+ (base32
+ "1fwqwbi0dnla16x6zj14rf95qr5gmilfmlrwnv7s960h4yiw4n97"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-rcpp" ,r-rcpp)))
+ (home-page "https://github.com/imbs-hl/ranger")
+ (synopsis "Fast implementation of random forests")
+ (description
+ "This package provides a fast implementation of Random Forests,
+particularly suited for high dimensional data. Ensembles of classification,
+regression, survival and probability prediction trees are supported. Data from
+genome-wide association studies can be analyzed efficiently.")
+ (license license:gpl3)))
+
+(define-public r-tsne
+ (package
+ (name "r-tsne")
+ (version "0.1-3")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "tsne" version))
+ (sha256
+ (base32
+ "0s8cv2pndkddq62rzlgzgfdjp1vjv5hz5i5957sllnb97vbzbzb6"))))
+ (build-system r-build-system)
+ (home-page "https://github.com/jdonaldson/rtsne/")
+ (synopsis "t-Distributed Stochastic Neighbor Embedding for R")
+ (description
+ "This package provides a pure R implementation of the t-SNE algorithm.")
+ (license license:gpl2+)))
diff --git a/gnu/packages/video.scm b/gnu/packages/video.scm
index 9f73a7ad59..34ffabb483 100644
--- a/gnu/packages/video.scm
+++ b/gnu/packages/video.scm
@@ -980,7 +980,7 @@ access to mpv's powerful playback capabilities.")
(define-public youtube-dl
(package
(name "youtube-dl")
- (version "2017.03.02")
+ (version "2017.03.07")
(source (origin
(method url-fetch)
(uri (string-append "https://yt-dl.org/downloads/"
@@ -988,7 +988,7 @@ access to mpv's powerful playback capabilities.")
version ".tar.gz"))
(sha256
(base32
- "0f86qnppxnbh2c8bmpf0c1xhwk5vqjdzz7pqh9sydhscv8r0209g"))))
+ "19acz9m3gazd1ims4l9a9ni1p7jw8z4y0ncqn99xlx9kna8ryjnv"))))
(build-system python-build-system)
(arguments
;; The problem here is that the directory for the man page and completion
diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm
index dab30df13d..a0e76d52c4 100644
--- a/gnu/packages/web.scm
+++ b/gnu/packages/web.scm
@@ -4459,10 +4459,9 @@ functions of Tidy.")
(home-page "https://www.hiawatha-webserver.org")
(synopsis "Webserver with focus on security")
(description
- "Hiawatha has been written with security in mind. This resulted in a
-highly secure webserver in both code and features. Hiawatha can stop SQL
-injections, XSS and CSRF attacks and exploit attempts. Via a specially
-crafted monitoring tool, you can keep track of all your webservers.")
+ "Hiawatha has been written with security in mind.
+Features include the ability to stop SQL injections, XSS and CSRF attacks and
+exploit attempts.")
(license l:gpl2)))
(define-public qutebrowser
diff --git a/gnu/packages/wget.scm b/gnu/packages/wget.scm
index 9ac21b4db1..1c56e14a66 100644
--- a/gnu/packages/wget.scm
+++ b/gnu/packages/wget.scm
@@ -20,6 +20,7 @@
(define-module (gnu packages wget)
#:use-module (guix licenses)
+ #:use-module (gnu packages)
#:use-module (gnu packages libidn)
#:use-module (gnu packages python)
#:use-module (gnu packages perl)
@@ -39,6 +40,7 @@
(method url-fetch)
(uri (string-append "mirror://gnu/wget/wget-"
version ".tar.xz"))
+ (patches (search-patches "wget-CVE-2017-6508.patch"))
(sha256
(base32
"1ljcfhbkdsd0zjfm520rbl1ai62fc34i7c45sfj244l8f6b0p58c"))))
diff --git a/gnu/packages/wine.scm b/gnu/packages/wine.scm
index d28e2dd4e4..40e1dd5cfc 100644
--- a/gnu/packages/wine.scm
+++ b/gnu/packages/wine.scm
@@ -54,15 +54,14 @@
(define-public wine
(package
(name "wine")
- (version "2.0")
+ (version "2.3")
(source (origin
(method url-fetch)
- (uri (string-append "https://dl.winehq.org/wine/source/"
- (version-major+minor version)
- "/wine-" version ".tar.bz2"))
+ (uri (string-append "https://dl.winehq.org/wine/source/2.x"
+ "/wine-" version ".tar.xz"))
(sha256
(base32
- "1ik6q0h3ph3jizmp7bxhf6kcm1pzrdrn2m0yf2x86slv2aigamlp"))))
+ "0zh6kvs4d6d99x5qgxbb5jq2wilwzifhmib2nhq0g3ychxx5rjdg"))))
(build-system gnu-build-system)
(native-inputs `(("pkg-config" ,pkg-config)
("gettext" ,gettext-minimal)
diff --git a/gnu/packages/xorg.scm b/gnu/packages/xorg.scm
index 18354271ee..191dc7dd19 100644
--- a/gnu/packages/xorg.scm
+++ b/gnu/packages/xorg.scm
@@ -2392,7 +2392,7 @@ including most mice, keyboards, tablets and touchscreens.")
(define-public xf86-input-libinput
(package
(name "xf86-input-libinput")
- (version "0.24.0")
+ (version "0.25.0")
(source (origin
(method url-fetch)
(uri (string-append
@@ -2400,7 +2400,7 @@ including most mice, keyboards, tablets and touchscreens.")
name "-" version ".tar.bz2"))
(sha256
(base32
- "0a1nn65qq71bbfhxq39zdb4b1h6ickzv98cjdacv4ngd18shgjyx"))))
+ "0vsmijamfzf6vcljrr0am2qcz33zl2l0lj2mzmbwgrm7ixjx2zxv"))))
(build-system gnu-build-system)
(arguments
'(#:configure-flags
@@ -2811,10 +2811,10 @@ X server.")
(define-public xf86-video-intel
- (let ((commit "e4fe79cf0d9a05ee3f3a027148ef0aeb2b1b34e1"))
+ (let ((commit "7e9e92c86b0fc4c848d164fe571798add5e1e36e"))
(package
(name "xf86-video-intel")
- (version (string-append "2.99.917-3-" (string-take commit 7)))
+ (version (string-append "2.99.917-4-" (string-take commit 7)))
(source
(origin
;; there's no current tarball
@@ -2824,7 +2824,7 @@ X server.")
(commit commit)))
(sha256
(base32
- "0hf3fxv5jchyh820h449c1ld9x19gc8081w1yk98mab6zr89zswp"))
+ "0igfw8vpz1q0a2526j81fl65z6avfh6lzzrijcs72gwihqqhb1sv"))
(file-name (string-append name "-" version))))
(build-system gnu-build-system)
(inputs `(("mesa" ,mesa)
@@ -2994,7 +2994,7 @@ supported, and the RENDER extension is not accelerated by this driver.")
(define-public xf86-video-nouveau
(package
(name "xf86-video-nouveau")
- (version "1.0.13")
+ (version "1.0.14")
(source
(origin
(method url-fetch)
@@ -3004,7 +3004,7 @@ supported, and the RENDER extension is not accelerated by this driver.")
".tar.bz2"))
(sha256
(base32
- "1js7vak68g2800f1cy5r41wl5x2j7dbmbd7zxypzfgcw2fx454kd"))))
+ "1h9izq510m2pvg77d0y9krc0cvvbhp2y3xlrrz6id7y47jdzkpsd"))))
(build-system gnu-build-system)
(inputs `(("xorg-server" ,xorg-server)))
(native-inputs `(("pkg-config" ,pkg-config)))