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Merge branch 'master' into core-updates

master
Mark H Weaver 2016-01-24 21:04:54 -05:00
parent 6871628999 880d647d0f
commit 412bee5e29
45 changed files with 1143 additions and 172 deletions
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4
Makefile.am
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@ -240,8 +240,10 @@ SCM_TESTS = \
tests/challenge.scm \ tests/challenge.scm \
tests/cve.scm \ tests/cve.scm \
tests/file-systems.scm \ tests/file-systems.scm \
tests/system.scm \
tests/services.scm \ tests/services.scm \
tests/containers.scm tests/containers.scm \
tests/import-utils.scm
if HAVE_GUILE_JSON if HAVE_GUILE_JSON

5
build-aux/hydra/gnu-system.scm
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@ -1,5 +1,5 @@
;;; GNU Guix --- Functional package management for GNU ;;; 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. ;;; This file is part of GNU Guix.
;;; ;;;
@ -78,6 +78,9 @@
(license . ,(package-license package)) (license . ,(package-license package))
(home-page . ,(package-home-page package)) (home-page . ,(package-home-page package))
(maintainers . ("bug-guix@gnu.org")) (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) (timeout . ,(or (assoc-ref (package-properties package) 'timeout)
72000)))) ; 20 hours by default 72000)))) ; 20 hours by default

143
doc/guix.texi
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@ -399,6 +399,21 @@ for instance with:
# ln -s /var/guix/profiles/per-user/root/guix-profile/bin/guix # ln -s /var/guix/profiles/per-user/root/guix-profile/bin/guix
@end example @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 @item
To use substitutes from @code{hydra.gnu.org} (@pxref{Substitutes}), To use substitutes from @code{hydra.gnu.org} (@pxref{Substitutes}),
authorize them: authorize them:
@ -754,7 +769,7 @@ machines, since offloading works by invoking the @code{guix archive} and
this is the case by running: this is the case by running:
@example @example
lsh build-machine guile -c '(use-modules (guix config))' lsh build-machine guile -c "'(use-modules (guix config))'"
@end example @end example
There's one last thing to do once @file{machines.scm} is in place. As 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 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. 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 @item --dry-run
@itemx -n @itemx -n
Do not build the derivations. Do not build the derivations.
@ -4271,11 +4294,12 @@ guix import cpan Acme::Boolean
@item cran @item cran
@cindex CRAN @cindex CRAN
@cindex Bioconductor
Import meta-data from @uref{http://cran.r-project.org/, CRAN}, the Import meta-data from @uref{http://cran.r-project.org/, CRAN}, the
central repository for the @uref{http://r-project.org, GNU@tie{}R central repository for the @uref{http://r-project.org, GNU@tie{}R
statistical and graphical environment}. 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} The command command below imports meta-data for the @code{Cairo}
R package: R package:
@ -4284,6 +4308,21 @@ R package:
guix import cran Cairo guix import cran Cairo
@end example @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 @item nix
Import meta-data from a local copy of the source of the Import meta-data from a local copy of the source of the
@uref{http://nixos.org/nixpkgs/, Nixpkgs distribution}@footnote{This @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; the updater for @uref{http://elpa.gnu.org/, ELPA} packages;
@item cran @item cran
the updater for @uref{http://cran.r-project.org/, CRAN} packages; 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 @item pypi
the updater for @uref{https://pypi.python.org, PyPI} packages. the updater for @uref{https://pypi.python.org, PyPI} packages.
@end table @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 Others, such as @code{packages} and @code{services}, can be omitted, in
which case they get a default value. 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 @vindex %base-packages
The @code{packages} field lists The @code{packages} field lists packages that will be globally visible
packages that will be globally visible on the system, for all user on the system, for all user accounts---i.e., in every user's @code{PATH}
accounts---i.e., in every user's @code{PATH} environment variable---in environment variable---in addition to the per-user profiles
addition to the per-user profiles (@pxref{Invoking guix package}). The (@pxref{Invoking guix package}). The @var{%base-packages} variable
@var{%base-packages} variable provides all the tools one would expect provides all the tools one would expect for basic user and administrator
for basic user and administrator tasks---including the GNU Core tasks---including the GNU Core Utilities, the GNU Networking Utilities,
Utilities, the GNU Networking Utilities, the GNU Zile lightweight text the GNU Zile lightweight text editor, @command{find}, @command{grep},
editor, @command{find}, @command{grep}, etc. The example above adds etc. The example above adds tcpdump to those, taken from the @code{(gnu
tcpdump to those, taken from the @code{(gnu packages admin)} module packages admin)} module (@pxref{Package Modules}).
(@pxref{Package Modules}).
@findex specification->package @findex specification->package
Referring to packages by variable name, like @var{tcpdump} above, has Referring to packages by variable name, like @var{tcpdump} above, has
@ -5706,6 +5753,8 @@ version:
%base-packages))) %base-packages)))
@end lisp @end lisp
@unnumberedsubsubsec System Services
@vindex %base-services @vindex %base-services
The @code{services} field lists @dfn{system services} to be made The @code{services} field lists @dfn{system services} to be made
available when the system starts (@pxref{Services}). 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 @xref{Desktop Services}, for the exact list of services provided by
@var{%desktop-services}. @xref{X.509 Certificates}, for background @var{%desktop-services}. @xref{X.509 Certificates}, for background
information about the @code{nss-certs} package that is used here. 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 file, the @command{guix system reconfigure my-system-config.scm} command
instantiates that configuration, and makes it the default GRUB boot instantiates that configuration, and makes it the default GRUB boot
entry (@pxref{Invoking guix system}). 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 @command{guix system list-generations} command lists the system
generations available on disk. generations available on disk.
@unnumberedsubsubsec The Programming Interface
At the Scheme level, the bulk of an @code{operating-system} declaration At the Scheme level, the bulk of an @code{operating-system} declaration
is instantiated with the following monadic procedure (@pxref{The Store is instantiated with the following monadic procedure (@pxref{The Store
Monad}): Monad}):
@ -5792,6 +5857,11 @@ the packages, configuration files, and other supporting files needed to
instantiate @var{os}. instantiate @var{os}.
@end deffn @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 @node operating-system Reference
@subsection @code{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 That locale must be among the @dfn{locale definitions} that are known to
the system---and these are specified in the @code{locale-definitions} the system---and these are specified in the @code{locale-definitions}
slot of @code{operating-system}. The default value includes locale 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. locales, in order to save space.
If the locale specified in the @code{locale} field is not among the 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. @command{man tor} for information about the configuration file.
@end deffn @end deffn
@cindex hidden service
@deffn {Scheme Procedure} tor-hidden-service @var{name} @var{mapping} @deffn {Scheme Procedure} tor-hidden-service @var{name} @var{mapping}
Define a new Tor @dfn{hidden service} called @var{name} and implementing 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: @var{mapping}. @var{mapping} is a list of port/host tuples, such as:
@example @example
'((22 \"127.0.0.1:22\") '((22 "127.0.0.1:22")
(80 \"127.0.0.1:8080\")) (80 "127.0.0.1:8080"))
@end example @end example
In this example, port 22 of the hidden service is mapped to local port 22, and 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. further.
@deffn {Monadic Procedure} base-initrd @var{file-systems} @ @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 '()] [#:extra-modules '()] [#:mapped-devices '()]
Return a monadic derivation that builds a generic initrd. @var{file-systems} is 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 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 @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 @node Synopses and Descriptions
@subsection Synopses and Descriptions @subsection Synopses and Descriptions

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

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

@ -41,7 +41,7 @@
"Return #t if user namespaces can be created by unprivileged users." "Return #t if user namespaces can be created by unprivileged users."
(let ((userns-file "/proc/sys/kernel/unprivileged_userns_clone")) (let ((userns-file "/proc/sys/kernel/unprivileged_userns_clone"))
(if (file-exists? userns-file) (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))) #t)))
(define (setgroups-supported?) (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 Taylan Ulrich Bayırlı/Kammer <taylanbayirli@gmail.com>
;;; Copyright © 2015 Alex Sassmannshausen <alex.sassmannshausen@gmail.com> ;;; Copyright © 2015 Alex Sassmannshausen <alex.sassmannshausen@gmail.com>
;;; Copyright © 2015 Eric Dvorsak <eric@dvorsak.fr> ;;; Copyright © 2015 Eric Dvorsak <eric@dvorsak.fr>
;;; Copyright © 2016 Leo Famulari <leo@famulari.name>
;;; ;;;
;;; This file is part of GNU Guix. ;;; This file is part of GNU Guix.
;;; ;;;
@ -392,7 +393,7 @@ connection alive.")
(bind-minor-version "9") (bind-minor-version "9")
(bind-patch-version "8") (bind-patch-version "8")
(bind-release-type "-P") (bind-release-type "-P")
(bind-release-version "2") (bind-release-version "3")
(bind-version (string-append bind-major-version (bind-version (string-append bind-major-version
"." "."
bind-minor-version bind-minor-version
@ -508,7 +509,7 @@ connection alive.")
"/bind-" bind-version ".tar.gz")) "/bind-" bind-version ".tar.gz"))
(sha256 (sha256
(base32 (base32
"0agkpmpna7s67la13krn4xlhwhdjpazmljxlq0zbjdwnw4k1k17m")))) "01qa17479jghy90lb2j8b1bpg3ay6k6aaajpigyirwzsvyc9yj3a"))))
;; When cross-compiling, we need the cross Coreutils and sed. ;; When cross-compiling, we need the cross Coreutils and sed.
;; Otherwise just use those from %FINAL-INPUTS. ;; Otherwise just use those from %FINAL-INPUTS.
@ -1377,3 +1378,25 @@ command that learns\". It works by maintaining a database of the directories
you use the most from the command line and allows you to \"jump\" to you use the most from the command line and allows you to \"jump\" to
frequently used directories by typing only a small pattern.") frequently used directories by typing only a small pattern.")
(license license:gpl3+))) (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 @@ fast arithmetic.")
(define-public arb (define-public arb
(package (package
(name "arb") (name "arb")
(version "2.7.0") (version "2.8.1")
(source (origin (source (origin
(method url-fetch) (method url-fetch)
(uri (string-append (uri (string-append
@ -247,7 +247,8 @@ fast arithmetic.")
(file-name (string-append name "-" version ".tar.gz")) (file-name (string-append name "-" version ".tar.gz"))
(sha256 (sha256
(base32 (base32
"1rwkffs57v8mry63rq8l2dyw69zfs9rg5fpbfllqp3nkjnkp1fly")))) "04hhcpshfkcq9fr4hixbhpps50yf9drk62xgkvlcaj5kb4nyrx7l"))
(patches (map search-patch '("arb-ldconfig.patch")))))
(build-system gnu-build-system) (build-system gnu-build-system)
(propagated-inputs (propagated-inputs
`(("flint" ,flint))) ; flint.h is included by arf.h `(("flint" ,flint))) ; flint.h is included by arf.h

6
gnu/packages/audio.scm
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@ -3,7 +3,7 @@
;;; Copyright © 2015 Taylan Ulrich Bayırlı/Kammer <taylanbayirli@gmail.com> ;;; Copyright © 2015 Taylan Ulrich Bayırlı/Kammer <taylanbayirli@gmail.com>
;;; Copyright © 2015 Andreas Enge <andreas@enge.fr> ;;; Copyright © 2015 Andreas Enge <andreas@enge.fr>
;;; Copyright © 2015 Alex Kost <alezost@gmail.com> ;;; 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. ;;; This file is part of GNU Guix.
;;; ;;;
@ -1535,14 +1535,14 @@ surround and reverb.")
(define-public libxmp (define-public libxmp
(package (package
(name "libxmp") (name "libxmp")
(version "4.3.8") (version "4.3.10")
(source (origin (source (origin
(method url-fetch) (method url-fetch)
(uri (string-append "mirror://sourceforge/xmp/libxmp/" (uri (string-append "mirror://sourceforge/xmp/libxmp/"
name "-" version ".tar.gz")) name "-" version ".tar.gz"))
(sha256 (sha256
(base32 (base32
"0h06091hlpgc6ds4pjmfq8sx4snw7av3nhny180q4pwfyasjb6ny")))) "1gm5xa0ca7ypcbj3bkmj3k1vvzl7nkch8gjyrm8p1a9vgzr0n761"))))
(build-system gnu-build-system) (build-system gnu-build-system)
(home-page "http://xmp.sourceforge.net/") (home-page "http://xmp.sourceforge.net/")
(synopsis "Module player library") (synopsis "Module player library")

230
gnu/packages/bioinformatics.scm
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@ -654,6 +654,73 @@ gapped, local, and paired-end alignment modes.")
(supported-systems '("x86_64-linux")) (supported-systems '("x86_64-linux"))
(license license:gpl3+))) (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 (define-public bwa
(package (package
(name "bwa") (name "bwa")
@ -915,6 +982,64 @@ files between different genome assemblies. It supports most commonly used
file formats including SAM/BAM, Wiggle/BigWig, BED, GFF/GTF, VCF.") file formats including SAM/BAM, Wiggle/BigWig, BED, GFF/GTF, VCF.")
(license license:gpl2+))) (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 (define-public cutadapt
(package (package
(name "cutadapt") (name "cutadapt")
@ -3016,40 +3141,107 @@ optimized for modern read lengths of 100 bases or higher, and takes advantage
of these reads to align data quickly through a hash-based indexing scheme.") of these reads to align data quickly through a hash-based indexing scheme.")
(license license:asl2.0))) (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 (define-public star
(package (package
(name "star") (name "star")
(version "2.4.2a") (version "2.5.1b")
(source (origin (source (origin
(method url-fetch) (method url-fetch)
(uri (string-append (uri (string-append "https://github.com/alexdobin/STAR/archive/"
"https://github.com/alexdobin/STAR/archive/STAR_" version ".tar.gz"))
version ".tar.gz")) (file-name (string-append name "-" version ".tar.gz"))
(sha256 (sha256
(base32 (base32
"1c3rnm7r5l0kl3d04gl1g7938xqf1c2l0mla87rlplqg1hcns5mc")) "0wzcfhkg10apnh0y73xlarfa79xxwxdizicbdl11wb48awk44iq4"))
(modules '((guix build utils))) (modules '((guix build utils)))
(snippet (snippet
'(substitute* "source/Makefile" '(begin
(("/bin/rm") "rm"))))) (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) (build-system gnu-build-system)
(arguments (arguments
'(#:tests? #f ;no check target '(#:tests? #f ;no check target
#:make-flags '("STAR") #:make-flags '("STAR")
#:phases #:phases
(alist-cons-after (modify-phases %standard-phases
'unpack 'enter-source-dir (lambda _ (chdir "source")) (add-after 'unpack 'enter-source-dir
(alist-replace (lambda _ (chdir "source") #t))
'install (add-after 'enter-source-dir 'do-not-use-bundled-htslib
(lambda* (#:key outputs #:allow-other-keys) (lambda _
(let ((bin (string-append (assoc-ref outputs "out") "/bin/"))) (substitute* "Makefile"
(install-file "STAR" bin))) (("(Depend.list: \\$\\(SOURCES\\) parametersDefault\\.xxd) htslib"
(alist-delete _ prefix) prefix))
'configure %standard-phases))))) (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 (native-inputs
`(("vim" ,vim))) ; for xxd `(("vim" ,vim))) ; for xxd
(inputs (inputs
`(("zlib" ,zlib))) `(("htslib" ,htslib)
("zlib" ,zlib)))
(home-page "https://github.com/alexdobin/STAR") (home-page "https://github.com/alexdobin/STAR")
(synopsis "Universal RNA-seq aligner") (synopsis "Universal RNA-seq aligner")
(description (description
@ -4002,7 +4194,7 @@ genomic intervals. In addition, it can use BAM or BigWig files as input.")
(define-public r-qtl (define-public r-qtl
(package (package
(name "r-qtl") (name "r-qtl")
(version "1.37-11") (version "1.38-4")
(source (source
(origin (origin
(method url-fetch) (method url-fetch)
@ -4010,7 +4202,7 @@ genomic intervals. In addition, it can use BAM or BigWig files as input.")
version ".tar.gz")) version ".tar.gz"))
(sha256 (sha256
(base32 (base32
"0h20d36mww7ljp51pfs66xq33yq4b4fwq9nsh02dpmfhlaxgx1xi")))) "0rv9xhp8lyldpgwxqirhyjqvg07dr5x4x1x2jpyj37dada9ccyx3"))))
(build-system r-build-system) (build-system r-build-system)
(home-page "http://rqtl.org/") (home-page "http://rqtl.org/")
(synopsis "R package for analyzing QTL experiments in genetics") (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 ;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2014 Taylan Ulrich Bayirli/Kammer <taylanbayirli@gmail.com> ;;; Copyright © 2014 Taylan Ulrich Bayirli/Kammer <taylanbayirli@gmail.com>
;;; Copyright © 2014, 2015 Ludovic Courtès <ludo@gnu.org> ;;; Copyright © 2014, 2015 Ludovic Courtès <ludo@gnu.org>
;;; Copyright © 2016 Leo Famulari <leo@famulari.name>
;;; ;;;
;;; This file is part of GNU Guix. ;;; This file is part of GNU Guix.
;;; ;;;
@ -21,6 +22,7 @@
#:use-module (guix packages) #:use-module (guix packages)
#:use-module (guix download) #:use-module (guix download)
#:use-module (guix build-system gnu) #:use-module (guix build-system gnu)
#:use-module (guix build-system python)
#:use-module (guix build-system glib-or-gtk) #:use-module (guix build-system glib-or-gtk)
#:use-module ((guix licenses) #:prefix l:) #:use-module ((guix licenses) #:prefix l:)
#:use-module (gnu packages libevent) #:use-module (gnu packages libevent)
@ -33,6 +35,7 @@
#:use-module (gnu packages gtk) #:use-module (gnu packages gtk)
#:use-module (gnu packages check) #:use-module (gnu packages check)
#:use-module (gnu packages ncurses) #:use-module (gnu packages ncurses)
#:use-module (gnu packages python)
#:use-module (gnu packages curl) #:use-module (gnu packages curl)
#:use-module (gnu packages cyrus-sasl) #:use-module (gnu packages cyrus-sasl)
#:use-module (gnu packages tls)) #:use-module (gnu packages tls))
@ -148,3 +151,44 @@ full encryption, DHT, PEX, and Magnet Links. It can also be controlled via
XML-RPC over SCGI.") XML-RPC over SCGI.")
(home-page "https://github.com/rakshasa/rtorrent") (home-page "https://github.com/rakshasa/rtorrent")
(license l:gpl2+))) (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 ;;; 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. ;;; This file is part of GNU Guix.
;;; ;;;
@ -169,7 +169,7 @@ tools that process C/C++ code.")
(_ "UNSUPPORTED")))) (_ "UNSUPPORTED"))))
(package (package
(name "american-fuzzy-lop") (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 (source
(origin (origin
(method url-fetch) (method url-fetch)
@ -177,7 +177,7 @@ tools that process C/C++ code.")
"afl-" version ".tgz")) "afl-" version ".tgz"))
(sha256 (sha256
(base32 (base32
"1by9ncf6lgcyibzqwyla34jv64sd66mn8zhgjz2pcgsds51qwn0r")))) "0z7j231p6v2h1dxxijgdzj1lq1lxr8cxllwf6iyv7p4ki5pv1gh3"))))
(build-system gnu-build-system) (build-system gnu-build-system)
(inputs (inputs
`(("custom-qemu" `(("custom-qemu"
@ -190,11 +190,13 @@ tools that process C/C++ code.")
;; afl only supports using a single afl-qemu-trace executable, so ;; afl only supports using a single afl-qemu-trace executable, so
;; we only build qemu for the native target. ;; we only build qemu for the native target.
(arguments (arguments
`(#:configure-flags `(#:modules ((srfi srfi-1)
(list (string-append "--target-list=" ,machine "-linux-user"))
#:modules ((srfi srfi-1)
,@%gnu-build-system-modules) ,@%gnu-build-system-modules)
,@(substitute-keyword-arguments (package-arguments qemu-2.3.0) ,@(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) ((#:phases qemu-phases)
`(modify-phases ,qemu-phases `(modify-phases ,qemu-phases
(add-after (add-after
@ -236,8 +238,8 @@ tools that process C/C++ code.")
(lambda* (#:key inputs outputs #:allow-other-keys) (lambda* (#:key inputs outputs #:allow-other-keys)
(let ((qemu (assoc-ref inputs "custom-qemu")) (let ((qemu (assoc-ref inputs "custom-qemu"))
(out (assoc-ref outputs "out"))) (out (assoc-ref outputs "out")))
(copy-file (string-append qemu "/bin/qemu-" ,machine) (symlink (string-append qemu "/bin/qemu-" ,machine)
(string-append out "/bin/afl-qemu-trace")) (string-append out "/bin/afl-qemu-trace"))
#t))) #t)))
(delete 'check)))) (delete 'check))))
(supported-systems (fold delete (supported-systems (fold delete

36
gnu/packages/dns.scm
View File

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

4
gnu/packages/ebook.scm
View File

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

6
gnu/packages/enlightenment.scm
View File

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

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

@ -32,7 +32,7 @@
(source (source
(origin (origin
(method url-fetch) (method url-fetch)
(uri (string-append "http://jxself.org/" name ".tar.gz")) (uri (string-append "https://jxself.org/" name ".tar.gz"))
(sha256 (sha256
(base32 (base32
"1hjcpy5439qs3v2zykis7hsi0i17zjs62gks3zd8mnfw9ni4i2h3")))) "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 © 2012, 2013, 2014, 2015 Ludovic Courtès <ludo@gnu.org>
;;; Copyright © 2013, 2014, 2015 Andreas Enge <andreas@enge.fr> ;;; Copyright © 2013, 2014, 2015 Andreas Enge <andreas@enge.fr>
;;; Copyright © 2012 Nikita Karetnikov <nikita@karetnikov.org> ;;; 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 Federico Beffa <beffa@fbengineering.ch>
;;; Copyright © 2015 Taylan Ulrich Bayırlı/Kammer <taylanbayirli@gmail.com> ;;; 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> ;;; Copyright © 2016 Christopher Allan Webber <cwebber@dustycloud.org>
;;; ;;;
;;; This file is part of GNU Guix. ;;; This file is part of GNU Guix.
@ -286,7 +286,9 @@ for SYSTEM, or #f if there is no configuration for SYSTEM."
(uri (linux-libre-urls version)) (uri (linux-libre-urls version))
(sha256 (sha256
(base32 (base32
"1839xsaifs7vvyblzin8jps0gqi10xmz1l9p4x0j27vmdj39jgpm")))) "1839xsaifs7vvyblzin8jps0gqi10xmz1l9p4x0j27vmdj39jgpm"))
(patches
(list (search-patch "linux-libre-CVE-2016-0728.patch")))))
(build-system gnu-build-system) (build-system gnu-build-system)
(supported-systems '("x86_64-linux" "i686-linux")) (supported-systems '("x86_64-linux" "i686-linux"))
(native-inputs `(("perl" ,perl) (native-inputs `(("perl" ,perl)
@ -1234,7 +1236,7 @@ processes currently causing I/O.")
(define-public fuse (define-public fuse
(package (package
(name "fuse") (name "fuse")
(version "2.9.4") (version "2.9.5")
(source (origin (source (origin
(method url-fetch) (method url-fetch)
(uri (let ((version-with-underscores (uri (let ((version-with-underscores
@ -1245,7 +1247,7 @@ processes currently causing I/O.")
"/fuse-" version ".tar.gz"))) "/fuse-" version ".tar.gz")))
(sha256 (sha256
(base32 (base32
"1qbwp63a2bp0bchabkwiyzszi9x5krlk2pwk2is6g35gyszw1sbb")))) "1dfvbi1p57svbv2sfnbqwpnsk219spvjnlapf35azhgzqlf3g7sp"))))
(build-system gnu-build-system) (build-system gnu-build-system)
(inputs `(("util-linux" ,util-linux))) (inputs `(("util-linux" ,util-linux)))
(arguments (arguments

35
gnu/packages/mail.scm
View File

@ -8,7 +8,8 @@
;;; Copyright © 2015 Paul van der Walt <paul@denknerd.org> ;;; Copyright © 2015 Paul van der Walt <paul@denknerd.org>
;;; Copyright © 2015 Eric Bavier <bavier@member.fsf.org> ;;; Copyright © 2015 Eric Bavier <bavier@member.fsf.org>
;;; Copyright © 2015 Andreas Enge <andreas@enge.fr> ;;; 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. ;;; This file is part of GNU Guix.
;;; ;;;
@ -519,7 +520,7 @@ MailCore 2.")
(define-public claws-mail (define-public claws-mail
(package (package
(name "claws-mail") (name "claws-mail")
(version "3.13.1") (version "3.13.2")
(source (origin (source (origin
(method url-fetch) (method url-fetch)
(uri (string-append (uri (string-append
@ -527,7 +528,7 @@ MailCore 2.")
".tar.xz")) ".tar.xz"))
(sha256 (sha256
(base32 (base32
"049av7r0xhjjjm1p93l2ns3xisvn125v3ncqar23cqjzgcichg5d")))) "1l8ankx0qpq1ix1an8viphcf11ksh53jsrm1xjmq8cjbh5910wva"))))
(build-system gnu-build-system) (build-system gnu-build-system)
(native-inputs `(("pkg-config" ,pkg-config))) (native-inputs `(("pkg-config" ,pkg-config)))
(inputs `(("bogofilter" ,bogofilter) (inputs `(("bogofilter" ,bogofilter)
@ -1014,4 +1015,32 @@ compatibility shims for the @command{sendmail}, @command{mailq}, and
@command{newaliases} commands.") @command{newaliases} commands.")
(license gpl2+))) (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 ;;; mail.scm ends here

15
gnu/packages/messaging.scm
View File

@ -1,5 +1,5 @@
;;; GNU Guix --- Functional package management for GNU ;;; 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 © 2014 Julien Lepiller <julien@lepiller.eu>
;;; Copyright © 2015 Taylan Ulrich Bayırlı/Kammer <taylanbayirli@gmail.com> ;;; Copyright © 2015 Taylan Ulrich Bayırlı/Kammer <taylanbayirli@gmail.com>
;;; Copyright © 2015 Andreas Enge <andreas@enge.fr> ;;; Copyright © 2015 Andreas Enge <andreas@enge.fr>
@ -425,7 +425,7 @@ was initially a fork of xmpppy, but is using non-blocking sockets.")
(define-public gajim (define-public gajim
(package (package
(name "gajim") (name "gajim")
(version "0.16.4") (version "0.16.5")
(source (origin (source (origin
(method url-fetch) (method url-fetch)
(uri (string-append "https://gajim.org/downloads/" (uri (string-append "https://gajim.org/downloads/"
@ -433,10 +433,17 @@ was initially a fork of xmpppy, but is using non-blocking sockets.")
"/gajim-" version ".tar.bz2")) "/gajim-" version ".tar.bz2"))
(sha256 (sha256
(base32 (base32
"0zyfs7q1qg8iqszr8l1gb18gqla6zrrfsgpmbxblpi9maqxas5i1")))) "14fhcqnkqygh91132dnf1idayj4r3iqbwb44sd3mxv20n6ribh55"))))
(build-system gnu-build-system) (build-system gnu-build-system)
(arguments (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 (modify-phases %standard-phases
(add-after 'install 'wrap-program (add-after 'install 'wrap-program
(lambda* (#:key outputs #:allow-other-keys) (lambda* (#:key outputs #:allow-other-keys)

50
gnu/packages/music.scm
View File

@ -1,6 +1,6 @@
;;; GNU Guix --- Functional package management for GNU ;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2014 Eric Bavier <bavier@member.fsf.org> ;;; 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> ;;; Copyright © 2015 Paul van der Walt <paul@denknerd.org>
;;; ;;;
;;; This file is part of GNU Guix. ;;; This file is part of GNU Guix.
@ -328,7 +328,11 @@ you to define complex tempo maps for entire songs or performances.")
music. Music is input in a text file containing control sequences which are 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 interpreted by LilyPond to produce the final document. It is extendable with
Guile.") 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 (define-public non-sequencer
;; The latest tagged release is three years old and uses a custom build ;; The latest tagged release is three years old and uses a custom build
@ -957,7 +961,7 @@ capabilities, custom envelopes, effects, etc.")
(define-public yoshimi (define-public yoshimi
(package (package
(name "yoshimi") (name "yoshimi")
(version "1.3.7.1") (version "1.3.8.2")
(source (origin (source (origin
(method url-fetch) (method url-fetch)
(uri (string-append "mirror://sourceforge/yoshimi/" (uri (string-append "mirror://sourceforge/yoshimi/"
@ -965,7 +969,7 @@ capabilities, custom envelopes, effects, etc.")
"/yoshimi-" version ".tar.bz2")) "/yoshimi-" version ".tar.bz2"))
(sha256 (sha256
(base32 (base32
"13xc1x8jrr2rn26jx4dini692ww3771d5j5xf7f56ixqr7mmdhvz")))) "0wl4ln6v1nkkx56kfah23chyrhga2vi93i82g0s200c4s4184xr8"))))
(build-system cmake-build-system) (build-system cmake-build-system)
(arguments (arguments
`(#:tests? #f ; there are no tests `(#:tests? #f ; there are no tests
@ -1036,3 +1040,41 @@ graphically in the terminal. It is built on a full-featured subtractive
synthesis engine. Notes and parameter changes may be entered via MIDI or the synthesis engine. Notes and parameter changes may be entered via MIDI or the
computer's keyboard.") computer's keyboard.")
(license license:gpl3+))) (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 ;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2012 Nikita Karetnikov <nikita@karetnikov.org> ;;; 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. ;;; This file is part of GNU Guix.
;;; ;;;
@ -28,7 +28,7 @@
(define-public nano (define-public nano
(package (package
(name "nano") (name "nano")
(version "2.5.0") (version "2.5.1")
(source (source
(origin (origin
(method url-fetch) (method url-fetch)
@ -36,7 +36,7 @@
version ".tar.gz")) version ".tar.gz"))
(sha256 (sha256
(base32 (base32
"1vl9bim56k1b4zwc3icxp46w6pn6gb042j1h4jlz1jklxxpkwcpz")))) "1piv8prj6w3rvsrrx41ra8c10b8fzkgjhnm6399lsgqqpw0wlvz0"))))
(build-system gnu-build-system) (build-system gnu-build-system)
(inputs (inputs
`(("gettext" ,gnu-gettext) `(("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 @@ security, and applying best practice development processes.")
(define-public acme (define-public acme
(package (package
(name "acme") (name "acme")
(version "0.1.1") (version "0.2.0")
(source (origin (source (origin
(method url-fetch) (method url-fetch)
(uri (pypi-uri "acme" version)) (uri (pypi-uri "acme" version))
(sha256 (sha256
(base32 (base32
"1yv0gy8akaqp5p2wjpfj8r5i0da04a9qdmlh06rczdkrmk6q680w")))) "1xcbywzrwrj2cmqhaj4k6b11wfkbm3i7za2k9j1sd74rs1zh5abl"))))
(build-system python-build-system) (build-system python-build-system)
(arguments (arguments
`(#:python ,python-2)) `(#:python ,python-2))
@ -371,13 +371,13 @@ security, and applying best practice development processes.")
(define-public letsencrypt (define-public letsencrypt
(package (package
(name "letsencrypt") (name "letsencrypt")
(version "0.1.1") (version "0.2.0")
(source (origin (source (origin
(method url-fetch) (method url-fetch)
(uri (pypi-uri "letsencrypt" version)) (uri (pypi-uri "letsencrypt" version))
(sha256 (sha256
(base32 (base32
"1kia3wk66lxyi2fghp9sd7cqgr5qiwdfayz153hi4wpa3q1q8rwf")))) "0q57ylx00b6kl9zvawgag5yl03vlv1cjhp18xm96682pdibbgjci"))))
(build-system python-build-system) (build-system python-build-system)
(arguments (arguments
`(#:python ,python-2)) `(#:python ,python-2))

9
gnu/packages/tor.scm
View File

@ -1,6 +1,7 @@
;;; GNU Guix --- Functional package management for GNU ;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2013, 2014, 2015 Ludovic Courtès <ludo@gnu.org> ;;; Copyright © 2013, 2014, 2015 Ludovic Courtès <ludo@gnu.org>
;;; Copyright © 2014, 2015 Mark H Weaver <mhw@netris.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. ;;; This file is part of GNU Guix.
;;; ;;;
@ -36,14 +37,14 @@
(define-public tor (define-public tor
(package (package
(name "tor") (name "tor")
(version "0.2.7.5") (version "0.2.7.6")
(source (origin (source (origin
(method url-fetch) (method url-fetch)
(uri (string-append "https://www.torproject.org/dist/tor-" (uri (string-append "https://www.torproject.org/dist/tor-"
version ".tar.gz")) version ".tar.gz"))
(sha256 (sha256
(base32 (base32
"0pxayvcab4cb107ynbpzx4g0qyr1mjfba2an76wdx6dxn56rwakx")))) "0p8hjlfi8dwghlyjif5s0q98cmpgz9kn9jja25430l04z5wqcfj9"))))
(build-system gnu-build-system) (build-system gnu-build-system)
(native-inputs (native-inputs
`(("python" ,python-2))) ; for tests `(("python" ,python-2))) ; for tests
@ -103,7 +104,7 @@ rejects UDP traffic from the application you're using.")
(define-public privoxy (define-public privoxy
(package (package
(name "privoxy") (name "privoxy")
(version "3.0.21") (version "3.0.24")
(source (origin (source (origin
(method url-fetch) (method url-fetch)
(uri (string-append "mirror://sourceforge/ijbswa/Sources/" (uri (string-append "mirror://sourceforge/ijbswa/Sources/"
@ -111,7 +112,7 @@ rejects UDP traffic from the application you're using.")
version "-stable-src.tar.gz")) version "-stable-src.tar.gz"))
(sha256 (sha256
(base32 (base32
"1f6xb7aa47p90c26vqaw74y6drs9gpnhxsgby3mx0awdjh0ydisy")))) "04mhkz5g713i2crvjd6s783hhrlsjjjlfb9llbaf13ghg3fgd0d3"))))
(build-system gnu-build-system) (build-system gnu-build-system)
(arguments (arguments
'(;; The default 'sysconfdir' is $out/etc; change that to '(;; 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 © 2015 Mathieu Lirzin <mthl@openmailbox.org>
;;; Copyright © 2014, 2015 Mark H Weaver <mhw@netris.org> ;;; Copyright © 2014, 2015 Mark H Weaver <mhw@netris.org>
;;; Copyright © 2014 Eric Bavier <bavier@member.fsf.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 Kyle Meyer <kyle@kyleam.com>
;;; Copyright © 2015 Ricardo Wurmus <rekado@elephly.net> ;;; Copyright © 2015 Ricardo Wurmus <rekado@elephly.net>
;;; ;;;
@ -1004,7 +1004,7 @@ modification time.")
(define-public myrepos (define-public myrepos
(package (package
(name "myrepos") (name "myrepos")
(version "1.20151022") (version "1.20160123")
(source (source
(origin (origin
(method url-fetch) (method url-fetch)
@ -1013,7 +1013,7 @@ modification time.")
version ".tar.gz")) version ".tar.gz"))
(file-name (string-append name "-" version ".tar.gz")) (file-name (string-append name "-" version ".tar.gz"))
(sha256 (sha256
(base32 "0c93lqsngpsxsca7nygk4qhidr40ijgih86q81x1mfcwbs0gbds8")))) (base32 "1723cg5haplz2w9dwdzp6ds1ip33cx3awmj4wnb0h4yq171v5lqk"))))
(build-system gnu-build-system) (build-system gnu-build-system)
(inputs (inputs
`(("perl" ,perl))) `(("perl" ,perl)))

36
gnu/packages/video.scm
View File

@ -1,6 +1,6 @@
;;; GNU Guix --- Functional package management for GNU ;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2013, 2014, 2015 Andreas Enge <andreas@enge.fr> ;;; 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 © 2014, 2015, 2016 Mark H Weaver <mhw@netris.org>
;;; Copyright © 2015 Taylan Ulrich Bayırlı/Kammer <taylanbayirli@gmail.com> ;;; Copyright © 2015 Taylan Ulrich Bayırlı/Kammer <taylanbayirli@gmail.com>
;;; Copyright © 2015, 2016 Efraim Flashner <efraim@flashner.co.il> ;;; Copyright © 2015, 2016 Efraim Flashner <efraim@flashner.co.il>
@ -1265,6 +1265,39 @@ functionality of the system is provided via an assortment of ready to use
tools, XML authoring components, and an extensible plug-in based API.") tools, XML authoring components, and an extensible plug-in based API.")
(license license:lgpl2.1+))) (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 (define-public obs
(package (package
(name "obs") (name "obs")
@ -1293,6 +1326,7 @@ tools, XML authoring components, and an extensible plug-in based API.")
("mesa" ,mesa) ("mesa" ,mesa)
("pulseaudio" ,pulseaudio) ("pulseaudio" ,pulseaudio)
("qt" ,qt) ("qt" ,qt)
("v4l-utils" ,v4l-utils)
("zlib" ,zlib))) ("zlib" ,zlib)))
(synopsis "Live streaming software") (synopsis "Live streaming software")
(description "Open Broadcaster Software provides a graphical interface for (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 Sree Harsha Totakura <sreeharsha@totakura.in>
;;; Copyright © 2014 Mark H Weaver <mhw@netris.org> ;;; Copyright © 2014 Mark H Weaver <mhw@netris.org>
;;; Copyright © 2015 Paul van der Walt <paul@denknerd.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. ;;; This file is part of GNU Guix.
;;; ;;;
@ -293,7 +293,7 @@ ogginfo, to obtain information (tags, bitrate, length, etc.) about
(define opus (define opus
(package (package
(name "opus") (name "opus")
(version "1.1.1") (version "1.1.2")
(source (origin (source (origin
(method url-fetch) (method url-fetch)
(uri (string-append (uri (string-append
@ -301,7 +301,7 @@ ogginfo, to obtain information (tags, bitrate, length, etc.) about
".tar.gz")) ".tar.gz"))
(sha256 (sha256
(base32 (base32
"07iplfwim26b6k1bqjyciaqvihps9rk5gi8385axa83ppmbgz14v")))) "1z87x5c5x951lhnm70iqr2gqn15wns5cqsw8nnkvl48jwdw00a8f"))))
(build-system gnu-build-system) (build-system gnu-build-system)
(synopsis "Versatile audio codec") (synopsis "Versatile audio codec")
(description (description
@ -349,7 +349,7 @@ decoding .opus files.")
(define opusfile (define opusfile
(package (package
(name "opusfile") (name "opusfile")
(version "0.6") (version "0.7")
(source (origin (source (origin
(method url-fetch) (method url-fetch)
(uri (string-append (uri (string-append
@ -357,7 +357,7 @@ decoding .opus files.")
".tar.gz")) ".tar.gz"))
(sha256 (sha256
(base32 (base32
"19iys2kld75k0210b807i4illrdmj3cmmnrgxlc9y4vf6mxp2a14")))) "00f3wwjv3hxwg05g22s6mkkxikz80ljsn70g39cmi43jph9ysawy"))))
(build-system gnu-build-system) (build-system gnu-build-system)
(propagated-inputs (propagated-inputs
`(("opus" ,opus))) `(("opus" ,opus)))
@ -409,7 +409,7 @@ things in between.")
(define-public libshout (define-public libshout
(package (package
(name "libshout") (name "libshout")
(version "2.3.1") (version "2.4.1")
(source (origin (source (origin
(method url-fetch) (method url-fetch)
(uri (string-append (uri (string-append
@ -417,7 +417,7 @@ things in between.")
name "-" version ".tar.gz")) name "-" version ".tar.gz"))
(sha256 (sha256
(base32 (base32
"0vlj4dxfxg06xhvv0z2zjjlrjh5di2m28w7v16zcygsy99mmyg6g")))) "0kgjpf8jkgyclw11nilxi8vyjk4s8878x23qyxnvybbgqbgbib7k"))))
(build-system gnu-build-system) (build-system gnu-build-system)
(native-inputs (native-inputs
`(("pkg-config" ,pkg-config))) `(("pkg-config" ,pkg-config)))

5
gnu/services/avahi.scm
View File

@ -1,5 +1,5 @@
;;; GNU Guix --- Functional package management for GNU ;;; 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. ;;; This file is part of GNU Guix.
;;; ;;;
@ -26,7 +26,8 @@
#:use-module (gnu packages admin) #:use-module (gnu packages admin)
#:use-module (guix records) #:use-module (guix records)
#:use-module (guix gexp) #:use-module (guix gexp)
#:export (avahi-service)) #:export (avahi-service
avahi-service-type))
;;; Commentary: ;;; Commentary:
;;; ;;;

26
gnu/system.scm
View File

@ -79,6 +79,7 @@
operating-system-locale-libcs operating-system-locale-libcs
operating-system-mapped-devices operating-system-mapped-devices
operating-system-file-systems operating-system-file-systems
operating-system-store-file-system
operating-system-activation-script operating-system-activation-script
operating-system-derivation operating-system-derivation
@ -678,12 +679,34 @@ listed in OS. The C library expects to find it under
(package-version kernel) (package-version kernel)
" (alpha)")) " (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 '())) (define* (operating-system-grub.cfg os #:optional (old-entries '()))
"Return the GRUB configuration file for OS. Use OLD-ENTRIES to populate the "Return the GRUB configuration file for OS. Use OLD-ENTRIES to populate the
\"old entries\" menu." \"old entries\" menu."
(mlet* %store-monad (mlet* %store-monad
((system (operating-system-derivation os)) ((system (operating-system-derivation os))
(root-fs -> (operating-system-root-file-system os)) (root-fs -> (operating-system-root-file-system os))
(store-fs -> (operating-system-store-file-system os))
(kernel -> (operating-system-kernel os)) (kernel -> (operating-system-kernel os))
(root-device -> (if (eq? 'uuid (file-system-title root-fs)) (root-device -> (if (eq? 'uuid (file-system-title root-fs))
(uuid->string (file-system-device root-fs)) (uuid->string (file-system-device root-fs))
@ -698,7 +721,8 @@ listed in OS. The C library expects to find it under
"/boot") "/boot")
(operating-system-kernel-arguments os))) (operating-system-kernel-arguments os)))
(initrd #~(string-append #$system "/initrd")))))) (initrd #~(string-append #$system "/initrd"))))))
(grub-configuration-file (operating-system-bootloader os) entries (grub-configuration-file (operating-system-bootloader os)
store-fs entries
#:old-entries old-entries))) #:old-entries old-entries)))
(define (operating-system-parameters-file os) (define (operating-system-parameters-file os)

54
gnu/system/grub.scm
View File

@ -1,5 +1,5 @@
;;; GNU Guix --- Functional package management for GNU ;;; 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. ;;; This file is part of GNU Guix.
;;; ;;;
@ -25,6 +25,7 @@
#:use-module (guix gexp) #:use-module (guix gexp)
#:use-module (guix download) #:use-module (guix download)
#:use-module (gnu artwork) #:use-module (gnu artwork)
#:use-module (gnu system file-systems)
#:autoload (gnu packages grub) (grub) #:autoload (gnu packages grub) (grub)
#:autoload (gnu packages inkscape) (inkscape) #:autoload (gnu packages inkscape) (inkscape)
#:autoload (gnu packages imagemagick) (imagemagick) #:autoload (gnu packages imagemagick) (imagemagick)
@ -153,10 +154,12 @@ WIDTH/HEIGHT, or #f if none was found."
(with-monad %store-monad (with-monad %store-monad
(return #f))))) (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 "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 '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 (define setup-gfxterm-body
;; Intel systems need to be switched into graphics mode, whereas most ;; Intel systems need to be switched into graphics mode, whereas most
;; other modern architectures have no other mode and therefore don't need ;; other modern architectures have no other mode and therefore don't need
@ -179,15 +182,18 @@ all that."
(string-append (symbol->string (assoc-ref colors 'fg)) "/" (string-append (symbol->string (assoc-ref colors 'fg)) "/"
(symbol->string (assoc-ref colors 'bg))))) (symbol->string (assoc-ref colors 'bg)))))
(define font-file
#~(string-append #$grub "/share/grub/unicode.pf2"))
(mlet* %store-monad ((image (grub-background-image config))) (mlet* %store-monad ((image (grub-background-image config)))
(return (and image (return (and image
#~(format #$port " #~(format #$port "
function setup_gfxterm {~a} function setup_gfxterm {~a}
# Set 'root' to the partition that contains /gnu/store. # Set 'root' to the partition that contains /gnu/store.
search --file --set ~a/share/grub/unicode.pf2 ~a
if loadfont ~a/share/grub/unicode.pf2; then if loadfont ~a; then
setup_gfxterm setup_gfxterm
fi fi
@ -200,7 +206,9 @@ else
set menu_color_highlight=white/blue set menu_color_highlight=white/blue
fi~%" fi~%"
#$setup-gfxterm-body #$setup-gfxterm-body
#$grub #$grub #$(grub-root-search root-fs font-file)
#$font-file
#$image #$image
#$(theme-colors grub-theme-color-normal) #$(theme-colors grub-theme-color-normal)
#$(theme-colors grub-theme-color-highlight)))))) #$(theme-colors grub-theme-color-highlight))))))
@ -210,13 +218,31 @@ fi~%"
;;; Configuration file. ;;; Configuration file.
;;; ;;;
(define* (grub-configuration-file config entries (define (grub-root-search root-fs file)
"Return the GRUB 'search' command to look for ROOT-FS, which contains FILE,
a gexp. The result is a gexp that can be inserted in the grub.cfg-generation
code."
(case (file-system-title root-fs)
;; Preferably refer to ROOT-FS by its UUID or label. This is more
;; efficient and less ambiguous, see <>.
((uuid)
(format #f "search --fs-uuid --set ~a"
(uuid->string (file-system-device root-fs))))
((label)
(format #f "search --label --set ~a"
(file-system-device root-fs)))
(else
;; As a last resort, look for any device containing FILE.
#~(format #f "search --file --set ~a" #$file))))
(define* (grub-configuration-file config store-fs entries
#:key #:key
(system (%current-system)) (system (%current-system))
(old-entries '())) (old-entries '()))
"Return the GRUB configuration file corresponding to CONFIG, a "Return the GRUB configuration file corresponding to CONFIG, a
<grub-configuration> object. OLD-ENTRIES is taken to be a list of menu <grub-configuration> object, and where the store is available at STORE-FS, a
entries corresponding to old generations of the system." <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 (define linux-image-name
(if (string-prefix? "mips" system) (if (string-prefix? "mips" system)
"vmlinuz" "vmlinuz"
@ -229,18 +255,18 @@ entries corresponding to old generations of the system."
(match-lambda (match-lambda
(($ <menu-entry> label linux arguments initrd) (($ <menu-entry> label linux arguments initrd)
#~(format port "menuentry ~s { #~(format port "menuentry ~s {
# Set 'root' to the partition that contains the kernel. ~a
search --file --set ~a/~a~%
linux ~a/~a ~a linux ~a/~a ~a
initrd ~a initrd ~a
}~%" }~%"
#$label #$label
#$linux #$linux-image-name #$(grub-root-search store-fs
#~(string-append #$linux "/"
#$linux-image-name))
#$linux #$linux-image-name (string-join (list #$@arguments)) #$linux #$linux-image-name (string-join (list #$@arguments))
#$initrd)))) #$initrd))))
(mlet %store-monad ((sugar (eye-candy config system #~port))) (mlet %store-monad ((sugar (eye-candy config store-fs system #~port)))
(define builder (define builder
#~(call-with-output-file #$output #~(call-with-output-file #$output
(lambda (port) (lambda (port)

103
guix/import/cran.scm
View File

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

7
guix/import/gem.scm
View File

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

8
guix/licenses.scm
View File

@ -4,6 +4,7 @@
;;; Copyright © 2012, 2013 Nikita Karetnikov <nikita@karetnikov.org> ;;; Copyright © 2012, 2013 Nikita Karetnikov <nikita@karetnikov.org>
;;; Copyright © 2015 Mark H Weaver <mhw@netris.org> ;;; Copyright © 2015 Mark H Weaver <mhw@netris.org>
;;; Copyright © 2015 Ricardo Wurmus <rekado@elephly.net> ;;; Copyright © 2015 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2016 Eric Bavier <bavier@member.fsf.org>
;;; ;;;
;;; This file is part of GNU Guix. ;;; This file is part of GNU Guix.
;;; ;;;
@ -49,7 +50,7 @@
imlib2 imlib2
ipa ipa
lgpl2.0 lgpl2.0+ lgpl2.1 lgpl2.1+ lgpl3 lgpl3+ lgpl2.0 lgpl2.0+ lgpl2.1 lgpl2.1+ lgpl3 lgpl3+
mpl1.1 mpl2.0 mpl1.0 mpl1.1 mpl2.0
ms-pl ms-pl
ncsa ncsa
openldap2.8 openssl openldap2.8 openssl
@ -302,6 +303,11 @@ at URI, which may be a file:// URI pointing the package's tree."
"https://www.gnu.org/licenses/lgpl.html" "https://www.gnu.org/licenses/lgpl.html"
"https://www.gnu.org/licenses/license-list#LGPLv3")) "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 (define mpl1.1
(license "MPL 1.1" (license "MPL 1.1"
"http://directory.fsf.org/wiki/License:MPLv1.1" "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 ;;; 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> ;;; Copyright © 2013 Mark H Weaver <mhw@netris.org>
;;; ;;;
;;; This file is part of GNU Guix. ;;; This file is part of GNU Guix.
@ -153,6 +153,8 @@ options handled by 'set-build-options-from-command-line', and listed in
(display (_ " (display (_ "
-K, --keep-failed keep build tree of failed builds")) -K, --keep-failed keep build tree of failed builds"))
(display (_ " (display (_ "
-k, --keep-going keep going when some of the derivations fail"))
(display (_ "
-n, --dry-run do not build the derivations")) -n, --dry-run do not build the derivations"))
(display (_ " (display (_ "
--fallback fall back to building when the substituter fails")) --fallback fall back to building when the substituter fails"))
@ -183,6 +185,7 @@ options handled by 'set-build-options-from-command-line', and listed in
;; TODO: Add more options. ;; TODO: Add more options.
(set-build-options store (set-build-options store
#:keep-failed? (assoc-ref opts 'keep-failed?) #:keep-failed? (assoc-ref opts 'keep-failed?)
#:keep-going? (assoc-ref opts 'keep-going?)
#:rounds (assoc-ref opts 'rounds) #:rounds (assoc-ref opts 'rounds)
#:build-cores (or (assoc-ref opts 'cores) 0) #:build-cores (or (assoc-ref opts 'cores) 0)
#:max-build-jobs (or (assoc-ref opts 'max-jobs) 1) #:max-build-jobs (or (assoc-ref opts 'max-jobs) 1)
@ -214,6 +217,11 @@ options handled by 'set-build-options-from-command-line', and listed in
(apply values (apply values
(alist-cons 'keep-failed? #t result) (alist-cons 'keep-failed? #t result)
rest))) 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 (option '("rounds") #t #f
(lambda (opt name arg result . rest) (lambda (opt name arg result . rest)
(apply values (apply values

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

@ -41,6 +41,8 @@
(define (show-help) (define (show-help)
(display (_ "Usage: guix import cran PACKAGE-NAME (display (_ "Usage: guix import cran PACKAGE-NAME
Import and convert the CRAN package for PACKAGE-NAME.\n")) Import and convert the CRAN package for PACKAGE-NAME.\n"))
(display (_ "
-a, --archive=ARCHIVE specify the archive repository"))
(display (_ " (display (_ "
-h, --help display this help and exit")) -h, --help display this help and exit"))
(display (_ " (display (_ "
@ -57,6 +59,10 @@ Import and convert the CRAN package for PACKAGE-NAME.\n"))
(option '(#\V "version") #f #f (option '(#\V "version") #f #f
(lambda args (lambda args
(show-version-and-exit "guix import cran"))) (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)) %standard-import-options))
@ -82,7 +88,8 @@ Import and convert the CRAN package for PACKAGE-NAME.\n"))
(reverse opts)))) (reverse opts))))
(match args (match args
((package-name) ((package-name)
(let ((sexp (cran->guix-package package-name))) (let ((sexp (cran->guix-package package-name
(or (assoc-ref opts 'repo) 'cran))))
(unless sexp (unless sexp
(leave (_ "failed to download description for package '~a'~%") (leave (_ "failed to download description for package '~a'~%")
package-name)) package-name))

1
guix/scripts/refresh.scm
View File

@ -195,6 +195,7 @@ unavailable optional dependencies such as Guile-JSON."
%gnome-updater %gnome-updater
%elpa-updater %elpa-updater
%cran-updater %cran-updater
%bioconductor-updater
((guix import pypi) => %pypi-updater))) ((guix import pypi) => %pypi-updater)))
(define (lookup-updater name) (define (lookup-updater name)

12
tests/cran.scm
View File

@ -86,16 +86,6 @@ Date/Publication: 2015-07-14 14:15:16
'() '()
((@@ (guix import cran) listify) simple-alist "BadList")) ((@@ (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" (test-assert "description->package"
;; Replace network resources with sample data. ;; Replace network resources with sample data.
(mock ((guix build download) url-fetch (mock ((guix build download) url-fetch
@ -107,7 +97,7 @@ Date/Publication: 2015-07-14 14:15:16
("mirror://cran/src/contrib/My-Example_1.2.3.tar.gz" ("mirror://cran/src/contrib/My-Example_1.2.3.tar.gz"
"source") "source")
(_ (error "Unexpected URL: " url)))))))) (_ (error "Unexpected URL: " url))))))))
(match ((@@ (guix import cran) description->package) description-alist) (match ((@@ (guix import cran) description->package) 'cran description-alist)
(('package (('package
('name "r-my-example") ('name "r-my-example")
('version "1.2.3") ('version "1.2.3")

27
tests/derivations.scm
View File

@ -151,6 +151,33 @@
;; the contents. ;; the contents.
(valid-path? %store (derivation->output-path drv))))) (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" (test-assert "identical files are deduplicated"
(let* ((build1 (add-text-to-store %store "one.sh" (let* ((build1 (add-text-to-store %store "one.sh"
"echo hello, world > \"$out\"\n" "echo hello, world > \"$out\"\n"

2
tests/gem.scm
View File

@ -69,7 +69,7 @@
(("bundler" ('unquote 'bundler)) (("bundler" ('unquote 'bundler))
("ruby-bar" ('unquote 'ruby-bar))))) ("ruby-bar" ('unquote 'ruby-bar)))))
('synopsis "A cool gem") ('synopsis "A cool gem")
('description "A cool gem") ('description "This package provides a cool gem")
('home-page "https://example.com") ('home-page "https://example.com")
('license ('list 'expat 'asl2.0))) ('license ('list 'expat 'asl2.0)))
#t) #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 ;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2012, 2013 Cyril Roelandt <tipecaml@gmail.com> ;;; Copyright © 2012, 2013 Cyril Roelandt <tipecaml@gmail.com>
;;; Copyright © 2014, 2015 Eric Bavier <bavier@member.fsf.org> ;;; 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> ;;; Copyright © 2015 Mathieu Lirzin <mthl@openmailbox.org>
;;; ;;;
;;; This file is part of GNU Guix. ;;; This file is part of GNU Guix.
@ -19,6 +19,9 @@
;;; You should have received a copy of the GNU General Public License ;;; You should have received a copy of the GNU General Public License
;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>. ;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
;; Avoid interference.
(unsetenv "http_proxy")
(define-module (test-lint) (define-module (test-lint)
#:use-module (guix tests) #:use-module (guix tests)
#:use-module (guix download) #: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 ;;; You should have received a copy of the GNU General Public License
;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>. ;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
;; Avoid interference.
(unsetenv "http_proxy")
(define-module (test-publish) (define-module (test-publish)
#:use-module (guix scripts publish) #:use-module (guix scripts publish)
#:use-module (guix tests) #:use-module (guix tests)
@ -62,6 +65,7 @@
(connect conn AF_INET (inet-pton AF_INET "127.0.0.1") 6789)) (connect conn AF_INET (inet-pton AF_INET "127.0.0.1") 6789))
(loop)))) (loop))))
(test-begin "publish") (test-begin "publish")
(test-equal "/nix-cache-info" (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))