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Merge branch 'master' into core-updates

master
Mark H Weaver 2016-10-27 20:21:26 -04:00
parent f9a65318dd 7500e42b3e
commit 3d82676919
No known key found for this signature in database
GPG Key ID: 7CEF29847562C516
19 changed files with 455 additions and 74 deletions
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3
build-aux/run-system-tests.scm
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@ -68,7 +68,8 @@
(out -> (map derivation->output-path drv)))
(mbegin %store-monad
(show-what-to-build* drv)
(set-build-options* #:keep-going? #t #:keep-failed? #t)
(set-build-options* #:keep-going? #t #:keep-failed? #t
#:fallback? #t)
(built-derivations* drv)
(mlet %store-monad ((valid (filterm (store-lift valid-path?)
out))

35
gnu/build/file-systems.scm
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@ -192,15 +192,15 @@ not valid header was found."
(define (disk-partitions)
"Return the list of device names corresponding to valid disk partitions."
(define (partition? major minor)
(let ((marker (format #f "/sys/dev/block/~a:~a/partition" major minor)))
(catch 'system-error
(lambda ()
(not (zero? (call-with-input-file marker read))))
(lambda args
(if (= ENOENT (system-error-errno args))
#f
(apply throw args))))))
(define (last-character str)
(string-ref str (- (string-length str) 1)))
(define (partition? name major minor)
;; Select device names that end in a digit, like libblkid's 'probe_all'
;; function does. Checking for "/sys/dev/block/MAJOR:MINOR/partition"
;; doesn't work for partitions coming from mapped devices.
(and (char-set-contains? char-set:digit (last-character name))
(> major 2))) ;ignore RAM disks and floppy disks
(call-with-input-file "/proc/partitions"
(lambda (port)
@ -217,7 +217,7 @@ not valid header was found."
(match (string-tokenize line)
(((= string->number major) (= string->number minor)
blocks name)
(if (partition? major minor)
(if (partition? name major minor)
(loop (cons name parts))
(loop parts))))))))))
@ -232,12 +232,15 @@ warning and #f as the result."
;; When running on the hand-made /dev,
;; 'disk-partitions' could return partitions for which
;; we have no /dev node. Handle that gracefully.
(if (= ENOENT (system-error-errno args))
(begin
(format (current-error-port)
"warning: device '~a' not found~%" device)
#f)
(apply throw args))))))
(let ((errno (system-error-errno args)))
(cond ((= ENOENT errno)
(format (current-error-port)
"warning: device '~a' not found~%" device)
#f)
((= ENOMEDIUM errno) ;for removable media
#f)
(else
(apply throw args))))))))
(define (partition-predicate read field =)
"Return a predicate that returns true if the FIELD of partition header that

33
gnu/packages/bioinformatics.scm
View File

@ -7394,6 +7394,39 @@ library implementing most of the pipeline's features.")
@dfn{RNA-centric annotation system} (RCAS).")
(license license:agpl3+)))
(define-public r-mutationalpatterns
(package
(name "r-mutationalpatterns")
(version "1.0.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "MutationalPatterns" version))
(sha256
(base32
"1a3c2bm0xx0q4gf98jiw74msmdf2fr8rbsdysd5ww9kqlzmsbr17"))))
(build-system r-build-system)
(propagated-inputs
`(("r-biocgenerics" ,r-biocgenerics)
("r-biostrings" ,r-biostrings)
("r-genomicranges" ,r-genomicranges)
("r-genomeinfodb" ,r-genomeinfodb)
("r-ggplot2" ,r-ggplot2)
("r-gridextra" ,r-gridextra)
("r-iranges" ,r-iranges)
("r-nmf" ,r-nmf)
("r-plyr" ,r-plyr)
("r-pracma" ,r-pracma)
("r-reshape2" ,r-reshape2)
("r-summarizedexperiment" ,r-summarizedexperiment)
("r-variantannotation" ,r-variantannotation)))
(home-page "http://bioconductor.org/packages/MutationalPatterns/")
(synopsis "Extract and visualize mutational patterns in genomic data")
(description "This package provides an extensive toolset for the
characterization and visualization of a wide range of mutational patterns
in SNV base substitution data.")
(license license:expat)))
(define-public emboss
(package
(name "emboss")

4
gnu/packages/dav.scm
View File

@ -60,13 +60,13 @@ clients.")
(define-public vdirsyncer
(package
(name "vdirsyncer")
(version "0.13.1")
(version "0.14.0")
(source (origin
(method url-fetch)
(uri (pypi-uri name version))
(sha256
(base32
"1c4kipcc7dx1rn5j1a1x7wckz09mm9ihwakf3ramwn1y78q5zanb"))))
"1mbh2gykx9sqsnyfa962ifxksx4afl2lb9rcsbd6rsh3gj2il898"))))
(build-system python-build-system)
(arguments
`(#:phases (modify-phases %standard-phases

7
gnu/packages/gnome.scm
View File

@ -3868,7 +3868,7 @@ metadata in photo and video files of various formats.")
(define-public shotwell
(package
(name "shotwell")
(version "0.23.5")
(version "0.25.0")
(source (origin
(method url-fetch)
(uri (string-append "mirror://gnome/sources/" name "/"
@ -3876,7 +3876,7 @@ metadata in photo and video files of various formats.")
name "-" version ".tar.xz"))
(sha256
(base32
"0fgs1rgvkmy79bmpxrsvm5w8rvqml4l1vnwma0xqx5zzm02p8a07"))))
"0f3ly7nxy3kqwgs40avsqkxcz98bfmlhlk30n0d7j7ndk67zz57h"))))
(build-system glib-or-gtk-build-system)
(propagated-inputs
`(("dconf" ,dconf)))
@ -3899,7 +3899,8 @@ metadata in photo and video files of various formats.")
("libsoup" ,libsoup)
("libxml2" ,libxml2)
("libgudev" ,libgudev)
("libgphoto2" ,libgphoto2)))
("libgphoto2" ,libgphoto2)
("gcr" ,gcr)))
(home-page "https://wiki.gnome.org/Apps/Shotwell")
(synopsis "Photo manager for GNOME 3")
(description

11
gnu/packages/gnupg.scm
View File

@ -9,6 +9,7 @@
;;; Copyright © 2016 Christopher Allan Webber <cwebber@dustycloud.org>
;;; Copyright © 2016 Nils Gillmann <ng0@libertad.pw>
;;; Copyright © 2016 Christopher Baines <mail@cbaines.net>
;;; Copyright © 2016 Mike Gerwitz <mtg@gnu.org>
;;;
;;; This file is part of GNU Guix.
;;;
@ -43,6 +44,7 @@
#:use-module (gnu packages gnome)
#:use-module (gnu packages pkg-config)
#:use-module (gnu packages ncurses)
#:use-module (gnu packages security-token)
#:use-module (gnu packages tls)
#:use-module (guix packages)
#:use-module (guix download)
@ -233,6 +235,7 @@ compatible to GNU Pth.")
("libksba" ,libksba)
("npth" ,npth)
("openldap" ,openldap)
("pcsc-lite" ,pcsc-lite)
("readline" ,readline)
("sqlite" ,sqlite)
("zlib" ,zlib)))
@ -240,10 +243,14 @@ compatible to GNU Pth.")
`(#:configure-flags '("--enable-gpg2-is-gpg")
#:phases
(modify-phases %standard-phases
(add-before 'configure 'patch-config-files
(lambda _
(add-before 'configure 'patch-paths
(lambda* (#:key inputs #:allow-other-keys)
(substitute* "tests/openpgp/defs.inc"
(("/bin/pwd") (which "pwd")))
(substitute* "scd/scdaemon.c"
(("\"(libpcsclite\\.so[^\"]*)\"" _ name)
(string-append "\"" (assoc-ref inputs "pcsc-lite")
"/lib/" name "\"")))
#t))
(add-after 'build 'patch-scheme-tests
(lambda _

5
gnu/packages/gnustep.scm
View File

@ -76,7 +76,10 @@
("libxft" ,libxft)
("libx11" ,libx11)
("fontconfig" ,fontconfig)
("libjpeg" ,libjpeg)))
("libjpeg" ,libjpeg)
("giflib" ,giflib)
("libpng" ,libpng)
("libtiff" ,libtiff)))
(native-inputs
`(("pkg-config" ,pkg-config)))
(home-page "http://windowmaker.org/")

4
gnu/packages/image.scm
View File

@ -770,14 +770,14 @@ convert, manipulate, filter and display a wide variety of image formats.")
(define-public jasper
(package
(name "jasper")
(version "1.900.13")
(version "1.900.16")
(source (origin
(method url-fetch)
(uri (string-append "https://www.ece.uvic.ca/~frodo/jasper"
"/software/jasper-" version ".tar.gz"))
(sha256
(base32
"0nmy5248gar057s94a30fssvq70m3jy4vdrfcispvn01ih33fa19"))))
"0wgrz6970sf8apyld35vrxamzx46fq15l0ipkvjsjlbwfrhj57rl"))))
(build-system gnu-build-system)
(arguments
'(#:make-flags '("CFLAGS=-std=c99"))) ; 1.900.13 added c++ style comments

33
gnu/packages/linux.scm
View File

@ -2396,6 +2396,35 @@ assemble, report on, and monitor arrays. It can also move spares between raid
arrays when needed.")
(license license:gpl2+)))
(define-public mdadm-static
(package
(inherit mdadm)
(name "mdadm-static")
(arguments
(substitute-keyword-arguments (package-arguments mdadm)
((#:make-flags flags)
`(cons "LDFLAGS = -static" ,flags))
((#:phases phases)
`(modify-phases ,phases
(add-after 'install 'remove-cruft
(lambda* (#:key outputs #:allow-other-keys)
(let* ((out (assoc-ref outputs "out"))
(precious? (lambda (file)
(member file '("." ".." "sbin"))))
(directories (scandir out (negate precious?))))
(with-directory-excursion out
(for-each delete-file-recursively directories)
(remove-store-references "sbin/mdadm")
(delete-file "sbin/mdmon")
#t))))))
((#:modules modules %gnu-build-system-modules)
`((ice-9 ftw) ,@modules))
((#:strip-flags _ '())
''("--strip-all")) ;strip a few extra KiB
((#:allowed-references _ '("out"))
'("out")))) ;refer only self
(synopsis "Statically-linked 'mdadm' command for use in an initrd")))
(define-public libaio
(package
(name "libaio")
@ -2975,14 +3004,14 @@ the default @code{nsswitch} and the experimental @code{umich_ldap}.")
(define-public mcelog
(package
(name "mcelog")
(version "143")
(version "144")
(source (origin
(method url-fetch)
(uri (string-append "https://git.kernel.org/cgit/utils/cpu/mce/"
"mcelog.git/snapshot/v" version ".tar.gz"))
(sha256
(base32
"1mn5i1d6ybfxqgr6smlpxcx1wb53h0r2rp90ild7919b9yqxpk0x"))
"03jyhsl0s59sfqykj5p6gkb03k4w1h9ay31yxym1dnzis5sq99pa"))
(file-name (string-append name "-" version ".tar.gz"))
(modules '((guix build utils)))
(snippet

9
gnu/packages/python.scm
View File

@ -7773,14 +7773,14 @@ concurrent.futures package from Python 3.2")
(define-public python-urllib3
(package
(name "python-urllib3")
(version "1.13.1")
(version "1.18.1")
(source
(origin
(method url-fetch)
(uri (pypi-uri "urllib3" version))
(sha256
(base32
"10rrbr6c6k7j5dvfsyj4b2gsgxg9gggnn708qixf6ll57xqivfkf"))))
"1wb8aqnq53vzh2amrv8kc66f3h6fx217y0q62y6n30a64p2yqmam"))))
(build-system python-build-system)
(arguments `(#:tests? #f))
(native-inputs
@ -7795,7 +7795,7 @@ concurrent.futures package from Python 3.2")
("python-ndg-httpsclient" ,python-ndg-httpsclient)
("python-pyasn1" ,python-pyasn1)
("python-pyopenssl" ,python-pyopenssl)))
(home-page "http://urllib3.readthedocs.org/")
(home-page "https://urllib3.readthedocs.org/")
(synopsis "HTTP library with thread-safe connection pooling")
(description
"Urllib3 supports features left out of urllib and urllib2 libraries. It
@ -8984,6 +8984,9 @@ anymore.")
(base32
"0p050msg5c8d0kadv702jnfshaxrb0il765cpkgnhn6mq5hakcyy"))))
(build-system python-build-system)
;; We only need the the Python 2 variant, since for Python 3 our minimum
;; version is 3.4 which already includes this package as part of the
;; standard library.
(arguments
`(#:python ,python-2))
(native-inputs

35
gnu/packages/sdl.scm
View File

@ -3,6 +3,7 @@
;;; Copyright © 2014 Mark H Weaver <mhw@netris.org>
;;; Copyright © 2015 Sou Bunnbu <iyzsong@gmail.com>
;;; Copyright © 2015 Alex Kost <alezost@gmail.com>
;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il>
;;;
;;; This file is part of GNU Guix.
;;;
@ -47,7 +48,7 @@
(source (origin
(method url-fetch)
(uri
(string-append "http://libsdl.org/release/SDL-"
(string-append "https://libsdl.org/release/SDL-"
version ".tar.gz"))
(sha256
(base32
@ -81,34 +82,34 @@
(description "Simple DirectMedia Layer is a cross-platform development
library designed to provide low level access to audio, keyboard, mouse,
joystick, and graphics hardware.")
(home-page "http://libsdl.org/")
(home-page "https://libsdl.org/")
(license lgpl2.1)))
(define-public sdl2
(package (inherit sdl)
(name "sdl2")
(version "2.0.4")
(version "2.0.5")
(source (origin
(method url-fetch)
(uri
(string-append "http://libsdl.org/release/SDL2-"
(string-append "https://libsdl.org/release/SDL2-"
version ".tar.gz"))
(sha256
(base32
"0jqp46mxxbh9lhpx1ih6sp93k752j2smhpc0ad0q4cb3px0famfs"))))
"11c75qj1qxmx67iwkvf9z4x69phk301pdn86zzr6jncnap7kh824"))))
(license bsd-3)))
(define-public libmikmod
(package
(name "libmikmod")
(version "3.3.7")
(version "3.3.10")
(source (origin
(method url-fetch)
(uri (string-append "mirror://sourceforge/mikmod/libmikmod/"
version "/libmikmod-" version ".tar.gz"))
(sha256
(base32
"18nrkf5l50hfg0y50yxr7bvik9f002lhn8c00nbcp6dgm5011x2c"))))
"0j7g4jpa2zgzw7x6s3rldypa7zlwjvn97rwx0sylx1iihhlzbcq0"))))
(build-system gnu-build-system)
(arguments
;; By default, libmikmod tries to dlopen libasound etc., which won't work
@ -154,7 +155,7 @@ other supporting functions for SDL.")
(source (origin
(method url-fetch)
(uri
(string-append "http://www.libsdl.org/projects/SDL_image/release/SDL_image-"
(string-append "https://www.libsdl.org/projects/SDL_image/release/SDL_image-"
version ".tar.gz"))
(sha256
(base32
@ -180,7 +181,7 @@ other supporting functions for SDL.")
(description "SDL_image is an image file loading library for SDL that
supports the following formats: BMP, GIF, JPEG, LBM, PCX, PNG, PNM, TGA, TIFF,
WEBP, XCF, XPM, and XV.")
(home-page "http://www.libsdl.org/projects/SDL_image/")
(home-page "https://www.libsdl.org/projects/SDL_image/")
(license zlib)))
(define-public sdl-mixer
@ -190,7 +191,7 @@ WEBP, XCF, XPM, and XV.")
(source (origin
(method url-fetch)
(uri
(string-append "http://www.libsdl.org/projects/SDL_mixer/release/SDL_mixer-"
(string-append "https://www.libsdl.org/projects/SDL_mixer/release/SDL_mixer-"
version ".tar.gz"))
(sha256
(base32
@ -218,7 +219,7 @@ WEBP, XCF, XPM, and XV.")
It supports any number of simultaneously playing channels of 16 bit stereo
audio, plus a single channel of music. Supported format include FLAC, MOD,
MIDI, Ogg Vorbis, and MP3.")
(home-page "http://www.libsdl.org/projects/SDL_mixer/")
(home-page "https://www.libsdl.org/projects/SDL_mixer/")
(license zlib)))
(define-public sdl-net
@ -228,7 +229,7 @@ MIDI, Ogg Vorbis, and MP3.")
(source (origin
(method url-fetch)
(uri
(string-append "http://www.libsdl.org/projects/SDL_net/release/SDL_net-"
(string-append "https://www.libsdl.org/projects/SDL_net/release/SDL_net-"
version ".tar.gz"))
(sha256
(base32
@ -239,7 +240,7 @@ MIDI, Ogg Vorbis, and MP3.")
(synopsis "SDL networking library")
(description "SDL_net is a small, cross-platform networking library for
SDL.")
(home-page "http://www.libsdl.org/projects/SDL_net/")
(home-page "https://www.libsdl.org/projects/SDL_net/")
(license zlib)))
(define-public sdl-ttf
@ -249,7 +250,7 @@ SDL.")
(source (origin
(method url-fetch)
(uri
(string-append "http://www.libsdl.org/projects/SDL_ttf/release/SDL_ttf-"
(string-append "https://www.libsdl.org/projects/SDL_ttf/release/SDL_ttf-"
version ".tar.gz"))
(sha256
(base32
@ -261,7 +262,7 @@ SDL.")
(native-inputs `(("pkg-config" ,pkg-config)))
(synopsis "SDL TrueType font library")
(description "SDL_ttf is a TrueType font rendering library for SDL.")
(home-page "http://www.libsdl.org/projects/SDL_ttf/")
(home-page "https://www.libsdl.org/projects/SDL_ttf/")
(license zlib)))
(define* (sdl-union #:optional (packages (list sdl sdl-gfx sdl-net sdl-ttf
@ -308,7 +309,7 @@ directory.")
(source (origin
(method url-fetch)
(uri
(string-append "http://www.libsdl.org/projects/SDL_image/release/SDL2_image-"
(string-append "https://www.libsdl.org/projects/SDL_image/release/SDL2_image-"
version ".tar.gz"))
(sha256
(base32
@ -342,7 +343,7 @@ directory.")
(source (origin
(method url-fetch)
(uri
(string-append "http://www.libsdl.org/projects/SDL_ttf/release/SDL2_ttf-"
(string-append "https://www.libsdl.org/projects/SDL_ttf/release/SDL2_ttf-"
version ".tar.gz"))
(modules '((guix build utils)))
(snippet

38
gnu/packages/security-token.scm
View File

@ -1,6 +1,7 @@
;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2014 Ludovic Courtès <ludo@gnu.org>
;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il>
;;; Copyright © 2016 Mike Gerwitz <mtg@gnu.org>
;;;
;;; This file is part of GNU Guix.
;;;
@ -23,9 +24,11 @@
#:use-module (guix packages)
#:use-module (guix download)
#:use-module (guix build-system gnu)
#:use-module (gnu packages pkg-config)
#:use-module (gnu packages curl)
#:use-module (gnu packages linux)
#:use-module (gnu packages man)
#:use-module (gnu packages curl))
#:use-module (gnu packages perl)
#:use-module (gnu packages pkg-config))
(define-public libyubikey
(package
@ -47,6 +50,37 @@ the low-level development kit for the Yubico YubiKey authentication device.")
(home-page "https://developers.yubico.com/yubico-c/")
(license license:bsd-2)))
(define-public pcsc-lite
(package
(name "pcsc-lite")
(version "1.8.18")
(source (origin
(method url-fetch)
(uri (string-append
"https://alioth.debian.org/frs/download.php/file/4179/"
"pcsc-lite-" version ".tar.bz2"))
(sha256
(base32
"0189s10xsgcmdvc2sixakncwlv47cg6by6m9vdm038gn32q34bdj"))))
(build-system gnu-build-system)
(arguments
`(#:configure-flags '("--enable-usbdropdir=/var/lib/pcsc/drivers")))
(native-inputs
`(("perl" ,perl) ; for pod2man
("pkg-config" ,pkg-config)))
(inputs
`(("libudev" ,eudev)))
(home-page "https://pcsclite.alioth.debian.org/pcsclite.html")
(synopsis "Middleware to access a smart card using PC/SC")
(description
"pcsc-lite provides an interface to communicate with smartcards and
readers using the SCard API. pcsc-lite is used to connect to the PC/SC daemon
from a client application and provide access to the desired reader.")
(license (list license:bsd-3 ; pcsc-lite
license:expat ; src/sd-daemon.[ch]
license:isc ; src/strlcat.c src/strlcpy.c
license:gpl3+)))) ; src/spy/*
(define-public ykclient
(package
(name "ykclient")

8
gnu/packages/statistics.scm
View File

@ -118,6 +118,13 @@ be output in text, PostScript, PDF or HTML.")
"/lib/R/lib"))
#:phases
(modify-phases %standard-phases
(add-before 'configure 'patch-uname
(lambda* (#:key inputs #:allow-other-keys)
(let ((uname-bin (string-append (assoc-ref inputs "coreutils")
"/bin/uname")))
(substitute* "src/scripts/R.sh.in"
(("uname") uname-bin)))
#t))
(add-before
'configure 'set-default-pager
;; Set default pager to "cat", because otherwise it is "false",
@ -170,6 +177,7 @@ be output in text, PostScript, PDF or HTML.")
`(;; We need not only cairo here, but pango to ensure that tests for the
;; "cairo" bitmapType plotting backend succeed.
("pango" ,pango)
("coreutils" ,coreutils)
("curl" ,curl)
("tzdata" ,tzdata)
("openblas" ,openblas)

86
gnu/packages/textutils.scm
View File

@ -6,6 +6,7 @@
;;; Copyright © 2016 Jelle Licht <jlicht@fsfe.org>
;;; Copyright © 2016 Alex Griffin <a@ajgrf.com>
;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il>
;;; Copyright © 2016 ng0 <ng0@we.make.ritual.n0.is>
;;;
;;; This file is part of GNU Guix.
;;;
@ -32,7 +33,12 @@
#:use-module (guix build-system trivial)
#:use-module (gnu packages)
#:use-module (gnu packages autotools)
#:use-module (gnu packages ncurses)
#:use-module (gnu packages perl)
#:use-module (gnu packages pkg-config)
#:use-module (gnu packages python)
#:use-module (gnu packages readline)
#:use-module (gnu packages slang)
#:use-module (gnu packages zip))
(define-public recode
@ -373,3 +379,83 @@ runs Word\".")
(description "UTF8-CPP is a C++ library for handling UTF-8 encoded text
in a portable way.")
(license license:boost1.0)))
(define-public dbacl
(package
(name "dbacl")
(version "1.14")
(source
(origin
(method url-fetch)
(uri (string-append "http://www.lbreyer.com/gpl/"
name "-" version ".tar.gz"))
(sha256
(base32
"0224g6x71hyvy7jikfxmgcwww1r5lvk0jx36cva319cb9nmrbrq7"))))
(build-system gnu-build-system)
(arguments
`(#:make-flags
(list
(string-append "-I" (assoc-ref %build-inputs "slang")
"/include/slang")
(string-append "-I" (assoc-ref %build-inputs "ncurses")
"/include/ncurses"))
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'delete-sample6-and-japanese
(lambda _
(substitute* "doc/Makefile.am"
(("sample6.txt") "")
(("japanese.txt") ""))
(delete-file "doc/sample6.txt")
(delete-file "doc/japanese.txt")
(substitute* (list "src/tests/Makefile.am"
"src/tests/Makefile.in")
(("dbacl-jap.shin") "")
(("dbacl-jap.sh") ""))
#t))
(add-after 'unpack 'delete-test
;; See comments about the license.
(lambda _
(delete-file "src/tests/dbacl-jap.shin")))
(add-after 'delete-sample6-and-japanese 'autoreconf
(lambda _
(zero? (system* "autoreconf" "-vif"))))
(add-after 'unpack 'fix-test-files
(lambda* (#:key inputs outputs #:allow-other-keys)
(let* ((out (assoc-ref outputs "out"))
(bin (string-append out "/bin")))
(substitute* (find-files "src/tests/" "\\.shin$")
(("PATH=/bin:/usr/bin")
"#PATH=/bin:/usr/bin")
(("diff") (string-append (which "diff")))
(("tr") (string-append (which "tr"))))
#t))))))
(inputs
`(("ncurses" ,ncurses)
("perl" ,perl)
("readline" ,readline)
("slang" ,slang)))
(native-inputs
`(("libtool" ,libtool)
("autoconf" ,autoconf)
("automake" ,automake)
("pkg-config" ,pkg-config)))
(home-page "http://www.lbreyer.com/dbacl.html")
(synopsis "Bayesian text and email classifier")
(description
"dbacl is a fast Bayesian text and email classifier. It builds a variety
of language models using maximum entropy (minimum divergence) principles, and
these can then be used to categorize input data automatically among multiple
categories.")
;; The software is licensed as GPLv3 or later, but
;; includes various sample texts in the doc dir:
;; - sample1.txt, sample3 and sampe5.txt are in the public domain,
;; by Mark Twain.
;; - sample2.txt, sample4.txt are in the public domain, by Aristotle.
;; - sample6.txt is a forwarded email, copyright unknown.
;; Guix does exclude sample6.txt.
;; - japanese.txt is a Japanese unoffical translation of the
;; GNU General Public License, (c) by the Free Software Foundation.
;; Guix excludes this file.
(license (list license:gpl3+ license:public-domain))))

29
gnu/packages/valgrind.scm
View File

@ -2,6 +2,7 @@
;;; Copyright © 2013, 2014 Ludovic Courtès <ludo@gnu.org>
;;; Copyright © 2015 Andreas Enge <andreas@enge.fr>
;;; Copyright © 2015 Mark H Weaver <mhw@netris.org>
;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il>
;;;
;;; This file is part of GNU Guix.
;;;
@ -30,29 +31,29 @@
(define-public valgrind
(package
(name "valgrind")
(version "3.11.0")
(version "3.12.0")
(source (origin
(method url-fetch)
(uri (string-append "http://valgrind.org/downloads/valgrind-"
version ".tar.bz2"))
(sha256
(base32
"0hiv871b9bk689mv42mkhp76za78l5773glszfkdbpf1m1qn4fbc"))
"18bnrw9b1d55wi1wnl68n25achsp9w48n51n1xw4fwjjnaal7jk7"))
(patches (search-patches "valgrind-enable-arm.patch"))))
(build-system gnu-build-system)
(arguments
'(#:phases (alist-cons-after
'install 'patch-suppression-files
(lambda* (#:key outputs #:allow-other-keys)
;; Don't assume the FHS.
(let* ((out (assoc-ref outputs "out"))
(dir (string-append out "/lib/valgrind")))
(substitute* (find-files dir "\\.supp$")
(("obj:/lib") "obj:*/lib")
(("obj:/usr/X11R6/lib") "obj:*/lib")
(("obj:/usr/lib") "obj:*/lib"))
#t))
%standard-phases)))
'(#:phases
(modify-phases %standard-phases
(add-after 'install 'patch-suppression-files
(lambda* (#:key outputs #:allow-other-keys)
;; Don't assume the FHS.
(let* ((out (assoc-ref outputs "out"))
(dir (string-append out "/lib/valgrind")))
(substitute* (find-files dir "\\.supp$")
(("obj:/lib") "obj:*/lib")
(("obj:/usr/X11R6/lib") "obj:*/lib")
(("obj:/usr/lib") "obj:*/lib"))
#t))))))
(inputs `(;; GDB is needed to provide a sane default for `--db-command'.
("gdb" ,gdb)))
(native-inputs `(("perl" ,perl)))

8
gnu/system/mapped-devices.scm
View File

@ -24,7 +24,7 @@
#:use-module (gnu services)
#:use-module (gnu services shepherd)
#:autoload (gnu packages cryptsetup) (cryptsetup)
#:autoload (gnu packages linux) (mdadm)
#:autoload (gnu packages linux) (mdadm-static)
#:use-module (srfi srfi-1)
#:use-module (ice-9 match)
#:export (mapped-device
@ -150,12 +150,14 @@ TARGET (e.g., \"/dev/md0\"), using 'mdadm'."
(sleep 1)
(loop (+ 1 attempts))))
(zero? (apply system* (string-append #$mdadm "/sbin/mdadm")
;; Use 'mdadm-static' rather than 'mdadm' to avoid pulling its whole
;; closure (80 MiB) in the initrd when a RAID device is needed for boot.
(zero? (apply system* #$(file-append mdadm-static "/sbin/mdadm")
"--assemble" #$target sources))))
(define (close-raid-device sources target)
"Return a gexp that stops the RAID device TARGET."
#~(zero? (system* (string-append #$mdadm "/sbin/mdadm")
#~(zero? (system* #$(file-append mdadm-static "/sbin/mdadm")
"--stop" #$target)))
(define raid-device-mapping

172
gnu/tests/install.scm
View File

@ -33,6 +33,8 @@
#:use-module (guix gexp)
#:use-module (guix utils)
#:export (%test-installed-os
%test-separate-store-os
%test-raid-root-os
%test-encrypted-os))
;;; Commentary:
@ -190,9 +192,9 @@ the installed system."
(gexp->derivation "installation" install)))
(define (qemu-command/writable-image image)
(define* (qemu-command/writable-image image #:key (memory-size 256))
"Return as a monadic value the command to run QEMU on a writable copy of
IMAGE, a disk image."
IMAGE, a disk image. The QEMU VM is has access to MEMORY-SIZE MiB of RAM."
(mlet %store-monad ((system (current-system)))
(return #~(let ((image #$image))
;; First we need a writable copy of the image.
@ -204,7 +206,7 @@ IMAGE, a disk image."
,@(if (file-exists? "/dev/kvm")
'("-enable-kvm")
'())
"-no-reboot" "-m" "256"
"-no-reboot" "-m" #$(number->string memory-size)
"-drive" "file=disk.img,if=virtio")))))
@ -222,6 +224,170 @@ build (current-guix) and then store a couple of full system images.")
"installed-os")))))
;;;
;;; Separate /gnu/store partition.
;;;
(define-os-with-source (%separate-store-os %separate-store-os-source)
;; The OS we want to install.
(use-modules (gnu) (gnu tests) (srfi srfi-1))
(operating-system
(host-name "liberigilo")
(timezone "Europe/Paris")
(locale "en_US.UTF-8")
(bootloader (grub-configuration (device "/dev/vdb")))
(kernel-arguments '("console=ttyS0"))
(file-systems (cons* (file-system
(device "root-fs")
(title 'label)
(mount-point "/")
(type "ext4"))
(file-system
(device "store-fs")
(title 'label)
(mount-point "/gnu")
(type "ext4")
(needed-for-boot? #t)) ;definitely!
%base-file-systems))
(users %base-user-accounts)
(services (cons (service marionette-service-type
(marionette-configuration
(imported-modules '((gnu services herd)
(guix combinators)))))
%base-services))))
(define %separate-store-installation-script
;; Installation with a separate /gnu partition.
"\
. /etc/profile
set -e -x
guix --version
export GUIX_BUILD_OPTIONS=--no-grafts
guix build isc-dhcp
parted --script /dev/vdb mklabel gpt \\
mkpart primary ext2 1M 3M \\
mkpart primary ext2 3M 100M \\
mkpart primary ext2 100M 1G \\
set 1 boot on \\
set 1 bios_grub on
mkfs.ext4 -L root-fs /dev/vdb2
mkfs.ext4 -L store-fs /dev/vdb3
mount /dev/vdb2 /mnt
mkdir /mnt/gnu
mount /dev/vdb3 /mnt/gnu
df -h /mnt
herd start cow-store /mnt
mkdir /mnt/etc
cp /etc/target-config.scm /mnt/etc/config.scm
guix system init /mnt/etc/config.scm /mnt --no-substitutes
sync
reboot\n")
(define %test-separate-store-os
(system-test
(name "separate-store-os")
(description
"Test basic functionality of an OS installed like one would do by hand,
where /gnu lives on a separate partition.")
(value
(mlet* %store-monad ((image (run-install %separate-store-os
%separate-store-os-source
#:script
%separate-store-installation-script))
(command (qemu-command/writable-image image)))
(run-basic-test %separate-store-os command "separate-store-os")))))
;;;
;;; RAID root device.
;;;
(define-os-with-source (%raid-root-os %raid-root-os-source)
;; An OS whose root partition is a RAID partition.
(use-modules (gnu) (gnu tests))
(operating-system
(host-name "raidified")
(timezone "Europe/Paris")
(locale "en_US.utf8")
(bootloader (grub-configuration (device "/dev/vdb")))
(kernel-arguments '("console=ttyS0"))
(initrd (lambda (file-systems . rest)
;; Add a kernel module for RAID-0 (aka. "stripe").
(apply base-initrd file-systems
#:extra-modules '("raid0")
rest)))
(mapped-devices (list (mapped-device
(source (list "/dev/vda2" "/dev/vda3"))
(target "/dev/md0")
(type raid-device-mapping))))
(file-systems (cons (file-system
(device "root-fs")
(title 'label)
(mount-point "/")
(type "ext4")
(dependencies mapped-devices))
%base-file-systems))
(users %base-user-accounts)
(services (cons (service marionette-service-type
(marionette-configuration
(imported-modules '((gnu services herd)
(guix combinators)))))
%base-services))))
(define %raid-root-installation-script
;; Installation with a separate /gnu partition. See
;; <https://raid.wiki.kernel.org/index.php/RAID_setup> for more on RAID and
;; mdadm.
"\
. /etc/profile
set -e -x
guix --version
export GUIX_BUILD_OPTIONS=--no-grafts
parted --script /dev/vdb mklabel gpt \\
mkpart primary ext2 1M 3M \\
mkpart primary ext2 3M 600M \\
mkpart primary ext2 600M 1200M \\
set 1 boot on \\
set 1 bios_grub on
mdadm --create /dev/md0 --verbose --level=stripe --raid-devices=2 \\
/dev/vdb2 /dev/vdb3
mkfs.ext4 -L root-fs /dev/md0
mount /dev/md0 /mnt
df -h /mnt
herd start cow-store /mnt
mkdir /mnt/etc
cp /etc/target-config.scm /mnt/etc/config.scm
guix system init /mnt/etc/config.scm /mnt --no-substitutes
sync
reboot\n")
(define %test-raid-root-os
(system-test
(name "raid-root-os")
(description
"Test functionality of an OS installed with a RAID root partition managed
by 'mdadm'.")
(value
(mlet* %store-monad ((image (run-install %raid-root-os
%raid-root-os-source
#:script
%raid-root-installation-script
#:target-size (* 1300 MiB)))
(command (qemu-command/writable-image image)))
(run-basic-test %raid-root-os
`(,@command) "raid-root-os")))))
;;;
;;; LUKS-encrypted root file system.
;;;
(define-os-with-source (%encrypted-root-os %encrypted-root-os-source)
;; The OS we want to install.
(use-modules (gnu) (gnu tests) (srfi srfi-1))

4
tests/pypi.scm
View File

@ -122,7 +122,7 @@ baz > 13.37")
('base32
(? string? hash)))))
('build-system 'python-build-system)
('inputs
('propagated-inputs
('quasiquote
(("python-bar" ('unquote 'python-bar))
("python-baz" ('unquote 'python-baz))
@ -182,7 +182,7 @@ baz > 13.37")
('base32
(? string? hash)))))
('build-system 'python-build-system)
('inputs
('propagated-inputs
('quasiquote
(("python-bar" ('unquote 'python-bar))
("python-baz" ('unquote 'python-baz))

5
tests/syscalls.scm
View File

@ -146,7 +146,10 @@
(waitpid fork-pid)
result))))))))
(unless perform-container-tests?
;; XXX: Skip this test when running Linux > 4.7.5 to work around
;; <https://bugzilla.kernel.org/show_bug.cgi?id=183461>.
(when (or (not perform-container-tests?)
(version>? (utsname:release (uname)) "4.7.5"))
(test-skip 1))
(test-equal "pivot-root"
#t