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Merge branch 'master' into core-updates

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Mark H Weaver 2016-01-24 21:04:54 -05:00
commit 412bee5e29
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4
Makefile.am
View file

@ -240,8 +240,10 @@ SCM_TESTS = \
tests/challenge.scm \
tests/cve.scm \
tests/file-systems.scm \
tests/system.scm \
tests/services.scm \
tests/containers.scm
tests/containers.scm \
tests/import-utils.scm
if HAVE_GUILE_JSON

5
build-aux/hydra/gnu-system.scm
View file

@ -1,5 +1,5 @@
;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2012, 2013, 2014, 2015 Ludovic Courtès <ludo@gnu.org>
;;; Copyright © 2012, 2013, 2014, 2015, 2016 Ludovic Courtès <ludo@gnu.org>
;;;
;;; This file is part of GNU Guix.
;;;
@ -78,6 +78,9 @@ (define* (package->alist store package system
(license . ,(package-license package))
(home-page . ,(package-home-page package))
(maintainers . ("bug-guix@gnu.org"))
(max-silent-time . ,(or (assoc-ref (package-properties package)
'max-silent-time)
3600)) ; 1 hour by default
(timeout . ,(or (assoc-ref (package-properties package) 'timeout)
72000)))) ; 20 hours by default

143
doc/guix.texi
View file

@ -399,6 +399,21 @@ for instance with:
# ln -s /var/guix/profiles/per-user/root/guix-profile/bin/guix
@end example
It is also a good idea to make the Info version of this manual available
there:
@example
# mkdir -p /usr/local/share/info
# cd /usr/local/share/info
# for i in /var/guix/profiles/per-user/root/guix-profile/share/info/* ;
do ln -s $i ; done
@end example
That way, assuming @file{/usr/local/share/info} is in the search path,
running @command{info guix} will open this manual (@pxref{Other Info
Directories,,, texinfo, GNU Texinfo}, for more details on changing the
Info search path.)
@item
To use substitutes from @code{hydra.gnu.org} (@pxref{Substitutes}),
authorize them:
@ -754,7 +769,7 @@ machines, since offloading works by invoking the @code{guix archive} and
this is the case by running:
@example
lsh build-machine guile -c '(use-modules (guix config))'
lsh build-machine guile -c "'(use-modules (guix config))'"
@end example
There's one last thing to do once @file{machines.scm} is in place. As
@ -3973,6 +3988,14 @@ Keep the build tree of failed builds. Thus, if a build fail, its build
tree is kept under @file{/tmp}, in a directory whose name is shown at
the end of the build log. This is useful when debugging build issues.
@item --keep-going
@itemx -k
Keep going when some of the derivations fail to build; return only once
all the builds have either completed or failed.
The default behavior is to stop as soon as one of the specified
derivations has failed.
@item --dry-run
@itemx -n
Do not build the derivations.
@ -4271,11 +4294,12 @@ guix import cpan Acme::Boolean
@item cran
@cindex CRAN
@cindex Bioconductor
Import meta-data from @uref{http://cran.r-project.org/, CRAN}, the
central repository for the @uref{http://r-project.org, GNU@tie{}R
statistical and graphical environment}.
Information is extracted from the package's DESCRIPTION file.
Information is extracted from the package's @code{DESCRIPTION} file.
The command command below imports meta-data for the @code{Cairo}
R package:
@ -4284,6 +4308,21 @@ R package:
guix import cran Cairo
@end example
When @code{--archive=bioconductor} is added, meta-data is imported from
@uref{http://www.bioconductor.org/, Bioconductor}, a repository of R
packages for for the analysis and comprehension of high-throughput
genomic data in bioinformatics.
Information is extracted from a package's @code{DESCRIPTION} file
published on the web interface of the Bioconductor SVN repository.
The command command below imports meta-data for the @code{GenomicRanges}
R package:
@example
guix import cran --archive=bioconductor GenomicRanges
@end example
@item nix
Import meta-data from a local copy of the source of the
@uref{http://nixos.org/nixpkgs/, Nixpkgs distribution}@footnote{This
@ -4482,6 +4521,8 @@ the updater for GNOME packages;
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;
@item pypi
the updater for @uref{https://pypi.python.org, PyPI} packages.
@end table
@ -5674,17 +5715,23 @@ above, such as @code{host-name} and @code{bootloader}, are mandatory.
Others, such as @code{packages} and @code{services}, can be omitted, in
which case they get a default value.
Below we discuss the effect of some of the most important fields
(@pxref{operating-system Reference}, for details about all the available
fields), and how to @dfn{instantiate} the operating system using
@command{guix system}.
@unnumberedsubsubsec Globally-Visible Packages
@vindex %base-packages
The @code{packages} field lists
packages that will be globally visible on the system, for all user
accounts---i.e., in every user's @code{PATH} environment variable---in
addition to the per-user profiles (@pxref{Invoking guix package}). The
@var{%base-packages} variable provides all the tools one would expect
for basic user and administrator tasks---including the GNU Core
Utilities, the GNU Networking Utilities, the GNU Zile lightweight text
editor, @command{find}, @command{grep}, etc. The example above adds
tcpdump to those, taken from the @code{(gnu packages admin)} module
(@pxref{Package Modules}).
The @code{packages} field lists packages that will be globally visible
on the system, for all user accounts---i.e., in every user's @code{PATH}
environment variable---in addition to the per-user profiles
(@pxref{Invoking guix package}). The @var{%base-packages} variable
provides all the tools one would expect for basic user and administrator
tasks---including the GNU Core Utilities, the GNU Networking Utilities,
the GNU Zile lightweight text editor, @command{find}, @command{grep},
etc. The example above adds tcpdump to those, taken from the @code{(gnu
packages admin)} module (@pxref{Package Modules}).
@findex specification->package
Referring to packages by variable name, like @var{tcpdump} above, has
@ -5706,6 +5753,8 @@ version:
%base-packages)))
@end lisp
@unnumberedsubsubsec System Services
@vindex %base-services
The @code{services} field lists @dfn{system services} to be made
available when the system starts (@pxref{Services}).
@ -5754,10 +5803,24 @@ more, would look like this:
@xref{Desktop Services}, for the exact list of services provided by
@var{%desktop-services}. @xref{X.509 Certificates}, for background
information about the @code{nss-certs} package that is used here.
@xref{operating-system Reference}, for details about all the available
@code{operating-system} fields.
Assuming the above snippet is stored in the @file{my-system-config.scm}
Again, @var{%desktop-services} is just a list of service objects. If
you want to remove services from there, you can do so using the
procedures for list filtering (@pxref{SRFI-1 Filtering and
Partitioning,,, guile, GNU Guile Reference Manual}). For instance, the
following expression returns a list that contains all the services in
@var{%desktop-services} minus the Avahi service:
@example
(remove (lambda (service)
(eq? (service-kind service) avahi-service-type))
%desktop-services)
@end example
@unnumberedsubsubsec Instantiating the System
Assuming the @code{operating-system} declaration
is stored in the @file{my-system-config.scm}
file, the @command{guix system reconfigure my-system-config.scm} command
instantiates that configuration, and makes it the default GRUB boot
entry (@pxref{Invoking guix system}).
@ -5779,6 +5842,8 @@ something went wrong with the latest generation. Reassuring, no? The
@command{guix system list-generations} command lists the system
generations available on disk.
@unnumberedsubsubsec The Programming Interface
At the Scheme level, the bulk of an @code{operating-system} declaration
is instantiated with the following monadic procedure (@pxref{The Store
Monad}):
@ -5792,6 +5857,11 @@ the packages, configuration files, and other supporting files needed to
instantiate @var{os}.
@end deffn
This procedure is provided by the @code{(gnu system)} module. Along
with @code{(gnu services)} (@pxref{Services}), this module contains the
guts of GuixSD. Make sure to visit it!
@node operating-system Reference
@subsection @code{operating-system} Reference
@ -6288,7 +6358,7 @@ using the @code{locale} field of the @code{operating-system} declaration
That locale must be among the @dfn{locale definitions} that are known to
the system---and these are specified in the @code{locale-definitions}
slot of @code{operating-system}. The default value includes locale
definition for some widely used locales, but not for all the available
definitions for some widely used locales, but not for all the available
locales, in order to save space.
If the locale specified in the @code{locale} field is not among the
@ -6762,13 +6832,14 @@ and lines for hidden services added via @code{tor-hidden-service}. Run
@command{man tor} for information about the configuration file.
@end deffn
@cindex hidden service
@deffn {Scheme Procedure} tor-hidden-service @var{name} @var{mapping}
Define a new Tor @dfn{hidden service} called @var{name} and implementing
@var{mapping}. @var{mapping} is a list of port/host tuples, such as:
@example
'((22 \"127.0.0.1:22\")
(80 \"127.0.0.1:8080\"))
'((22 "127.0.0.1:22")
(80 "127.0.0.1:8080"))
@end example
In this example, port 22 of the hidden service is mapped to local port 22, and
@ -8907,7 +8978,7 @@ Now that you know all the features that initial RAM disks produced by
further.
@deffn {Monadic Procedure} base-initrd @var{file-systems} @
[#:qemu-networking? #f] [#:virtio? #f] [#:volatile-root? #f] @
[#:qemu-networking? #f] [#:virtio? #t] [#:volatile-root? #f] @
[#:extra-modules '()] [#:mapped-devices '()]
Return a monadic derivation that builds a generic initrd. @var{file-systems} is
a list of file-systems to be mounted by the initrd, possibly in addition to
@ -10060,6 +10131,40 @@ If we also wanted GTK+ 3.8.2, this would be packaged as
...))
@end example
@c See <https://lists.gnu.org/archive/html/guix-devel/2016-01/msg00425.html>,
@c for a discussion of what follows.
@cindex version number, for VCS snapshots
Occasionally, we package snapshots of upstream's version control system
(VCS) instead of formal releases. This should remain exceptional,
because it is up to upstream developers to clarify what the stable
release is. Yet, it is sometimes necessary. So, what should we put in
the @code{version} field?
Clearly, we need to make the commit identifier of the VCS snapshot
visible in the version string, but we also need to make sure that the
version string is monotonically increasing so that @command{guix package
--upgrade} can determine which version is newer. Since commit
identifiers, notably with Git, are not monotonically increasing, we add
a revision number that we increase each time we upgrade to a newer
snapshot. The resulting version string looks like this:
@example
2.0.11-3.cabba9e
^ ^ ^
| | `-- upstream commit ID
| |
| `--- Guix package revision
|
latest upstream version
@end example
It is a good idea to strip commit identifiers in the @code{version}
field to, say, 7 digits. It avoids an aesthetic annoyance (assuming
aesthetics have a role to play here) as well as problems related to OS
limits such as the maximum shebang length (127 bytes for the Linux
kernel.) It is best to use the full commit identifiers in
@code{origin}s, though, to avoid ambiguities.
@node Synopses and Descriptions
@subsection Synopses and Descriptions

6
gnu-system.am
View file

@ -1,6 +1,6 @@
# GNU Guix --- Functional package management for GNU
# Copyright © 2012, 2013, 2014, 2015, 2016 Ludovic Courtès <ludo@gnu.org>
# Copyright © 2013, 2014, 2015 Andreas Enge <andreas@enge.fr>
# Copyright © 2013, 2014, 2015, 2016 Andreas Enge <andreas@enge.fr>
# Copyright © 2013, 2014, 2015, 2016 Mark H Weaver <mhw@netris.org>
#
# This file is part of GNU Guix.
@ -177,6 +177,7 @@ GNU_SYSTEM_MODULES = \
gnu/packages/kodi.scm \
gnu/packages/language.scm \
gnu/packages/ldc.scm \
gnu/packages/lego.scm \
gnu/packages/less.scm \
gnu/packages/lesstif.scm \
gnu/packages/libcanberra.scm \
@ -408,6 +409,7 @@ dist_patch_DATA = \
gnu/packages/patches/agg-am_c_prototype.patch \
gnu/packages/patches/alsa-lib-mips-atomic-fix.patch \
gnu/packages/patches/apr-skip-getservbyname-test.patch \
gnu/packages/patches/arb-ldconfig.patch \
gnu/packages/patches/asymptote-gsl2.patch \
gnu/packages/patches/ath9k-htc-firmware-binutils.patch \
gnu/packages/patches/ath9k-htc-firmware-gcc.patch \
@ -568,6 +570,7 @@ dist_patch_DATA = \
gnu/packages/patches/libwmf-CVE-2015-4695.patch \
gnu/packages/patches/libwmf-CVE-2015-4696.patch \
gnu/packages/patches/libxslt-CVE-2015-7995.patch \
gnu/packages/patches/linux-libre-CVE-2016-0728.patch \
gnu/packages/patches/lirc-localstatedir.patch \
gnu/packages/patches/libpthread-glibc-preparation.patch \
gnu/packages/patches/lm-sensors-hwmon-attrs.patch \
@ -686,6 +689,7 @@ dist_patch_DATA = \
gnu/packages/patches/tidy-CVE-2015-5522+5523.patch \
gnu/packages/patches/tinyxml-use-stl.patch \
gnu/packages/patches/tk-find-library.patch \
gnu/packages/patches/tophat-build-with-later-seqan.patch \
gnu/packages/patches/torsocks-dns-test.patch \
gnu/packages/patches/tvtime-gcc41.patch \
gnu/packages/patches/tvtime-pngoutput.patch \

2
gnu/build/linux-container.scm
View file

@ -41,7 +41,7 @@ (define (unprivileged-user-namespace-supported?)
"Return #t if user namespaces can be created by unprivileged users."
(let ((userns-file "/proc/sys/kernel/unprivileged_userns_clone"))
(if (file-exists? userns-file)
(string=? "1" (call-with-input-file userns-file read-string))
(eqv? #\1 (call-with-input-file userns-file read-char))
#t)))
(define (setgroups-supported?)

27
gnu/packages/admin.scm
View file

@ -6,6 +6,7 @@
;;; Copyright © 2015 Taylan Ulrich Bayırlı/Kammer <taylanbayirli@gmail.com>
;;; Copyright © 2015 Alex Sassmannshausen <alex.sassmannshausen@gmail.com>
;;; Copyright © 2015 Eric Dvorsak <eric@dvorsak.fr>
;;; Copyright © 2016 Leo Famulari <leo@famulari.name>
;;;
;;; This file is part of GNU Guix.
;;;
@ -392,7 +393,7 @@ (define-public isc-dhcp
(bind-minor-version "9")
(bind-patch-version "8")
(bind-release-type "-P")
(bind-release-version "2")
(bind-release-version "3")
(bind-version (string-append bind-major-version
"."
bind-minor-version
@ -508,7 +509,7 @@ (define-public isc-dhcp
"/bind-" bind-version ".tar.gz"))
(sha256
(base32
"0agkpmpna7s67la13krn4xlhwhdjpazmljxlq0zbjdwnw4k1k17m"))))
"01qa17479jghy90lb2j8b1bpg3ay6k6aaajpigyirwzsvyc9yj3a"))))
;; When cross-compiling, we need the cross Coreutils and sed.
;; Otherwise just use those from %FINAL-INPUTS.
@ -1377,3 +1378,25 @@ (define-public autojump
you use the most from the command line and allows you to \"jump\" to
frequently used directories by typing only a small pattern.")
(license license:gpl3+)))
(define-public iftop
(package
(name "iftop")
(version "1.0pre4")
(source (origin
(method url-fetch)
(uri (string-append "http://www.ex-parrot.com/~pdw/iftop/download"
"/iftop-" version ".tar.gz"))
(sha256
(base32
"15sgkdyijb7vbxpxjavh5qm5nvyii3fqcg9mzvw7fx8s6zmfwczp"))))
(build-system gnu-build-system)
(inputs
`(("libpcap" ,libpcap)
("ncurses" ,ncurses)))
(synopsis "Monitor network usage")
(description "Iftop does for network usage what @command{top} does
for CPU usage. It listens to network traffic on a named interface and
displays a table of current bandwidth usage by pairs of hosts.")
(home-page "http://www.ex-parrot.com/~pdw/iftop/")
(license license:gpl3)))

5
gnu/packages/algebra.scm
View file

@ -238,7 +238,7 @@ (define-public flint
(define-public arb
(package
(name "arb")
(version "2.7.0")
(version "2.8.1")
(source (origin
(method url-fetch)
(uri (string-append
@ -247,7 +247,8 @@ (define-public arb
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
"1rwkffs57v8mry63rq8l2dyw69zfs9rg5fpbfllqp3nkjnkp1fly"))))
"04hhcpshfkcq9fr4hixbhpps50yf9drk62xgkvlcaj5kb4nyrx7l"))
(patches (map search-patch '("arb-ldconfig.patch")))))
(build-system gnu-build-system)
(propagated-inputs
`(("flint" ,flint))) ; flint.h is included by arf.h

6
gnu/packages/audio.scm
View file

@ -3,7 +3,7 @@
;;; Copyright © 2015 Taylan Ulrich Bayırlı/Kammer <taylanbayirli@gmail.com>
;;; Copyright © 2015 Andreas Enge <andreas@enge.fr>
;;; Copyright © 2015 Alex Kost <alezost@gmail.com>
;;; Copyright © 2015 Mark H Weaver <mhw@netris.org>
;;; Copyright © 2015, 2016 Mark H Weaver <mhw@netris.org>
;;;
;;; This file is part of GNU Guix.
;;;
@ -1535,14 +1535,14 @@ (define-public libmodplug
(define-public libxmp
(package
(name "libxmp")
(version "4.3.8")
(version "4.3.10")
(source (origin
(method url-fetch)
(uri (string-append "mirror://sourceforge/xmp/libxmp/"
name "-" version ".tar.gz"))
(sha256
(base32
"0h06091hlpgc6ds4pjmfq8sx4snw7av3nhny180q4pwfyasjb6ny"))))
"1gm5xa0ca7ypcbj3bkmj3k1vvzl7nkch8gjyrm8p1a9vgzr0n761"))))
(build-system gnu-build-system)
(home-page "http://xmp.sourceforge.net/")
(synopsis "Module player library")

230
gnu/packages/bioinformatics.scm
View file

@ -654,6 +654,73 @@ (define-public bowtie
(supported-systems '("x86_64-linux"))
(license license:gpl3+)))
(define-public tophat
(package
(name "tophat")
(version "2.1.0")
(source (origin
(method url-fetch)
(uri (string-append
"http://ccb.jhu.edu/software/tophat/downloads/tophat-"
version ".tar.gz"))
(sha256
(base32
"168zlzykq622zbgkh90a90f1bdgsxkscq2zxzbj8brq80hbjpyp7"))
(patches (list (search-patch "tophat-build-with-later-seqan.patch")))
(modules '((guix build utils)))
(snippet
'(begin
;; Remove bundled SeqAn and samtools
(delete-file-recursively "src/SeqAn-1.3")
(delete-file-recursively "src/samtools-0.1.18")
#t))))
(build-system gnu-build-system)
(arguments
'(#:parallel-build? #f ; not supported
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'use-system-samtools
(lambda* (#:key inputs #:allow-other-keys)
(substitute* "src/Makefile.in"
(("(noinst_LIBRARIES = )\\$\\(SAMLIB\\)" _ prefix) prefix)
(("\\$\\(SAMPROG\\): \\$\\(SAMLIB\\)") "")
(("SAMPROG = samtools_0\\.1\\.18") "")
(("\\$\\(samtools_0_1_18_SOURCES\\)") "")
(("am__EXEEXT_1 = samtools_0\\.1\\.18\\$\\(EXEEXT\\)") ""))
(substitute* '("src/common.cpp"
"src/tophat.py")
(("samtools_0.1.18") (which "samtools")))
(substitute* '("src/common.h"
"src/bam2fastx.cpp")
(("#include \"bam.h\"") "#include <samtools/bam.h>")
(("#include \"sam.h\"") "#include <samtools/sam.h>"))
(substitute* '("src/bwt_map.h"
"src/map2gtf.h"
"src/align_status.h")
(("#include <bam.h>") "#include <samtools/bam.h>")
(("#include <sam.h>") "#include <samtools/sam.h>"))
#t)))))
(inputs
`(("boost" ,boost)
("bowtie" ,bowtie)
("samtools" ,samtools-0.1)
("ncurses" ,ncurses)
("python" ,python-2)
("perl" ,perl)
("zlib" ,zlib)
("seqan" ,seqan)))
(home-page "http://ccb.jhu.edu/software/tophat/index.shtml")
(synopsis "Spliced read mapper for RNA-Seq data")
(description
"TopHat is a fast splice junction mapper for nucleotide sequence
reads produced by the RNA-Seq method. It aligns RNA-Seq reads to
mammalian-sized genomes using the ultra high-throughput short read
aligner Bowtie, and then analyzes the mapping results to identify
splice junctions between exons.")
;; TopHat is released under the Boost Software License, Version 1.0
;; See https://github.com/infphilo/tophat/issues/11#issuecomment-121589893
(license license:boost1.0)))
(define-public bwa
(package
(name "bwa")
@ -915,6 +982,64 @@ (define-public crossmap
file formats including SAM/BAM, Wiggle/BigWig, BED, GFF/GTF, VCF.")
(license license:gpl2+)))
(define-public cufflinks
(package
(name "cufflinks")
(version "2.2.1")
(source (origin
(method url-fetch)
(uri (string-append "http://cole-trapnell-lab.github.io/"
"cufflinks/assets/downloads/cufflinks-"
version ".tar.gz"))
(sha256
(base32
"1bnm10p8m7zq4qiipjhjqb24csiqdm1pwc8c795z253r2xk6ncg8"))))
(build-system gnu-build-system)
(arguments
`(#:make-flags
(list
;; The includes for "eigen" are located in a subdirectory.
(string-append "EIGEN_CPPFLAGS="
"-I" (assoc-ref %build-inputs "eigen")
"/include/eigen3/")
;; Cufflinks must be linked with various boost libraries.
(string-append "LDFLAGS="
(string-join '("-lboost_system"
"-lboost_serialization"
"-lboost_thread"))))
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'fix-search-for-bam
(lambda _
(substitute* '("ax_bam.m4"
"configure"
"src/hits.h")
(("<bam/sam\\.h>") "<samtools/sam.h>")
(("<bam/bam\\.h>") "<samtools/bam.h>")
(("<bam/version\\.hpp>") "<samtools/version.h>"))
#t)))
#:configure-flags
(list (string-append "--with-bam="
(assoc-ref %build-inputs "samtools")))))
(inputs
`(("eigen" ,eigen)
("samtools" ,samtools-0.1)
("htslib" ,htslib)
("boost" ,boost)
("python" ,python-2)
("zlib" ,zlib)))
(home-page "http://cole-trapnell-lab.github.io/cufflinks/")
(synopsis "Transcriptome assembly and RNA-Seq expression analysis")
(description
"Cufflinks assembles RNA transcripts, estimates their abundances,
and tests for differential expression and regulation in RNA-Seq
samples. It accepts aligned RNA-Seq reads and assembles the
alignments into a parsimonious set of transcripts. Cufflinks then
estimates the relative abundances of these transcripts based on how
many reads support each one, taking into account biases in library
preparation protocols.")
(license license:boost1.0)))
(define-public cutadapt
(package
(name "cutadapt")
@ -3016,40 +3141,107 @@ (define-public snap-aligner
of these reads to align data quickly through a hash-based indexing scheme.")
(license license:asl2.0)))
(define-public sortmerna
(package
(name "sortmerna")
(version "2.0")
(source
(origin
(method url-fetch)
(uri (string-append
"https://github.com/biocore/sortmerna/archive/"
version ".tar.gz"))
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
"1670a92x1vvkacnvgr2i5xac3ls6lp4pc3n0bccnmllsnymggcf0"))))
(build-system gnu-build-system)
(outputs '("out" ;for binaries
"db")) ;for sequence databases
(arguments
`(#:phases
(modify-phases %standard-phases
(replace 'install
(lambda* (#:key outputs #:allow-other-keys)
(let* ((out (assoc-ref outputs "out"))
(bin (string-append out "/bin"))
(db (assoc-ref outputs "db"))
(share
(string-append db "/share/sortmerna/rRNA_databases")))
(install-file "sortmerna" bin)
(install-file "indexdb_rna" bin)
(for-each (lambda (file)
(install-file file share))
(find-files "rRNA_databases" ".*fasta"))
#t))))))
(home-page "http://bioinfo.lifl.fr/RNA/sortmerna")
(synopsis "Biological sequence analysis tool for NGS reads")
(description
"SortMeRNA is a biological sequence analysis tool for filtering, mapping
and operational taxonomic unit (OTU) picking of next generation
sequencing (NGS) reads. The core algorithm is based on approximate seeds and
allows for fast and sensitive analyses of nucleotide sequences. The main
application of SortMeRNA is filtering rRNA from metatranscriptomic data.")
(license license:lgpl3)))
(define-public star
(package
(name "star")
(version "2.4.2a")
(version "2.5.1b")
(source (origin
(method url-fetch)
(uri (string-append
"https://github.com/alexdobin/STAR/archive/STAR_"
version ".tar.gz"))
(uri (string-append "https://github.com/alexdobin/STAR/archive/"
version ".tar.gz"))
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
"1c3rnm7r5l0kl3d04gl1g7938xqf1c2l0mla87rlplqg1hcns5mc"))
"0wzcfhkg10apnh0y73xlarfa79xxwxdizicbdl11wb48awk44iq4"))
(modules '((guix build utils)))
(snippet
'(substitute* "source/Makefile"
(("/bin/rm") "rm")))))
'(begin
(substitute* "source/Makefile"
(("/bin/rm") "rm"))
;; Remove pre-built binaries and bundled htslib sources.
(delete-file-recursively "bin/MacOSX_x86_64")
(delete-file-recursively "bin/Linux_x86_64")
(delete-file-recursively "source/htslib")
#t))))
(build-system gnu-build-system)
(arguments
'(#:tests? #f ;no check target
#:make-flags '("STAR")
#:phases
(alist-cons-after
'unpack 'enter-source-dir (lambda _ (chdir "source"))
(alist-replace
'install
(lambda* (#:key outputs #:allow-other-keys)
(let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
(install-file "STAR" bin)))
(alist-delete
'configure %standard-phases)))))
(modify-phases %standard-phases
(add-after 'unpack 'enter-source-dir
(lambda _ (chdir "source") #t))
(add-after 'enter-source-dir 'do-not-use-bundled-htslib
(lambda _
(substitute* "Makefile"
(("(Depend.list: \\$\\(SOURCES\\) parametersDefault\\.xxd) htslib"
_ prefix) prefix))
(substitute* '("BAMfunctions.cpp"
"signalFromBAM.h"
"bam_cat.h"
"bam_cat.c"
"STAR.cpp"
"bamRemoveDuplicates.cpp")
(("#include \"htslib/([^\"]+\\.h)\"" _ header)
(string-append "#include <" header ">")))
(substitute* "IncludeDefine.h"
(("\"htslib/(htslib/[^\"]+.h)\"" _ header)
(string-append "<" header ">")))
#t))
(replace 'install
(lambda* (#:key outputs #:allow-other-keys)
(let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
(install-file "STAR" bin))
#t))
(delete 'configure))))
(native-inputs
`(("vim" ,vim))) ; for xxd
(inputs
`(("zlib" ,zlib)))
`(("htslib" ,htslib)
("zlib" ,zlib)))
(home-page "https://github.com/alexdobin/STAR")
(synopsis "Universal RNA-seq aligner")
(description
@ -4002,7 +4194,7 @@ (define-public r-genomation
(define-public r-qtl
(package
(name "r-qtl")
(version "1.37-11")
(version "1.38-4")
(source
(origin
(method url-fetch)
@ -4010,7 +4202,7 @@ (define-public r-qtl
version ".tar.gz"))
(sha256
(base32
"0h20d36mww7ljp51pfs66xq33yq4b4fwq9nsh02dpmfhlaxgx1xi"))))
"0rv9xhp8lyldpgwxqirhyjqvg07dr5x4x1x2jpyj37dada9ccyx3"))))
(build-system r-build-system)
(home-page "http://rqtl.org/")
(synopsis "R package for analyzing QTL experiments in genetics")

44
gnu/packages/bittorrent.scm
View file

@ -1,6 +1,7 @@
;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2014 Taylan Ulrich Bayirli/Kammer <taylanbayirli@gmail.com>
;;; Copyright © 2014, 2015 Ludovic Courtès <ludo@gnu.org>
;;; Copyright © 2016 Leo Famulari <leo@famulari.name>
;;;
;;; This file is part of GNU Guix.
;;;
@ -21,6 +22,7 @@ (define-module (gnu packages bittorrent)
#:use-module (guix packages)
#:use-module (guix download)
#:use-module (guix build-system gnu)
#:use-module (guix build-system python)
#:use-module (guix build-system glib-or-gtk)
#:use-module ((guix licenses) #:prefix l:)
#:use-module (gnu packages libevent)
@ -33,6 +35,7 @@ (define-module (gnu packages bittorrent)
#:use-module (gnu packages gtk)
#:use-module (gnu packages check)
#:use-module (gnu packages ncurses)
#:use-module (gnu packages python)
#:use-module (gnu packages curl)
#:use-module (gnu packages cyrus-sasl)
#:use-module (gnu packages tls))
@ -148,3 +151,44 @@ (define-public rtorrent
XML-RPC over SCGI.")
(home-page "https://github.com/rakshasa/rtorrent")
(license l:gpl2+)))
(define-public transmission-remote-cli
(package
(name "transmission-remote-cli")
(version "1.7.1")
(source (origin
(method url-fetch)
(uri (string-append "https://github.com/fagga/"
"transmission-remote-cli/archive/v"
version ".tar.gz"))
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
"1y0hkpcjf6jw9xig8yf484hbhy63nip0pkchx401yxj81m25l4z9"))))
(build-system python-build-system)
(arguments
`(#:python ,python-2 ; only supports Python 2
#:tests? #f ; no test suite
#:phases (modify-phases %standard-phases
;; The software is just a Python script that must be
;; copied into place.
(delete 'build)
(replace 'install
(lambda* (#:key outputs #:allow-other-keys)
(let* ((out (assoc-ref outputs "out"))
(bin (string-append out "/bin"))
(man (string-append out "/share/man/man1"))
;; FIXME install zsh completions
(completions (string-append out "/etc/bash_completion.d")))
(install-file "transmission-remote-cli" bin)
(install-file "transmission-remote-cli.1" man)
(install-file
(string-append
"completion/bash/"
"transmission-remote-cli-bash-completion.sh")
completions)))))))
(synopsis "Console client for the Transmission BitTorrent daemon")
(description "Transmission-remote-cli is a console client, with a curses
interface, for the Transmission BitTorrent daemon.")
(home-page "https://github.com/fagga/transmission-remote-cli")
(license l:gpl3+)))

18
gnu/packages/debug.scm
View file

@ -1,5 +1,5 @@
;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2014, 2015 Eric Bavier <bavier@member.fsf.org>
;;; Copyright © 2014, 2015, 2016 Eric Bavier <bavier@member.fsf.org>
;;;
;;; This file is part of GNU Guix.
;;;
@ -169,7 +169,7 @@ (define-public american-fuzzy-lop
(_ "UNSUPPORTED"))))
(package
(name "american-fuzzy-lop")
(version "1.86b") ;It seems all releases have the 'b' suffix
(version "1.96b") ;It seems all releases have the 'b' suffix
(source
(origin
(method url-fetch)
@ -177,7 +177,7 @@ (define-public american-fuzzy-lop
"afl-" version ".tgz"))
(sha256
(base32
"1by9ncf6lgcyibzqwyla34jv64sd66mn8zhgjz2pcgsds51qwn0r"))))
"0z7j231p6v2h1dxxijgdzj1lq1lxr8cxllwf6iyv7p4ki5pv1gh3"))))
(build-system gnu-build-system)
(inputs
`(("custom-qemu"
@ -190,11 +190,13 @@ (define-public american-fuzzy-lop
;; afl only supports using a single afl-qemu-trace executable, so
;; we only build qemu for the native target.
(arguments
`(#:configure-flags
(list (string-append "--target-list=" ,machine "-linux-user"))
#:modules ((srfi srfi-1)
`(#:modules ((srfi srfi-1)
,@%gnu-build-system-modules)
,@(substitute-keyword-arguments (package-arguments qemu-2.3.0)
((#:configure-flags config-flags)
``(,(string-append "--target-list=" ,machine "-linux-user")
,@(remove (λ (f) (string-prefix? "--target-list=" f))
,config-flags)))
((#:phases qemu-phases)
`(modify-phases ,qemu-phases
(add-after
@ -236,8 +238,8 @@ (define-public american-fuzzy-lop
(lambda* (#:key inputs outputs #:allow-other-keys)
(let ((qemu (assoc-ref inputs "custom-qemu"))
(out (assoc-ref outputs "out")))
(copy-file (string-append qemu "/bin/qemu-" ,machine)
(string-append out "/bin/afl-qemu-trace"))
(symlink (string-append qemu "/bin/qemu-" ,machine)
(string-append out "/bin/afl-qemu-trace"))
#t)))
(delete 'check))))
(supported-systems (fold delete

36
gnu/packages/dns.scm
View file

@ -1,5 +1,7 @@
;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2015 Taylan Ulrich Bayırlı/Kammer <taylanbayirli@gmail.com>
;;; Copyright © 2016 Mark H Weaver <mhw@netris.org>
;;; Copyright © 2016 Ricardo Wurmus <rekado@elephly.net>
;;;
;;; This file is part of GNU Guix.
;;;
@ -63,14 +65,14 @@ (define-public dnsmasq
(define-public bind-utils
(package
(name "bind-utils")
(version "9.10.3-P2")
(version "9.10.3-P3")
(source (origin
(method url-fetch)
(uri (string-append "http://ftp.isc.org/isc/bind9/" version
"/bind-" version ".tar.gz"))
(sha256
(base32
"1kbfzml37sx4r2xi4gq48ji8w5kckd1f6gdn6pk6njqdmh8ijv2a"))))
"10yblk8qbb85qxakzdjy5qmqvqj4rlcqsqvlkriglampzg8i0239"))))
(build-system gnu-build-system)
(inputs
;; it would be nice to add GeoIP and gssapi once there is package
@ -89,20 +91,24 @@ (define-public bind-utils
(assoc-ref %build-inputs "mysql"))
(string-append "--with-pkcs11="
(assoc-ref %build-inputs "p11-kit")))
#:modules ((srfi srfi-1)
(srfi srfi-26)
,@%gnu-build-system-modules)
#:phases
(alist-replace
'build
(lambda _
(and (zero? (system* "make" "-C" "lib/dns"))
(zero? (system* "make" "-C" "lib/isc"))
(zero? (system* "make" "-C" "lib/bind9"))
(zero? (system* "make" "-C" "lib/isccfg"))
(zero? (system* "make" "-C" "lib/lwres"))
(zero? (system* "make" "-C" "bin/dig"))))
(alist-replace
'install
(lambda _ (zero? (system* "make" "-C" "bin/dig" "install")))
%standard-phases))))
(let ((libs '("dns" "isc" "bind9" "isccfg" "lwres"))
(bins '("dig" "nsupdate")))
(modify-phases %standard-phases
(replace 'build
(lambda _
(every (lambda (dir)
(zero? (system* "make" "-C" dir)))
(append (map (cut string-append "lib/" <>) libs)
(map (cut string-append "bin/" <>) bins)))))
(replace 'install
(lambda _
(every (lambda (dir)
(zero? (system* "make" "-C" dir "install")))
(map (cut string-append "bin/" <>) bins))))))))
(home-page "https://www.isc.org/downloads/bind/")
(synopsis "Tools for querying nameservers")
(description

4
gnu/packages/ebook.scm
View file

@ -60,7 +60,7 @@ (define-public chmlib
(define-public calibre
(package
(name "calibre")
(version "2.48.0")
(version "2.49.0")
(source
(origin
(method url-fetch)
@ -69,7 +69,7 @@ (define-public calibre
version ".tar.xz"))
(sha256
(base32
"0bjzw806czqxkhq9qqkhff8bhfc428pijkidb1h6gr47jqdp4hpg"))
"0jc476pg07c0nwccprhwgjdlvvb2fdzza9xrjqzc0c42c5v7qzxa"))
;; Remove non-free or doubtful code, see
;; https://lists.gnu.org/archive/html/guix-devel/2015-02/msg00478.html
(modules '((guix build utils)))

6
gnu/packages/enlightenment.scm
View file

@ -1,7 +1,7 @@
;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2015 Tomáš Čech <sleep_walker@suse.cz>
;;; Copyright © 2015 Daniel Pimentel <d4n1@member.fsf.org>
;;; Copyright © 2015 Efraim Flashner <efraim@flashner.co.il>
;;; Copyright © 2015, 2016 Efraim Flashner <efraim@flashner.co.il>
;;;
;;; This file is part of GNU Guix.
;;;
@ -271,7 +271,7 @@ (define-public rage
(define-public enlightenment
(package
(name "enlightenment")
(version "0.20.2")
(version "0.20.3")
(source (origin
(method url-fetch)
(uri
@ -279,7 +279,7 @@ (define-public enlightenment
name "/" name "-" version ".tar.xz"))
(sha256
(base32
"0faxky7lqd133jjjkr4c40kwwjhqc51ww10l3yy63671rfjhj424"))))
"19z3bwdzwpzwi330l5g5mj7xy6wy8xrc39zivjhm0d1ql3fh649j"))))
(build-system gnu-build-system)
(arguments
`(#:configure-flags '("--enable-mount-eeze")))

2
gnu/packages/grue-hunter.scm
View file

@ -32,7 +32,7 @@ (define-public grue-hunter
(source
(origin
(method url-fetch)
(uri (string-append "http://jxself.org/" name ".tar.gz"))
(uri (string-append "https://jxself.org/" name ".tar.gz"))
(sha256
(base32
"1hjcpy5439qs3v2zykis7hsi0i17zjs62gks3zd8mnfw9ni4i2h3"))))

67
gnu/packages/lego.scm Normal file
View file

@ -0,0 +1,67 @@
;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2016 Eric Bavier <bavier@member.fsf.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 (gnu packages lego)
#:use-module ((guix licenses) #:prefix license:)
#:use-module (guix download)
#:use-module (guix packages)
#:use-module (guix build-system gnu)
#:use-module (gnu packages)
#:use-module (gnu packages bison)
#:use-module (gnu packages flex))
(define-public nqc
(package
(name "nqc")
(version "3.1.r6")
(source (origin
(method url-fetch)
(uri (string-append "http://bricxcc.sourceforge.net/nqc/release/"
"nqc-" version ".tgz"))
(sha256
(base32
"0rp7pzr8xrdxpv75c2mi8zszzz2ypli4vvzxiic7mbrryrafdmdz"))))
(build-system gnu-build-system)
(native-inputs
`(("bison" ,bison)
("flex" ,flex)))
(arguments
'(#:tests? #f ;no tests
#:make-flags (list (string-append "PREFIX=" %output))
#:phases (modify-phases %standard-phases
(delete 'configure)
(add-before 'build 'rm-generated
;; Regenerating compiler/lexer.cpp avoids an 'undefined
;; reference to `isatty(int)'' error.
(lambda _
(for-each delete-file
'("compiler/lexer.cpp"
"compiler/parse.cpp"))
#t))
(add-after 'unpack 'deal-with-tarbomb
(lambda _
(chdir "..") ;tarbomb
#t)))))
(home-page "http://bricxcc.sourceforge.net/nqc/")
(synopsis "C-like language for Lego's MINDSTORMS")
(description
"Not Quite C (NQC) is a simple language for programming several Lego
MINDSTORMS products. The preprocessor and control structures of NQC are very
similar to C. NQC is not a general purpose language -- there are many
restrictions that stem from limitations of the standard RCX firmware.")
(license license:mpl1.0)))

12
gnu/packages/linux.scm
View file

@ -2,10 +2,10 @@
;;; Copyright © 2012, 2013, 2014, 2015 Ludovic Courtès <ludo@gnu.org>
;;; Copyright © 2013, 2014, 2015 Andreas Enge <andreas@enge.fr>
;;; Copyright © 2012 Nikita Karetnikov <nikita@karetnikov.org>
;;; Copyright © 2014, 2015 Mark H Weaver <mhw@netris.org>
;;; Copyright © 2014, 2015, 2016 Mark H Weaver <mhw@netris.org>
;;; Copyright © 2015 Federico Beffa <beffa@fbengineering.ch>
;;; Copyright © 2015 Taylan Ulrich Bayırlı/Kammer <taylanbayirli@gmail.com>
;;; Copyright © 2015 Efraim Flashner <efraim@flashner.co.il>
;;; Copyright © 2015, 2016 Efraim Flashner <efraim@flashner.co.il>
;;; Copyright © 2016 Christopher Allan Webber <cwebber@dustycloud.org>
;;;
;;; This file is part of GNU Guix.
@ -286,7 +286,9 @@ (define-public linux-libre
(uri (linux-libre-urls version))
(sha256
(base32
"1839xsaifs7vvyblzin8jps0gqi10xmz1l9p4x0j27vmdj39jgpm"))))
"1839xsaifs7vvyblzin8jps0gqi10xmz1l9p4x0j27vmdj39jgpm"))
(patches
(list (search-patch "linux-libre-CVE-2016-0728.patch")))))
(build-system gnu-build-system)
(supported-systems '("x86_64-linux" "i686-linux"))
(native-inputs `(("perl" ,perl)
@ -1234,7 +1236,7 @@ (define-public iotop
(define-public fuse
(package
(name "fuse")
(version "2.9.4")
(version "2.9.5")
(source (origin
(method url-fetch)
(uri (let ((version-with-underscores
@ -1245,7 +1247,7 @@ (define-public fuse
"/fuse-" version ".tar.gz")))
(sha256
(base32
"1qbwp63a2bp0bchabkwiyzszi9x5krlk2pwk2is6g35gyszw1sbb"))))
"1dfvbi1p57svbv2sfnbqwpnsk219spvjnlapf35azhgzqlf3g7sp"))))
(build-system gnu-build-system)
(inputs `(("util-linux" ,util-linux)))
(arguments

35
gnu/packages/mail.scm
View file

@ -8,7 +8,8 @@
;;; Copyright © 2015 Paul van der Walt <paul@denknerd.org>
;;; Copyright © 2015 Eric Bavier <bavier@member.fsf.org>
;;; Copyright © 2015 Andreas Enge <andreas@enge.fr>
;;; Copyright © 2015 Efraim Flashner <efraim@flashner.co.il>
;;; Copyright © 2015, 2016 Efraim Flashner <efraim@flashner.co.il>
;;; Copyright © 2016 Christopher Allan Webber <cwebber@dustycloud.org>
;;;
;;; This file is part of GNU Guix.
;;;
@ -519,7 +520,7 @@ (define-public libetpan
(define-public claws-mail
(package
(name "claws-mail")
(version "3.13.1")
(version "3.13.2")
(source (origin
(method url-fetch)
(uri (string-append
@ -527,7 +528,7 @@ (define-public claws-mail
".tar.xz"))
(sha256
(base32
"049av7r0xhjjjm1p93l2ns3xisvn125v3ncqar23cqjzgcichg5d"))))
"1l8ankx0qpq1ix1an8viphcf11ksh53jsrm1xjmq8cjbh5910wva"))))
(build-system gnu-build-system)
(native-inputs `(("pkg-config" ,pkg-config)))
(inputs `(("bogofilter" ,bogofilter)
@ -1014,4 +1015,32 @@ (define-public esmtp
@command{newaliases} commands.")
(license gpl2+)))
(define-public fdm
(package
(name "fdm")
(version "1.9")
(source (origin
(method url-fetch)
(uri (string-append "https://github.com/nicm/fdm/releases/download/"
version "/fdm-"
version ".tar.gz"))
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32 "054rscijahiza5f9qha79rg3siji3bk5mk10f8c2vqx7m4w6qh8n"))))
(build-system gnu-build-system)
(inputs
`(("tdb" ,tdb)
("openssl" ,openssl)
("zlib" ,zlib)))
(home-page "https://github.com/nicm/fdm")
(synopsis "Mail Retrieval Agent (MRA) and Mail Delivery Agent (MDA)")
(description "fdm is a program designed to fetch mail from POP3
or IMAP servers, or receive local mail from stdin, and
deliver it in various ways.")
(license
;; Why point to a source file? Well, all the individual files have a
;; copy of this license in their headers, but there's no seprate file
;; with that information.
(non-copyleft "https://github.com/nicm/fdm/blob/master/command.c"))))
;;; mail.scm ends here

15
gnu/packages/messaging.scm
View file

@ -1,5 +1,5 @@
;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2014, 2015 Mark H Weaver <mhw@netris.org>
;;; Copyright © 2014, 2015, 2016 Mark H Weaver <mhw@netris.org>
;;; Copyright © 2014 Julien Lepiller <julien@lepiller.eu>
;;; Copyright © 2015 Taylan Ulrich Bayırlı/Kammer <taylanbayirli@gmail.com>
;;; Copyright © 2015 Andreas Enge <andreas@enge.fr>
@ -425,7 +425,7 @@ (define-public python2-nbxmpp
(define-public gajim
(package
(name "gajim")
(version "0.16.4")
(version "0.16.5")
(source (origin
(method url-fetch)
(uri (string-append "https://gajim.org/downloads/"
@ -433,10 +433,17 @@ (define-public gajim
"/gajim-" version ".tar.bz2"))
(sha256
(base32
"0zyfs7q1qg8iqszr8l1gb18gqla6zrrfsgpmbxblpi9maqxas5i1"))))
"14fhcqnkqygh91132dnf1idayj4r3iqbwb44sd3mxv20n6ribh55"))))
(build-system gnu-build-system)
(arguments
`(#:phases
`(;; The only check done by gajim-0.16.x is to check that the
;; translations are up-to-date, and in 0.16.5 they are not, so
;; "make check" fails. Therefore, we disable tests for now.
;;
;; XXX TODO Try re-enabling tests in gajim-0.16.6 or later.
;;
#:tests? #f
#:phases
(modify-phases %standard-phases
(add-after 'install 'wrap-program
(lambda* (#:key outputs #:allow-other-keys)

50
gnu/packages/music.scm
View file

@ -1,6 +1,6 @@
;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2014 Eric Bavier <bavier@member.fsf.org>
;;; Copyright © 2015 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2015, 2016 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2015 Paul van der Walt <paul@denknerd.org>
;;;
;;; This file is part of GNU Guix.
@ -328,7 +328,11 @@ (define-public lilypond
music. Music is input in a text file containing control sequences which are
interpreted by LilyPond to produce the final document. It is extendable with
Guile.")
(license license:gpl3+)))
(license license:gpl3+)
;; On armhf and mips64el, building the documentation sometimes leads to
;; more than an hour of silence, so double the max silent time.
(properties `((max-silent-time . 7200)))))
(define-public non-sequencer
;; The latest tagged release is three years old and uses a custom build
@ -957,7 +961,7 @@ (define-public zynaddsubfx
(define-public yoshimi
(package
(name "yoshimi")
(version "1.3.7.1")
(version "1.3.8.2")
(source (origin
(method url-fetch)
(uri (string-append "mirror://sourceforge/yoshimi/"
@ -965,7 +969,7 @@ (define-public yoshimi
"/yoshimi-" version ".tar.bz2"))
(sha256
(base32
"13xc1x8jrr2rn26jx4dini692ww3771d5j5xf7f56ixqr7mmdhvz"))))
"0wl4ln6v1nkkx56kfah23chyrhga2vi93i82g0s200c4s4184xr8"))))
(build-system cmake-build-system)
(arguments
`(#:tests? #f ; there are no tests
@ -1036,3 +1040,41 @@ (define-public cursynth
synthesis engine. Notes and parameter changes may be entered via MIDI or the
computer's keyboard.")
(license license:gpl3+)))
(define-public qtractor
(package
(name "qtractor")
(version "0.7.3")
(source (origin
(method url-fetch)
(uri (string-append "http://downloads.sourceforge.net/qtractor/"
"qtractor-" version ".tar.gz"))
(sha256
(base32
"1vy4297myyqk0k58nzybgvgklckhngpdcnmp98k0rq98dirclbl7"))))
(build-system gnu-build-system)
(arguments `(#:tests? #f)) ; no "check" target
(inputs
`(("qt" ,qt)
("alsa-lib" ,alsa-lib)
("jack" ,jack-1)
("libsndfile" ,libsndfile)
("ladspa" ,ladspa)
("lv2" ,lv2)
("lilv" ,lilv)
("suil" ,suil)
("libsamplerate" ,libsamplerate)
("libvorbis" ,libvorbis)
("libmad" ,libmad)
("rubberband" ,rubberband)
("liblo" ,liblo)
("zlib" ,zlib)))
(native-inputs
`(("pkg-config" ,pkg-config)))
(home-page "http://qtractor.sourceforge.net/")
(synopsis "Audio/MIDI multi-track sequencer")
(description
"Qtractor is an Audio/MIDI multi-track sequencer application. It uses
JACK for audio and ALSA sequencer for MIDI as multimedia infrastructures and
follows a traditional multi-track tape recorder control paradigm.")
(license license:gpl2+)))

6
gnu/packages/nano.scm
View file

@ -1,6 +1,6 @@
;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2012 Nikita Karetnikov <nikita@karetnikov.org>
;;; Copyright © 2015 Efraim Flashner <efraim@flashner.co.il>
;;; Copyright © 2015, 2016 Efraim Flashner <efraim@flashner.co.il>
;;;
;;; This file is part of GNU Guix.
;;;
@ -28,7 +28,7 @@ (define-module (gnu packages nano)
(define-public nano
(package
(name "nano")
(version "2.5.0")
(version "2.5.1")
(source
(origin
(method url-fetch)
@ -36,7 +36,7 @@ (define-public nano
version ".tar.gz"))
(sha256
(base32
"1vl9bim56k1b4zwc3icxp46w6pn6gb042j1h4jlz1jklxxpkwcpz"))))
"1piv8prj6w3rvsrrx41ra8c10b8fzkgjhnm6399lsgqqpw0wlvz0"))))
(build-system gnu-build-system)
(inputs
`(("gettext" ,gnu-gettext)

22
gnu/packages/patches/arb-ldconfig.patch Normal file
View file

@ -0,0 +1,22 @@
diff -u -r arb-2.8.1.orig/configure arb-2.8.1/configure
--- arb-2.8.1.orig/configure 2015-12-31 17:30:01.000000000 +0100
+++ arb-2.8.1/configure 2016-01-20 16:41:41.336726596 +0100
@@ -647,6 +647,7 @@
echo "ARB_SHARED=$SHARED" >> Makefile
echo "ARB_LIB=$ARB_LIB" >> Makefile
echo "ARB_LIBNAME=$ARB_LIBNAME" >> Makefile
+echo "ARB_MAJOR=$ARB_MAJOR" >> Makefile
echo "ARB_SOLIB=$ARB_SOLIB" >> Makefile
echo "EXEEXT=$EXEEXT" >> Makefile
echo "PREFIX=$PREFIX" >> Makefile
diff -u -r arb-2.8.1.orig/Makefile.in arb-2.8.1/Makefile.in
--- arb-2.8.1.orig/Makefile.in 2015-12-31 17:30:01.000000000 +0100
+++ arb-2.8.1/Makefile.in 2016-01-20 16:30:32.575298517 +0100
@@ -101,6 +101,7 @@
$(LDCONFIG) -n "$(CURDIR)"; \
fi
ln -sf "$(ARB_LIB)" "$(ARB_LIBNAME)"; \
+ ln -sf "$(ARB_LIB)" "$(ARB_LIBNAME).$(ARB_MAJOR)"; \
libarb.a: $(OBJS) $(LIB_SOURCES) $(EXT_SOURCES) $(HEADERS) $(EXT_HEADERS) | build build/interfaces
$(AT)$(foreach ext, $(EXTENSIONS), $(foreach dir, $(patsubst $(ext)/%.h, %, $(wildcard $(ext)/*.h)), mkdir -p build/$(dir); BUILD_DIR=$(CURDIR)/build/$(dir); export BUILD_DIR; MOD_DIR=$(dir); export MOD_DIR; $(MAKE) -f $(CURDIR)/Makefile.subdirs -C $(ext)/$(dir) static || exit $$?;))

84
gnu/packages/patches/linux-libre-CVE-2016-0728.patch Normal file
View file

@ -0,0 +1,84 @@
Copied from
https://git.kernel.org/cgit/linux/kernel/git/torvalds/linux.git/patch/?id=23567fd052a9abb6d67fe8e7a9ccdd9800a540f2
From 23567fd052a9abb6d67fe8e7a9ccdd9800a540f2 Mon Sep 17 00:00:00 2001
From: Yevgeny Pats <yevgeny@perception-point.io>
Date: Tue, 19 Jan 2016 22:09:04 +0000
Subject: KEYS: Fix keyring ref leak in join_session_keyring()
This fixes CVE-2016-0728.
If a thread is asked to join as a session keyring the keyring that's already
set as its session, we leak a keyring reference.
This can be tested with the following program:
#include <stddef.h>
#include <stdio.h>
#include <sys/types.h>
#include <keyutils.h>
int main(int argc, const char *argv[])
{
int i = 0;
key_serial_t serial;
serial = keyctl(KEYCTL_JOIN_SESSION_KEYRING,
"leaked-keyring");
if (serial < 0) {
perror("keyctl");
return -1;
}
if (keyctl(KEYCTL_SETPERM, serial,
KEY_POS_ALL | KEY_USR_ALL) < 0) {
perror("keyctl");
return -1;
}
for (i = 0; i < 100; i++) {
serial = keyctl(KEYCTL_JOIN_SESSION_KEYRING,
"leaked-keyring");
if (serial < 0) {
perror("keyctl");
return -1;
}
}
return 0;
}
If, after the program has run, there something like the following line in
/proc/keys:
3f3d898f I--Q--- 100 perm 3f3f0000 0 0 keyring leaked-keyring: empty
with a usage count of 100 * the number of times the program has been run,
then the kernel is malfunctioning. If leaked-keyring has zero usages or
has been garbage collected, then the problem is fixed.
Reported-by: Yevgeny Pats <yevgeny@perception-point.io>
Signed-off-by: David Howells <dhowells@redhat.com>
Acked-by: Don Zickus <dzickus@redhat.com>
Acked-by: Prarit Bhargava <prarit@redhat.com>
Acked-by: Jarod Wilson <jarod@redhat.com>
Signed-off-by: James Morris <james.l.morris@oracle.com>
---
security/keys/process_keys.c | 1 +
1 file changed, 1 insertion(+)
diff --git a/security/keys/process_keys.c b/security/keys/process_keys.c
index a3f85d2..e6d50172 100644
--- a/security/keys/process_keys.c
+++ b/security/keys/process_keys.c
@@ -794,6 +794,7 @@ long join_session_keyring(const char *name)
ret = PTR_ERR(keyring);
goto error2;
} else if (keyring == new->session_keyring) {
+ key_put(keyring);
ret = 0;
goto error2;
}
--
cgit v0.12

24
gnu/packages/patches/tophat-build-with-later-seqan.patch Normal file
View file

@ -0,0 +1,24 @@
This patch resolves a build failure when building TopHat 2.1.0 with SeqAn 1.4.
This is the relevant part of a patch originally posted here:
https://lists.fu-berlin.de/pipermail/seqan-dev/2014-July/msg00001.html
--- a/src/segment_juncs.cpp
+++ b/src/segment_juncs.cpp
@@ -2050,10 +2050,13 @@ void juncs_from_ref_segs(RefSequenceTabl
typedef map<uint32_t, IntronMotifs> MotifMap;
MotifMap ims;
-
- seqan::DnaStringReverseComplement rev_donor_dinuc(donor_dinuc);
- seqan::DnaStringReverseComplement rev_acceptor_dinuc(acceptor_dinuc);
-
+
+ typedef seqan::ModifiedString<
+ seqan::ModifiedString<seqan::DnaString const, seqan::ModView<seqan::FunctorComplement<seqan::Dna> > >,
+ seqan::ModReverse> ConstDnaStringReverseComplement;
+ ConstDnaStringReverseComplement rev_donor_dinuc(donor_dinuc);
+ ConstDnaStringReverseComplement rev_acceptor_dinuc(acceptor_dinuc);
+
if (talkative)
fprintf(stderr, "Collecting potential splice sites in islands\n");

8
gnu/packages/tls.scm
View file

@ -339,13 +339,13 @@ (define-public libressl
(define-public acme
(package
(name "acme")
(version "0.1.1")
(version "0.2.0")
(source (origin
(method url-fetch)
(uri (pypi-uri "acme" version))
(sha256
(base32
"1yv0gy8akaqp5p2wjpfj8r5i0da04a9qdmlh06rczdkrmk6q680w"))))
"1xcbywzrwrj2cmqhaj4k6b11wfkbm3i7za2k9j1sd74rs1zh5abl"))))
(build-system python-build-system)
(arguments
`(#:python ,python-2))
@ -371,13 +371,13 @@ (define-public acme
(define-public letsencrypt
(package
(name "letsencrypt")
(version "0.1.1")
(version "0.2.0")
(source (origin
(method url-fetch)
(uri (pypi-uri "letsencrypt" version))
(sha256
(base32
"1kia3wk66lxyi2fghp9sd7cqgr5qiwdfayz153hi4wpa3q1q8rwf"))))
"0q57ylx00b6kl9zvawgag5yl03vlv1cjhp18xm96682pdibbgjci"))))
(build-system python-build-system)
(arguments
`(#:python ,python-2))

9
gnu/packages/tor.scm
View file

@ -1,6 +1,7 @@
;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2013, 2014, 2015 Ludovic Courtès <ludo@gnu.org>
;;; Copyright © 2014, 2015 Mark H Weaver <mhw@netris.org>
;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il>
;;;
;;; This file is part of GNU Guix.
;;;
@ -36,14 +37,14 @@ (define-module (gnu packages tor)
(define-public tor
(package
(name "tor")
(version "0.2.7.5")
(version "0.2.7.6")
(source (origin
(method url-fetch)
(uri (string-append "https://www.torproject.org/dist/tor-"
version ".tar.gz"))
(sha256
(base32
"0pxayvcab4cb107ynbpzx4g0qyr1mjfba2an76wdx6dxn56rwakx"))))
"0p8hjlfi8dwghlyjif5s0q98cmpgz9kn9jja25430l04z5wqcfj9"))))
(build-system gnu-build-system)
(native-inputs
`(("python" ,python-2))) ; for tests
@ -103,7 +104,7 @@ (define-public torsocks
(define-public privoxy
(package
(name "privoxy")
(version "3.0.21")
(version "3.0.24")
(source (origin
(method url-fetch)
(uri (string-append "mirror://sourceforge/ijbswa/Sources/"
@ -111,7 +112,7 @@ (define-public privoxy
version "-stable-src.tar.gz"))
(sha256
(base32
"1f6xb7aa47p90c26vqaw74y6drs9gpnhxsgby3mx0awdjh0ydisy"))))
"04mhkz5g713i2crvjd6s783hhrlsjjjlfb9llbaf13ghg3fgd0d3"))))
(build-system gnu-build-system)
(arguments
'(;; The default 'sysconfdir' is $out/etc; change that to

6
gnu/packages/version-control.scm
View file

@ -6,7 +6,7 @@
;;; Copyright © 2015 Mathieu Lirzin <mthl@openmailbox.org>
;;; Copyright © 2014, 2015 Mark H Weaver <mhw@netris.org>
;;; Copyright © 2014 Eric Bavier <bavier@member.fsf.org>
;;; Copyright © 2015 Efraim Flashner <efraim@flashner.co.il>
;;; Copyright © 2015, 2016 Efraim Flashner <efraim@flashner.co.il>
;;; Copyright © 2015 Kyle Meyer <kyle@kyleam.com>
;;; Copyright © 2015 Ricardo Wurmus <rekado@elephly.net>
;;;
@ -1004,7 +1004,7 @@ (define-public findnewest
(define-public myrepos
(package
(name "myrepos")
(version "1.20151022")
(version "1.20160123")
(source
(origin
(method url-fetch)
@ -1013,7 +1013,7 @@ (define-public myrepos
version ".tar.gz"))
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32 "0c93lqsngpsxsca7nygk4qhidr40ijgih86q81x1mfcwbs0gbds8"))))
(base32 "1723cg5haplz2w9dwdzp6ds1ip33cx3awmj4wnb0h4yq171v5lqk"))))
(build-system gnu-build-system)
(inputs
`(("perl" ,perl)))

36
gnu/packages/video.scm
View file

@ -1,6 +1,6 @@
;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2013, 2014, 2015 Andreas Enge <andreas@enge.fr>
;;; Copyright © 2014, 2015 David Thompson <davet@gnu.org>
;;; Copyright © 2014, 2015, 2016 David Thompson <davet@gnu.org>
;;; Copyright © 2014, 2015, 2016 Mark H Weaver <mhw@netris.org>
;;; Copyright © 2015 Taylan Ulrich Bayırlı/Kammer <taylanbayirli@gmail.com>
;;; Copyright © 2015, 2016 Efraim Flashner <efraim@flashner.co.il>
@ -1265,6 +1265,39 @@ (define-public mlt
tools, XML authoring components, and an extensible plug-in based API.")
(license license:lgpl2.1+)))
(define-public v4l-utils
(package
(name "v4l-utils")
(version "1.8.1")
(source (origin
(method url-fetch)
(uri (string-append "http://linuxtv.org/downloads/v4l-utils"
"/v4l-utils-" version ".tar.bz2"))
(sha256
(base32
"0cqv8drw0z0kfmz4f50a8kzbrz6vbj6j6q78030hgshr7yq1jqig"))))
(build-system gnu-build-system)
(arguments
'(#:configure-flags
(list (string-append "--with-udevdir="
(assoc-ref %outputs "out")
"/lib/udev"))))
(native-inputs
`(("pkg-config" ,pkg-config)))
(inputs
`(("alsa-lib" ,alsa-lib)
("glu" ,glu)
("libjpeg" ,libjpeg)
("libx11" ,libx11)
("qt" ,qt)
("eudev" ,eudev)))
(synopsis "Realtime video capture utilities for Linux")
(description "The v4l-utils provide a series of libraries and utilities to
be used for realtime video capture via Linux-specific APIs.")
(home-page "https://linuxtv.org/wiki/index.php/V4l-utils")
;; libv4l2 is LGPL2.1+, while utilities are GPL2 only.
(license (list license:lgpl2.1+ license:gpl2))))
(define-public obs
(package
(name "obs")
@ -1293,6 +1326,7 @@ (define-public obs
("mesa" ,mesa)
("pulseaudio" ,pulseaudio)
("qt" ,qt)
("v4l-utils" ,v4l-utils)
("zlib" ,zlib)))
(synopsis "Live streaming software")
(description "Open Broadcaster Software provides a graphical interface for

14
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 Efraim Flashner <efraim@flashner.co.il>
;;; Copyright © 2015, 2016 Efraim Flashner <efraim@flashner.co.il>
;;;
;;; This file is part of GNU Guix.
;;;
@ -293,7 +293,7 @@ (define vorbis-tools
(define opus
(package
(name "opus")
(version "1.1.1")
(version "1.1.2")
(source (origin
(method url-fetch)
(uri (string-append
@ -301,7 +301,7 @@ (define opus
".tar.gz"))
(sha256
(base32
"07iplfwim26b6k1bqjyciaqvihps9rk5gi8385axa83ppmbgz14v"))))
"1z87x5c5x951lhnm70iqr2gqn15wns5cqsw8nnkvl48jwdw00a8f"))))
(build-system gnu-build-system)
(synopsis "Versatile audio codec")
(description
@ -349,7 +349,7 @@ (define opus-tools
(define opusfile
(package
(name "opusfile")
(version "0.6")
(version "0.7")
(source (origin
(method url-fetch)
(uri (string-append
@ -357,7 +357,7 @@ (define opusfile
".tar.gz"))
(sha256
(base32
"19iys2kld75k0210b807i4illrdmj3cmmnrgxlc9y4vf6mxp2a14"))))
"00f3wwjv3hxwg05g22s6mkkxikz80ljsn70g39cmi43jph9ysawy"))))
(build-system gnu-build-system)
(propagated-inputs
`(("opus" ,opus)))
@ -409,7 +409,7 @@ (define-public icecast
(define-public libshout
(package
(name "libshout")
(version "2.3.1")
(version "2.4.1")
(source (origin
(method url-fetch)
(uri (string-append
@ -417,7 +417,7 @@ (define-public libshout
name "-" version ".tar.gz"))
(sha256
(base32
"0vlj4dxfxg06xhvv0z2zjjlrjh5di2m28w7v16zcygsy99mmyg6g"))))
"0kgjpf8jkgyclw11nilxi8vyjk4s8878x23qyxnvybbgqbgbib7k"))))
(build-system gnu-build-system)
(native-inputs
`(("pkg-config" ,pkg-config)))

5
gnu/services/avahi.scm
View file

@ -1,5 +1,5 @@
;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2014, 2015 Ludovic Courtès <ludo@gnu.org>
;;; Copyright © 2014, 2015, 2016 Ludovic Courtès <ludo@gnu.org>
;;;
;;; This file is part of GNU Guix.
;;;
@ -26,7 +26,8 @@ (define-module (gnu services avahi)
#:use-module (gnu packages admin)
#:use-module (guix records)
#:use-module (guix gexp)
#:export (avahi-service))
#:export (avahi-service
avahi-service-type))
;;; Commentary:
;;;

26
gnu/system.scm
View file

@ -79,6 +79,7 @@ (define-module (gnu system)
operating-system-locale-libcs
operating-system-mapped-devices
operating-system-file-systems
operating-system-store-file-system
operating-system-activation-script
operating-system-derivation
@ -678,12 +679,34 @@ (define (kernel->grub-label kernel)
(package-version kernel)
" (alpha)"))
(define (store-file-system file-systems)
"Return the file system object among FILE-SYSTEMS that contains the store."
(match (filter (lambda (fs)
(and (file-system-mount? fs)
(not (memq 'bind-mount (file-system-flags fs)))
(string-prefix? (file-system-mount-point fs)
(%store-prefix))))
file-systems)
((and candidates (head . tail))
(reduce (lambda (fs1 fs2)
(if (> (string-length (file-system-mount-point fs1))
(string-length (file-system-mount-point fs2)))
fs1
fs2))
head
candidates))))
(define (operating-system-store-file-system os)
"Return the file system that contains the store of OS."
(store-file-system (operating-system-file-systems os)))
(define* (operating-system-grub.cfg os #:optional (old-entries '()))
"Return the GRUB configuration file for OS. Use OLD-ENTRIES to populate the
\"old entries\" menu."
(mlet* %store-monad
((system (operating-system-derivation os))
(root-fs -> (operating-system-root-file-system os))
(store-fs -> (operating-system-store-file-system os))
(kernel -> (operating-system-kernel os))
(root-device -> (if (eq? 'uuid (file-system-title root-fs))
(uuid->string (file-system-device root-fs))
@ -698,7 +721,8 @@ (define* (operating-system-grub.cfg os #:optional (old-entries '()))
"/boot")
(operating-system-kernel-arguments os)))
(initrd #~(string-append #$system "/initrd"))))))
(grub-configuration-file (operating-system-bootloader os) entries
(grub-configuration-file (operating-system-bootloader os)
store-fs entries
#:old-entries old-entries)))
(define (operating-system-parameters-file os)

54
gnu/system/grub.scm
View file

@ -1,5 +1,5 @@
;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2013, 2014, 2015 Ludovic Courtès <ludo@gnu.org>
;;; Copyright © 2013, 2014, 2015, 2016 Ludovic Courtès <ludo@gnu.org>
;;;
;;; This file is part of GNU Guix.
;;;
@ -25,6 +25,7 @@ (define-module (gnu system grub)
#:use-module (guix gexp)
#:use-module (guix download)
#:use-module (gnu artwork)
#:use-module (gnu system file-systems)
#:autoload (gnu packages grub) (grub)
#:autoload (gnu packages inkscape) (inkscape)
#:autoload (gnu packages imagemagick) (imagemagick)
@ -153,10 +154,12 @@ (define* (grub-background-image config #:key (width 1024) (height 768))
(with-monad %store-monad
(return #f)))))
(define (eye-candy config system port)
(define (eye-candy config root-fs system port)
"Return in %STORE-MONAD a gexp that writes to PORT (a port-valued gexp) the
'grub.cfg' part concerned with graphics mode, background images, colors, and
all that."
all that. ROOT-FS is a file-system object denoting the root file system where
the store is. SYSTEM must be the target system string---e.g.,
\"x86_64-linux\"."
(define setup-gfxterm-body
;; Intel systems need to be switched into graphics mode, whereas most
;; other modern architectures have no other mode and therefore don't need
@ -179,15 +182,18 @@ (define (theme-colors type)
(string-append (symbol->string (assoc-ref colors 'fg)) "/"
(symbol->string (assoc-ref colors 'bg)))))
(define font-file
#~(string-append #$grub "/share/grub/unicode.pf2"))
(mlet* %store-monad ((image (grub-background-image config)))
(return (and image
#~(format #$port "
function setup_gfxterm {~a}
# Set 'root' to the partition that contains /gnu/store.
search --file --set ~a/share/grub/unicode.pf2
~a
if loadfont ~a/share/grub/unicode.pf2; then
if loadfont ~a; then
setup_gfxterm
fi
@ -200,7 +206,9 @@ (define (theme-colors type)
set menu_color_highlight=white/blue
fi~%"
#$setup-gfxterm-body
#$grub #$grub
#$(grub-root-search root-fs font-file)
#$font-file
#$image
#$(theme-colors grub-theme-color-normal)
#$(theme-colors grub-theme-color-highlight))))))
@ -210,13 +218,31 @@ (define (theme-colors type)
;;; Configuration file.
;;;
(define* (grub-configuration-file config entries
(define (grub-root-search root-fs file)
"Return the GRUB 'search' command to look for ROOT-FS, which contains FILE,
a gexp. The result is a gexp that can be inserted in the grub.cfg-generation
code."
(case (file-system-title root-fs)
;; Preferably refer to ROOT-FS by its UUID or label. This is more
;; efficient and less ambiguous, see <>.
((uuid)
(format #f "search --fs-uuid --set ~a"
(uuid->string (file-system-device root-fs))))
((label)
(format #f "search --label --set ~a"
(file-system-device root-fs)))
(else
;; As a last resort, look for any device containing FILE.
#~(format #f "search --file --set ~a" #$file))))
(define* (grub-configuration-file config store-fs entries
#:key
(system (%current-system))
(old-entries '()))
"Return the GRUB configuration file corresponding to CONFIG, a
<grub-configuration> object. OLD-ENTRIES is taken to be a list of menu
entries corresponding to old generations of the system."
<grub-configuration> object, and where the store is available at STORE-FS, a
<file-system> object. OLD-ENTRIES is taken to be a list of menu entries
corresponding to old generations of the system."
(define linux-image-name
(if (string-prefix? "mips" system)
"vmlinuz"
@ -229,18 +255,18 @@ (define entry->gexp
(match-lambda
(($ <menu-entry> label linux arguments initrd)
#~(format port "menuentry ~s {
# Set 'root' to the partition that contains the kernel.
search --file --set ~a/~a~%
~a
linux ~a/~a ~a
initrd ~a
}~%"
#$label
#$linux #$linux-image-name
#$(grub-root-search store-fs
#~(string-append #$linux "/"
#$linux-image-name))
#$linux #$linux-image-name (string-join (list #$@arguments))
#$initrd))))
(mlet %store-monad ((sugar (eye-candy config system #~port)))
(mlet %store-monad ((sugar (eye-candy config store-fs system #~port)))
(define builder
#~(call-with-output-file #$output
(lambda (port)

103
guix/import/cran.scm
View file

@ -29,12 +29,14 @@ (define-module (guix import cran)
#:use-module (guix base32)
#:use-module ((guix download) #:select (download-to-store))
#:use-module (guix import utils)
#:use-module ((guix build-system r) #:select (cran-uri))
#:use-module ((guix build-system r) #:select (cran-uri bioconductor-uri))
#:use-module (guix upstream)
#:use-module (guix packages)
#:use-module (gnu packages)
#:export (cran->guix-package
%cran-updater))
bioconductor->guix-package
%cran-updater
%bioconductor-updater))
;;; Commentary:
;;;
@ -108,6 +110,15 @@ (define* (maybe-inputs package-inputs #:optional (type 'inputs))
`((,type (,'quasiquote ,(format-inputs package-inputs)))))))
(define %cran-url "http://cran.r-project.org/web/packages/")
(define %bioconductor-url "http://bioconductor.org/packages/")
;; The latest Bioconductor release is 3.2. Bioconductor packages should be
;; updated together.
(define %bioconductor-svn-url
(string-append "https://readonly:readonly@"
"hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/"
"madman/Rpacks/"))
(define (fetch-description base-url name)
"Return an alist of the contents of the DESCRIPTION file for the R package
@ -136,24 +147,31 @@ (define (listify meta field)
(string-any char-set:whitespace item)))
(map string-trim-both items))))))
(define (description->package meta)
"Return the `package' s-expression for a CRAN package from the alist META,
which was derived from the R package's DESCRIPTION file."
(define (description->package repository meta)
"Return the `package' s-expression for an R package published on REPOSITORY
from the alist META, which was derived from the R package's DESCRIPTION file."
(define (guix-name name)
(if (string-prefix? "r-" name)
(string-downcase name)
(string-append "r-" (string-downcase name))))
(let* ((name (assoc-ref meta "Package"))
(let* ((base-url (case repository
((cran) %cran-url)
((bioconductor) %bioconductor-url)))
(uri-helper (case repository
((cran) cran-uri)
((bioconductor) bioconductor-uri)))
(name (assoc-ref meta "Package"))
(synopsis (assoc-ref meta "Title"))
(version (assoc-ref meta "Version"))
(license (string->license (assoc-ref meta "License")))
;; Some packages have multiple home pages. Some have none.
(home-page (match (listify meta "URL")
((url rest ...) url)
(_ (string-append %cran-url name))))
(source-url (match (cran-uri name version)
(_ (string-append base-url name))))
(source-url (match (uri-helper name version)
((url rest ...) url)
((? string? url) url)
(_ #f)))
(tarball (with-store store (download-to-store store source-url)))
(sysdepends (map string-downcase (listify meta "SystemRequirements")))
@ -167,26 +185,32 @@ (define (guix-name name)
(version ,version)
(source (origin
(method url-fetch)
(uri (cran-uri ,name version))
(uri (,(procedure-name uri-helper) ,name version))
(sha256
(base32
,(bytevector->nix-base32-string (file-sha256 tarball))))))
(properties ,`(,'quasiquote ((,'upstream-name . ,name))))
,@(if (not (equal? (string-append "r-" name)
(guix-name name)))
`((properties ,`(,'quasiquote ((,'upstream-name . ,name)))))
'())
(build-system r-build-system)
,@(maybe-inputs sysdepends)
,@(maybe-inputs propagate 'propagated-inputs)
(home-page ,(if (string-null? home-page)
(string-append %cran-url name)
(string-append base-url name)
home-page))
(synopsis ,synopsis)
(description ,(beautify-description (assoc-ref meta "Description")))
(license ,license))))
(define (cran->guix-package package-name)
"Fetch the metadata for PACKAGE-NAME from cran.r-project.org, and return the
`package' s-expression corresponding to that package, or #f on failure."
(let ((module-meta (fetch-description %cran-url package-name)))
(and=> module-meta description->package)))
(define* (cran->guix-package package-name #:optional (repo 'cran))
"Fetch the metadata for PACKAGE-NAME from REPO and return the `package'
s-expression corresponding to that package, or #f on failure."
(let* ((url (case repo
((cran) %cran-url)
((bioconductor) %bioconductor-svn-url)))
(module-meta (fetch-description url package-name)))
(and=> module-meta (cut description->package repo <>))))
;;;
@ -212,7 +236,7 @@ (define (package->upstream-name package)
(_ #f)))
(_ #f)))))
(define (latest-release package)
(define (latest-cran-release package)
"Return an <upstream-source> for the latest release of PACKAGE."
(define upstream-name
@ -229,16 +253,55 @@ (define meta
(version version)
(urls (cran-uri upstream-name version))))))
(define (latest-bioconductor-release package)
"Return an <upstream-source> for the latest release of PACKAGE."
(define upstream-name
(package->upstream-name (specification->package package)))
(define meta
(fetch-description %bioconductor-svn-url upstream-name))
(and meta
(let ((version (assoc-ref meta "Version")))
;; Bioconductor does not provide signatures.
(upstream-source
(package package)
(version version)
(urls (bioconductor-uri upstream-name version))))))
(define (cran-package? package)
"Return true if PACKAGE is an R package from CRAN."
;; Assume all R packages are available on CRAN.
(string-prefix? "r-" (package-name package)))
(and (string-prefix? "r-" (package-name package))
(match (and=> (package-source package) origin-uri)
((? string? uri)
(string-prefix? "mirror://cran" uri))
((? list? uris)
(any (cut string-prefix? "mirror://cran" <>) uris))
(_ #f))))
(define (bioconductor-package? package)
"Return true if PACKAGE is an R package from Bioconductor."
(and (string-prefix? "r-" (package-name package))
(match (and=> (package-source package) origin-uri)
((? string? uri)
(string-prefix? "http://bioconductor.org" uri))
((? list? uris)
(any (cut string-prefix? "http://bioconductor.org" <>) uris))
(_ #f))))
(define %cran-updater
(upstream-updater
(name 'cran)
(description "Updater for CRAN packages")
(pred cran-package?)
(latest latest-release)))
(latest latest-cran-release)))
(define %bioconductor-updater
(upstream-updater
(name 'bioconductor)
(description "Updater for Bioconductor packages")
(pred bioconductor-package?)
(latest latest-bioconductor-release)))
;;; cran.scm ends here

7
guix/import/gem.scm
View file

@ -77,7 +77,7 @@ (define (read-byte i)
(bytevector-u8-set! bv i (read-byte i))
(loop (1+ i)))))))
(define (make-gem-sexp name version hash home-page description
(define (make-gem-sexp name version hash home-page synopsis description
dependencies licenses)
"Return the `package' s-expression for a Ruby package with the given NAME,
VERSION, HASH, HOME-PAGE, DESCRIPTION, DEPENDENCIES, and LICENSES."
@ -101,7 +101,7 @@ (define (make-gem-sexp name version hash home-page description
(,'unquote
,(string->symbol name))))
dependencies)))))
(synopsis ,description) ; nothing better to use
(synopsis ,synopsis)
(description ,description)
(home-page ,home-page)
(license ,(match licenses
@ -117,6 +117,7 @@ (define* (gem->guix-package package-name #:optional version)
(let ((name (assoc-ref package "name"))
(version (assoc-ref package "version"))
(hash (assoc-ref package "sha"))
(synopsis (assoc-ref package "info")) ; nothing better to use
(description (beautify-description
(assoc-ref package "info")))
(home-page (assoc-ref package "homepage_uri"))
@ -129,5 +130,5 @@ (define* (gem->guix-package package-name #:optional version)
"runtime")))
(licenses (map string->license
(assoc-ref package "licenses"))))
(make-gem-sexp name version hash home-page
(make-gem-sexp name version hash home-page synopsis
description dependencies licenses)))))

8
guix/licenses.scm
View file

@ -4,6 +4,7 @@
;;; Copyright © 2012, 2013 Nikita Karetnikov <nikita@karetnikov.org>
;;; Copyright © 2015 Mark H Weaver <mhw@netris.org>
;;; Copyright © 2015 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2016 Eric Bavier <bavier@member.fsf.org>
;;;
;;; This file is part of GNU Guix.
;;;
@ -49,7 +50,7 @@ (define-module (guix licenses)
imlib2
ipa
lgpl2.0 lgpl2.0+ lgpl2.1 lgpl2.1+ lgpl3 lgpl3+
mpl1.1 mpl2.0
mpl1.0 mpl1.1 mpl2.0
ms-pl
ncsa
openldap2.8 openssl
@ -302,6 +303,11 @@ (define lgpl3+
"https://www.gnu.org/licenses/lgpl.html"
"https://www.gnu.org/licenses/license-list#LGPLv3"))
(define mpl1.0
(license "MPL 1.0"
"http://www.mozilla.org/MPL/1.0/"
"https://www.gnu.org/licenses/license-list.html#MPL"))
(define mpl1.1
(license "MPL 1.1"
"http://directory.fsf.org/wiki/License:MPLv1.1"

10
guix/scripts/build.scm
View file

@ -1,5 +1,5 @@
;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2012, 2013, 2014, 2015 Ludovic Courtès <ludo@gnu.org>
;;; Copyright © 2012, 2013, 2014, 2015, 2016 Ludovic Courtès <ludo@gnu.org>
;;; Copyright © 2013 Mark H Weaver <mhw@netris.org>
;;;
;;; This file is part of GNU Guix.
@ -153,6 +153,8 @@ (define (show-build-options-help)
(display (_ "
-K, --keep-failed keep build tree of failed builds"))
(display (_ "
-k, --keep-going keep going when some of the derivations fail"))
(display (_ "
-n, --dry-run do not build the derivations"))
(display (_ "
--fallback fall back to building when the substituter fails"))
@ -183,6 +185,7 @@ (define (set-build-options-from-command-line store opts)
;; TODO: Add more options.
(set-build-options store
#:keep-failed? (assoc-ref opts 'keep-failed?)
#:keep-going? (assoc-ref opts 'keep-going?)
#:rounds (assoc-ref opts 'rounds)
#:build-cores (or (assoc-ref opts 'cores) 0)
#:max-build-jobs (or (assoc-ref opts 'max-jobs) 1)
@ -214,6 +217,11 @@ (define %standard-build-options
(apply values
(alist-cons 'keep-failed? #t result)
rest)))
(option '(#\k "keep-going") #f #f
(lambda (opt name arg result . rest)
(apply values
(alist-cons 'keep-going? #t result)
rest)))
(option '("rounds") #t #f
(lambda (opt name arg result . rest)
(apply values

9
guix/scripts/import/cran.scm
View file

@ -41,6 +41,8 @@ (define %default-options
(define (show-help)
(display (_ "Usage: guix import cran PACKAGE-NAME
Import and convert the CRAN package for PACKAGE-NAME.\n"))
(display (_ "
-a, --archive=ARCHIVE specify the archive repository"))
(display (_ "
-h, --help display this help and exit"))
(display (_ "
@ -57,6 +59,10 @@ (define %options
(option '(#\V "version") #f #f
(lambda args
(show-version-and-exit "guix import cran")))
(option '(#\a "archive") #t #f
(lambda (opt name arg result)
(alist-cons 'repo (string->symbol arg)
(alist-delete 'repo result))))
%standard-import-options))
@ -82,7 +88,8 @@ (define (parse-options)
(reverse opts))))
(match args
((package-name)
(let ((sexp (cran->guix-package package-name)))
(let ((sexp (cran->guix-package package-name
(or (assoc-ref opts 'repo) 'cran))))
(unless sexp
(leave (_ "failed to download description for package '~a'~%")
package-name))

1
guix/scripts/refresh.scm
View file

@ -195,6 +195,7 @@ (define %updaters
%gnome-updater
%elpa-updater
%cran-updater
%bioconductor-updater
((guix import pypi) => %pypi-updater)))
(define (lookup-updater name)

12
tests/cran.scm
View file

@ -86,16 +86,6 @@ (define simple-alist
'()
((@@ (guix import cran) listify) simple-alist "BadList"))
(test-equal "beautify-description: use double spacing"
"This is a package. It is great. Trust me Mr. Hendrix."
((@@ (guix import cran) beautify-description)
"This is a package. It is great. Trust me Mr. Hendrix."))
(test-equal "beautify-description: transform fragment into sentence"
"This package provides a function to establish world peace"
((@@ (guix import cran) beautify-description)
"A function to establish world peace"))
(test-assert "description->package"
;; Replace network resources with sample data.
(mock ((guix build download) url-fetch
@ -107,7 +97,7 @@ (define simple-alist
("mirror://cran/src/contrib/My-Example_1.2.3.tar.gz"
"source")
(_ (error "Unexpected URL: " url))))))))
(match ((@@ (guix import cran) description->package) description-alist)
(match ((@@ (guix import cran) description->package) 'cran description-alist)
(('package
('name "r-my-example")
('version "1.2.3")

27
tests/derivations.scm
View file

@ -151,6 +151,33 @@ (define prefix-len (string-length dir))
;; the contents.
(valid-path? %store (derivation->output-path drv)))))
(test-assert "derivation fails but keep going"
;; In keep-going mode, 'build-derivations' should fail because of D1, but it
;; must return only after D2 has succeeded.
(with-store store
(let* ((d1 (derivation %store "fails"
%bash `("-c" "false")
#:inputs `((,%bash))))
(d2 (build-expression->derivation %store "sleep-then-succeed"
`(begin
,(random-text)
;; XXX: Hopefully that's long
;; enough that D1 has already
;; failed.
(sleep 2)
(mkdir %output)))))
(set-build-options %store
#:use-substitutes? #f
#:keep-going? #t)
(guard (c ((nix-protocol-error? c)
(and (= 100 (nix-protocol-error-status c))
(string-contains (nix-protocol-error-message c)
(derivation-file-name d1))
(not (valid-path? %store (derivation->output-path d1)))
(valid-path? %store (derivation->output-path d2)))))
(build-derivations %store (list d1 d2))
#f))))
(test-assert "identical files are deduplicated"
(let* ((build1 (add-text-to-store %store "one.sh"
"echo hello, world > \"$out\"\n"

2
tests/gem.scm
View file

@ -69,7 +69,7 @@ (define test-json
(("bundler" ('unquote 'bundler))
("ruby-bar" ('unquote 'ruby-bar)))))
('synopsis "A cool gem")
('description "A cool gem")
('description "This package provides a cool gem")
('home-page "https://example.com")
('license ('list 'expat 'asl2.0)))
#t)

39
tests/import-utils.scm Normal file
View file

@ -0,0 +1,39 @@
;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2015 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2016 Ben Woodcroft <donttrustben@gmail.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 (test-import-utils)
#:use-module (guix tests)
#:use-module (guix import utils)
#:use-module (srfi srfi-64))
(test-begin "import-utils")
(test-equal "beautify-description: use double spacing"
"This is a package. It is great. Trust me Mr. Hendrix."
(beautify-description
"This is a package. It is great. Trust me Mr. Hendrix."))
(test-equal "beautify-description: transform fragment into sentence"
"This package provides a function to establish world peace"
(beautify-description "A function to establish world peace"))
(test-end "import-utils")
(exit (= (test-runner-fail-count (test-runner-current)) 0))

5
tests/lint.scm
View file

@ -1,7 +1,7 @@
;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2012, 2013 Cyril Roelandt <tipecaml@gmail.com>
;;; Copyright © 2014, 2015 Eric Bavier <bavier@member.fsf.org>
;;; Copyright © 2014, 2015 Ludovic Courtès <ludo@gnu.org>
;;; Copyright © 2014, 2015, 2016 Ludovic Courtès <ludo@gnu.org>
;;; Copyright © 2015 Mathieu Lirzin <mthl@openmailbox.org>
;;;
;;; This file is part of GNU Guix.
@ -19,6 +19,9 @@
;;; You should have received a copy of the GNU General Public License
;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
;; Avoid interference.
(unsetenv "http_proxy")
(define-module (test-lint)
#:use-module (guix tests)
#:use-module (guix download)

4
tests/publish.scm
View file

@ -16,6 +16,9 @@
;;; You should have received a copy of the GNU General Public License
;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
;; Avoid interference.
(unsetenv "http_proxy")
(define-module (test-publish)
#:use-module (guix scripts publish)
#:use-module (guix tests)
@ -62,6 +65,7 @@ (define (publish-uri route)
(connect conn AF_INET (inet-pton AF_INET "127.0.0.1") 6789))
(loop))))
(test-begin "publish")
(test-equal "/nix-cache-info"

77
tests/system.scm Normal file
View file

@ -0,0 +1,77 @@
;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2016 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 (test-system)
#:use-module (gnu)
#:use-module (guix store)
#:use-module (srfi srfi-1)
#:use-module (srfi srfi-64))
;; Test the (gnu system) module.
(define %root-fs
(file-system
(device "my-root")
(title 'label)
(mount-point "/")
(type "ext4")))
(define %os
(operating-system
(host-name "komputilo")
(timezone "Europe/Berlin")
(locale "en_US.utf8")
(bootloader (grub-configuration (device "/dev/sdX")))
(file-systems (cons %root-fs %base-file-systems))
(users %base-user-accounts)))
(test-begin "system")
(test-assert "operating-system-store-file-system"
;; %BASE-FILE-SYSTEMS defines a bind-mount for /gnu/store, but this
;; shouldn't be a problem.
(eq? %root-fs
(operating-system-store-file-system %os)))
(test-assert "operating-system-store-file-system, prefix"
(let* ((gnu (file-system
(device "foobar")
(mount-point (dirname (%store-prefix)))
(type "ext5")))
(os (operating-system
(inherit %os)
(file-systems (cons* gnu %root-fs
%base-file-systems)))))
(eq? gnu (operating-system-store-file-system os))))
(test-assert "operating-system-store-file-system, store"
(let* ((gnu (file-system
(device "foobar")
(mount-point (%store-prefix))
(type "ext5")))
(os (operating-system
(inherit %os)
(file-systems (cons* gnu %root-fs
%base-file-systems)))))
(eq? gnu (operating-system-store-file-system os))))
(test-end)
(exit (= (test-runner-fail-count (test-runner-current)) 0))