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-rw-r--r--build-aux/run-system-tests.scm3
-rw-r--r--gnu/build/file-systems.scm35
-rw-r--r--gnu/packages/bioinformatics.scm33
-rw-r--r--gnu/packages/dav.scm4
-rw-r--r--gnu/packages/gnome.scm7
-rw-r--r--gnu/packages/gnupg.scm11
-rw-r--r--gnu/packages/gnustep.scm5
-rw-r--r--gnu/packages/image.scm4
-rw-r--r--gnu/packages/linux.scm33
-rw-r--r--gnu/packages/python.scm9
-rw-r--r--gnu/packages/sdl.scm35
-rw-r--r--gnu/packages/security-token.scm38
-rw-r--r--gnu/packages/statistics.scm8
-rw-r--r--gnu/packages/textutils.scm86
-rw-r--r--gnu/packages/valgrind.scm29
-rw-r--r--gnu/system/mapped-devices.scm8
-rw-r--r--gnu/tests/install.scm172
-rw-r--r--tests/pypi.scm4
-rw-r--r--tests/syscalls.scm5
19 files changed, 455 insertions, 74 deletions
diff --git a/build-aux/run-system-tests.scm b/build-aux/run-system-tests.scm
index 3f3a70e7b4..b582bc5e57 100644
--- a/build-aux/run-system-tests.scm
+++ b/build-aux/run-system-tests.scm
@@ -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))
diff --git a/gnu/build/file-systems.scm b/gnu/build/file-systems.scm
index f1fccbdf2e..bfc353ae6b 100644
--- a/gnu/build/file-systems.scm
+++ b/gnu/build/file-systems.scm
@@ -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
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index fa35531868..4e9397e14e 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -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")
diff --git a/gnu/packages/dav.scm b/gnu/packages/dav.scm
index ba56d0d852..835b8fcf39 100644
--- a/gnu/packages/dav.scm
+++ b/gnu/packages/dav.scm
@@ -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
diff --git a/gnu/packages/gnome.scm b/gnu/packages/gnome.scm
index a4ae777383..8b7da30152 100644
--- a/gnu/packages/gnome.scm
+++ b/gnu/packages/gnome.scm
@@ -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
diff --git a/gnu/packages/gnupg.scm b/gnu/packages/gnupg.scm
index dd75ea5c34..a3a42cc2f2 100644
--- a/gnu/packages/gnupg.scm
+++ b/gnu/packages/gnupg.scm
@@ -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 _
diff --git a/gnu/packages/gnustep.scm b/gnu/packages/gnustep.scm
index f49b25492e..6c365cbbc4 100644
--- a/gnu/packages/gnustep.scm
+++ b/gnu/packages/gnustep.scm
@@ -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/")
diff --git a/gnu/packages/image.scm b/gnu/packages/image.scm
index 286708cb1d..d97e853828 100644
--- a/gnu/packages/image.scm
+++ b/gnu/packages/image.scm
@@ -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
diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm
index 1a4b50359d..d9189b12a0 100644
--- a/gnu/packages/linux.scm
+++ b/gnu/packages/linux.scm
@@ -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
diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 73cabe8228..9b25b3ff62 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -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
diff --git a/gnu/packages/sdl.scm b/gnu/packages/sdl.scm
index 161689bf24..bb4ad1c90b 100644
--- a/gnu/packages/sdl.scm
+++ b/gnu/packages/sdl.scm
@@ -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
diff --git a/gnu/packages/security-token.scm b/gnu/packages/security-token.scm
index 36ccaa5203..735b2fe0ec 100644
--- a/gnu/packages/security-token.scm
+++ b/gnu/packages/security-token.scm
@@ -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")
diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index ee6e69346a..4df1e2457a 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -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)
diff --git a/gnu/packages/textutils.scm b/gnu/packages/textutils.scm
index a9725b47d3..2259a16c91 100644
--- a/gnu/packages/textutils.scm
+++ b/gnu/packages/textutils.scm
@@ -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))))
diff --git a/gnu/packages/valgrind.scm b/gnu/packages/valgrind.scm
index ed847c2def..5f2bef16df 100644
--- a/gnu/packages/valgrind.scm
+++ b/gnu/packages/valgrind.scm
@@ -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$")
+ (("obj:/lib") "obj:*/lib")
+ (("obj:/usr/X11R6/lib") "obj:*/lib")
+ (("obj:/usr/lib") "obj:*/lib"))
+ #t))))))
(inputs `(;; GDB is needed to provide a sane default for `--db-command'.
("gdb" ,gdb)))
(native-inputs `(("perl" ,perl)))
diff --git a/gnu/system/mapped-devices.scm b/gnu/system/mapped-devices.scm
index 2487638c52..e44f2693a7 100644
--- a/gnu/system/mapped-devices.scm
+++ b/gnu/system/mapped-devices.scm
@@ -24,7 +24,7 @@
#:use-module (gnu services)
#:use-module (gnu services shepherd)
#:autoload (gnu packages cryptsetup) (cryptsetup)
- #:autoload (gnu packages linux) (mdadm)
+ #:autoload (gnu packages linux) (mdadm-static)
#:use-module (srfi srfi-1)
#:use-module (ice-9 match)
#:export (mapped-device
@@ -150,12 +150,14 @@ TARGET (e.g., \"/dev/md0\"), using 'mdadm'."
(sleep 1)
(loop (+ 1 attempts))))
- (zero? (apply system* (string-append #$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" #$target)))
(define raid-device-mapping
diff --git a/gnu/tests/install.scm b/gnu/tests/install.scm
index 4e79fdb294..98f8649af8 100644
--- a/gnu/tests/install.scm
+++ b/gnu/tests/install.scm
@@ -33,6 +33,8 @@
#:use-module (guix gexp)
#:use-module (guix utils)
#:export (%test-installed-os
+ %test-separate-store-os
+ %test-raid-root-os
%test-encrypted-os))
;;; Commentary:
@@ -190,9 +192,9 @@ the installed system."
(gexp->derivation "installation" install)))
-(define (qemu-command/writable-image image)
+(define* (qemu-command/writable-image image #:key (memory-size 256))
"Return as a monadic value the command to run QEMU on a writable copy of
-IMAGE, a disk image."
+IMAGE, a disk image. The QEMU VM is has access to MEMORY-SIZE MiB of RAM."
(mlet %store-monad ((system (current-system)))
(return #~(let ((image #$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))
diff --git a/tests/pypi.scm b/tests/pypi.scm
index ab4e9c958b..9d2fcc7391 100644
--- a/tests/pypi.scm
+++ b/tests/pypi.scm
@@ -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))
diff --git a/tests/syscalls.scm b/tests/syscalls.scm
index 1b31d87f23..9eb19f9c80 100644
--- a/tests/syscalls.scm
+++ b/tests/syscalls.scm
@@ -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
generated by cgit v1.2.3 (git 2.25.4) at 2024-06-28 08:01:37 +0000