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Merge branch 'master' into core-updates

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Mark H Weaver 2015-04-13 01:25:28 -04:00
commit 1ca8ff285b
11 changed files with 421 additions and 11 deletions
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4
Makefile.am
View file

@ -51,6 +51,7 @@ MODULES = \
guix/build-system/cmake.scm \
guix/build-system/glib-or-gtk.scm \
guix/build-system/gnu.scm \
guix/build-system/haskell.scm \
guix/build-system/perl.scm \
guix/build-system/python.scm \
guix/build-system/waf.scm \
@ -240,6 +241,9 @@ tests/guix-gc.log: \
# Public key used to sign substitutes from hydra.gnu.org.
dist_pkgdata_DATA = hydra.gnu.org.pub
# Bash completion file.
dist_bashcompletion_DATA = etc/completion/bash/guix
EXTRA_DIST = \
HACKING \
ROADMAP \

7
configure.ac
View file

@ -34,6 +34,13 @@ AC_ARG_WITH(store-dir,
[storedir="/gnu/store"])
AC_SUBST(storedir)
AC_ARG_WITH([bash-completion-dir],
AC_HELP_STRING([--with-bash-completion-dir=DIR],
[name of the Bash completion directory]),
[bashcompletiondir="$withval"],
[bashcompletiondir='${sysconfdir}/bash_completion.d'])
AC_SUBST([bashcompletiondir])
dnl Better be verbose.
AC_MSG_CHECKING([for the store directory])
AC_MSG_RESULT([$storedir])

38
doc/guix.texi
View file

@ -4531,7 +4531,8 @@ the ``message of the day''.
Return a service that runs libc's name service cache daemon (nscd) with
the given @var{config}---an @code{<nscd-configuration>} object.
Optionally, @code{#:name-services} is a list of packages that provide
name service switch (NSS) modules needed by nscd.
name service switch (NSS) modules needed by nscd. @xref{Name Service
Switch}, for an example.
@end deffn
@defvr {Scheme Variable} %nscd-default-configuration
@ -4929,9 +4930,12 @@ next method in the list. The NSS configuration is given in the
@code{name-service-switch} field of @code{operating-system} declarations
(@pxref{operating-system Reference, @code{name-service-switch}}).
@c See <http://0pointer.de/lennart/projects/nss-mdns/>.
@cindex nss-mdns
@cindex .local, host name lookup
As an example, the declaration below configures the NSS to use the
@code{nss-mdns} back-end for host name lookups:
@uref{http://0pointer.de/lennart/projects/nss-mdns/, @code{nss-mdns}
back-end}, which supports host name lookups over multicast DNS (mDNS)
for host names ending in @code{.local}:
@example
(name-service-switch
@ -4957,6 +4961,34 @@ As an example, the declaration below configures the NSS to use the
(name "mdns")))))
@end example
Note that, in this case, in addition to setting the
@code{name-service-switch} of the @code{operating-system} declaration,
@code{nscd-service} must be told where to find the @code{nss-mdns}
shared library (@pxref{Base Services, @code{nscd-service}}). Since the
@code{nscd} service is part of @var{%base-services}, you may want to
customize it by adding this snippet in the operating system
configuration file:
@example
(use-modules (guix) (gnu))
(define %my-base-services
;; Replace the default nscd service with one that knows
;; about nss-mdns.
(map (lambda (mservice)
;; "Bind" the MSERVICE monadic value to inspect it.
(mlet %store-monad ((service mservice))
(if (member 'nscd (service-provision service))
(nscd-service (nscd-configuration)
#:name-services (list nss-mdns))
mservice)))
%base-services))
@end example
@noindent
@dots{} and then refer to @var{%my-base-services} instead of
@var{%base-services} in the @code{operating-system} declaration.
The reference for name service switch configuration is given below. It
is a direct mapping of the C library's configuration file format, so
please refer to the C library manual for more information (@pxref{NSS

139
etc/completion/bash/guix Normal file
View file

@ -0,0 +1,139 @@
# GNU Guix --- Functional package management for GNU
# Copyright © 2015 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/>.
# Bash completion for Guix commands.
_guix_complete_available_package ()
{
local prefix="$1"
local packages="$(${COMP_WORDS[0]} package -A "^$prefix" | cut -f1)"
COMPREPLY=($(compgen -W "$packages" -- "$prefix"))
}
_guix_complete_installed_package ()
{
local prefix="$1"
local packages="$(${COMP_WORDS[0]} package -I "^$prefix" | cut -f1)"
COMPREPLY=($(compgen -W "$packages" -- "$prefix"))
}
_guix_complete_option ()
{
local options="$(${COMP_WORDS[0]} ${COMP_WORDS[1]} --help \
| grep '^ -' \
| sed -e's/^.*--\([a-zA-Z0-9_-]\+\)\(=\?\).*/--\1\2/g' )"
compopt -o nospace
COMPREPLY=($(compgen -W "$options" -- "${COMP_WORDS[$word_count - 1]}"))
}
_guix_is_command ()
{
local word
local result="false"
for word in ${COMP_WORDS[*]}
do
if [ "$word" = "$1" ]
then
result=true
break
fi
done
$result
}
_guix_is_removing ()
{
local word
local result="false"
for word in ${COMP_WORDS[*]}
do
case "$word" in
--remove|--remove=*|-r)
result=true
break
;;
esac
done
$result
}
_guix_is_dash_L ()
{
[ "${COMP_WORDS[$COMP_CWORD - 1]}" = "-L" ] \
|| { case "${COMP_WORDS[$COMP_CWORD]}" in
--load-path=*) true;;
*) false;;
esac }
}
_guix_complete_file ()
{
# Let Readline complete file names.
compopt -o default
COMPREPLY=()
}
_guix_complete ()
{
local word_count=${#COMP_WORDS[*]}
local word_at_point="${COMP_WORDS[$COMP_CWORD]}"
if [ "$COMP_CWORD" -gt 1 ]
then
case "$word_at_point" in
-*)
_guix_complete_option "$word_at_point"
return
;;
esac
fi
case $COMP_CWORD in
1)
local subcommands="$(guix --help | grep '^ ' | cut -c 2-)"
COMPREPLY=($(compgen -W "$subcommands" -- "$word_at_point"))
;;
*)
if _guix_is_command "package"
then
if _guix_is_dash_L
then
_guix_complete_file
elif _guix_is_removing
then
_guix_complete_installed_package "$word_at_point"
else
_guix_complete_available_package "$word_at_point"
fi
elif _guix_is_command "system"
then
_guix_complete_file # TODO: complete sub-commands
elif _guix_is_command "hash"
then
_guix_complete_file
elif _guix_is_command "import" # TODO: complete sub-commands
then
_guix_complete_file
else
_guix_complete_available_package "$word_at_point"
fi
;;
esac
}
complete -F _guix_complete guix

13
gnu/build/activation.scm
View file

@ -30,6 +30,7 @@ (define-module (gnu build activation)
activate-/bin/sh
activate-modprobe
activate-firmware
activate-ptrace-attach
activate-current-system))
;;; Commentary:
@ -335,6 +336,18 @@ (define (activate-firmware directory)
(lambda (port)
(display directory port))))
(define (activate-ptrace-attach)
"Allow users to PTRACE_ATTACH their own processes.
This works around a regression introduced in the default \"security\" policy
found in Linux 3.4 onward that prevents users from attaching to their own
processes--see Yama.txt in the Linux source tree for the rationale. This
sounds like an unacceptable restriction for little or no security
improvement."
(call-with-output-file "/proc/sys/kernel/yama/ptrace_scope"
(lambda (port)
(display 0 port))))
(define %current-system
;; The system that is current (a symlink.) This is not necessarily the same

160
gnu/packages/bioinformatics.scm
View file

@ -30,13 +30,17 @@ (define-module (gnu packages bioinformatics)
#:use-module (gnu packages base)
#:use-module (gnu packages compression)
#:use-module (gnu packages java)
#:use-module (gnu packages maths)
#:use-module (gnu packages ncurses)
#:use-module (gnu packages perl)
#:use-module (gnu packages pkg-config)
#:use-module (gnu packages popt)
#:use-module (gnu packages python)
#:use-module (gnu packages statistics)
#:use-module (gnu packages swig)
#:use-module (gnu packages tbb)
#:use-module (gnu packages vim)
#:use-module (gnu packages xml)
#:use-module (gnu packages zip))
(define-public bedops
@ -507,6 +511,57 @@ (define-public flexbar
Illumina, Roche 454, and the SOLiD platform.")
(license license:gpl3)))
(define-public grit
(package
(name "grit")
(version "2.0.2")
(source (origin
(method url-fetch)
(uri (string-append
"https://github.com/nboley/grit/archive/"
version ".tar.gz"))
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
"157in84dj70wimbind3x7sy1whs3h57qfgcnj2s6lrd38fbrb7mj"))))
(build-system python-build-system)
(arguments
`(#:python ,python-2
#:phases
(alist-cons-after
'unpack 'generate-from-cython-sources
(lambda* (#:key inputs outputs #:allow-other-keys)
;; Delete these C files to force fresh generation from pyx sources.
(delete-file "grit/sparsify_support_fns.c")
(delete-file "grit/call_peaks_support_fns.c")
(substitute* "setup.py"
(("Cython.Setup") "Cython.Build")
;; Add numpy include path to fix compilation
(("pyx\", \\]")
(string-append "pyx\", ], include_dirs = ['"
(assoc-ref inputs "python-numpy")
"/lib/python2.7/site-packages/numpy/core/include/"
"']"))) #t)
%standard-phases)))
(inputs
`(("python-scipy" ,python2-scipy)
("python-numpy" ,python2-numpy)
("python-pysam" ,python2-pysam)
("python-networkx" ,python2-networkx)))
(native-inputs
`(("python-cython" ,python2-cython)
("python-setuptools" ,python2-setuptools)))
(home-page "http://grit-bio.org")
(synopsis "Tool for integrative analysis of RNA-seq type assays")
(description
"GRIT is designed to use RNA-seq, TES, and TSS data to build and quantify
full length transcript models. When none of these data sources are available,
GRIT can be run by providing a candidate set of TES or TSS sites. In
addition, GRIT can merge in reference junctions and gene boundaries. GRIT can
also be run in quantification mode, where it uses a provided GTF file and just
estimates transcript expression.")
(license license:gpl3+)))
(define-public hisat
(package
(name "hisat")
@ -1001,6 +1056,111 @@ (define-public star
;; STAR is licensed under GPLv3 or later; htslib is MIT-licensed.
(license license:gpl3+)))
(define-public shogun
(package
(name "shogun")
(version "4.0.0")
(source
(origin
(method url-fetch)
(uri (string-append
"ftp://shogun-toolbox.org/shogun/releases/"
(version-major+minor version)
"/sources/shogun-" version ".tar.bz2"))
(sha256
(base32
"159nlijnb7mnrv9za80wnm1shwvy45hgrqzn51hxy7gw4z6d6fdb"))))
(build-system cmake-build-system)
(arguments
'(#:tests? #f ;no check target
#:phases
(alist-cons-after
'unpack 'delete-broken-symlinks
(lambda _
(for-each delete-file '("applications/arts/data"
"applications/asp/data"
"applications/easysvm/data"
"applications/msplicer/data"
"applications/ocr/data"
"examples/documented/data"
"examples/documented/matlab_static"
"examples/documented/octave_static"
"examples/undocumented/data"
"examples/undocumented/matlab_static"
"examples/undocumented/octave_static"
"tests/integration/data"
"tests/integration/matlab_static"
"tests/integration/octave_static"
"tests/integration/python_modular/tests"))
#t)
(alist-cons-after
'unpack 'change-R-target-path
(lambda* (#:key outputs #:allow-other-keys)
(substitute* '("src/interfaces/r_modular/CMakeLists.txt"
"src/interfaces/r_static/CMakeLists.txt"
"examples/undocumented/r_modular/CMakeLists.txt")
(("\\$\\{R_COMPONENT_LIB_PATH\\}")
(string-append (assoc-ref outputs "out")
"/lib/R/library/")))
#t)
(alist-cons-after
'unpack 'fix-octave-modules
(lambda* (#:key outputs #:allow-other-keys)
(substitute* '("src/interfaces/octave_modular/CMakeLists.txt"
"src/interfaces/octave_static/CMakeLists.txt")
(("^include_directories\\(\\$\\{OCTAVE_INCLUDE_DIRS\\}")
"include_directories(${OCTAVE_INCLUDE_DIRS} ${OCTAVE_INCLUDE_DIRS}/octave"))
;; change target directory
(substitute* "src/interfaces/octave_modular/CMakeLists.txt"
(("\\$\\{OCTAVE_OCT_LOCAL_API_FILE_DIR\\}")
(string-append (assoc-ref outputs "out")
"/share/octave/packages")))
#t)
(alist-cons-before
'build 'set-HOME
;; $HOME needs to be set at some point during the build phase
(lambda _ (setenv "HOME" "/tmp") #t)
%standard-phases))))
#:configure-flags
(list "-DUSE_SVMLIGHT=OFF" ;disable proprietary SVMLIGHT
;;"-DJavaModular=ON" ;requires unpackaged jblas
;;"-DRubyModular=ON" ;requires unpackaged ruby-narray
;;"-DPerlModular=ON" ;"FindPerlLibs" does not exist
;;"-DLuaModular=ON" ;fails because lua doesn't build pkgconfig file
"-DOctaveModular=ON"
"-DOctaveStatic=ON"
"-DPythonModular=ON"
"-DPythonStatic=ON"
"-DRModular=ON"
"-DRStatic=ON"
"-DCmdLineStatic=ON")))
(inputs
`(("python" ,python)
("numpy" ,python-numpy)
("r" ,r)
("octave" ,octave)
("swig" ,swig)
("hdf5" ,hdf5)
("atlas" ,atlas)
("arpack" ,arpack-ng)
("lapack" ,lapack)
("glpk" ,glpk)
("libxml2" ,libxml2)
("lzo" ,lzo)
("zlib" ,zlib)))
(native-inputs
`(("pkg-config" ,pkg-config)))
(home-page "http://shogun-toolbox.org/")
(synopsis "Machine learning toolbox")
(description
"The Shogun Machine learning toolbox provides a wide range of unified and
efficient Machine Learning (ML) methods. The toolbox seamlessly allows to
combine multiple data representations, algorithm classes, and general purpose
tools. This enables both rapid prototyping of data pipelines and extensibility
in terms of new algorithms.")
(license license:gpl3+)))
(define-public vcftools
(package
(name "vcftools")

6
gnu/packages/emacs.scm
View file

@ -1,7 +1,7 @@
;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2014 Taylan Ulrich Bayirli/Kammer <taylanbayirli@gmail.com>
;;; Copyright © 2013, 2014, 2015 Ludovic Courtès <ludo@gnu.org>
;;; Copyright © 2014 Mark H Weaver <mhw@netris.org>
;;; Copyright © 2014, 2015 Mark H Weaver <mhw@netris.org>
;;; Copyright © 2014 Alex Kost <alezost@gmail.com>
;;;
;;; This file is part of GNU Guix.
@ -57,14 +57,14 @@ (define-module (gnu packages emacs)
(define-public emacs
(package
(name "emacs")
(version "24.4")
(version "24.5")
(source (origin
(method url-fetch)
(uri (string-append "mirror://gnu/emacs/emacs-"
version ".tar.xz"))
(sha256
(base32
"1zflm6ac34s6v166p58ilxrxbxjm0q2wfc25f8y0mjml1lbr3qs7"))))
"0kn3rzm91qiswi0cql89kbv6mqn27rwsyjfb8xmwy9m5s8fxfiyx"))))
(build-system glib-or-gtk-build-system)
(arguments
'(#:phases (alist-cons-before

39
gnu/packages/gstreamer.scm
View file

@ -20,7 +20,7 @@
;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
(define-module (gnu packages gstreamer)
#:use-module ((guix licenses) #:select (lgpl2.0+ bsd-2 bsd-3))
#:use-module ((guix licenses) #:select (lgpl2.0+ bsd-2 bsd-3 gpl2+))
#:use-module (guix packages)
#:use-module (guix download)
#:use-module (guix build-system gnu)
@ -39,6 +39,7 @@ (define-module (gnu packages gstreamer)
#:use-module (gnu packages xiph)
#:use-module (gnu packages pkg-config)
#:use-module (gnu packages python)
#:use-module (gnu packages yasm)
#:use-module (gnu packages xml))
(define-public orc
@ -247,6 +248,42 @@ (define-public gst-plugins-good
developers consider to have good quality code and correct functionality.")
(license lgpl2.0+)))
(define-public gst-libav
(package
(name "gst-libav")
(version "1.4.5")
(source (origin
(method url-fetch)
(uri (string-append
"http://gstreamer.freedesktop.org/src/" name "/"
name "-" version ".tar.xz"))
(sha256
(base32
"1g7vg9amh3cc3nmc415h6g2rqxqi4wgwqi08hxfbpwq48ri64p30"))))
(build-system gnu-build-system)
(arguments
'(#:phases
(modify-phases %standard-phases
(add-before configure patch-/bin/sh
(lambda _
(substitute* "gst-libs/ext/libav/configure"
(("#! /bin/sh")
(string-append "#! "(which "sh")))))))))
(native-inputs
`(("pkg-config" ,pkg-config)
("python" ,python)
("yasm" ,yasm)))
(inputs
`(("gst-plugins-base" ,gst-plugins-base)
("orc" ,orc)
("zlib" ,zlib)))
(home-page "http://gstreamer.freedesktop.org/")
(synopsis "Plugins for the GStreamer multimedia library")
(description
"This GStreamer plugin supports a large number of audio and video
compression formats through the use of the libav library.")
(license gpl2+)))
(define-public gst-plugins-base-0.10
(package (inherit gst-plugins-base)
(version "0.10.36")

6
gnu/packages/man.scm
View file

@ -1,5 +1,5 @@
;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2012, 2014 Ludovic Courtès <ludo@gnu.org>
;;; Copyright © 2012, 2014, 2015 Ludovic Courtès <ludo@gnu.org>
;;; Copyright © 2014 David Thompson <dthompson2@worcester.edu>
;;; Copyright © 2015 Ricardo Wurmus <rekado@elephly.net>
;;;
@ -119,7 +119,7 @@ (define-public man-db
(define-public man-pages
(package
(name "man-pages")
(version "3.69")
(version "3.82")
(source (origin
(method url-fetch)
(uri (string-append
@ -127,7 +127,7 @@ (define-public man-pages
version ".tar.xz"))
(sha256
(base32
"18zzmdzjihdnyg4vamk0jp6v6826vrsgal3kqqxvfq9bzyrh8xm2"))))
"1c8q618shf469nfp55qrwjv9630fgq5abfk946xya9hw1bfp6wjl"))))
(build-system gnu-build-system)
(arguments
'(#:phases (alist-delete 'configure %standard-phases)

2
gnu/services/base.scm
View file

@ -499,7 +499,7 @@ (define* (nscd-service #:optional (config %nscd-default-configuration)
"Return a service that runs libc's name service cache daemon (nscd) with the
given @var{config}---an @code{<nscd-configuration>} object. Optionally,
@code{#:name-services} is a list of packages that provide name service switch
(NSS) modules needed by nscd."
(NSS) modules needed by nscd. @xref{Name Service Switch}, for an example."
(mlet %store-monad ((nscd.conf (nscd.conf-file config)))
(return (service
(documentation "Run libc's name service cache daemon (nscd).")

18
gnu/system.scm
View file

@ -1,5 +1,6 @@
;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2013, 2014, 2015 Ludovic Courtès <ludo@gnu.org>
;;; Copyright © 2015 Mark H Weaver <mhw@netris.org>
;;;
;;; This file is part of GNU Guix.
;;;
@ -680,6 +681,9 @@ (define group-specs
(activate-firmware
(string-append #$firmware "/lib/firmware"))
;; Let users debug their own processes!
(activate-ptrace-attach)
;; Run the services' activation snippets.
;; TODO: Use 'load-compiled'.
(for-each primitive-load '#$actions)
@ -695,6 +699,20 @@ (define (operating-system-boot-script os)
(dmd-conf (dmd-configuration-file services)))
(gexp->file "boot"
#~(begin
(use-modules (guix build utils))
;; Clean out /tmp and /var/run.
;;
;; XXX This needs to happen before service activations, so
;; it has to be here, but this also implicitly assumes
;; that /tmp and /var/run are on the root partition.
(false-if-exception (delete-file-recursively "/tmp"))
(false-if-exception (delete-file-recursively "/var/run"))
(false-if-exception (mkdir "/tmp"))
(false-if-exception (chmod "/tmp" #o1777))
(false-if-exception (mkdir "/var/run"))
(false-if-exception (chmod "/var/run" #o755))
;; Activate the system.
;; TODO: Use 'load-compiled'.
(primitive-load #$activate)