futurile/guix-play
1
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

Merge branch 'master' into core-updates

Browse Source
This commit is contained in:
Marius Bakke 2017-10-22 20:12:52 +02:00
commit 119a749db9
No known key found for this signature in database
GPG Key ID: A2A06DF2A33A54FA
81 changed files with 3039 additions and 653 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

2
Makefile.am
View File

@ -47,6 +47,7 @@ MODULES = \
guix/hash.scm \
guix/pk-crypto.scm \
guix/pki.scm \
guix/progress.scm \
guix/combinators.scm \
guix/memoization.scm \
guix/utils.scm \
@ -105,6 +106,7 @@ MODULES = \
guix/ui.scm \
guix/build/ant-build-system.scm \
guix/build/download.scm \
guix/build/download-nar.scm \
guix/build/cargo-build-system.scm \
guix/build/cmake-build-system.scm \
guix/build/dub-build-system.scm \

7
doc/guix.texi
View File

@ -5881,7 +5881,7 @@ dependency graph of the given upstream package recursively and generate
package expressions for all those packages that are not yet in Guix.
When @code{--archive=bioconductor} is added, metadata is imported from
@uref{http://www.bioconductor.org/, Bioconductor}, a repository of R
@uref{https://www.bioconductor.org/, Bioconductor}, a repository of R
packages for for the analysis and comprehension of high-throughput
genomic data in bioinformatics.
@ -6236,7 +6236,7 @@ the updater for @uref{http://elpa.gnu.org/, ELPA} packages;
@item cran
the updater for @uref{http://cran.r-project.org/, CRAN} packages;
@item bioconductor
the updater for @uref{http://www.bioconductor.org/, Bioconductor} R packages;
the updater for @uref{https://www.bioconductor.org/, Bioconductor} R packages;
@item cpan
the updater for @uref{http://www.cpan.org/, CPAN} packages;
@item pypi
@ -18605,7 +18605,8 @@ The boot script is what the initial RAM disk runs when booting.
@end defvr
@defvr {Scheme Variable} etc-service-type
The type of the @file{/etc} service. This service can be extended by
The type of the @file{/etc} service. This service is used to create
files under @file{/etc} and can be extended by
passing it name/file tuples such as:
@example

10
gnu/local.mk
View File

@ -66,6 +66,7 @@ GNU_SYSTEM_MODULES = \
%D%/packages/autotools.scm \
%D%/packages/avahi.scm \
%D%/packages/avr.scm \
%D%/packages/axoloti.scm \
%D%/packages/backup.scm \
%D%/packages/base.scm \
%D%/packages/bash.scm \
@ -810,6 +811,8 @@ dist_patch_DATA = \
%D%/packages/patches/libtool-skip-tests2.patch \
%D%/packages/patches/libunistring-gnulib-multi-core.patch \
%D%/packages/patches/libusb-0.1-disable-tests.patch \
%D%/packages/patches/libusb-for-axoloti.patch \
%D%/packages/patches/libvirt-CVE-2017-1000256.patch \
%D%/packages/patches/libvisio-fix-tests.patch \
%D%/packages/patches/libvpx-CVE-2016-2818.patch \
%D%/packages/patches/libxcb-python-3.5-compat.patch \
@ -864,8 +867,8 @@ dist_patch_DATA = \
%D%/packages/patches/mozjs38-version-detection.patch \
%D%/packages/patches/mumps-build-parallelism.patch \
%D%/packages/patches/mupdf-build-with-openjpeg-2.1.patch \
%D%/packages/patches/mupdf-CVE-2017-15587.patch \
%D%/packages/patches/mupen64plus-ui-console-notice.patch \
%D%/packages/patches/musl-CVE-2016-8859.patch \
%D%/packages/patches/mutt-store-references.patch \
%D%/packages/patches/ncurses-CVE-2017-10684-10685.patch \
%D%/packages/patches/net-tools-bitrot.patch \
@ -1092,6 +1095,11 @@ dist_patch_DATA = \
%D%/packages/patches/wordnet-CVE-2008-2149.patch \
%D%/packages/patches/wordnet-CVE-2008-3908-pt1.patch \
%D%/packages/patches/wordnet-CVE-2008-3908-pt2.patch \
%D%/packages/patches/wpa-supplicant-CVE-2017-13082.patch \
%D%/packages/patches/wpa-supplicant-fix-key-reuse.patch \
%D%/packages/patches/wpa-supplicant-fix-zeroed-keys.patch \
%D%/packages/patches/wpa-supplicant-fix-nonce-reuse.patch \
%D%/packages/patches/wpa-supplicant-krack-followups.patch \
%D%/packages/patches/xcb-proto-python3-print.patch \
%D%/packages/patches/xcb-proto-python3-whitespace.patch \
%D%/packages/patches/xdotool-fix-makefile.patch \

26
gnu/packages/admin.scm
View File

@ -783,6 +783,11 @@ over ssh connections.")
"/etc"))
#:phases (modify-phases %standard-phases
(add-after 'unpack 'patch-paths
(lambda _
(substitute* "rc/rc"
(("/usr/sbin/sendmail") "sendmail"))
#t))
(add-after 'build 'set-packdir
(lambda _
;; Set a default location for archived logs.
@ -902,6 +907,11 @@ commands and their arguments.")
"http://w1.fi/releases/wpa_supplicant-"
version
".tar.gz"))
(patches (search-patches "wpa-supplicant-CVE-2017-13082.patch"
"wpa-supplicant-fix-key-reuse.patch"
"wpa-supplicant-fix-zeroed-keys.patch"
"wpa-supplicant-fix-nonce-reuse.patch"
"wpa-supplicant-krack-followups.patch"))
(sha256
(base32
"0l0l5gz3d5j9bqjsbjlfcv4w4jwndllp9fmyai4x9kg6qhs6v4xl"))))
@ -2134,7 +2144,7 @@ tool for remote execution and deployment.")
(define-public neofetch
(package
(name "neofetch")
(version "3.2.0")
(version "3.3.0")
(source (origin
(method url-fetch)
(uri (string-append "https://github.com/dylanaraps/neofetch/"
@ -2142,10 +2152,10 @@ tool for remote execution and deployment.")
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
"07a32rzmch51znxspzyc7zyaldmr383v70b49wmnjdjs2qfdbv3a"))))
"15p69q0jchfms1fpb4i7kq8b28w2xpgh2zmynln618qxv1myf228"))))
(build-system gnu-build-system)
(arguments
'(#:tests? #f ; there are no tests
`(#:tests? #f ; there are no tests
#:make-flags
(list (string-append "PREFIX=" %output))
#:phases
@ -2162,7 +2172,15 @@ tool for remote execution and deployment.")
(("\"/usr/share/neofetch")
(string-append "\"" out "/share/neofetch"))))
#t))
(delete 'configure))))
(delete 'configure) ; no configure script
(replace 'install
(lambda* (#:key make-flags outputs #:allow-other-keys)
(let* ((out (assoc-ref outputs "out"))
(doc (string-append out "/share/doc/" ,name "-" ,version))
(etc (string-append doc "/examples/etc")))
(zero? (apply system* `("make" ,@make-flags
,(string-append "SYSCONFDIR=" etc)
"install")))))))))
(home-page "https://github.com/dylanaraps/neofetch")
(synopsis "System info script")
(description "Neofetch is a CLI system information tool written in Bash.

32
gnu/packages/audio.scm
View File

@ -580,7 +580,7 @@ emulation (valve, tape), bit fiddling (decimator, pointer-cast), etc.")
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
"0f67vyy3r29hn26qkkcwnizrnzzy8p7gmg3say5q3wjhxns3b5yl"))))
"0xqpqws4jsv7fyawcjzwaw544qbfh29xq164kdf30a9v1n3yklp4"))))
(build-system cmake-build-system)
(inputs
`(("alsa-lib" ,alsa-lib)
@ -1660,6 +1660,21 @@ add functionality to support the needs of increasingly powerful audio
software.")
(license license:isc)))
(define-public lv2-devel
(let ((commit "39c7c726cd52b2863fcea356cafe1bcab2ba7f37")
(revision "1"))
(package (inherit lv2)
(name "lv2-devel")
(version (string-append "1.15.3-" revision "." (string-take commit 7)))
(source (origin
(method git-fetch)
(uri (git-reference
(url "http://lv2plug.in/git/lv2.git")
(commit commit)))
(sha256
(base32
"1gp2rd99dfmpibvpixrqn115mrhybzf3if3h8bssf6siyi13f29r")))))))
(define-public lv2-mda-piano
(package
(name "lv2-mda-piano")
@ -1916,11 +1931,11 @@ aimed at audio/musical applications.")
(license license:gpl2+)))
(define-public raul-devel
(let ((commit "f8bf77d3c3b77830aedafb9ebb5cdadfea7ed07a")
(let ((commit "4db870b2b20b0a608ec0283139056b836c5b1624")
(revision "1"))
(package (inherit raul)
(name "raul")
(version (string-append "0.8.4-" revision "."
(version (string-append "0.8.9-" revision "."
(string-take commit 9)))
(source (origin
(method git-fetch)
@ -1930,7 +1945,7 @@ aimed at audio/musical applications.")
(file-name (string-append name "-" version "-checkout"))
(sha256
(base32
"1lby508fb0n8ks6iz959sh18fc37br39d6pbapwvbcw5nckdrxwj")))))))
"04fajrass3ymr72flx5js5vxc601ccrmx8ny8scp0rw7j0igyjdr")))))))
(define-public rubberband
(package
@ -2040,14 +2055,14 @@ the Turtle syntax.")
(define-public suil
(package
(name "suil")
(version "0.8.4")
(version "0.10.0")
(source (origin
(method url-fetch)
(uri (string-append "http://download.drobilla.net/suil-"
version ".tar.bz2"))
(sha256
(base32
"1kji3lhha26qr6xm9j8ic5c40zbrrb5qnwm2qxzmsfxgmrz29wkf"))))
"0j489gm3fhnmwmbgw30bvd4byw1vsy4yazdlnji8jzhcz0qwb5cq"))))
(build-system waf-build-system)
(arguments
`(#:tests? #f ; no check target
@ -2055,7 +2070,8 @@ the Turtle syntax.")
'("CXXFLAGS=-std=gnu++11")))
(inputs
`(("lv2" ,lv2)
("gtk+-2" ,gtk+-2)
("gtk+" ,gtk+-2)
("gtk+" ,gtk+)
("qt" ,qtbase)))
(native-inputs
`(("pkg-config" ,pkg-config)))
@ -2069,7 +2085,7 @@ toolkit. The API is designed such that hosts do not need to explicitly
support specific toolkits – if Suil supports a particular toolkit, then UIs in
that toolkit will work in all hosts that use Suil automatically.
Suil currently supports every combination of Gtk 2, Qt 4, and X11.")
Suil currently supports every combination of Gtk, Qt, and X11.")
(license license:isc)))
(define-public timidity++

352
gnu/packages/axoloti.scm Normal file
View File

@ -0,0 +1,352 @@
;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2016, 2017 Ricardo Wurmus <rekado@elephly.net>
;;;
;;; This file is part of GNU Guix.
;;;
;;; GNU Guix is free software; you can redistribute it and/or modify it
;;; under the terms of the GNU General Public License as published by
;;; the Free Software Foundation; either version 3 of the License, or (at
;;; your option) any later version.
;;;
;;; GNU Guix is distributed in the hope that it will be useful, but
;;; WITHOUT ANY WARRANTY; without even the implied warranty of
;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
;;; GNU General Public License for more details.
;;;
;;; You should have received a copy of the GNU General Public License
;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
(define-module (gnu packages axoloti)
#:use-module (guix utils)
#:use-module (guix packages)
#:use-module (guix download)
#:use-module ((guix licenses) #:prefix license:)
#:use-module (guix build-system gnu)
#:use-module (guix build-system ant)
#:use-module (gnu packages)
#:use-module (gnu packages base)
#:use-module (gnu packages compression)
#:use-module (gnu packages cross-base)
#:use-module (gnu packages embedded)
#:use-module (gnu packages flashing-tools)
#:use-module (gnu packages java)
#:use-module (gnu packages libusb)
#:use-module (gnu packages pkg-config)
#:use-module (gnu packages textutils)
#:use-module (gnu packages version-control)
#:use-module (gnu packages xml))
(define libusb-for-axoloti
(package (inherit libusb)
(name "axoloti-libusb")
(version (package-version libusb))
(source
(origin
(inherit (package-source libusb))
(patches (list (search-patch "libusb-for-axoloti.patch")))))))
(define dfu-util-for-axoloti
(package (inherit dfu-util)
(name "axoloti-dfu-util")
(version "0.8")
(source
(origin
(method url-fetch)
(uri (string-append "http://dfu-util.sourceforge.net/releases/"
"dfu-util-" version ".tar.gz"))
(sha256
(base32
"0n7h08avlzin04j93m6hkq9id6hxjiiix7ff9gc2n89aw6dxxjsm"))))
(inputs
`(("libusb" ,libusb-for-axoloti)))))
(define-public axoloti-runtime
(package
(name "axoloti-runtime")
(version "1.0.12")
(source (origin
(method url-fetch)
(uri (string-append "https://github.com/axoloti/axoloti/"
"archive/" version ".tar.gz"))
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
"1dynk6h0nixp4zihpirpqa4vi8fq1lhm443jsmvhk135ykhf364p"))
(modules '((guix build utils)))
(snippet
'(begin
;; Remove pre-built Java binaries.
(delete-file-recursively "lib/")
#t))))
(build-system gnu-build-system)
(arguments
`(#:tests? #f ; no check target
#:modules ((guix build gnu-build-system)
(guix build utils)
(srfi srfi-1)
(srfi srfi-26)
(ice-9 match)
(ice-9 regex))
#:imported-modules ((guix build syscalls)
,@%gnu-build-system-modules)
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'patch-paths
(lambda* (#:key inputs #:allow-other-keys)
;; prepare ChibiOS
(and (zero? (system* "unzip" "-o" (assoc-ref inputs "chibios")))
(zero? (system* "mv" "ChibiOS_2.6.9" "chibios"))
(with-directory-excursion "chibios/ext"
(zero? (system* "unzip" "-o" "fatfs-0.9-patched.zip"))))
;; Remove source of non-determinism in ChibiOS
(substitute* "chibios/os/various/shell.c"
(("#ifdef __DATE__") "#if 0"))
;; Patch shell paths
(substitute* '("src/main/java/qcmds/QCmdCompileFirmware.java"
"src/main/java/qcmds/QCmdCompilePatch.java"
"src/main/java/qcmds/QCmdFlashDFU.java")
(("/bin/sh") (which "sh")))
;; Override cross compiler base name
(substitute* "firmware/Makefile.patch"
(("arm-none-eabi-(gcc|g\\+\\+|objcopy|objdump)" tool)
(which tool)))
;; Hardcode full path to compiler tools
(substitute* '("firmware/Makefile"
"firmware/flasher/Makefile"
"firmware/mounter/Makefile")
(("TRGT =.*")
(string-append "TRGT = "
(assoc-ref inputs "cross-toolchain")
"/bin/arm-none-eabi-\n")))
;; Hardcode path to "make"
(substitute* '("firmware/compile_firmware_linux.sh"
"firmware/compile_patch_linux.sh")
(("make") (which "make")))
;; Hardcode path to "dfu-util"
(substitute* "platform_linux/upload_fw_dfu.sh"
(("-f \"\\$\\{platformdir\\}/bin/dfu-util\"") "-z \"\"")
(("\\./dfu-util") (which "dfu-util")))
#t))
(delete 'configure)
(replace 'build
;; Build Axoloti firmware with cross-compiler
(lambda* (#:key inputs #:allow-other-keys)
(let* ((toolchain (assoc-ref inputs "cross-toolchain"))
(headers (string-append
toolchain
"/arm-none-eabi/include:"
toolchain
"/arm-none-eabi/include/arm-none-eabi/armv7e-m")))
(setenv "CROSS_CPATH" headers)
(setenv "CROSS_CPLUS_INCLUDE_PATH" headers)
(setenv "CROSS_LIBRARY_PATH"
(string-append toolchain
"/arm-none-eabi/lib")))
(with-directory-excursion "platform_linux"
(zero? (system* "sh" "compile_firmware.sh")))))
(replace 'install
(lambda* (#:key inputs outputs #:allow-other-keys)
(let* ((out (assoc-ref outputs "out"))
(share (string-append out "/share/axoloti/"))
(doc (string-append share "doc"))
(dir (getcwd))
(pats '("/doc/[^/]+$"
"/patches/[^/]+/[^/]+$"
"/objects/[^/]+/[^/]+$"
"/firmware/.+"
"/chibios/[^/]+$"
"/chibios/boards/ST_STM32F4_DISCOVERY/[^/]+$"
"/chibios/(ext|os|docs)/.+"
"/CMSIS/[^/]+/[^/]+$"
"/patch/[^/]+/[^/]+$"
"/[^/]+\\.txt$"))
(pattern (string-append
"(" (string-join
(map (cut string-append dir <>)
pats)
"|") ")"))
(files (find-files dir
(lambda (file stat)
(and (eq? 'regular (stat:type stat))
(string-match pattern file))))))
(for-each (lambda (file)
(install-file file
(string-append
share
(regexp-substitute
#f
(string-match dir (dirname file))
'pre 'post))))
files)
#t))))))
(inputs
`(("chibios"
,(origin
(method url-fetch)
(uri "mirror://sourceforge/chibios/ChibiOS_RT%20stable/Version%202.6.9/ChibiOS_2.6.9.zip")
(sha256
(base32
"0lb5s8pkj80mqhsy47mmq0lqk34s2a2m3xagzihalvabwd0frhlj"))))
;; for compiling patches
("make" ,gnu-make)
;; for compiling firmware
("cross-toolchain" ,arm-none-eabi-nano-toolchain-4.9)
;; for uploading compiled patches and firmware
("dfu-util" ,dfu-util-for-axoloti)))
(native-inputs
`(("unzip" ,unzip)))
(home-page "http://www.axoloti.com/")
(synopsis "Audio development environment for the Axoloti core board")
(description
"The Axoloti patcher offers a “patcher” environment similar to Pure Data
for sketching digital audio algorithms. The patches run on a standalone
powerful microcontroller board: Axoloti Core. This package provides the
runtime.")
(license license:gpl3+)))
(define-public axoloti-patcher
(package (inherit axoloti-runtime)
(name "axoloti-patcher")
(version (package-version axoloti-runtime))
(arguments
`(#:tests? #f ; no check target
#:modules ((guix build gnu-build-system)
((guix build ant-build-system) #:prefix ant:)
(guix build utils)
(srfi srfi-1)
(srfi srfi-26)
(ice-9 match)
(ice-9 regex)
(sxml simple)
(sxml xpath)
(sxml transform))
#:imported-modules ((guix build ant-build-system)
(guix build syscalls)
,@%gnu-build-system-modules)
#:phases
(modify-phases %standard-phases
(delete 'configure)
(replace 'build
(lambda* (#:key inputs #:allow-other-keys)
(setenv "JAVA_HOME" (assoc-ref inputs "icedtea"))
;; We want to use our own jar files instead of the pre-built
;; stuff in lib. So we replace the zipfileset tags in the
;; build.xml with new ones that reference our jars.
(let* ((build.xml (with-input-from-file "build.xml"
(lambda _
(xml->sxml #:trim-whitespace? #t))))
(jars (append-map (match-lambda
(((? (cut string-prefix? "java-" <>)
label) . directory)
(find-files directory "\\.jar$"))
(_ '()))
inputs))
(classpath (string-join jars ":"))
(fileset (map (lambda (jar)
`(zipfileset (@ (excludes "META-INF/*.SF")
(src ,jar))))
jars)))
(call-with-output-file "build.xml"
(lambda (port)
(sxml->xml
(pre-post-order
build.xml
`(;; Remove all zipfileset tags from the "jar" tree and
;; inject our own tags.
(jar . ,(lambda (tag . kids)
`(jar ,@(append-map
(filter (lambda (e)
(not (eq? 'zipfileset (car e)))))
kids)
,@fileset)))
;; Skip the "bundle" target (and the "-post-jar" target
;; that depends on it), because we don't need it and it
;; confuses sxml->xml.
(target . ,(lambda (tag . kids)
(let ((name ((sxpath '(name *text*))
(car kids))))
(if (or (member "bundle" name)
(member "-post-jar" name))
'() ; skip
`(,tag ,@kids)))))
(*default* . ,(lambda (tag . kids) `(,tag ,@kids)))
(*text* . ,(lambda (_ txt)
(match txt
;; Remove timestamp.
("${TODAY}" "(unknown)")
(_ txt))))))
port)))
;; Build it!
(zero? (system* "ant"
(string-append "-Djavac.classpath=" classpath)
"-Dbuild.runtime=true"
"-Dbuild.time=01/01/1970 00:00:00"
"-Djavac.source=1.7"
"-Djavac.target=1.7"
(string-append "-Dtag.short.version="
,version))))))
(replace 'install
(lambda* (#:key inputs outputs #:allow-other-keys)
(let* ((out (assoc-ref outputs "out"))
(share (string-append out "/share/axoloti/")))
(install-file "dist/Axoloti.jar" share)
;; We do this to ensure that this package retains references to
;; other Java packages' jar files.
(install-file "build.xml" share)
;; Create a launcher script
(mkdir (string-append out "/bin"))
(let ((target (string-append out "/bin/Axoloti")))
(with-output-to-file target
(lambda ()
(let* ((dir (string-append (assoc-ref outputs "out")
"/share/axoloti"))
(runtime (string-append (assoc-ref inputs "axoloti-runtime")
"/share/axoloti"))
(toolchain (assoc-ref inputs "cross-toolchain"))
(includes (string-append
toolchain
"/arm-none-eabi/include:"
toolchain
"/arm-none-eabi/include/arm-none-eabi/armv7e-m")))
(display
(string-append "#!" (which "sh") "\n"
"export CROSS_CPATH=" includes "\n"
"export CROSS_CPLUS_INCLUDE_PATH=" includes "\n"
"export CROSS_LIBRARY_PATH="
toolchain "/arm-none-eabi/lib" "\n"
(which "java")
" -Daxoloti_release=" runtime
" -Daxoloti_runtime=" runtime
" -jar " dir "/Axoloti.jar")))))
(chmod target #o555))
#t)))
(add-after 'install 'strip-jar-timestamps
(assoc-ref ant:%standard-phases 'strip-jar-timestamps)))))
(inputs
`(("icedtea" ,icedtea "jdk")
("cross-toolchain" ,arm-none-eabi-nano-toolchain-4.9)
("java-simple-xml" ,java-simple-xml)
("java-rsyntaxtextarea" ,java-rsyntaxtextarea)
("java-usb4java" ,java-usb4java)
("java-jsch" ,java-jsch)
("java-slf4j-api" ,java-slf4j-api)
("java-jgit" ,java-jgit-4.2)
("axoloti-runtime" ,axoloti-runtime)))
(native-inputs
`(("ant" ,ant)
("zip" ,zip) ; for repacking the jar
("unzip" ,unzip)))
(description
"The Axoloti patcher offers a “patcher” environment similar to Pure Data
for sketching digital audio algorithms. The patches run on a standalone
powerful microcontroller board: Axoloti Core. This package provides the
patcher application.")))

108
gnu/packages/backup.scm
View File

@ -7,6 +7,7 @@
;;; Copyright © 2017 Arun Isaac <arunisaac@systemreboot.net>
;;; Copyright © 2017 Kei Kebreau <kkebreau@posteo.net>
;;; Copyright © 2017 Efraim Flashner <efraim@flashner.co.il>
;;; Copyright © 2017 Christopher Allan Webber <cwebber@dustycloud.org>
;;;
;;; This file is part of GNU Guix.
;;;
@ -676,3 +677,110 @@ 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+)))
(define-public dirvish
(package
(name "dirvish")
(version "1.2.1")
(build-system gnu-build-system)
(source (origin
(method url-fetch)
(uri (string-append
"http://dirvish.org/dirvish-" version ".tgz"))
(sha256
(base32
"1kbxa1irszp2zw8hd5qzqnrrzb4vxfivs1vn64yxnj0lak1jjzvb"))))
(arguments
`(#:modules ((ice-9 match) (ice-9 rdelim)
,@%gnu-build-system-modules)
#:phases
;; This mostly mirrors the steps taken in the install.sh that ships
;; with dirvish, but simplified because we aren't prompting interactively
(modify-phases %standard-phases
(delete 'configure)
(delete 'build)
(delete 'check)
(replace 'install
(lambda* (#:key inputs outputs #:allow-other-keys)
;; These are mostly the same steps the install.sh that comes with
;; dirvish does
(let* (;; Files we'll be copying
(executables
'("dirvish" "dirvish-runall"
"dirvish-expire" "dirvish-locate"))
(man-pages
'(("dirvish" "8") ("dirvish-runall" "8")
("dirvish-expire" "8") ("dirvish-locate" "8")
("dirvish.conf" "5")))
(output-dir
(assoc-ref outputs "out"))
;; Just a default... not so useful on guixsd though
;; You probably want to a service with file(s) to point to.
(confdir "/etc/dirvish")
(perl (string-append (assoc-ref %build-inputs "perl")
"/bin/perl"))
(loadconfig.pl (call-with-input-file "loadconfig.pl"
read-string)))
(define (write-pl filename)
(define pl-header
(string-append "#!" perl "\n\n"
"$CONFDIR = \"" confdir "\";\n\n"))
(define input-file-location
(string-append filename ".pl"))
(define target-file-location
(string-append output-dir "/bin/" filename ".pl"))
(define text-to-write
(string-append pl-header
(call-with-input-file input-file-location
read-string)
"\n" loadconfig.pl))
(with-output-to-file target-file-location
(lambda ()
(display text-to-write)))
(chmod target-file-location #o755)
(wrap-program target-file-location
`("PERL5LIB" ":" prefix
,(map (lambda (l) (string-append (assoc-ref %build-inputs l)
"/lib/perl5/site_perl"))
'("perl-libtime-period"
"perl-libtime-parsedate")))))
(define write-man
(match-lambda
((file-base man-num)
(let* ((filename
(string-append file-base "." man-num))
(output-path
(string-append output-dir
"/share/man/man" man-num
"/" filename)))
(copy-file filename output-path)))))
;; Make directories
(mkdir-p (string-append output-dir "/bin/"))
(mkdir-p (string-append output-dir "/share/man/man8/"))
(mkdir-p (string-append output-dir "/share/man/man5/"))
;; Write out executables
(for-each write-pl executables)
;; Write out man pages
(for-each write-man man-pages)
#t))))))
(inputs
`(("perl" ,perl)
("rsync" ,rsync)
("perl-libtime-period" ,perl-libtime-period)
("perl-libtime-parsedate" ,perl-libtime-parsedate)))
(home-page "http://dirvish.org/")
(synopsis "Fast, disk based, rotating network backup system")
(description
"With dirvish you can maintain a set of complete images of your
filesystems with unattended creation and expiration. A dirvish backup vault
is like a time machine for your data. ")
(license (license:fsf-free "file://COPYING"
"Open Software License 2.0"))))

173
gnu/packages/bioinformatics.scm
View File

@ -5747,7 +5747,7 @@ data types as well.")
("r-xml" ,r-xml)
("r-xtable" ,r-xtable)))
(home-page
"http://bioconductor.org/packages/annotate")
"https://bioconductor.org/packages/annotate")
(synopsis "Annotation for microarrays")
(description "This package provides R environments for the annotation of
microarrays.")
@ -5772,7 +5772,7 @@ microarrays.")
("r-biocgenerics" ,r-biocgenerics)
("r-lattice" ,r-lattice)
("r-rcolorbrewer" ,r-rcolorbrewer)))
(home-page "http://bioconductor.org/packages/geneplotter")
(home-page "https://bioconductor.org/packages/geneplotter")
(synopsis "Graphics functions for genomic data")
(description
"This package provides functions for plotting genomic data.")
@ -5798,7 +5798,7 @@ microarrays.")
("r-biobase" ,r-biobase)
("r-s4vectors" ,r-s4vectors)
("r-survival" ,r-survival)))
(home-page "http://bioconductor.org/packages/genefilter")
(home-page "https://bioconductor.org/packages/genefilter")
(synopsis "Filter genes from high-throughput experiments")
(description
"This package provides basic functions for filtering genes from
@ -5833,7 +5833,7 @@ high-throughput sequencing experiments.")
("r-rcpparmadillo" ,r-rcpparmadillo)
("r-s4vectors" ,r-s4vectors)
("r-summarizedexperiment" ,r-summarizedexperiment)))
(home-page "http://bioconductor.org/packages/DESeq2")
(home-page "https://bioconductor.org/packages/DESeq2")
(synopsis "Differential gene expression analysis")
(description
"This package provides functions to estimate variance-mean dependence in
@ -5873,7 +5873,7 @@ distribution.")
("r-statmod" ,r-statmod)
("r-stringr" ,r-stringr)
("r-summarizedexperiment" ,r-summarizedexperiment)))
(home-page "http://bioconductor.org/packages/DEXSeq")
(home-page "https://bioconductor.org/packages/DEXSeq")
(synopsis "Inference of differential exon usage in RNA-Seq")
(description
"This package is focused on finding differential exon usage using RNA-seq
@ -5908,7 +5908,7 @@ exploration of the results.")
("r-rsqlite" ,r-rsqlite)
("r-s4vectors" ,r-s4vectors)
("r-xml" ,r-xml)))
(home-page "http://bioconductor.org/packages/AnnotationForge")
(home-page "https://bioconductor.org/packages/AnnotationForge")
(synopsis "Code for building annotation database packages")
(description
"This package provides code for generating Annotation packages and their
@ -5929,7 +5929,7 @@ databases. Packages produced are intended to be used with AnnotationDbi.")
(properties `((upstream-name . "RBGL")))
(build-system r-build-system)
(propagated-inputs `(("r-graph" ,r-graph)))
(home-page "http://www.bioconductor.org/packages/RBGL")
(home-page "https://www.bioconductor.org/packages/RBGL")
(synopsis "Interface to the Boost graph library")
(description
"This package provides a fairly extensive and comprehensive interface to
@ -5956,7 +5956,7 @@ the graph algorithms contained in the Boost library.")
("r-biocgenerics" ,r-biocgenerics)
("r-graph" ,r-graph)
("r-xml" ,r-xml)))
(home-page "http://bioconductor.org/packages/GSEABase")
(home-page "https://bioconductor.org/packages/GSEABase")
(synopsis "Gene set enrichment data structures and methods")
(description
"This package provides classes and methods to support @dfn{Gene Set
@ -5987,7 +5987,7 @@ Enrichment Analysis} (GSEA).")
("r-matrix" ,r-matrix)
("r-rbgl" ,r-rbgl)
("r-rsqlite" ,r-rsqlite)))
(home-page "http://bioconductor.org/packages/Category")
(home-page "https://bioconductor.org/packages/Category")
(synopsis "Category analysis")
(description
"This package provides a collection of tools for performing category
@ -6016,7 +6016,7 @@ analysis.")
("r-go-db" ,r-go-db)
("r-graph" ,r-graph)
("r-rbgl" ,r-rbgl)))
(home-page "http://bioconductor.org/packages/GOstats")
(home-page "https://bioconductor.org/packages/GOstats")
(synopsis "Tools for manipulating GO and microarrays")
(description
"This package provides a set of tools for interacting with GO and
@ -6055,7 +6055,7 @@ testing and other simple calculations.")
("r-s4vectors" ,r-s4vectors)
("r-xvector" ,r-xvector)
("r-zlibbioc" ,r-zlibbioc)))
(home-page "http://bioconductor.org/packages/ShortRead")
(home-page "https://bioconductor.org/packages/ShortRead")
(synopsis "FASTQ input and manipulation tools")
(description
"This package implements sampling, iteration, and input of FASTQ files.
@ -6147,7 +6147,7 @@ annotation infrastructure.")
(method url-fetch)
;; We cannot use bioconductor-uri here because this tarball is
;; located under "data/annotation/" instead of "bioc/".
(uri (string-append "http://bioconductor.org/packages/"
(uri (string-append "https://bioconductor.org/packages/"
"release/data/annotation/src/contrib"
"/TxDb.Hsapiens.UCSC.hg19.knownGene_"
version ".tar.gz"))
@ -6163,7 +6163,7 @@ annotation infrastructure.")
(propagated-inputs
`(("r-genomicfeatures" ,r-genomicfeatures)))
(home-page
"http://bioconductor.org/packages/TxDb.Hsapiens.UCSC.hg19.knownGene/")
"https://bioconductor.org/packages/TxDb.Hsapiens.UCSC.hg19.knownGene/")
(synopsis "Annotation package for human genome in TxDb format")
(description
"This package provides an annotation database of Homo sapiens genome
@ -6444,7 +6444,7 @@ barplots or heatmaps.")
(properties
`((upstream-name . "BiocGenerics")))
(build-system r-build-system)
(home-page "http://bioconductor.org/packages/BiocGenerics")
(home-page "https://bioconductor.org/packages/BiocGenerics")
(synopsis "S4 generic functions for Bioconductor")
(description
"This package provides S4 generic functions needed by many Bioconductor
@ -6464,7 +6464,7 @@ packages.")
(properties
`((upstream-name . "BiocInstaller")))
(build-system r-build-system)
(home-page "http://bioconductor.org/packages/BiocInstaller")
(home-page "https://bioconductor.org/packages/BiocInstaller")
(synopsis "Install Bioconductor packages")
(description "This package is used to install and update R packages from
Bioconductor, CRAN, and Github.")
@ -6491,7 +6491,7 @@ Bioconductor, CRAN, and Github.")
("r-xml" ,r-xml)
("r-knitr" ,r-knitr)
("r-runit" ,r-runit)))
(home-page "http://bioconductor.org/packages/biocViews")
(home-page "https://bioconductor.org/packages/biocViews")
(synopsis "Bioconductor package categorization helper")
(description "The purpose of biocViews is to create HTML pages that
categorize packages in a Bioconductor package repository according to keywords,
@ -6538,7 +6538,7 @@ authoring books and technical documents with R Markdown.")
("r-knitr" ,r-knitr)
("r-rmarkdown" ,r-rmarkdown)
("r-yaml" ,r-yaml)))
(home-page "http://bioconductor.org/packages/BiocStyle")
(home-page "https://bioconductor.org/packages/BiocStyle")
(synopsis "Bioconductor formatting styles")
(description "This package provides standard formatting styles for
Bioconductor PDF and HTML documents. Package vignettes illustrate use and
@ -6586,7 +6586,7 @@ functionality.")
("r-optparse" ,r-optparse)
("r-biocinstaller" ,r-biocinstaller)
("r-biocviews" ,r-biocviews)))
(home-page "http://bioconductor.org/packages/BiocCheck")
(home-page "https://bioconductor.org/packages/BiocCheck")
(synopsis "Executes Bioconductor-specific package checks")
(description "This package contains tools to perform additional quality
checks on R packages that are to be submitted to the Bioconductor repository.")
@ -6674,7 +6674,7 @@ abnormal copy number.")
(build-system r-build-system)
(propagated-inputs
`(("r-biocgenerics" ,r-biocgenerics)))
(home-page "http://bioconductor.org/packages/S4Vectors")
(home-page "https://bioconductor.org/packages/S4Vectors")
(synopsis "S4 implementation of vectors and lists")
(description
"The S4Vectors package defines the @code{Vector} and @code{List} virtual
@ -6727,7 +6727,7 @@ utilities for sequence data management under the ACNUC system.")
(propagated-inputs
`(("r-biocgenerics" ,r-biocgenerics)
("r-s4vectors" ,r-s4vectors)))
(home-page "http://bioconductor.org/packages/IRanges")
(home-page "https://bioconductor.org/packages/IRanges")
(synopsis "Infrastructure for manipulating intervals on sequences")
(description
"This package provides efficient low-level and highly reusable S4 classes
@ -6757,7 +6757,7 @@ possible.")
(properties
`((upstream-name . "GenomeInfoDbData")))
(build-system r-build-system)
(home-page "http://bioconductor.org/packages/GenomeInfoDbData")
(home-page "https://bioconductor.org/packages/GenomeInfoDbData")
(synopsis "Species and taxonomy ID look up tables for GenomeInfoDb")
(description "This package contains data for mapping between NCBI taxonomy
ID and species. It is used by functions in the GenomeInfoDb package.")
@ -6782,7 +6782,7 @@ ID and species. It is used by functions in the GenomeInfoDb package.")
("r-iranges" ,r-iranges)
("r-rcurl" ,r-rcurl)
("r-s4vectors" ,r-s4vectors)))
(home-page "http://bioconductor.org/packages/GenomeInfoDb")
(home-page "https://bioconductor.org/packages/GenomeInfoDb")
(synopsis "Utilities for manipulating chromosome identifiers")
(description
"This package contains data and functions that define and allow
@ -6904,7 +6904,7 @@ different technologies, including microarrays, RNA-seq, and quantitative PCR.")
`(("r-biocgenerics" ,r-biocgenerics)
("r-iranges" ,r-iranges)
("r-s4vectors" ,r-s4vectors)))
(home-page "http://bioconductor.org/packages/XVector")
(home-page "https://bioconductor.org/packages/XVector")
(synopsis "Representation and manpulation of external sequences")
(description
"This package provides memory efficient S4 classes for storing sequences
@ -6930,7 +6930,7 @@ different technologies, including microarrays, RNA-seq, and quantitative PCR.")
("r-iranges" ,r-iranges)
("r-s4vectors" ,r-s4vectors)
("r-xvector" ,r-xvector)))
(home-page "http://bioconductor.org/packages/GenomicRanges")
(home-page "https://bioconductor.org/packages/GenomicRanges")
(synopsis "Representation and manipulation of genomic intervals")
(description
"This package provides tools to efficiently represent and manipulate
@ -6955,7 +6955,7 @@ manipulating genomic intervals and variables defined along a genome.")
(build-system r-build-system)
(propagated-inputs
`(("r-biocgenerics" ,r-biocgenerics)))
(home-page "http://bioconductor.org/packages/Biobase")
(home-page "https://bioconductor.org/packages/Biobase")
(synopsis "Base functions for Bioconductor")
(description
"This package provides functions that are needed by many other packages
@ -6982,7 +6982,7 @@ on Bioconductor or which replace R functions.")
("r-iranges" ,r-iranges)
("r-rsqlite" ,r-rsqlite)
("r-s4vectors" ,r-s4vectors)))
(home-page "http://bioconductor.org/packages/AnnotationDbi")
(home-page "https://bioconductor.org/packages/AnnotationDbi")
(synopsis "Annotation database interface")
(description
"This package provides user interface and database connection code for
@ -7006,7 +7006,7 @@ annotation data packages using SQLite data storage.")
`(("r-annotationdbi" ,r-annotationdbi)
("r-rcurl" ,r-rcurl)
("r-xml" ,r-xml)))
(home-page "http://bioconductor.org/packages/biomaRt")
(home-page "https://bioconductor.org/packages/biomaRt")
(synopsis "Interface to BioMart databases")
(description
"biomaRt provides an interface to a growing collection of databases
@ -7035,7 +7035,7 @@ powerful online queries from gene annotation to database mining.")
(propagated-inputs
`(("r-futile-logger" ,r-futile-logger)
("r-snow" ,r-snow)))
(home-page "http://bioconductor.org/packages/BiocParallel")
(home-page "https://bioconductor.org/packages/BiocParallel")
(synopsis "Bioconductor facilities for parallel evaluation")
(description
"This package provides modified versions and novel implementation of
@ -7061,7 +7061,7 @@ objects.")
("r-iranges" ,r-iranges)
("r-s4vectors" ,r-s4vectors)
("r-xvector" ,r-xvector)))
(home-page "http://bioconductor.org/packages/Biostrings")
(home-page "https://bioconductor.org/packages/Biostrings")
(synopsis "String objects and algorithms for biological sequences")
(description
"This package provides memory efficient string containers, string
@ -7104,7 +7104,7 @@ biological sequences or sets of sequences.")
("r-iranges" ,r-iranges)
("r-s4vectors" ,r-s4vectors)
("r-xvector" ,r-xvector)))
(home-page "http://bioconductor.org/packages/release/bioc/html/Rsamtools.html")
(home-page "https://bioconductor.org/packages/release/bioc/html/Rsamtools.html")
(synopsis "Interface to samtools, bcftools, and tabix")
(description
"This package provides an interface to the 'samtools', 'bcftools', and
@ -7131,7 +7131,7 @@ files.")
("r-s4vectors" ,r-s4vectors)
("r-iranges" ,r-iranges)
("r-matrixstats" ,r-matrixstats)))
(home-page "http://bioconductor.org/packages/DelayedArray")
(home-page "https://bioconductor.org/packages/DelayedArray")
(synopsis "Delayed operations on array-like objects")
(description
"Wrapping an array-like object (typically an on-disk object) in a
@ -7165,7 +7165,7 @@ array-like objects like @code{DataFrame} objects (typically with Rle columns),
("r-iranges" ,r-iranges)
("r-matrix" ,r-matrix)
("r-s4vectors" ,r-s4vectors)))
(home-page "http://bioconductor.org/packages/SummarizedExperiment")
(home-page "https://bioconductor.org/packages/SummarizedExperiment")
(synopsis "Container for representing genomic ranges by sample")
(description
"The SummarizedExperiment container contains one or more assays, each
@ -7197,7 +7197,7 @@ samples.")
("r-rsamtools" ,r-rsamtools)
("r-s4vectors" ,r-s4vectors)
("r-summarizedexperiment" ,r-summarizedexperiment)))
(home-page "http://bioconductor.org/packages/GenomicAlignments")
(home-page "https://bioconductor.org/packages/GenomicAlignments")
(synopsis "Representation and manipulation of short genomic alignments")
(description
"This package provides efficient containers for storing and manipulating
@ -7242,7 +7242,7 @@ alignments.")
("r-s4vectors" ,r-s4vectors)
("r-xml" ,r-xml)
("r-xvector" ,r-xvector)))
(home-page "http://bioconductor.org/packages/rtracklayer")
(home-page "https://bioconductor.org/packages/rtracklayer")
(synopsis "R interface to genome browsers and their annotation tracks")
(description
"rtracklayer is an extensible framework for interacting with multiple
@ -7280,7 +7280,7 @@ as well as query and modify the browser state, such as the current viewport.")
("r-rtracklayer" ,r-rtracklayer)
("r-s4vectors" ,r-s4vectors)
("r-xvector" ,r-xvector)))
(home-page "http://bioconductor.org/packages/GenomicFeatures")
(home-page "https://bioconductor.org/packages/GenomicFeatures")
(synopsis "Tools for working with transcript centric annotations")
(description
"This package provides a set of tools and methods for making and
@ -7299,7 +7299,7 @@ extracting the desired features in a convenient format.")
(version "3.4.0")
(source (origin
(method url-fetch)
(uri (string-append "http://www.bioconductor.org/packages/"
(uri (string-append "https://www.bioconductor.org/packages/"
"release/data/annotation/src/contrib/GO.db_"
version ".tar.gz"))
(sha256
@ -7310,7 +7310,7 @@ extracting the desired features in a convenient format.")
(build-system r-build-system)
(propagated-inputs
`(("r-annotationdbi" ,r-annotationdbi)))
(home-page "http://bioconductor.org/packages/GO.db")
(home-page "https://bioconductor.org/packages/GO.db")
(synopsis "Annotation maps describing the entire Gene Ontology")
(description
"The purpose of this GO.db annotation package is to provide detailed
@ -7330,7 +7330,7 @@ information about the latest version of the Gene Ontologies.")
(build-system r-build-system)
(propagated-inputs
`(("r-biocgenerics" ,r-biocgenerics)))
(home-page "http://bioconductor.org/packages/graph")
(home-page "https://bioconductor.org/packages/graph")
(synopsis "Handle graph data structures in R")
(description
"This package implements some simple graph handling capabilities for R.")
@ -7359,7 +7359,7 @@ information about the latest version of the Gene Ontologies.")
("r-lattice" ,r-lattice)
("r-matrixstats" ,r-matrixstats)
("r-sparsem" ,r-sparsem)))
(home-page "http://bioconductor.org/packages/topGO")
(home-page "https://bioconductor.org/packages/topGO")
(synopsis "Enrichment analysis for gene ontology")
(description
"The topGO package provides tools for testing @dfn{gene ontology} (GO)
@ -7392,7 +7392,7 @@ dependencies between GO terms can be implemented and applied.")
("r-rtracklayer" ,r-rtracklayer)
("r-s4vectors" ,r-s4vectors)
("r-xvector" ,r-xvector)))
(home-page "http://bioconductor.org/packages/BSgenome")
(home-page "https://bioconductor.org/packages/BSgenome")
(synopsis "Infrastructure for Biostrings-based genome data packages")
(description
"This package provides infrastructure shared by all Biostrings-based
@ -7407,7 +7407,7 @@ genome data packages and support for efficient SNP representation.")
(method url-fetch)
;; We cannot use bioconductor-uri here because this tarball is
;; located under "data/annotation/" instead of "bioc/".
(uri (string-append "http://www.bioconductor.org/packages/"
(uri (string-append "https://www.bioconductor.org/packages/"
"release/data/annotation/src/contrib/"
"BSgenome.Hsapiens.1000genomes.hs37d5_"
version ".tar.gz"))
@ -7423,7 +7423,7 @@ genome data packages and support for efficient SNP representation.")
(propagated-inputs
`(("r-bsgenome" ,r-bsgenome)))
(home-page
"http://www.bioconductor.org/packages/BSgenome.Hsapiens.1000genomes.hs37d5/")
"https://www.bioconductor.org/packages/BSgenome.Hsapiens.1000genomes.hs37d5/")
(synopsis "Full genome sequences for Homo sapiens")
(description
"This package provides full genome sequences for Homo sapiens from
@ -7443,7 +7443,7 @@ genome data packages and support for efficient SNP representation.")
(inputs
`(("gfortran" ,gfortran)))
(build-system r-build-system)
(home-page "http://bioconductor.org/packages/impute")
(home-page "https://bioconductor.org/packages/impute")
(synopsis "Imputation for microarray data")
(description
"This package provides a function to impute missing gene expression
@ -7469,7 +7469,7 @@ microarray data, using nearest neighbor averaging.")
("r-iranges" ,r-iranges)
("r-kernsmooth" ,r-kernsmooth)
("r-plotrix" ,r-plotrix)))
(home-page "http://bioconductor.org/packages/seqPattern")
(home-page "https://bioconductor.org/packages/seqPattern")
(synopsis "Visualising oligonucleotide patterns and motif occurrences")
(description
"This package provides tools to visualize oligonucleotide patterns and
@ -7562,7 +7562,7 @@ downloaded from Encode.")
(method url-fetch)
;; We cannot use bioconductor-uri here because this tarball is
;; located under "data/annotation/" instead of "bioc/".
(uri (string-append "http://www.bioconductor.org/packages/"
(uri (string-append "https://www.bioconductor.org/packages/"
"release/data/annotation/src/contrib/"
"org.Hs.eg.db_" version ".tar.gz"))
(sha256
@ -7573,7 +7573,7 @@ downloaded from Encode.")
(build-system r-build-system)
(propagated-inputs
`(("r-annotationdbi" ,r-annotationdbi)))
(home-page "http://www.bioconductor.org/packages/org.Hs.eg.db/")
(home-page "https://www.bioconductor.org/packages/org.Hs.eg.db/")
(synopsis "Genome wide annotation for Human")
(description
"This package provides mappings from Entrez gene identifiers to various
@ -7588,7 +7588,7 @@ annotations for the human genome.")
(method url-fetch)
;; We cannot use bioconductor-uri here because this tarball is
;; located under "data/annotation/" instead of "bioc/".
(uri (string-append "http://www.bioconductor.org/packages/"
(uri (string-append "https://www.bioconductor.org/packages/"
"release/data/annotation/src/contrib/"
"org.Ce.eg.db_" version ".tar.gz"))
(sha256
@ -7599,7 +7599,7 @@ annotations for the human genome.")
(build-system r-build-system)
(propagated-inputs
`(("r-annotationdbi" ,r-annotationdbi)))
(home-page "http://www.bioconductor.org/packages/org.Ce.eg.db/")
(home-page "https://www.bioconductor.org/packages/org.Ce.eg.db/")
(synopsis "Genome wide annotation for Worm")
(description
"This package provides mappings from Entrez gene identifiers to various
@ -7614,7 +7614,7 @@ annotations for the genome of the model worm Caenorhabditis elegans.")
(method url-fetch)
;; We cannot use bioconductor-uri here because this tarball is
;; located under "data/annotation/" instead of "bioc/".
(uri (string-append "http://www.bioconductor.org/packages/"
(uri (string-append "https://www.bioconductor.org/packages/"
"release/data/annotation/src/contrib/"
"org.Dm.eg.db_" version ".tar.gz"))
(sha256
@ -7625,7 +7625,7 @@ annotations for the genome of the model worm Caenorhabditis elegans.")
(build-system r-build-system)
(propagated-inputs
`(("r-annotationdbi" ,r-annotationdbi)))
(home-page "http://www.bioconductor.org/packages/org.Dm.eg.db/")
(home-page "https://www.bioconductor.org/packages/org.Dm.eg.db/")
(synopsis "Genome wide annotation for Fly")
(description
"This package provides mappings from Entrez gene identifiers to various
@ -7640,7 +7640,7 @@ annotations for the genome of the model fruit fly Drosophila melanogaster.")
(method url-fetch)
;; We cannot use bioconductor-uri here because this tarball is
;; located under "data/annotation/" instead of "bioc/".
(uri (string-append "http://www.bioconductor.org/packages/"
(uri (string-append "https://www.bioconductor.org/packages/"
"release/data/annotation/src/contrib/"
"org.Mm.eg.db_" version ".tar.gz"))
(sha256
@ -7651,7 +7651,7 @@ annotations for the genome of the model fruit fly Drosophila melanogaster.")
(build-system r-build-system)
(propagated-inputs
`(("r-annotationdbi" ,r-annotationdbi)))
(home-page "http://www.bioconductor.org/packages/org.Mm.eg.db/")
(home-page "https://www.bioconductor.org/packages/org.Mm.eg.db/")
(synopsis "Genome wide annotation for Mouse")
(description
"This package provides mappings from Entrez gene identifiers to various
@ -7671,7 +7671,7 @@ annotations for the genome of the model mouse Mus musculus.")
"19d5zmy7m8svljwgbmrb4vxkq18slq0f3all6k2ayv42b8w44h6q"))))
(properties `((upstream-name . "seqLogo")))
(build-system r-build-system)
(home-page "http://bioconductor.org/packages/seqLogo")
(home-page "https://bioconductor.org/packages/seqLogo")
(synopsis "Sequence logos for DNA sequence alignments")
(description
"seqLogo takes the position weight matrix of a DNA sequence motif and
@ -7687,7 +7687,7 @@ Stephens (1990).")
(method url-fetch)
;; We cannot use bioconductor-uri here because this tarball is
;; located under "data/annotation/" instead of "bioc/".
(uri (string-append "http://www.bioconductor.org/packages/"
(uri (string-append "https://www.bioconductor.org/packages/"
"release/data/annotation/src/contrib/"
"BSgenome.Hsapiens.UCSC.hg19_"
version ".tar.gz"))
@ -7703,7 +7703,7 @@ Stephens (1990).")
(propagated-inputs
`(("r-bsgenome" ,r-bsgenome)))
(home-page
"http://www.bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19/")
"https://www.bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19/")
(synopsis "Full genome sequences for Homo sapiens")
(description
"This package provides full genome sequences for Homo sapiens as provided
@ -7718,7 +7718,7 @@ by UCSC (hg19, February 2009) and stored in Biostrings objects.")
(method url-fetch)
;; We cannot use bioconductor-uri here because this tarball is
;; located under "data/annotation/" instead of "bioc/".
(uri (string-append "http://www.bioconductor.org/packages/"
(uri (string-append "https://www.bioconductor.org/packages/"
"release/data/annotation/src/contrib/"
"BSgenome.Mmusculus.UCSC.mm9_"
version ".tar.gz"))
@ -7734,7 +7734,7 @@ by UCSC (hg19, February 2009) and stored in Biostrings objects.")
(propagated-inputs
`(("r-bsgenome" ,r-bsgenome)))
(home-page
"http://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9/")
"https://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9/")
(synopsis "Full genome sequences for Mouse")
(description
"This package provides full genome sequences for Mus musculus (Mouse) as
@ -7749,7 +7749,7 @@ provided by UCSC (mm9, July 2007) and stored in Biostrings objects.")
(method url-fetch)
;; We cannot use bioconductor-uri here because this tarball is
;; located under "data/annotation/" instead of "bioc/".
(uri (string-append "http://www.bioconductor.org/packages/"
(uri (string-append "https://www.bioconductor.org/packages/"
"release/data/annotation/src/contrib/"
"BSgenome.Mmusculus.UCSC.mm10_"
version ".tar.gz"))
@ -7765,7 +7765,7 @@ provided by UCSC (mm9, July 2007) and stored in Biostrings objects.")
(propagated-inputs
`(("r-bsgenome" ,r-bsgenome)))
(home-page
"http://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm10/")
"https://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm10/")
(synopsis "Full genome sequences for Mouse")
(description
"This package provides full genome sequences for Mus
@ -7781,7 +7781,7 @@ in Biostrings objects.")
(method url-fetch)
;; We cannot use bioconductor-uri here because this tarball is
;; located under "data/annotation/" instead of "bioc/".
(uri (string-append "http://www.bioconductor.org/packages/"
(uri (string-append "https://www.bioconductor.org/packages/"
"release/data/annotation/src/contrib/"
"TxDb.Mmusculus.UCSC.mm10.knownGene_"
version ".tar.gz"))
@ -7799,7 +7799,7 @@ in Biostrings objects.")
("r-genomicfeatures" ,r-genomicfeatures)
("r-annotationdbi" ,r-annotationdbi)))
(home-page
"http://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm10.knownGene/")
"https://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm10.knownGene/")
(synopsis "Annotation package for TxDb knownGene object(s) for Mouse")
(description
"This package loads a TxDb object, which is an R interface to
@ -7816,7 +7816,7 @@ based on the knownGene track.")
(method url-fetch)
;; We cannot use bioconductor-uri here because this tarball is
;; located under "data/annotation/" instead of "bioc/".
(uri (string-append "http://www.bioconductor.org/packages/"
(uri (string-append "https://www.bioconductor.org/packages/"
"release/data/annotation/src/contrib/"
"BSgenome.Celegans.UCSC.ce6_"
version ".tar.gz"))
@ -7832,7 +7832,7 @@ based on the knownGene track.")
(propagated-inputs
`(("r-bsgenome" ,r-bsgenome)))
(home-page
"http://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce6/")
"https://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce6/")
(synopsis "Full genome sequences for Worm")
(description
"This package provides full genome sequences for Caenorhabditis
@ -7848,7 +7848,7 @@ objects.")
(method url-fetch)
;; We cannot use bioconductor-uri here because this tarball is
;; located under "data/annotation/" instead of "bioc/".
(uri (string-append "http://www.bioconductor.org/packages/"
(uri (string-append "https://www.bioconductor.org/packages/"
"release/data/annotation/src/contrib/"
"BSgenome.Celegans.UCSC.ce10_"
version ".tar.gz"))
@ -7864,7 +7864,7 @@ objects.")
(propagated-inputs
`(("r-bsgenome" ,r-bsgenome)))
(home-page
"http://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce10/")
"https://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce10/")
(synopsis "Full genome sequences for Worm")
(description
"This package provides full genome sequences for Caenorhabditis
@ -7880,7 +7880,7 @@ objects.")
(method url-fetch)
;; We cannot use bioconductor-uri here because this tarball is
;; located under "data/annotation/" instead of "bioc/".
(uri (string-append "http://www.bioconductor.org/packages/"
(uri (string-append "https://www.bioconductor.org/packages/"
"release/data/annotation/src/contrib/"
"BSgenome.Dmelanogaster.UCSC.dm3_"
version ".tar.gz"))
@ -7896,7 +7896,7 @@ objects.")
(propagated-inputs
`(("r-bsgenome" ,r-bsgenome)))
(home-page
"http://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm3/")
"https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm3/")
(synopsis "Full genome sequences for Fly")
(description
"This package provides full genome sequences for Drosophila
@ -7924,7 +7924,7 @@ Biostrings objects.")
("r-iranges" ,r-iranges)
("r-seqlogo" ,r-seqlogo)
("r-xvector" ,r-xvector)))
(home-page "http://bioconductor.org/packages/motifRG")
(home-page "https://bioconductor.org/packages/motifRG")
(synopsis "Discover motifs in high throughput sequencing data")
(description
"This package provides tools for discriminative motif discovery in high
@ -8046,7 +8046,7 @@ of other R packages who wish to make use of HTSlib.")
("r-zlibbioc" ,r-zlibbioc)))
(inputs
`(("zlib" ,zlib)))
(home-page "http://bioconductor.org/packages/bamsignals")
(home-page "https://bioconductor.org/packages/bamsignals")
(synopsis "Extract read count signals from bam files")
(description
"This package allows to efficiently obtain count vectors from indexed bam
@ -8175,7 +8175,7 @@ library implementing most of the pipeline's features.")
("r-reshape2" ,r-reshape2)
("r-summarizedexperiment" ,r-summarizedexperiment)
("r-variantannotation" ,r-variantannotation)))
(home-page "http://bioconductor.org/packages/MutationalPatterns/")
(home-page "https://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
@ -8331,7 +8331,7 @@ kernels, including: gkmSVM, kmer-SVM, mismatch kernel and wildcard kernel.")
(base32
"1mklb02bj4gnbjlmb7vv6k4lr3w9fp3pzli9rddbrwd0y5n8fcpx"))))
(build-system r-build-system)
(home-page "http://bioconductor.org/packages/tximport")
(home-page "https://bioconductor.org/packages/tximport")
(synopsis "Import and summarize transcript-level estimates for gene-level analysis")
(description
"This package provides tools to import transcript-level abundance,
@ -8373,7 +8373,7 @@ of gene-level counts.")
(inputs
`(("perl" ,perl)
("zlib" ,zlib)))
(home-page "http://bioconductor.org/packages/rhdf5")
(home-page "https://bioconductor.org/packages/rhdf5")
(synopsis "HDF5 interface to R")
(description
"This R/Bioconductor package provides an interface between HDF5 and R.
@ -8692,7 +8692,7 @@ common bioinformatics tools.")
("r-iranges" ,r-iranges)
("r-s4vectors" ,r-s4vectors)
("r-shortread" ,r-shortread)))
(home-page "http://bioconductor.org/packages/chipseq")
(home-page "https://bioconductor.org/packages/chipseq")
(synopsis "Package for analyzing ChIPseq data")
(description
"This package provides tools for processing short read data from ChIPseq
@ -8706,7 +8706,7 @@ experiments.")
(source
(origin
(method url-fetch)
(uri (string-append "http://bioconductor.org/packages/release/"
(uri (string-append "https://bioconductor.org/packages/release/"
"data/experiment/src/contrib/CopyhelpeR_"
version ".tar.gz"))
(sha256
@ -8714,7 +8714,7 @@ experiments.")
"0x7cyynjmxls9as2gg0iyp9x5fpalxmdjq914ss7i84i9zyk5bhq"))))
(properties `((upstream-name . "CopyhelpeR")))
(build-system r-build-system)
(home-page "http://bioconductor.org/packages/CopyhelpeR/")
(home-page "https://bioconductor.org/packages/CopyhelpeR/")
(synopsis "Helper files for CopywriteR")
(description
"This package contains the helper files that are required to run the
@ -8829,7 +8829,7 @@ TAB-Seq.")
("r-biocparallel" ,r-biocparallel)
("r-matrixstats" ,r-matrixstats)
("r-limma" ,r-limma)))
(home-page "http://bioconductor.org/packages/sva")
(home-page "https://bioconductor.org/packages/sva")
(synopsis "Surrogate variable analysis")
(description
"This package contains functions for removing batch effects and other
@ -9017,7 +9017,7 @@ CDF file formats.")
("r-biocinstaller" ,r-biocinstaller)
("r-preprocesscore" ,r-preprocesscore)
("r-zlibbioc" ,r-zlibbioc)))
(home-page "http://bioconductor.org/packages/affy")
(home-page "https://bioconductor.org/packages/affy")
(synopsis "Methods for affymetrix oligonucleotide arrays")
(description
"This package contains functions for exploratory oligonucleotide array
@ -9043,7 +9043,7 @@ analysis.")
("r-hexbin" ,r-hexbin)
("r-lattice" ,r-lattice)
("r-limma" ,r-limma)))
(home-page "http://bioconductor.org/packages/release/bioc/html/vsn.html")
(home-page "https://bioconductor.org/packages/release/bioc/html/vsn.html")
(synopsis "Variance stabilization and calibration for microarray data")
(description
"The package implements a method for normalising microarray intensities,
@ -9080,7 +9080,7 @@ and specific in detecting differential transcription.")
("r-protgenerics" ,r-protgenerics)
("r-rcpp" ,r-rcpp)
("r-xml" ,r-xml)))
(home-page "http://bioconductor.org/packages/mzID")
(home-page "https://bioconductor.org/packages/mzID")
(synopsis "Parser for mzIdentML files")
(description
"This package provides a parser for mzIdentML files implemented using the
@ -9187,7 +9187,7 @@ of mass spectrometry based proteomics data.")
("r-r-cache" ,r-r-cache)
("r-rcpp" ,r-rcpp)
("r-reshape2" ,r-reshape2)))
(home-page "http://bioconductor.org/packages/MSnID")
(home-page "https://bioconductor.org/packages/MSnID")
(synopsis "Utilities for LC-MSn proteomics identifications")
(description
"This package extracts @dfn{tandem mass spectrometry} (MS/MS) ID data
@ -9391,7 +9391,7 @@ global-scaling and full-quantile normalization.")
(propagated-inputs
`(("r-biocgenerics" ,r-biocgenerics)
("r-shiny" ,r-shiny)))
(home-page "http://bioconductor.org/packages/interactiveDisplayBase")
(home-page "https://bioconductor.org/packages/interactiveDisplayBase")
(synopsis "Base package for web displays of Bioconductor objects")
(description
"This package contains the basic methods needed to generate interactive
@ -9420,7 +9420,7 @@ Shiny-based display methods for Bioconductor objects.")
("r-rsqlite" ,r-rsqlite)
("r-s4vectors" ,r-s4vectors)
("r-yaml" ,r-yaml)))
(home-page "http://bioconductor.org/packages/AnnotationHub")
(home-page "https://bioconductor.org/packages/AnnotationHub")
(synopsis "Client to access AnnotationHub resources")
(description
"This package provides a client for the Bioconductor AnnotationHub web
@ -10035,13 +10035,18 @@ browser.")
#:phases
(modify-phases %standard-phases
(replace 'install
(lambda* (#:key outputs #:allow-other-keys)
(lambda* (#:key inputs outputs #:allow-other-keys)
(let* ((target (assoc-ref outputs "out"))
(doc (string-append target "/share/doc/f-seq/")))
(mkdir-p target)
(mkdir-p doc)
(substitute* "bin/linux/fseq"
(("java") (which "java")))
(("java") (which "java"))
(("\\$REALDIR/../lib/commons-cli-1.1.jar")
(string-append (assoc-ref inputs "java-commons-cli")
"/share/java/commons-cli.jar"))
(("REALDIR=.*")
(string-append "REALDIR=" target "/bin\n")))
(install-file "README.txt" doc)
(install-file "bin/linux/fseq" (string-append target "/bin"))
(install-file "build~/fseq.jar" (string-append target "/lib"))

4
gnu/packages/check.scm
View File

@ -244,13 +244,13 @@ format.")
(define-public cppcheck
(package
(name "cppcheck")
(version "1.80")
(version "1.81")
(source (origin
(method url-fetch)
(uri (string-append "https://github.com/danmar/cppcheck/archive/"
version ".tar.gz"))
(sha256
(base32 "007hs15i2pn49l6kycy49h3bj66qh6fxrp6yidj3776n32q3v1i0"))
(base32 "0miamqk7pa2dzmnmi5wb6hjp2a3zya1x8afnlcxby8jb6gp6wf8j"))
(file-name (string-append name "-" version ".tar.gz"))))
(build-system cmake-build-system)
(home-page "http://cppcheck.sourceforge.net")

38
gnu/packages/compression.scm
View File

@ -17,6 +17,7 @@
;;; Copyright © 2017 ng0 <contact.ng0@cryptolab.net>
;;; Copyright © 2017 Manolis Fragkiskos Ragkousis <manolis837@gmail.com>
;;; Copyright © 2017 Theodoros Foradis <theodoros@foradis.org>
;;; Copyright © 2017 Stefan Reichör <stefan@xsteve.at>
;;;
;;; This file is part of GNU Guix.
;;;
@ -50,6 +51,7 @@
#:use-module (gnu packages base)
#:use-module (gnu packages check)
#:use-module (gnu packages curl)
#:use-module (gnu packages file)
#:use-module (gnu packages perl)
#:use-module (gnu packages pkg-config)
#:use-module (gnu packages python)
@ -1574,3 +1576,39 @@ zip archives. Files can be added from data buffers, files, or compressed data
copied directly from other zip archives. Changes made without closing the
archive can be reverted.")
(license license:bsd-3)))
(define-public atool
(package
(name "atool")
(version "0.39.0")
(source
(origin
(method url-fetch)
(uri (string-append "http://savannah.nongnu.org/download/atool/atool-"
version ".tar.gz"))
(sha256
(base32
"0fvhzip2v08jgnlfpyj6rapan39xlsl1ksgq4lp8gfsai2ah1xma"))))
(build-system gnu-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
(add-after 'unpack 'embed-absolute-file-name
(lambda* (#:key inputs #:allow-other-keys)
(substitute* "atool"
(("(^\\$::cfg_path_file.*= )'file'" _ pre)
(string-append pre "'" (assoc-ref inputs "file")
"/bin/file'")))
#t)))))
(inputs
`(("perl" ,perl)
("file" ,file)))
(home-page "http://www.nongnu.org/atool/")
(synopsis "Universal tool to manage file archives of various types")
(description "The main command is @command{aunpack} which extracts files
from an archive. The other commands provided are @command{apack} (to create
archives), @command{als} (to list files in archives), and @command{acat} (to
extract files to standard out). As @command{atool} invokes external programs
to handle the archives, not all commands may be supported for a certain type
of archives.")
(license license:gpl2+)))

24
gnu/packages/cran.scm
View File

@ -1217,3 +1217,27 @@ initial data set and then applied to other data sets. The resulting design
matrices can then be used as inputs into statistical or machine learning
models.")
(license license:gpl2)))
(define-public r-pdist
(package
(name "r-pdist")
(version "1.2")
(source
(origin
(method url-fetch)
(uri (cran-uri "pdist" version))
(sha256
(base32
"18nd3mgad11f2zmwcp0w3sxlch4a9y6wp8dfdyzvjn7y4b4bq0dd"))))
(build-system r-build-system)
(home-page "https://github.com/jeffwong/pdist")
(synopsis "Partitioned distance function")
(description
"Pdist computes the euclidean distance between rows of a matrix X and
rows of another matrix Y. Previously, this could be done by binding the two
matrices together and calling @code{dist}, but this creates unnecessary
computation by computing the distances between a row of X and another row of
X, and likewise for Y. Pdist strictly computes distances across the two
matrices, not within the same matrix, making computations significantly faster
for certain use cases.")
(license license:gpl3+)))

2
gnu/packages/crypto.scm
View File

@ -556,7 +556,7 @@ generator.")
(synopsis "Get weak or strong random data from pluggable sources")
(description "This module provides implementations for a number of
byte-oriented sources of random data.")
(license (package-license perl))))
(license license:perl-license)))
(define-public perl-math-random-secure
(package

4
gnu/packages/cups.scm
View File

@ -377,14 +377,14 @@ device-specific programs to convert and print many types of files.")
(define-public hplip
(package
(name "hplip")
(version "3.17.7")
(version "3.17.10")
(source (origin
(method url-fetch)
(uri (string-append "mirror://sourceforge/hplip/hplip/" version
"/hplip-" version ".tar.gz"))
(sha256
(base32
"03a0vkbrzvgj15il9rvr93kf5pc706gxcjk6akbkzds0zmdbsxrm"))))
"0v27hg856b5z2rilczcbfgz8ksxn0n810g1glac3mxkj8qbl8wqg"))))
(build-system gnu-build-system)
(home-page "http://hplipopensource.com/")
(synopsis "HP Printer Drivers")

4
gnu/packages/databases.scm
View File

@ -453,7 +453,7 @@ RDBMS systems (which are deep in functionality).")
(define-public mysql
(package
(name "mysql")
(version "5.7.19")
(version "5.7.20")
(source (origin
(method url-fetch)
(uri (list (string-append
@ -465,7 +465,7 @@ RDBMS systems (which are deep in functionality).")
name "-" version ".tar.gz")))
(sha256
(base32
"1c8y54yk756179nx4dgg79dijmjdq5n8l057cnqsg70pjdpyfl9y"))))
"11v4g3igigv3zvknv67qml8in6fjrbs2vnr3q6bg6f62nydm95sk"))))
(build-system cmake-build-system)
(arguments
`(#:configure-flags

9
gnu/packages/display-managers.scm
View File

@ -4,6 +4,7 @@
;;; Copyright © 2014 Andreas Enge <andreas@enge.fr>
;;; Copyright © 2017 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2017 Sou Bunnbu <iyzsong@gmail.com>
;;; Copyright © 2017 Marius Bakke <mbakke@fastmail.com>
;;;
;;; This file is part of GNU Guix.
;;;
@ -188,6 +189,14 @@ Qt-style API for Wayland clients.")
(substitute* "CMakeLists.txt"
(("/usr/bin/loginctl") (which "loginctl")))
#t))
(add-before 'configure 'fix-qml-include
(lambda _
;; Make sure QtQml is found when building the helper.
;; See <https://github.com/sddm/sddm/pull/918>.
(substitute* "src/helper/CMakeLists.txt"
(("target_link_libraries\\(sddm-helper")
"target_link_libraries(sddm-helper Qt5::Qml"))
#t))
(add-after 'install 'wrap-programs
(lambda* (#:key outputs #:allow-other-keys)
(let ((out (assoc-ref outputs "out")))

10
gnu/packages/dns.scm
View File

@ -284,7 +284,7 @@ asynchronous fashion.")
(define-public unbound
(package
(name "unbound")
(version "1.6.3")
(version "1.6.7")
(source
(origin
(method url-fetch)
@ -292,7 +292,7 @@ asynchronous fashion.")
version ".tar.gz"))
(sha256
(base32
"0pw4m4z5qspsagxzbjb61xq5bhd57amw26xqvqzi6b8d3mf6azjc"))))
"17qwfmlls0w9kpkya3dlpn44b3kr87wsswzg3gawc13hh8yx8ysf"))))
(build-system gnu-build-system)
(outputs '("out" "python"))
(native-inputs
@ -443,9 +443,9 @@ served by AS112. Stub and forward zones are supported.")
(define-public yadifa
(package
(name "yadifa")
(version "2.2.5")
(version "2.2.6")
(source
(let ((build "6937"))
(let ((build "7246"))
(origin
(method url-fetch)
(uri
@ -453,7 +453,7 @@ served by AS112. Stub and forward zones are supported.")
name "-" version "-" build ".tar.gz"))
(sha256
(base32
"146fs52izf6dfwsxal3srpwin2yyl41g31cy4pyvbi5mqy2craj7")))))
"041a35f5jz2wcn8pxk1m7b2qln2wbvj4ddwb0a53lqabl912xi6p")))))
(build-system gnu-build-system)
(native-inputs
`(("which" ,which)))

32
gnu/packages/emacs.scm
View File

@ -135,7 +135,17 @@
(format #f "(tramp-default-remote-path ~s ~s ~s ~s "
"~/.guix-profile/bin" "~/.guix-profile/sbin"
"/run/current-system/profile/bin"
"/run/current-system/profile/sbin")))))))
"/run/current-system/profile/sbin")))
;; Make sure Man looks for C header files in the right
;; places.
(substitute* "man.el"
(("\"/usr/local/include\"" line)
(string-join
(list line
"\"~/.guix-profile/include\""
"\"/var/guix/profiles/system/profile/include\"")
" ")))))))
(build-system glib-or-gtk-build-system)
(arguments
`(#:phases
@ -5657,6 +5667,26 @@ pair of minor modes which suppress all mouse events by intercepting them and
running a customisable handler command (@code{ignore} by default). ")
(license license:gpl3+)))
(define-public emacs-json-snatcher
(package
(name "emacs-json-snatcher")
(version "1.0.0")
(source
(origin
(method url-fetch)
(uri (string-append "https://github.com/Sterlingg/json-snatcher/archive/"
version ".tar.gz"))
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
"1nfiwsifpdiz0lbrqa77nl0crnfrv5h85ans9b0g5rggnmyshcfb"))))
(build-system emacs-build-system)
(home-page "https://github.com/sterlingg/json-snatcher")
(synopsis "Grabs the path to JSON values in a JSON file")
(description "@code{emacs-json-snatcher} grabs the path to JSON values in
a @url{http://json.org/, JSON} file.")
(license license:gpl3+)))
(define-public emacs-restclient
(let ((commit "07a3888bb36d0e29608142ebe743b4362b800f40")
(revision "1")) ;Guix package revision,

2
gnu/packages/engineering.scm
View File

@ -429,7 +429,7 @@ multipole-accelerated algorithm.")
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
"0pvk57z2pxz89pcwwm61lkpvj4w9qxqz8mi0zkpj6pnaljabp7bf"))))
"15rwjp4xdj9w1z9f709rz9p0k2mi9k9idma9hvzkj5j8p04mg7yd"))))
(build-system gnu-build-system)
(arguments
`(#:phases

2
gnu/packages/erlang.scm
View File

@ -46,7 +46,7 @@
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
"1azjjyb743i6vjq7rnh5qnslsqg0x60a9zrlhg9n3dpm13z1b22l"))
"11xp6vv1v7iay9dg1xc6xm7izfsanbn5pgwp96ba0j1fmlkhjw92"))
(patches (search-patches "erlang-man-path.patch"))))
(build-system gnu-build-system)
(native-inputs

21
gnu/packages/fonts.scm
View File

@ -764,17 +764,15 @@ glyph designs, not just an added slant.")
(define-public font-hack
(package
(name "font-hack")
(version "2.020")
(version "3.000")
(source (origin
(method url-fetch/zipbomb)
(uri (string-append
"https://github.com/chrissimpkins/Hack/releases/download/v"
version "/Hack-v"
(string-replace-substring version "." "_")
"-ttf.zip"))
"https://github.com/source-foundry/Hack/releases/download/v"
version "/Hack-v" version "-ttf.zip"))
(sha256
(base32
"16kkmc3psckw1b7k07ccn1gi5ymhlg9djh43nqjzg065g6p6d184"))))
"0h6slqg25a6cq57k6rh5hmnk8dxbprmf8shs4iyj1pc83sw6b1r3"))))
(build-system font-build-system)
(home-page "https://sourcefoundry.org/hack/")
(synopsis "Typeface designed for source code")
@ -782,9 +780,12 @@ glyph designs, not just an added slant.")
"Hack is designed to be a workhorse typeface for code. It expands upon
the Bitstream Vera & DejaVu projects, provides 1561 glyphs, and includes
Powerline support.")
(license (license:x11-style
"https://github.com/chrissimpkins/Hack/blob/master/LICENSE.md"
"Hack Open Font License v2.0"))))
(license
;; See https://github.com/source-foundry/Hack/issues/271 for details.
(list license:expat ; the Hack modifications to...
license:public-domain ; ...the DejaVu modifications to...
(license:x11-style ; ...the Bitstream Vera typeface
"file://LICENSE.md" "Bitstream Vera License")))))
(define-public font-adobe-source-code-pro
(package
@ -1026,7 +1027,7 @@ monospace, slab-serif fonts.")
version ".tar.gz"))
(sha256
(base32
"183n0qv3q8w6n27libarq1fhc4mqv2d3sasbfmbn7x9r5pw9c6ga"))
"018i3za9r6kf6svci33z09lc5pr5yz4164m8gzzwjzzqcrng0p5j"))
(file-name (string-append name "-" version ".tar.gz"))))
(build-system font-build-system)
(home-page "http://google.github.io/material-design-icons")

5
gnu/packages/game-development.scm
View File

@ -280,7 +280,10 @@ files) into @file{.grf} and/or @file{.nfo} files.")
(source
(origin
(method url-fetch)
(uri (pypi-uri "sge-pygame" version))
(uri (string-append "mirror://savannah/stellarengine/"
(version-major+minor version) "/sge-pygame-"
version ".tar.gz"))
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
"1rl3xjzh78sl0sq3xl8rl7cgp9v9v3h7s2pfwn7nj1vrmffzkcpd"))))

22
gnu/packages/games.scm
View File

@ -248,22 +248,22 @@ the others like yourself, that want what you have.")
(define-public cowsay
(package
(name "cowsay")
(version "3.03")
(version "3.04")
(source (origin
(method url-fetch)
(uri (string-append "https://web.archive.org/web/20071026043648/"
"http://www.nog.net:80/~tony/warez/"
"cowsay-" version ".tar.gz"))
(uri (string-append "https://github.com/tnalpgge/"
"rank-amateur-cowsay/archive/"
name "-" version ".tar.gz"))
(sha256
(base32
"1bxj802na2si2bk5zh7n0b7c33mg8a5n2wnvh0vihl9bmjkp51hb"))))
"12w7apbf6a9qffk92r32b16w22na2fjcqbl32rn0n7zw5hrp3f6q"))))
(build-system gnu-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
(delete 'configure)
(delete 'install)
(replace 'build
(delete 'configure) ; no configure script
(delete 'build) ; nothing to be built
(replace 'install
(lambda* (#:key outputs #:allow-other-keys)
(zero? (system* "sh" "install.sh"
(assoc-ref outputs "out")))))
@ -275,12 +275,12 @@ the others like yourself, that want what you have.")
(inputs
`(("perl" ,perl)))
(home-page (string-append "https://web.archive.org/web/20071026043648/"
"http://www.nog.net:80/~tony/warez/"))
"http://www.nog.net:80/~tony/warez/cowsay.shtml"))
(synopsis "Speaking cow text filter")
(description "Cowsay is basically a text filter. Send some text into it,
and you get a cow saying your text. If you think a talking cow isn't enough,
cows can think too. All you have to do is run @code{cowthink}.")
;; Any version of the GPL.
cows can think too: all you have to do is run @command{cowthink}. If you're
tired of cows, a variety of other ASCII-art messengers are available.")
(license license:gpl3+)))
(define-public freedoom

19
gnu/packages/gnome.scm
View File

@ -517,7 +517,7 @@ and keep up to date translations of documentation.")
(define-public gnome-disk-utility
(package
(name "gnome-disk-utility")
(version "3.24.1")
(version "3.26.1")
(source (origin
(method url-fetch)
(uri (string-append "mirror://gnome/sources/" name "/"
@ -525,10 +525,11 @@ and keep up to date translations of documentation.")
name "-" version ".tar.xz"))
(sha256
(base32
"18akarcbhm8djlmz49jzavc7qx8dg71gvxc9xd23p0bwjj4h93w7"))))
(build-system gnu-build-system)
"10spllvcq2q71xk3dnhzjk8v4qx9am8y1h68k8z2j0l94g1c8bi3"))))
(build-system meson-build-system)
(native-inputs
`(("glib:bin" ,glib "bin")
("gtk+" ,gtk+ "bin") ; gtk-update-icon-cache
("intltool" ,intltool)
("pkg-config" ,pkg-config)
("docbook-xml" ,docbook-xml)
@ -2371,7 +2372,7 @@ library.")
(define-public rest
(package
(name "rest")
(version "0.8.0")
(version "0.8.1")
(source (origin
(method url-fetch)
(uri (string-append "mirror://gnome/sources/rest/"
@ -2379,7 +2380,7 @@ library.")
name "-" version ".tar.xz"))
(sha256
(base32
"0iznvzhab1jq9z3nwy97dh2pid9azwkqm7kkxwx0f5ql1hh9pf77"))))
"1j81bgqmd55s5lxyaxcplym9n6xywcs1cm9wmvafsg2xiv9sl4q5"))))
(build-system gnu-build-system)
(arguments
'(#:tests? #f ; tests require internet connection
@ -3769,7 +3770,7 @@ supports playlists, song ratings, and any codecs installed through gstreamer.")
(define-public eog
(package
(name "eog")
(version "3.24.1")
(version "3.26.1")
(source (origin
(method url-fetch)
(uri (string-append "mirror://gnome/sources/" name "/"
@ -3777,7 +3778,7 @@ supports playlists, song ratings, and any codecs installed through gstreamer.")
name "-" version ".tar.xz"))
(sha256
(base32
"1rr7zy8afqgl15j1zz8l37svyv6bw4r3l04yf70zlnf1w8bf27pm"))))
"125wzr1mai4raybfb2hwjzxv59q20bjpw9j4wn682nn5bd9ypnwq"))))
(build-system glib-or-gtk-build-system)
(arguments
`(#:phases
@ -3824,7 +3825,7 @@ supports image conversion, rotation, and slideshows.")
;; 'XDG_DATA_DIRS' appropriately set.
(package
(name "eog-plugins")
(version "3.25.1")
(version "3.26.1")
(source (origin
(method url-fetch)
(uri (string-append "mirror://gnome/sources/" name "/"
@ -3832,7 +3833,7 @@ supports image conversion, rotation, and slideshows.")
name "-" version ".tar.xz"))
(sha256
(base32
"0an04z8v83qa6j950rbwdzf1s86y7zd8h1r4p2x36fwbkk1m617q"))))
"0v45f2m3b60ygkwpq6jrl49nwrivw6qy0ciibpv821qrm73hsgd7"))))
(build-system gnu-build-system)
(home-page "https://wiki.gnome.org/Apps/EyeOfGnome/Plugins")
(synopsis "Extensions for the Eye of GNOME image viewer")

30
gnu/packages/graph.scm
View File

@ -25,7 +25,9 @@
#:use-module ((guix licenses) #:prefix license:)
#:use-module (gnu packages)
#:use-module (gnu packages gcc)
#:use-module (gnu packages bioinformatics)
#:use-module (gnu packages compression)
#:use-module (gnu packages graphviz)
#:use-module (gnu packages maths)
#:use-module (gnu packages multiprecision)
#:use-module (gnu packages pkg-config)
@ -116,3 +118,31 @@ It can handle large graphs very well and provides functions for generating
random and regular graphs, graph visualization, centrality methods and much
more.")
(license license:gpl2+)))
(define-public r-rgraphviz
(package
(name "r-rgraphviz")
(version "2.20.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "Rgraphviz" version))
(sha256
(base32
"0mwdqsmmhpk8szp3pf3bw66nv2sazpjiflpwdvqwjamvxyynmp67"))))
(properties `((upstream-name . "Rgraphviz")))
(build-system r-build-system)
;; FIXME: Rgraphviz bundles the sources of an older variant of
;; graphviz. It does not build with the latest version of graphviz, so
;; we do not add graphviz to the inputs.
(inputs `(("zlib" ,zlib)))
(propagated-inputs
`(("r-graph" ,r-graph)))
(native-inputs
`(("pkg-config" ,pkg-config)))
(home-page "http://bioconductor.org/packages/Rgraphviz")
(synopsis "Plotting capabilities for R graph objects")
(description
"This package interfaces R with the graphviz library for plotting R graph
objects from the @code{graph} package.")
(license license:epl1.0)))

2
gnu/packages/graphics.scm
View File

@ -244,7 +244,7 @@ exception-handling library.")
"/archive/v" version ".tar.gz"))
(sha256
(base32
"1ab354bmwwryxr4zgxchfkm6h4z38mjgif8yn89x640rsrgw5ipj"))
"1p0c91cc7zg3c00wjaibnxb0a0xm14mkg0h65pzpw93m0d6nc8wd"))
(file-name (string-append name "-" version ".tar.gz"))))
(build-system cmake-build-system)
(arguments

6
gnu/packages/gtk.scm
View File

@ -306,12 +306,12 @@ diagrams.")
(license license:gpl3+)))
(define-public ganv-devel
(let ((commit "31685d283e9b811b61014f820c42807f4effa071")
(let ((commit "12f7d6b0438c94dd87f773a92eee3453d971846e")
(revision "1"))
(package
(inherit ganv)
(name "ganv")
(version (string-append "1.4.2-" revision "."
(version (string-append "1.5.4-" revision "."
(string-take commit 9)))
(source (origin
(method git-fetch)
@ -320,7 +320,7 @@ diagrams.")
(commit commit)))
(sha256
(base32
"0xmbykdl42jn9cgzrqrys5lng67d26nk5xq10wkkvjqldiwdck56")))))))
"1cr8w02lr6bk9mkxa12j3imq721b2an2yn4bj5wnwmpm91ddn2gi")))))))
(define-public gtksourceview-2
(package

6
gnu/packages/haskell.scm
View File

@ -4,7 +4,7 @@
;;; Copyright © 2015 Paul van der Walt <paul@denknerd.org>
;;; Copyright © 2015 Eric Bavier <bavier@member.fsf.org>
;;; Copyright © 2016 Ludovic Courtès <ludo@gnu.org>
;;; Copyright © 2016 ng0 <ng0@we.make.ritual.n0.is>
;;; Copyright © 2016, 2017 ng0 <ng0@infotropique.org>
;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il>
;;; Copyright © 2015, 2016, 2017 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2016, 2017 David Craven <david@craven.ch>
@ -8601,7 +8601,7 @@ JSON (JavaScript Object Notation) is a lightweight data-interchange format.")
(define-public shellcheck
(package
(name "shellcheck")
(version "0.4.5")
(version "0.4.6")
(source
(origin
(method url-fetch)
@ -8609,7 +8609,7 @@ JSON (JavaScript Object Notation) is a lightweight data-interchange format.")
"v" version ".tar.gz"))
(sha256
(base32
"14r84fcn28rin339avlvca5g0kz832f01x8dpmwb5ql8mbc4rlxr"))
"1qkd69lc34n3l23ss9rq1azvx49bfq4hi4bmaj76rgxybscxhg0w"))
(file-name (string-append name "-" version ".tar.gz"))))
(build-system haskell-build-system)
(inputs

4
gnu/packages/irc.scm
View File

@ -110,7 +110,7 @@ irssi, but graphical.")
(define-public irssi
(package
(name "irssi")
(version "1.0.4")
(version "1.0.5")
(source (origin
(method url-fetch)
(uri (string-append "https://github.com/irssi/irssi/"
@ -118,7 +118,7 @@ irssi, but graphical.")
version ".tar.xz"))
(sha256
(base32
"1jl6p431rv4iixk48wn607m4s0mcy3wgasfwrhz22y71mzdhfp5q"))))
"055r9fhbfcfkzinsnprnlqd8psspdyn3j26lzsmnrc1fw4kn8mf2"))))
(build-system gnu-build-system)
(arguments
`(#:phases

4
gnu/packages/java.scm
View File

@ -2299,7 +2299,7 @@ more.")
"plexus-interpolation-" version ".tar.gz"))
(sha256
(base32
"1w79ljwk42ymrgy8kqxq4l82pgdj6287gabpfnpkyzbrnclsnfrp"))))
"03377yzlx5q440m6sxxgv6a5qb8fl30zzcgxgc0hxk5qgl2z1jjn"))))
(build-system ant-build-system)
(arguments
`(#:jar-name "plexus-interpolation.jar"
@ -4429,7 +4429,7 @@ StringTemplate also powers ANTLR.")
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
"07zff5frmjd53rnqdx31h0pmswz1lv0p2lp28cspfszh25ysz6sj"))))
"0218v683081lg54z9hvjxinhxd4dqp870jx6n39gslm0bkyi4vd6"))))
(build-system ant-build-system)
(arguments
`(#:jar-name (string-append ,name "-" ,version ".jar")

2
gnu/packages/kde-frameworks.scm
View File

@ -2780,7 +2780,7 @@ typed.")
("ki18n" ,ki18n)
("qtbase" ,qtbase)))
(arguments
`(#:tests? #f ; FIXME: 8/10 tests fail.
`(#:tests? #f ; FIXME: 6/10 tests fail.
#:phases
(modify-phases %standard-phases
(add-before 'check 'check-setup

5
gnu/packages/lighting.scm
View File

@ -1,5 +1,6 @@
;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2016 John J. Foerch <jjfoerch@earthlink.net>
;;; Copyright © 2017 Tobias Geerinckx-Rice <me@tobias.gr>
;;;
;;; This file is part of GNU Guix.
;;;
@ -59,7 +60,9 @@
("libuuid" ,util-linux)
("zlib" ,zlib)))
(propagated-inputs
`(("protobuf" ,protobuf))) ;; for pkg-config --libs libola
;; Ola 0.10.5 only supports protobuf 2.x, and building it with 3.x breaks.
;; XXX Remove protobuf-2 when it is no longer needed.
`(("protobuf" ,protobuf-2))) ;; for pkg-config --libs libola
(arguments
`(;; G++ >= 4.8 macro expansion tracking requires lots of memory, causing
;; build to fail on low memory systems. We disable that with the

37
gnu/packages/linux.scm
View File

@ -72,6 +72,7 @@
#:use-module (gnu packages gnuzilla)
#:use-module (gnu packages gperf)
#:use-module (gnu packages gtk)
#:use-module (gnu packages libunwind)
#:use-module (gnu packages libusb)
#:use-module (gnu packages man)
#:use-module (gnu packages maths)
@ -367,8 +368,8 @@ It has been modified to remove all non-free binary blobs.")
(define %intel-compatible-systems '("x86_64-linux" "i686-linux"))
(define %linux-libre-version "4.13.7")
(define %linux-libre-hash "1znf2zrhfb6wmlv09c14y6sawl4nb0jr7gzwwnakspvy0yjs95r3")
(define %linux-libre-version "4.13.8")
(define %linux-libre-hash "0qi2n5lczqwq2v0q5zl08ac3x4lixpj1dmb0kza6hsllmx8hbybw")
(define-public linux-libre
(make-linux-libre %linux-libre-version
@ -377,32 +378,22 @@ It has been modified to remove all non-free binary blobs.")
#:configuration-file kernel-config))
(define-public linux-libre-4.9
(make-linux-libre "4.9.56"
"05wy73yh4jbn1881djs21wl4hws62lyc1frb5di6cg6m3z7j658i"
(make-linux-libre "4.9.57"
"02ldxzbazdbhvgkwxl6xblkwj75s5cm33fpm77kv394w35jan3by"
%intel-compatible-systems
#:configuration-file kernel-config))
(define-public linux-libre-4.4
(make-linux-libre "4.4.92"
"038mrv36n2521xd1f4nlpn00ar4vwzbwkldf6pk7rflbc3zi0p8g"
(make-linux-libre "4.4.93"
"1llpqkm7vvwi5fm92y4n6qrc89ps7kdfl83s7m38a2yivm3kgzr6"
%intel-compatible-systems
#:configuration-file kernel-config))
(define-public linux-libre-4.1
(make-linux-libre "4.1.44"
"1h1v2n8fxnn98y0jz9pnr4xdmc0v4l5d3hfxa5n5r3xmjksf1xs3"
(make-linux-libre "4.1.45"
"1ifpyyq86x0imjdfb9vm7m8dbnkw82a7bqczx166zrssc1fc677l"
%intel-compatible-systems
#:configuration-file kernel-config
#:patches
(list %boot-logo-patch
(origin
(method url-fetch)
(uri "\
https://git.kernel.org/pub/scm/linux/kernel/git/stable/linux-stable.git/patch/?id=f7ec367c8ea7021517c9c04b0022c225d2d0785a")
(file-name "linux-libre-4.4-CVE-2017-1000251.patch")
(sha256
(base32
"1glnjvs3xkvana2wfdv47dxi7jz2s4dz3v0b8ryglf2vbflm388w"))))))
#:configuration-file kernel-config))
(define-public linux-libre-arm-generic
(make-linux-libre %linux-libre-version
@ -2525,7 +2516,7 @@ in a digital read-out.")
(setenv "SHELL_PATH" (which "bash"))
(chdir "tools/perf")
#t)))
#:make-flags (list (string-append "DESTDIR="
#:make-flags (list (string-append "prefix="
(assoc-ref %outputs "out"))
"WERROR=0"
@ -2547,6 +2538,8 @@ in a digital read-out.")
("python" ,python-2) ;'perf' links against libpython
("elfutils" ,elfutils)
("libiberty" ,libiberty) ;used alongside BDF for symbol demangling
("libunwind" ,libunwind) ;better stack walking
("numactl" ,numactl) ;for 'perf bench numa mem'
;; Documentation.
("libxml2" ,libxml2) ;for $XML_CATALOG_FILES
@ -3186,7 +3179,7 @@ and copy/paste text in the console and in xterm.")
(define-public btrfs-progs
(package
(name "btrfs-progs")
(version "4.13.2")
(version "4.13.3")
(source (origin
(method url-fetch)
(uri (string-append "mirror://kernel.org/linux/kernel/"
@ -3194,7 +3187,7 @@ and copy/paste text in the console and in xterm.")
"btrfs-progs-v" version ".tar.xz"))
(sha256
(base32
"1ga8jk2hkaxpm17z3gdfrpq0i62kqpv2wm5yzbzmsj862cgk7ivm"))))
"10yp0b4pwrw5mcd81yn3d0d87fnqpp4si5d25dfhl6n2640dnnw0"))))
(build-system gnu-build-system)
(outputs '("out"
"static")) ; static versions of the binaries in "out"

23
gnu/packages/mail.scm
View File

@ -1,5 +1,5 @@
;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2013, 2014, 2015, 2016 Ludovic Courtès <ludo@gnu.org>
;;; Copyright © 2013, 2014, 2015, 2016, 2017 Ludovic Courtès <ludo@gnu.org>
;;; Copyright © 2014, 2015, 2017 Mark H Weaver <mhw@netris.org>
;;; Copyright © 2014 Ian Denhardt <ian@zenhack.net>
;;; Copyright © 2014 Sou Bunnbu <iyzsong@gmail.com>
@ -117,19 +117,19 @@
(define-public mailutils
(package
(name "mailutils")
(version "3.2")
(version "3.3")
(source (origin
(method url-fetch)
(uri (string-append "mirror://gnu/mailutils/mailutils-"
version ".tar.bz2"))
(sha256
(base32
"0c06yj5hgqibi24ib9sx865kq6i1h18wn201g6iwcfbpi2a7psdm"))))
"1v110avpdz0bvz3yh3cfvvd0dnn7sa6hrpql2h8dgnri8fww6cag"))))
(build-system gnu-build-system)
(arguments
'(#:phases
(modify-phases %standard-phases
(add-before 'build 'pre-build
(add-before 'check 'prepare-test-suite
(lambda _
;; Use the right file name for `cat'.
(substitute* "testsuite/lib/mailutils.exp"
@ -162,6 +162,17 @@
(("\\$\\(SHELL\\) \\$\\(TESTSUITE\\)" all)
(string-append "-" all)))
;; 'frm' tests expect write access to $HOME.
(setenv "HOME" (getcwd))
;; Avoid the message "I'm going to create the standard MH path
;; for you", which would lead to one test failure (when diffing
;; stdout of 'fmtcheck'.)
(call-with-output-file ".mh_profile"
(lambda (port)
(format port "Path: ~a/Mail-for-tests~%"
(getcwd))))
#t)))
;; TODO: Add `--with-sql'.
#:configure-flags '("--sysconfdir=/etc")
@ -1097,7 +1108,7 @@ facilities for checking incoming mail.")
(define-public dovecot
(package
(name "dovecot")
(version "2.2.33.1")
(version "2.2.33.2")
(source
(origin
(method url-fetch)
@ -1105,7 +1116,7 @@ facilities for checking incoming mail.")
(version-major+minor version) "/"
name "-" version ".tar.gz"))
(sha256 (base32
"02w932hq8v9889k709gbg94jl983lzwd3nh51vkxq041821a3ng4"))))
"117f9i62liz2pm96zi2lpldzlj2knzj7g410zhifwmlsc1w3n7py"))))
(build-system gnu-build-system)
(native-inputs
`(("pkg-config" ,pkg-config)))

32
gnu/packages/mate.scm
View File

@ -27,28 +27,28 @@
#:use-module (guix build-system glib-or-gtk)
#:use-module (guix build-system trivial)
#:use-module (gnu packages)
#:use-module (gnu packages pkg-config)
#:use-module (gnu packages freedesktop)
#:use-module (gnu packages fontutils)
#:use-module (gnu packages fonts)
#:use-module (gnu packages libcanberra)
#:use-module (gnu packages linux)
#:use-module (gnu packages glib)
#:use-module (gnu packages gtk)
#:use-module (gnu packages gettext)
#:use-module (gnu packages gnome)
#:use-module (gnu packages base)
#:use-module (gnu packages docbook)
#:use-module (gnu packages documentation)
#:use-module (gnu packages fonts)
#:use-module (gnu packages fontutils)
#:use-module (gnu packages freedesktop)
#:use-module (gnu packages gettext)
#:use-module (gnu packages glib)
#:use-module (gnu packages gnome)
#:use-module (gnu packages gnupg)
#:use-module (gnu packages gnuzilla)
#:use-module (gnu packages xorg)
#:use-module (gnu packages documentation)
#:use-module (gnu packages xdisorg)
#:use-module (gnu packages base)
#:use-module (gnu packages xml)
#:use-module (gnu packages gtk)
#:use-module (gnu packages libcanberra)
#:use-module (gnu packages linux)
#:use-module (gnu packages pkg-config)
#:use-module (gnu packages photo)
#:use-module (gnu packages polkit)
#:use-module (gnu packages pulseaudio)
#:use-module (gnu packages python))
#:use-module (gnu packages python)
#:use-module (gnu packages xdisorg)
#:use-module (gnu packages xml)
#:use-module (gnu packages xorg))
(define-public mate-icon-theme
(package

4
gnu/packages/messaging.scm
View File

@ -801,14 +801,14 @@ instant messenger with audio and video chat capabilities.")
(define-public qtox
(package
(name "qtox")
(version "1.12.0")
(version "1.12.1")
(source (origin
(method url-fetch)
(uri (string-append "https://github.com/qTox/qTox/archive/v"
version ".tar.gz"))
(sha256
(base32
"0ycgvcfn8hchc775dcn1wpdqff8chvzz1svx9g99wa5vcns9pflg"))
"0dwy0abcxzzcybww2xi33cla71a7752cq02qswcks5kbxnf5pck5"))
(file-name (string-append name "-" version ".tar.gz"))))
(build-system cmake-build-system)
(arguments

8
gnu/packages/mp3.scm
View File

@ -43,6 +43,7 @@
#:use-module (gnu packages video) ;ffmpeg
#:use-module (guix packages)
#:use-module (guix download)
#:use-module (guix utils)
#:use-module (guix build-system gnu)
#:use-module (guix build-system python)
#:use-module (guix build-system cmake))
@ -348,14 +349,15 @@ use with CD-recording software).")
(define-public lame
(package
(name "lame")
(version "3.99.5")
(version "3.100")
(source (origin
(method url-fetch)
(uri (string-append "mirror://sourceforge/lame/lame/3.99/lame-"
(uri (string-append "mirror://sourceforge/lame/lame/"
(version-major+minor version) "/lame-"
version ".tar.gz"))
(sha256
(base32
"1zr3kadv35ii6liia0bpfgxpag27xcivp571ybckpbz4b10nnd14"))))
"07nsn5sy3a8xbmw1bidxnsj5fj6kg9ai04icmqw40ybkp353dznx"))))
(build-system gnu-build-system)
;; XXX FIXME: Use gcc-4.8 on i686 to work around
;; <http://bugs.gnu.org/20856>.

12
gnu/packages/music.scm
View File

@ -2300,7 +2300,7 @@ for improved Amiga ProTracker 2/3 compatibility.")
(define-public schismtracker
(package
(name "schismtracker")
(version "20170420")
(version "20170910")
(source (origin
(method url-fetch)
(uri (string-append
@ -2309,7 +2309,7 @@ for improved Amiga ProTracker 2/3 compatibility.")
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
"0k06vri29ayaq7mzsik3yywh6zdar2nfpkav2sp6g2rjl6k6vi5z"))
"01gfcjngbpv87y9w5jln8k313hycpkb1d617hdy2cdw2hxqzlclz"))
(modules '((guix build utils)))
(snippet
;; Remove use of __DATE__ and __TIME__ for reproducibility.
@ -2807,8 +2807,8 @@ plugins, a switch trigger, a toggle switch, and a peakmeter.")
(license license:gpl2+))))
(define-public ingen
(let ((commit "fd147d0b888090bfb897505852c1f25dbdf77e18")
(revision "1"))
(let ((commit "cc4a4db33f4d126a07a4a498e053c5fb9a883be3")
(revision "2"))
(package
(name "ingen")
(version (string-append "0.0.0-" revision "."
@ -2822,7 +2822,7 @@ plugins, a switch trigger, a toggle switch, and a peakmeter.")
(file-name (string-append name "-" version "-checkout"))
(sha256
(base32
"1qmg79962my82c43vyrv5sxbqci9c7gc2s9bwaaqd0fcf08xcz1z"))))
"1wg47vjw9djn99gbnsl2bcwj4xhdid61m4wrbn2nlp797flj91ic"))))
(build-system waf-build-system)
(arguments
`(#:tests? #f ; no "check" target
@ -2866,7 +2866,7 @@ plugins, a switch trigger, a toggle switch, and a peakmeter.")
("python-rdflib" ,python-rdflib)
("python" ,python)
("jack" ,jack-1)
("lv2" ,lv2)
("lv2" ,lv2-devel)
("lilv" ,lilv)
("raul" ,raul-devel)
("ganv" ,ganv-devel)

5
gnu/packages/musl.scm
View File

@ -27,15 +27,14 @@
(define-public musl
(package
(name "musl")
(version "1.1.15")
(version "1.1.17")
(source (origin
(method url-fetch)
(uri (string-append "http://www.musl-libc.org/releases/"
name "-" version ".tar.gz"))
(patches (search-patches "musl-CVE-2016-8859.patch"))
(sha256
(base32
"1ymhxkskivzph0q34zadwfglc5gyahqajm7chqqn2zraxv3lgr4p"))))
"0r0lyp2w6v2bvm8h1si7w3p2qx037szl14qnxm5p00568z3m3an8"))))
(build-system gnu-build-system)
(arguments
`(#:tests? #f ; Musl has no tests

8
gnu/packages/networking.scm
View File

@ -875,7 +875,7 @@ offline emulation of DNS.")
(define-public perl-geo-ip
(package
(name "perl-geo-ip")
(version "1.50")
(version "1.51")
(source
(origin
(method url-fetch)
@ -885,7 +885,7 @@ offline emulation of DNS.")
".tar.gz"))
(sha256
(base32
"0ar69lrm26rp6sqxjf0p6cvjfprjx8gkxx11r399lvh99rqfl7zr"))))
"1fka8fr7fw6sh3xa9glhs1zjg3s2gfkhi7n7da1l2m2wblqj0c0n"))))
(build-system perl-build-system)
(home-page "http://search.cpan.org/dist/Geo-IP")
(synopsis
@ -1267,7 +1267,7 @@ networks.")
(define-public speedtest-cli
(package
(name "speedtest-cli")
(version "1.0.6")
(version "1.0.7")
(source
(origin
(method url-fetch)
@ -1276,7 +1276,7 @@ networks.")
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
"1alambi1ljng6j04k7pq58jqwd0wh1q9630f17nl34ljabji5lwy"))))
"1fbq4kpx8sj50g74hwpixisfjjgxq6zyn40d3m28dxhn7mxbnlrq"))))
(build-system python-build-system)
(home-page "https://github.com/sivel/speedtest-cli")
(synopsis "Internet bandwidth tester")

76
gnu/packages/ocaml.scm
View File

@ -401,7 +401,12 @@ syntax of OCaml.")
(lambda _
(zero? (system* "make" "-j" (number->string
(parallel-job-count))
"world.opt")))))))
"world.opt"))))
;; Required for findlib to find camlp5's libraries
(add-after 'install 'install-meta
(lambda* (#:key outputs #:allow-other-keys)
(install-file "etc/META" (string-append (assoc-ref outputs "out")
"/lib/ocaml/camlp5/")))))))
(home-page "http://camlp5.gforge.inria.fr/")
(synopsis "Pre-processor Pretty Printer for OCaml")
(description
@ -445,26 +450,25 @@ written in Objective Caml.")
(define-public coq
(package
(name "coq")
(version "8.5pl2")
(version "8.7.0")
(source (origin
(method url-fetch)
(uri (string-append "https://coq.inria.fr/distrib/V" version
"/files/" name "-" version ".tar.gz"))
(sha256
(base32
"0wyywia0darak2zmc5v0ra9rn0b9whwdfiahralm8v5za499s8w3"))))
"15wjngjd5pyfqdl5yw92rvdxvy15xcjlpx0rqlkzvcsis1z20xpk"))))
(native-search-paths
(list (search-path-specification
(variable "COQPATH")
(files (list "lib/coq/user-contrib")))))
(build-system gnu-build-system)
(build-system ocaml-build-system)
(native-inputs
`(("texlive" ,texlive)
("findlib" ,ocaml-findlib)
("hevea" ,hevea)))
(inputs
`(("ocaml" ,ocaml)
("lablgtk" ,lablgtk)
`(("lablgtk" ,lablgtk)
("python" ,python-2)
("camlp5" ,camlp5)))
(arguments
`(#:phases
@ -488,6 +492,11 @@ written in Objective Caml.")
(add-after 'install 'check
(lambda _
(with-directory-excursion "test-suite"
;; These two tests fail.
;; This one fails because the output is not formatted as expected.
(delete-file-recursively "coq-makefile/timing")
;; This one fails because we didn't build coqtop.byte.
(delete-file-recursively "coq-makefile/findlib-package")
(zero? (system* "make"))))))))
(home-page "https://coq.inria.fr")
(synopsis "Proof assistant for higher-order logic")
@ -3551,14 +3560,14 @@ library is currently designed for Unicode Standard 3.2.")
(define-public coq-flocq
(package
(name "coq-flocq")
(version "2.5.2")
(version "2.6.0")
(source (origin
(method url-fetch)
(uri (string-append "https://gforge.inria.fr/frs/download.php/file"
"/36199/flocq-" version ".tar.gz"))
"/37054/flocq-" version ".tar.gz"))
(sha256
(base32
"0h5mlasirfzc0wwn2isg4kahk384n73145akkpinrxq5jsn5d22h"))))
"13fv150dcwnjrk00d7zj2c5x9jwmxgrq0ay440gkr730l8mvk3l3"))))
(build-system gnu-build-system)
(native-inputs
`(("ocaml" ,ocaml)
@ -3648,14 +3657,14 @@ assistant.")
(define-public coq-mathcomp
(package
(name "coq-mathcomp")
(version "1.6.1")
(version "1.6.2")
(source (origin
(method url-fetch)
(uri (string-append "https://github.com/math-comp/math-comp/archive/mathcomp-"
version ".tar.gz"))
(sha256
(base32
"1j9ylggjzrxz1i2hdl2yhsvmvy5z6l4rprwx7604401080p5sgjw"))))
"0lg5ncr7p4y8qqq6pfw6brqc6a9xzlfa0drprwfdn0rnyaq5nca6"))))
(build-system gnu-build-system)
(native-inputs
`(("ocaml" ,ocaml)
@ -3690,14 +3699,14 @@ part of the distribution.")
(define-public coq-coquelicot
(package
(name "coq-coquelicot")
(version "3.0.0")
(version "3.0.1")
(source (origin
(method url-fetch)
(uri (string-append "https://gforge.inria.fr/frs/download.php/"
"file/36537/coquelicot-" version ".tar.gz"))
"file/37045/coquelicot-" version ".tar.gz"))
(sha256
(base32
"0fx99bvsbdizj00gx2im8939y4wwl05f4qhw184j90kcx5vjxxv9"))))
"0hsyhsy2lwqxxx2r8xgi5csmirss42lp9bkb9yy35mnya0w78c8r"))))
(build-system gnu-build-system)
(native-inputs
`(("ocaml" ,ocaml)
@ -3737,17 +3746,49 @@ conservative extension of Coq's standard library and provides correspondence
theorems between the two libraries.")
(license license:lgpl3+)))
(define-public coq-bignums
(package
(name "coq-bignums")
(version "8.7.0")
(source (origin
(method url-fetch)
(uri (string-append "https://github.com/coq/bignums/archive/V"
version ".tar.gz"))
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
"03iw9jiwq9jx45gsvp315y3lxr8m9ksppmcjvxs5c23qnky6zqjx"))))
(build-system gnu-build-system)
(native-inputs
`(("ocaml" ,ocaml)
("coq" ,coq)))
(inputs
`(("camlp5" ,camlp5)))
(arguments
`(#:tests? #f; No test target
#:make-flags
(list (string-append "COQLIBINSTALL=" (assoc-ref %outputs "out")
"/lib/coq/user-contrib"))
#:phases
(modify-phases %standard-phases
(delete 'configure))))
(home-page "https://github.com/coq/bignums")
(synopsis "Coq library for arbitrary large numbers")
(description "Bignums is a coq library of arbitrary large numbers. It
provides BigN, BigZ, BigQ that used to be part of Coq standard library.")
(license license:lgpl2.1+)))
(define-public coq-interval
(package
(name "coq-interval")
(version "3.2.0")
(version "3.3.0")
(source (origin
(method url-fetch)
(uri (string-append "https://gforge.inria.fr/frs/download.php/"
"file/36538/interval-" version ".tar.gz"))
(sha256
(base32
"16ir7mizl18kwa1ls8fwjih6r87894bvc1r6lh85cd43la7nriq3"))))
"08fdcf3hbwqphglvwprvqzgkg0qbimpyhnqsgv3gac4y1ap0f903"))))
(build-system gnu-build-system)
(native-inputs
`(("ocaml" ,ocaml)
@ -3755,6 +3796,7 @@ theorems between the two libraries.")
("coq" ,coq)))
(propagated-inputs
`(("flocq" ,coq-flocq)
("bignums" ,coq-bignums)
("coquelicot" ,coq-coquelicot)
("mathcomp" ,coq-mathcomp)))
(arguments

6
gnu/packages/package-management.scm
View File

@ -79,8 +79,8 @@
;; Note: the 'update-guix-package.scm' script expects this definition to
;; start precisely like this.
(let ((version "0.13.0")
(commit "8b920d707ed07a3251227f77526cf875d86a4417")
(revision 7))
(commit "357ab93aacbd882a48cd7961ab301afa78c941d0")
(revision 8))
(package
(name "guix")
@ -96,7 +96,7 @@
(commit commit)))
(sha256
(base32
"15phwcadkw44mr4hnv1dxzzw9an6x7sbdfzwy4iciqw6y2wckncd"))
"19cf4gpdkqv8lxpqg4ibmxhmnsm2ggi3wrhaslfmypa2a5b5jls1"))
(file-name (string-append "guix-" version "-checkout"))))
(build-system gnu-build-system)
(arguments

5
gnu/packages/password-utils.scm
View File

@ -12,6 +12,7 @@
;;; Copyright © 2017 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2017 Jelle Licht <jlicht@fsfe.org>
;;; Copyright © 2017 Eric Bavier <bavier@member.fsf.org>
;;; Copyright © 2017 Nicolas Goaziou <mail@nicolasgoaziou.fr>
;;;
;;; This file is part of GNU Guix.
;;;
@ -83,7 +84,7 @@ human.")
(define-public keepassxc
(package
(name "keepassxc")
(version "2.2.0")
(version "2.2.1")
(source
(origin
(method url-fetch)
@ -92,7 +93,7 @@ human.")
version "-src.tar.xz"))
(sha256
(base32
"0nby6aq6w8g7c9slzahf7i34sbj8majf8rhmqqww87v6kaypxi3i"))))
"1gkxsv3g4pkzbjkd1c27k15m2b5y2fqnnijphnaiv542yk7csqb7"))))
(build-system cmake-build-system)
(inputs
`(("libgcrypt" ,libgcrypt)

14
gnu/packages/patches/libusb-for-axoloti.patch Normal file
View File

@ -0,0 +1,14 @@
diff -rp -u4 libusb-1.0.19-orig/libusb/descriptor.c libusb-1.0.19/libusb/descriptor.c
--- libusb-1.0.19-orig/libusb/descriptor.c 2015-05-12 00:15:19 +0200
+++ libusb-1.0.19/libusb/descriptor.c 2015-05-12 00:17:09 +0200
@@ -1181,9 +1181,9 @@ int API_EXPORTED libusb_get_string_descr
if (tbuf[1] != LIBUSB_DT_STRING)
return LIBUSB_ERROR_IO;
if (tbuf[0] > r)
- return LIBUSB_ERROR_IO;
+ tbuf[0] = r;
for (di = 0, si = 2; si < tbuf[0]; si += 2) {
if (di >= (length - 1))
break;

84
gnu/packages/patches/libvirt-CVE-2017-1000256.patch Normal file
View File

@ -0,0 +1,84 @@
Fix CVE-2017-1000256:
https://security.libvirt.org/2017/0002.html
https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2017-1000256
Patch copied from upstream source repository:
https://libvirt.org/git/?p=libvirt.git;a=commit;h=dc6c41798d1eb5c52c75365ffa22f7672709dfa7
From dc6c41798d1eb5c52c75365ffa22f7672709dfa7 Mon Sep 17 00:00:00 2001
From: Daniel P. Berrange <berrange@redhat.com>
Date: Thu, 5 Oct 2017 17:54:28 +0100
Subject: [PATCH] qemu: ensure TLS clients always verify the server certificate
The default_tls_x509_verify (and related) parameters in qemu.conf
control whether the QEMU TLS servers request & verify certificates
from clients. This works as a simple access control system for
servers by requiring the CA to issue certs to permitted clients.
This use of client certificates is disabled by default, since it
requires extra work to issue client certificates.
Unfortunately the code was using this configuration parameter when
setting up both TLS clients and servers in QEMU. The result was that
TLS clients for character devices and disk devices had verification
turned off, meaning they would ignore errors while validating the
server certificate.
This allows for trivial MITM attacks between client and server,
as any certificate returned by the attacker will be accepted by
the client.
This is assigned CVE-2017-1000256 / LSN-2017-0002
Reviewed-by: Eric Blake <eblake@redhat.com>
Signed-off-by: Daniel P. Berrange <berrange@redhat.com>
(cherry picked from commit 441d3eb6d1be940a67ce45a286602a967601b157)
---
src/qemu/qemu_command.c | 2 +-
.../qemuxml2argv-serial-tcp-tlsx509-chardev.args | 2 +-
...xml2argv-serial-tcp-tlsx509-secret-chardev.args | 2 +-
3 files changed, 3 insertions(+), 3 deletions(-)
diff --git a/src/qemu/qemu_command.c b/src/qemu/qemu_command.c
index 9a27987..ae78cd1 100644
--- a/src/qemu/qemu_command.c
+++ b/src/qemu/qemu_command.c
@@ -718,7 +718,7 @@ qemuBuildTLSx509BackendProps(const char *tlspath,
if (virJSONValueObjectCreate(propsret,
"s:dir", path,
"s:endpoint", (isListen ? "server": "client"),
- "b:verify-peer", verifypeer,
+ "b:verify-peer", (isListen ? verifypeer : true),
NULL) < 0)
goto cleanup;
diff --git a/tests/qemuxml2argvdata/qemuxml2argv-serial-tcp-tlsx509-chardev.args b/tests/qemuxml2argvdata/qemuxml2argv-serial-tcp-tlsx509-chardev.args
index 5aff773..ab5f7e2 100644
--- a/tests/qemuxml2argvdata/qemuxml2argv-serial-tcp-tlsx509-chardev.args
+++ b/tests/qemuxml2argvdata/qemuxml2argv-serial-tcp-tlsx509-chardev.args
@@ -26,7 +26,7 @@ server,nowait \
localport=1111 \
-device isa-serial,chardev=charserial0,id=serial0 \
-object tls-creds-x509,id=objcharserial1_tls0,dir=/etc/pki/libvirt-chardev,\
-endpoint=client,verify-peer=no \
+endpoint=client,verify-peer=yes \
-chardev socket,id=charserial1,host=127.0.0.1,port=5555,\
tls-creds=objcharserial1_tls0 \
-device isa-serial,chardev=charserial1,id=serial1 \
diff --git a/tests/qemuxml2argvdata/qemuxml2argv-serial-tcp-tlsx509-secret-chardev.args b/tests/qemuxml2argvdata/qemuxml2argv-serial-tcp-tlsx509-secret-chardev.args
index 91f1fe0..2567abb 100644
--- a/tests/qemuxml2argvdata/qemuxml2argv-serial-tcp-tlsx509-secret-chardev.args
+++ b/tests/qemuxml2argvdata/qemuxml2argv-serial-tcp-tlsx509-secret-chardev.args
@@ -31,7 +31,7 @@ localport=1111 \
data=9eao5F8qtkGt+seB1HYivWIxbtwUu6MQtg1zpj/oDtUsPr1q8wBYM91uEHCn6j/1,\
keyid=masterKey0,iv=AAECAwQFBgcICQoLDA0ODw==,format=base64 \
-object tls-creds-x509,id=objcharserial1_tls0,dir=/etc/pki/libvirt-chardev,\
-endpoint=client,verify-peer=no,passwordid=charserial1-secret0 \
+endpoint=client,verify-peer=yes,passwordid=charserial1-secret0 \
-chardev socket,id=charserial1,host=127.0.0.1,port=5555,\
tls-creds=objcharserial1_tls0 \
-device isa-serial,chardev=charserial1,id=serial1 \
--
1.7.1

21
gnu/packages/patches/mupdf-CVE-2017-15587.patch Normal file
View File

@ -0,0 +1,21 @@
Fix CVE-2017-15587.
https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2017-15587
https://nandynarwhals.org/CVE-2017-15587/
Copied from upstream:
<https://git.ghostscript.com/?p=mupdf.git;h=82df2631d7d0446b206ea6b434ea609b6c28b0e8>
diff --git a/source/pdf/pdf-xref.c b/source/pdf/pdf-xref.c
index 66bd0ed..6292793 100644
--- a/source/pdf/pdf-xref.c
+++ b/source/pdf/pdf-xref.c
@@ -924,7 +924,7 @@ pdf_read_new_xref_section(fz_context *ctx, pdf_document *doc, fz_stream *stm, fz
pdf_xref_entry *table;
int i, n;
- if (i0 < 0 || i1 < 0)
+ if (i0 < 0 || i1 < 0 || (i0+i1) < 0)
fz_throw(ctx, FZ_ERROR_GENERIC, "negative xref stream entry index");
//if (i0 + i1 > pdf_xref_len(ctx, doc))
// fz_throw(ctx, FZ_ERROR_GENERIC, "xref stream has too many entries");

81
gnu/packages/patches/musl-CVE-2016-8859.patch
View File

@ -1,81 +0,0 @@
Fix CVE-2016-8859:
https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2016-8859
Patch copied from upstream source repository:
http://git.musl-libc.org/cgit/musl/commit/?id=c3edc06d1e1360f3570db9155d6b318ae0d0f0f7
From c3edc06d1e1360f3570db9155d6b318ae0d0f0f7 Mon Sep 17 00:00:00 2001
From: Rich Felker <dalias@aerifal.cx>
Date: Thu, 6 Oct 2016 18:34:58 -0400
Subject: [PATCH] fix missing integer overflow checks in regexec buffer size
computations
most of the possible overflows were already ruled out in practice by
regcomp having already succeeded performing larger allocations.
however at least the num_states*num_tags multiplication can clearly
overflow in practice. for safety, check them all, and use the proper
type, size_t, rather than int.
also improve comments, use calloc in place of malloc+memset, and
remove bogus casts.
---
src/regex/regexec.c | 23 ++++++++++++++++++-----
1 file changed, 18 insertions(+), 5 deletions(-)
diff --git a/src/regex/regexec.c b/src/regex/regexec.c
index 16c5d0a..dd52319 100644
--- a/src/regex/regexec.c
+++ b/src/regex/regexec.c
@@ -34,6 +34,7 @@
#include <wchar.h>
#include <wctype.h>
#include <limits.h>
+#include <stdint.h>
#include <regex.h>
@@ -206,11 +207,24 @@ tre_tnfa_run_parallel(const tre_tnfa_t *tnfa, const void *string,
/* Allocate memory for temporary data required for matching. This needs to
be done for every matching operation to be thread safe. This allocates
- everything in a single large block from the stack frame using alloca()
- or with malloc() if alloca is unavailable. */
+ everything in a single large block with calloc(). */
{
- int tbytes, rbytes, pbytes, xbytes, total_bytes;
+ size_t tbytes, rbytes, pbytes, xbytes, total_bytes;
char *tmp_buf;
+
+ /* Ensure that tbytes and xbytes*num_states cannot overflow, and that
+ * they don't contribute more than 1/8 of SIZE_MAX to total_bytes. */
+ if (num_tags > SIZE_MAX/(8 * sizeof(int) * tnfa->num_states))
+ goto error_exit;
+
+ /* Likewise check rbytes. */
+ if (tnfa->num_states+1 > SIZE_MAX/(8 * sizeof(*reach_next)))
+ goto error_exit;
+
+ /* Likewise check pbytes. */
+ if (tnfa->num_states > SIZE_MAX/(8 * sizeof(*reach_pos)))
+ goto error_exit;
+
/* Compute the length of the block we need. */
tbytes = sizeof(*tmp_tags) * num_tags;
rbytes = sizeof(*reach_next) * (tnfa->num_states + 1);
@@ -221,10 +235,9 @@ tre_tnfa_run_parallel(const tre_tnfa_t *tnfa, const void *string,
+ (rbytes + xbytes * tnfa->num_states) * 2 + tbytes + pbytes;
/* Allocate the memory. */
- buf = xmalloc((unsigned)total_bytes);
+ buf = calloc(total_bytes, 1);
if (buf == NULL)
return REG_ESPACE;
- memset(buf, 0, (size_t)total_bytes);
/* Get the various pointers within tmp_buf (properly aligned). */
tmp_tags = (void *)buf;
--
2.10.1

182
gnu/packages/patches/wpa-supplicant-CVE-2017-13082.patch Normal file
View File

@ -0,0 +1,182 @@
Fix CVE-2017-13082:
https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2017-13082
https://w1.fi/security/2017-1/wpa-packet-number-reuse-with-replayed-messages.txt
Patch copied from upstream:
https://w1.fi/security/2017-1/rebased-v2.6-0001-hostapd-Avoid-key-reinstallation-in-FT-handshake.patch
From cf4cab804c7afd5c45505528a8d16e46163243a2 Mon Sep 17 00:00:00 2001
From: Mathy Vanhoef <Mathy.Vanhoef@cs.kuleuven.be>
Date: Fri, 14 Jul 2017 15:15:35 +0200
Subject: [PATCH 1/8] hostapd: Avoid key reinstallation in FT handshake
Do not reinstall TK to the driver during Reassociation Response frame
processing if the first attempt of setting the TK succeeded. This avoids
issues related to clearing the TX/RX PN that could result in reusing
same PN values for transmitted frames (e.g., due to CCM nonce reuse and
also hitting replay protection on the receiver) and accepting replayed
frames on RX side.
This issue was introduced by the commit
0e84c25434e6a1f283c7b4e62e483729085b78d2 ('FT: Fix PTK configuration in
authenticator') which allowed wpa_ft_install_ptk() to be called multiple
times with the same PTK. While the second configuration attempt is
needed with some drivers, it must be done only if the first attempt
failed.
Signed-off-by: Mathy Vanhoef <Mathy.Vanhoef@cs.kuleuven.be>
---
src/ap/ieee802_11.c | 16 +++++++++++++---
src/ap/wpa_auth.c | 11 +++++++++++
src/ap/wpa_auth.h | 3 ++-
src/ap/wpa_auth_ft.c | 10 ++++++++++
src/ap/wpa_auth_i.h | 1 +
5 files changed, 37 insertions(+), 4 deletions(-)
diff --git a/src/ap/ieee802_11.c b/src/ap/ieee802_11.c
index 4e04169..333035f 100644
--- a/src/ap/ieee802_11.c
+++ b/src/ap/ieee802_11.c
@@ -1841,6 +1841,7 @@ static int add_associated_sta(struct hostapd_data *hapd,
{
struct ieee80211_ht_capabilities ht_cap;
struct ieee80211_vht_capabilities vht_cap;
+ int set = 1;
/*
* Remove the STA entry to ensure the STA PS state gets cleared and
@@ -1848,9 +1849,18 @@ static int add_associated_sta(struct hostapd_data *hapd,
* FT-over-the-DS, where a station re-associates back to the same AP but
* skips the authentication flow, or if working with a driver that
* does not support full AP client state.
+ *
+ * Skip this if the STA has already completed FT reassociation and the
+ * TK has been configured since the TX/RX PN must not be reset to 0 for
+ * the same key.
*/
- if (!sta->added_unassoc)
+ if (!sta->added_unassoc &&
+ (!(sta->flags & WLAN_STA_AUTHORIZED) ||
+ !wpa_auth_sta_ft_tk_already_set(sta->wpa_sm))) {
hostapd_drv_sta_remove(hapd, sta->addr);
+ wpa_auth_sm_event(sta->wpa_sm, WPA_DRV_STA_REMOVED);
+ set = 0;
+ }
#ifdef CONFIG_IEEE80211N
if (sta->flags & WLAN_STA_HT)
@@ -1873,11 +1883,11 @@ static int add_associated_sta(struct hostapd_data *hapd,
sta->flags & WLAN_STA_VHT ? &vht_cap : NULL,
sta->flags | WLAN_STA_ASSOC, sta->qosinfo,
sta->vht_opmode, sta->p2p_ie ? 1 : 0,
- sta->added_unassoc)) {
+ set)) {
hostapd_logger(hapd, sta->addr,
HOSTAPD_MODULE_IEEE80211, HOSTAPD_LEVEL_NOTICE,
"Could not %s STA to kernel driver",
- sta->added_unassoc ? "set" : "add");
+ set ? "set" : "add");
if (sta->added_unassoc) {
hostapd_drv_sta_remove(hapd, sta->addr);
diff --git a/src/ap/wpa_auth.c b/src/ap/wpa_auth.c
index 3587086..707971d 100644
--- a/src/ap/wpa_auth.c
+++ b/src/ap/wpa_auth.c
@@ -1745,6 +1745,9 @@ int wpa_auth_sm_event(struct wpa_state_machine *sm, enum wpa_event event)
#else /* CONFIG_IEEE80211R */
break;
#endif /* CONFIG_IEEE80211R */
+ case WPA_DRV_STA_REMOVED:
+ sm->tk_already_set = FALSE;
+ return 0;
}
#ifdef CONFIG_IEEE80211R
@@ -3250,6 +3253,14 @@ int wpa_auth_sta_wpa_version(struct wpa_state_machine *sm)
}
+int wpa_auth_sta_ft_tk_already_set(struct wpa_state_machine *sm)
+{
+ if (!sm || !wpa_key_mgmt_ft(sm->wpa_key_mgmt))
+ return 0;
+ return sm->tk_already_set;
+}
+
+
int wpa_auth_sta_clear_pmksa(struct wpa_state_machine *sm,
struct rsn_pmksa_cache_entry *entry)
{
diff --git a/src/ap/wpa_auth.h b/src/ap/wpa_auth.h
index 0de8d97..97461b0 100644
--- a/src/ap/wpa_auth.h
+++ b/src/ap/wpa_auth.h
@@ -267,7 +267,7 @@ void wpa_receive(struct wpa_authenticator *wpa_auth,
u8 *data, size_t data_len);
enum wpa_event {
WPA_AUTH, WPA_ASSOC, WPA_DISASSOC, WPA_DEAUTH, WPA_REAUTH,
- WPA_REAUTH_EAPOL, WPA_ASSOC_FT
+ WPA_REAUTH_EAPOL, WPA_ASSOC_FT, WPA_DRV_STA_REMOVED
};
void wpa_remove_ptk(struct wpa_state_machine *sm);
int wpa_auth_sm_event(struct wpa_state_machine *sm, enum wpa_event event);
@@ -280,6 +280,7 @@ int wpa_auth_pairwise_set(struct wpa_state_machine *sm);
int wpa_auth_get_pairwise(struct wpa_state_machine *sm);
int wpa_auth_sta_key_mgmt(struct wpa_state_machine *sm);
int wpa_auth_sta_wpa_version(struct wpa_state_machine *sm);
+int wpa_auth_sta_ft_tk_already_set(struct wpa_state_machine *sm);
int wpa_auth_sta_clear_pmksa(struct wpa_state_machine *sm,
struct rsn_pmksa_cache_entry *entry);
struct rsn_pmksa_cache_entry *
diff --git a/src/ap/wpa_auth_ft.c b/src/ap/wpa_auth_ft.c
index 42242a5..e63b99a 100644
--- a/src/ap/wpa_auth_ft.c
+++ b/src/ap/wpa_auth_ft.c
@@ -780,6 +780,14 @@ void wpa_ft_install_ptk(struct wpa_state_machine *sm)
return;
}
+ if (sm->tk_already_set) {
+ /* Must avoid TK reconfiguration to prevent clearing of TX/RX
+ * PN in the driver */
+ wpa_printf(MSG_DEBUG,
+ "FT: Do not re-install same PTK to the driver");
+ return;
+ }
+
/* FIX: add STA entry to kernel/driver here? The set_key will fail
* most likely without this.. At the moment, STA entry is added only
* after association has been completed. This function will be called
@@ -792,6 +800,7 @@ void wpa_ft_install_ptk(struct wpa_state_machine *sm)
/* FIX: MLME-SetProtection.Request(TA, Tx_Rx) */
sm->pairwise_set = TRUE;
+ sm->tk_already_set = TRUE;
}
@@ -898,6 +907,7 @@ static int wpa_ft_process_auth_req(struct wpa_state_machine *sm,
sm->pairwise = pairwise;
sm->PTK_valid = TRUE;
+ sm->tk_already_set = FALSE;
wpa_ft_install_ptk(sm);
buflen = 2 + sizeof(struct rsn_mdie) + 2 + sizeof(struct rsn_ftie) +
diff --git a/src/ap/wpa_auth_i.h b/src/ap/wpa_auth_i.h
index 72b7eb3..7fd8f05 100644
--- a/src/ap/wpa_auth_i.h
+++ b/src/ap/wpa_auth_i.h
@@ -65,6 +65,7 @@ struct wpa_state_machine {
struct wpa_ptk PTK;
Boolean PTK_valid;
Boolean pairwise_set;
+ Boolean tk_already_set;
int keycount;
Boolean Pair;
struct wpa_key_replay_counter {
--
2.7.4

448
gnu/packages/patches/wpa-supplicant-fix-key-reuse.patch Normal file
View File

@ -0,0 +1,448 @@
Fix CVE-2017-{13078,13079,13080,13081,13087,13088}:
https://w1.fi/security/2017-1/wpa-packet-number-reuse-with-replayed-messages.txt
https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2017-13078
https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2017-13079
https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2017-13080
https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2017-13081
https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2017-13087
https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2017-13088
These two patches are copied from upstream:
https://w1.fi/security/2017-1/rebased-v2.6-0002-Prevent-reinstallation-of-an-already-in-use-group-ke.patch
https://w1.fi/security/2017-1/rebased-v2.6-0003-Extend-protection-of-GTK-IGTK-reinstallation-of-WNM-.patch
From 927f891007c402fefd1ff384645b3f07597c3ede Mon Sep 17 00:00:00 2001
From: Mathy Vanhoef <Mathy.Vanhoef@cs.kuleuven.be>
Date: Wed, 12 Jul 2017 16:03:24 +0200
Subject: [PATCH 2/8] Prevent reinstallation of an already in-use group key
Track the current GTK and IGTK that is in use and when receiving a
(possibly retransmitted) Group Message 1 or WNM-Sleep Mode Response, do
not install the given key if it is already in use. This prevents an
attacker from trying to trick the client into resetting or lowering the
sequence counter associated to the group key.
Signed-off-by: Mathy Vanhoef <Mathy.Vanhoef@cs.kuleuven.be>
---
src/common/wpa_common.h | 11 +++++
src/rsn_supp/wpa.c | 116 ++++++++++++++++++++++++++++++------------------
src/rsn_supp/wpa_i.h | 4 ++
3 files changed, 87 insertions(+), 44 deletions(-)
diff --git a/src/common/wpa_common.h b/src/common/wpa_common.h
index af1d0f0..d200285 100644
--- a/src/common/wpa_common.h
+++ b/src/common/wpa_common.h
@@ -217,6 +217,17 @@ struct wpa_ptk {
size_t tk_len;
};
+struct wpa_gtk {
+ u8 gtk[WPA_GTK_MAX_LEN];
+ size_t gtk_len;
+};
+
+#ifdef CONFIG_IEEE80211W
+struct wpa_igtk {
+ u8 igtk[WPA_IGTK_MAX_LEN];
+ size_t igtk_len;
+};
+#endif /* CONFIG_IEEE80211W */
/* WPA IE version 1
* 00-50-f2:1 (OUI:OUI type)
diff --git a/src/rsn_supp/wpa.c b/src/rsn_supp/wpa.c
index 3c47879..95bd7be 100644
--- a/src/rsn_supp/wpa.c
+++ b/src/rsn_supp/wpa.c
@@ -714,6 +714,15 @@ static int wpa_supplicant_install_gtk(struct wpa_sm *sm,
const u8 *_gtk = gd->gtk;
u8 gtk_buf[32];
+ /* Detect possible key reinstallation */
+ if (sm->gtk.gtk_len == (size_t) gd->gtk_len &&
+ os_memcmp(sm->gtk.gtk, gd->gtk, sm->gtk.gtk_len) == 0) {
+ wpa_dbg(sm->ctx->msg_ctx, MSG_DEBUG,
+ "WPA: Not reinstalling already in-use GTK to the driver (keyidx=%d tx=%d len=%d)",
+ gd->keyidx, gd->tx, gd->gtk_len);
+ return 0;
+ }
+
wpa_hexdump_key(MSG_DEBUG, "WPA: Group Key", gd->gtk, gd->gtk_len);
wpa_dbg(sm->ctx->msg_ctx, MSG_DEBUG,
"WPA: Installing GTK to the driver (keyidx=%d tx=%d len=%d)",
@@ -748,6 +757,9 @@ static int wpa_supplicant_install_gtk(struct wpa_sm *sm,
}
os_memset(gtk_buf, 0, sizeof(gtk_buf));
+ sm->gtk.gtk_len = gd->gtk_len;
+ os_memcpy(sm->gtk.gtk, gd->gtk, sm->gtk.gtk_len);
+
return 0;
}
@@ -854,6 +866,48 @@ static int wpa_supplicant_pairwise_gtk(struct wpa_sm *sm,
}
+#ifdef CONFIG_IEEE80211W
+static int wpa_supplicant_install_igtk(struct wpa_sm *sm,
+ const struct wpa_igtk_kde *igtk)
+{
+ size_t len = wpa_cipher_key_len(sm->mgmt_group_cipher);
+ u16 keyidx = WPA_GET_LE16(igtk->keyid);
+
+ /* Detect possible key reinstallation */
+ if (sm->igtk.igtk_len == len &&
+ os_memcmp(sm->igtk.igtk, igtk->igtk, sm->igtk.igtk_len) == 0) {
+ wpa_dbg(sm->ctx->msg_ctx, MSG_DEBUG,
+ "WPA: Not reinstalling already in-use IGTK to the driver (keyidx=%d)",
+ keyidx);
+ return 0;
+ }
+
+ wpa_dbg(sm->ctx->msg_ctx, MSG_DEBUG,
+ "WPA: IGTK keyid %d pn %02x%02x%02x%02x%02x%02x",
+ keyidx, MAC2STR(igtk->pn));
+ wpa_hexdump_key(MSG_DEBUG, "WPA: IGTK", igtk->igtk, len);
+ if (keyidx > 4095) {
+ wpa_msg(sm->ctx->msg_ctx, MSG_WARNING,
+ "WPA: Invalid IGTK KeyID %d", keyidx);
+ return -1;
+ }
+ if (wpa_sm_set_key(sm, wpa_cipher_to_alg(sm->mgmt_group_cipher),
+ broadcast_ether_addr,
+ keyidx, 0, igtk->pn, sizeof(igtk->pn),
+ igtk->igtk, len) < 0) {
+ wpa_msg(sm->ctx->msg_ctx, MSG_WARNING,
+ "WPA: Failed to configure IGTK to the driver");
+ return -1;
+ }
+
+ sm->igtk.igtk_len = len;
+ os_memcpy(sm->igtk.igtk, igtk->igtk, sm->igtk.igtk_len);
+
+ return 0;
+}
+#endif /* CONFIG_IEEE80211W */
+
+
static int ieee80211w_set_keys(struct wpa_sm *sm,
struct wpa_eapol_ie_parse *ie)
{
@@ -864,30 +918,14 @@ static int ieee80211w_set_keys(struct wpa_sm *sm,
if (ie->igtk) {
size_t len;
const struct wpa_igtk_kde *igtk;
- u16 keyidx;
+
len = wpa_cipher_key_len(sm->mgmt_group_cipher);
if (ie->igtk_len != WPA_IGTK_KDE_PREFIX_LEN + len)
return -1;
+
igtk = (const struct wpa_igtk_kde *) ie->igtk;
- keyidx = WPA_GET_LE16(igtk->keyid);
- wpa_dbg(sm->ctx->msg_ctx, MSG_DEBUG, "WPA: IGTK keyid %d "
- "pn %02x%02x%02x%02x%02x%02x",
- keyidx, MAC2STR(igtk->pn));
- wpa_hexdump_key(MSG_DEBUG, "WPA: IGTK",
- igtk->igtk, len);
- if (keyidx > 4095) {
- wpa_msg(sm->ctx->msg_ctx, MSG_WARNING,
- "WPA: Invalid IGTK KeyID %d", keyidx);
- return -1;
- }
- if (wpa_sm_set_key(sm, wpa_cipher_to_alg(sm->mgmt_group_cipher),
- broadcast_ether_addr,
- keyidx, 0, igtk->pn, sizeof(igtk->pn),
- igtk->igtk, len) < 0) {
- wpa_msg(sm->ctx->msg_ctx, MSG_WARNING,
- "WPA: Failed to configure IGTK to the driver");
+ if (wpa_supplicant_install_igtk(sm, igtk) < 0)
return -1;
- }
}
return 0;
@@ -2307,7 +2345,7 @@ void wpa_sm_deinit(struct wpa_sm *sm)
*/
void wpa_sm_notify_assoc(struct wpa_sm *sm, const u8 *bssid)
{
- int clear_ptk = 1;
+ int clear_keys = 1;
if (sm == NULL)
return;
@@ -2333,11 +2371,11 @@ void wpa_sm_notify_assoc(struct wpa_sm *sm, const u8 *bssid)
/* Prepare for the next transition */
wpa_ft_prepare_auth_request(sm, NULL);
- clear_ptk = 0;
+ clear_keys = 0;
}
#endif /* CONFIG_IEEE80211R */
- if (clear_ptk) {
+ if (clear_keys) {
/*
* IEEE 802.11, 8.4.10: Delete PTK SA on (re)association if
* this is not part of a Fast BSS Transition.
@@ -2347,6 +2385,10 @@ void wpa_sm_notify_assoc(struct wpa_sm *sm, const u8 *bssid)
os_memset(&sm->ptk, 0, sizeof(sm->ptk));
sm->tptk_set = 0;
os_memset(&sm->tptk, 0, sizeof(sm->tptk));
+ os_memset(&sm->gtk, 0, sizeof(sm->gtk));
+#ifdef CONFIG_IEEE80211W
+ os_memset(&sm->igtk, 0, sizeof(sm->igtk));
+#endif /* CONFIG_IEEE80211W */
}
#ifdef CONFIG_TDLS
@@ -2877,6 +2919,10 @@ void wpa_sm_drop_sa(struct wpa_sm *sm)
os_memset(sm->pmk, 0, sizeof(sm->pmk));
os_memset(&sm->ptk, 0, sizeof(sm->ptk));
os_memset(&sm->tptk, 0, sizeof(sm->tptk));
+ os_memset(&sm->gtk, 0, sizeof(sm->gtk));
+#ifdef CONFIG_IEEE80211W
+ os_memset(&sm->igtk, 0, sizeof(sm->igtk));
+#endif /* CONFIG_IEEE80211W */
#ifdef CONFIG_IEEE80211R
os_memset(sm->xxkey, 0, sizeof(sm->xxkey));
os_memset(sm->pmk_r0, 0, sizeof(sm->pmk_r0));
@@ -2949,29 +2995,11 @@ int wpa_wnmsleep_install_key(struct wpa_sm *sm, u8 subelem_id, u8 *buf)
os_memset(&gd, 0, sizeof(gd));
#ifdef CONFIG_IEEE80211W
} else if (subelem_id == WNM_SLEEP_SUBELEM_IGTK) {
- struct wpa_igtk_kde igd;
- u16 keyidx;
-
- os_memset(&igd, 0, sizeof(igd));
- keylen = wpa_cipher_key_len(sm->mgmt_group_cipher);
- os_memcpy(igd.keyid, buf + 2, 2);
- os_memcpy(igd.pn, buf + 4, 6);
-
- keyidx = WPA_GET_LE16(igd.keyid);
- os_memcpy(igd.igtk, buf + 10, keylen);
-
- wpa_hexdump_key(MSG_DEBUG, "Install IGTK (WNM SLEEP)",
- igd.igtk, keylen);
- if (wpa_sm_set_key(sm, wpa_cipher_to_alg(sm->mgmt_group_cipher),
- broadcast_ether_addr,
- keyidx, 0, igd.pn, sizeof(igd.pn),
- igd.igtk, keylen) < 0) {
- wpa_printf(MSG_DEBUG, "Failed to install the IGTK in "
- "WNM mode");
- os_memset(&igd, 0, sizeof(igd));
+ const struct wpa_igtk_kde *igtk;
+
+ igtk = (const struct wpa_igtk_kde *) (buf + 2);
+ if (wpa_supplicant_install_igtk(sm, igtk) < 0)
return -1;
- }
- os_memset(&igd, 0, sizeof(igd));
#endif /* CONFIG_IEEE80211W */
} else {
wpa_printf(MSG_DEBUG, "Unknown element id");
diff --git a/src/rsn_supp/wpa_i.h b/src/rsn_supp/wpa_i.h
index f653ba6..afc9e37 100644
--- a/src/rsn_supp/wpa_i.h
+++ b/src/rsn_supp/wpa_i.h
@@ -31,6 +31,10 @@ struct wpa_sm {
u8 rx_replay_counter[WPA_REPLAY_COUNTER_LEN];
int rx_replay_counter_set;
u8 request_counter[WPA_REPLAY_COUNTER_LEN];
+ struct wpa_gtk gtk;
+#ifdef CONFIG_IEEE80211W
+ struct wpa_igtk igtk;
+#endif /* CONFIG_IEEE80211W */
struct eapol_sm *eapol; /* EAPOL state machine from upper level code */
--
2.7.4
From 8280294e74846ea342389a0cd17215050fa5afe8 Mon Sep 17 00:00:00 2001
From: Jouni Malinen <j@w1.fi>
Date: Sun, 1 Oct 2017 12:12:24 +0300
Subject: [PATCH 3/8] Extend protection of GTK/IGTK reinstallation of WNM-Sleep
Mode cases
This extends the protection to track last configured GTK/IGTK value
separately from EAPOL-Key frames and WNM-Sleep Mode frames to cover a
corner case where these two different mechanisms may get used when the
GTK/IGTK has changed and tracking a single value is not sufficient to
detect a possible key reconfiguration.
Signed-off-by: Jouni Malinen <j@w1.fi>
---
src/rsn_supp/wpa.c | 53 +++++++++++++++++++++++++++++++++++++---------------
src/rsn_supp/wpa_i.h | 2 ++
2 files changed, 40 insertions(+), 15 deletions(-)
diff --git a/src/rsn_supp/wpa.c b/src/rsn_supp/wpa.c
index 95bd7be..7a2c68d 100644
--- a/src/rsn_supp/wpa.c
+++ b/src/rsn_supp/wpa.c
@@ -709,14 +709,17 @@ struct wpa_gtk_data {
static int wpa_supplicant_install_gtk(struct wpa_sm *sm,
const struct wpa_gtk_data *gd,
- const u8 *key_rsc)
+ const u8 *key_rsc, int wnm_sleep)
{
const u8 *_gtk = gd->gtk;
u8 gtk_buf[32];
/* Detect possible key reinstallation */
- if (sm->gtk.gtk_len == (size_t) gd->gtk_len &&
- os_memcmp(sm->gtk.gtk, gd->gtk, sm->gtk.gtk_len) == 0) {
+ if ((sm->gtk.gtk_len == (size_t) gd->gtk_len &&
+ os_memcmp(sm->gtk.gtk, gd->gtk, sm->gtk.gtk_len) == 0) ||
+ (sm->gtk_wnm_sleep.gtk_len == (size_t) gd->gtk_len &&
+ os_memcmp(sm->gtk_wnm_sleep.gtk, gd->gtk,
+ sm->gtk_wnm_sleep.gtk_len) == 0)) {
wpa_dbg(sm->ctx->msg_ctx, MSG_DEBUG,
"WPA: Not reinstalling already in-use GTK to the driver (keyidx=%d tx=%d len=%d)",
gd->keyidx, gd->tx, gd->gtk_len);
@@ -757,8 +760,14 @@ static int wpa_supplicant_install_gtk(struct wpa_sm *sm,
}
os_memset(gtk_buf, 0, sizeof(gtk_buf));
- sm->gtk.gtk_len = gd->gtk_len;
- os_memcpy(sm->gtk.gtk, gd->gtk, sm->gtk.gtk_len);
+ if (wnm_sleep) {
+ sm->gtk_wnm_sleep.gtk_len = gd->gtk_len;
+ os_memcpy(sm->gtk_wnm_sleep.gtk, gd->gtk,
+ sm->gtk_wnm_sleep.gtk_len);
+ } else {
+ sm->gtk.gtk_len = gd->gtk_len;
+ os_memcpy(sm->gtk.gtk, gd->gtk, sm->gtk.gtk_len);
+ }
return 0;
}
@@ -852,7 +861,7 @@ static int wpa_supplicant_pairwise_gtk(struct wpa_sm *sm,
(wpa_supplicant_check_group_cipher(sm, sm->group_cipher,
gtk_len, gtk_len,
&gd.key_rsc_len, &gd.alg) ||
- wpa_supplicant_install_gtk(sm, &gd, key_rsc))) {
+ wpa_supplicant_install_gtk(sm, &gd, key_rsc, 0))) {
wpa_dbg(sm->ctx->msg_ctx, MSG_DEBUG,
"RSN: Failed to install GTK");
os_memset(&gd, 0, sizeof(gd));
@@ -868,14 +877,18 @@ static int wpa_supplicant_pairwise_gtk(struct wpa_sm *sm,
#ifdef CONFIG_IEEE80211W
static int wpa_supplicant_install_igtk(struct wpa_sm *sm,
- const struct wpa_igtk_kde *igtk)
+ const struct wpa_igtk_kde *igtk,
+ int wnm_sleep)
{
size_t len = wpa_cipher_key_len(sm->mgmt_group_cipher);
u16 keyidx = WPA_GET_LE16(igtk->keyid);
/* Detect possible key reinstallation */
- if (sm->igtk.igtk_len == len &&
- os_memcmp(sm->igtk.igtk, igtk->igtk, sm->igtk.igtk_len) == 0) {
+ if ((sm->igtk.igtk_len == len &&
+ os_memcmp(sm->igtk.igtk, igtk->igtk, sm->igtk.igtk_len) == 0) ||
+ (sm->igtk_wnm_sleep.igtk_len == len &&
+ os_memcmp(sm->igtk_wnm_sleep.igtk, igtk->igtk,
+ sm->igtk_wnm_sleep.igtk_len) == 0)) {
wpa_dbg(sm->ctx->msg_ctx, MSG_DEBUG,
"WPA: Not reinstalling already in-use IGTK to the driver (keyidx=%d)",
keyidx);
@@ -900,8 +913,14 @@ static int wpa_supplicant_install_igtk(struct wpa_sm *sm,
return -1;
}
- sm->igtk.igtk_len = len;
- os_memcpy(sm->igtk.igtk, igtk->igtk, sm->igtk.igtk_len);
+ if (wnm_sleep) {
+ sm->igtk_wnm_sleep.igtk_len = len;
+ os_memcpy(sm->igtk_wnm_sleep.igtk, igtk->igtk,
+ sm->igtk_wnm_sleep.igtk_len);
+ } else {
+ sm->igtk.igtk_len = len;
+ os_memcpy(sm->igtk.igtk, igtk->igtk, sm->igtk.igtk_len);
+ }
return 0;
}
@@ -924,7 +943,7 @@ static int ieee80211w_set_keys(struct wpa_sm *sm,
return -1;
igtk = (const struct wpa_igtk_kde *) ie->igtk;
- if (wpa_supplicant_install_igtk(sm, igtk) < 0)
+ if (wpa_supplicant_install_igtk(sm, igtk, 0) < 0)
return -1;
}
@@ -1574,7 +1593,7 @@ static void wpa_supplicant_process_1_of_2(struct wpa_sm *sm,
if (wpa_supplicant_rsc_relaxation(sm, key->key_rsc))
key_rsc = null_rsc;
- if (wpa_supplicant_install_gtk(sm, &gd, key_rsc) ||
+ if (wpa_supplicant_install_gtk(sm, &gd, key_rsc, 0) ||
wpa_supplicant_send_2_of_2(sm, key, ver, key_info) < 0)
goto failed;
os_memset(&gd, 0, sizeof(gd));
@@ -2386,8 +2405,10 @@ void wpa_sm_notify_assoc(struct wpa_sm *sm, const u8 *bssid)
sm->tptk_set = 0;
os_memset(&sm->tptk, 0, sizeof(sm->tptk));
os_memset(&sm->gtk, 0, sizeof(sm->gtk));
+ os_memset(&sm->gtk_wnm_sleep, 0, sizeof(sm->gtk_wnm_sleep));
#ifdef CONFIG_IEEE80211W
os_memset(&sm->igtk, 0, sizeof(sm->igtk));
+ os_memset(&sm->igtk_wnm_sleep, 0, sizeof(sm->igtk_wnm_sleep));
#endif /* CONFIG_IEEE80211W */
}
@@ -2920,8 +2941,10 @@ void wpa_sm_drop_sa(struct wpa_sm *sm)
os_memset(&sm->ptk, 0, sizeof(sm->ptk));
os_memset(&sm->tptk, 0, sizeof(sm->tptk));
os_memset(&sm->gtk, 0, sizeof(sm->gtk));
+ os_memset(&sm->gtk_wnm_sleep, 0, sizeof(sm->gtk_wnm_sleep));
#ifdef CONFIG_IEEE80211W
os_memset(&sm->igtk, 0, sizeof(sm->igtk));
+ os_memset(&sm->igtk_wnm_sleep, 0, sizeof(sm->igtk_wnm_sleep));
#endif /* CONFIG_IEEE80211W */
#ifdef CONFIG_IEEE80211R
os_memset(sm->xxkey, 0, sizeof(sm->xxkey));
@@ -2986,7 +3009,7 @@ int wpa_wnmsleep_install_key(struct wpa_sm *sm, u8 subelem_id, u8 *buf)
wpa_hexdump_key(MSG_DEBUG, "Install GTK (WNM SLEEP)",
gd.gtk, gd.gtk_len);
- if (wpa_supplicant_install_gtk(sm, &gd, key_rsc)) {
+ if (wpa_supplicant_install_gtk(sm, &gd, key_rsc, 1)) {
os_memset(&gd, 0, sizeof(gd));
wpa_printf(MSG_DEBUG, "Failed to install the GTK in "
"WNM mode");
@@ -2998,7 +3021,7 @@ int wpa_wnmsleep_install_key(struct wpa_sm *sm, u8 subelem_id, u8 *buf)
const struct wpa_igtk_kde *igtk;
igtk = (const struct wpa_igtk_kde *) (buf + 2);
- if (wpa_supplicant_install_igtk(sm, igtk) < 0)
+ if (wpa_supplicant_install_igtk(sm, igtk, 1) < 0)
return -1;
#endif /* CONFIG_IEEE80211W */
} else {
diff --git a/src/rsn_supp/wpa_i.h b/src/rsn_supp/wpa_i.h
index afc9e37..9a54631 100644
--- a/src/rsn_supp/wpa_i.h
+++ b/src/rsn_supp/wpa_i.h
@@ -32,8 +32,10 @@ struct wpa_sm {
int rx_replay_counter_set;
u8 request_counter[WPA_REPLAY_COUNTER_LEN];
struct wpa_gtk gtk;
+ struct wpa_gtk gtk_wnm_sleep;
#ifdef CONFIG_IEEE80211W
struct wpa_igtk igtk;
+ struct wpa_igtk igtk_wnm_sleep;
#endif /* CONFIG_IEEE80211W */
struct eapol_sm *eapol; /* EAPOL state machine from upper level code */
--
2.7.4

72
gnu/packages/patches/wpa-supplicant-fix-nonce-reuse.patch Normal file
View File

@ -0,0 +1,72 @@
Fix a nonce re-use bug:
https://w1.fi/security/2017-1/wpa-packet-number-reuse-with-replayed-messages.txt
Patch copied from upstream:
https://w1.fi/security/2017-1/rebased-v2.6-0005-Fix-PTK-rekeying-to-generate-a-new-ANonce.patch
From 12fac09b437a1dc8a0f253e265934a8aaf4d2f8b Mon Sep 17 00:00:00 2001
From: Jouni Malinen <j@w1.fi>
Date: Sun, 1 Oct 2017 12:32:57 +0300
Subject: [PATCH 5/8] Fix PTK rekeying to generate a new ANonce
The Authenticator state machine path for PTK rekeying ended up bypassing
the AUTHENTICATION2 state where a new ANonce is generated when going
directly to the PTKSTART state since there is no need to try to
determine the PMK again in such a case. This is far from ideal since the
new PTK would depend on a new nonce only from the supplicant.
Fix this by generating a new ANonce when moving to the PTKSTART state
for the purpose of starting new 4-way handshake to rekey PTK.
Signed-off-by: Jouni Malinen <j@w1.fi>
---
src/ap/wpa_auth.c | 24 +++++++++++++++++++++---
1 file changed, 21 insertions(+), 3 deletions(-)
diff --git a/src/ap/wpa_auth.c b/src/ap/wpa_auth.c
index 707971d..bf10cc1 100644
--- a/src/ap/wpa_auth.c
+++ b/src/ap/wpa_auth.c
@@ -1901,6 +1901,21 @@ SM_STATE(WPA_PTK, AUTHENTICATION2)
}
+static int wpa_auth_sm_ptk_update(struct wpa_state_machine *sm)
+{
+ if (random_get_bytes(sm->ANonce, WPA_NONCE_LEN)) {
+ wpa_printf(MSG_ERROR,
+ "WPA: Failed to get random data for ANonce");
+ sm->Disconnect = TRUE;
+ return -1;
+ }
+ wpa_hexdump(MSG_DEBUG, "WPA: Assign new ANonce", sm->ANonce,
+ WPA_NONCE_LEN);
+ sm->TimeoutCtr = 0;
+ return 0;
+}
+
+
SM_STATE(WPA_PTK, INITPMK)
{
u8 msk[2 * PMK_LEN];
@@ -2458,9 +2473,12 @@ SM_STEP(WPA_PTK)
SM_ENTER(WPA_PTK, AUTHENTICATION);
else if (sm->ReAuthenticationRequest)
SM_ENTER(WPA_PTK, AUTHENTICATION2);
- else if (sm->PTKRequest)
- SM_ENTER(WPA_PTK, PTKSTART);
- else switch (sm->wpa_ptk_state) {
+ else if (sm->PTKRequest) {
+ if (wpa_auth_sm_ptk_update(sm) < 0)
+ SM_ENTER(WPA_PTK, DISCONNECTED);
+ else
+ SM_ENTER(WPA_PTK, PTKSTART);
+ } else switch (sm->wpa_ptk_state) {
case WPA_PTK_INITIALIZE:
break;
case WPA_PTK_DISCONNECT:
--
2.7.4

86
gnu/packages/patches/wpa-supplicant-fix-zeroed-keys.patch Normal file
View File

@ -0,0 +1,86 @@
Don't install a zeroed encryption key:
https://w1.fi/security/2017-1/wpa-packet-number-reuse-with-replayed-messages.txt
Patch copied from upstream:
https://w1.fi/security/2017-1/rebased-v2.6-0004-Prevent-installation-of-an-all-zero-TK.patch
From 8f82bc94e8697a9d47fa8774dfdaaede1084912c Mon Sep 17 00:00:00 2001
From: Mathy Vanhoef <Mathy.Vanhoef@cs.kuleuven.be>
Date: Fri, 29 Sep 2017 04:22:51 +0200
Subject: [PATCH 4/8] Prevent installation of an all-zero TK
Properly track whether a PTK has already been installed to the driver
and the TK part cleared from memory. This prevents an attacker from
trying to trick the client into installing an all-zero TK.
This fixes the earlier fix in commit
ad00d64e7d8827b3cebd665a0ceb08adabf15e1e ('Fix TK configuration to the
driver in EAPOL-Key 3/4 retry case') which did not take into account
possibility of an extra message 1/4 showing up between retries of
message 3/4.
Signed-off-by: Mathy Vanhoef <Mathy.Vanhoef@cs.kuleuven.be>
---
src/common/wpa_common.h | 1 +
src/rsn_supp/wpa.c | 5 ++---
src/rsn_supp/wpa_i.h | 1 -
3 files changed, 3 insertions(+), 4 deletions(-)
diff --git a/src/common/wpa_common.h b/src/common/wpa_common.h
index d200285..1021ccb 100644
--- a/src/common/wpa_common.h
+++ b/src/common/wpa_common.h
@@ -215,6 +215,7 @@ struct wpa_ptk {
size_t kck_len;
size_t kek_len;
size_t tk_len;
+ int installed; /* 1 if key has already been installed to driver */
};
struct wpa_gtk {
diff --git a/src/rsn_supp/wpa.c b/src/rsn_supp/wpa.c
index 7a2c68d..0550a41 100644
--- a/src/rsn_supp/wpa.c
+++ b/src/rsn_supp/wpa.c
@@ -510,7 +510,6 @@ static void wpa_supplicant_process_1_of_4(struct wpa_sm *sm,
os_memset(buf, 0, sizeof(buf));
}
sm->tptk_set = 1;
- sm->tk_to_set = 1;
kde = sm->assoc_wpa_ie;
kde_len = sm->assoc_wpa_ie_len;
@@ -615,7 +614,7 @@ static int wpa_supplicant_install_ptk(struct wpa_sm *sm,
enum wpa_alg alg;
const u8 *key_rsc;
- if (!sm->tk_to_set) {
+ if (sm->ptk.installed) {
wpa_dbg(sm->ctx->msg_ctx, MSG_DEBUG,
"WPA: Do not re-install same PTK to the driver");
return 0;
@@ -659,7 +658,7 @@ static int wpa_supplicant_install_ptk(struct wpa_sm *sm,
/* TK is not needed anymore in supplicant */
os_memset(sm->ptk.tk, 0, WPA_TK_MAX_LEN);
- sm->tk_to_set = 0;
+ sm->ptk.installed = 1;
if (sm->wpa_ptk_rekey) {
eloop_cancel_timeout(wpa_sm_rekey_ptk, sm, NULL);
diff --git a/src/rsn_supp/wpa_i.h b/src/rsn_supp/wpa_i.h
index 9a54631..41f371f 100644
--- a/src/rsn_supp/wpa_i.h
+++ b/src/rsn_supp/wpa_i.h
@@ -24,7 +24,6 @@ struct wpa_sm {
struct wpa_ptk ptk, tptk;
int ptk_set, tptk_set;
unsigned int msg_3_of_4_ok:1;
- unsigned int tk_to_set:1;
u8 snonce[WPA_NONCE_LEN];
u8 anonce[WPA_NONCE_LEN]; /* ANonce from the last 1/4 msg */
int renew_snonce;
--
2.7.4

275
gnu/packages/patches/wpa-supplicant-krack-followups.patch Normal file
View File

@ -0,0 +1,275 @@
These three patches are follow-ups to the bug fixes for the 'KRACK' key
re-installation attacks on Wi-Fi's WPA2 security protocol. See upstream
security announcement for more information:
https://w1.fi/security/2017-1/wpa-packet-number-reuse-with-replayed-messages.txt
These three patches copied from upstream:
https://w1.fi/security/2017-1/rebased-v2.6-0006-TDLS-Reject-TPK-TK-reconfiguration.patch
https://w1.fi/security/2017-1/rebased-v2.6-0007-WNM-Ignore-WNM-Sleep-Mode-Response-without-pending-r.patch
https://w1.fi/security/2017-1/rebased-v2.6-0008-FT-Do-not-allow-multiple-Reassociation-Response-fram.patch
From 6c4bed4f47d1960ec04981a9d50e5076aea5223d Mon Sep 17 00:00:00 2001
From: Jouni Malinen <j@w1.fi>
Date: Fri, 22 Sep 2017 11:03:15 +0300
Subject: [PATCH 6/8] TDLS: Reject TPK-TK reconfiguration
Do not try to reconfigure the same TPK-TK to the driver after it has
been successfully configured. This is an explicit check to avoid issues
related to resetting the TX/RX packet number. There was already a check
for this for TPK M2 (retries of that message are ignored completely), so
that behavior does not get modified.
For TPK M3, the TPK-TK could have been reconfigured, but that was
followed by immediate teardown of the link due to an issue in updating
the STA entry. Furthermore, for TDLS with any real security (i.e.,
ignoring open/WEP), the TPK message exchange is protected on the AP path
and simple replay attacks are not feasible.
As an additional corner case, make sure the local nonce gets updated if
the peer uses a very unlikely "random nonce" of all zeros.
Signed-off-by: Jouni Malinen <j@w1.fi>
---
src/rsn_supp/tdls.c | 38 ++++++++++++++++++++++++++++++++++++--
1 file changed, 36 insertions(+), 2 deletions(-)
diff --git a/src/rsn_supp/tdls.c b/src/rsn_supp/tdls.c
index e424168..9eb9738 100644
--- a/src/rsn_supp/tdls.c
+++ b/src/rsn_supp/tdls.c
@@ -112,6 +112,7 @@ struct wpa_tdls_peer {
u8 tk[16]; /* TPK-TK; assuming only CCMP will be used */
} tpk;
int tpk_set;
+ int tk_set; /* TPK-TK configured to the driver */
int tpk_success;
int tpk_in_progress;
@@ -192,6 +193,20 @@ static int wpa_tdls_set_key(struct wpa_sm *sm, struct wpa_tdls_peer *peer)
u8 rsc[6];
enum wpa_alg alg;
+ if (peer->tk_set) {
+ /*
+ * This same TPK-TK has already been configured to the driver
+ * and this new configuration attempt (likely due to an
+ * unexpected retransmitted frame) would result in clearing
+ * the TX/RX sequence number which can break security, so must
+ * not allow that to happen.
+ */
+ wpa_printf(MSG_INFO, "TDLS: TPK-TK for the peer " MACSTR
+ " has already been configured to the driver - do not reconfigure",
+ MAC2STR(peer->addr));
+ return -1;
+ }
+
os_memset(rsc, 0, 6);
switch (peer->cipher) {
@@ -209,12 +224,15 @@ static int wpa_tdls_set_key(struct wpa_sm *sm, struct wpa_tdls_peer *peer)
return -1;
}
+ wpa_printf(MSG_DEBUG, "TDLS: Configure pairwise key for peer " MACSTR,
+ MAC2STR(peer->addr));
if (wpa_sm_set_key(sm, alg, peer->addr, -1, 1,
rsc, sizeof(rsc), peer->tpk.tk, key_len) < 0) {
wpa_printf(MSG_WARNING, "TDLS: Failed to set TPK to the "
"driver");
return -1;
}
+ peer->tk_set = 1;
return 0;
}
@@ -696,7 +714,7 @@ static void wpa_tdls_peer_clear(struct wpa_sm *sm, struct wpa_tdls_peer *peer)
peer->cipher = 0;
peer->qos_info = 0;
peer->wmm_capable = 0;
- peer->tpk_set = peer->tpk_success = 0;
+ peer->tk_set = peer->tpk_set = peer->tpk_success = 0;
peer->chan_switch_enabled = 0;
os_memset(&peer->tpk, 0, sizeof(peer->tpk));
os_memset(peer->inonce, 0, WPA_NONCE_LEN);
@@ -1159,6 +1177,7 @@ skip_rsnie:
wpa_tdls_peer_free(sm, peer);
return -1;
}
+ peer->tk_set = 0; /* A new nonce results in a new TK */
wpa_hexdump(MSG_DEBUG, "TDLS: Initiator Nonce for TPK handshake",
peer->inonce, WPA_NONCE_LEN);
os_memcpy(ftie->Snonce, peer->inonce, WPA_NONCE_LEN);
@@ -1751,6 +1770,19 @@ static int wpa_tdls_addset_peer(struct wpa_sm *sm, struct wpa_tdls_peer *peer,
}
+static int tdls_nonce_set(const u8 *nonce)
+{
+ int i;
+
+ for (i = 0; i < WPA_NONCE_LEN; i++) {
+ if (nonce[i])
+ return 1;
+ }
+
+ return 0;
+}
+
+
static int wpa_tdls_process_tpk_m1(struct wpa_sm *sm, const u8 *src_addr,
const u8 *buf, size_t len)
{
@@ -2004,7 +2036,8 @@ skip_rsn:
peer->rsnie_i_len = kde.rsn_ie_len;
peer->cipher = cipher;
- if (os_memcmp(peer->inonce, ftie->Snonce, WPA_NONCE_LEN) != 0) {
+ if (os_memcmp(peer->inonce, ftie->Snonce, WPA_NONCE_LEN) != 0 ||
+ !tdls_nonce_set(peer->inonce)) {
/*
* There is no point in updating the RNonce for every obtained
* TPK M1 frame (e.g., retransmission due to timeout) with the
@@ -2020,6 +2053,7 @@ skip_rsn:
"TDLS: Failed to get random data for responder nonce");
goto error;
}
+ peer->tk_set = 0; /* A new nonce results in a new TK */
}
#if 0
--
2.7.4
From 53c5eb58e95004f86e65ee9fbfccbc291b139057 Mon Sep 17 00:00:00 2001
From: Jouni Malinen <j@w1.fi>
Date: Fri, 22 Sep 2017 11:25:02 +0300
Subject: [PATCH 7/8] WNM: Ignore WNM-Sleep Mode Response without pending
request
Commit 03ed0a52393710be6bdae657d1b36efa146520e5 ('WNM: Ignore WNM-Sleep
Mode Response if WNM-Sleep Mode has not been used') started ignoring the
response when no WNM-Sleep Mode Request had been used during the
association. This can be made tighter by clearing the used flag when
successfully processing a response. This adds an additional layer of
protection against unexpected retransmissions of the response frame.
Signed-off-by: Jouni Malinen <j@w1.fi>
---
wpa_supplicant/wnm_sta.c | 4 +++-
1 file changed, 3 insertions(+), 1 deletion(-)
diff --git a/wpa_supplicant/wnm_sta.c b/wpa_supplicant/wnm_sta.c
index 1b3409c..67a07ff 100644
--- a/wpa_supplicant/wnm_sta.c
+++ b/wpa_supplicant/wnm_sta.c
@@ -260,7 +260,7 @@ static void ieee802_11_rx_wnmsleep_resp(struct wpa_supplicant *wpa_s,
if (!wpa_s->wnmsleep_used) {
wpa_printf(MSG_DEBUG,
- "WNM: Ignore WNM-Sleep Mode Response frame since WNM-Sleep Mode has not been used in this association");
+ "WNM: Ignore WNM-Sleep Mode Response frame since WNM-Sleep Mode operation has not been requested");
return;
}
@@ -299,6 +299,8 @@ static void ieee802_11_rx_wnmsleep_resp(struct wpa_supplicant *wpa_s,
return;
}
+ wpa_s->wnmsleep_used = 0;
+
if (wnmsleep_ie->status == WNM_STATUS_SLEEP_ACCEPT ||
wnmsleep_ie->status == WNM_STATUS_SLEEP_EXIT_ACCEPT_GTK_UPDATE) {
wpa_printf(MSG_DEBUG, "Successfully recv WNM-Sleep Response "
--
2.7.4
https://w1.fi/security/2017-1/wpa-packet-number-reuse-with-replayed-messages.txt
Patch copied from upstream:
https://w1.fi/security/2017-1/rebased-v2.6-0008-FT-Do-not-allow-multiple-Reassociation-Response-fram.patch
From b372ab0b7daea719749194dc554b26e6367603f2 Mon Sep 17 00:00:00 2001
From: Jouni Malinen <j@w1.fi>
Date: Fri, 22 Sep 2017 12:06:37 +0300
Subject: [PATCH 8/8] FT: Do not allow multiple Reassociation Response frames
The driver is expected to not report a second association event without
the station having explicitly request a new association. As such, this
case should not be reachable. However, since reconfiguring the same
pairwise or group keys to the driver could result in nonce reuse issues,
be extra careful here and do an additional state check to avoid this
even if the local driver ends up somehow accepting an unexpected
Reassociation Response frame.
Signed-off-by: Jouni Malinen <j@w1.fi>
---
src/rsn_supp/wpa.c | 3 +++
src/rsn_supp/wpa_ft.c | 8 ++++++++
src/rsn_supp/wpa_i.h | 1 +
3 files changed, 12 insertions(+)
diff --git a/src/rsn_supp/wpa.c b/src/rsn_supp/wpa.c
index 0550a41..2a53c6f 100644
--- a/src/rsn_supp/wpa.c
+++ b/src/rsn_supp/wpa.c
@@ -2440,6 +2440,9 @@ void wpa_sm_notify_disassoc(struct wpa_sm *sm)
#ifdef CONFIG_TDLS
wpa_tdls_disassoc(sm);
#endif /* CONFIG_TDLS */
+#ifdef CONFIG_IEEE80211R
+ sm->ft_reassoc_completed = 0;
+#endif /* CONFIG_IEEE80211R */
/* Keys are not needed in the WPA state machine anymore */
wpa_sm_drop_sa(sm);
diff --git a/src/rsn_supp/wpa_ft.c b/src/rsn_supp/wpa_ft.c
index 205793e..d45bb45 100644
--- a/src/rsn_supp/wpa_ft.c
+++ b/src/rsn_supp/wpa_ft.c
@@ -153,6 +153,7 @@ static u8 * wpa_ft_gen_req_ies(struct wpa_sm *sm, size_t *len,
u16 capab;
sm->ft_completed = 0;
+ sm->ft_reassoc_completed = 0;
buf_len = 2 + sizeof(struct rsn_mdie) + 2 + sizeof(struct rsn_ftie) +
2 + sm->r0kh_id_len + ric_ies_len + 100;
@@ -681,6 +682,11 @@ int wpa_ft_validate_reassoc_resp(struct wpa_sm *sm, const u8 *ies,
return -1;
}
+ if (sm->ft_reassoc_completed) {
+ wpa_printf(MSG_DEBUG, "FT: Reassociation has already been completed for this FT protocol instance - ignore unexpected retransmission");
+ return 0;
+ }
+
if (wpa_ft_parse_ies(ies, ies_len, &parse) < 0) {
wpa_printf(MSG_DEBUG, "FT: Failed to parse IEs");
return -1;
@@ -781,6 +787,8 @@ int wpa_ft_validate_reassoc_resp(struct wpa_sm *sm, const u8 *ies,
return -1;
}
+ sm->ft_reassoc_completed = 1;
+
if (wpa_ft_process_gtk_subelem(sm, parse.gtk, parse.gtk_len) < 0)
return -1;
diff --git a/src/rsn_supp/wpa_i.h b/src/rsn_supp/wpa_i.h
index 41f371f..56f88dc 100644
--- a/src/rsn_supp/wpa_i.h
+++ b/src/rsn_supp/wpa_i.h
@@ -128,6 +128,7 @@ struct wpa_sm {
size_t r0kh_id_len;
u8 r1kh_id[FT_R1KH_ID_LEN];
int ft_completed;
+ int ft_reassoc_completed;
int over_the_ds_in_progress;
u8 target_ap[ETH_ALEN]; /* over-the-DS target AP */
int set_ptk_after_assoc;
--
2.7.4

2
gnu/packages/patchutils.scm
View File

@ -171,7 +171,7 @@ refreshed, and more.")
(inputs
`(("perl" ,perl)
("xmlto" ,xmlto)))
(home-page "http://www.colordiff.org")
(home-page "https://www.colordiff.org")
(synopsis "Display diff output with colors")
(description
"Colordiff is Perl script wrapper on top of diff command which provides

38
gnu/packages/pdf.scm
View File

@ -413,6 +413,41 @@ using libspectre.")
using the DjVuLibre library.")
(license license:zlib)))
(define-public zathura-pdf-mupdf
(package
(name "zathura-pdf-mupdf")
(version "0.3.1")
(source (origin
(method url-fetch)
(uri
(string-append "https://pwmt.org/projects/zathura-pdf-mupdf"
"/download/zathura-pdf-mupdf-" version ".tar.gz"))
(sha256
(base32
"06zqn8z6a0hfsx3s1kzqvqzb73afgcl6z5r062sxv7kv570fvffr"))))
(native-inputs `(("pkg-config" ,pkg-config)))
(propagated-inputs `(("girara" ,girara)))
(inputs
`(("gtk+" ,gtk+)
("jbig2dec" ,jbig2dec)
("libjpeg" ,libjpeg)
("mupdf" ,mupdf)
("openjpeg" ,openjpeg)
("openssl" ,openssl)
("zathura" ,zathura)))
(build-system gnu-build-system)
(arguments
`(#:make-flags (list (string-append "PREFIX=" %output)
(string-append "PLUGINDIR=" %output "/lib/zathura")
"CC=gcc")
#:tests? #f ;No tests.
#:phases (modify-phases %standard-phases (delete 'configure))))
(home-page "https://pwmt.org/projects/zathura-pdf-mupdf/")
(synopsis "PDF support for zathura (mupdf backend)")
(description "The zathura-pdf-mupdf plugin adds PDF support to zathura
by using the @code{mupdf} rendering library.")
(license license:zlib)))
(define-public zathura-pdf-poppler
(package
(name "zathura-pdf-poppler")
@ -540,7 +575,8 @@ extracting content or merging files.")
(sha256
(base32
"02phamcchgsmvjnb3ir7r5sssvx9fcrscn297z73b82n1jl79510"))
(patches (search-patches "mupdf-build-with-openjpeg-2.1.patch"))
(patches (search-patches "mupdf-build-with-openjpeg-2.1.patch"
"mupdf-CVE-2017-15587.patch"))
(modules '((guix build utils)))
(snippet
;; Delete all the bundled libraries except for mujs, which is

67
gnu/packages/perl.scm
View File

@ -17,6 +17,7 @@
;;; Copyright © 2017 Adriano Peluso <catonano@gmail.com>
;;; Copyright © 2017 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2017 Leo Famulari <leo@famulari.name>
;;; Copyright © 2017 Christopher Allan Webber <cwebber@dustycloud.org>
;;;
;;; This file is part of GNU Guix.
;;;
@ -40,6 +41,7 @@
#:use-module (guix download)
#:use-module (guix build-system gnu)
#:use-module (guix build-system perl)
#:use-module (gnu packages base)
#:use-module (gnu packages perl-web)
#:use-module (gnu packages pkg-config))
@ -9187,3 +9189,68 @@ interface to File::Find::Object.")
(description "Test::TrailingSpace tests for trailing spaces
in Perl source files.")
(license x11)))
(define-public perl-libtime-parsedate
(package
(name "perl-libtime-parsedate")
(version "2015.103")
(source
(origin
(method url-fetch)
(uri (string-append
"mirror://cpan/authors/id/M/MU/MUIR/modules/Time-ParseDate-"
version ".tar.gz"))
(sha256
(base32 "1lgfr87j4qwqnln0hyyzgik5ixqslzdaksn9m8y824gqbcihc6ic"))))
(build-system perl-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
;; This is needed for tests
(add-after 'unpack 'set-TZDIR
(lambda* (#:key inputs #:allow-other-keys)
(setenv "TZDIR" (string-append (assoc-ref inputs "tzdata")
"/share/zoneinfo"))
#t)))))
(native-inputs
`(("perl-module-build" ,perl-module-build)
("tzdata" ,tzdata-2017a)))
(home-page "https://metacpan.org/release/Time-ParseDate")
(synopsis "Collection of Perl modules for time/date manipulation")
(description "Provides several perl modules for date/time manipulation:
@code{Time::CTime.pm}, @code{Time::JulianDay.pm}, @code{Time::ParseDate.pm},
@code{Time::Timezone.pm}, and @code{Time::DaysInMonth.pm}.")
;; License text:
;; "License hereby granted for anyone to use, modify or redistribute this
;; module at their own risk. Please feed useful changes back to
;; cpan@dave.sharnoff.org."
(license (non-copyleft "http://metadata.ftp-master.debian.org/\
changelogs/main/libt/libtime-parsedate-perl/\
libtime-parsedate-perl_2015.103-2_copyright"))))
(define-public perl-libtime-period
(package
(name "perl-libtime-period")
(version "1.20")
(source
(origin
(method url-fetch)
(uri (string-append
"http://http.debian.net/debian/pool/main/libt/"
"libtime-period-perl/libtime-period-perl_"
version ".orig.tar.gz"))
(sha256
(base32 "0c0yd999h0ikj88c9j95wa087m87i0qh7vja3715y2kd7vixkci2"))))
(build-system perl-build-system)
(native-inputs
`(("perl-module-build" ,perl-module-build)))
;; Unless some other homepage is out there...
(home-page "https://packages.debian.org/stretch/libtime-period-perl")
(synopsis "Perl library for testing if a time() is in a specific period")
(description "This Perl library provides a function which tells whether a
specific time falls within a specified time period. Its syntax for specifying
time periods allows you to test for conditions like \"Monday to Friday, 9am
till 5pm\" and \"on the second Tuesday of the month\" and \"between 4pm and
4:15pm\" and \"in the first half of each minute\" and \"in January of
1998\".")
(license perl-license)))

55
gnu/packages/protobuf.scm
View File

@ -2,6 +2,8 @@
;;; Copyright © 2014 Ludovic Courtès <ludo@gnu.org>
;;; Copyright © 2016 Daniel Pimentel <d4n1@d4n1.org>
;;; Copyright © 2016 Leo Famulari <leo@famulari.name>
;;; Copyright © 2017 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2017 Tobias Geerinckx-Rice <me@tobias.gr>
;;;
;;; This file is part of GNU Guix.
;;;
@ -24,23 +26,24 @@
#:use-module (guix build-system gnu)
#:use-module (guix build-system python)
#:use-module ((guix licenses)
#:select (bsd-3))
#:select (bsd-2 bsd-3))
#:use-module (gnu packages compression)
#:use-module (gnu packages gcc)
#:use-module (gnu packages pkg-config)
#:use-module (gnu packages python))
(define-public protobuf
(package
(name "protobuf")
(version "2.6.1")
(version "3.4.1")
(source (origin
(method url-fetch)
(uri (string-append "https://github.com/google/protobuf/releases/"
"download/v" version "/protobuf-"
version ".tar.bz2"))
"download/v" version "/protobuf-cpp-"
version ".tar.gz"))
(sha256
(base32
"040rcs9fpv4bslhiy43v7dcrzakz4vwwpyqg4jp8bn24sl95ci7f"))))
"0y6cr4l7bwa6zvjv5flzr4cx28shk5h8dz99xw90v8qih954pcrb"))))
(build-system gnu-build-system)
(inputs `(("zlib" ,zlib)))
(home-page "https://github.com/google/protobuf")
@ -51,17 +54,55 @@ yet extensible format. Google uses Protocol Buffers for almost all of its
internal RPC protocols and file formats.")
(license bsd-3)))
;; XXX Remove this old version when no other packages depend on it.
(define-public protobuf-2
(package (inherit protobuf)
(version "2.6.1")
(source (origin
(method url-fetch)
(uri (string-append "https://github.com/google/protobuf/releases/"
"download/v" version "/protobuf-"
version ".tar.bz2"))
(sha256
(base32
"040rcs9fpv4bslhiy43v7dcrzakz4vwwpyqg4jp8bn24sl95ci7f"))))))
(define-public protobuf-c
(package
(name "protobuf-c")
(version "1.3.0")
(source (origin
(method url-fetch)
(uri (string-append "https://github.com/protobuf-c/protobuf-c/"
"releases/download/v" version
"/protobuf-c-" version ".tar.gz"))
(sha256
(base32
"18aj4xfv26zjmj44zbb01wk90jl7y4aj5xvbzz4gg748kdxavjax"))))
(build-system gnu-build-system)
(inputs `(("protobuf" ,protobuf)))
(native-inputs `(("pkg-config" ,pkg-config)))
(home-page "https://github.com/protobuf-c/protobuf-c")
(synopsis "Protocol Buffers implementation in C")
(description
"This is protobuf-c, a C implementation of the Google Protocol Buffers
data serialization format. It includes @code{libprotobuf-c}, a pure C library
that implements protobuf encoding and decoding, and @code{protoc-c}, a code
generator that converts Protocol Buffer @code{.proto} files to C descriptor
code.")
(license bsd-2)))
(define-public python-protobuf
(package
(name "python-protobuf")
(version "3.0.0")
(version "3.4.0")
(source
(origin
(method url-fetch)
(uri (pypi-uri "protobuf" version))
(sha256
(base32
"1xbgbfg4g43bihkyw1a2giqa2gxmqc5wkh0fzqcb90qi1z1hpi7c"))))
"0x33xz85cy5ilg1n2rn92l4qwlcw25vzysx2ldv7k625yjg600pg"))))
(build-system python-build-system)
(propagated-inputs
`(("python-six" ,python-six)))

58
gnu/packages/python.scm
View File

@ -7550,6 +7550,48 @@ and MAC network addresses.")
(define-public python2-netaddr
(package-with-python2 python-netaddr))
(define-public python2-neo4j-driver
(package
(name "python2-neo4j-driver")
;; NOTE: When upgrading to 1.5.0, please add a python3 variant.
(version "1.4.0")
(source (origin
(method url-fetch)
(uri (pypi-uri "neo4j-driver" version))
(sha256
(base32
"011r1vh182p8mm83d8dz9rfnc3l7rf7fd00cyrbyfzi71jmc4g98"))))
(build-system python-build-system)
(arguments
`(#:python ,python-2))
(home-page "https://neo4j.com/developer/python/")
(synopsis "Neo4j driver code written in Python")
(description "This package provides the Neo4j Python driver that connects
to the database using Neo4j's binary protocol. It aims to be minimal, while
being idiomatic to Python.")
(license license:asl2.0)))
(define-public python2-py2neo
(package
(name "python2-py2neo")
(version "3.1.2")
(source (origin
(method url-fetch)
(uri (pypi-uri "py2neo" version))
(sha256
(base32
"1f1q95vqcvlc3nsc33p841swnjdcjazddlq2dzi3qfnjqjrajxw1"))))
(build-system python-build-system)
(arguments
`(#:python ,python-2))
(home-page "http://py2neo.org")
(synopsis "Library and toolkit for working with Neo4j in Python")
(description "This package provides a client library and toolkit for
working with Neo4j from within Python applications and from the command
line. The core library has no external dependencies and has been carefully
designed to be easy and intuitive to use.")
(license license:asl2.0)))
(define-public python-wrapt
(package
(name "python-wrapt")
@ -8578,7 +8620,7 @@ simulation, statistical modeling, machine learning and much more.")
(define-public python-chardet
(package
(name "python-chardet")
(version "2.3.0")
(version "3.0.4")
(source
(origin
(method url-fetch)
@ -8588,7 +8630,11 @@ simulation, statistical modeling, machine learning and much more.")
".tar.gz"))
(sha256
(base32
"1ak87ikcw34fivcgiz2xvi938dmclh078az65l9x3rmgljrkhgp5"))))
"1bpalpia6r5x1kknbk11p1fzph56fmmnp405ds8icksd3knr5aw4"))))
(native-inputs
`(("python-hypothesis" ,python-hypothesis)
("python-pytest" ,python-pytest)
("python-pytest-runner" ,python-pytest-runner)))
(build-system python-build-system)
(home-page "https://github.com/chardet/chardet")
(synopsis "Universal encoding detector for Python 2 and 3")
@ -9672,13 +9718,13 @@ with a new public API, and RPython support.")
(define-public python-hy
(package
(name "python-hy")
(version "0.11.1")
(version "0.13.0")
(source (origin
(method url-fetch)
(uri (pypi-uri "hy" version))
(sha256
(base32
"1msqv747iz12r73mz4qvsmlwkddwjvrahlrk7ysrcz07h7dsscxs"))))
"19sfymaksx9jhksfnb15ahid46mzrhdfzz6yy2craz2qnzvpmky8"))))
(build-system python-build-system)
(arguments
'(#:phases
@ -10109,9 +10155,9 @@ seamlessly into your existing Python unit testing work flow.")
(let ((hypothesis (package-with-python2
(strip-python2-variant python-hypothesis))))
(package (inherit hypothesis)
(native-inputs
(propagated-inputs
`(("python2-enum34" ,python2-enum34)
,@(package-native-inputs hypothesis))))))
,@(package-propagated-inputs hypothesis))))))
(define-public python-pytest-subtesthack
(package

14
gnu/packages/qt.scm
View File

@ -617,7 +617,11 @@ HostPrefix=~a
HostData=lib/qt5
HostBinaries=bin
HostLibraries=lib
" out out)))
[EffectiveSourcePaths]
HostPrefix=~a
HostData=lib/qt5
" out out qtbase)))
#t)))
(replace 'configure
(lambda* (#:key inputs outputs #:allow-other-keys)
@ -1443,7 +1447,7 @@ message.")))
(define-public python-sip
(package
(name "python-sip")
(version "4.19.2")
(version "4.19.3")
(source
(origin
(method url-fetch)
@ -1452,7 +1456,7 @@ message.")))
"sip-" version "/sip-" version ".tar.gz"))
(sha256
(base32
"0cq5r21fmjyw5v7a6l4sfbaj3zgm7k5b2cryj6bnjki54nnllas3"))))
"0x2bghbprwl3az1ni3p87i0bq8r99694la93kg65vi0cz12gh3bl"))))
(build-system gnu-build-system)
(native-inputs
`(("python" ,python-wrapper)))
@ -1506,7 +1510,7 @@ module provides support functions to the automatically generated code.")
(define-public python-pyqt
(package
(name "python-pyqt")
(version "5.8.2")
(version "5.9")
(source
(origin
(method url-fetch)
@ -1516,7 +1520,7 @@ module provides support functions to the automatically generated code.")
version ".tar.gz"))
(sha256
(base32
"1s1nalcspam9dc7f63jkqn1i2sv9lrqn57p2zsc61g8bncahbmzb"))
"15hh4z5vd45dcswjla58q6rrfr6ic7jfz2n7c8lwfb10rycpj3mb"))
(patches (search-patches "pyqt-configure.patch"))))
(build-system gnu-build-system)
(native-inputs

2
gnu/packages/serialization.scm
View File

@ -248,7 +248,7 @@ that implements both the msgpack and msgpack-rpc specifications.")
"yaml-cpp-" version ".tar.gz"))
(sha256
(base32
"1vk6pjh0f5k6jwk2sszb9z5169whmiha9ainbdpa1arxlkq7v3b6"))))
"1ck7jk0wjfigrf4cgcjqsir4yp1s6vamhhxhpsgfvs46pgm5pk6y"))))
(build-system cmake-build-system)
(arguments
'(#:configure-flags '("-DBUILD_SHARED_LIBS=ON")))

4
gnu/packages/spice.scm
View File

@ -162,6 +162,7 @@ which allows users to view a desktop computing environment.")
("spice-protocol" ,spice-protocol)))
(inputs
`(("glib-networking" ,glib-networking)
("gobject-introspection" ,gobject-introspection)
("gtk+" ,gtk+)
("libepoxy" ,libepoxy)
("libjpeg" ,libjpeg)
@ -182,7 +183,8 @@ which allows users to view a desktop computing environment.")
`(#:configure-flags
'("--enable-gstaudio"
"--enable-gstvideo"
"--enable-pulse")
"--enable-pulse"
"--enable-introspection")
#:phases
(modify-phases %standard-phases
(add-after

28
gnu/packages/statistics.scm
View File

@ -1578,13 +1578,13 @@ and printing capabilities than traditional data frames.")
(define-public r-dplyr
(package
(name "r-dplyr")
(version "0.7.3")
(version "0.7.4")
(source (origin
(method url-fetch)
(uri (cran-uri "dplyr" version))
(sha256
(base32
"0wz5vrcsxzmxpxvs1raz9kyfc7mq3591nadq4rb4hx4sc97ysrxf"))))
"1hm8ml7yaraag1ak6kvz2mxx6if568c759ix8a1n9d7va03wj7vv"))))
(build-system r-build-system)
(propagated-inputs
`(("r-assertthat" ,r-assertthat)
@ -1730,13 +1730,13 @@ and density estimation.")
(define-public r-chron
(package
(name "r-chron")
(version "2.3-50")
(version "2.3-51")
(source (origin
(method url-fetch)
(uri (cran-uri "chron" version))
(sha256
(base32
"1w3sl60gsirniqslb3pa75caiqbzbvc44phpd4czvwkb62xx1vx9"))))
"05aznigw9nwv3hbwjnjbvqhfjqkwsw2csgrjx8500gzr2fvla5w8"))))
(build-system r-build-system)
(home-page "http://cran.r-project.org/web/packages/chron")
(synopsis "Chronological R objects which can handle dates and times")
@ -1748,13 +1748,13 @@ times.")
(define-public r-data-table
(package
(name "r-data-table")
(version "1.10.4")
(version "1.10.4-2")
(source (origin
(method url-fetch)
(uri (cran-uri "data.table" version))
(sha256
(base32
"0ykbjr1x50ajxbri385vi3mnxj7zg1dcgh9y0snp341qmmmdypw6"))))
"159dgcjlrpq17iy7y3a6v2wnlrszjlz031cj4aqcl9bbfkh07mr7"))))
(build-system r-build-system)
(home-page "https://github.com/Rdatatable/data.table/wiki")
(synopsis "Enhanced version of data.frame R object")
@ -2480,15 +2480,17 @@ well as additional utilities such as panel and axis annotation functions.")
(define-public r-rcpparmadillo
(package
(name "r-rcpparmadillo")
(version "0.7.960.1.2")
(version "0.8.100.1.0")
(source (origin
(method url-fetch)
(uri (cran-uri "RcppArmadillo" version))
(sha256
(base32
"0kg8vbamaz3413h283f23hzgqkmfpf6fs0vbklmpj0l3ricvp9cc"))))
"19sghlkslz6llcrjk5pd8c6dsb338jsi4dnwrbbrjkfq6jdr5jlp"))))
(properties `((upstream-name . "RcppArmadillo")))
(build-system r-build-system)
(native-inputs
`(("r-knitr" ,r-knitr))) ; needed for vignettes
(propagated-inputs
`(("r-rcpp" ,r-rcpp)))
(home-page "https://github.com/RcppCore/RcppArmadillo")
@ -2716,7 +2718,7 @@ engine (version 3.8.8.2) is included.")
(version "1.95-0.1.2")
(source (origin
(method url-fetch)
(uri (string-append "http://www.bioconductor.org/packages/"
(uri (string-append "https://www.bioconductor.org/packages/"
"release/extra/src/"
"contrib/RCurl_" version ".tar.gz"))
(sha256
@ -3586,14 +3588,14 @@ the 'lite' version of the more complete @code{viridis} package.")
(define-public r-tidyselect
(package
(name "r-tidyselect")
(version "0.2.0")
(version "0.2.2")
(source
(origin
(method url-fetch)
(uri (cran-uri "tidyselect" version))
(sha256
(base32
"1h10qc5bxk5v0zhmip3gwnzy50fs2gbdvcg2163is0k9a8rifq9r"))))
"1lndr0ajd3fhycmrw2fdaiyf32in5pgl5ig901q221g24n87vmnd"))))
(build-system r-build-system)
(propagated-inputs
`(("r-glue" ,r-glue)
@ -3612,14 +3614,14 @@ selection.")
(define-public r-tidyr
(package
(name "r-tidyr")
(version "0.7.1")
(version "0.7.2")
(source
(origin
(method url-fetch)
(uri (cran-uri "tidyr" version))
(sha256
(base32
"18fii18f967xaw6swn0w744sncx37rfq6gd8d9dccrpyf8647hmr"))))
"1700fry2b3d3ksj7x2f09xl6agjrdnx1rqsc1r8gvzsp5cpflb06"))))
(build-system r-build-system)
(propagated-inputs
`(("r-dplyr" ,r-dplyr)

41
gnu/packages/textutils.scm
View File

@ -38,6 +38,7 @@
#:use-module (guix build-system gnu)
#:use-module (guix build-system cmake)
#:use-module (guix build-system trivial)
#:use-module (guix build-system python)
#:use-module (gnu packages)
#:use-module (gnu packages autotools)
#:use-module (gnu packages compression)
@ -53,14 +54,14 @@
(define-public dos2unix
(package
(name "dos2unix")
(version "7.3.4")
(version "7.4.0")
(source
(origin
(method url-fetch)
(uri (string-append "https://waterlan.home.xs4all.nl/" name "/"
name "-" version ".tar.gz"))
(sha256
(base32 "1i9hbxn0br7xa18z4bjpkdv7mrzmbfxhm44mzpd07yd2qnxsgkcc"))))
(base32 "12h4c61g376bhq03y5g2xszkrkrj5hwd928rly3xsp6rvfmnbixs"))))
(build-system gnu-build-system)
(arguments
'(#:make-flags (list "CC=gcc"
@ -623,3 +624,39 @@ completely with the standard @code{javax.swing.text} package. It is fast and
efficient, and can be used in any application that needs to edit or view
source code.")
(license license:bsd-3)))
;; We use the sources from git instead of the tarball from pypi, because the
;; latter does not include the Cython source file from which bycython.cpp is
;; generated.
(define-public python-editdistance
(let ((commit "3ea84a7dd3258c76aa3be851ef3d50e59c886846")
(revision "1"))
(package
(name "python-editdistance")
(version (string-append "0.3.1-" revision "." (string-take commit 7)))
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/aflc/editdistance.git")
(commit commit)))
(sha256
(base32
"1l43svsv12crvzphrgi6x435z6xg8m086c64armp8wzb4l8ccm7g"))))
(build-system python-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
(add-after 'unpack 'build-cython-code
(lambda _
(with-directory-excursion "editdistance"
(delete-file "bycython.cpp")
(zero? (system* "cython" "--cplus" "bycython.pyx"))))))))
(native-inputs
`(("python-cython" ,python-cython)))
(home-page "https://www.github.com/aflc/editdistance")
(synopsis "Fast implementation of the edit distance (Levenshtein distance)")
(description
"This library simply implements Levenshtein distance algorithm with C++
and Cython.")
(license license:expat))))

32
gnu/packages/version-control.scm
View File

@ -363,7 +363,7 @@ everything from small to very large projects with speed and efficiency.")
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
"1fdk9yhwvl1w1z71ykzcvgh4nsf8scxcbclz5anh98zpplmhmisa"))
"1b3figbhp5l83vd37vq6j2narrq4yl9pfw6mw0px0dzb1hz3jqka"))
(patches (search-patches "libgit2-0.25.1-mtime-0.patch"))))
(build-system cmake-build-system)
(outputs '("out" "debug"))
@ -1650,7 +1650,17 @@ unique algebra of patches called @url{http://darcs.net/Theory,Patchtheory}.
;; JGit must be built with a JDK supporting Java 8.
#:jdk ,icedtea-8
;; Target our older default JDK.
#:make-flags (list "-Dtarget=1.7")))
#:make-flags (list "-Dtarget=1.7")
#:phases
(modify-phases %standard-phases
;; The jar file generated by the default build.xml does not include
;; the text properties files, so we need to add them.
(add-after 'build 'add-properties
(lambda* (#:key jar-name #:allow-other-keys)
(with-directory-excursion "src"
(zero? (apply system* "jar" "-uf"
(string-append "../build/jar/" jar-name)
(find-files "." "\\.properties$")))))))))
(inputs
`(("java-classpathx-servletapi" ,java-classpathx-servletapi)
("java-javaewah" ,java-javaewah)
@ -1679,16 +1689,16 @@ network protocols, and core version control algorithms.")
"15gm537iivhnzlkjym4x3wn5jqdjdragsw9pdpzqqg21nrc817mm"))))
(build-system ant-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
(add-after 'unpack 'use-latest-javaewah-API
(lambda _
(substitute* "src/org/eclipse/jgit/internal/storage/file/BitmapIndexImpl.java"
(("wordinbits") "WORD_IN_BITS"))
#t)))
(substitute-keyword-arguments (package-arguments java-jgit)
;; Build for default JDK.
,@(substitute-keyword-arguments (package-arguments java-jgit)
((#:jdk _) icedtea-7))))
((#:jdk _) icedtea-7)
((#:phases phases)
`(modify-phases ,phases
(add-after 'unpack 'use-latest-javaewah-API
(lambda _
(substitute* "src/org/eclipse/jgit/internal/storage/file/BitmapIndexImpl.java"
(("wordinbits") "WORD_IN_BITS"))
#t))))))
(inputs
`(("java-javaewah" ,java-javaewah)
("java-jsch" ,java-jsch)

91
gnu/packages/video.scm
View File

@ -85,6 +85,7 @@
#:use-module (gnu packages gtk)
#:use-module (gnu packages image)
#:use-module (gnu packages imagemagick)
#:use-module (gnu packages libreoffice)
#:use-module (gnu packages linux)
#:use-module (gnu packages lua)
#:use-module (gnu packages m4)
@ -1115,7 +1116,7 @@ access to mpv's powerful playback capabilities.")
(define-public youtube-dl
(package
(name "youtube-dl")
(version "2017.10.15.1")
(version "2017.10.20")
(source (origin
(method url-fetch)
(uri (string-append "https://yt-dl.org/downloads/"
@ -1123,7 +1124,7 @@ access to mpv's powerful playback capabilities.")
version ".tar.gz"))
(sha256
(base32
"0zr9sx0nxk36si8xbvhlnazb69xzlygrhsxcyiydm0dy5y5ycsns"))))
"0npr8b1xg1dylz717kfllw433h1y16251npzch48lchq69bhm4iy"))))
(build-system python-build-system)
(arguments
;; The problem here is that the directory for the man page and completion
@ -2385,3 +2386,89 @@ tables")
generation of MPEG TS and DVB PSI tables according to standards ISO/IEC 13818s
and ITU-T H.222.0.")
(license license:lgpl2.1)))
(define-public ffms2
(package
(name "ffms2")
(version "2.23")
(home-page "https://github.com/FFMS/ffms2/")
(source (origin
(method url-fetch)
(uri (string-append home-page "archive/" version ".tar.gz"))
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
"1vbkab8vrplxz5xgag8ggzkwp4f7nf285pd0l2a7zy66n6i2m6xh"))))
(build-system gnu-build-system)
(arguments
'(#:configure-flags
(list "--enable-avresample")))
(inputs
`(("zlib" ,zlib)))
(propagated-inputs
`(("ffmpeg" ,ffmpeg)))
(native-inputs
`(("pkg-config" ,pkg-config)))
(synopsis "Cross-platform wrapper around ffmpeg/libav")
(description
"FFMpegSource is a wrapper library around ffmpeg/libav that allows
programmers to access a standard API to open and decompress media files.")
;; sources are distributed under a different license that the binary.
;; see https://github.com/FFMS/ffms2/blob/master/COPYING
(license license:gpl2+))); inherits from ffmpeg
(define-public aegisub
(package
(name "aegisub")
(version "3.2.2")
(source (origin
(method url-fetch)
(uri (string-append
"http://ftp.aegisub.org/pub/archives/releases/source/"
name "-" version ".tar.xz"))
(sha256
(base32
"11b83qazc8h0iidyj1rprnnjdivj1lpphvpa08y53n42bfa36pn5"))))
(build-system gnu-build-system)
(arguments
`(#:configure-flags
(list "--disable-update-checker"
"--without-portaudio"
"--without-openal"
"--without-oss")
;; tests require busted, a lua package we don't have yet
#:tests? #f
#:phases
(modify-phases %standard-phases
(add-before 'configure 'fix-ldflags
(lambda _
(setenv "LDFLAGS" "-pthread"))))))
(inputs
`(("boost" ,boost)
("desktop-file-utils" ,desktop-file-utils)
("ffms2" ,ffms2)
("fftw" ,fftw)
("hunspell" ,hunspell)
("mesa" ,mesa)
("libass" ,libass)
("alsa-lib" ,alsa-lib)
("pulseaudio" ,pulseaudio)
("libx11" ,libx11)
("freetype" ,freetype)
("wxwidgets-gtk2" ,wxwidgets-gtk2)))
(native-inputs
`(("intltool" ,intltool)
("pkg-config" ,pkg-config)))
(home-page "http://www.aegisub.org/")
(synopsis "Subtitle engine")
(description
"Aegisub is a tool for creating and modifying subtitles. Aegisub makes
it quick and easy to time subtitles to audio, and features many powerful
tools for styling them, including a built-in real-time video preview.")
(license (list license:bsd-3 ; the package is licensed under the bsd-3, except
license:mpl1.1 ; for vendor/universalchardet under the mpl1.1
license:expat)))) ; and src/gl that is under a license similar
; the the Expat license, with a rewording (Software -> Materials). (called MIT
; by upstream). See https://github.com/Aegisub/Aegisub/blob/master/LICENCE
; src/MatroskaParser.(c|h) is under bsd-3 with permission from the author

4
gnu/packages/vim.scm
View File

@ -60,7 +60,7 @@
(define-public vim
(package
(name "vim")
(version "8.0.1130")
(version "8.0.1207")
(source (origin
(method url-fetch)
(uri (string-append "https://github.com/vim/vim/archive/v"
@ -68,7 +68,7 @@
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
"0zqyk7086crc6q5fil38szppx9sgd14fs3wb9h4ak13jg6s2ir90"))))
"0zq740d0crybva00dk0rxsa9q1gafvc438syxqlmlxgnk5f0xd11"))))
(build-system gnu-build-system)
(arguments
`(#:test-target "test"

31
gnu/packages/virtualization.scm
View File

@ -4,6 +4,7 @@
;;; Copyright © 2016, 2017 Efraim Flashner <efraim@flashner.co.il>
;;; Copyright © 2016 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2017 Alex Vong <alexvong1995@gmail.com>
;;; Copyright © 2017 Andy Patterson <ajpatter@uwaterloo.ca>
;;;
;;; This file is part of GNU Guix.
;;;
@ -85,7 +86,7 @@
'(;; Running tests in parallel can occasionally lead to failures, like:
;; boot_sector_test: assertion failed (signature == SIGNATURE): (0x00000000 == 0x0000dead)
#:parallel-tests? #f
#:configure-flags '("--enable-usb-redir" "--enable-opengl")
#:phases
(modify-phases %standard-phases
(replace 'configure
@ -143,7 +144,9 @@
("libaio" ,libaio)
("libattr" ,attr)
("libcap" ,libcap) ; virtfs support requires libcap & libattr
("libjpeg" ,libjpeg-8)
("libdrm" ,libdrm)
("libepoxy" ,libepoxy)
("libjpeg" ,libjpeg-turbo)
("libpng" ,libpng)
("libusb" ,libusb) ;USB pass-through support
("mesa" ,mesa)
@ -152,6 +155,7 @@
("pixman" ,pixman)
("sdl" ,sdl)
("spice" ,spice)
("usbredir" ,usbredir)
("util-linux" ,util-linux)
;; ("vde2" ,vde2)
("virglrenderer" ,virglrenderer)
@ -188,14 +192,15 @@ server and embedded PowerPC, and S390 guests.")
(name "qemu-minimal")
(synopsis "Machine emulator and virtualizer (without GUI)")
(arguments
`(#:configure-flags
;; Restrict to the targets supported by Guix.
'("--target-list=i386-softmmu,x86_64-softmmu,mips64el-softmmu,arm-softmmu,aarch64-softmmu")
,@(package-arguments qemu)))
(substitute-keyword-arguments (package-arguments qemu)
((#:configure-flags _ '(list))
;; Restrict to the targets supported by Guix.
''("--target-list=i386-softmmu,x86_64-softmmu,mips64el-softmmu,arm-softmmu,aarch64-softmmu"))))
;; Remove dependencies on optional libraries, notably GUI libraries.
(inputs (fold alist-delete (package-inputs qemu)
'("libusb" "mesa" "sdl" "spice" "virglrenderer")))))
'("libusb" "mesa" "sdl" "spice" "virglrenderer"
"usbredir" "libdrm" "libepoxy")))))
(define-public libosinfo
(package
@ -317,6 +322,7 @@ manage system or application containers.")
(method url-fetch)
(uri (string-append "https://libvirt.org/sources/libvirt-"
version ".tar.xz"))
(patches (search-patches "libvirt-CVE-2017-1000256.patch"))
(sha256
(base32
"1fk75cdzg59y9hnfdpdwv83fsc1yffy3lac4ch19zygfkqhcnysf"))))
@ -510,6 +516,13 @@ virtualization library.")
(substitute* "virtcli/cliconfig.py"
(("/usr") (assoc-ref outputs "out")))
#t))
(add-after 'unpack 'fix-default-uri
(lambda* (#:key inputs #:allow-other-keys)
;; xen is not available for now - so only patch qemu
(substitute* "virtManager/connect.py"
(("/usr(/bin/qemu-system)" _ suffix)
(string-append (assoc-ref inputs "qemu") suffix)))
#t))
(add-before 'wrap 'wrap-with-GI_TYPELIB_PATH
(lambda* (#:key inputs outputs #:allow-other-keys)
(let* ((bin (string-append (assoc-ref outputs "out") "/bin"))
@ -540,8 +553,10 @@ virtualization library.")
("python2-libvirt" ,python2-libvirt)
("python2-requests" ,python2-requests)
("python2-ipaddr" ,python2-ipaddr)
("python2-pycairo" ,python2-pycairo)
("python2-pygobject" ,python2-pygobject)
("python2-libxml2" ,python2-libxml2)))
("python2-libxml2" ,python2-libxml2)
("spice-gtk" ,spice-gtk)))
;; virt-manager searches for qemu-img or kvm-img in the PATH.
(propagated-inputs
`(("qemu" ,qemu)))

8
gnu/packages/web.scm
View File

@ -142,14 +142,14 @@ and its related documentation.")
(name "nginx")
;; Consider updating the nginx-docs package if the nginx package is
;; updated.
(version "1.12.1")
(version "1.12.2")
(source (origin
(method url-fetch)
(uri (string-append "https://nginx.org/download/nginx-"
version ".tar.gz"))
(sha256
(base32
"1yvnmj7vlykrqdi6amkvs63lva6qkxd98sqv0a8hz8w5ci1bz4w7"))))
"05h4rwja7170z0l979yjghy9i9ichllwhicylzpmmyyml6fkfprh"))))
(build-system gnu-build-system)
(inputs `(("pcre" ,pcre)
("openssl" ,openssl)
@ -3788,13 +3788,13 @@ LaTeX.")
(define-public r-curl
(package
(name "r-curl")
(version "2.8.1")
(version "3.0")
(source (origin
(method url-fetch)
(uri (cran-uri "curl" version))
(sha256
(base32
"0dgfl7wn4r8inv55xnk4ybf1y2x4qmi4cbr6phr3lfi1dnjm4hsm"))))
"01m52jz2q38yc32xbnmpm48hck2xj9fyhxq262p04y67gjpf7y3v"))))
(build-system r-build-system)
(arguments
`(#:phases

4
gnu/packages/webkit.scm
View File

@ -54,14 +54,14 @@
(define-public webkitgtk
(package
(name "webkitgtk")
(version "2.18.0")
(version "2.18.1")
(source (origin
(method url-fetch)
(uri (string-append "https://www.webkitgtk.org/releases/"
name "-" version ".tar.xz"))
(sha256
(base32
"1383wlv98l8fwmhzy0fad82a44h5svm89c1kpa03wsp37mmf90xm"))))
"15fp7szmkpannx7avsynf0nv3y343qwq0fvq3rz2m2mw5wq7pnww"))))
(build-system cmake-build-system)
(arguments
'(#:tests? #f ; no tests

4
gnu/packages/xdisorg.scm
View File

@ -1073,7 +1073,7 @@ connectivity of the X server running on a particular @code{DISPLAY}.")
(define-public rofi
(package
(name "rofi")
(version "1.4.1")
(version "1.4.2")
(source (origin
(method url-fetch)
(uri (string-append "https://github.com/DaveDavenport/rofi/"
@ -1081,7 +1081,7 @@ connectivity of the X server running on a particular @code{DISPLAY}.")
version "/rofi-" version ".tar.xz"))
(sha256
(base32
"0xnfzbwhxd2cd4lxkc24mbx3f4b1h3l1alcdbbsymi2b9fdwmywh"))))
"1129cbg76g56c6ckzj5y5haf92jxhx3b71cr3qmhrb0n8g4gi38s"))))
(build-system gnu-build-system)
(inputs
`(("pango" ,pango)

13
gnu/packages/xiph.scm
View File

@ -5,7 +5,7 @@
;;; Copyright © 2014 Sree Harsha Totakura <sreeharsha@totakura.in>
;;; Copyright © 2014 Mark H Weaver <mhw@netris.org>
;;; Copyright © 2015 Paul van der Walt <paul@denknerd.org>
;;; Copyright © 2015, 2016 Efraim Flashner <efraim@flashner.co.il>
;;; Copyright © 2015, 2016, 2017 Efraim Flashner <efraim@flashner.co.il>
;;; Copyright © 2017 Marius Bakke <mbakke@fastmail.com>
;;;
;;; This file is part of GNU Guix.
@ -139,7 +139,11 @@ compressed video format.")
(base32
"150047wnllz4r94whb9r73l5qf0z5z3rlhy98bawfbblmkq8mbpa"))))
(build-system gnu-build-system)
(inputs `(("libogg" ,libogg)))
(native-inputs
`(("pkg-config" ,pkg-config)))
(inputs
`(("libogg" ,libogg)
("speexdsp" ,speexdsp)))
(home-page "https://gnu.org/software/speex")
(synopsis "Library for patent-free audio compression format")
(description
@ -163,6 +167,11 @@ stereo encoding, and voice activity detection.")
(base32
"1wcjyrnwlkayb20zdhp48y260rfyzg925qpjpljd5x9r01h8irja"))))
(build-system gnu-build-system)
(arguments
`(#:configure-flags '(,@(if (string=? "aarch64-linux"
(%current-system))
'("--enable-neon=no") ; neon defaults to armv7-a
'()))))
(home-page "https://speex.org/")
(synopsis "Speex processing library")
(description

10
gnu/system/vm.scm
View File

@ -49,7 +49,7 @@
#:use-module (gnu packages admin)
#:use-module (gnu bootloader)
#:use-module ((gnu bootloader grub) #:select (grub-mkrescue-bootloader))
#:use-module (gnu bootloader grub)
#:use-module (gnu system shadow)
#:use-module (gnu system pam)
#:use-module (gnu system linux-initrd)
@ -565,6 +565,14 @@ environment with the store shared with the host. MAPPINGS is a list of
user-file-systems)))
(operating-system (inherit os)
;; XXX: Until we run QEMU with UEFI support (with the OVMF firmware),
;; force the traditional i386/BIOS method.
;; See <https://bugs.gnu.org/28768>.
(bootloader (bootloader-configuration
(bootloader grub-bootloader)
(target "/dev/vda")))
(initrd (lambda (file-systems . rest)
(apply base-initrd file-systems
#:volatile-root? #t

2
guix/build-system/r.scm
View File

@ -50,7 +50,7 @@ available via the first URI, the second URI points to the archived version."
(define (bioconductor-uri name version)
"Return a URI string for the R package archive on Bioconductor for the
release corresponding to NAME and VERSION."
(string-append "http://bioconductor.org/packages/release/bioc/src/contrib/"
(string-append "https://bioconductor.org/packages/release/bioc/src/contrib/"
name "_" version ".tar.gz"))
(define %r-build-system-modules

125
guix/build/download-nar.scm Normal file
View File

@ -0,0 +1,125 @@
;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2017 Ludovic Courtès <ludo@gnu.org>
;;;
;;; This file is part of GNU Guix.
;;;
;;; GNU Guix is free software; you can redistribute it and/or modify it
;;; under the terms of the GNU General Public License as published by
;;; the Free Software Foundation; either version 3 of the License, or (at
;;; your option) any later version.
;;;
;;; GNU Guix is distributed in the hope that it will be useful, but
;;; WITHOUT ANY WARRANTY; without even the implied warranty of
;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
;;; GNU General Public License for more details.
;;;
;;; You should have received a copy of the GNU General Public License
;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
(define-module (guix build download-nar)
#:use-module (guix build download)
#:use-module (guix build utils)
#:use-module (guix serialization)
#:use-module (guix zlib)
#:use-module (guix progress)
#:use-module (web uri)
#:use-module (srfi srfi-11)
#:use-module (srfi srfi-26)
#:use-module (ice-9 format)
#:use-module (ice-9 match)
#:export (download-nar))
;;; Commentary:
;;;
;;; Download a normalized archive or "nar", similar to what 'guix substitute'
;;; does. The intent here is to use substitute servers as content-addressed
;;; mirrors of VCS checkouts. This is mostly useful for users who have
;;; disabled substitutes.
;;;
;;; Code:
(define (urls-for-item item)
"Return the fallback nar URL for ITEM--e.g.,
\"/gnu/store/cabbag3…-foo-1.2-checkout\"."
;; Here we hard-code nar URLs without checking narinfos. That's probably OK
;; though.
;; TODO: Use HTTPS? The downside is the extra dependency.
(let ((bases '("http://mirror.hydra.gnu.org/guix"
"http://berlin.guixsd.org"))
(item (basename item)))
(append (map (cut string-append <> "/nar/gzip/" item) bases)
(map (cut string-append <> "/nar/" item) bases))))
(define (restore-gzipped-nar port item size)
"Restore the gzipped nar read from PORT, of SIZE bytes (compressed), to
ITEM."
;; Since PORT is typically a non-file port (for instance because 'http-get'
;; returns a delimited port), create a child process so we're back to a file
;; port that can be passed to 'call-with-gzip-input-port'.
(match (pipe)
((input . output)
(match (primitive-fork)
(0
(dynamic-wind
(const #t)
(lambda ()
(close-port output)
(close-port port)
(catch #t
(lambda ()
(call-with-gzip-input-port input
(cut restore-file <> item)))
(lambda (key . args)
(print-exception (current-error-port)
(stack-ref (make-stack #t) 1)
key args)
(primitive-exit 1))))
(lambda ()
(primitive-exit 0))))
(child
(close-port input)
(dump-port* port output
#:reporter (progress-reporter/file item size
#:abbreviation
store-path-abbreviation))
(close-port output)
(newline)
(match (waitpid child)
((_ . status)
(unless (zero? status)
(error "nar decompression failed" status)))))))))
(define (download-nar item)
"Download and extract the normalized archive for ITEM. Return #t on
success, #f otherwise."
;; Let progress reports go through.
(setvbuf (current-error-port) _IONBF)
(setvbuf (current-output-port) _IONBF)
(let loop ((urls (urls-for-item item)))
(match urls
((url rest ...)
(format #t "Trying content-addressed mirror at ~a...~%"
(uri-host (string->uri url)))
(let-values (((port size)
(catch #t
(lambda ()
(http-fetch (string->uri url)))
(lambda args
(values #f #f)))))
(if (not port)
(loop rest)
(begin
(if size
(format #t "Downloading from ~a (~,2h MiB)...~%" url
(/ size (expt 2 20.)))
(format #t "Downloading from ~a...~%" url))
(if (string-contains url "/gzip")
(restore-gzipped-nar port item size)
(begin
;; FIXME: Add progress report.
(restore-file port item)
(close-port port)))
#t))))
(()
#f))))

216
guix/build/download.scm
View File

@ -1,7 +1,6 @@
;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2012, 2013, 2014, 2015, 2016, 2017 Ludovic Courtès <ludo@gnu.org>
;;; Copyright © 2015 Mark H Weaver <mhw@netris.org>
;;; Copyright © 2015 Steve Sprang <scs@stevesprang.com>
;;; Copyright © 2017 Tobias Geerinckx-Rice <me@tobias.gr>
;;;
;;; This file is part of GNU Guix.
@ -27,7 +26,7 @@
#:use-module (guix base64)
#:use-module (guix ftp-client)
#:use-module (guix build utils)
#:use-module (guix utils)
#:use-module (guix progress)
#:use-module (rnrs io ports)
#:use-module (rnrs bytevectors)
#:use-module (srfi srfi-1)
@ -39,14 +38,13 @@
#:use-module (ice-9 format)
#:export (open-socket-for-uri
open-connection-for-uri
http-fetch
%x509-certificate-directory
close-connection
resolve-uri-reference
maybe-expand-mirrors
url-fetch
byte-count->string
current-terminal-columns
progress-reporter/file
uri-abbreviation
nar-uri-abbreviation
store-path-abbreviation))
@ -61,69 +59,6 @@
;; Size of the HTTP receive buffer.
65536)
(define current-terminal-columns
;; Number of columns of the terminal.
(make-parameter 80))
(define (nearest-exact-integer x)
"Given a real number X, return the nearest exact integer, with ties going to
the nearest exact even integer."
(inexact->exact (round x)))
(define (duration->seconds duration)
"Return the number of seconds represented by DURATION, a 'time-duration'
object, as an inexact number."
(+ (time-second duration)
(/ (time-nanosecond duration) 1e9)))
(define (seconds->string duration)
"Given DURATION in seconds, return a string representing it in 'mm:ss' or
'hh:mm:ss' format, as needed."
(if (not (number? duration))
"00:00"
(let* ((total-seconds (nearest-exact-integer duration))
(extra-seconds (modulo total-seconds 3600))
(num-hours (quotient total-seconds 3600))
(hours (and (positive? num-hours) num-hours))
(mins (quotient extra-seconds 60))
(secs (modulo extra-seconds 60)))
(format #f "~@[~2,'0d:~]~2,'0d:~2,'0d" hours mins secs))))
(define (byte-count->string size)
"Given SIZE in bytes, return a string representing it in a human-readable
way."
(let ((KiB 1024.)
(MiB (expt 1024. 2))
(GiB (expt 1024. 3))
(TiB (expt 1024. 4)))
(cond
((< size KiB) (format #f "~dB" (nearest-exact-integer size)))
((< size MiB) (format #f "~dKiB" (nearest-exact-integer (/ size KiB))))
((< size GiB) (format #f "~,1fMiB" (/ size MiB)))
((< size TiB) (format #f "~,2fGiB" (/ size GiB)))
(else (format #f "~,3fTiB" (/ size TiB))))))
(define* (progress-bar % #:optional (bar-width 20))
"Return % as a string representing an ASCII-art progress bar. The total
width of the bar is BAR-WIDTH."
(let* ((fraction (/ % 100))
(filled (inexact->exact (floor (* fraction bar-width))))
(empty (- bar-width filled)))
(format #f "[~a~a]"
(make-string filled #\#)
(make-string empty #\space))))
(define (string-pad-middle left right len)
"Combine LEFT and RIGHT with enough padding in the middle so that the
resulting string has length at least LEN (it may overflow). If the string
does not overflow, the last char in RIGHT will be flush with the LEN
column."
(let* ((total-used (+ (string-length left)
(string-length right)))
(num-spaces (max 1 (- len total-used)))
(padding (make-string num-spaces #\space)))
(string-append left padding right)))
(define* (ellipsis #:optional (port (current-output-port)))
"Make a rough guess at whether Unicode's HORIZONTAL ELLIPSIS can be written
in PORT's encoding, and return either that or ASCII dots."
@ -142,105 +77,6 @@ Otherwise return STORE-PATH."
(string-drop base 32)))
store-path))
(cond-expand
(guile-2.2
;; Guile 2.2.2 has a bug whereby 'time-monotonic' objects have seconds and
;; nanoseconds swapped (fixed in Guile commit 886ac3e). Work around it.
(define time-monotonic time-tai))
(else #t))
;; TODO: replace '(@ (guix build utils) dump-port))'.
(define* (dump-port* in out
#:key (buffer-size 16384)
(reporter (make-progress-reporter noop noop noop)))
"Read as much data as possible from IN and write it to OUT, using chunks of
BUFFER-SIZE bytes. After each successful transfer of BUFFER-SIZE bytes or
less, report the total number of bytes transferred to the REPORTER, which
should be a <progress-reporter> object."
(define buffer
(make-bytevector buffer-size))
(call-with-progress-reporter reporter
(lambda (report)
(let loop ((total 0)
(bytes (get-bytevector-n! in buffer 0 buffer-size)))
(or (eof-object? bytes)
(let ((total (+ total bytes)))
(put-bytevector out buffer 0 bytes)
(report total)
(loop total (get-bytevector-n! in buffer 0 buffer-size))))))))
(define (rate-limited proc interval)
"Return a procedure that will forward the invocation to PROC when the time
elapsed since the previous forwarded invocation is greater or equal to
INTERVAL (a time-duration object), otherwise does nothing and returns #f."
(let ((previous-at #f))
(lambda args
(let* ((now (current-time time-monotonic))
(forward-invocation (lambda ()
(set! previous-at now)
(apply proc args))))
(if previous-at
(let ((elapsed (time-difference now previous-at)))
(if (time>=? elapsed interval)
(forward-invocation)
#f))
(forward-invocation))))))
(define* (progress-reporter/file file size
#:optional (log-port (current-output-port))
#:key (abbreviation basename))
"Return a <progress-reporter> object to show the progress of FILE's download,
which is SIZE bytes long. The progress report is written to LOG-PORT, with
ABBREVIATION used to shorten FILE for display."
(let ((start-time (current-time time-monotonic))
(transferred 0))
(define (render)
"Write the progress report to LOG-PORT."
(define elapsed
(duration->seconds
(time-difference (current-time time-monotonic) start-time)))
(if (number? size)
(let* ((% (* 100.0 (/ transferred size)))
(throughput (/ transferred elapsed))
(left (format #f " ~a ~a"
(abbreviation file)
(byte-count->string size)))
(right (format #f "~a/s ~a ~a~6,1f%"
(byte-count->string throughput)
(seconds->string elapsed)
(progress-bar %) %)))
(display "\r\x1b[K" log-port)
(display (string-pad-middle left right
(current-terminal-columns))
log-port)
(flush-output-port log-port))
(let* ((throughput (/ transferred elapsed))
(left (format #f " ~a"
(abbreviation file)))
(right (format #f "~a/s ~a | ~a transferred"
(byte-count->string throughput)
(seconds->string elapsed)
(byte-count->string transferred))))
(display "\r\x1b[K" log-port)
(display (string-pad-middle left right
(current-terminal-columns))
log-port)
(flush-output-port log-port))))
(progress-reporter
(start render)
;; Report the progress every 300ms or longer.
(report
(let ((rate-limited-render
(rate-limited render (make-time time-monotonic 300000000 0))))
(lambda (value)
(set! transferred value)
(rate-limited-render))))
;; Don't miss the last report.
(stop render))))
(define* (uri-abbreviation uri #:optional (max-length 42))
"If URI's string representation is larger than MAX-LENGTH, return an
abbreviation of URI showing the scheme, host, and basename of the file."
@ -745,11 +581,11 @@ Return the resulting target URI."
#:query (uri-query ref)
#:fragment (uri-fragment ref)))))
(define* (http-fetch uri file #:key timeout (verify-certificate? #t))
"Fetch data from URI and write it to FILE; when TIMEOUT is true, bail out if
the connection could not be established in less than TIMEOUT seconds. Return
FILE on success. When VERIFY-CERTIFICATE? is true, verify HTTPS
certificates; otherwise simply ignore them."
(define* (http-fetch uri #:key timeout (verify-certificate? #t))
"Return an input port containing the data at URI, and the expected number of
bytes available or #f. When TIMEOUT is true, bail out if the connection could
not be established in less than TIMEOUT seconds. When VERIFY-CERTIFICATE? is
true, verify HTTPS certificates; otherwise simply ignore them."
(define headers
`(;; Some web sites, such as http://dist.schmorp.de, would block you if
@ -774,28 +610,15 @@ certificates; otherwise simply ignore them."
#:timeout timeout
#:verify-certificate?
verify-certificate?))
((resp bv-or-port)
((resp port)
(http-get uri #:port connection #:decode-body? #f
#:streaming? #t
#:headers headers))
((code)
(response-code resp))
((size)
(response-content-length resp)))
(response-code resp)))
(case code
((200) ; OK
(begin
(call-with-output-file file
(lambda (p)
(if (port? bv-or-port)
(begin
(dump-port* bv-or-port p
#:buffer-size %http-receive-buffer-size
#:reporter (progress-reporter/file
(uri-abbreviation uri) size))
(newline))
(put-bytevector p bv-or-port))))
file))
(values port (response-content-length resp)))
((301 ; moved permanently
302 ; found (redirection)
303 ; see other
@ -805,7 +628,7 @@ certificates; otherwise simply ignore them."
(format #t "following redirection to `~a'...~%"
(uri->string uri))
(close connection)
(http-fetch uri file
(http-fetch uri
#:timeout timeout
#:verify-certificate? verify-certificate?)))
(else
@ -876,10 +699,19 @@ otherwise simply ignore them."
file (uri->string uri))
(case (uri-scheme uri)
((http https)
(false-if-exception* (http-fetch uri file
#:verify-certificate?
verify-certificate?
#:timeout timeout)))
(false-if-exception*
(let-values (((port size)
(http-fetch uri
#:verify-certificate? verify-certificate?
#:timeout timeout)))
(call-with-output-file file
(lambda (output)
(dump-port* port output
#:buffer-size %http-receive-buffer-size
#:reporter (progress-reporter/file
(uri-abbreviation uri) size))
(newline)))
#t)))
((ftp)
(false-if-exception* (ftp-fetch uri file
#:timeout timeout)))

38
guix/cvs-download.scm
View File

@ -1,5 +1,5 @@
;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2014, 2015, 2016 Ludovic Courtès <ludo@gnu.org>
;;; Copyright © 2014, 2015, 2016, 2017 Ludovic Courtès <ludo@gnu.org>
;;; Copyright © 2014 Sree Harsha Totakura <sreeharsha@totakura.in>
;;; Copyright © 2015 Mark H Weaver <mhw@netris.org>
;;;
@ -23,6 +23,7 @@
#:use-module (guix gexp)
#:use-module (guix store)
#:use-module (guix monads)
#:use-module (guix modules)
#:use-module (guix packages)
#:use-module (ice-9 match)
#:export (cvs-reference
@ -59,16 +60,35 @@
"Return a fixed-output derivation that fetches REF, a <cvs-reference>
object. The output is expected to have recursive hash HASH of type
HASH-ALGO (a symbol). Use NAME as the file name, or a generic name if #f."
(define zlib
(module-ref (resolve-interface '(gnu packages compression)) 'zlib))
(define config.scm
(scheme-file "config.scm"
#~(begin
(define-module (guix config)
#:export (%libz))
(define %libz
#+(file-append zlib "/lib/libz")))))
(define modules
(cons `((guix config) => ,config.scm)
(delete '(guix config)
(source-module-closure '((guix build cvs)
(guix build download-nar))))))
(define build
(with-imported-modules '((guix build cvs)
(guix build utils))
(with-imported-modules modules
#~(begin
(use-modules (guix build cvs))
(cvs-fetch '#$(cvs-reference-root-directory ref)
'#$(cvs-reference-module ref)
'#$(cvs-reference-revision ref)
#$output
#:cvs-command (string-append #+cvs "/bin/cvs")))))
(use-modules (guix build cvs)
(guix build download-nar))
(or (cvs-fetch '#$(cvs-reference-root-directory ref)
'#$(cvs-reference-module ref)
'#$(cvs-reference-revision ref)
#$output
#:cvs-command (string-append #+cvs "/bin/cvs"))
(download-nar #$output)))))
(mlet %store-monad ((guile (package->derivation guile system)))
(gexp->derivation (or name "cvs-checkout") build

37
guix/git-download.scm
View File

@ -25,6 +25,7 @@
#:use-module (guix monads)
#:use-module (guix records)
#:use-module (guix packages)
#:use-module (guix modules)
#:autoload (guix build-system gnu) (standard-packages)
#:use-module (ice-9 match)
#:use-module (ice-9 popen)
@ -77,12 +78,31 @@ HASH-ALGO (a symbol). Use NAME as the file name, or a generic name if #f."
(standard-packages)
'()))
(define zlib
(module-ref (resolve-interface '(gnu packages compression)) 'zlib))
(define config.scm
(scheme-file "config.scm"
#~(begin
(define-module (guix config)
#:export (%libz))
(define %libz
#+(file-append zlib "/lib/libz")))))
(define modules
(cons `((guix config) => ,config.scm)
(delete '(guix config)
(source-module-closure '((guix build git)
(guix build utils)
(guix build download-nar))))))
(define build
(with-imported-modules '((guix build git)
(guix build utils))
(with-imported-modules modules
#~(begin
(use-modules (guix build git)
(guix build utils)
(guix build download-nar)
(ice-9 match))
;; The 'git submodule' commands expects Coreutils, sed,
@ -92,12 +112,13 @@ HASH-ALGO (a symbol). Use NAME as the file name, or a generic name if #f."
(((names dirs) ...)
dirs)))
(git-fetch (getenv "git url") (getenv "git commit")
#$output
#:recursive? (call-with-input-string
(getenv "git recursive?")
read)
#:git-command (string-append #+git "/bin/git")))))
(or (git-fetch (getenv "git url") (getenv "git commit")
#$output
#:recursive? (call-with-input-string
(getenv "git recursive?")
read)
#:git-command (string-append #+git "/bin/git"))
(download-nar #$output)))))
(mlet %store-monad ((guile (package->derivation guile system)))
(gexp->derivation (or name "git-checkout") build

36
guix/hg-download.scm
View File

@ -1,5 +1,5 @@
;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2014, 2015, 2016 Ludovic Courtès <ludo@gnu.org>
;;; Copyright © 2014, 2015, 2016, 2017 Ludovic Courtès <ludo@gnu.org>
;;; Copyright © 2016 Ricardo Wurmus <rekado@elephly.net>
;;;
;;; This file is part of GNU Guix.
@ -22,6 +22,7 @@
#:use-module (guix store)
#:use-module (guix monads)
#:use-module (guix records)
#:use-module (guix modules)
#:use-module (guix packages)
#:autoload (guix build-system gnu) (standard-packages)
#:use-module (ice-9 match)
@ -59,18 +60,35 @@
"Return a fixed-output derivation that fetches REF, a <hg-reference>
object. The output is expected to have recursive hash HASH of type
HASH-ALGO (a symbol). Use NAME as the file name, or a generic name if #f."
(define zlib
(module-ref (resolve-interface '(gnu packages compression)) 'zlib))
(define config.scm
(scheme-file "config.scm"
#~(begin
(define-module (guix config)
#:export (%libz))
(define %libz
#+(file-append zlib "/lib/libz")))))
(define modules
(cons `((guix config) => ,config.scm)
(delete '(guix config)
(source-module-closure '((guix build hg)
(guix build download-nar))))))
(define build
(with-imported-modules '((guix build hg)
(guix build utils))
(with-imported-modules modules
#~(begin
(use-modules (guix build hg)
(guix build utils)
(ice-9 match))
(guix build download-nar))
(hg-fetch '#$(hg-reference-url ref)
'#$(hg-reference-changeset ref)
#$output
#:hg-command (string-append #+hg "/bin/hg")))))
(or (hg-fetch '#$(hg-reference-url ref)
'#$(hg-reference-changeset ref)
#$output
#:hg-command (string-append #+hg "/bin/hg"))
(download-nar #$output)))))
(mlet %store-monad ((guile (package->derivation guile system)))
(gexp->derivation (or name "hg-checkout") build

8
guix/import/cran.scm
View File

@ -126,7 +126,7 @@ package definition."
`((,type (,'quasiquote ,(format-inputs package-inputs)))))))
(define %cran-url "http://cran.r-project.org/web/packages/")
(define %bioconductor-url "http://bioconductor.org/packages/")
(define %bioconductor-url "https://bioconductor.org/packages/")
;; The latest Bioconductor release is 3.5. Bioconductor packages should be
;; updated together.
@ -446,7 +446,7 @@ dependencies."
(define (bioconductor-package? package)
"Return true if PACKAGE is an R package from Bioconductor."
(let ((predicate (lambda (uri)
(and (string-prefix? "http://bioconductor.org" uri)
(and (string-prefix? "https://bioconductor.org" uri)
;; Data packages are neither listed in SVN nor on
;; the Github mirror, so we have to exclude them
;; from the set of bioconductor packages that can be
@ -465,7 +465,7 @@ dependencies."
(define (bioconductor-data-package? package)
"Return true if PACKAGE is an R data package from Bioconductor."
(let ((predicate (lambda (uri)
(and (string-prefix? "http://bioconductor.org" uri)
(and (string-prefix? "https://bioconductor.org" uri)
(string-contains uri "/data/annotation/")))))
(and (string-prefix? "r-" (package-name package))
(match (and=> (package-source package) origin-uri)
@ -478,7 +478,7 @@ dependencies."
(define (bioconductor-experiment-package? package)
"Return true if PACKAGE is an R experiment package from Bioconductor."
(let ((predicate (lambda (uri)
(and (string-prefix? "http://bioconductor.org" uri)
(and (string-prefix? "https://bioconductor.org" uri)
(string-contains uri "/data/experiment/")))))
(and (string-prefix? "r-" (package-name package))
(match (and=> (package-source package) origin-uri)

228
guix/progress.scm Normal file
View File

@ -0,0 +1,228 @@
;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2017 Sou Bunnbu <iyzsong@gmail.com>
;;; Copyright © 2015 Steve Sprang <scs@stevesprang.com>
;;;
;;; This file is part of GNU Guix.
;;;
;;; GNU Guix is free software; you can redistribute it and/or modify it
;;; under the terms of the GNU General Public License as published by
;;; the Free Software Foundation; either version 3 of the License, or (at
;;; your option) any later version.
;;;
;;; GNU Guix is distributed in the hope that it will be useful, but
;;; WITHOUT ANY WARRANTY; without even the implied warranty of
;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
;;; GNU General Public License for more details.
;;;
;;; You should have received a copy of the GNU General Public License
;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
(define-module (guix progress)
#:use-module (guix records)
#:use-module (srfi srfi-19)
#:use-module (rnrs io ports)
#:use-module (rnrs bytevectors)
#:use-module (ice-9 format)
#:use-module (ice-9 match)
#:export (<progress-reporter>
progress-reporter
make-progress-reporter
progress-reporter?
call-with-progress-reporter
progress-reporter/silent
progress-reporter/file
byte-count->string
current-terminal-columns
dump-port*))
;;; Commentary:
;;;
;;; Helper to write progress report code for downloads, etc.
;;;
;;; Code:
(define-record-type* <progress-reporter>
progress-reporter make-progress-reporter progress-reporter?
(start progress-reporter-start) ; thunk
(report progress-reporter-report) ; procedure
(stop progress-reporter-stop)) ; thunk
(define (call-with-progress-reporter reporter proc)
"Start REPORTER for progress reporting, and call @code{(@var{proc} report)}
with the resulting report procedure. When @var{proc} returns, the REPORTER is
stopped."
(match reporter
(($ <progress-reporter> start report stop)
(dynamic-wind start (lambda () (proc report)) stop))))
(define progress-reporter/silent
(make-progress-reporter noop noop noop))
;;;
;;; File download progress report.
;;;
(cond-expand
(guile-2.2
;; Guile 2.2.2 has a bug whereby 'time-monotonic' objects have seconds and
;; nanoseconds swapped (fixed in Guile commit 886ac3e). Work around it.
(define time-monotonic time-tai))
(else #t))
(define (nearest-exact-integer x)
"Given a real number X, return the nearest exact integer, with ties going to
the nearest exact even integer."
(inexact->exact (round x)))
(define (duration->seconds duration)
"Return the number of seconds represented by DURATION, a 'time-duration'
object, as an inexact number."
(+ (time-second duration)
(/ (time-nanosecond duration) 1e9)))
(define (seconds->string duration)
"Given DURATION in seconds, return a string representing it in 'mm:ss' or
'hh:mm:ss' format, as needed."
(if (not (number? duration))
"00:00"
(let* ((total-seconds (nearest-exact-integer duration))
(extra-seconds (modulo total-seconds 3600))
(num-hours (quotient total-seconds 3600))
(hours (and (positive? num-hours) num-hours))
(mins (quotient extra-seconds 60))
(secs (modulo extra-seconds 60)))
(format #f "~@[~2,'0d:~]~2,'0d:~2,'0d" hours mins secs))))
(define (byte-count->string size)
"Given SIZE in bytes, return a string representing it in a human-readable
way."
(let ((KiB 1024.)
(MiB (expt 1024. 2))
(GiB (expt 1024. 3))
(TiB (expt 1024. 4)))
(cond
((< size KiB) (format #f "~dB" (nearest-exact-integer size)))
((< size MiB) (format #f "~dKiB" (nearest-exact-integer (/ size KiB))))
((< size GiB) (format #f "~,1fMiB" (/ size MiB)))
((< size TiB) (format #f "~,2fGiB" (/ size GiB)))
(else (format #f "~,3fTiB" (/ size TiB))))))
(define (string-pad-middle left right len)
"Combine LEFT and RIGHT with enough padding in the middle so that the
resulting string has length at least LEN (it may overflow). If the string
does not overflow, the last char in RIGHT will be flush with the LEN
column."
(let* ((total-used (+ (string-length left)
(string-length right)))
(num-spaces (max 1 (- len total-used)))
(padding (make-string num-spaces #\space)))
(string-append left padding right)))
(define (rate-limited proc interval)
"Return a procedure that will forward the invocation to PROC when the time
elapsed since the previous forwarded invocation is greater or equal to
INTERVAL (a time-duration object), otherwise does nothing and returns #f."
(let ((previous-at #f))
(lambda args
(let* ((now (current-time time-monotonic))
(forward-invocation (lambda ()
(set! previous-at now)
(apply proc args))))
(if previous-at
(let ((elapsed (time-difference now previous-at)))
(if (time>=? elapsed interval)
(forward-invocation)
#f))
(forward-invocation))))))
(define current-terminal-columns
;; Number of columns of the terminal.
(make-parameter 80))
(define* (progress-bar % #:optional (bar-width 20))
"Return % as a string representing an ASCII-art progress bar. The total
width of the bar is BAR-WIDTH."
(let* ((fraction (/ % 100))
(filled (inexact->exact (floor (* fraction bar-width))))
(empty (- bar-width filled)))
(format #f "[~a~a]"
(make-string filled #\#)
(make-string empty #\space))))
(define* (progress-reporter/file file size
#:optional (log-port (current-output-port))
#:key (abbreviation basename))
"Return a <progress-reporter> object to show the progress of FILE's download,
which is SIZE bytes long. The progress report is written to LOG-PORT, with
ABBREVIATION used to shorten FILE for display."
(let ((start-time (current-time time-monotonic))
(transferred 0))
(define (render)
"Write the progress report to LOG-PORT."
(define elapsed
(duration->seconds
(time-difference (current-time time-monotonic) start-time)))
(if (number? size)
(let* ((% (* 100.0 (/ transferred size)))
(throughput (/ transferred elapsed))
(left (format #f " ~a ~a"
(abbreviation file)
(byte-count->string size)))
(right (format #f "~a/s ~a ~a~6,1f%"
(byte-count->string throughput)
(seconds->string elapsed)
(progress-bar %) %)))
(display "\r\x1b[K" log-port)
(display (string-pad-middle left right
(current-terminal-columns))
log-port)
(force-output log-port))
(let* ((throughput (/ transferred elapsed))
(left (format #f " ~a"
(abbreviation file)))
(right (format #f "~a/s ~a | ~a transferred"
(byte-count->string throughput)
(seconds->string elapsed)
(byte-count->string transferred))))
(display "\r\x1b[K" log-port)
(display (string-pad-middle left right
(current-terminal-columns))
log-port)
(force-output log-port))))
(progress-reporter
(start render)
;; Report the progress every 300ms or longer.
(report
(let ((rate-limited-render
(rate-limited render (make-time time-monotonic 300000000 0))))
(lambda (value)
(set! transferred value)
(rate-limited-render))))
;; Don't miss the last report.
(stop render))))
;; TODO: replace '(@ (guix build utils) dump-port))'.
(define* (dump-port* in out
#:key (buffer-size 16384)
(reporter progress-reporter/silent))
"Read as much data as possible from IN and write it to OUT, using chunks of
BUFFER-SIZE bytes. After each successful transfer of BUFFER-SIZE bytes or
less, report the total number of bytes transferred to the REPORTER, which
should be a <progress-reporter> object."
(define buffer
(make-bytevector buffer-size))
(call-with-progress-reporter reporter
(lambda (report)
(let loop ((total 0)
(bytes (get-bytevector-n! in buffer 0 buffer-size)))
(or (eof-object? bytes)
(let ((total (+ total bytes)))
(put-bytevector out buffer 0 bytes)
(report total)
(loop total (get-bytevector-n! in buffer 0 buffer-size))))))))

4
guix/scripts/download.scm
View File

@ -25,7 +25,9 @@
#:use-module (guix base32)
#:use-module ((guix download) #:hide (url-fetch))
#:use-module ((guix build download)
#:select (url-fetch current-terminal-columns))
#:select (url-fetch))
#:use-module ((guix progress)
#:select (current-terminal-columns))
#:use-module ((guix build syscalls)
#:select (terminal-columns))
#:use-module (web uri)

16
guix/scripts/substitute.scm
View File

@ -33,13 +33,12 @@
#:use-module (guix pki)
#:use-module ((guix build utils) #:select (mkdir-p dump-port))
#:use-module ((guix build download)
#:select (current-terminal-columns
progress-reporter/file
uri-abbreviation nar-uri-abbreviation
#:select (uri-abbreviation nar-uri-abbreviation
(open-connection-for-uri
. guix:open-connection-for-uri)
close-connection
store-path-abbreviation byte-count->string))
#:use-module (guix progress)
#:use-module ((guix build syscalls)
#:select (set-thread-name))
#:use-module (ice-9 rdelim)
@ -956,19 +955,22 @@ DESTINATION as a nar file. Verify the substitute against ACL."
#:abbreviation nar-uri-abbreviation)))
(progress-report-port reporter raw)))
((input pids)
;; NOTE: This 'progress' port of current process will be
;; closed here, while the child process doing the
;; reporting will close it upon exit.
(decompressed-port (and=> (narinfo-compression narinfo)
string->symbol)
progress)))
;; Unpack the Nar at INPUT into DESTINATION.
(restore-file input destination)
(close-port input)
(close-port progress)
;; Wait for the reporter to finish.
(every (compose zero? cdr waitpid) pids)
;; Skip a line after what 'progress-reporter/file' printed, and another
;; one to visually separate substitutions.
(display "\n\n" (current-error-port))
(every (compose zero? cdr waitpid) pids))))
(display "\n\n" (current-error-port)))))
;;;

30
guix/utils.scm
View File

@ -33,7 +33,6 @@
#:autoload (rnrs io ports) (make-custom-binary-input-port)
#:use-module ((rnrs bytevectors) #:select (bytevector-u8-set!))
#:use-module (guix memoization)
#:use-module (guix records)
#:use-module ((guix build utils) #:select (dump-port mkdir-p))
#:use-module ((guix build syscalls) #:select (mkdtemp! fdatasync))
#:use-module (ice-9 format)
@ -95,13 +94,7 @@
call-with-decompressed-port
compressed-output-port
call-with-compressed-output-port
canonical-newline-port
<progress-reporter>
progress-reporter
make-progress-reporter
progress-reporter?
call-with-progress-reporter))
canonical-newline-port))
;;;
@ -153,9 +146,11 @@ buffered data is lost."
(close-port in)
(dump-port input out))
(lambda ()
(close-port input)
(false-if-exception (close out))
(primitive-_exit 0))))
(child
(close-port input)
(close-port out)
(loop in (cons child pids)))))))))
@ -755,25 +750,6 @@ a location object."
(column . ,(location-column loc))
(filename . ,(location-file loc))))
;;;
;;; Progress reporter.
;;;
(define-record-type* <progress-reporter>
progress-reporter make-progress-reporter progress-reporter?
(start progress-reporter-start) ; thunk
(report progress-reporter-report) ; procedure
(stop progress-reporter-stop)) ; thunk
(define (call-with-progress-reporter reporter proc)
"Start REPORTER for progress reporting, and call @code{(@var{proc} report)}
with the resulting report procedure. When @var{proc} returns, the REPORTER is
stopped."
(match reporter
(($ <progress-reporter> start report stop)
(dynamic-wind start (lambda () (proc report)) stop))))
;;; Local Variables:
;;; eval: (put 'call-with-progress-reporter 'scheme-indent-function 1)
;;; End: