From 59ef20304b1b3b05fb4262e9e94b605d0b8f6e0d Mon Sep 17 00:00:00 2001 From: Mathieu Lirzin Date: Sun, 13 Sep 2015 14:33:00 +0200 Subject: gnu: Add cvs-fast-export. * gnu/packages/version-control.scm (cvs-fast-export): New variable. --- gnu/packages/version-control.scm | 42 ++++++++++++++++++++++++++++++++++++++++ 1 file changed, 42 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/version-control.scm b/gnu/packages/version-control.scm index 3c0571bac6..e0b3c53858 100644 --- a/gnu/packages/version-control.scm +++ b/gnu/packages/version-control.scm @@ -3,6 +3,7 @@ ;;; Copyright © 2013 Cyril Roelandt ;;; Copyright © 2013, 2014, 2015 Ludovic Courtès ;;; Copyright © 2013, 2014 Andreas Enge +;;; Copyright © 2015 Mathieu Lirzin ;;; Copyright © 2014, 2015 Mark H Weaver ;;; Copyright © 2014 Eric Bavier ;;; @@ -34,10 +35,12 @@ #:use-module (guix build-system trivial) #:use-module (guix build utils) #:use-module (gnu packages apr) + #:use-module (gnu packages asciidoc) #:use-module (gnu packages base) #:use-module (gnu packages bison) #:use-module (gnu packages cook) #:use-module (gnu packages curl) + #:use-module (gnu packages docbook) #:use-module (gnu packages ed) #:use-module (gnu packages file) #:use-module (gnu packages flex) @@ -683,6 +686,45 @@ sources files, and documents. It fills a similar role to the free software RCS, PRCS, and Aegis packages.") (license gpl1+))) +(define-public cvs-fast-export + (package + (name "cvs-fast-export") + (version "1.33") + (source (origin + (method url-fetch) + (uri (string-append "http://www.catb.org/~esr/" + name "/" name "-" version ".tar.gz")) + (sha256 + (base32 + "1c3s4nacbwlaaccx1fr7hf72kxxrzy49y2rdz5hhqbk8r29vm8w1")))) + (build-system gnu-build-system) + (arguments + `(#:phases (modify-phases %standard-phases (delete 'configure)) + #:make-flags + (list "CC=gcc" (string-append "prefix?=" (assoc-ref %outputs "out"))))) + (inputs `(("git" ,git))) + (native-inputs `(("asciidoc" ,asciidoc) + ("docbook-xml" ,docbook-xml) + ("docbook-xsl" ,docbook-xsl) + ("xmllint" ,libxml2) + ("xsltproc" ,libxslt) + ;; These are needed for the tests. + ("cvs" ,cvs) + ("python" ,python-2) + ("rcs" ,rcs))) + (home-page "http://www.catb.org/esr/cvs-fast-export/") + (synopsis "Export an RCS or CVS history as a fast-import stream") + (description "This program analyzes a collection of RCS files in a CVS +repository (or outside of one) and, when possible, emits an equivalent history +in the form of a fast-import stream. Not all possible histories can be +rendered this way; the program tries to emit useful warnings when it can't. + +The program can also produce a visualization of the resulting commit directed +acyclic graph (DAG) in the input format of @uref{http://www.graphviz.org, +Graphviz}. The package also includes @command{cvssync}, a tool for mirroring +masters from remote CVS hosts.") + (license gpl2+))) + (define-public vc-dwim (package (name "vc-dwim") -- cgit v1.2.3 From 6e5e39f4063b30fcea6d5a9af6769236d8a57cd3 Mon Sep 17 00:00:00 2001 From: Cyril Roelandt Date: Tue, 8 Sep 2015 00:22:49 +0200 Subject: gnu: Add python-netaddr. * gnu/packages/python.scm (python-netaddr, python2-netaddr): New variables. --- gnu/packages/python.scm | 28 ++++++++++++++++++++++++++++ 1 file changed, 28 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index feddd1a46a..f85c788f43 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -4739,3 +4739,31 @@ reading and writing MessagePack data.") (define-public python2-msgpack (package-with-python2 python-msgpack)) + +(define-public python-netaddr + (package + (name "python-netaddr") + (version "0.7.18") + (source + (origin + (method url-fetch) + (uri (string-append + "https://pypi.python.org/packages/source/n/netaddr/netaddr-" + version + ".tar.gz")) + (sha256 + (base32 + "06dxjlbcicq7q3vqy8agq11ra01kvvd47j4mk6dmghjsyzyckxd1")))) + (build-system python-build-system) + (arguments `(#:tests? #f)) ;; No tests. + (inputs + `(("python-setuptools" ,python-setuptools))) + (home-page "https://github.com/drkjam/netaddr/") + (synopsis "Pythonic manipulation of network addresses") + (description + "A Python library for representing and manipulating IPv4, IPv6, CIDR, EUI +and MAC network addresses.") + (license bsd-3))) + +(define-public python2-netaddr + (package-with-python2 python-netaddr)) -- cgit v1.2.3 From 673d1a9deb0bd15870cc39ae9fe032074fb033fb Mon Sep 17 00:00:00 2001 From: Cyril Roelandt Date: Tue, 8 Sep 2015 00:27:45 +0200 Subject: gnu: Add python-stevedore. * gnu/packages/openstack.scm (python-stevedore, python2-stevedore): New variables. --- gnu/packages/openstack.scm | 41 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 41 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/openstack.scm b/gnu/packages/openstack.scm index 91686441ba..6c845887f0 100644 --- a/gnu/packages/openstack.scm +++ b/gnu/packages/openstack.scm @@ -139,6 +139,47 @@ and sensible default behaviors into your setuptools run.") (define-public python2-pbr (package-with-python2 python-pbr)) +(define-public python-stevedore + (package + (name "python-stevedore") + (version "1.7.0") + (source + (origin + (method url-fetch) + (uri (string-append + "https://pypi.python.org/packages/source/s/stevedore/stevedore-" + version + ".tar.gz")) + (sha256 + (base32 + "149pjc0c3z6khjisn4yil3f94qjnzwafz093wc8rrzbw828qdkv8")))) + (build-system python-build-system) + (propagated-inputs + `(("python-six" ,python-six))) + (inputs + `(("python-pbr" ,python-pbr) + ("python-setuptools" ,python-setuptools) + ;; Tests + ("python-docutils" ,python-docutils) + ("python-mock" ,python-mock) + ("python-oslotest" ,python-oslotest) + ("python-sphinx" ,python-sphinx))) + (home-page "https://github.com/dreamhost/stevedore") + (synopsis "Manage dynamic plugins for Python applications") + (description + "Python makes loading code dynamically easy, allowing you to configure +and extend your application by discovering and loading extensions (“plugins”) +at runtime. Many applications implement their own library for doing this, +using __import__ or importlib. stevedore avoids creating yet another extension +mechanism by building on top of setuptools entry points. The code for managing +entry points tends to be repetitive, though, so stevedore provides manager +classes for implementing common patterns for using dynamically loaded +extensions.") + (license asl2.0))) + +(define-public python2-stevedore + (package-with-python2 python-stevedore)) + ;; Packages from the Oslo library (define-public python-oslo.i18n (package -- cgit v1.2.3 From ed56af06bc9ecc240f5334df26ebca679fbabd00 Mon Sep 17 00:00:00 2001 From: Cyril Roelandt Date: Tue, 8 Sep 2015 00:33:05 +0200 Subject: gnu: Add python-oslo.config. * gnu/packages/openstack.scm (python-oslo.config, python2-oslo.config): New variables. --- gnu/packages/openstack.scm | 37 +++++++++++++++++++++++++++++++++++++ 1 file changed, 37 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/openstack.scm b/gnu/packages/openstack.scm index 6c845887f0..1f321bf312 100644 --- a/gnu/packages/openstack.scm +++ b/gnu/packages/openstack.scm @@ -181,6 +181,43 @@ extensions.") (package-with-python2 python-stevedore)) ;; Packages from the Oslo library +(define-public python-oslo.config + (package + (name "python-oslo.config") + (version "2.4.0") + (source + (origin + (method url-fetch) + (uri (string-append + "https://pypi.python.org/packages/source/o/oslo.config/oslo.config-" + version + ".tar.gz")) + (sha256 + (base32 + "13r778jfb0fhna37c2pd1f2xipnsbd7zli7qhn96acrzymrwj5k1")))) + (build-system python-build-system) + (propagated-inputs + `(("python-netaddr" ,python-netaddr) + ("python-six" ,python-six) + ("python-stevedore" ,python-stevedore))) + (inputs + `(("python-pbr" ,python-pbr) + ("python-setuptools" ,python-setuptools) + ;; Tests + ("python-oslo.i18n" ,python-oslo.i18n) + ("python-mock" ,python-mock) + ("python-oslotest" ,python-oslotest) + ("python-testscenarios" ,python-testscenarios))) + (home-page "https://launchpad.net/oslo") + (synopsis "Oslo Configuration API") + (description + "The Oslo configuration API supports parsing command line arguments and +.ini style configuration files.") + (license asl2.0))) + +(define-public python2-oslo.config + (package-with-python2 python-oslo.config)) + (define-public python-oslo.i18n (package (name "python-oslo.i18n") -- cgit v1.2.3 From 8c692a52586937a58627ae609f08aaabb102b64f Mon Sep 17 00:00:00 2001 From: Cyril Roelandt Date: Wed, 9 Sep 2015 00:26:26 +0200 Subject: gnu: Add python-wrapt * gnu/packages/python.scm (python-wrapt, python2-wrapt): New variables. --- gnu/packages/python.scm | 32 ++++++++++++++++++++++++++++++++ 1 file changed, 32 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index f85c788f43..04c842bc83 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -4767,3 +4767,35 @@ and MAC network addresses.") (define-public python2-netaddr (package-with-python2 python-netaddr)) + +(define-public python-wrapt + (package + (name "python-wrapt") + (version "1.10.5") + (source + (origin + (method url-fetch) + (uri (string-append + "https://pypi.python.org/packages/source/w/wrapt/wrapt-" + version + ".tar.gz")) + (sha256 + (base32 + "0cq8rlpzkxzk48b50yrfhzn1d1hrq4gjcdqlrgq4v5palgiv9jwr")))) + (build-system python-build-system) + (arguments + ;; Tests are not included in the tarball, they are only available in the + ;; git repository. + `(#:tests? #f)) + (inputs + `(("python-setuptools" ,python-setuptools))) + (home-page "https://github.com/GrahamDumpleton/wrapt") + (synopsis "Module for decorators, wrappers and monkey patching") + (description + "The aim of the wrapt module is to provide a transparent object proxy for + Python, which can be used as the basis for the construction of function + wrappers and decorator functions.") + (license bsd-2))) + +(define-public python2-wrapt + (package-with-python2 python-wrapt)) -- cgit v1.2.3 From b85c85becd36aa3abbd80dbb5b22705f10e5e57a Mon Sep 17 00:00:00 2001 From: Cyril Roelandt Date: Wed, 9 Sep 2015 00:44:14 +0200 Subject: gnu: Add python-iso8601. * gnu/packages/python.scm (python-iso8601, python2-iso8601): New variables. --- gnu/packages/python.scm | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 04c842bc83..85ab88c709 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -4799,3 +4799,30 @@ and MAC network addresses.") (define-public python2-wrapt (package-with-python2 python-wrapt)) + +(define-public python-iso8601 + (package + (name "python-iso8601") + (version "0.1.10") + (source + (origin + (method url-fetch) + (uri (string-append + "https://pypi.python.org/packages/source/i/iso8601/iso8601-" + version + ".tar.gz")) + (sha256 + (base32 + "1qf01afxh7j4gja71vxv345if8avg6nnm0ry0zsk6j3030xgy4p7")))) + (build-system python-build-system) + (inputs + `(("python-setuptools" ,python-setuptools))) + (home-page "https://bitbucket.org/micktwomey/pyiso8601") + (synopsis "Module to parse ISO 8601 dates") + (description + "This module parses the most common forms of ISO 8601 date strings (e.g. +@code{2007-01-14T20:34:22+00:00}) into @code{datetime} objects.") + (license license:expat))) + +(define-public python2-iso8601 + (package-with-python2 python-iso8601)) -- cgit v1.2.3 From 5e412b6383fbdceb971d940ecb534f187a59a443 Mon Sep 17 00:00:00 2001 From: Cyril Roelandt Date: Wed, 9 Sep 2015 00:51:45 +0200 Subject: gnu: Add python-monotonic. * gnu/packages/python.scm (python-monotonic, python2-monotonic): New variables. --- gnu/packages/python.scm | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 85ab88c709..c58d7f3fc1 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -4826,3 +4826,30 @@ and MAC network addresses.") (define-public python2-iso8601 (package-with-python2 python-iso8601)) + +(define-public python-monotonic + (package + (name "python-monotonic") + (version "0.3") + (source + (origin + (method url-fetch) + (uri (string-append + "https://pypi.python.org/packages/source/m/monotonic/monotonic-" + version + ".tar.gz")) + (sha256 + (base32 + "0yz0bcbwx8r2c01czzfpbrxddynxyk9k95jj8h6sgcb7xmfvl998")))) + (build-system python-build-system) + (inputs + `(("python-setuptools" ,python-setuptools))) + (home-page "https://github.com/atdt/monotonic") + (synopsis "Implementation of time.monotonic() for Python 2 & < 3.3") + (description + "This module provides a monotonic() function which returns the value (in +fractional seconds) of a clock which never goes backwards.") + (license asl2.0))) + +(define-public python2-monotonic + (package-with-python2 python-monotonic)) -- cgit v1.2.3 From 2713527e0694112a3970e22eac66dc938bea0463 Mon Sep 17 00:00:00 2001 From: Cyril Roelandt Date: Wed, 9 Sep 2015 00:59:10 +0200 Subject: gnu: Add python-debtcollector. * gnu/packages/openstack.scm (python-debtcollector, python2-debtcollector): New variables. --- gnu/packages/openstack.scm | 35 +++++++++++++++++++++++++++++++++++ 1 file changed, 35 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/openstack.scm b/gnu/packages/openstack.scm index 1f321bf312..c099846bac 100644 --- a/gnu/packages/openstack.scm +++ b/gnu/packages/openstack.scm @@ -25,6 +25,41 @@ #:select (asl2.0)) #:use-module (guix packages)) +(define-public python-debtcollector + (package + (name "python-debtcollector") + (version "0.5.0") + (source + (origin + (method url-fetch) + (uri (string-append + "https://pypi.python.org/packages/source/d/debtcollector/" + "debtcollector-" version ".tar.gz")) + (sha256 + (base32 + "0amlcg5f98lk2mfzdg44slh1nsi2y4ds123g5d57376fjk2b3njd")))) + (build-system python-build-system) + (propagated-inputs + `(("python-six" ,python-six) + ("python-wrapt" ,python-wrapt))) + (inputs + `(("python-babel" ,python-babel) + ("python-pbr" ,python-pbr) + ("python-setuptools" ,python-setuptools) + ;; Tests. + ("python-oslotest" ,python-oslotest))) + (home-page "http://www.openstack.org/") + (synopsis + "Find deprecated patterns and strategies in Python code") + (description + "This package provides a collection of Python deprecation patterns and +strategies that help you collect your technical debt in a non-destructive +manner.") + (license asl2.0))) + +(define-public python2-debtcollector + (package-with-python2 python-debtcollector)) + (define-public python-mox3 (package (name "python-mox3") -- cgit v1.2.3 From 27cc9f2544295659fd6cca0572841cd3aa5e9456 Mon Sep 17 00:00:00 2001 From: Cyril Roelandt Date: Wed, 9 Sep 2015 01:33:40 +0200 Subject: gnu: Add python-oslo.utils. * gnu/packages/openstack.scm (python-oslo.utils, python2-oslo.utils): New variables. --- gnu/packages/openstack.scm | 49 ++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 49 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/openstack.scm b/gnu/packages/openstack.scm index c099846bac..a9db3f2414 100644 --- a/gnu/packages/openstack.scm +++ b/gnu/packages/openstack.scm @@ -327,3 +327,52 @@ and better support for mocking results.") (define-public python2-oslotest (package-with-python2 python-oslotest)) + +(define-public python-oslo.utils + (package + (name "python-oslo.utils") + (version "2.5.0") + (source + (origin + (method url-fetch) + (uri (string-append + "https://pypi.python.org/packages/source/o/oslo.utils/oslo.utils-" + version + ".tar.gz")) + (sha256 + (base32 + "11b073gblhzkxhi1j6sqk3apq2ll8xhi9h9g9kxzx9dycqdq0qp0")) + (snippet + '(begin + ;; FIXME: setuptools fails to import this file during the test + ;; phase. + (delete-file "oslo_utils/tests/test_netutils.py"))))) + (build-system python-build-system) + (propagated-inputs + `(("python-debtcollector" ,python-debtcollector) + ("python-oslo.i18n" ,python-oslo.i18n) + ("python-iso8601" ,python-iso8601) + ("python-monotonic" ,python-monotonic) + ("python-netaddr" ,python-netaddr) + ("python-netifaces" ,python-netifaces) + ("python-pytz" ,python-pytz) + ("python-six" ,python-six))) + (inputs + `(("python-babel" ,python-babel) + ("python-pbr" ,python-pbr) + ("python-setuptools" ,python-setuptools) + ;; Tests. + ("python-oslotest" ,python-oslotest) + ("python-mock" ,python-mock) + ("python-mox3" ,python-mox3) + ("python-testscenarios" ,python-testscenarios))) + (home-page "http://launchpad.net/oslo") + (synopsis "Oslo utility library") + (description + "The @code{oslo.utils} library provides support for common utility type +functions, such as encoding, exception handling, string manipulation, and time +handling.") + (license asl2.0))) + +(define-public python2-oslo.utils + (package-with-python2 python-oslo.utils)) -- cgit v1.2.3 From 239db054a731a8e35ab239a025219a16bba2deb3 Mon Sep 17 00:00:00 2001 From: David Thompson Date: Mon, 8 Jun 2015 08:59:00 -0400 Subject: gnu: system: Add Linux container module. * gnu/system/linux-container.scm: New file. * gnu-system.am (GNU_SYSTEM_MODULES): Add it. * gnu/system.scm: Export 'operating-system-etc-directory', 'operating-system-boot-script', 'operating-system-locale-directory', and 'file-union'. (operating-system-boot-script): Add #:container? keyword argument. (operating-system-activation-script): Add #:container? keyword argument. Don't call 'activate-firmware' or 'activate-ptrace-attach' when activating a container. --- gnu-system.am | 1 + gnu/system.scm | 30 +++++++---- gnu/system/linux-container.scm | 119 +++++++++++++++++++++++++++++++++++++++++ 3 files changed, 140 insertions(+), 10 deletions(-) create mode 100644 gnu/system/linux-container.scm (limited to 'gnu') diff --git a/gnu-system.am b/gnu-system.am index cd9561e8b4..d3c63cad33 100644 --- a/gnu-system.am +++ b/gnu-system.am @@ -360,6 +360,7 @@ GNU_SYSTEM_MODULES = \ gnu/system/grub.scm \ gnu/system/install.scm \ gnu/system/linux.scm \ + gnu/system/linux-container.scm \ gnu/system/linux-initrd.scm \ gnu/system/locale.scm \ gnu/system/nss.scm \ diff --git a/gnu/system.scm b/gnu/system.scm index ea6e9c13ea..cee5f37bcb 100644 --- a/gnu/system.scm +++ b/gnu/system.scm @@ -83,6 +83,11 @@ operating-system-derivation operating-system-profile operating-system-grub.cfg + operating-system-etc-directory + operating-system-locale-directory + operating-system-boot-script + + file-union local-host-aliases %setuid-programs @@ -689,7 +694,7 @@ variable is not set---hence the need for this wrapper." (apply execl #$modprobe (cons #$modprobe (cdr (command-line)))))))) -(define (operating-system-activation-script os) +(define* (operating-system-activation-script os #:key container?) "Return the activation script for OS---i.e., the code that \"activates\" the stateful part of OS, including user accounts and groups, special directories, etc." @@ -763,12 +768,15 @@ etc." ;; Tell the kernel to use our 'modprobe' command. (activate-modprobe #$modprobe) - ;; Tell the kernel where firmware is. - (activate-firmware - (string-append #$firmware "/lib/firmware")) - - ;; Let users debug their own processes! - (activate-ptrace-attach) + ;; Tell the kernel where firmware is, unless we are + ;; activating a container. + #$@(if container? + #~() + ;; Tell the kernel where firmware is. + #~((activate-firmware + (string-append #$firmware "/lib/firmware")) + ;; Let users debug their own processes! + (activate-ptrace-attach))) ;; Run the services' activation snippets. ;; TODO: Use 'load-compiled'. @@ -777,11 +785,13 @@ etc." ;; Set up /run/current-system. (activate-current-system))))) -(define (operating-system-boot-script os) +(define* (operating-system-boot-script os #:key container?) "Return the boot script for OS---i.e., the code started by the initrd once -we're running in the final root." +we're running in the final root. When CONTAINER? is true, skip all +hardware-related operations as necessary when booting a Linux container." (mlet* %store-monad ((services (operating-system-services os)) - (activate (operating-system-activation-script os)) + (activate (operating-system-activation-script + os #:container? container?)) (dmd-conf (dmd-configuration-file services))) (gexp->file "boot" #~(begin diff --git a/gnu/system/linux-container.scm b/gnu/system/linux-container.scm new file mode 100644 index 0000000000..fdf7460872 --- /dev/null +++ b/gnu/system/linux-container.scm @@ -0,0 +1,119 @@ +;;; GNU Guix --- Functional package management for GNU +;;; Copyright © 2015 David Thompson +;;; +;;; 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 . + +(define-module (gnu system linux-container) + #:use-module (ice-9 match) + #:use-module (srfi srfi-1) + #:use-module (guix config) + #:use-module (guix store) + #:use-module (guix gexp) + #:use-module (guix derivations) + #:use-module (guix monads) + #:use-module (gnu build linux-container) + #:use-module (gnu system) + #:use-module (gnu system file-systems) + #:export (mapping->file-system + system-container + containerized-operating-system + container-script)) + +(define (mapping->file-system mapping) + "Return a file system that realizes MAPPING." + (match mapping + (($ source target writable?) + (file-system + (mount-point target) + (device source) + (type "none") + (flags (if writable? + '(bind-mount) + '(bind-mount read-only))) + (check? #f) + (create-mount-point? #t))))) + +(define (system-container os) + "Return a derivation that builds OS as a Linux container." + (mlet* %store-monad + ((profile (operating-system-profile os)) + (etc (operating-system-etc-directory os)) + (boot (operating-system-boot-script os #:container? #t)) + (locale (operating-system-locale-directory os))) + (file-union "system-container" + `(("boot" ,#~#$boot) + ("profile" ,#~#$profile) + ("locale" ,#~#$locale) + ("etc" ,#~#$etc))))) + +(define (containerized-operating-system os mappings) + "Return an operating system based on OS for use in a Linux container +environment. MAPPINGS is a list of to realize in the +containerized OS." + (define user-file-systems + (remove (lambda (fs) + (let ((target (file-system-mount-point fs)) + (source (file-system-device fs))) + (or (string=? target (%store-prefix)) + (string=? target "/") + (string-prefix? "/dev/" source) + (string-prefix? "/dev" target) + (string-prefix? "/sys" target)))) + (operating-system-file-systems os))) + + (define (mapping->fs fs) + (file-system (inherit (mapping->file-system fs)) + (needed-for-boot? #t))) + + (operating-system (inherit os) + (swap-devices '()) ; disable swap + (file-systems (append (map mapping->fs (cons %store-mapping mappings)) + %container-file-systems + user-file-systems)))) + +(define* (container-script os #:key (mappings '())) + "Return a derivation of a script that runs OS as a Linux container. +MAPPINGS is a list of objects that specify the files/directories +that will be shared with the host system." + (let* ((os (containerized-operating-system os mappings)) + (file-systems (filter file-system-needed-for-boot? + (operating-system-file-systems os))) + (specs (map file-system->spec file-systems))) + + (mlet* %store-monad ((os-drv (system-container os))) + + (define script + #~(begin + (use-modules (gnu build linux-container) + (guix build utils)) + + (call-with-container '#$specs + (lambda () + (setenv "HOME" "/root") + (setenv "TMPDIR" "/tmp") + (setenv "GUIX_NEW_SYSTEM" #$os-drv) + (for-each mkdir-p '("/run" "/bin" "/etc" "/home" "/var")) + (primitive-load (string-append #$os-drv "/boot")))))) + + (gexp->script "run-container" script + #:modules '((ice-9 match) + (srfi srfi-98) + (guix config) + (guix utils) + (guix build utils) + (guix build syscalls) + (gnu build file-systems) + (gnu build linux-container)))))) -- cgit v1.2.3 From b429c4fbb06299ce10ecc113a7818bf777c63a6e Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Mon, 14 Sep 2015 16:32:27 +0200 Subject: gnu: Add bio-locus. * gnu/packages/bioinformatics.scm (bio-locus): New variable. --- gnu/packages/bioinformatics.scm | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 03eb2dfe30..c4ba0e082f 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -2616,3 +2616,27 @@ data in the form of VCF files.") ;; The license is declared as LGPLv3 in the README and ;; at http://vcftools.sourceforge.net/license.html (license license:lgpl3))) + +(define-public bio-locus + (package + (name "bio-locus") + (version "0.0.7") + (source + (origin + (method url-fetch) + (uri (rubygems-uri "bio-locus" version)) + (sha256 + (base32 + "02vmrxyimkj9sahsp4zhfhnmbvz6dbbqz1y01vglf8cbwvkajfl0")))) + (build-system ruby-build-system) + (native-inputs + `(("ruby-rspec" ,ruby-rspec))) + (synopsis "Tool for fast querying of genome locations") + (description + "Bio-locus is a tabix-like tool for fast querying of genome +locations. Many file formats in bioinformatics contain records that +start with a chromosome name and a position for a SNP, or a start-end +position for indels. Bio-locus allows users to store this chr+pos or +chr+pos+alt information in a fast database.") + (home-page "https://github.com/pjotrp/bio-locus") + (license license:expat))) -- cgit v1.2.3 From 801a0a221956dfeeddf7a8c85a66ff106dc33d7a Mon Sep 17 00:00:00 2001 From: David Thompson Date: Mon, 14 Sep 2015 12:05:15 -0400 Subject: Revert "gnu: Add bio-locus." This reverts commit b429c4fbb06299ce10ecc113a7818bf777c63a6e. --- gnu/packages/bioinformatics.scm | 24 ------------------------ 1 file changed, 24 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index c4ba0e082f..03eb2dfe30 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -2616,27 +2616,3 @@ data in the form of VCF files.") ;; The license is declared as LGPLv3 in the README and ;; at http://vcftools.sourceforge.net/license.html (license license:lgpl3))) - -(define-public bio-locus - (package - (name "bio-locus") - (version "0.0.7") - (source - (origin - (method url-fetch) - (uri (rubygems-uri "bio-locus" version)) - (sha256 - (base32 - "02vmrxyimkj9sahsp4zhfhnmbvz6dbbqz1y01vglf8cbwvkajfl0")))) - (build-system ruby-build-system) - (native-inputs - `(("ruby-rspec" ,ruby-rspec))) - (synopsis "Tool for fast querying of genome locations") - (description - "Bio-locus is a tabix-like tool for fast querying of genome -locations. Many file formats in bioinformatics contain records that -start with a chromosome name and a position for a SNP, or a start-end -position for indels. Bio-locus allows users to store this chr+pos or -chr+pos+alt information in a fast database.") - (home-page "https://github.com/pjotrp/bio-locus") - (license license:expat))) -- cgit v1.2.3 From 9c38b54027ee009f9ff604342ae99c4ebd7958a6 Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Mon, 14 Sep 2015 16:32:27 +0200 Subject: gnu: Add bio-locus. * gnu/packages/bioinformatics.scm (bio-locus): New variable. --- gnu/packages/bioinformatics.scm | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 03eb2dfe30..1f3421126c 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -27,6 +27,7 @@ #:use-module (guix build-system cmake) #:use-module (guix build-system perl) #:use-module (guix build-system python) + #:use-module (guix build-system ruby) #:use-module (guix build-system trivial) #:use-module (gnu packages) #:use-module (gnu packages algebra) @@ -45,6 +46,7 @@ #:use-module (gnu packages popt) #:use-module (gnu packages protobuf) #:use-module (gnu packages python) + #:use-module (gnu packages ruby) #:use-module (gnu packages statistics) #:use-module (gnu packages tbb) #:use-module (gnu packages textutils) @@ -2616,3 +2618,27 @@ data in the form of VCF files.") ;; The license is declared as LGPLv3 in the README and ;; at http://vcftools.sourceforge.net/license.html (license license:lgpl3))) + +(define-public bio-locus + (package + (name "bio-locus") + (version "0.0.7") + (source + (origin + (method url-fetch) + (uri (rubygems-uri "bio-locus" version)) + (sha256 + (base32 + "02vmrxyimkj9sahsp4zhfhnmbvz6dbbqz1y01vglf8cbwvkajfl0")))) + (build-system ruby-build-system) + (native-inputs + `(("ruby-rspec" ,ruby-rspec))) + (synopsis "Tool for fast querying of genome locations") + (description + "Bio-locus is a tabix-like tool for fast querying of genome +locations. Many file formats in bioinformatics contain records that +start with a chromosome name and a position for a SNP, or a start-end +position for indels. Bio-locus allows users to store this chr+pos or +chr+pos+alt information in a database.") + (home-page "https://github.com/pjotrp/bio-locus") + (license license:expat))) -- cgit v1.2.3 From 17d8e33f316b7e88aa06452f873b59770989f1b6 Mon Sep 17 00:00:00 2001 From: Mathieu Lirzin Date: Sun, 13 Sep 2015 22:26:37 +0200 Subject: doc: Use the recommended Scheme format. Apply the recommended formatting rules from '.dir-locals.el' to the examples in the manual in order to fulfill it's purpose of being a reference. * doc/package-hello.scm: Indent it. * doc/guix.texi (Defining Packages, Version Numbers): Likewise. * gnu/packages/base.scm (hello): Be consistent with the manual. --- doc/guix.texi | 31 ++++++++++++++++--------------- doc/package-hello.scm | 5 +++-- gnu/packages/base.scm | 29 +++++++++++++++-------------- 3 files changed, 34 insertions(+), 31 deletions(-) (limited to 'gnu') diff --git a/doc/guix.texi b/doc/guix.texi index ff3a9c47b7..51f7cb24b9 100644 --- a/doc/guix.texi +++ b/doc/guix.texi @@ -1963,13 +1963,14 @@ package looks like this: (define-public hello (package (name "hello") - (version "2.8") + (version "2.10") (source (origin - (method url-fetch) - (uri (string-append "mirror://gnu/hello/hello-" version - ".tar.gz")) - (sha256 - (base32 "0wqd8sjmxfskrflaxywc7gqw7sfawrfvdxd9skxawzfgyy0pzdz6")))) + (method url-fetch) + (uri (string-append "mirror://gnu/hello/hello-" version + ".tar.gz")) + (sha256 + (base32 + "0ssi1wpaf7plaswqqjwigppsg5fyh99vdlb9kzl7c9lng89ndq1i")))) (build-system gnu-build-system) (arguments `(#:configure-flags '("--enable-silent-rules"))) (inputs `(("gawk" ,gawk))) @@ -7232,22 +7233,22 @@ For instance, the versions 2.24.20 and 3.9.12 of GTK+ may be packaged as follows @example (define-public gtk+ (package - (name "gtk+") - (version "3.9.12") - ...)) + (name "gtk+") + (version "3.9.12") + ...)) (define-public gtk+-2 (package - (name "gtk+") - (version "2.24.20") - ...)) + (name "gtk+") + (version "2.24.20") + ...)) @end example If we also wanted GTK+ 3.8.2, this would be packaged as @example (define-public gtk+-3.8 (package - (name "gtk+") - (version "3.8.2") - ...)) + (name "gtk+") + (version "3.8.2") + ...)) @end example diff --git a/doc/package-hello.scm b/doc/package-hello.scm index b3fcd4ff73..c57eb89108 100644 --- a/doc/package-hello.scm +++ b/doc/package-hello.scm @@ -4,13 +4,14 @@ (package (name "hello") - (version "2.8") + (version "2.10") (source (origin (method url-fetch) (uri (string-append "mirror://gnu/hello/hello-" version ".tar.gz")) (sha256 - (base32 "0wqd8sjmxfskrflaxywc7gqw7sfawrfvdxd9skxawzfgyy0pzdz6")))) + (base32 + "0ssi1wpaf7plaswqqjwigppsg5fyh99vdlb9kzl7c9lng89ndq1i")))) (build-system gnu-build-system) (synopsis "Hello, GNU world: An example GNU package") (description "Guess what GNU Hello prints!") diff --git a/gnu/packages/base.scm b/gnu/packages/base.scm index f35f619201..c5f447736a 100644 --- a/gnu/packages/base.scm +++ b/gnu/packages/base.scm @@ -49,22 +49,23 @@ (define-public hello (package - (name "hello") - (version "2.10") - (source (origin - (method url-fetch) - (uri (string-append "mirror://gnu/hello/hello-" version - ".tar.gz")) - (sha256 - (base32 "0ssi1wpaf7plaswqqjwigppsg5fyh99vdlb9kzl7c9lng89ndq1i")))) - (build-system gnu-build-system) - (synopsis "Hello, GNU world: An example GNU package") - (description - "GNU Hello prints the message \"Hello, world!\" and then exits. It + (name "hello") + (version "2.10") + (source (origin + (method url-fetch) + (uri (string-append "mirror://gnu/hello/hello-" version + ".tar.gz")) + (sha256 + (base32 + "0ssi1wpaf7plaswqqjwigppsg5fyh99vdlb9kzl7c9lng89ndq1i")))) + (build-system gnu-build-system) + (synopsis "Hello, GNU world: An example GNU package") + (description + "GNU Hello prints the message \"Hello, world!\" and then exits. It serves as an example of standard GNU coding practices. As such, it supports command-line arguments, multiple languages, and so on.") - (home-page "http://www.gnu.org/software/hello/") - (license gpl3+))) + (home-page "http://www.gnu.org/software/hello/") + (license gpl3+))) (define-public grep (package -- cgit v1.2.3 From 62e4cc5aa19e4c64fc244e3c6724d8e4d97f8599 Mon Sep 17 00:00:00 2001 From: "pjotr.public12@thebird.nl" Date: Tue, 15 Sep 2015 16:48:35 +0200 Subject: gnu: Add ruby-gherkin3. * gnu/packages/ruby.scm (ruby-gherkin3): New variable. --- gnu/packages/ruby.scm | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/ruby.scm b/gnu/packages/ruby.scm index ee0acc8639..7dc46b6caa 100644 --- a/gnu/packages/ruby.scm +++ b/gnu/packages/ruby.scm @@ -1124,3 +1124,26 @@ it unifies the API for web servers, web frameworks, and software in between into a single method call.") (home-page "http://rack.github.io/") (license license:expat))) + +(define-public ruby-gherkin3 + (package + (name "ruby-gherkin3") + (version "3.1.1") + (source + (origin + (method url-fetch) + (uri (rubygems-uri "gherkin3" version)) + (sha256 + (base32 + "0xsyxhqa1gwcxzvsdy4didaiq5vam8ma3fbwbw2w60via4k6r1z9")))) + (build-system ruby-build-system) + (native-inputs + `(("bundler" ,bundler))) + (arguments + '(#:tests? #f)) ; needs simplecov, among others + (synopsis "Gherkin parser for Ruby") + (description "Gherkin 3 is a parser and compiler for the Gherkin language. +It is intended to replace Gherkin 2 and be used by all Cucumber +implementations to parse '.feature' files.") + (home-page "https://github.com/cucumber/gherkin3") + (license license:expat))) -- cgit v1.2.3 From ed6094fc77267b14510e6fb589fca663e7e1ce04 Mon Sep 17 00:00:00 2001 From: Vicente Vera Parra Date: Tue, 15 Sep 2015 14:11:12 -0300 Subject: gnu: Add r-assertthat. * gnu/packages/statistics.scm (r-assertthat): New variable. --- gnu/packages/statistics.scm | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 29cd34a4f3..1c3d696028 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -1,5 +1,6 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2015 Ricardo Wurmus +;;; Copyright © 2015 Vicente Vera Parra ;;; ;;; This file is part of GNU Guix. ;;; @@ -498,3 +499,24 @@ by step from multiple data sources. It also implements a sophisticated multidimensional conditioning system and a consistent interface to map data to aesthetic attributes.") (license license:gpl2+))) + +(define-public r-assertthat + (package + (name "r-assertthat") + (version "0.1") + (source (origin + (method url-fetch) + (uri (string-append "mirror://cran/src/contrib/assertthat_" + version ".tar.gz")) + (sha256 + (base32 + "0dwsqajyglfscqilj843qfqn1ndbqpswa7b4l1d633qjk9d68qqk")))) + (build-system r-build-system) + (home-page "https://github.com/hadley/assertthat") + (synopsis "Easy pre and post assertions") + (description + "Assertthat is an extension to stopifnot() that makes it easy to declare +the pre and post conditions that your code should satisfy, while also +producing friendly error messages so that your users know what they've done +wrong.") + (license license:gpl3+))) -- cgit v1.2.3 From 6af481343001c552f1c12f1e3128159685abef07 Mon Sep 17 00:00:00 2001 From: Vicente Vera Parra Date: Tue, 15 Sep 2015 14:12:32 -0300 Subject: gnu: Add r-lazyeval. * gnu/packages/statistics.scm (r-lazyeval): New variable. --- gnu/packages/statistics.scm | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 1c3d696028..6bd8e767ec 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -520,3 +520,22 @@ the pre and post conditions that your code should satisfy, while also producing friendly error messages so that your users know what they've done wrong.") (license license:gpl3+))) + +(define-public r-lazyeval + (package + (name "r-lazyeval") + (version "0.1.10") + (source (origin + (method url-fetch) + (uri (string-append "mirror://cran/src/contrib/lazyeval_" + version ".tar.gz")) + (sha256 + (base32 + "02qfpn2fmy78vx4jxr7g7rhqzcm1kcivfwai7lbh0vvpawia0qwh")))) + (build-system r-build-system) + (home-page "https://github.com/hadley/lazyeval") + (synopsis "Lazy (non-standard) evaluation in R") + (description + "This package provides the tools necessary to do non-standard +evaluation (NSE) in R.") + (license license:gpl3+))) -- cgit v1.2.3 From f4e92db3cb25d44ca3db96e960790f856c2887f1 Mon Sep 17 00:00:00 2001 From: Ludovic Courtès Date: Tue, 15 Sep 2015 22:46:56 +0200 Subject: nls: Add "TRANSLATORS:" comment about Texinfo. * gnu/packages/abiword.scm: Add comment above 'description'. --- gnu/packages/abiword.scm | 15 +++++++++++---- 1 file changed, 11 insertions(+), 4 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/abiword.scm b/gnu/packages/abiword.scm index a76b16c5af..c6f259a2dd 100644 --- a/gnu/packages/abiword.scm +++ b/gnu/packages/abiword.scm @@ -99,8 +99,15 @@ ("pkg-config" ,pkg-config))) (home-page "http://abisource.org/") (synopsis "Word processing program") - (description - "AbiWord is a word processing program. It is rapidly becoming a state -of the art word processor, with lots of features useful for your daily work, -personal needs, or for just some good old typing fun.") + + ;; HACKERS: The comment below is here so that it shows up early in the + ;; .pot file. + + ;; TRANSLATORS: Dear translator, We would like to inform you that package + ;; descriptions may occasionally include Texinfo markup. Texinfo markup + ;; looks like "@code{rm -rf}", "@emph{important}", etc. When translating, + ;; please leave markup as is. + (description "AbiWord is a word processing program. It is rapidly +becoming a state of the art word processor, with lots of features useful for +your daily work, personal needs, or for just some good old typing fun.") (license license:gpl2+))) -- cgit v1.2.3 From 8ea6b30fea9637c5568c310d384bc13bc225648b Mon Sep 17 00:00:00 2001 From: Vicente Vera Parra Date: Tue, 15 Sep 2015 14:14:11 -0300 Subject: gnu: Add r-dbi. * gnu/packages/statistics.scm (r-dbi): New variable. --- gnu/packages/statistics.scm | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 6bd8e767ec..6ccb97f375 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -539,3 +539,24 @@ wrong.") "This package provides the tools necessary to do non-standard evaluation (NSE) in R.") (license license:gpl3+))) + +(define-public r-dbi + (package + (name "r-dbi") + (version "0.3.1") + (source (origin + (method url-fetch) + (uri (string-append "mirror://cran/src/contrib/DBI_" + version ".tar.gz")) + (sha256 + (base32 + "0xj5baxwnhl23rd5nskhjvranrwrc68f3xlyrklglipi41bm69hw")))) + (build-system r-build-system) + (home-page "https://github.com/rstats-db/DBI") + (synopsis "R database interface") + (description + "The DBI package provides a database interface (DBI) definition for +communication between R and relational database management systems. All +classes in this package are virtual and need to be extended by the various +R/DBMS implementations.") + (license license:lgpl2.0+))) -- cgit v1.2.3 From f9ae2c068dc5228f4f5072bcfbb214cfb8373069 Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Wed, 16 Sep 2015 07:56:44 +0200 Subject: gnu: Add ruby-log4r. * gnu/packages/ruby.scm (ruby-log4r): New variable. --- gnu/packages/ruby.scm | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/ruby.scm b/gnu/packages/ruby.scm index 7dc46b6caa..e61332f6aa 100644 --- a/gnu/packages/ruby.scm +++ b/gnu/packages/ruby.scm @@ -421,6 +421,30 @@ Java Native Interface.") (home-page "http://www.artonx.org/collabo/backyard/?RubyJavaBridge") (license license:lgpl2.1+))) +(define-public ruby-log4r + (package + (name "ruby-log4r") + (version "1.1.10") + (source + (origin + (method url-fetch) + (uri (rubygems-uri "log4r" version)) + (sha256 + (base32 + "0ri90q0frfmigkirqv5ihyrj59xm8pq5zcmf156cbdv4r4l2jicv")))) + (build-system ruby-build-system) + (arguments + '(#:tests? #f)) ; no Rakefile in gem + (synopsis "Flexible logging library for Ruby") + (description "Comprehensive and flexible logging library written +in Ruby for use in Ruby programs. It features a hierarchical logging +system of any number of levels, custom level names, logger +inheritance, multiple output destinations per log event, execution +tracing, custom formatting, thread safteyness, XML and YAML +configuration, and more.") + (home-page "http://log4r.rubyforge.org/") + (license license:bsd-3))) + (define-public ruby-atoulme-antwrap (package (name "ruby-atoulme-antwrap") -- cgit v1.2.3 From 979f9e8aed754151d2e89b841c99d3a4afce50af Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 16 Sep 2015 22:41:10 +0200 Subject: gnu: sfarklib: Update to 2.24. * gnu/packages/compression.scm (sfarklib): Update to 2.24. --- gnu/packages/compression.scm | 14 ++++++-------- 1 file changed, 6 insertions(+), 8 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/compression.scm b/gnu/packages/compression.scm index a60eef1143..2ab1e2955c 100644 --- a/gnu/packages/compression.scm +++ b/gnu/packages/compression.scm @@ -357,17 +357,15 @@ This package is mostly for compatibility and historical interest.") (define-public sfarklib (package (name "sfarklib") - (version "2.23.5ca96b779") + (version "2.24") (source (origin - ;; The 2.23 tarball does not include the Makefile, but only - ;; Makefile.am. - (method git-fetch) - (uri (git-reference - (url "https://github.com/raboof/sfArkLib.git") - (commit (last (string-split version #\.))))) + (method url-fetch) + (uri (string-append "https://github.com/raboof/sfArkLib/archive/" + version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "1hk1x88dl5b9jq016r6rx5wyszxknyv0sa7gmil4m4alnhwl4h7h")))) + "0bzs2d98rk1xw9qwpnc7gmlbxwmwc3dg1rpn310afy9pq1k9clzi")))) (build-system gnu-build-system) (arguments `(#:tests? #f ;no "check" target -- cgit v1.2.3 From 5702efe3e9df94348a365813ac63f8cdaf8a3354 Mon Sep 17 00:00:00 2001 From: Cyril Roelandt Date: Mon, 14 Sep 2015 20:39:18 +0200 Subject: gnu: Add python-oslo.serialization. * gnu/packages/openstack.scm (python-oslo.serialization, python2-oslo.serialization): New variables. --- gnu/packages/openstack.scm | 39 +++++++++++++++++++++++++++++++++++++++ 1 file changed, 39 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/openstack.scm b/gnu/packages/openstack.scm index a9db3f2414..b268c619f3 100644 --- a/gnu/packages/openstack.scm +++ b/gnu/packages/openstack.scm @@ -290,6 +290,45 @@ in an application or library.") (define-public python2-oslo.i18n (package-with-python2 python-oslo.i18n)) +(define-public python-oslo.serialization + (package + (name "python-oslo.serialization") + (version "1.9.0") + (source + (origin + (method url-fetch) + (uri (string-append + "https://pypi.python.org/packages/source/o/oslo.serialization/" + "oslo.serialization-" version ".tar.gz")) + (sha256 + (base32 + "00qaxg155s61ylh4fqc7m5fh0gijf33khhai9xvcsc9k106i3c9c")))) + (build-system python-build-system) + (propagated-inputs + `(("python-iso8601" ,python-iso8601) + ("python-netaddr" ,python-netaddr) + ("python-oslo.utils" ,python-oslo.utils) + ("python-simplejson" ,python-simplejson) + ("python-six" ,python-six) + ("python-pytz" ,python-pytz))) + (inputs + `(("python-babel" ,python-babel) + ("python-pbr" ,python-pbr) + ("python-setuptools" ,python-setuptools) + ;; Tests. + ("python-mock" ,python-mock) + ("python-oslo.i18n" ,python-oslo.i18n) + ("python-oslotest" ,python-oslotest))) + (home-page "http://launchpad.net/oslo") + (synopsis "Oslo serialization library") + (description + "The oslo.serialization library provides support for representing objects +in transmittable and storable formats, such as JSON and MessagePack.") + (license asl2.0))) + +(define-public python2-oslo.serialization + (package-with-python2 python-oslo.serialization)) + (define-public python-oslotest (package (name "python-oslotest") -- cgit v1.2.3 From c7c7a93621ad38e8302ccf3f52e182b65ef3715d Mon Sep 17 00:00:00 2001 From: Cyril Roelandt Date: Mon, 14 Sep 2015 20:50:35 +0200 Subject: gnu: Add python-oslo.context. * gnu/packages/openstack.scm (python-oslo.context, python2-oslo.context): New variables. --- gnu/packages/openstack.scm | 31 +++++++++++++++++++++++++++++++ 1 file changed, 31 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/openstack.scm b/gnu/packages/openstack.scm index b268c619f3..a0e6952e2a 100644 --- a/gnu/packages/openstack.scm +++ b/gnu/packages/openstack.scm @@ -253,6 +253,37 @@ extensions.") (define-public python2-oslo.config (package-with-python2 python-oslo.config)) +(define-public python-oslo.context + (package + (name "python-oslo.context") + (version "0.6.0") + (source + (origin + (method url-fetch) + (uri (string-append + "https://pypi.python.org/packages/source/o/oslo.context/" + "oslo.context-" version ".tar.gz")) + (sha256 + (base32 + "16wr9qrkc3lb94ssb14qid4liza66x316fvzjw0izg67h1a0fm86")))) + (build-system python-build-system) + (inputs + `(("python-babel" ,python-babel) + ("python-pbr" ,python-pbr) + ("python-setuptools" ,python-setuptools) + ;; Tests. + ("python-oslotest" ,python-oslotest))) + (home-page "http://launchpad.net/oslo") + (synopsis "Oslo context library") + (description + "The Oslo context library has helpers to maintain useful information +about a request context. The request context is usually populated in the WSGI +pipeline and used by various modules such as logging.") + (license asl2.0))) + +(define-public python2-oslo.context + (package-with-python2 python-oslo.context)) + (define-public python-oslo.i18n (package (name "python-oslo.i18n") -- cgit v1.2.3 From de34aface7e0c83b02c3def1ec55630e29bed6b7 Mon Sep 17 00:00:00 2001 From: Cyril Roelandt Date: Mon, 14 Sep 2015 22:16:53 +0200 Subject: gnu: Add python-webob. * gnu/packages/python.scm (python-webob, python2-webob): New variables. --- gnu/packages/python.scm | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index c58d7f3fc1..408064d9be 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -4853,3 +4853,30 @@ fractional seconds) of a clock which never goes backwards.") (define-public python2-monotonic (package-with-python2 python-monotonic)) + +(define-public python-webob + (package + (name "python-webob") + (version "1.5.0b0") + (source + (origin + (method url-fetch) + (uri (string-append + "https://pypi.python.org/packages/source/W/WebOb/WebOb-" + version ".tar.gz")) + (sha256 + (base32 + "140b3iczclk1j0405rvw5gxshqfkhcc8254fj520z3m23cwbql4a")))) + (build-system python-build-system) + (inputs + `(("python-nose" ,python-nose) + ("python-setuptools" ,python-setuptools))) + (home-page "http://webob.org/") + (synopsis "WSGI request and response object") + (description + "WebOb provides wrappers around the WSGI request environment, and an +object to help create WSGI responses.") + (license license:expat))) + +(define-public python2-webob + (package-with-python2 python-webob)) -- cgit v1.2.3 From 2c9d96767a8ad616d61f0548b6ebba0b762589dd Mon Sep 17 00:00:00 2001 From: Cyril Roelandt Date: Mon, 14 Sep 2015 22:53:32 +0200 Subject: gnu: Add python-requests-mock. * gnu/packages/openstack.scm (python-requests-mock, python2-requests-mock): New variables. --- gnu/packages/openstack.scm | 31 +++++++++++++++++++++++++++++++ 1 file changed, 31 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/openstack.scm b/gnu/packages/openstack.scm index a0e6952e2a..39584d566f 100644 --- a/gnu/packages/openstack.scm +++ b/gnu/packages/openstack.scm @@ -174,6 +174,37 @@ and sensible default behaviors into your setuptools run.") (define-public python2-pbr (package-with-python2 python-pbr)) +(define-public python-requests-mock + (package + (name "python-requests-mock") + (version "0.6.0") + (source + (origin + (method url-fetch) + (uri (string-append + "https://pypi.python.org/packages/source/r/requests-mock/" + "requests-mock-" version ".tar.gz")) + (sha256 + (base32 + "0gmd88c224y53b1ai8cfsrcxm9kw3gdqzysclmnaqspg7zjhxwd1")))) + (build-system python-build-system) + (propagated-inputs + `(("python-requests" ,python-requests) + ("python-six" ,python-six))) + (inputs + `(("python-mock" ,python-mock) + ("python-pbr" ,python-pbr) + ("python-setuptools" ,python-setuptools))) + (home-page "https://requests-mock.readthedocs.org/") + (synopsis "Mock out responses from the requests package") + (description + "This module provides a building block to stub out the HTTP requests +portions of your testing code.") + (license asl2.0))) + +(define-public python2-requests-mock + (package-with-python2 python-requests-mock)) + (define-public python-stevedore (package (name "python-stevedore") -- cgit v1.2.3 From e8647227315653728435ba0673cc2aa690c40138 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Wed, 16 Sep 2015 13:18:40 +0300 Subject: gnu: Add keepassx. * gnu/packages/password-utils.scm (keepassx): New variable. --- gnu/packages/password-utils.scm | 37 ++++++++++++++++++++++++++++++++++++- 1 file changed, 36 insertions(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/packages/password-utils.scm b/gnu/packages/password-utils.scm index 4aef371615..8619f14f38 100644 --- a/gnu/packages/password-utils.scm +++ b/gnu/packages/password-utils.scm @@ -1,5 +1,6 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2015 Steve Sprang +;;; Copyright © 2015 Efraim Flashner ;;; ;;; This file is part of GNU Guix. ;;; @@ -18,9 +19,14 @@ (define-module (gnu packages password-utils) #:use-module ((guix licenses) #:prefix license:) + #:use-module (guix build-system cmake) #:use-module (guix build-system gnu) #:use-module (guix download) - #:use-module (guix packages)) + #:use-module (guix packages) + #:use-module (gnu packages compression) + #:use-module (gnu packages gnupg) + #:use-module (gnu packages qt) + #:use-module (gnu packages xorg)) (define-public pwgen (package @@ -41,3 +47,32 @@ (description "Pwgen generates passwords which can be easily memorized by a human.") (license license:gpl2))) + +(define-public keepassx + (package + (name "keepassx") + (version "2.0-beta2") + (source + (origin + (method url-fetch) + (uri (string-append "https://github.com/keepassx/keepassx/archive/" + version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 "0ljf9ws3wh62zd0gyb0vk2qw6pqsmxrlybrfs5mqahf44q92ca2q")))) + (build-system cmake-build-system) + (inputs + `(("libgcrypt" ,libgcrypt) + ("libxtst" ,libxtst) + ("qt" ,qt-4))) + (native-inputs + `(("zlib" ,zlib))) + (home-page "https://www.keepassx.org") + (synopsis "Password manager") + (description "KeePassX is a password manager or safe which helps you to +manage your passwords in a secure way. You can put all your passwords in one +database, which is locked with one master key or a key-file which can be stored +on an external storage device. The databases are encrypted using the +algorithms AES or Twofish.") + ;; Non functional parts use various licences. + (license license:gpl3))) -- cgit v1.2.3 From 41ddebdd2a94da127369ab13fb1ccaf226b30a43 Mon Sep 17 00:00:00 2001 From: Ben Woodcroft Date: Sat, 12 Sep 2015 22:10:20 +1000 Subject: gnu: Add mafft. * gnu/packages/bioinformatics.scm (mafft): New variable. --- gnu/packages/bioinformatics.scm | 58 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 58 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 1f3421126c..a13fd7a91d 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1545,6 +1545,64 @@ resolution of binding sites through combining the information of both sequencing tag position and orientation.") (license license:bsd-3))) +(define-public mafft + (package + (name "mafft") + (version "7.221") + (source (origin + (method url-fetch) + (uri (string-append + "http://mafft.cbrc.jp/alignment/software/mafft-" version + "-without-extensions-src.tgz")) + (file-name (string-append name "-" version ".tgz")) + (sha256 + (base32 + "0xi7klbsgi049vsrk6jiwh9wfj3b770gz3c8c7zwij448v0dr73d")))) + (build-system gnu-build-system) + (arguments + `(#:tests? #f ; no automated tests, though there are tests in the read me + #:make-flags (let ((out (assoc-ref %outputs "out"))) + (list (string-append "PREFIX=" out) + (string-append "BINDIR=" + (string-append out "/bin")))) + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'enter-dir + (lambda _ (chdir "core") #t)) + (add-after 'enter-dir 'patch-makefile + (lambda _ + ;; on advice from the MAFFT authors, there is no need to + ;; distribute mafft-profile, mafft-distance, or + ;; mafft-homologs.rb as they are too "specialised". + (substitute* "Makefile" + ;; remove mafft-homologs.rb from SCRIPTS + (("^SCRIPTS = mafft mafft-homologs.rb") + "SCRIPTS = mafft") + ;; remove mafft-distance from PROGS + (("^PROGS = dvtditr dndfast7 dndblast sextet5 mafft-distance") + "PROGS = dvtditr dndfast7 dndblast sextet5") + ;; remove mafft-profile from PROGS + (("splittbfast disttbfast tbfast mafft-profile 2cl mccaskillwrap") + "splittbfast disttbfast tbfast f2cl mccaskillwrap") + (("^rm -f mafft-profile mafft-profile.exe") "#") + (("^rm -f mafft-distance mafft-distance.exe") ")#") + ;; do not install MAN pages in libexec folder + (("^\t\\$\\(INSTALL\\) -m 644 \\$\\(MANPAGES\\) \ +\\$\\(DESTDIR\\)\\$\\(LIBDIR\\)") "#")) + #t)) + (delete 'configure)))) + (inputs + `(("perl" ,perl))) + (home-page "http://mafft.cbrc.jp/alignment/software/") + (synopsis "Multiple sequence alignment program") + (description + "MAFFT offers a range of multiple alignment methods for nucleotide and +protein sequences. For instance, it offers L-INS-i (accurate; for alignment +of <~200 sequences) and FFT-NS-2 (fast; for alignment of <~30,000 +sequences).") + (license (license:non-copyleft + "http://mafft.cbrc.jp/alignment/software/license.txt" + "BSD-3 with different formatting")))) (define-public metabat (package -- cgit v1.2.3 From cd89fecbe71a1f72c676eb0589d218237ccbf43b Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Wed, 16 Sep 2015 05:03:48 +0200 Subject: gnu: Add ruby-cucumber-core. * gnu/packages/ruby.scm (ruby-cucumber-core): New variable. --- gnu/packages/ruby.scm | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/ruby.scm b/gnu/packages/ruby.scm index e61332f6aa..a4702289c9 100644 --- a/gnu/packages/ruby.scm +++ b/gnu/packages/ruby.scm @@ -1171,3 +1171,30 @@ It is intended to replace Gherkin 2 and be used by all Cucumber implementations to parse '.feature' files.") (home-page "https://github.com/cucumber/gherkin3") (license license:expat))) + +(define-public ruby-cucumber-core + (package + (name "ruby-cucumber-core") + (version "1.3.0") + (source + (origin + (method url-fetch) + (uri (rubygems-uri "cucumber-core" version)) + (sha256 + (base32 + "12mrzf0s96izpq0k10lahlkgwc4fjs0zfs344rh8r8h3w3jyppr8")))) + (build-system ruby-build-system) + (propagated-inputs + `(("ruby-gherkin3" ,ruby-gherkin3))) + (native-inputs + `(("bundler" ,bundler))) + (arguments + '(#:tests? #f)) ; needs simplecov, among others + (synopsis "Core library for the Cucumber BDD app") + (description "Cucumber is a tool for running automated tests +written in plain language. Because they're written in plain language, +they can be read by anyone on your team. Because they can be read by +anyone, you can use them to help improve communication, collaboration +and trust on your team.") + (home-page "https://cucumber.io/") + (license license:expat))) -- cgit v1.2.3 From 3ffe36f5349bfed523ef7405c5b3c45da7195802 Mon Sep 17 00:00:00 2001 From: Ludovic Courtès Date: Thu, 17 Sep 2015 10:38:12 +0200 Subject: gnu: Add emacs-deferred. * gnu/packages/emacs.scm (emacs-deferred): New variable. --- gnu/packages/emacs.scm | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/emacs.scm b/gnu/packages/emacs.scm index f7ad4e3a19..2ab1ebe4a0 100644 --- a/gnu/packages/emacs.scm +++ b/gnu/packages/emacs.scm @@ -1098,3 +1098,27 @@ prefer the listing of bugs as TODO items of @code{org-mode}, you could use A minor mode @code{debbugs-browse-mode} let you browse URLs to the GNU Bug Tracker as well as bug identifiers prepared for @code{bug-reference-mode}.") (license license:gpl3+))) + +(define-public emacs-deferred + (package + (name "emacs-deferred") + (version "0.3.2") + (home-page "https://github.com/kiwanami/emacs-deferred") + (source (origin + (method git-fetch) + (uri (git-reference + (url home-page) + (commit (string-append "v" version)))) + (sha256 + (base32 + "0059jy01ni5irpgrj9fa81ayd9j25nvmjjm79ms3210ysx4pgqdr")) + (file-name (string-append name "-" version)))) + (build-system emacs-build-system) + ;; FIXME: Would need 'el-expectations' to actually run tests. + (synopsis "Simple asynchronous functions for Emacs Lisp") + (description + "The @code{deferred.el} library provides support for asynchronous tasks. +The API is almost the same as that of +@uref{https://github.com/cho45/jsdeferred, JSDeferred}, a JavaScript library +for asynchronous tasks.") + (license license:gpl3+))) -- cgit v1.2.3 From d001bb5ab54b4e174392be6137e7acaec1e6f0f3 Mon Sep 17 00:00:00 2001 From: Ludovic Courtès Date: Thu, 17 Sep 2015 10:45:01 +0200 Subject: gnu: Add emacs-butler. * gnu/packages/emacs.scm (butler): New variable. --- gnu/packages/emacs.scm | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/emacs.scm b/gnu/packages/emacs.scm index 2ab1ebe4a0..cdd73206c4 100644 --- a/gnu/packages/emacs.scm +++ b/gnu/packages/emacs.scm @@ -1122,3 +1122,29 @@ The API is almost the same as that of @uref{https://github.com/cho45/jsdeferred, JSDeferred}, a JavaScript library for asynchronous tasks.") (license license:gpl3+))) + +(define-public butler + (package + (name "emacs-butler") + (version "0.2.4") + (home-page "https://github.com/AshtonKem/Butler") + (source (origin + (method git-fetch) + (uri (git-reference + (url home-page) + (commit version))) + (sha256 + (base32 + "1pii9dw4skq7nr4na6qxqasl36av8cwjp71bf1fgppqpcd9z8skj")) + (file-name (string-append name "-" version)))) + (build-system emacs-build-system) + (propagated-inputs + `(("emacs-deferred" ,emacs-deferred))) + (synopsis "Emacs client for Jenkins") + (description + "Butler provides an interface to connect to Jenkins continuous +integration servers. Users can specify a list of server in the +@code{butler-server-list} variable and then use @code{M-x butler-status} to +view the build status of those servers' build jobs, and possibly to trigger +build jobs.") + (license license:gpl3+))) -- cgit v1.2.3 From 2d1db448bdbce9cd8a6df39097f56c3840754949 Mon Sep 17 00:00:00 2001 From: Ludovic Courtès Date: Thu, 17 Sep 2015 11:15:23 +0200 Subject: gnu: Add emacs-typo. * gnu/packages/emacs.scm (typo): New variable. --- gnu/packages/emacs.scm | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/emacs.scm b/gnu/packages/emacs.scm index cdd73206c4..a342f4861b 100644 --- a/gnu/packages/emacs.scm +++ b/gnu/packages/emacs.scm @@ -1148,3 +1148,27 @@ integration servers. Users can specify a list of server in the view the build status of those servers' build jobs, and possibly to trigger build jobs.") (license license:gpl3+))) + +(define-public typo + (package + (name "emacs-typo") + (version "1.1") + (home-page "https://github.com/jorgenschaefer/typoel") + (source (origin + (method git-fetch) + (uri (git-reference + (url home-page) + (commit (string-append "v" version)))) + (sha256 + (base32 + "1jhd4grch5iz12gyxwfbsgh4dmz5hj4bg4gnvphccg8dsnni05k2")) + (file-name (string-append name "-" version)))) + (build-system emacs-build-system) + (synopsis "Minor mode for typographic editing") + (description + "This package provides two Emacs modes, @code{typo-mode} and +@code{typo-global-mode}. These modes automatically insert Unicode characters +for quotation marks, dashes, and ellipses. For example, typing @kbd{\"} +automatically inserts a Unicode opening or closing quotation mark, depending +on context.") + (license license:gpl3+))) -- cgit v1.2.3 From be3feafedf4b040680b3b5a23646b81ecefaf9a0 Mon Sep 17 00:00:00 2001 From: Christopher Allan Webber Date: Wed, 16 Sep 2015 15:49:06 -0500 Subject: gnu: guile: Add guile-next MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/guile.scm (guile-next): New variable. * gnu/packages/guile.scm (guile-for-guile-emacs): Adjust to inherit from guile-next rather than guile-2.0 Signed-off-by: Ludovic Courtès --- gnu/packages/guile.scm | 27 +++++++++++++++++++++------ 1 file changed, 21 insertions(+), 6 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/guile.scm b/gnu/packages/guile.scm index 7b4f4c65c2..60af92dceb 100644 --- a/gnu/packages/guile.scm +++ b/gnu/packages/guile.scm @@ -185,18 +185,19 @@ without requiring the source code to be rewritten.") ;; in the `base' module, and thus changing it entails a full rebuild. guile-2.0) -(define-public guile-for-guile-emacs +(define-public guile-next (package (inherit guile-2.0) - (name "guile-for-guile-emacs") - (version "20150510.d8d9a8d") + (name "guile-next") + (version "20150815.00884bb") (source (origin (method git-fetch) (uri (git-reference - (url "git://git.hcoop.net/git/bpt/guile.git") - (commit "d8d9a8da05ec876acba81a559798eb5eeceb5a17"))) + (url "git://git.sv.gnu.org/guile.git") + (commit "00884bb79fff41fdf5f22f24a74e366a94a14c9b"))) (sha256 (base32 - "00sprsshy16y8pxjy126hr2adqcvvzzz96hjyjwgg8swva1qh6b0")))) + "0qk8m9aq3i7pzw6npim58xmsvjqfz5kl1pkyb6b43awn2vydydi5")))) + (arguments (substitute-keyword-arguments `(;; Tests aren't passing for now. ;; Obviously we should re-enable this! @@ -212,6 +213,7 @@ without requiring the source code to be rewritten.") (substitute* "build-aux/git-version-gen" (("#!/bin/sh") (string-append "#!" (which "sh")))) #t)))))) + (synopsis "Snapshot of what will become version 2.2 of GNU Guile") (native-inputs `(("autoconf" ,autoconf) ("automake" ,automake) @@ -221,6 +223,19 @@ without requiring the source code to be rewritten.") ("gettext" ,gnu-gettext) ,@(package-native-inputs guile-2.0))))) +(define-public guile-for-guile-emacs + (package (inherit guile-next) + (name "guile-for-guile-emacs") + (version "20150510.d8d9a8d") + (source (origin + (method git-fetch) + (uri (git-reference + (url "git://git.hcoop.net/git/bpt/guile.git") + (commit "d8d9a8da05ec876acba81a559798eb5eeceb5a17"))) + (sha256 + (base32 + "00sprsshy16y8pxjy126hr2adqcvvzzz96hjyjwgg8swva1qh6b0")))))) + ;;; ;;; Extensions. -- cgit v1.2.3 From 212d563d260171054fec007d68cc0d4b1811ee4c Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Wed, 16 Sep 2015 06:06:26 +0000 Subject: gnu: Add ruby-bio-logger. * gnu/packages/ruby.scm (ruby-bio-logger): New variable. --- gnu/packages/ruby.scm | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/ruby.scm b/gnu/packages/ruby.scm index a4702289c9..fa4f345882 100644 --- a/gnu/packages/ruby.scm +++ b/gnu/packages/ruby.scm @@ -1198,3 +1198,25 @@ anyone, you can use them to help improve communication, collaboration and trust on your team.") (home-page "https://cucumber.io/") (license license:expat))) + +(define-public ruby-bio-logger + (package + (name "ruby-bio-logger") + (version "1.0.1") + (source + (origin + (method url-fetch) + (uri (rubygems-uri "bio-logger" version)) + (sha256 + (base32 + "02pylfy8nkdqzyzplvnhn1crzmfkj1zmi3qjhrj2f2imlxvycd28")))) + (build-system ruby-build-system) + (arguments + `(#:tests? #f)) ; rake errors, missing shoulda + (propagated-inputs + `(("ruby-log4r" ,ruby-log4r))) + (synopsis "Log4r wrapper for Ruby") + (description "Bio-logger is a wrapper around Log4r adding extra logging +features such as filtering and fine grained logging.") + (home-page "https://github.com/pjotrp/bioruby-logger-plugin") + (license license:expat))) -- cgit v1.2.3 From c093f9f63a57ae8fa9d230249f0b724f80763dc5 Mon Sep 17 00:00:00 2001 From: Federico Beffa Date: Thu, 13 Aug 2015 18:58:01 +0200 Subject: gnu: Add scmutils. * gnu/packages/scheme.scm (scmutils): New variable. --- gnu/packages/scheme.scm | 177 ++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 177 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/scheme.scm b/gnu/packages/scheme.scm index 803b8d5a20..7465b1b58c 100644 --- a/gnu/packages/scheme.scm +++ b/gnu/packages/scheme.scm @@ -1,6 +1,7 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2013, 2014, 2015 Ludovic Courtès ;;; Copyright © 2015 Taylan Ulrich Bayırlı/Kammer +;;; Copyright © 2015 Federico Beffa ;;; ;;; This file is part of GNU Guix. ;;; @@ -486,3 +487,179 @@ addition to support for lightweight VM-based threads, each VM itself runs in an isolated heap allowing multiple VMs to run simultaneously in different OS threads.") (license bsd-3))) + +;; FIXME: This function is temporarily in the engineering module and not +;; exported. It will be moved to an utility module for general use. Once +;; this is done, we should remove this definition. +(define broken-tarball-fetch + (@@ (gnu packages engineering) broken-tarball-fetch)) + +(define-public scmutils + (let () + (define (system-suffix) + (cond + ((string-prefix? "x86_64" (or (%current-target-system) + (%current-system))) + "x86-64") + (else "i386"))) + + (package + (name "scmutils") + (version "20140302") + (source + (origin + (method broken-tarball-fetch) + (modules '((guix build utils))) + (snippet + ;; Remove binary code + '(delete-file-recursively "scmutils/mit-scheme")) + (file-name (string-append name "-" version ".tar.gz")) + (uri (string-append "http://groups.csail.mit.edu/mac/users/gjs/6946" + "/scmutils-tarballs/" name "-" version + "-x86-64-gnu-linux.tar.gz")) + (sha256 + (base32 "10cnbm7nh78m5mrl1di85s29gny81jb1am9zd9f9yx725xb6dnfg")))) + (build-system gnu-build-system) + (inputs + `(("mit-scheme" ,mit-scheme) + ("emacs" ,emacs-no-x))) + (arguments + `(#:tests? #f ;; no tests-suite + #:modules ((guix build gnu-build-system) + (guix build utils) + (guix build emacs-utils)) + #:imported-modules (,@%gnu-build-system-modules + (guix build emacs-utils)) + #:phases + (modify-phases %standard-phases + (replace 'configure + ;; No standard build procedure is used. We set the correct + ;; runtime path in the custom build system. + (lambda* (#:key outputs #:allow-other-keys) + (let ((out (assoc-ref outputs "out"))) + ;; Required to find .bci files at runtime. + (with-directory-excursion "scmutils" + (rename-file "src" "scmutils")) + (substitute* "scmutils/scmutils/load.scm" + (("/usr/local/scmutils/") + (string-append out "/lib/mit-scheme-" + ,(system-suffix) "/"))) + #t))) + (replace 'build + ;; Compile the code and build a band. + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (make-img (string-append + "echo '(load \"load\") " + "(disk-save \"edwin-mechanics.com\")'" + "| mit-scheme"))) + (with-directory-excursion "scmutils/scmutils" + (and (zero? (system "mit-scheme < compile.scm")) + (zero? (system make-img))))))) + (add-before 'install 'fix-directory-names + ;; Correct directory names in the startup script. + (lambda* (#:key inputs outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (scm-root (assoc-ref inputs "mit-scheme"))) + (substitute* "bin/mechanics" + (("ROOT=\"\\$\\{SCMUTILS_ROOT:-/.*\\}\"") + (string-append + "ROOT=\"${SCMUTILS_ROOT:-" scm-root "}\"\n" + "LIB=\"${ROOT}/lib/mit-scheme-" + ,(system-suffix) ":" + out "/lib/mit-scheme-" ,(system-suffix) "\"")) + (("EDWIN_INFO_DIRECTORY=.*\n") "") + (("SCHEME=.*\n") + (string-append "SCHEME=\"${ROOT}/bin/scheme " + "--library ${LIB}\"\n")) + (("export EDWIN_INFO_DIRECTORY") "")) + #t))) + (add-before 'install 'emacs-tags + ;; Generate Emacs's tags for easy reference to source + ;; code. + (lambda* (#:key inputs outputs #:allow-other-keys) + (with-directory-excursion "scmutils/scmutils" + (zero? (apply system* "etags" + (find-files "." "\\.scm")))))) + (replace 'install + ;; Copy files to the store. + (lambda* (#:key outputs #:allow-other-keys) + (define* (copy-files-to-directory files dir + #:optional (delete? #f)) + (for-each (lambda (f) + (copy-file f (string-append dir "/" f)) + (when delete? (delete-file f))) + files)) + + (let* ((out (assoc-ref outputs "out")) + (bin (string-append out "/bin")) + (doc (string-append out "/share/doc/" + ,name "-" ,version)) + (lib (string-append out "/lib/mit-scheme-" + ,(system-suffix) + "/scmutils"))) + (for-each mkdir-p (list lib doc bin)) + (with-directory-excursion "scmutils/scmutils" + (copy-files-to-directory '("COPYING" "LICENSE") + doc #t) + (for-each delete-file (find-files "." "\\.bin")) + (copy-files-to-directory '("edwin-mechanics.com") + (string-append lib "/..") #t) + (copy-recursively "." lib)) + (with-directory-excursion "bin" + (copy-files-to-directory (find-files ".") bin)) + (with-directory-excursion "scmutils/manual" + (copy-files-to-directory (find-files ".") doc)) + #t))) + (add-after 'install 'emacs-helpers + ;; Add convenience Emacs commands to easily load the + ;; Scmutils band in an MIT-Scheme buffer inside of Emacs + ;; and to easily load code tags. + (lambda* (#:key inputs outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (mit-root (assoc-ref inputs "mit-scheme")) + (emacs-lisp-dir + (string-append out "/share/emacs/site-lisp" + "/guix.d/" ,name "-" ,version)) + (el-file (string-append emacs-lisp-dir + "/scmutils.el")) + (lib-relative-path + (string-append "/lib/mit-scheme-" + ,(system-suffix)))) + (mkdir-p emacs-lisp-dir) + (call-with-output-file el-file + (lambda (p) + (format p + ";;;###autoload +(defun scmutils-load () + (interactive) + (require 'xscheme) + (let ((mit-root \"~a\") + (scmutils \"~a\")) + (run-scheme + (concat mit-root \"/bin/scheme --library \" + mit-root \"~a:\" scmutils \"~a\" + \" --band edwin-mechanics.com\" + \" --emacs\")))) + +;;;###autoload +(defun scmutils-load-tags () + (interactive) + (let ((scmutils \"~a\")) + (visit-tags-table (concat scmutils \"/TAGS\")))) +" + mit-root out + lib-relative-path + lib-relative-path + (string-append out lib-relative-path + "/scmutils")))) + (emacs-byte-compile-directory (dirname el-file)) + #t)))))) + (home-page + "http://groups.csail.mit.edu/mac/users/gjs/6946/linux-install.htm") + (synopsis "Scmutils library for MIT Scheme") + (description "The Scmutils system is an integrated library of +procedures, embedded in the programming language Scheme, and intended to +support teaching and research in mathematical physics and electrical +engineering.") + (license gpl2+)))) -- cgit v1.2.3 From 24a848c8e36e762968e6e2803a72ae570e9edbec Mon Sep 17 00:00:00 2001 From: Stefan Reichoer Date: Tue, 15 Sep 2015 10:39:49 +0200 Subject: gnu: Add ifstatus. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/networking.scm (ifstatus): New variable. Signed-off-by: Ludovic Courtès --- gnu/packages/networking.scm | 43 ++++++++++++++++++++++++++++++++++++++++++- 1 file changed, 42 insertions(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/packages/networking.scm b/gnu/packages/networking.scm index dc139e28fe..08380b1f87 100644 --- a/gnu/packages/networking.scm +++ b/gnu/packages/networking.scm @@ -2,6 +2,7 @@ ;;; Copyright © 2014 Ludovic Courtès ;;; Copyright © 2015 Ricardo Wurmus ;;; Copyright © 2015 Mark H Weaver +;;; Copyright © 2015 Stefan Reichör ;;; ;;; This file is part of GNU Guix. ;;; @@ -23,7 +24,8 @@ #:use-module (guix packages) #:use-module (guix download) #:use-module (guix build-system gnu) - #:use-module (gnu packages tls)) + #:use-module (gnu packages tls) + #:use-module (gnu packages ncurses)) (define-public miredo (package @@ -146,3 +148,42 @@ receiving NDP messages.") auto-negotiation and checksum offload on many network devices, especially Ethernet devices.") (license license:gpl2))) + +(define-public ifstatus + (package + (name "ifstatus") + (version "1.1.0") + (source (origin + (method url-fetch) + (uri (string-append "mirror://sourceforge/ifstatus/ifstatus-v" + version ".tar.gz")) + (sha256 + (base32 + "045cbsq9ps32j24v8y5hpyqxnqn9mpaf3mgvirlhgpqyb9jsia0c")) + (modules '((guix build utils))) + (snippet + '(substitute* "Main.h" + (("#include ") + "#include \n#include "))))) + (build-system gnu-build-system) + (arguments + '(#:tests? #f ; no "check" target + #:phases + (modify-phases %standard-phases + (delete 'configure) ; no configure script + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (bin (string-append out "/bin"))) + (mkdir-p bin) + (copy-file "ifstatus" + (string-append bin "/ifstatus")))))))) + (inputs `(("ncurses" ,ncurses))) + (home-page "http://ifstatus.sourceforge.net/graphic/index.html") + (synopsis "Text based network interface status monitor") + (description + "IFStatus is a simple, easy-to-use program for displaying commonly +needed / wanted real-time traffic statistics of multiple network +interfaces, with a simple and efficient view on the command line. It is +intended as a substitute for the PPPStatus and EthStatus projects.") + (license license:bsd-2))) -- cgit v1.2.3 From 8874f7668ae93bec2805fd823bfcbe80a977e78c Mon Sep 17 00:00:00 2001 From: Ludovic Courtès Date: Fri, 18 Sep 2015 21:57:53 +0200 Subject: gnu: ifstatus: Fix license. * gnu/packages/networking.scm (ifstatus)[license]: Set to GPL2+. --- gnu/packages/networking.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/networking.scm b/gnu/packages/networking.scm index 08380b1f87..0a7cde0b0d 100644 --- a/gnu/packages/networking.scm +++ b/gnu/packages/networking.scm @@ -183,7 +183,7 @@ Ethernet devices.") (synopsis "Text based network interface status monitor") (description "IFStatus is a simple, easy-to-use program for displaying commonly -needed / wanted real-time traffic statistics of multiple network +needed/wanted real-time traffic statistics of multiple network interfaces, with a simple and efficient view on the command line. It is intended as a substitute for the PPPStatus and EthStatus projects.") - (license license:bsd-2))) + (license license:gpl2+))) -- cgit v1.2.3 From 6aaa815e9fae8fccb98c243936210c17cd9609ed Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Wed, 16 Sep 2015 06:06:40 +0200 Subject: gnu: Add ruby-docile. * gnu/packages/ruby.scm (ruby-docile): New variable. --- gnu/packages/ruby.scm | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/ruby.scm b/gnu/packages/ruby.scm index fa4f345882..9c081624b6 100644 --- a/gnu/packages/ruby.scm +++ b/gnu/packages/ruby.scm @@ -1149,6 +1149,27 @@ into a single method call.") (home-page "http://rack.github.io/") (license license:expat))) +(define-public ruby-docile + (package + (name "ruby-docile") + (version "1.1.5") + (source + (origin + (method url-fetch) + (uri (rubygems-uri "docile" version)) + (sha256 + (base32 + "0m8j31whq7bm5ljgmsrlfkiqvacrw6iz9wq10r3gwrv5785y8gjx")))) + (build-system ruby-build-system) + (arguments + '(#:tests? #f)) ; needs github-markup, among others + (synopsis "Ruby EDSL helper library") + (description "Docile is a Ruby library that provides an interface for +creating embedded domain specific languages (EDSLs) that manipulate existing +Ruby classes.") + (home-page "https://ms-ati.github.io/docile/") + (license license:expat))) + (define-public ruby-gherkin3 (package (name "ruby-gherkin3") -- cgit v1.2.3 From ec79018e6831babef249ab883e9f9a71bebe1193 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 16 Sep 2015 10:58:49 +0200 Subject: gnu: Add ruby-lumberjack. * gnu/packages/ruby.scm (ruby-lumberjack): New variable. --- gnu/packages/ruby.scm | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/ruby.scm b/gnu/packages/ruby.scm index 9c081624b6..6aaa5dd5ec 100644 --- a/gnu/packages/ruby.scm +++ b/gnu/packages/ruby.scm @@ -529,6 +529,27 @@ interfaces.") (home-page "http://whatisthor.com/") (license license:expat))) +(define-public ruby-lumberjack + (package + (name "ruby-lumberjack") + (version "1.0.9") + (source (origin + (method url-fetch) + (uri (rubygems-uri "lumberjack" version)) + (sha256 + (base32 + "162frm2bwy58pj8ccsdqa4a6i0csrhb9h5l3inhkl1ivgfc8814l")))) + (build-system ruby-build-system) + (native-inputs + `(("ruby-rspec" ,ruby-rspec))) + (synopsis "Logging utility library for Ruby") + (description "Lumberjack is a simple logging utility that can be a drop in +replacement for Logger or ActiveSupport::BufferedLogger. It provides support +for automatically rolling log files even with multiple processes writing the +same log file.") + (home-page "http://github.com/bdurand/lumberjack") + (license license:expat))) + (define-public ruby-useragent (package (name "ruby-useragent") -- cgit v1.2.3 From 70b4cf3818c9fb5abfb49df77bcafbd5406ee700 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 16 Sep 2015 10:59:21 +0200 Subject: gnu: Add ruby-nenv. * gnu/packages/ruby.scm (ruby-nenv): New variable. --- gnu/packages/ruby.scm | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/ruby.scm b/gnu/packages/ruby.scm index 6aaa5dd5ec..0127a616de 100644 --- a/gnu/packages/ruby.scm +++ b/gnu/packages/ruby.scm @@ -550,6 +550,28 @@ same log file.") (home-page "http://github.com/bdurand/lumberjack") (license license:expat))) +(define-public ruby-nenv + (package + (name "ruby-nenv") + (version "0.2.0") + (source (origin + (method url-fetch) + (uri (rubygems-uri "nenv" version)) + (sha256 + (base32 + "152wxwri0afwgnxdf93gi6wjl9rr5z7vwp8ln0gpa3rddbfc27s6")))) + (build-system ruby-build-system) + (arguments + `(#:tests? #f)) ; no tests included + (native-inputs + `(("ruby-rspec" ,ruby-rspec) + ("bundler" ,bundler))) + (synopsis "Ruby interface for modifying the environment") + (description "Nenv provides a convenient wrapper for Ruby's ENV to modify +and inspect the environment.") + (home-page "https://github.com/e2/nenv") + (license license:expat))) + (define-public ruby-useragent (package (name "ruby-useragent") -- cgit v1.2.3 From c5d14d42282fe9d4123f1efa0f995123781e17da Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 16 Sep 2015 11:00:45 +0200 Subject: gnu: Add ruby-shellany. * gnu/packages/ruby.scm (ruby-shellany): New variable. --- gnu/packages/ruby.scm | 30 ++++++++++++++++++++++++++++++ 1 file changed, 30 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/ruby.scm b/gnu/packages/ruby.scm index 0127a616de..e8ec6ed870 100644 --- a/gnu/packages/ruby.scm +++ b/gnu/packages/ruby.scm @@ -572,6 +572,36 @@ and inspect the environment.") (home-page "https://github.com/e2/nenv") (license license:expat))) +(define-public ruby-shellany + (package + (name "ruby-shellany") + (version "0.0.1") + (source (origin + (method url-fetch) + (uri (rubygems-uri "shellany" version)) + (sha256 + (base32 + "1ryyzrj1kxmnpdzhlv4ys3dnl2r5r3d2rs2jwzbnd1v96a8pl4hf")))) + (build-system ruby-build-system) + (arguments + `(#:test-target "default" + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'fix-version-test + (lambda _ + (substitute* "spec/shellany_spec.rb" + (("^RSpec") "require \"shellany\"\nRSpec")) + #t))))) + (native-inputs + `(("ruby-rspec" ,ruby-rspec) + ("ruby-nenv" ,ruby-nenv) + ("bundler" ,bundler))) + (synopsis "Capture command output") + (description "Shellany is a Ruby library providing functions to capture +the output produced by running shell commands.") + (home-page "https://rubygems.org/gems/shellany") + (license license:expat))) + (define-public ruby-useragent (package (name "ruby-useragent") -- cgit v1.2.3 From d152162fc1bbd1dea4379239537cde7ca893880a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 16 Sep 2015 11:01:34 +0200 Subject: gnu: Add ruby-notiffany. * gnu/packages/ruby.scm (ruby-notiffany): New variable. --- gnu/packages/ruby.scm | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/ruby.scm b/gnu/packages/ruby.scm index e8ec6ed870..88eeb76a10 100644 --- a/gnu/packages/ruby.scm +++ b/gnu/packages/ruby.scm @@ -602,6 +602,30 @@ the output produced by running shell commands.") (home-page "https://rubygems.org/gems/shellany") (license license:expat))) +(define-public ruby-notiffany + (package + (name "ruby-notiffany") + (version "0.0.7") + (source (origin + (method url-fetch) + (uri (rubygems-uri "notiffany" version)) + (sha256 + (base32 + "1v5x1w59qq85r6dpv3y9ga34dfd7hka1qxyiykaw7gm0i6kggbhi")))) + (build-system ruby-build-system) + ;; Tests are not included in the gem. + (arguments `(#:tests? #f)) + (propagated-inputs + `(("ruby-shellany" ,ruby-shellany) + ("ruby-nenv" ,ruby-nenv))) + (native-inputs + `(("bundler" ,bundler))) + (synopsis "Wrapper libray for notification libraries") + (description "Notiffany is a Ruby wrapper libray for notification +libraries such as Libnotify.") + (home-page "https://github.com/guard/notiffany") + (license license:expat))) + (define-public ruby-useragent (package (name "ruby-useragent") -- cgit v1.2.3 From 8528365b0ebd7f7f4cb532165aa509b80e87c236 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 16 Sep 2015 11:02:32 +0200 Subject: gnu: Add ruby-formatador. * gnu/packages/ruby.scm (ruby-formatador): New variable. --- gnu/packages/ruby.scm | 20 ++++++++++++++++++++ 1 file changed, 20 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/ruby.scm b/gnu/packages/ruby.scm index 88eeb76a10..d73e854774 100644 --- a/gnu/packages/ruby.scm +++ b/gnu/packages/ruby.scm @@ -626,6 +626,26 @@ libraries such as Libnotify.") (home-page "https://github.com/guard/notiffany") (license license:expat))) +(define-public ruby-formatador + (package + (name "ruby-formatador") + (version "0.2.5") + (source (origin + (method url-fetch) + (uri (rubygems-uri "formatador" version)) + (sha256 + (base32 + "1gc26phrwlmlqrmz4bagq1wd5b7g64avpx0ghxr9xdxcvmlii0l0")))) + (build-system ruby-build-system) + ;; Circular dependency: Tests require ruby-shindo, which requires + ;; ruby-formatador at runtime. + (arguments `(#:tests? #f)) + (synopsis "Ruby library to format text on stdout") + (description "Formatador is a Ruby library to format text printed to the +standard output stream.") + (home-page "http://github.com/geemus/formatador") + (license license:expat))) + (define-public ruby-useragent (package (name "ruby-useragent") -- cgit v1.2.3 From 7ac4610f7e00a08e3d05eb49b488043b3f0005a7 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 16 Sep 2015 11:03:10 +0200 Subject: gnu: Add ruby-shindo. * gnu/packages/ruby.scm (ruby-shindo): New variable. --- gnu/packages/ruby.scm | 29 +++++++++++++++++++++++++++++ 1 file changed, 29 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/ruby.scm b/gnu/packages/ruby.scm index d73e854774..d80d3aa424 100644 --- a/gnu/packages/ruby.scm +++ b/gnu/packages/ruby.scm @@ -646,6 +646,35 @@ standard output stream.") (home-page "http://github.com/geemus/formatador") (license license:expat))) +(define-public ruby-shindo + (package + (name "ruby-shindo") + (version "0.3.8") + (source (origin + (method url-fetch) + (uri (rubygems-uri "shindo" version)) + (sha256 + (base32 + "0s8v1jbz8i0jh92f2fgxb3p51l1azrpkc8nv4mhrqy4vndpvd7wq")))) + (build-system ruby-build-system) + (arguments + `(#:test-target "shindo_tests" + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'fix-tests + (lambda _ + (substitute* "Rakefile" + (("system \"shindo") "system \"./bin/shindo") + ;; This test doesn't work, so we disable it. + (("fail \"The build_error test should fail") "#")) + #t))))) + (propagated-inputs + `(("ruby-formatador" ,ruby-formatador))) + (synopsis "Simple depth first Ruby testing") + (description "Shindo is a simple depth first testing library for Ruby.") + (home-page "https://github.com/geemus/shindo") + (license license:expat))) + (define-public ruby-useragent (package (name "ruby-useragent") -- cgit v1.2.3 From 28c5d42d354c6e902529d3c6e55138ee942461d0 Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Tue, 15 Sep 2015 13:32:34 +0000 Subject: gnu: Add ruby-libxml. * gnu/packages/ruby.scm (ruby-libxml): New variable. --- gnu/packages/ruby.scm | 28 ++++++++++++++++++++++++++++ 1 file changed, 28 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/ruby.scm b/gnu/packages/ruby.scm index d80d3aa424..c906361971 100644 --- a/gnu/packages/ruby.scm +++ b/gnu/packages/ruby.scm @@ -489,6 +489,34 @@ extensions.") (home-page "http://codeforpeople.com/lib/ruby/orderedhash/") (license license:public-domain))) +(define-public ruby-libxml + (package + (name "ruby-libxml") + (version "2.8.0") + (source + (origin + (method url-fetch) + (uri (rubygems-uri "libxml-ruby" version)) + (sha256 + (base32 + "1dhjqp4r9vkdp00l6h1cj8qfndzxlhlxk6b9g0w4v55gz857ilhb")))) + (build-system ruby-build-system) + (inputs + `(("zlib" ,zlib) + ("libxml2" ,libxml2))) + (arguments + '(#:tests? #f ; test suite hangs for unknown reason + #:gem-flags + (list "--" + (string-append "--with-xml2-include=" + (assoc-ref %build-inputs "libxml2") + "/include/libxml2" )))) + (synopsis "Ruby bindings for GNOME Libxml2") + (description "The Libxml-Ruby project provides Ruby language bindings for +the GNOME Libxml2 XML toolkit.") + (home-page "http://xml4r.github.com/libxml-ruby") + (license license:expat))) + (define-public ruby-xml-simple (package (name "ruby-xml-simple") -- cgit v1.2.3 From edb15985f1123e54199bac7228e49fb84371e0cb Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Thu, 17 Sep 2015 06:17:44 +0000 Subject: gnu: Add bioruby. * gnu/packages/bioinformatics.scm (bioruby): New variable. --- gnu/packages/bioinformatics.scm | 43 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 43 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index a13fd7a91d..37bd3339d3 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -2700,3 +2700,46 @@ position for indels. Bio-locus allows users to store this chr+pos or chr+pos+alt information in a database.") (home-page "https://github.com/pjotrp/bio-locus") (license license:expat))) + +(define-public bioruby + (package + (name "bioruby") + (version "1.5.0") + (source + (origin + (method url-fetch) + (uri (rubygems-uri "bio" version)) + (sha256 + (base32 + "01k2fyjl5fpx4zn8g6gqiqvsg2j1fgixrs9p03vzxckynxdq3wmc")))) + (build-system ruby-build-system) + (propagated-inputs + `(("ruby-libxml" ,ruby-libxml))) + (native-inputs + `(("which" ,which))) ; required for test phase + (arguments + `(#:phases + (modify-phases %standard-phases + (add-before 'build 'patch-test-command + (lambda _ + (substitute* '("test/functional/bio/test_command.rb") + (("/bin/sh") (which "sh"))) + (substitute* '("test/functional/bio/test_command.rb") + (("/bin/ls") (which "ls"))) + (substitute* '("test/functional/bio/test_command.rb") + (("which") (which "which"))) + (substitute* '("test/functional/bio/test_command.rb", + "test/data/command/echoarg2.sh") + (("/bin/echo") (which "echo"))) + #t))))) + (synopsis "Ruby library, shell and utilities for bioinformatics") + (description "BioRuby comes with a comprehensive set of Ruby development +tools and libraries for bioinformatics and molecular biology. BioRuby has +components for sequence analysis, pathway analysis, protein modelling and +phylogenetic analysis; it supports many widely used data formats and provides +easy access to databases, external programs and public web services, including +BLAST, KEGG, GenBank, MEDLINE and GO.") + (home-page "http://bioruby.org/") + ;; Code is released under Ruby license, except for setup + ;; (LGPLv2.1+) and scripts in samples (which have GPL2 and GPL2+) + (license (list license:ruby license:lgpl2.1+ license:gpl2+ )))) -- cgit v1.2.3 From e49b339608d63ea980c24fec01dc94cd59f19335 Mon Sep 17 00:00:00 2001 From: Andreas Enge Date: Sat, 19 Sep 2015 23:19:32 +0200 Subject: gnu: libmtp: Add additional MTP devices. * gnu/packages/patches/libmtp-devices.patch: New file. * gnu-system.am (dist_patch_DATA): Register patch. * gnu/packages/patches/libmtp-devices.patch (libmtp)[source]: Add patch. --- gnu-system.am | 1 + gnu/packages/libusb.scm | 3 +- gnu/packages/patches/libmtp-devices.patch | 554 ++++++++++++++++++++++++++++++ 3 files changed, 557 insertions(+), 1 deletion(-) create mode 100644 gnu/packages/patches/libmtp-devices.patch (limited to 'gnu') diff --git a/gnu-system.am b/gnu-system.am index d3c63cad33..2d261315ef 100644 --- a/gnu-system.am +++ b/gnu-system.am @@ -518,6 +518,7 @@ dist_patch_DATA = \ gnu/packages/patches/libbonobo-activation-test-race.patch \ gnu/packages/patches/libcanberra-sound-theme-freedesktop.patch \ gnu/packages/patches/libevent-dns-tests.patch \ + gnu/packages/patches/libmtp-devices.patch \ gnu/packages/patches/liboop-mips64-deplibs-fix.patch \ gnu/packages/patches/liblxqt-include.patch \ gnu/packages/patches/libmad-armv7-thumb-pt1.patch \ diff --git a/gnu/packages/libusb.scm b/gnu/packages/libusb.scm index e7f5b8b119..266669061e 100644 --- a/gnu/packages/libusb.scm +++ b/gnu/packages/libusb.scm @@ -96,7 +96,8 @@ version of libusb to run with newer libusb.") "/libmtp-" version ".tar.gz")) (sha256 (base32 - "12dinqic0ljnhrwx3rc61jc7q24ybr0mckc2ya5kh1s1np0d7w93")))) + "12dinqic0ljnhrwx3rc61jc7q24ybr0mckc2ya5kh1s1np0d7w93")) + (patches (list (search-patch "libmtp-devices.patch"))))) (build-system gnu-build-system) (native-inputs `(("pkg-config" ,pkg-config))) diff --git a/gnu/packages/patches/libmtp-devices.patch b/gnu/packages/patches/libmtp-devices.patch new file mode 100644 index 0000000000..9b985e526d --- /dev/null +++ b/gnu/packages/patches/libmtp-devices.patch @@ -0,0 +1,554 @@ +Add additional devices; the patched file corresponds to git commit 8e471b, +to which one additional device has been added as reported at + http://sourceforge.net/p/libmtp/bugs/1422/ + +diff -u -r libmtp-1.1.9.orig/src/music-players.h libmtp-1.1.9/src/music-players.h +--- libmtp-1.1.9.orig/src/music-players.h 2015-09-19 22:54:24.537330594 +0200 ++++ libmtp-1.1.9/src/music-players.h 2015-09-19 23:16:41.079206331 +0200 +@@ -47,82 +47,61 @@ + * and properties. + */ + { "Creative", 0x041e, "ZEN Vision", 0x411f, +- DEVICE_FLAG_BROKEN_MTPGETOBJPROPLIST_ALL | +- DEVICE_FLAG_BROKEN_GET_OBJECT_PROPVAL }, ++ DEVICE_FLAG_BROKEN_MTPGETOBJPROPLIST_ALL }, + { "Creative", 0x041e, "Portable Media Center", 0x4123, +- DEVICE_FLAG_BROKEN_MTPGETOBJPROPLIST_ALL | +- DEVICE_FLAG_BROKEN_GET_OBJECT_PROPVAL }, ++ DEVICE_FLAG_BROKEN_MTPGETOBJPROPLIST_ALL }, + { "Creative", 0x041e, "ZEN Xtra (MTP mode)", 0x4128, +- DEVICE_FLAG_BROKEN_MTPGETOBJPROPLIST_ALL | +- DEVICE_FLAG_BROKEN_GET_OBJECT_PROPVAL }, ++ DEVICE_FLAG_BROKEN_MTPGETOBJPROPLIST_ALL }, + { "Dell", 0x041e, "DJ (2nd generation)", 0x412f, +- DEVICE_FLAG_BROKEN_MTPGETOBJPROPLIST_ALL | +- DEVICE_FLAG_BROKEN_GET_OBJECT_PROPVAL }, ++ DEVICE_FLAG_BROKEN_MTPGETOBJPROPLIST_ALL }, + { "Creative", 0x041e, "ZEN Micro (MTP mode)", 0x4130, +- DEVICE_FLAG_BROKEN_MTPGETOBJPROPLIST_ALL | +- DEVICE_FLAG_BROKEN_GET_OBJECT_PROPVAL }, ++ DEVICE_FLAG_BROKEN_MTPGETOBJPROPLIST_ALL }, + { "Creative", 0x041e, "ZEN Touch (MTP mode)", 0x4131, +- DEVICE_FLAG_BROKEN_MTPGETOBJPROPLIST_ALL | +- DEVICE_FLAG_BROKEN_GET_OBJECT_PROPVAL }, ++ DEVICE_FLAG_BROKEN_MTPGETOBJPROPLIST_ALL }, + { "Dell", 0x041e, "Dell Pocket DJ (MTP mode)", 0x4132, +- DEVICE_FLAG_BROKEN_MTPGETOBJPROPLIST_ALL | +- DEVICE_FLAG_BROKEN_GET_OBJECT_PROPVAL }, +- { "Creative", 0x041e, "ZEN MicroPhoto (alternate version)", 0x4133, +- DEVICE_FLAG_BROKEN_MTPGETOBJPROPLIST_ALL | +- DEVICE_FLAG_BROKEN_GET_OBJECT_PROPVAL }, ++ DEVICE_FLAG_BROKEN_MTPGETOBJPROPLIST_ALL }, ++ { "Creative", 0x041e, "ZEN MicroPhoto (alternate version)", 0x4133, ++ DEVICE_FLAG_BROKEN_MTPGETOBJPROPLIST_ALL }, + { "Creative", 0x041e, "ZEN Sleek (MTP mode)", 0x4137, +- DEVICE_FLAG_BROKEN_MTPGETOBJPROPLIST_ALL | +- DEVICE_FLAG_BROKEN_GET_OBJECT_PROPVAL }, ++ DEVICE_FLAG_BROKEN_MTPGETOBJPROPLIST_ALL }, + { "Creative", 0x041e, "ZEN MicroPhoto", 0x413c, +- DEVICE_FLAG_BROKEN_MTPGETOBJPROPLIST_ALL | +- DEVICE_FLAG_BROKEN_GET_OBJECT_PROPVAL }, ++ DEVICE_FLAG_BROKEN_MTPGETOBJPROPLIST_ALL }, + { "Creative", 0x041e, "ZEN Sleek Photo", 0x413d, +- DEVICE_FLAG_BROKEN_MTPGETOBJPROPLIST_ALL | +- DEVICE_FLAG_BROKEN_GET_OBJECT_PROPVAL }, ++ DEVICE_FLAG_BROKEN_MTPGETOBJPROPLIST_ALL }, + { "Creative", 0x041e, "ZEN Vision:M", 0x413e, +- DEVICE_FLAG_BROKEN_MTPGETOBJPROPLIST_ALL | +- DEVICE_FLAG_BROKEN_GET_OBJECT_PROPVAL }, ++ DEVICE_FLAG_BROKEN_MTPGETOBJPROPLIST_ALL }, + // Reported by marazm@o2.pl + { "Creative", 0x041e, "ZEN V", 0x4150, +- DEVICE_FLAG_BROKEN_MTPGETOBJPROPLIST_ALL | +- DEVICE_FLAG_BROKEN_GET_OBJECT_PROPVAL }, ++ DEVICE_FLAG_BROKEN_MTPGETOBJPROPLIST_ALL }, + // Reported by danielw@iinet.net.au + // This version of the Vision:M needs the no release interface flag, + // unclear whether the other version above need it too or not. + { "Creative", 0x041e, "ZEN Vision:M (DVP-HD0004)", 0x4151, + DEVICE_FLAG_NO_RELEASE_INTERFACE | +- DEVICE_FLAG_BROKEN_MTPGETOBJPROPLIST_ALL | +- DEVICE_FLAG_BROKEN_GET_OBJECT_PROPVAL }, ++ DEVICE_FLAG_BROKEN_MTPGETOBJPROPLIST_ALL }, + // Reported by Darel on the XNJB forums + { "Creative", 0x041e, "ZEN V Plus", 0x4152, +- DEVICE_FLAG_BROKEN_MTPGETOBJPROPLIST_ALL | +- DEVICE_FLAG_BROKEN_GET_OBJECT_PROPVAL }, ++ DEVICE_FLAG_BROKEN_MTPGETOBJPROPLIST_ALL }, + { "Creative", 0x041e, "ZEN Vision W", 0x4153, +- DEVICE_FLAG_BROKEN_MTPGETOBJPROPLIST_ALL | +- DEVICE_FLAG_BROKEN_GET_OBJECT_PROPVAL }, ++ DEVICE_FLAG_BROKEN_MTPGETOBJPROPLIST_ALL }, + // Don't add 0x4155: this is a Zen Stone device which is not MTP + // Reported by Paul Kurczaba + { "Creative", 0x041e, "ZEN", 0x4157, + DEVICE_FLAG_IGNORE_HEADER_ERRORS | + DEVICE_FLAG_BROKEN_SET_SAMPLE_DIMENSIONS | +- DEVICE_FLAG_BROKEN_MTPGETOBJPROPLIST_ALL | +- DEVICE_FLAG_BROKEN_GET_OBJECT_PROPVAL }, ++ DEVICE_FLAG_BROKEN_MTPGETOBJPROPLIST_ALL }, + // Reported by Ringofan + { "Creative", 0x041e, "ZEN V 2GB", 0x4158, +- DEVICE_FLAG_BROKEN_MTPGETOBJPROPLIST_ALL | +- DEVICE_FLAG_BROKEN_GET_OBJECT_PROPVAL }, ++ DEVICE_FLAG_BROKEN_MTPGETOBJPROPLIST_ALL }, + // Reported by j norment + { "Creative", 0x041e, "ZEN Mozaic", 0x4161, +- DEVICE_FLAG_BROKEN_MTPGETOBJPROPLIST_ALL | +- DEVICE_FLAG_BROKEN_GET_OBJECT_PROPVAL }, ++ DEVICE_FLAG_BROKEN_MTPGETOBJPROPLIST_ALL }, + // Reported by Aaron F. Gonzalez + { "Creative", 0x041e, "ZEN X-Fi", 0x4162, +- DEVICE_FLAG_BROKEN_MTPGETOBJPROPLIST_ALL | +- DEVICE_FLAG_BROKEN_GET_OBJECT_PROPVAL }, ++ DEVICE_FLAG_BROKEN_MTPGETOBJPROPLIST_ALL }, + // Reported by farmerstimuli + { "Creative", 0x041e, "ZEN X-Fi 3", 0x4169, +- DEVICE_FLAG_BROKEN_MTPGETOBJPROPLIST_ALL | +- DEVICE_FLAG_BROKEN_GET_OBJECT_PROPVAL }, ++ DEVICE_FLAG_BROKEN_MTPGETOBJPROPLIST_ALL }, + // Reported by Todor Gyumyushev + { "ZiiLABS", 0x041e, "Zii EGG", 0x6000, + DEVICE_FLAG_UNLOAD_DRIVER | +@@ -607,8 +586,17 @@ + /* https://sourceforge.net/p/libmtp/bugs/1251/ */ + { "Acer", 0x0502, "E39", 0x3643, + DEVICE_FLAGS_ANDROID_BUGS }, ++ /* https://sourceforge.net/p/libmtp/bugs/1369/ */ ++ { "Acer", 0x0502, "liquid e700", 0x3644, ++ DEVICE_FLAGS_ANDROID_BUGS }, + { "Acer", 0x0502, "One 7", 0x3657, + DEVICE_FLAGS_ANDROID_BUGS }, ++ /* https://sourceforge.net/p/libmtp/support-requests/183/ */ ++ { "Acer", 0x0502, "Z200", 0x3683, ++ DEVICE_FLAGS_ANDROID_BUGS }, ++ /* https://sourceforge.net/p/libmtp/bugs/1341/ */ ++ { "Acer", 0x0502, "Liquid S56", 0x3725, ++ DEVICE_FLAGS_ANDROID_BUGS }, + + /* + * SanDisk +@@ -952,6 +940,7 @@ + { "Archos", 0x0e79, "SPOD (MTP mode)", 0x1341, DEVICE_FLAG_UNLOAD_DRIVER }, + { "Archos", 0x0e79, "5S IT (MTP mode)", 0x1351, DEVICE_FLAG_UNLOAD_DRIVER }, + { "Archos", 0x0e79, "5H IT (MTP mode)", 0x1357, DEVICE_FLAG_UNLOAD_DRIVER }, ++ { "Archos", 0x0e79, "48 (MTP mode)", 0x1421, DEVICE_FLAGS_ANDROID_BUGS }, + { "Archos", 0x0e79, "Arnova Childpad", 0x1458, DEVICE_FLAGS_ANDROID_BUGS }, + { "Archos", 0x0e79, "Arnova 8c G3", 0x145e, DEVICE_FLAGS_ANDROID_BUGS }, + { "Archos", 0x0e79, "Arnova 10bG3 Tablet", 0x146b, DEVICE_FLAGS_ANDROID_BUGS }, +@@ -973,9 +962,17 @@ + { "Archos", 0x0e79, "70it2 (ID 2)", 0x1569, DEVICE_FLAGS_ANDROID_BUGS }, + { "Archos", 0x0e79, "50c", 0x2008, DEVICE_FLAGS_ANDROID_BUGS }, + { "Archos", 0x0e79, "C40", 0x31ab, DEVICE_FLAGS_ANDROID_BUGS }, ++ /* https://sourceforge.net/p/libmtp/bugs/1393/ */ ++ { "Archos", 0x0e79, "Phone", 0x31e1, DEVICE_FLAGS_ANDROID_BUGS }, ++ /* https://sourceforge.net/p/libmtp/bugs/1325/ */ ++ { "Archos", 0x0e79, "45 Neon", 0x31f3, DEVICE_FLAGS_ANDROID_BUGS }, ++ /* https://sourceforge.net/p/libmtp/bugs/1352/ */ ++ { "Archos", 0x0e79, "50 Diamond", 0x3229, DEVICE_FLAGS_ANDROID_BUGS }, + { "Archos", 0x0e79, "101 G4", 0x4002, DEVICE_FLAGS_ANDROID_BUGS }, + { "Archos (for Tesco)", 0x0e79, "Hudl (ID1)", 0x5008, DEVICE_FLAGS_ANDROID_BUGS }, + { "Archos (for Tesco)", 0x0e79, "Hudl (ID2)", 0x5009, DEVICE_FLAGS_ANDROID_BUGS }, ++ /* https://sourceforge.net/p/libmtp/bugs/1404/ */ ++ { "Archos", 0x0e79, "AC40DTI", 0x5217, DEVICE_FLAGS_ANDROID_BUGS }, + + /* + * Dunlop (OEM of EGOMAN ltd?) reported by Nanomad +@@ -1181,6 +1178,10 @@ + { "Qualcomm (for OnePlus)", 0x05c6, "One (MTP+ADB)", + 0x6765, DEVICE_FLAGS_ANDROID_BUGS }, + ++ /* https://sourceforge.net/p/libmtp/bugs/1377/ */ ++ { "Qualcomm (for Xolo)", 0x901b, "Xolo Black (MTP)", ++ 0x9039, DEVICE_FLAGS_ANDROID_BUGS }, ++ + { "Qualcomm (for PhiComm)", 0x05c6, "C230w (MTP)", + 0x9039, DEVICE_FLAGS_ANDROID_BUGS }, + +@@ -1221,6 +1222,9 @@ + // Reported by Thomas Bretthauer + { "Fujitsu, Ltd", 0x04c5, "STYLISTIC M532", 0x133b, + DEVICE_FLAGS_ANDROID_BUGS }, ++ /* https://sourceforge.net/p/libmtp/feature-requests/137/ */ ++ { "Fujitsu, Ltd", 0x04c5, "F02-E", 0x1378, ++ DEVICE_FLAGS_ANDROID_BUGS }, + + /* + * Palm device userland program named Pocket Tunes +@@ -1247,6 +1251,9 @@ + // Reported by anonymous SourceForge user + { "Medion", 0x066f, "MD8333 (ID2)", 0x8588, + DEVICE_FLAG_UNLOAD_DRIVER | DEVICE_FLAG_BROKEN_MTPGETOBJPROPLIST }, ++ /* https://sourceforge.net/p/libmtp/bugs/1359/ */ ++ { "Verizon", 0x0408, "Ellipsis 7", 0x3899, ++ DEVICE_FLAGS_ANDROID_BUGS }, + // The vendor ID is "Quanta Computer, Inc." + // same as Olivetti Olipad 110 + // Guessing on device flags +@@ -1403,6 +1410,9 @@ + DEVICE_FLAGS_ANDROID_BUGS }, + { "LG Electronics Inc.", 0x1004, "LG2 Optimus", 0x6225, + DEVICE_FLAGS_ANDROID_BUGS }, ++ /* https://sourceforge.net/p/libmtp/bugs/1386/ */ ++ { "LG Electronics Inc.", 0x1004, "LG VS950", 0x622a, ++ DEVICE_FLAGS_ANDROID_BUGS }, + { "LG Electronics Inc.", 0x1004, "LG VS870", 0x6239, + DEVICE_FLAGS_ANDROID_BUGS }, + /* https://sourceforge.net/p/libmtp/bugs/992/ */ +@@ -1410,6 +1420,8 @@ + DEVICE_FLAGS_ANDROID_BUGS }, + { "LG Electronics Inc.", 0x1004, "VK810", 0x6265, + DEVICE_FLAGS_ANDROID_BUGS }, ++ { "LG Electronics Inc.", 0x1004, "G3", 0x627f, ++ DEVICE_FLAGS_ANDROID_BUGS }, + /* https://sourceforge.net/p/libmtp/support-requests/134/ */ + { "LG Electronics Inc.", 0x1004, "G3 (VS985)", 0x626e, + DEVICE_FLAGS_ANDROID_BUGS }, +@@ -1723,8 +1735,12 @@ + DEVICE_FLAG_NONE }, + { "SONY", 0x0fce, "Xperia M2 MTP", 0x01aa, + DEVICE_FLAG_NONE }, ++ { "SONY", 0x0fce, "Xperia M2 Dual MTP", 0x01ab, ++ DEVICE_FLAG_NONE }, + { "SONY", 0x0fce, "Xperia Z2 MTP", 0x01af, + DEVICE_FLAG_NONE }, ++ { "SONY", 0x0fce, "Xperia Z2 Tablet MTP", 0x01b1, ++ DEVICE_FLAGS_ANDROID_BUGS }, + { "SONY", 0x0fce, "Xperia Z Ultra MTP", 0x01b6, + DEVICE_FLAGS_ANDROID_BUGS }, + { "SONY", 0x0fce, "Xperia Z3 MTP", 0x01ba, +@@ -1733,6 +1749,10 @@ + DEVICE_FLAG_NONE }, + { "SONY", 0x0fce, "Xperia E3 MTP", 0x01bc, + DEVICE_FLAG_NONE }, ++ { "SONY", 0x0fce, "XPeria Z3+ MTP", 0x01c9, ++ DEVICE_FLAG_NONE }, ++ { "SONY", 0x0fce, "XPeria E4g MTP", 0x01cb, ++ DEVICE_FLAG_NONE }, + + + /* +@@ -1788,6 +1808,8 @@ + DEVICE_FLAG_NONE }, + { "SONY", 0x0fce, "Xperia M MTP+CDROM", 0x419b, + DEVICE_FLAG_NONE }, ++ { "SONY", 0x0fce, "Xperia Z Ultra MTP+CDROM (ID3)", 0x419c, ++ DEVICE_FLAG_NONE }, + { "SONY", 0x0fce, "Xperia Z1 MTP+CDROM", 0x419e, + DEVICE_FLAG_NONE }, + { "SONY", 0x0fce, "Xperia C MTP+CDROM", 0x41a3, +@@ -1796,10 +1818,20 @@ + DEVICE_FLAG_NONE }, + { "SONY", 0x0fce, "Xperia M2 MTP+CDROM", 0x41aa, + DEVICE_FLAG_NONE }, ++ { "SONY", 0x0fce, "Xperia M2 Dual MTP+CDROM", 0x41ab, ++ DEVICE_FLAG_NONE }, + { "SONY", 0x0fce, "Xperia Z2 MTP+CDROM", 0x41af, + DEVICE_FLAG_NONE }, + { "SONY", 0x0fce, "Xperia Z3 MTP+CDROM", 0x41ba, + DEVICE_FLAG_NONE }, ++ { "SONY", 0x0fce, "Xperia Z3 Compact MTP+CDROM", 0x41bb, ++ DEVICE_FLAG_NONE }, ++ { "SONY", 0x0fce, "Xperia E3 MTP+CDROM", 0x01bc, ++ DEVICE_FLAG_NONE }, ++ { "SONY", 0x0fce, "XPeria Z3+ MTP+CDROM", 0x41c9, ++ DEVICE_FLAG_NONE }, ++ { "SONY", 0x0fce, "XPeria E4g MTP+CDROM", 0x41cb, ++ DEVICE_FLAG_NONE }, + + /* + * MTP+ADB personalities of MTP devices (see above) +@@ -1888,6 +1920,8 @@ + DEVICE_FLAG_NONE }, + { "SONY", 0x0fce, "Xperia M2 MTP+ADB", 0x51aa, + DEVICE_FLAG_NONE }, ++ { "SONY", 0x0fce, "Xperia M2 Dual MTP+ADB", 0x51ab, ++ DEVICE_FLAG_NONE }, + { "SONY", 0x0fce, "Xperia Z2 MTP+ADB", 0x51af, + DEVICE_FLAG_NONE }, + { "SONY", 0x0fce, "Xperia Z Ultra MTP+ADB", 0x51b6, +@@ -1898,6 +1932,10 @@ + DEVICE_FLAG_NONE }, + { "SONY", 0x0fce, "Xperia E3 MTP+ADB", 0x51bc, + DEVICE_FLAG_NONE }, ++ { "SONY", 0x0fce, "XPeria Z3+ MTP+ADB", 0x51c9, ++ DEVICE_FLAG_NONE }, ++ { "SONY", 0x0fce, "XPeria E4g MTP+ADB", 0x51cb, ++ DEVICE_FLAG_NONE }, + + /* + * MTP+UMS modes +@@ -1936,6 +1974,9 @@ + * Motorola + * Assume DEVICE_FLAG_BROKEN_SET_OBJECT_PROPLIST on all of these. + */ ++ /* https://sourceforge.net/p/libmtp/feature-requests/136/ */ ++ { "Motorola", 0x22b8, "XT1524 (MTP)", 0x002e, ++ DEVICE_FLAGS_ANDROID_BUGS }, + // Reported by David Boyd + { "Motorola", 0x22b8, "V3m/V750 verizon", 0x2a65, + DEVICE_FLAG_BROKEN_SET_OBJECT_PROPLIST | +@@ -1952,6 +1993,9 @@ + DEVICE_FLAGS_ANDROID_BUGS }, + { "Motorola", 0x22b8, "Moto X (XT1058)", 0x2e63, + DEVICE_FLAGS_ANDROID_BUGS }, ++ /* https://sourceforge.net/p/libmtp/bugs/1323/ */ ++ { "Motorola", 0x22b8, "Moto X (XT1080)", 0x2e66, ++ DEVICE_FLAGS_ANDROID_BUGS }, + { "Motorola", 0x22b8, "Droid Maxx (XT1080)", 0x2e67, + DEVICE_FLAGS_ANDROID_BUGS }, + { "Motorola", 0x22b8, "Droid Ultra", 0x2e68, +@@ -2345,6 +2389,14 @@ + /* https://sourceforge.net/p/libmtp/bugs/1244/ */ + { "Asus", 0x0b05, "MemoPad 8 ME181 CX (MTP)", 0x5561, + DEVICE_FLAGS_ANDROID_BUGS }, ++ /* https://sourceforge.net/p/libmtp/bugs/1406/ */ ++ { "Asus", 0x0b05, "Zenfone 2 (MTP)", 0x5600, ++ DEVICE_FLAGS_ANDROID_BUGS }, ++ /* https://sourceforge.net/p/libmtp/bugs/1364/ */ ++ { "Asus", 0x0b05, "Z00AD (MTP)", 0x5601, ++ DEVICE_FLAGS_ANDROID_BUGS }, ++ { "Asus", 0x0b05, "TX201LA (MTP)", 0x561f, ++ DEVICE_FLAGS_ANDROID_BUGS }, + /* https://sourceforge.net/p/libmtp/bugs/1271/ */ + { "Asus", 0x0b05, "ZenFone 4 (MTP)", 0x580f, + DEVICE_FLAGS_ANDROID_BUGS }, +@@ -2354,9 +2406,20 @@ + /* https://sourceforge.net/p/libmtp/bugs/1258/ */ + { "Asus", 0x0b05, "A450CG (MTP)", 0x5a0f, + DEVICE_FLAGS_ANDROID_BUGS }, ++ /* https://sourceforge.net/p/libmtp/bugs/1350/ */ ++ { "Asus", 0x0b05, "Zenfone 2 ZE550ML (MTP)", 0x5f02, ++ DEVICE_FLAGS_ANDROID_BUGS }, ++ /* https://sourceforge.net/p/libmtp/bugs/1364/ */ ++ { "Asus", 0x0b05, "Zenfone 2 ZE551ML (MTP)", 0x5f03, ++ DEVICE_FLAGS_ANDROID_BUGS }, + /* https://sourceforge.net/p/libmtp/bugs/1232/ */ + { "Asus", 0x0b05, "MemoPad 7 (ME572CL)", 0x7772, + DEVICE_FLAGS_ANDROID_BUGS }, ++ /* https://sourceforge.net/p/libmtp/bugs/1351/ */ ++ { "Asus", 0x0b05, "Fonepad 7 (FE375CXG)", 0x7773, ++ DEVICE_FLAGS_ANDROID_BUGS }, ++ { "Asus", 0x0b05, "ZenFone 5 A500KL (MTP)", 0x7780, ++ DEVICE_FLAGS_ANDROID_BUGS }, + /* https://sourceforge.net/p/libmtp/bugs/1247/ */ + { "Asus", 0x0b05, "ZenFone 5 A500KL (MTP+ADB)", 0x7781, + DEVICE_FLAGS_ANDROID_BUGS }, +@@ -2365,6 +2428,12 @@ + /* + * Lenovo + */ ++ /* https://sourceforge.net/p/libmtp/support-requests/178/ */ ++ { "Lenovo", 0x17ef, "P70-A", 0x0c02, ++ DEVICE_FLAGS_ANDROID_BUGS }, ++ /* https://sourceforge.net/p/libmtp/bugs/1415/ */ ++ { "Lenovo", 0x17ef, "P70", 0x2008, ++ DEVICE_FLAGS_ANDROID_BUGS }, + // Reported by Richard Körber + { "Lenovo", 0x17ef, "K1", 0x740a, + DEVICE_FLAGS_ANDROID_BUGS }, +@@ -2407,6 +2476,9 @@ + DEVICE_FLAGS_ANDROID_BUGS }, + { "Lenovo", 0x17ef, "Toga Tablet B6000-F", 0x76f2, + DEVICE_FLAGS_ANDROID_BUGS }, ++ /* https://sourceforge.net/p/libmtp/bugs/1122/ */ ++ { "Lenovo", 0x17ef, "S930", 0x7718, ++ DEVICE_FLAGS_ANDROID_BUGS }, + /* https://sourceforge.net/p/libmtp/bugs/1250/ */ + { "Lenovo", 0x17ef, "A5500-F", 0x772b, + DEVICE_FLAGS_ANDROID_BUGS }, +@@ -2417,15 +2489,24 @@ + /* https://sourceforge.net/p/libmtp/bugs/1155/ */ + { "Lenovo", 0x17ef, "Yoga Tablet 10 B8000-H", 0x76ff, + DEVICE_FLAGS_ANDROID_BUGS }, ++ /* https://sourceforge.net/p/libmtp/bugs/1391/ */ ++ { "Lenovo", 0x17ef, "A7600-F", 0x7731, ++ DEVICE_FLAGS_ANDROID_BUGS }, + /* https://sourceforge.net/p/libmtp/bugs/1291/ */ + { "Lenovo", 0x17ef, "A3500-F", 0x7737, + DEVICE_FLAGS_ANDROID_BUGS }, ++ /* https://sourceforge.net/p/libmtp/support-requests/186/ */ ++ { "Lenovo", 0x17ef, "Yoga Tablet 2 - 1050F", 0x77a4, ++ DEVICE_FLAGS_ANDROID_BUGS }, + /* https://sourceforge.net/p/libmtp/support-requests/168/ */ + { "Lenovo", 0x17ef, "Yoga Tablet 2 Pro", 0x77b1, + DEVICE_FLAGS_ANDROID_BUGS }, + /* https://sourceforge.net/p/libmtp/feature-requests/125/ */ + { "Lenovo", 0x17ef, "Vibe Z2", 0x77ea, + DEVICE_FLAGS_ANDROID_BUGS }, ++ /* https://sourceforge.net/p/libmtp/bugs/1360/ */ ++ { "Lenovo", 0x17ef, "K3 Note", 0x7883, ++ DEVICE_FLAGS_ANDROID_BUGS }, + + /* + * Huawei +@@ -2435,6 +2516,15 @@ + DEVICE_FLAGS_ANDROID_BUGS }, + { "Huawei", 0x12d1, "MTP device (ID2)", 0x1052, + DEVICE_FLAGS_ANDROID_BUGS }, ++ /* https://sourceforge.net/p/libmtp/bugs/1381/ */ ++ { "Huawei", 0x12d1, "H60-L11", 0x1079, ++ DEVICE_FLAGS_ANDROID_BUGS }, ++ /* https://sourceforge.net/p/libmtp/bugs/1361/ */ ++ { "Huawei", 0x12d1, "Ascend P8 ", 0x1082, ++ DEVICE_FLAGS_ANDROID_BUGS }, ++ /* https://sourceforge.net/p/libmtp/bugs/1418/ */ ++ { "Huawei", 0x12d1, "Honor 3C ", 0x2012, ++ DEVICE_FLAGS_ANDROID_BUGS }, + { "Huawei", 0x12d1, "Mediapad (mode 0)", 0x360f, + DEVICE_FLAGS_ANDROID_BUGS }, + // Reported by Bearsh +@@ -2452,6 +2542,8 @@ + /* https://sourceforge.net/p/libmtp/bugs/672/ */ + { "ZTE", 0x19d2, "Grand X In", 0x0343, DEVICE_FLAGS_ANDROID_BUGS }, + { "ZTE", 0x19d2, "V985", 0x0383, DEVICE_FLAGS_ANDROID_BUGS }, ++ /* https://sourceforge.net/p/libmtp/bugs/1328/ */ ++ { "ZTE", 0x19d2, "V5", 0xffce, DEVICE_FLAGS_ANDROID_BUGS }, + + /* + * HTC (High Tech Computer Corp) +@@ -2459,6 +2551,12 @@ + * Steven Eastland + * Kevin Cheng + */ ++ /* https://sourceforge.net/p/libmtp/support-requests/181/ */ ++ { "HTC", 0x0bb4, "HTC One M9 (MTP)", 0x040b, ++ DEVICE_FLAGS_ANDROID_BUGS }, ++ /* https://sourceforge.net/p/libmtp/bugs/1398/ */ ++ { "HTC", 0x0bb4, "Spreadtrum SH57MYZ03342 (MTP)", 0x05e3, ++ DEVICE_FLAGS_ANDROID_BUGS }, + /* reported by Mikkel Oscar Lyderik */ + { "HTC", 0x0bb4, "HTC Desire 510 (MTP+ADB)", 0x05fd, + DEVICE_FLAGS_ANDROID_BUGS }, +@@ -2545,6 +2643,9 @@ + /* https://sourceforge.net/p/libmtp/bugs/1182/ */ + { "HTC", 0x0bb4, "Desire 310 (MTP)", 0x0ec6, + DEVICE_FLAGS_ANDROID_BUGS }, ++ /* https://sourceforge.net/p/libmtp/bugs/1420/ */ ++ { "HTC", 0x0bb4, "Desire 816G (MTP)", 0x0edb, ++ DEVICE_FLAGS_ANDROID_BUGS }, + { "HTC", 0x0bb4, "HTC One (MTP+ADB+CDC)", 0x0f5f, + DEVICE_FLAGS_ANDROID_BUGS }, + { "HTC", 0x0bb4, "HTC One (MTP+CDC)", 0x0f60, +@@ -2658,6 +2759,9 @@ + DEVICE_FLAGS_ANDROID_BUGS }, + { "Amazon", 0x1949, "Kindle Fire (ID5)", 0x0012, + DEVICE_FLAGS_ANDROID_BUGS }, ++ /* https://sourceforge.net/p/libmtp/bugs/1353/ */ ++ { "Amazon", 0x1949, "Kindle Fire HD6", 0x00f2, ++ DEVICE_FLAGS_ANDROID_BUGS }, + { "Amazon", 0x1949, "Fire Phone", 0x0800, + DEVICE_FLAGS_ANDROID_BUGS }, + +@@ -2677,6 +2781,9 @@ + DEVICE_FLAGS_ANDROID_BUGS }, + { "YiFang", 0x2207, "BQ Tesla", 0x0006, + DEVICE_FLAGS_ANDROID_BUGS }, ++ /* https://sourceforge.net/p/libmtp/bugs/1354/ */ ++ { "Various", 0x2207, "Viewpia DR/bq Kepler Debugging", 0x0011, ++ DEVICE_FLAGS_ANDROID_BUGS }, + + /* + * Kobo +@@ -2708,6 +2815,8 @@ + { "Intel", 0x8087, "Foxconn iView i700", 0x0a15, DEVICE_FLAGS_ANDROID_BUGS }, + /* https://sourceforge.net/p/libmtp/bugs/1237/ */ + { "Intel", 0x8087, "Telcast Air 3G", 0x0a5e, DEVICE_FLAGS_ANDROID_BUGS }, ++ /* https://sourceforge.net/p/libmtp/bugs/1338/ */ ++ { "Intel", 0x8087, "Chuwi vi8", 0x0a5f, DEVICE_FLAGS_ANDROID_BUGS }, + + /* + * Xiaomi +@@ -2738,6 +2847,15 @@ + DEVICE_FLAGS_ANDROID_BUGS }, + { "Xiaomi", 0x2717, "Mi-2 (MTP)", 0xf003, + DEVICE_FLAGS_ANDROID_BUGS }, ++ /* https://sourceforge.net/p/libmtp/bugs/1397/ */ ++ { "Xiaomi", 0x2717, "Mi-2s (id2) (MTP)", 0xff40, ++ DEVICE_FLAGS_ANDROID_BUGS }, ++ /* https://sourceforge.net/p/libmtp/bugs/1339/ */ ++ { "Xiaomi", 0x2717, "Mi-2s (MTP)", 0xff48, ++ DEVICE_FLAGS_ANDROID_BUGS }, ++ /* https://sourceforge.net/p/libmtp/bugs/1402/ */ ++ { "Xiaomi", 0x2717, "Redmi 2 (MTP)", 0xff60, ++ DEVICE_FLAGS_ANDROID_BUGS }, + + /* + * XO Learning Tablet +@@ -2774,6 +2892,9 @@ + /* https://sourceforge.net/p/libmtp/bugs/1304/ */ + { "Alcatel", 0x1bbb, "OneTouch 5042D (MTP)", 0xa00e, + DEVICE_FLAGS_ANDROID_BUGS }, ++ /* https://sourceforge.net/p/libmtp/bugs/1401/ */ ++ { "Alcatel", 0x1bbb, "OneTouch Idol 3 (MTP)", 0xaf2b, ++ DEVICE_FLAGS_ANDROID_BUGS }, + /* https://sourceforge.net/p/libmtp/feature-requests/114/ */ + { "Alcatel", 0x1bbb, "OneTouch 6034R", 0xf003, + DEVICE_FLAGS_ANDROID_BUGS }, +@@ -2782,8 +2903,12 @@ + * Kyocera + */ + { "Kyocera", 0x0482, "Rise", 0x0571, DEVICE_FLAGS_ANDROID_BUGS }, ++ /* https://sourceforge.net/p/libmtp/feature-requests/134/ */ ++ { "Kyocera", 0x0482, "Torque Model E6715", 0x0059a, DEVICE_FLAGS_ANDROID_BUGS }, + /* https://sourceforge.net/p/libmtp/discussion/535190/thread/6270f5ce/ */ + { "Kyocera", 0x0482, "KYL22", 0x0810, DEVICE_FLAGS_ANDROID_BUGS }, ++ /* https://sourceforge.net/p/libmtp/bugs/1345/ */ ++ { "Kyocera", 0x0482, "DuraForce", 0x0979, DEVICE_FLAGS_ANDROID_BUGS }, + + /* + * HiSense +@@ -2798,12 +2923,20 @@ + DEVICE_FLAGS_ANDROID_BUGS }, + { "Hewlett-Packard", 0x03f0, "Slate 7 2800", 0x5d1d, + DEVICE_FLAGS_ANDROID_BUGS }, ++ /* https://sourceforge.net/p/libmtp/bugs/1366/ */ ++ { "Hewlett-Packard", 0x03f0, "Slate 10 HD", 0x7e1d, ++ DEVICE_FLAGS_ANDROID_BUGS }, + + /* + * MediaTek Inc. + */ + { "MediaTek Inc", 0x0e8d, "MT5xx and MT6xx SoCs", 0x0050, + DEVICE_FLAGS_ANDROID_BUGS }, ++ { "MediaTek Inc", 0x0e8d, "MT65xx", 0x2008, ++ DEVICE_FLAGS_ANDROID_BUGS }, ++ /* https://sourceforge.net/p/libmtp/feature-requests/79/ */ ++ { "MediaTek Inc", 0x0e8d, "Elephone P8000", 0x201d, ++ DEVICE_FLAGS_ANDROID_BUGS }, + + /* + * Jolla +@@ -2860,6 +2993,8 @@ + { "Prestigio", 0x29e4, "5505 DUO ", 0x1103, DEVICE_FLAGS_ANDROID_BUGS }, + /* https://sourceforge.net/p/libmtp/bugs/1243/ */ + { "Prestigio", 0x29e4, "5504 DUO ", 0x1203, DEVICE_FLAGS_ANDROID_BUGS }, ++ /* https://sourceforge.net/p/libmtp/feature-requests/141/ */ ++ { "Prestigio", 0x29e4, "3405 DUO ", 0x3201, DEVICE_FLAGS_ANDROID_BUGS }, + + /* https://sourceforge.net/p/libmtp/bugs/1283/ */ + { "Megafon", 0x201e, "MFLogin3T", 0x42ab, DEVICE_FLAGS_ANDROID_BUGS }, +@@ -2867,6 +3002,8 @@ + /* https://sourceforge.net/p/libmtp/bugs/1287/ */ + { "Gensis", 0x040d, "GT-7305 ", 0x885c, DEVICE_FLAGS_ANDROID_BUGS }, + ++ /* https://sourceforge.net/p/libmtp/support-requests/182/ */ ++ { "Oppo", 0x22d9, "Find 5", 0x2764, DEVICE_FLAGS_ANDROID_BUGS }, + /* https://sourceforge.net/p/libmtp/bugs/1207/ */ + { "Oppo", 0x22d9, "Find 7 (ID 1)", 0x2765, DEVICE_FLAGS_ANDROID_BUGS }, + /* https://sourceforge.net/p/libmtp/bugs/1277/ */ +@@ -2916,6 +3053,14 @@ + /* https://sourceforge.net/p/libmtp/bugs/1314/ */ + { "BenQ", 0x1d45, "F5", 0x459d, DEVICE_FLAGS_ANDROID_BUGS }, + ++ /* https://sourceforge.net/p/libmtp/bugs/1362/ */ ++ { "TomTom", 0x1390, "Rider 40", 0x5455, DEVICE_FLAGS_ANDROID_BUGS }, ++ ++ /* https://sourceforge.net/p/libmtp/feature-requests/135/. guessed android. */ ++ { "OUYA", 0x2836, "Videogame Console", 0x0010, DEVICE_FLAGS_ANDROID_BUGS }, ++ ++ /* https://sourceforge.net/p/libmtp/bugs/1383/ */ ++ { "BLU", 0x0e8d, "Studio HD", 0x2008, DEVICE_FLAGS_ANDROID_BUGS }, + /* + * Other strange stuff. + */ -- cgit v1.2.3 From a5002ae77c00693792ae0024b290cc24fb1d4328 Mon Sep 17 00:00:00 2001 From: Andreas Enge Date: Sun, 20 Sep 2015 00:32:45 +0200 Subject: gnu: Add R/qtl. * gnu/packages/bioinformatics.scm (r-qtl): New variable. Co-authored-by: Pjotr Prins --- gnu/packages/bioinformatics.scm | 28 ++++++++++++++++++++++++++++ 1 file changed, 28 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 37bd3339d3..2e31d85b2d 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1,6 +1,8 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2014, 2015 Ricardo Wurmus ;;; Copyright © 2015 Ben Woodcroft +;;; Copyright © 2015 Pjotr Prins +;;; Copyright © 2015 Andreas Enge ;;; ;;; This file is part of GNU Guix. ;;; @@ -27,6 +29,7 @@ #:use-module (guix build-system cmake) #:use-module (guix build-system perl) #:use-module (guix build-system python) + #:use-module (guix build-system r) #:use-module (guix build-system ruby) #:use-module (guix build-system trivial) #:use-module (gnu packages) @@ -2743,3 +2746,28 @@ BLAST, KEGG, GenBank, MEDLINE and GO.") ;; Code is released under Ruby license, except for setup ;; (LGPLv2.1+) and scripts in samples (which have GPL2 and GPL2+) (license (list license:ruby license:lgpl2.1+ license:gpl2+ )))) + +(define-public r-qtl + (package + (name "r-qtl") + (version "1.37-11") + (source + (origin + (method url-fetch) + (uri (string-append "mirror://cran/src/contrib/qtl_" + version ".tar.gz")) + (sha256 + (base32 + "0h20d36mww7ljp51pfs66xq33yq4b4fwq9nsh02dpmfhlaxgx1xi")))) + (build-system r-build-system) + (home-page "http://rqtl.org/") + (synopsis "R package for analyzing QTL experiments in genetics") + (description "R/qtl is an extension library for the R statistics +system. It is used to analyze experimental crosses for identifying +genes contributing to variation in quantitative traits (so-called +quantitative trait loci, QTLs). + +Using a hidden Markov model, R/qtl allows to estimate genetic maps, to +identify genotyping errors, and to perform single-QTL and two-QTL, +two-dimensional genome scans.") + (license license:gpl3))) -- cgit v1.2.3 From 350ba0a32b6d21acb974a1715d60df7839fd5acc Mon Sep 17 00:00:00 2001 From: Cyril Roelandt Date: Wed, 16 Sep 2015 23:02:11 +0200 Subject: gnu: Add python-prettytable * gnu/packages/python.scm (python-prettytable, python2-prettytable): New variables. --- gnu/packages/python.scm | 28 ++++++++++++++++++++++++++++ 1 file changed, 28 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 408064d9be..1818993399 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -4880,3 +4880,31 @@ object to help create WSGI responses.") (define-public python2-webob (package-with-python2 python-webob)) + +(define-public python-prettytable + (package + (name "python-prettytable") + (version "0.7.2") + (source + (origin + (method url-fetch) + (uri (string-append + "https://pypi.python.org/packages/source/P/PrettyTable/" + "prettytable-" version ".tar.bz2")) + (sha256 + (base32 + "0diwsicwmiq2cpzpxri7cyl5fmsvicafw6nfqf6p6p322dji2g45")))) + (build-system python-build-system) + (inputs + `(("python-setuptools" ,python-setuptools))) + (home-page "http://code.google.com/p/prettytable/") + (synopsis "Display tabular data in an ASCII table format") + (description + "A library designed to represent tabular data in visually appealing ASCII +tables. PrettyTable allows for selection of which columns are to be printed, +independent alignment of columns (left or right justified or centred) and +printing of sub-tables by specifying a row range.") + (license bsd-3))) + +(define-public python2-prettytable + (package-with-python2 python-prettytable)) -- cgit v1.2.3 From 7261d9eb16737c6cdf68ff4aa144541f752d24d6 Mon Sep 17 00:00:00 2001 From: Cyril Roelandt Date: Wed, 16 Sep 2015 23:24:36 +0200 Subject: gnu: Add python2-pyflakes and fix python2-pyflakes-0.8.1. * gnu/packages/python.scm (python2-pyflakes): New variable. * gnu/packages/python.scm (python2-pyflakes-0.8.1): Fix the definition. --- gnu/packages/python.scm | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 1818993399..0117eb79ef 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -4434,6 +4434,9 @@ PEP 8.") "Pyflakes statically checks Python source code for common errors.") (license license:expat))) +(define-public python2-pyflakes + (package-with-python2 python-pyflakes)) + (define-public python-mccabe (package (name "python-mccabe") @@ -4497,7 +4500,7 @@ complexity of Python source code.") "0sbpq6pqm1i9wqi41mlfrsc5rk92jv4mskvlyxmnhlbdnc80ma1z")))))) (define-public python2-pyflakes-0.8.1 - (package-with-python2 python-pyflakes)) + (package-with-python2 python-pyflakes-0.8.1)) (define-public python-flake8 (package -- cgit v1.2.3 From d7af1069876c66ee697941883c8fb654e642c49f Mon Sep 17 00:00:00 2001 From: Cyril Roelandt Date: Thu, 17 Sep 2015 01:41:50 +0200 Subject: gnu: Add python2-keyring. * gnu/packages/python.scm (python2-keyring): New variable. --- gnu/packages/python.scm | 3 +++ 1 file changed, 3 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 0117eb79ef..efda22b982 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -783,6 +783,9 @@ password storage.") ;; "MIT" and PSF dual license (license x11))) +(define-public python2-keyring + (package-with-python2 python-keyring)) + (define-public python-six (package (name "python-six") -- cgit v1.2.3 From 7d1b5022e959dcfc2bb0bd6a6507be3706b3f48a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 20 Sep 2015 10:07:00 +0200 Subject: gnu: sfml: Update to 2.3.2. * gnu/packages/game-development.scm (sfml): Update to 2.3.2. [native-inputs]: Remove. --- gnu/packages/game-development.scm | 14 ++++++++------ 1 file changed, 8 insertions(+), 6 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/game-development.scm b/gnu/packages/game-development.scm index 9c918dee35..c1757ac4de 100644 --- a/gnu/packages/game-development.scm +++ b/gnu/packages/game-development.scm @@ -102,19 +102,21 @@ clone.") (define-public sfml (package (name "sfml") - (version "2.3.1") + (version "2.3.2") (source (origin (method url-fetch) - (uri (string-append "http://mirror0.sfml-dev.org/files/SFML-" - version "-sources.zip")) + ;; Do not fetch the archives from + ;; http://mirror0.sfml-dev.org/files/ because files there seem + ;; to be changed in place. + (uri (string-append "https://github.com/SFML/SFML/archive/" + version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "0mjpkgfnz6ka4p0ir219pcqsbdy7gwcjydk7xxmjjfm2k5sw2qys")))) + "0k2fl5xk3ni2q8bsxl0551inx26ww3w6cp6hssvww0wfjdjcirsm")))) (build-system cmake-build-system) (arguments '(#:tests? #f)) ; no tests - (native-inputs - `(("unzip" ,unzip))) (inputs `(("mesa" ,mesa) ("glew" ,glew) -- cgit v1.2.3 From 127b04d74119f30da763cf035949941dc25015b2 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 31 Aug 2015 10:08:20 +0200 Subject: gnu: lilypond: Update to 2.19.27. * gnu/packages/music.scm (lilypond): Update to 2.19.27. [inputs]: Add font-tex-gyre. --- gnu/packages/music.scm | 14 ++++++++------ 1 file changed, 8 insertions(+), 6 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/music.scm b/gnu/packages/music.scm index 05a490574b..78310edf0e 100644 --- a/gnu/packages/music.scm +++ b/gnu/packages/music.scm @@ -187,7 +187,7 @@ you to define complex tempo maps for entire songs or performances.") (define-public lilypond (package (name "lilypond") - (version "2.18.2") + (version "2.19.27") (source (origin (method url-fetch) (uri (string-append @@ -196,14 +196,15 @@ you to define complex tempo maps for entire songs or performances.") name "-" version ".tar.gz")) (sha256 (base32 - "01xs9x2wjj7w9appaaqdhk15r1xvvdbz9qwahzhppfmhclvp779j")))) + "11v4jr4qj1jpqvjw1ww7riv8pxfyasif8mf16l447f1xq1ifhkhs")))) (build-system gnu-build-system) (arguments - `(;; Tests fail with this error: - ;; Undefined subroutine &main::get_index called at - ;; ./lilypond-2.18.2/Documentation/lilypond-texi2html.init line 2127. - #:tests? #f + `(#:tests? #f ; out-test/collated-files.html fails #:out-of-source? #t + #:configure-flags + (list (string-append "--with-texgyre-dir=" + (assoc-ref %build-inputs "font-tex-gyre") + "/share/fonts/opentype/")) #:phases (alist-cons-before 'configure 'prepare-configuration @@ -216,6 +217,7 @@ you to define complex tempo maps for entire songs or performances.") (inputs `(("guile" ,guile-1.8) ("font-dejavu" ,font-dejavu) + ("font-tex-gyre" ,font-tex-gyre) ("fontconfig" ,fontconfig) ("freetype" ,freetype) ("ghostscript" ,ghostscript) -- cgit v1.2.3 From 594360f508dad72dea67ecd28463e460fbe00f15 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 31 Aug 2015 10:11:09 +0200 Subject: gnu: vpnc: Use https for source URL. * gnu/packages/vpn.scm (vpnc)[source]: Use https protocol for source URL. --- gnu/packages/vpn.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/packages/vpn.scm b/gnu/packages/vpn.scm index 4cd5cd9b11..6af87d2657 100644 --- a/gnu/packages/vpn.scm +++ b/gnu/packages/vpn.scm @@ -63,7 +63,7 @@ endpoints.") (version "0.5.3") (source (origin (method url-fetch) - (uri (string-append "http://www.unix-ag.uni-kl.de/~massar/vpnc/vpnc-" + (uri (string-append "https://www.unix-ag.uni-kl.de/~massar/vpnc/vpnc-" version ".tar.gz")) (sha256 (base32 "1128860lis89g1s21hqxvap2nq426c9j4bvgghncc1zj0ays7kj6")) -- cgit v1.2.3 From 7ee5db15bfa336bb0472669b29eeb2c3b99449b8 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 20 Sep 2015 13:03:38 +0200 Subject: gnu: openal: Use full path to audio backend libraries. * gnu/packages/audio.scm (openal)[arguments]: Add build phase to patch in the full paths to backend audio libraries. --- gnu/packages/audio.scm | 20 +++++++++++++++++++- 1 file changed, 19 insertions(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm index eed72c31a9..029f40c37d 100644 --- a/gnu/packages/audio.scm +++ b/gnu/packages/audio.scm @@ -1052,7 +1052,25 @@ lv2-c++-tools.") "0mmhdqiyb3c9dzvxspm8h2v8jibhi8pfjxnf6m0wn744y1ia2a8f")))) (build-system cmake-build-system) (arguments - `(#:tests? #f)) ; no check target + `(#:tests? #f ; no check target + #:phases + (modify-phases %standard-phases + (add-after + 'unpack 'use-full-library-paths + (lambda* (#:key inputs #:allow-other-keys) + (substitute* "Alc/backends/pulseaudio.c" + (("#define PALIB \"libpulse\\.so\\.0\"") + (string-append "#define PALIB \"" + (assoc-ref inputs "pulseaudio") + "/lib/libpulse.so.0" + "\""))) + (substitute* "Alc/backends/alsa.c" + (("LoadLib\\(\"libasound\\.so\\.2\"\\)") + (string-append "LoadLib(\"" + (assoc-ref inputs "alsa-lib") + "/lib/libasound.so.2" + "\")"))) + #t))))) (inputs `(("alsa-lib" ,alsa-lib) ("pulseaudio" ,pulseaudio))) -- cgit v1.2.3 From cc0e575a94a4e22a0bf2bf1b0c7b0514f1c1fbb5 Mon Sep 17 00:00:00 2001 From: Ludovic Courtès Date: Sun, 20 Sep 2015 21:44:39 +0200 Subject: linux-boot: Mount /dev as a devtmpfs from the start. Suggested by Petter and Mark H Weaver . Reported by Duncan Keall . Partly fixes by populating /dev/mapper early enough. * gnu/build/linux-boot.scm (mount-essential-file-systems): Mount /dev as a devtmpfs. (move-essential-file-systems): Add /dev. (mount-root-file-system): Mount /rw-root/dev as a devtmpfs instead of calling 'make-essential-device-nodes'. (boot-system): Remove call to 'make-essential-device-nodes'. * gnu/system/file-systems.scm (%devtmpfs-file-system): Remove. * doc/guix.texi (File Systems): Adjust accordingly. --- doc/guix.texi | 7 +------ gnu/build/linux-boot.scm | 20 +++++++++----------- gnu/system/file-systems.scm | 15 +-------------- 3 files changed, 11 insertions(+), 31 deletions(-) (limited to 'gnu') diff --git a/doc/guix.texi b/doc/guix.texi index cfe83909da..3ca4cefa63 100644 --- a/doc/guix.texi +++ b/doc/guix.texi @@ -5295,16 +5295,11 @@ variables. @defvr {Scheme Variable} %base-file-systems These are essential file systems that are required on normal systems, -such as @var{%devtmpfs-file-system} and @var{%immutable-store} (see +such as @var{%pseudo-terminal-file-system} and @var{%immutable-store} (see below.) Operating system declarations should always contain at least these. @end defvr -@defvr {Scheme Variable} %devtmpfs-file-system -The @code{devtmpfs} file system to be mounted on @file{/dev}. This is a -requirement for udev (@pxref{Base Services, @code{udev-service}}). -@end defvr - @defvr {Scheme Variable} %pseudo-terminal-file-system This is the file system to be mounted as @file{/dev/pts}. It supports @dfn{pseudo-terminals} created @i{via} @code{openpty} and similar diff --git a/gnu/build/linux-boot.scm b/gnu/build/linux-boot.scm index 3081a93a97..30d6570b04 100644 --- a/gnu/build/linux-boot.scm +++ b/gnu/build/linux-boot.scm @@ -48,7 +48,7 @@ ;;; Code: (define* (mount-essential-file-systems #:key (root "/")) - "Mount /proc and /sys under ROOT." + "Mount /dev, /proc, and /sys under ROOT." (define (scope dir) (string-append root (if (string-suffix? "/" root) @@ -60,6 +60,10 @@ (mkdir (scope "proc"))) (mount "none" (scope "proc") "proc") + (unless (file-exists? (scope "dev")) + (mkdir (scope "dev"))) + (mount "none" (scope "dev") "devtmpfs") + (unless (file-exists? (scope "sys")) (mkdir (scope "sys"))) (mount "none" (scope "sys") "sysfs")) @@ -71,7 +75,7 @@ (unless (file-exists? target) (mkdir target)) (mount dir target "" MS_MOVE))) - '("/proc" "/sys"))) + '("/dev" "/proc" "/sys"))) (define (linux-command-line) "Return the Linux kernel command line as a list of strings." @@ -100,7 +104,7 @@ with the given MAJOR number, starting with MINOR." (define* (make-essential-device-nodes #:key (root "/")) "Make essential device nodes under ROOT/dev." - ;; The hand-made udev! + ;; The hand-made devtmpfs/udev! (define (scope dir) (string-append root @@ -255,7 +259,8 @@ UNIONFS." (mount "none" "/rw-root" "tmpfs") ;; We want read-write /dev nodes. - (make-essential-device-nodes #:root "/rw-root") + (mkdir-p "/rw-root/dev") + (mount "none" "/rw-root/dev" "devtmpfs") ;; Make /root a union of the tmpfs and the actual root. Use ;; 'max_files' to set a high RLIMIT_NOFILE for the unionfs process @@ -385,9 +390,6 @@ to it are lost." (unless (configure-qemu-networking) (display "network interface is DOWN\n"))) - ;; Make /dev nodes. - (make-essential-device-nodes) - ;; Prepare the real root file system under /root. (unless (file-exists? "/root") (mkdir "/root")) @@ -405,10 +407,6 @@ to it are lost." #:volatile-root? volatile-root?) (mount "none" "/root" "tmpfs")) - (unless (file-exists? "/root/dev") - (mkdir "/root/dev") - (make-essential-device-nodes #:root "/root")) - ;; Mount the specified file systems. (for-each mount-file-system (remove root-mount-point? mounts)) diff --git a/gnu/system/file-systems.scm b/gnu/system/file-systems.scm index b177f93398..8155b273e3 100644 --- a/gnu/system/file-systems.scm +++ b/gnu/system/file-systems.scm @@ -47,7 +47,6 @@ %binary-format-file-system %shared-memory-file-system %pseudo-terminal-file-system - %devtmpfs-file-system %immutable-store %control-groups %elogind-file-systems @@ -186,17 +185,6 @@ UUID representation." (type "binfmt_misc") (check? #f))) -(define %devtmpfs-file-system - ;; /dev as a 'devtmpfs' file system, needed for udev. - (file-system - (device "none") - (mount-point "/dev") - (type "devtmpfs") - (check? #f) - - ;; Mount it from the initrd so /dev/pts & co. can then be mounted over it. - (needed-for-boot? #t))) - (define %tty-gid ;; ID of the 'tty' group. Allocate it statically to make it easy to refer ;; to it from here and from the 'tty' group definitions. @@ -282,8 +270,7 @@ UUID representation." (define %base-file-systems ;; List of basic file systems to be mounted. Note that /proc and /sys are ;; currently mounted by the initrd. - (append (list %devtmpfs-file-system - %pseudo-terminal-file-system + (append (list %pseudo-terminal-file-system %shared-memory-file-system %immutable-store) %elogind-file-systems -- cgit v1.2.3 From 07779d0addd5bc52d0bc2e06054a158c5c6abb4b Mon Sep 17 00:00:00 2001 From: Ludovic Courtès Date: Sun, 20 Sep 2015 22:02:02 +0200 Subject: linux-initrd: Add LUKS/dm-crypt modules to the initrd. Suggested by Petter and Mark H Weaver . Partly fixes . * gnu/system/linux-initrd.scm (base-initrd)[linux-modules]: Add dm-crypt and xts. --- gnu/system/linux-initrd.scm | 1 + 1 file changed, 1 insertion(+) (limited to 'gnu') diff --git a/gnu/system/linux-initrd.scm b/gnu/system/linux-initrd.scm index 48b855b567..519373fe34 100644 --- a/gnu/system/linux-initrd.scm +++ b/gnu/system/linux-initrd.scm @@ -182,6 +182,7 @@ loaded at boot time in the order in which they appear." "isci" ;for SAS controllers like Intel C602 "usb-storage" "uas" ;for the installation image etc. "usbkbd" "usbhid" ;USB keyboards, for debugging + "dm-crypt" "xts" ;for encrypted root partitions ,@(if (or virtio? qemu-networking?) virtio-modules '()) -- cgit v1.2.3 From f210647da264a637716b004ddde713a2dbe9beb6 Mon Sep 17 00:00:00 2001 From: Eric Bavier Date: Sat, 19 Sep 2015 17:17:46 -0500 Subject: gnu: gnu-pw-mgr: Update to 1.5. * gnu/packages/gnu-pw-mgr.scm (gnu-pw-mgr): Update to 1.5. --- gnu/packages/gnu-pw-mgr.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/gnu-pw-mgr.scm b/gnu/packages/gnu-pw-mgr.scm index 7a9b0b9810..e7b93f024e 100644 --- a/gnu/packages/gnu-pw-mgr.scm +++ b/gnu/packages/gnu-pw-mgr.scm @@ -29,7 +29,7 @@ (define-public gnu-pw-mgr (package (name "gnu-pw-mgr") - (version "1.4") + (version "1.5") (source (origin (method url-fetch) @@ -37,7 +37,7 @@ version ".tar.xz")) (sha256 (base32 - "0a352y1m33vp6zmdbn96fdrq9gr9lchc9vcrj14mfx7g0dsvxjns")))) + "1winmckl4h8lypg57hd3nd7jscpdr7f1v8zi432k5h648izkf2dg")))) (build-system gnu-build-system) (native-inputs `(("which" ,which) -- cgit v1.2.3 From da494dad8e97c3241cf7702438b0047d502e551e Mon Sep 17 00:00:00 2001 From: Eric Bavier Date: Sat, 19 Sep 2015 17:42:31 -0500 Subject: gnu: autogen: Update to 5.18.6. * gnu/packages/autogen.scm (autogen): Update to 5.18.6. --- gnu/packages/autogen.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/autogen.scm b/gnu/packages/autogen.scm index 45b7cb81cc..615839f463 100644 --- a/gnu/packages/autogen.scm +++ b/gnu/packages/autogen.scm @@ -30,16 +30,16 @@ (define-public autogen (package (name "autogen") - (version "5.18.5") + (version "5.18.6") (source (origin (method url-fetch) (uri (string-append "mirror://gnu/autogen/rel" version "/autogen-" - version ".tar.gz")) + version ".tar.xz")) (sha256 (base32 - "1flnbnmkbqmbfgammkl8m36wrlk6rhpgnf9pdm6gdfhqalxvggbv")))) + "0sfmmy19k9z0j3f738fyk6ljf6b66410cvd5zzyplxi2683j10qs")))) (build-system gnu-build-system) (native-inputs `(("perl" ,perl) ;for doc generator mdoc ("pkg-config" ,pkg-config))) -- cgit v1.2.3 From af8f9f231ef49ba49fc75e4f5f123a62893fe670 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 1 Sep 2015 21:37:12 +0200 Subject: gnu: Add libgee. * gnu/packages/gnome.scm (libgee): New variable. --- gnu/packages/gnome.scm | 37 +++++++++++++++++++++++++++++++++++++ 1 file changed, 37 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/gnome.scm b/gnu/packages/gnome.scm index ca75fa82e0..73d8a4fb9d 100644 --- a/gnu/packages/gnome.scm +++ b/gnu/packages/gnome.scm @@ -3500,3 +3500,40 @@ manage, and publish documentation for Yelp and the web. Most of the heavy lifting is done by packages like yelp-xsl and itstool. This package just wraps things up in a developer-friendly way.") (license license:gpl2+))) + +(define-public libgee + (package + (name "libgee") + (version "0.18.0") + (source (origin + (method url-fetch) + (uri (string-append "mirror://gnome/sources/" name "/" + (version-major+minor version) "/" + name "-" version ".tar.xz")) + (sha256 + (base32 + "16a34js81w9m2bw4qd8csm4pcgr3zq5z87867j4b8wfh6zwrxnaa")))) + (build-system gnu-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'fix-introspection-install-dir + (lambda* (#:key outputs #:allow-other-keys) + (let ((out (assoc-ref outputs "out"))) + (substitute* "gee/Makefile.in" + (("@INTROSPECTION_GIRDIR@") + (string-append out "/share/gir-1.0/")) + (("@INTROSPECTION_TYPELIBDIR@") + (string-append out "/lib/girepository-1.0/"))))))))) + (native-inputs + `(("glib" ,glib "bin") + ("pkg-config" ,pkg-config))) + (inputs + `(("glib" ,glib) + ("gobject-introspection" ,gobject-introspection))) + (home-page "https://wiki.gnome.org/Projects/Libgee") + (synopsis "GObject collection library") + (description + "Libgee is a utility library providing GObject-based interfaces and +classes for commonly used data structures.") + (license license:lgpl2.1+))) -- cgit v1.2.3 From b0f9c4b86ca32cb3dd97b6dbf27a14ae2b5eaaeb Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 1 Sep 2015 21:38:06 +0200 Subject: gnu: Add gexiv2. * gnu/packages/gnome.scm (gexiv2): New variable. --- gnu/packages/gnome.scm | 31 +++++++++++++++++++++++++++++++ 1 file changed, 31 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/gnome.scm b/gnu/packages/gnome.scm index 73d8a4fb9d..eef54cc302 100644 --- a/gnu/packages/gnome.scm +++ b/gnu/packages/gnome.scm @@ -69,6 +69,7 @@ #:use-module (gnu packages scanner) #:use-module (gnu packages ssh) #:use-module (gnu packages xml) + #:use-module (gnu packages geeqie) #:use-module (gnu packages gl) #:use-module (gnu packages qt) ; for libxkbcommon #:use-module (gnu packages compression) @@ -3537,3 +3538,33 @@ wraps things up in a developer-friendly way.") "Libgee is a utility library providing GObject-based interfaces and classes for commonly used data structures.") (license license:lgpl2.1+))) + +(define-public gexiv2 + (package + (name "gexiv2") + (version "0.10.3") + (source (origin + (method url-fetch) + (uri (string-append "mirror://gnome/sources/" name "/" + (version-major+minor version) "/" + name "-" version ".tar.xz")) + (sha256 + (base32 + "121r5lv6l82pjr0ycdf2b01mdwy7sxwca2r068zrzylpc6bgn31r")))) + (build-system gnu-build-system) + (native-inputs + `(("glib" ,glib "bin") + ("pkg-config" ,pkg-config))) + (propagated-inputs + ;; Listed in "Requires" section of gexiv2.pc + `(("exiv2" ,exiv2))) + (inputs + `(("glib" ,glib) + ("gobject-introspection" ,gobject-introspection))) + (home-page "https://wiki.gnome.org/Projects/gexiv2") + (synopsis "GObject wrapper around the Exiv2 photo metadata library") + (description + "Gexiv2 is a GObject wrapper around the Exiv2 photo metadata library. It +allows for GNOME applications to easily inspect and update EXIF, IPTC, and XMP +metadata in photo and video files of various formats.") + (license license:gpl2+))) -- cgit v1.2.3 From fed5a6898b73919046665f9328f3d804823f3ba2 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 3 Sep 2015 13:09:34 +0200 Subject: gnu: Add shotwell. * gnu/packages/gnome.scm (shotwell): New variable. --- gnu/packages/gnome.scm | 57 ++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 57 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/gnome.scm b/gnu/packages/gnome.scm index eef54cc302..f9cb579e85 100644 --- a/gnu/packages/gnome.scm +++ b/gnu/packages/gnome.scm @@ -44,6 +44,7 @@ #:use-module (gnu packages djvu) #:use-module (gnu packages flex) #:use-module (gnu packages docbook) + #:use-module (gnu packages gettext) #:use-module (gnu packages glib) #:use-module (gnu packages gnupg) #:use-module (gnu packages gnuzilla) @@ -60,6 +61,7 @@ #:use-module (gnu packages libusb) #:use-module (gnu packages lirc) #:use-module (gnu packages lua) + #:use-module (gnu packages m4) #:use-module (gnu packages image) #:use-module (gnu packages perl) #:use-module (gnu packages photo) @@ -3568,3 +3570,58 @@ classes for commonly used data structures.") allows for GNOME applications to easily inspect and update EXIF, IPTC, and XMP metadata in photo and video files of various formats.") (license license:gpl2+))) + +(define-public shotwell + (package + (name "shotwell") + (version "0.22.0") + (source (origin + (method url-fetch) + (uri (string-append "mirror://gnome/sources/" name "/" + (version-major+minor version) "/" + name "-" version ".tar.xz")) + (sha256 + (base32 + "0cgqaaikrb10plhf6zxbgqy32zqpiwyi9dpx3g8yr261q72r5c81")))) + (build-system glib-or-gtk-build-system) + (arguments + `(#:tests? #f ;no "check" target + #:make-flags '("CC=gcc") + #:configure-flags '("--disable-gsettings-convert-install") + #:out-of-source? #f)) + (native-inputs + `(("pkg-config" ,pkg-config) + ("gettext" ,gnu-gettext) + ("m4" ,m4) + ("desktop-file-utils" ,desktop-file-utils) + ("vala" ,vala) + ("which" ,which) + ("gnome-doc-utils" ,gnome-doc-utils) + ;; FIXME: I only added python2-libxml2 because xml2po needs it at + ;; runtime. It should be propagated. + ("python2-libxml2" ,python2-libxml2) + ("python2" ,python-2))) + (inputs + `(("gstreamer" ,gstreamer) + ("gst-plugins-base" ,gst-plugins-base) + ("gst-plugins-good" ,gst-plugins-good) + ("libgee" ,libgee) + ("gexiv2" ,gexiv2) + ("libraw" ,libraw) + ("json-glib" ,json-glib) + ("rest" ,rest) + ("webkitgtk" ,webkitgtk-2.4) + ("sqlite" ,sqlite) + ("libsoup" ,libsoup) + ("libxml2" ,libxml2) + ("gtk+" ,gtk+) + ("libgudev" ,libgudev) + ("libgphoto2" ,libgphoto2))) + (home-page "https://wiki.gnome.org/Apps/Shotwell") + (synopsis "Photo manager for GNOME 3") + (description + "Shotwell is a digital photo manager designed for the GNOME desktop +environment. It allows you to import photos from disk or camera, organize +them by keywords and events, view them in full-window or fullscreen mode, and +share them with others via social networking and more.") + (license license:lgpl2.1+))) -- cgit v1.2.3 From 9cda36227b353854c5a753ed1e4eac2a8edb0c7a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 17 Sep 2015 17:04:35 +0200 Subject: gnu: Use cran-uri in source expressions. * gnu/packages/statistics.scm (r-colorspace, r-dichromat, r-digest, r-gtable, r-labeling, r-magrittr, r-munsell, r-rcpp, r-plyr, r-proto, r-rcolorbrewer, r-stringi, r-stringr, r-reshape2, r-scales, r-ggplot2, r-assertthat, r-lazyeval, r-dbi): Use cran-uri in source expressions. --- gnu/packages/statistics.scm | 58 +++++++++++++++------------------------------ 1 file changed, 19 insertions(+), 39 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 6ccb97f375..54c9abca40 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -141,8 +141,7 @@ available, greatly increasing its breadth and scope.") (source (origin (method url-fetch) - (uri (string-append "mirror://cran/src/contrib/colorspace_" - version ".tar.gz")) + (uri (cran-uri "colorspace" version)) (sha256 (base32 "0y8n4ljwhbdvkysdwgqzcnpv107pb3px1jip3k6svv86p72nacds")))) (build-system r-build-system) @@ -162,8 +161,7 @@ colors are provided.") (source (origin (method url-fetch) - (uri (string-append "mirror://cran/src/contrib/dichromat_" - version ".tar.gz")) + (uri (cran-uri "dichromat" version)) (sha256 (base32 "1l8db1nk29ccqg3mkbafvfiw0775iq4gapysf88xq2zp6spiw59i")))) (build-system r-build-system) @@ -181,8 +179,7 @@ effects of different types of color-blindness.") (source (origin (method url-fetch) - (uri (string-append "mirror://cran/src/contrib/digest_" - version ".tar.gz")) + (uri (cran-uri "digest" version)) (sha256 (base32 "0m9grqv67hhf51lz10whymhw0g0d98466ka694kya5x95hn44qih")))) (build-system r-build-system) @@ -207,8 +204,7 @@ OpenSSL should be used.") (source (origin (method url-fetch) - (uri (string-append "mirror://cran/src/contrib/gtable_" - version ".tar.gz")) + (uri (cran-uri "gtable" version)) (sha256 (base32 "0k9hfj6r5y238gqh92s3cbdn34biczx3zfh79ix5xq0c5vkai2xh")))) (build-system r-build-system) @@ -226,8 +222,7 @@ OpenSSL should be used.") (source (origin (method url-fetch) - (uri (string-append "mirror://cran/src/contrib/labeling_" - version ".tar.gz")) + (uri (cran-uri "labeling" version)) (sha256 (base32 "13sk7zrrrzry6ky1bp8mmnzcl9jhvkig8j4id9nny7z993mnk00d")))) (build-system r-build-system) @@ -244,8 +239,7 @@ algorithms.") (source (origin (method url-fetch) - (uri (string-append "mirror://cran/src/contrib/magrittr_" - version ".tar.gz")) + (uri (cran-uri "magrittr" version)) (sha256 (base32 "1s1ar6rag8m277qcqmdp02gn4awn9bdj9ax0r8s32i59mm1mki05")))) (build-system r-build-system) @@ -266,8 +260,7 @@ see package vignette. To quote Rene Magritte, \"Ceci n'est pas un pipe.\"") (source (origin (method url-fetch) - (uri (string-append "mirror://cran/src/contrib/munsell_" - version ".tar.gz")) + (uri (cran-uri "munsell" version)) (sha256 (base32 "1bi5yi0i80778bbzx2rm4f0glpc34kvh24pwwfhm4v32izsqgrw4")))) (build-system r-build-system) @@ -287,8 +280,7 @@ Munsell colour system.") (source (origin (method url-fetch) - (uri (string-append "mirror://cran/src/contrib/Rcpp_" - version ".tar.gz")) + (uri (cran-uri "Rcpp" version)) (sha256 (base32 "182109z0yc1snqgd833ssl2cix6cbq83bcxmy5344b15ym820y38")))) (build-system r-build-system) @@ -312,8 +304,7 @@ and Francois (2011, JSS), and the book by Eddelbuettel (2013, Springer); see (source (origin (method url-fetch) - (uri (string-append "mirror://cran/src/contrib/plyr_" - version ".tar.gz")) + (uri (cran-uri "plyr" version)) (sha256 (base32 "06v4zxawpjz37rp2q2ii5q43g664z9s29j4ydn0cz3crn7lzl6pk")))) (build-system r-build-system) @@ -335,7 +326,7 @@ panels or collapse high-dimensional arrays to simpler summary statistics.") (source (origin (method url-fetch) - (uri (string-append "mirror://cran/src/contrib/proto_" version ".tar.gz")) + (uri (cran-uri "proto" version)) (sha256 (base32 "03mvzi529y6kjcp9bkpk7zlgpcakb3iz73hca6rpjy14pyzl3nfh")))) (build-system r-build-system) @@ -353,8 +344,7 @@ prototype-based, rather than class-based object oriented ideas.") (source (origin (method url-fetch) - (uri (string-append "mirror://cran/src/contrib/RColorBrewer_" - version ".tar.gz")) + (uri (cran-uri "RColorBrewer" version)) (sha256 (base32 "1pfcl8z1pnsssfaaz9dvdckyfnnc6rcq56dhislbf571hhg7isgk")))) (build-system r-build-system) @@ -373,10 +363,7 @@ designed by Cynthia Brewer as described at http://colorbrewer2.org") (source (origin (method url-fetch) - (uri (string-append - "mirror://cran/src/contrib/stringi_" - version - ".tar.gz")) + (uri (cran-uri "stringi" version)) (sha256 (base32 "183wrrjhpgl1wbnn9lhghyvhz7l2mc64mpcmzplckal7y9j7pmhw")))) @@ -402,8 +389,7 @@ transliteration, concatenation, date-time formatting and parsing, etc.") (source (origin (method url-fetch) - (uri (string-append "mirror://cran/src/contrib/stringr_" - version ".tar.gz")) + (uri (cran-uri "stringr" version)) (sha256 (base32 "0jnz6r9yqyf7dschr2fnn1slg4wn6b4ik5q00j4zrh43bfw7s9pq")))) (build-system r-build-system) @@ -427,8 +413,7 @@ the input of another.") (source (origin (method url-fetch) - (uri (string-append "mirror://cran/src/contrib/reshape2_" - version ".tar.gz")) + (uri (cran-uri "reshape2" version)) (sha256 (base32 "0hl082dyk3pk07nqprpn5dvnrkqhnf6zjnjig1ijddxhlmsrzm7v")))) (build-system r-build-system) @@ -450,8 +435,7 @@ using just two functions: melt and dcast (or acast).") (source (origin (method url-fetch) - (uri (string-append "mirror://cran/src/contrib/scales_" - version ".tar.gz")) + (uri (cran-uri "scales" version)) (sha256 (base32 "12xrmn1vh64dl46bq7n7pa427aicb2ifjrby9in3m32nyvir0kac")))) (build-system r-build-system) @@ -477,8 +461,7 @@ legends.") (source (origin (method url-fetch) - (uri (string-append "mirror://cran/src/contrib/ggplot2_" - version ".tar.gz")) + (uri (cran-uri "ggplot2" version)) (sha256 (base32 "0794kjqi3lrxb33lr1mykd58959hlgkhdn259vj8fxrh65mqw920")))) (build-system r-build-system) @@ -506,8 +489,7 @@ aesthetic attributes.") (version "0.1") (source (origin (method url-fetch) - (uri (string-append "mirror://cran/src/contrib/assertthat_" - version ".tar.gz")) + (uri (cran-uri "assertthat" version)) (sha256 (base32 "0dwsqajyglfscqilj843qfqn1ndbqpswa7b4l1d633qjk9d68qqk")))) @@ -527,8 +509,7 @@ wrong.") (version "0.1.10") (source (origin (method url-fetch) - (uri (string-append "mirror://cran/src/contrib/lazyeval_" - version ".tar.gz")) + (uri (cran-uri "lazyeval" version)) (sha256 (base32 "02qfpn2fmy78vx4jxr7g7rhqzcm1kcivfwai7lbh0vvpawia0qwh")))) @@ -546,8 +527,7 @@ evaluation (NSE) in R.") (version "0.3.1") (source (origin (method url-fetch) - (uri (string-append "mirror://cran/src/contrib/DBI_" - version ".tar.gz")) + (uri (cran-uri "DBI" version)) (sha256 (base32 "0xj5baxwnhl23rd5nskhjvranrwrc68f3xlyrklglipi41bm69hw")))) -- cgit v1.2.3 From 675c9f447b264967ae9a9249e8281943f350cbc5 Mon Sep 17 00:00:00 2001 From: Vicente Vera Parra Date: Tue, 15 Sep 2015 14:15:16 -0300 Subject: gnu: Add r-bh. * gnu/packages/statistics.scm (r-bh): New variable. --- gnu/packages/statistics.scm | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 54c9abca40..911dc3de1e 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -540,3 +540,21 @@ communication between R and relational database management systems. All classes in this package are virtual and need to be extended by the various R/DBMS implementations.") (license license:lgpl2.0+))) + +(define-public r-bh + (package + (name "r-bh") + (version "1.58.0-1") + (source (origin + (method url-fetch) + (uri (cran-uri "BH" version)) + (sha256 + (base32 + "17rnwyw9ib2pvm60iixzkbz7ff4fslpifp1nlx4czp42hy67kqpf")))) + (build-system r-build-system) + (home-page "https://github.com/eddelbuettel/bh") + (synopsis "R package providing subset of Boost headers") + (description + "This package aims to provide the most useful subset of Boost libraries +for template use among CRAN packages.") + (license license:boost1.0))) -- cgit v1.2.3 From 256ccc926c31dbb5bb1a70af30a5403e91b132e3 Mon Sep 17 00:00:00 2001 From: Vicente Vera Parra Date: Tue, 15 Sep 2015 14:15:55 -0300 Subject: gnu: Add r-evaluate. * gnu/packages/statistics.scm (r-evaluate): New variable. --- gnu/packages/statistics.scm | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 911dc3de1e..9acc20b5eb 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -558,3 +558,25 @@ R/DBMS implementations.") "This package aims to provide the most useful subset of Boost libraries for template use among CRAN packages.") (license license:boost1.0))) + +(define-public r-evaluate + (package + (name "r-evaluate") + (version "0.8") + (source (origin + (method url-fetch) + (uri (cran-uri "evaluate" version)) + (sha256 + (base32 + "137gc35jlizhqnx19mxim3llrkm403abj8ghb2b7v5ls9rvd40pq")))) + (build-system r-build-system) + (propagated-inputs + `(("r-stringr" ,r-stringr))) + (home-page "https://github.com/hadley/evaluate") + (synopsis "Parsing and evaluation tools for R") + (description + "This package provides tools that allow you to recreate the parsing, +evaluation and display of R code, with enough information that you can +accurately recreate what happens at the command line. The tools can easily be +adapted for other output formats, such as HTML or LaTeX.") + (license license:gpl3+))) -- cgit v1.2.3 From c5bf3abe34718991a9441e0f036a6d1d86731bf7 Mon Sep 17 00:00:00 2001 From: Vicente Vera Parra Date: Tue, 15 Sep 2015 14:16:47 -0300 Subject: gnu: Add r-formatr. * gnu/packages/statistics.scm (r-formatr): New variable. --- gnu/packages/statistics.scm | 20 ++++++++++++++++++++ 1 file changed, 20 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 9acc20b5eb..ff7f0174e5 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -580,3 +580,23 @@ evaluation and display of R code, with enough information that you can accurately recreate what happens at the command line. The tools can easily be adapted for other output formats, such as HTML or LaTeX.") (license license:gpl3+))) + +(define-public r-formatr + (package + (name "r-formatr") + (version "1.2.1") + (source (origin + (method url-fetch) + (uri (cran-uri "formatR" version)) + (sha256 + (base32 + "0f4cv2zv5wayyqx99ybfyl0p83kgjvnsv8dhcwa4s49kw6jsx1lr")))) + (build-system r-build-system) + (home-page "http://yihui.name/formatR") + (synopsis "Format R code automatically") + (description + "This package provides a function to format R source code. Spaces and +indent will be added to the code automatically, and comments will be preserved +under certain conditions, so that R code will be more human-readable and tidy. +There is also a Shiny app as a user interface in this package.") + (license license:gpl3+))) -- cgit v1.2.3 From ad3f005bddcca58c9f4869fffb8aef0cf4efb598 Mon Sep 17 00:00:00 2001 From: Vicente Vera Parra Date: Tue, 15 Sep 2015 14:17:50 -0300 Subject: gnu: Add r-highr. * gnu/packages/statistics.scm (r-highr): New variable. --- gnu/packages/statistics.scm | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index ff7f0174e5..5cf094c0ee 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -600,3 +600,22 @@ indent will be added to the code automatically, and comments will be preserved under certain conditions, so that R code will be more human-readable and tidy. There is also a Shiny app as a user interface in this package.") (license license:gpl3+))) + +(define-public r-highr + (package + (name "r-highr") + (version "0.5.1") + (source (origin + (method url-fetch) + (uri (cran-uri "highr" version)) + (sha256 + (base32 + "11hyawzhaw3ph5y5xphi7alx6df1d0i6wh0a2n5m4sxxhdrzswnb")))) + (build-system r-build-system) + (home-page "https://github.com/yihui/highr") + (synopsis "Syntax highlighting for R source code") + (description + "This package provides syntax highlighting for R source code. Currently +it supports LaTeX and HTML output. Source code of other languages is +supported via Andre Simon's highlight package.") + (license license:gpl3+))) -- cgit v1.2.3 From acbb40fa2076c13aefa43c9d92474481cef110e4 Mon Sep 17 00:00:00 2001 From: Vicente Vera Parra Date: Tue, 15 Sep 2015 14:18:25 -0300 Subject: gnu: Add r-mime. * gnu/packages/statistics.scm (r-mime): New variable. --- gnu/packages/statistics.scm | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 5cf094c0ee..82a1fb8291 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -619,3 +619,21 @@ There is also a Shiny app as a user interface in this package.") it supports LaTeX and HTML output. Source code of other languages is supported via Andre Simon's highlight package.") (license license:gpl3+))) + +(define-public r-mime + (package + (name "r-mime") + (version "0.4") + (source (origin + (method url-fetch) + (uri (cran-uri "mime" version)) + (sha256 + (base32 + "145cdcg252w2zsq67dmvmsqka60msfp7agymlxs3gl3ihgiwg46p")))) + (build-system r-build-system) + (home-page "https://github.com/yihui/mime") + (synopsis "R package to map filenames to MIME types") + (description + "This package guesses the MIME type from a filename extension using the +data derived from /etc/mime.types in UNIX-type systems.") + (license license:gpl2))) -- cgit v1.2.3 From 3f8ac35330922507f4159b4bd670d5f50ea82673 Mon Sep 17 00:00:00 2001 From: Vicente Vera Parra Date: Tue, 15 Sep 2015 14:18:58 -0300 Subject: gnu: Add r-markdown. * gnu/packages/statistics.scm (r-markdown): New variable. --- gnu/packages/statistics.scm | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 82a1fb8291..84e5a21220 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -637,3 +637,29 @@ supported via Andre Simon's highlight package.") "This package guesses the MIME type from a filename extension using the data derived from /etc/mime.types in UNIX-type systems.") (license license:gpl2))) + +(define-public r-markdown + (package + (name "r-markdown") + (version "0.7.7") + (source (origin + (method url-fetch) + (uri (cran-uri "markdown" version)) + (sha256 + (base32 + "00j1hlib3il50azs2vlcyhi0bjpx1r50mxr9w9dl5g1bwjjc71hb")))) + (build-system r-build-system) + ;; Skip check phase because the tests require the r-knitr package to be + ;; installed. This prevents installation failures. Knitr normally + ;; shouldn't be available since r-markdown is a dependency of the r-knitr + ;; package. + (arguments `(#:tests? #f)) + (propagated-inputs + `(("r-mime" ,r-mime))) + (home-page "https://github.com/rstudio/markdown") + (synopsis "Markdown rendering for R") + (description + "This package provides R bindings to the Sundown Markdown rendering +library (https://github.com/vmg/sundown). Markdown is a plain-text formatting +syntax that can be converted to XHTML or other formats.") + (license license:gpl2))) -- cgit v1.2.3 From ea3a80957aa7b38cb8cf9c2a9cb104e724292384 Mon Sep 17 00:00:00 2001 From: Vicente Vera Parra Date: Tue, 15 Sep 2015 14:19:33 -0300 Subject: gnu: Add r-yaml. * gnu/packages/statistics.scm (r-yaml): New variable. --- gnu/packages/statistics.scm | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 84e5a21220..9c0c9fd11e 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -663,3 +663,21 @@ data derived from /etc/mime.types in UNIX-type systems.") library (https://github.com/vmg/sundown). Markdown is a plain-text formatting syntax that can be converted to XHTML or other formats.") (license license:gpl2))) + +(define-public r-yaml + (package + (name "r-yaml") + (version "2.1.13") + (source (origin + (method url-fetch) + (uri (cran-uri "yaml" version)) + (sha256 + (base32 + "18kz5mfn7qpif5pn91w4vbrc5bkycsj85vwm5wxwzjlb02i9mxi6")))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/yaml/") + (synopsis "Methods to convert R data to YAML and back") + (description + "This package implements the libyaml YAML 1.1 parser and +emitter (http://pyyaml.org/wiki/LibYAML) for R.") + (license license:bsd-3))) -- cgit v1.2.3 From 213656b95b3067c141e8d3fe458463326f2e7c6c Mon Sep 17 00:00:00 2001 From: Vicente Vera Parra Date: Tue, 15 Sep 2015 14:20:13 -0300 Subject: gnu: Add r-knitr. * gnu/packages/statistics.scm (r-knitr): New variable. --- gnu/packages/statistics.scm | 29 +++++++++++++++++++++++++++++ 1 file changed, 29 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 9c0c9fd11e..c3d98a6ca1 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -681,3 +681,32 @@ syntax that can be converted to XHTML or other formats.") "This package implements the libyaml YAML 1.1 parser and emitter (http://pyyaml.org/wiki/LibYAML) for R.") (license license:bsd-3))) + +(define-public r-knitr + (package + (name "r-knitr") + (version "1.11") + (source (origin + (method url-fetch) + (uri (cran-uri "knitr" version)) + (sha256 + (base32 + "1ikjla0hnpjfkdbydqhhqypc0aiizbi4nyn8c694sdk9ca4jasdd")))) + (build-system r-build-system) + (propagated-inputs + `(("r-evaluate" ,r-evaluate) + ("r-digest" ,r-digest) + ("r-formatr" ,r-formatr) + ("r-highr" ,r-highr) + ("r-markdown" ,r-markdown) + ("r-stringr" ,r-stringr) + ("r-yaml" ,r-yaml))) + (home-page "http://yihui.name/knitr/") + (synopsis "General-purpose package for dynamic report generation in R") + (description + "This package provides a general-purpose tool for dynamic report +generation in R using Literate Programming techniques.") + ;; The code is released under any version of the GPL. As it is used by + ;; r-markdown which is available under GPLv2 only, we have chosen GPLv2+ + ;; here. + (license license:gpl2+))) -- cgit v1.2.3 From 4f0e84845d4523e5801df12f24f2bd0570d8e549 Mon Sep 17 00:00:00 2001 From: Vicente Vera Parra Date: Tue, 15 Sep 2015 14:20:47 -0300 Subject: gnu: Add r-microbenchmark. * gnu/packages/statistics.scm (r-microbenchmark): New variable. --- gnu/packages/statistics.scm | 20 ++++++++++++++++++++ 1 file changed, 20 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index c3d98a6ca1..a9c8457b0c 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -710,3 +710,23 @@ generation in R using Literate Programming techniques.") ;; r-markdown which is available under GPLv2 only, we have chosen GPLv2+ ;; here. (license license:gpl2+))) + +(define-public r-microbenchmark + (package + (name "r-microbenchmark") + (version "1.4-2") + (source (origin + (method url-fetch) + (uri (cran-uri "microbenchmark" version)) + (sha256 + (base32 + "05yxvdnkxr2ll94h6f2m5sn3gg7vrlm9nbdxgmj2g8cp8gfxpfkg")))) + (build-system r-build-system) + (propagated-inputs + `(("r-ggplot2" ,r-ggplot2))) + (home-page "https://cran.r-project.org/web/packages/microbenchmark/") + (synopsis "Accurate timing functions for R") + (description + "This package provides infrastructure to accurately measure and compare +the execution time of R expressions.") + (license license:bsd-2))) -- cgit v1.2.3 From 1cf1cbb0ac650e297a4703df23d54f03391d96e6 Mon Sep 17 00:00:00 2001 From: Vicente Vera Parra Date: Tue, 15 Sep 2015 14:21:19 -0300 Subject: gnu: Add r-codetools. * gnu/packages/statistics.scm (r-codetools): New variable. --- gnu/packages/statistics.scm | 16 ++++++++++++++++ 1 file changed, 16 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index a9c8457b0c..6132b49f55 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -730,3 +730,19 @@ generation in R using Literate Programming techniques.") "This package provides infrastructure to accurately measure and compare the execution time of R expressions.") (license license:bsd-2))) + +(define-public r-codetools + (package + (name "r-codetools") + (version "0.2-14") + (source (origin + (method url-fetch) + (uri (cran-uri "codetools" version)) + (sha256 + (base32 + "0y9r4m2b8xgavr89sc179knzwpz54xljbc1dinpq2q07i4xn0397")))) + (build-system r-build-system) + (home-page "https://cran.r-project.org/web/packages/codetools/index.html") + (synopsis "Code analysis tools for R") + (description "This package provides code analysis tools for R.") + (license license:gpl3+))) -- cgit v1.2.3 From 0661b4db2e25f2e34de60335cb8398fcee3a09dd Mon Sep 17 00:00:00 2001 From: Vicente Vera Parra Date: Tue, 15 Sep 2015 14:22:35 -0300 Subject: gnu: Add r-pryr. * gnu/packages/statistics.scm (r-pryr): New variable. --- gnu/packages/statistics.scm | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 6132b49f55..a3710e0d9b 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -746,3 +746,26 @@ the execution time of R expressions.") (synopsis "Code analysis tools for R") (description "This package provides code analysis tools for R.") (license license:gpl3+))) + +(define-public r-pryr + (package + (name "r-pryr") + (version "0.1.2") + (source (origin + (method url-fetch) + (uri (cran-uri "pryr" version)) + (sha256 + (base32 + "1in350a8hxwf580afavasvn3jc7x2p1b7nlwmj1scakfz74vghk5")))) + (build-system r-build-system) + (propagated-inputs + `(("r-stringr" ,r-stringr) + ("r-codetools" ,r-codetools))) + (native-inputs + `(("r-rcpp" ,r-rcpp))) + (home-page "https://github.com/hadley/pryr") + (synopsis "Tools for computing on the R language") + (description + "This package provides useful tools to pry back the covers of R and +understand the language at a deeper level.") + (license license:gpl2))) -- cgit v1.2.3 From b668a95cf3104bedcb629f107b1c75e31ccfae91 Mon Sep 17 00:00:00 2001 From: Vicente Vera Parra Date: Tue, 15 Sep 2015 14:23:07 -0300 Subject: gnu: Add r-memoise. * gnu/packages/statistics.scm (r-memoise): New variable. --- gnu/packages/statistics.scm | 20 ++++++++++++++++++++ 1 file changed, 20 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index a3710e0d9b..1a99a09b48 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -769,3 +769,23 @@ the execution time of R expressions.") "This package provides useful tools to pry back the covers of R and understand the language at a deeper level.") (license license:gpl2))) + +(define-public r-memoise + (package + (name "r-memoise") + (version "0.2.1") + (source (origin + (method url-fetch) + (uri (cran-uri "memoise" version)) + (sha256 + (base32 + "19wm4b3kq6xva43kga3xydnl7ybl5mq7b4y2fczgzzjz63jd75y4")))) + (build-system r-build-system) + (propagated-inputs + `(("r-digest" ,r-digest))) + (home-page "http://github.com/hadley/memoise") + (synopsis "Memoise functions for R") + (description + "This R package allows to cache the results of a function so that when +you call it again with the same arguments it returns the pre-computed value.") + (license license:expat))) -- cgit v1.2.3 From 834f7ff3c0e3266beb13dde7356420960d9ff074 Mon Sep 17 00:00:00 2001 From: Vicente Vera Parra Date: Tue, 15 Sep 2015 14:23:46 -0300 Subject: gnu: Add r-crayon. * gnu/packages/statistics.scm (r-crayon): New variable. --- gnu/packages/statistics.scm | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 1a99a09b48..cf172ab58a 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -789,3 +789,26 @@ understand the language at a deeper level.") "This R package allows to cache the results of a function so that when you call it again with the same arguments it returns the pre-computed value.") (license license:expat))) + +(define-public r-crayon + (package + (name "r-crayon") + (version "1.3.1") + (source (origin + (method url-fetch) + (uri (cran-uri "crayon" version)) + (sha256 + (base32 + "0d38fm06h272a8iqlc0d45m2rh36giwqw7mwq4z8hkp4vs975fmm")))) + (build-system r-build-system) + (propagated-inputs + `(("r-memoise" ,r-memoise))) + (home-page "https://github.com/gaborcsardi/crayon") + (synopsis "Colored terminal output for R") + (description + "Colored terminal output on terminals that support ANSI color and +highlight codes. It also works in Emacs ESS. ANSI color support is +automatically detected. Colors and highlighting can be combined and nested. +New styles can also be created easily. This package was inspired by the +\"chalk\" JavaScript project.") + (license license:expat))) -- cgit v1.2.3 From 5b9789a6ff16e0cbe951bed3a3f3dbd96fe706ec Mon Sep 17 00:00:00 2001 From: Vicente Vera Parra Date: Tue, 15 Sep 2015 14:24:17 -0300 Subject: gnu: Add r-testthat. * gnu/packages/statistics.scm (r-testthat): New variable. --- gnu/packages/statistics.scm | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index cf172ab58a..53d3e28d27 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -812,3 +812,24 @@ automatically detected. Colors and highlighting can be combined and nested. New styles can also be created easily. This package was inspired by the \"chalk\" JavaScript project.") (license license:expat))) + +(define-public r-testthat + (package + (name "r-testthat") + (version "0.10.0") + (source (origin + (method url-fetch) + (uri (cran-uri "testthat" version)) + (sha256 + (base32 + "0b3akwcx5mv9dmi8vssbk91hr3yrrdxd2fm6zhr31fnyz8kjx4pw")))) + (build-system r-build-system) + (propagated-inputs + `(("r-digest" ,r-digest) + ("r-crayon" ,r-crayon))) + (home-page "https://github.com/hadley/testthat") + (synopsis "Unit testing for R") + (description + "This package provides a unit testing system for R designed to be fun, +flexible and easy to set up.") + (license license:expat))) -- cgit v1.2.3 From ffd4b478510b770966f5e5478d818be97a4ae06d Mon Sep 17 00:00:00 2001 From: Vicente Vera Parra Date: Tue, 15 Sep 2015 14:24:46 -0300 Subject: gnu: Add r-r6. * gnu/packages/statistics.scm (r-r6): New variable. --- gnu/packages/statistics.scm | 29 +++++++++++++++++++++++++++++ 1 file changed, 29 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 53d3e28d27..9e23cc720f 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -833,3 +833,32 @@ New styles can also be created easily. This package was inspired by the "This package provides a unit testing system for R designed to be fun, flexible and easy to set up.") (license license:expat))) + +(define-public r-r6 + (package + (name "r-r6") + (version "2.1.1") + (source (origin + (method url-fetch) + (uri (cran-uri "R6" version)) + (sha256 + (base32 + "16qq35bgxgswf989yvsqkb6fv7srpf8n8dv2s2c0z9n6zgmwq66m")))) + (build-system r-build-system) + (propagated-inputs + `(("r-knitr" ,r-knitr) + ("r-microbenchmark" ,r-microbenchmark) + ("r-pryr" ,r-pryr) + ("r-testthat" ,r-testthat) + ("r-ggplot2" ,r-ggplot2) + ("r-scales" ,r-scales))) + (home-page "https://github.com/wch/R6/") + (synopsis "Classes with reference semantics in R") + (description + "The R6 package allows the creation of classes with reference semantics, +similar to R's built-in reference classes. Compared to reference classes, R6 +classes are simpler and lighter-weight, and they are not built on S4 classes +so they do not require the methods package. These classes allow public and +private members, and they support inheritance, even when the classes are +defined in different packages.") + (license license:expat))) -- cgit v1.2.3 From 2a3a8ae753ec5c327b6831140795ecc28c10af7b Mon Sep 17 00:00:00 2001 From: Vicente Vera Parra Date: Tue, 15 Sep 2015 14:25:14 -0300 Subject: gnu: Add r-dplyr. * gnu/packages/statistics.scm (r-dplyr): New variable. --- gnu/packages/statistics.scm | 32 ++++++++++++++++++++++++++++++++ 1 file changed, 32 insertions(+) (limited to 'gnu') diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 9e23cc720f..473b5c2393 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -862,3 +862,35 @@ so they do not require the methods package. These classes allow public and private members, and they support inheritance, even when the classes are defined in different packages.") (license license:expat))) + +(define-public r-dplyr + (package + (name "r-dplyr") + (version "0.4.3") + (source (origin + (method url-fetch) + (uri (cran-uri "dplyr" version)) + (sha256 + (base32 + "1p8rbn4p4yrx2840dapwiahf9iqa8gnvd35nyc200wfhmrxlqdlc")))) + (build-system r-build-system) + (propagated-inputs + `(("r-assertthat" ,r-assertthat) + ("r-r6" ,r-r6) + ("r-magrittr" ,r-magrittr) + ("r-lazyeval" ,r-lazyeval) + ("r-dbi" ,r-dbi))) + (native-inputs + `(("r-rcpp" ,r-rcpp) + ("r-bh" ,r-bh))) + (home-page "https://github.com/hadley/dplyr") + (synopsis "Tools for working with data frames in R") + (description + "dplyr is the next iteration of plyr. It is focussed on tools for +working with data frames. It has three main goals: 1) identify the most +important data manipulation tools needed for data analysis and make them easy +to use in R; 2) provide fast performance for in-memory data by writing key +pieces of code in C++; 3) use the same code interface to work with data no +matter where it is stored, whether in a data frame, a data table or +database.") + (license license:expat))) -- cgit v1.2.3 From 91781b7498c0b8aff259f0ae7c24701a10089ebc Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 21 Sep 2015 11:03:36 +0200 Subject: gnu: r-scales: Update to 0.3.0. * gnu/packages/statistics.scm (r-scales): Update to 0.3.0. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 473b5c2393..cbcef49153 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -431,13 +431,13 @@ using just two functions: melt and dcast (or acast).") (define-public r-scales (package (name "r-scales") - (version "0.2.5") + (version "0.3.0") (source (origin (method url-fetch) (uri (cran-uri "scales" version)) (sha256 - (base32 "12xrmn1vh64dl46bq7n7pa427aicb2ifjrby9in3m32nyvir0kac")))) + (base32 "1kkgpqzb0a6lnpblhcprr4qzyfk5lhicdv4639xs5cq16n7bkqgl")))) (build-system r-build-system) (propagated-inputs `(("r-dichromat" ,r-dichromat) -- cgit v1.2.3 From 667d90dfee10ee03dd14e0ef479355eed302adbf Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 21 Sep 2015 16:24:51 +0200 Subject: gnu: python2-ipython: Override terminado in propagated inputs. * gnu/packages/python.scm (python2-ipython)[inputs, propagated-inputs]: Override inherited "python-terminado" in propagated inputs instead of regular inputs. --- gnu/packages/python.scm | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index efda22b982..798a22f5df 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -3724,13 +3724,15 @@ computing.") `(#:tests? #f ,@(package-arguments ipython))) ;; Make sure we use custom python2-NAME packages. ;; FIXME: add pyreadline once available. + (propagated-inputs + `(("python2-terminado" ,python2-terminado) + ,@(alist-delete "python-terminado" + (package-propagated-inputs ipython)))) (inputs `(("python2-mock" ,python2-mock) ("python2-matplotlib" ,python2-matplotlib) - ("python2-terminado" ,python2-terminado) - ,@(alist-delete "python-terminado" - (alist-delete "python-matplotlib" - (package-inputs ipython)))))))) + ,@(alist-delete "python-matplotlib" + (package-inputs ipython))))))) (define-public python-isodate (package -- cgit v1.2.3 From 7ae7ca0e2a030de558862a1e6cc13d5813f510df Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Mon, 21 Sep 2015 19:42:10 -0400 Subject: gnu: recutils: Add libuuid to native-inputs. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/databases.scm (recutils)[native-inputs]: Add "libuuid". Signed-off-by: Ludovic Courtès --- gnu/packages/databases.scm | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) (limited to 'gnu') diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm index c11395926a..9036d0445b 100644 --- a/gnu/packages/databases.scm +++ b/gnu/packages/databases.scm @@ -284,7 +284,8 @@ pictures, sounds, or video.") (arguments '(#:parallel-tests? #f)) (native-inputs `(("emacs" ,emacs-no-x) - ("bc" ,bc))) + ("bc" ,bc) + ("libuuid", util-linux))) ;; TODO: Add more optional inputs. ;; FIXME: Our Bash doesn't have development headers (need for the 'readrec' -- cgit v1.2.3 From ee1c4cbaf97927df4b353bd3ab35c96256eea01f Mon Sep 17 00:00:00 2001 From: Mark H Weaver Date: Tue, 22 Sep 2015 13:54:43 -0400 Subject: gnu: linux-libre: Update to 4.2.1. * gnu/packages/linux.scm (linux-libre): Update to 4.2.1. --- gnu/packages/linux.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu') diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index be7eec8af6..97e8bdcaec 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -210,7 +210,7 @@ for SYSTEM, or #f if there is no configuration for SYSTEM." #f))) (define-public linux-libre - (let* ((version "4.2") + (let* ((version "4.2.1") (build-phase '(lambda* (#:key system inputs #:allow-other-keys #:rest args) ;; Apply the neat patch. @@ -283,7 +283,7 @@ for SYSTEM, or #f if there is no configuration for SYSTEM." (uri (linux-libre-urls version)) (sha256 (base32 - "0jfgbr9qc92bk7hyfdvw030xyic2bg834l8cxp25rw9qbbdck3rs")))) + "140cqnk1hyhavfra572wwzwz7pddczc78j8anbxyciw35kh8z2hl")))) (build-system gnu-build-system) (native-inputs `(("perl" ,perl) ("bc" ,bc) -- cgit v1.2.3