From 9495cf9a804e63b7173a78c22b9c91991b9520a6 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Fri, 13 May 2016 23:22:53 -0400 Subject: gnu: Rename letsencrypt to certbot. Upgrade certbot and python-acme to 0.6.0. * gnu/packages/tls.scm (letsencrypt): Rename to... (certbot): ... this. (letsencrypt): Inherit from certbot. [source]: Update to 0.6.0 [arguments]: Adjust paths. (python-acme, python2-acme): Update to 0.6.0. --- gnu/packages/tls.scm | 40 +++++++++++++++++++++++++--------------- 1 file changed, 25 insertions(+), 15 deletions(-) diff --git a/gnu/packages/tls.scm b/gnu/packages/tls.scm index 885552bcb7..f122e7e3ef 100644 --- a/gnu/packages/tls.scm +++ b/gnu/packages/tls.scm @@ -358,13 +358,16 @@ (define-public libressl (define-public python-acme (package (name "python-acme") - (version "0.5.0") + (version "0.6.0") (source (origin - (method url-fetch) - (uri (pypi-uri "acme" version)) + (method url-fetch) + (uri (string-append + "https://pypi.python.org/packages/" + "af/33/703e5ec3d7efde7c4d2fcea9cdf88953a33d4e72aafd5b0a330173a7b395/" + "acme-" version ".tar.gz")) (sha256 (base32 - "1g8scfkhs3l06588h73py81xb1gvkkdzaxanl21whcvdclycc186")))) + "1ipck25c6nr0x54w2cc8ziwjmyyrpyz6pc1y8xc9nqmxvw4n0kpc")))) (build-system python-build-system) (arguments `(#:phases @@ -414,16 +417,19 @@ (define-public python-acme (define-public python2-acme (package-with-python2 python-acme)) -(define-public letsencrypt +(define-public certbot (package - (name "letsencrypt") - (version "0.5.0") + (name "certbot") + (version "0.6.0") (source (origin (method url-fetch) - (uri (pypi-uri "letsencrypt" version)) + (uri (string-append + "https://pypi.python.org/packages/" + "fc/eb/7594bf16d89909a9d52c46edbeae669d4b2ee6e12453bd97e674d0371920/" + name "-" version ".tar.gz")) (sha256 (base32 - "0nnijs26kkw07yylszc97p3jw09y98j54xihjp0rprrbp1q2p2p3")))) + "0ba95cf6shmyhi4vzvk64vbkrmr8qvkn32k3xwb2iv7ybbfbgc40")))) (build-system python-build-system) (arguments `(#:python ,python-2 @@ -435,14 +441,14 @@ (define-public letsencrypt (man1 (string-append out "/share/man/man1")) (man7 (string-append out "/share/man/man7")) (info (string-append out "/info"))) - (substitute* "docs/man/letsencrypt.rst" - (("letsencrypt --help all") - (string-append out "/bin/letsencrypt" " --help all"))) + (substitute* "docs/man/certbot.rst" + (("certbot --help all") + (string-append out "/bin/certbot" " --help all"))) (and (zero? (system* "make" "-C" "docs" "man" "info")) - (install-file "docs/_build/texinfo/LetsEncrypt.info" info) - (install-file "docs/_build/man/letsencrypt.1" man1) - (install-file "docs/_build/man/letsencrypt.7" man7) + (install-file "docs/_build/texinfo/Certbot.info" info) + (install-file "docs/_build/man/certbot.1" man1) + (install-file "docs/_build/man/certbot.7" man7) #t))))))) ;; TODO: Add optional inputs for testing. (native-inputs @@ -475,6 +481,10 @@ (define-public letsencrypt (home-page "https://letsencrypt.org/") (license license:asl2.0))) +(define-public letsencrypt + (package (inherit certbot) + (name "letsencrypt"))) + (define-public perl-net-ssleay (package (name "perl-net-ssleay") -- cgit v1.2.3 From 247783685beb6bc683a987d09cd2cfa398cf1e54 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Sat, 14 May 2016 01:35:04 -0400 Subject: gnu: certbot: Update home page URL. This is a followup to commit 9495cf9a804e63b7173a78c22b9c91991b9520a6. * gnu/packages/tls.scm (certbot)[home-page]: Update to new location. --- gnu/packages/tls.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/tls.scm b/gnu/packages/tls.scm index f122e7e3ef..0bce811112 100644 --- a/gnu/packages/tls.scm +++ b/gnu/packages/tls.scm @@ -478,7 +478,7 @@ (define-public certbot (description "Tool to automatically receive and install X.509 certificates to enable TLS on servers. The client will interoperate with the Let’s Encrypt CA which will be issuing browser-trusted certificates for free.") - (home-page "https://letsencrypt.org/") + (home-page "https://certbot.eff.org/") (license license:asl2.0))) (define-public letsencrypt -- cgit v1.2.3 From 6d461b21f0c3ce88feb44d2610950d5c5cf6157d Mon Sep 17 00:00:00 2001 From: Ludovic Courtès Date: Thu, 12 May 2016 14:25:30 +0200 Subject: gnu: git: Fix search path specification for 'GIT_SSL_CAINFO'. Reported by ng0 . * gnu/packages/version-control.scm (git)[native-search-paths]: Add 'file-type'. --- gnu/packages/version-control.scm | 1 + 1 file changed, 1 insertion(+) diff --git a/gnu/packages/version-control.scm b/gnu/packages/version-control.scm index 796fd7ad67..d47b3e86d2 100644 --- a/gnu/packages/version-control.scm +++ b/gnu/packages/version-control.scm @@ -265,6 +265,7 @@ (define-public git ;; FIXME: This variable designates a single file; it is not a search path. (list (search-path-specification (variable "GIT_SSL_CAINFO") + (file-type 'regular) (files '("etc/ssl/certs/ca-certificates.crt"))))) (synopsis "Distributed version control system") -- cgit v1.2.3 From 52e1defe02446b5f5d52f31ca17dddd13fa6353e Mon Sep 17 00:00:00 2001 From: Ludovic Courtès Date: Sat, 14 May 2016 15:50:25 +0200 Subject: gnu: guix: Update development snapshot. * gnu/packages/package-management.scm (guix-devel): Update to e9017c9. Use http URL. --- gnu/packages/package-management.scm | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/gnu/packages/package-management.scm b/gnu/packages/package-management.scm index 0a765cd080..314dc90888 100644 --- a/gnu/packages/package-management.scm +++ b/gnu/packages/package-management.scm @@ -203,17 +203,19 @@ (define guix-devel ;; ;; Note: use a very short commit id; with a longer one, the limit on ;; hash-bang lines would be exceeded while running the tests. - (let ((commit "80627f51f0238b9450745f4e642172d059ca5bb5")) + (let ((commit "e9017c98d61f305b624bacaa30e8891ec0100980")) (package (inherit guix-0.10.0) (version (string-append "0.10.0-0." (string-take commit 4))) (source (origin (method git-fetch) (uri (git-reference - (url "git://git.sv.gnu.org/guix.git") + ;; "git://git.sv.gnu.org/guix.git" temporarily + ;; unavailable (XXX). + (url "http://git.savannah.gnu.org/r/guix.git") (commit commit))) (sha256 (base32 - "102gdbx5imx0zab7i5dwa1z9j1diblinaaja09dp3q30770iyxj9")) + "13mfk10cw6fk4diclzld56xwabshanxjcczdrjlj0wisaz32h3nl")) (file-name (string-append "guix-" version "-checkout")))) (arguments (substitute-keyword-arguments (package-arguments guix-0.10.0) -- cgit v1.2.3 From 6e94a574787895cd74edd4ecca3fa347ed457330 Mon Sep 17 00:00:00 2001 From: Ludovic Courtès Date: Sat, 14 May 2016 16:47:12 +0200 Subject: guix build: Do not show what to build when '-d' is used. * guix/scripts/build.scm (guix-build): Don't call 'show-what-to-build' when OPTS contains 'derivations-only?'. --- guix/scripts/build.scm | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/guix/scripts/build.scm b/guix/scripts/build.scm index 320ec39be2..c38ffe6e89 100644 --- a/guix/scripts/build.scm +++ b/guix/scripts/build.scm @@ -681,7 +681,8 @@ (define quiet? (_ #f)) opts))) - (unless (assoc-ref opts 'log-file?) + (unless (or (assoc-ref opts 'log-file?) + (assoc-ref opts 'derivations-only?)) (show-what-to-build store drv #:use-substitutes? (assoc-ref opts 'substitutes?) -- cgit v1.2.3 From c22a475725b99463de6e163a212c9398116c8aa0 Mon Sep 17 00:00:00 2001 From: Ludovic Courtès Date: Sat, 14 May 2016 16:56:21 +0200 Subject: guix build: Catch 'getaddrinfo-error' for '--log-file'. * guix/scripts/build.scm (log-url)[valid-url?]: Catch 'getaddrinfo-error'. --- guix/scripts/build.scm | 10 +++++++--- 1 file changed, 7 insertions(+), 3 deletions(-) diff --git a/guix/scripts/build.scm b/guix/scripts/build.scm index c38ffe6e89..a02a0d5792 100644 --- a/guix/scripts/build.scm +++ b/guix/scripts/build.scm @@ -65,9 +65,13 @@ (define* (log-url store file #:key (base-urls %default-log-urls)) found. Return #f if no build log was found." (define (valid-url? url) ;; Probe URL and return #t if it is accessible. - (guard (c ((http-get-error? c) #f)) - (close-port (http-fetch url #:buffered? #f)) - #t)) + (catch 'getaddrinfo-error + (lambda () + (guard (c ((http-get-error? c) #f)) + (close-port (http-fetch url #:buffered? #f)) + #t)) + (lambda _ + #f))) (define (find-url file) (let ((base (basename file))) -- cgit v1.2.3 From cd436bf05a8344acf4462f3602e7d360821a902a Mon Sep 17 00:00:00 2001 From: Ludovic Courtès Date: Sat, 14 May 2016 17:37:47 +0200 Subject: download: Support content-addressed mirrors. * guix/download.scm (%content-addressed-mirrors) (%content-addressed-mirror-file): New variables. * guix/download.scm (url-fetch)[builder]: Define 'value-from-environment. Pass #:hashes and #:content-addressed-mirrors to 'url-fetch'. Define "guix download hashes" environment variable. * guix/build/download.scm (url-fetch): Add #:content-addressed-mirrors and #:hashes. [content-addressed-urls]: New variable. Use it. --- guix/build/download.scm | 26 +++++++++++++++++++++++--- guix/download.scm | 42 +++++++++++++++++++++++++++++++++++------- 2 files changed, 58 insertions(+), 10 deletions(-) diff --git a/guix/build/download.scm b/guix/build/download.scm index fec4cec3e8..824e1c354a 100644 --- a/guix/build/download.scm +++ b/guix/build/download.scm @@ -605,10 +605,22 @@ (define (maybe-expand-mirrors uri mirrors) (else (list uri)))) -(define* (url-fetch url file #:key (mirrors '())) +(define* (url-fetch url file + #:key + (mirrors '()) (content-addressed-mirrors '()) + (hashes '())) "Fetch FILE from URL; URL may be either a single string, or a list of string denoting alternate URLs for FILE. Return #f on failure, and FILE -on success." +on success. + +When MIRRORS is defined, it must be an alist of mirrors; it is used to resolve +'mirror://' URIs. + +HASHES must be a list of algorithm/hash pairs, where each algorithm is a +symbol such as 'sha256 and each hash is a bytevector. +CONTENT-ADDRESSED-MIRRORS must be a list of procedures that, given a hash +algorithm and a hash, return a URL where the specified data can be retrieved +or #f." (define uri (append-map (cut maybe-expand-mirrors <> mirrors) (match url @@ -628,13 +640,21 @@ (define (fetch uri file) uri) #f))) + (define content-addressed-urls + (append-map (lambda (make-url) + (filter-map (match-lambda + ((hash-algo . hash) + (make-url hash-algo hash))) + hashes)) + content-addressed-mirrors)) + ;; Make this unbuffered so 'progress-proc' works as expected. _IOLBF means ;; '\n', not '\r', so it's not appropriate here. (setvbuf (current-output-port) _IONBF) (setvbuf (current-error-port) _IOLBF) - (let try ((uri uri)) + (let try ((uri (append uri content-addressed-urls))) (match uri ((uri tail ...) (or (fetch uri file) diff --git a/guix/download.scm b/guix/download.scm index 88f285dc0a..ff0bef3c1f 100644 --- a/guix/download.scm +++ b/guix/download.scm @@ -210,6 +210,22 @@ (define %mirror-file ;; 'object->string'. (plain-file "mirrors" (object->string %mirrors))) +(define %content-addressed-mirrors + ;; List of content-addressed mirrors. Each mirror is represented as a + ;; procedure that takes an algorithm (symbol) and a hash (bytevector), and + ;; returns a URL or #f. + ;; TODO: Add more. + '(list (lambda (algo hash) + ;; 'tarballs.nixos.org' supports several algorithms. + (string-append "http://tarballs.nixos.org/" + (symbol->string algo) "/" + (bytevector->nix-base32-string hash))))) + +(define %content-addressed-mirror-file + ;; Content-addressed mirrors stored in a file. + (plain-file "content-addressed-mirrors" + (object->string %content-addressed-mirrors))) + (define (gnutls-package) "Return the default GnuTLS package." (let ((module (resolve-interface '(gnu packages tls)))) @@ -258,12 +274,21 @@ (define builder %load-path))) #~#t) - (use-modules (guix build download)) + (use-modules (guix build download) + (guix base32)) + + (let ((value-from-environment (lambda (variable) + (call-with-input-string + (getenv variable) + read)))) + (url-fetch (value-from-environment "guix download url") + #$output + #:mirrors (call-with-input-file #$%mirror-file read) - (url-fetch (call-with-input-string (getenv "guix download url") - read) - #$output - #:mirrors (call-with-input-file #$%mirror-file read)))) + ;; Content-addressed mirrors. + #:hashes (value-from-environment "guix download hashes") + #:content-addressed-mirrors + (primitive-load #$%content-addressed-mirror-file))))) (let ((uri (and (string? url) (string->uri url)))) (if (or (and (string? url) (not uri)) @@ -278,14 +303,17 @@ (define builder #:hash hash #:modules '((guix build download) (guix build utils) - (guix ftp-client)) + (guix ftp-client) + (guix base32)) ;; Use environment variables and a fixed script ;; name so there's only one script in store for ;; all the downloads. #:script-name "download" #:env-vars - `(("guix download url" . ,(object->string url))) + `(("guix download url" . ,(object->string url)) + ("guix download hashes" + . ,(object->string `((,hash-algo . ,hash))))) ;; Honor the user's proxy settings. #:leaked-env-vars '("http_proxy" "https_proxy") -- cgit v1.2.3 From 8a7680a759c3eb549378310ac53a9f5032423dac Mon Sep 17 00:00:00 2001 From: Jan Nieuwenhuizen Date: Sat, 14 May 2016 10:13:21 +0200 Subject: gnu: cross-base: Add srfi-26 for glibc. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Fixes a regression introduced in commit efc4eb147512fa7a2c6d74d9b296cfc22b1ef198. * gnu/packages/cross-base.scm (cross-libc)[arguments]: Add (srfi srfi-26). Signed-off-by: Ludovic Courtès --- gnu/packages/cross-base.scm | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/gnu/packages/cross-base.scm b/gnu/packages/cross-base.scm index 73ac76a48a..4856069e0f 100644 --- a/gnu/packages/cross-base.scm +++ b/gnu/packages/cross-base.scm @@ -323,6 +323,11 @@ (define xlinux-headers ;; itself. #:implicit-cross-inputs? #f + ;; We need SRFI 26. + #:modules ((guix build gnu-build-system) + (guix build utils) + (srfi srfi-26)) + ,@(package-arguments glibc)) ((#:configure-flags flags) `(cons ,(string-append "--host=" target) -- cgit v1.2.3 From e6a905070ad4a5f6c726e94e04b4a60b324a0dfc Mon Sep 17 00:00:00 2001 From: 宋文武 Date: Sun, 15 May 2016 14:09:17 +0800 Subject: gnu: wxmaxima: Update to 16.04.2. * gnu/packages/maths.scm (wxmaxima): Update to 16.04.2. --- gnu/packages/maths.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 10b1e9be45..73104a3487 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -1588,7 +1588,7 @@ (define-public maxima (define-public wxmaxima (package (name "wxmaxima") - (version "15.04.0") + (version "16.04.2") (source (origin (method url-fetch) @@ -1596,7 +1596,7 @@ (define-public wxmaxima version "/" name "-" version ".tar.gz")) (sha256 (base32 - "1fm47ah4aw5qdjqhkz67w5fwhy8yfffa5z896crp0d3hk2bh4180")))) + "1fpqzk1921isiqrpgpf433ldq41924qs9sy99fl1zn5661b2l73n")))) (build-system gnu-build-system) (inputs `(("wxwidgets" ,wxwidgets) -- cgit v1.2.3 From e91fd7f591cfc41412095876a3beeff286074852 Mon Sep 17 00:00:00 2001 From: 宋文武 Date: Sun, 15 May 2016 18:24:15 +0800 Subject: gnu: love: Update to 0.10.1. * gnu/packages/game-development.scm (love): Update to 0.10.1. --- gnu/packages/game-development.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/game-development.scm b/gnu/packages/game-development.scm index 8bfd2f1cb0..f6b3c0bbb7 100644 --- a/gnu/packages/game-development.scm +++ b/gnu/packages/game-development.scm @@ -272,14 +272,14 @@ (define-public physfs (define-public love (package (name "love") - (version "0.10.0") + (version "0.10.1") (source (origin (method url-fetch) (uri (string-append "https://bitbucket.org/rude/love/downloads/" "love-" version "-linux-src.tar.gz")) (sha256 (base32 - "1r2n1nrw3hcdvy14fjbwz3l9swcy65v3lqwpj2frnkkcwncdz94p")))) + "1ys18m7c4994k5s7avqlf17sc2icx5zgvfplz504q1ka16hwkc52")))) (build-system gnu-build-system) (native-inputs `(("pkg-config" ,pkg-config))) -- cgit v1.2.3 From 277a7d82b84c0b9ae86a9466479c34548209b0bf Mon Sep 17 00:00:00 2001 From: Jan Nieuwenhuizen Date: Sun, 3 Apr 2016 12:56:11 +0200 Subject: gnu: libnotify: Add dependency on gobject-introspection. * gnu/packages/gnome.scm (libnotify)[native-inputs]: Add gobject-introspection. Signed-off-by: Leo Famulari --- gnu/packages/gnome.scm | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/gnu/packages/gnome.scm b/gnu/packages/gnome.scm index 83e4f83163..6b78d0f720 100644 --- a/gnu/packages/gnome.scm +++ b/gnu/packages/gnome.scm @@ -16,6 +16,7 @@ ;;; Copyright © 2016 Jochem Raat ;;; Copyright © 2016 Rene Saavedra ;;; Copyright © 2016 Kei Yamashita +;;; Copyright © 2016 Jan Nieuwenhuizen ;;; ;;; This file is part of GNU Guix. ;;; @@ -682,7 +683,8 @@ (define-public libnotify ("libpng" ,libpng))) (native-inputs `(("pkg-config" ,pkg-config) - ("glib" ,glib "bin"))) + ("glib" ,glib "bin") + ("gobject-introspection" ,gobject-introspection))) (home-page "https://developer-next.gnome.org/libnotify/") (synopsis "GNOME desktop notification library") -- cgit v1.2.3 From 9365ee1c464b1a4bda5325b9c5a16f9c09029d2a Mon Sep 17 00:00:00 2001 From: Jan Nieuwenhuizen Date: Sun, 3 Apr 2016 12:52:37 +0200 Subject: gnu: Add gnome-tweak-tool. * gnu/packages/patches/gnome-tweak-tool-search-paths.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/gnome.scm (gnome-tweak-tool): New variable. Signed-off-by: Leo Famulari --- gnu/local.mk | 1 + gnu/packages/gnome.scm | 43 ++++++++++++++++++ .../patches/gnome-tweak-tool-search-paths.patch | 52 ++++++++++++++++++++++ 3 files changed, 96 insertions(+) create mode 100644 gnu/packages/patches/gnome-tweak-tool-search-paths.patch diff --git a/gnu/local.mk b/gnu/local.mk index acb979067b..553e0f39b0 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -509,6 +509,7 @@ dist_patch_DATA = \ gnu/packages/patches/glibc-versioned-locpath.patch \ gnu/packages/patches/gmp-arm-asm-nothumb.patch \ gnu/packages/patches/gmp-faulty-test.patch \ + gnu/packages/patches/gnome-tweak-tool-search-paths.patch \ gnu/packages/patches/gnucash-price-quotes-perl.patch \ gnu/packages/patches/gobject-introspection-absolute-shlib-path.patch \ gnu/packages/patches/gobject-introspection-cc.patch \ diff --git a/gnu/packages/gnome.scm b/gnu/packages/gnome.scm index 6b78d0f720..8963e3fca6 100644 --- a/gnu/packages/gnome.scm +++ b/gnu/packages/gnome.scm @@ -5024,3 +5024,46 @@ (define-public libzapojit "Libzapojit is a GLib-based library for accessing online service APIs of Microsoft SkyDrive and Hotmail, using their REST protocols.") (license license:lgpl2.1+))) + +(define-public gnome-tweak-tool + (package + (name "gnome-tweak-tool") + (version "3.20.1") + (source (origin + (method url-fetch) + (uri (string-append "mirror://gnome/sources/gnome-tweak-tool/" + (version-major+minor version) "/" + "gnome-tweak-tool-" version ".tar.xz")) + (patches (list + (search-patch "gnome-tweak-tool-search-paths.patch"))) + (sha256 + (base32 + "1fj6wjvnjygzm9br3sw9gya6d18yly1rm69yaiar9spfbkvv4wai")))) + (build-system gnu-build-system) + (arguments + `(#:configure-flags '("--localstatedir=/tmp" + "--sysconfdir=/tmp") + #:imported-modules ((guix build python-build-system) + ,@%gnu-build-system-modules) + #:phases (modify-phases %standard-phases + (add-after 'install 'wrap + (@@ (guix build python-build-system) wrap))))) + (native-inputs + `(("intltool" ,intltool) + ("pkg-config" ,pkg-config))) + (inputs + `(("python" ,python-2) + ("python2-pygobject" ,python2-pygobject))) + (propagated-inputs + `(("libnotify" ,libnotify) + ("gobject-introspection" ,gobject-introspection) + ("gsettings-desktop-schemas" ,gsettings-desktop-schemas) + ("gtk+" ,gtk+))) + (synopsis "Customize advanced GNOME 3 options") + (home-page "https://wiki.gnome.org/action/show/Apps/GnomeTweakTool") + (description + "GNOME Tweak Tool allows adjusting advanced configuration settings in +GNOME 3. This includes things like the fonts used in user interface elements, +alternative user interface themes, changes in window management behavior, +GNOME Shell appearance and extension, etc.") + (license license:gpl3+))) diff --git a/gnu/packages/patches/gnome-tweak-tool-search-paths.patch b/gnu/packages/patches/gnome-tweak-tool-search-paths.patch new file mode 100644 index 0000000000..027c61b3af --- /dev/null +++ b/gnu/packages/patches/gnome-tweak-tool-search-paths.patch @@ -0,0 +1,52 @@ +Gnome-tweak-tool does not look at GSETTINGS_SCHEMA_PATH or XDG_DATA_DIRS, it +assumes that schemas are installed in one global directory +(GSETTINGS_SCHEMA_DIR/gsettingsschemadir). + +Guix/GuixSD uses a different directory for every gir package and has +packages pick-up files using XDG_DATA_DIRS. + +Upstream ticket: https://bugzilla.gnome.org/show_bug.cgi?id=764537 +janneke@gnu.org + +--- gnome-tweak-tool-3.18.1.orig/gtweak/gsettings.py 2015-04-08 15:21:32.000000000 +0200 ++++ gnome-tweak-tool-3.18.1/gtweak/gsettings.py 2016-04-03 11:26:38.658482704 +0200 +@@ -16,7 +16,8 @@ + # along with gnome-tweak-tool. If not, see . + + import logging +-import os.path ++import os ++import sys + import xml.dom.minidom + import gettext + +@@ -31,6 +32,13 @@ + class GSettingsMissingError(Exception): + pass + ++def file_from_path(path, file_name): ++ for dir in path: ++ f = os.path.join(dir, file_name) ++ if os.path.exists(f): ++ return f ++ return None ++ + class _GSettingsSchema: + def __init__(self, schema_name, schema_dir=None, schema_filename=None, **options): + if not schema_dir: +@@ -38,9 +46,14 @@ + if not schema_filename: + schema_filename = schema_name + ".gschema.xml" + ++ schema_prefix = os.path.join('glib-2.0', 'schemas') + schema_path = os.path.join(schema_dir, schema_filename) + if not os.path.exists(schema_path): +- logging.critical("Could not find schema %s" % schema_path) ++ schema_path = file_from_path(os.environ.get ('GSETTINGS_SCHEMA_PATH', '').split(os.path.pathsep), schema_filename) ++ if not (schema_path and os.path.exists(schema_path)): ++ schema_path = file_from_path(os.environ.get ('XDG_DATA_DIRS', '').split(os.path.pathsep), os.path.join(schema_prefix, schema_filename)) ++ if not (schema_path and os.path.exists(schema_path)): ++ logging.critical("Could not find schema %s" % schema_filename) + assert(False) + + self._schema_name = schema_name -- cgit v1.2.3 From d8f3795622c892abd0ac023e40166ad4cd53646a Mon Sep 17 00:00:00 2001 From: David Thompson Date: Sun, 15 May 2016 18:32:36 -0400 Subject: gnu: minetest: Update to 0.4.14. * gnu/packages/games.scm (minetest-data, minetest): Update to 0.4.14. --- gnu/packages/games.scm | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/gnu/packages/games.scm b/gnu/packages/games.scm index 75f926edce..1af40e9409 100644 --- a/gnu/packages/games.scm +++ b/gnu/packages/games.scm @@ -1,6 +1,6 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2013 John Darrington -;;; Copyright © 2014, 2015 David Thompson +;;; Copyright © 2014, 2015, 2016 David Thompson ;;; Copyright © 2014, 2015, 2016 Eric Bavier ;;; Copyright © 2014 Cyrill Schenkel ;;; Copyright © 2014 Sylvain Beucler @@ -642,7 +642,7 @@ (define-public mars (define minetest-data (package (name "minetest-data") - (version "0.4.13") + (version "0.4.14") (source (origin (method url-fetch) (uri (string-append @@ -651,7 +651,7 @@ (define minetest-data (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "04xnyfap75v3p818kpqb07xshqwqzpws5xjvw5m96qnd9x4725ld")))) + "11fzdh4icx2yvjfz1skdql0d0wxpzdr006k993v33x72s0q2ig7f")))) (build-system trivial-build-system) (native-inputs `(("source" ,source) @@ -683,7 +683,7 @@ (define minetest-data (define-public minetest (package (name "minetest") - (version "0.4.13") + (version "0.4.14") (source (origin (method url-fetch) (uri (string-append @@ -692,7 +692,7 @@ (define-public minetest (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "1xzrvsg0fpbj5p4pz6lls11m3ab4y2bnjlsm4gnw68x9006ffznp")))) + "0m3hhk5icx4y4gd970z7ya2013fq4vvqbjljmck62ik03baf8g90")))) (build-system cmake-build-system) (arguments '(#:configure-flags -- cgit v1.2.3 From b7ab191ddd73f1e74294c98bb2f6a9697ea8a556 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Thu, 17 Mar 2016 03:58:01 -0400 Subject: gnu: Add libbsd. * gnu/packages/libbsd.scm: New file. * gnu/local.mk (GNU_SYSTEM_MODULES): Add it. --- gnu/local.mk | 1 + gnu/packages/libbsd.scm | 47 +++++++++++++++++++++++++++++++++++++++++++++++ 2 files changed, 48 insertions(+) create mode 100644 gnu/packages/libbsd.scm diff --git a/gnu/local.mk b/gnu/local.mk index 553e0f39b0..229785b2db 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -188,6 +188,7 @@ GNU_SYSTEM_MODULES = \ gnu/packages/lego.scm \ gnu/packages/less.scm \ gnu/packages/lesstif.scm \ + gnu/packages/libbsd.scm \ gnu/packages/libcanberra.scm \ gnu/packages/libdaemon.scm \ gnu/packages/libedit.scm \ diff --git a/gnu/packages/libbsd.scm b/gnu/packages/libbsd.scm new file mode 100644 index 0000000000..3bfa2a3fec --- /dev/null +++ b/gnu/packages/libbsd.scm @@ -0,0 +1,47 @@ +;;; GNU Guix --- Functional package management for GNU +;;; Copyright © 2016 Leo Famulari +;;; +;;; 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 packages libbsd) + #:use-module (guix build-system gnu) + #:use-module (guix download) + #:use-module (guix licenses) + #:use-module (guix packages)) + +(define-public libbsd + (package + (name "libbsd") + (version "0.8.3") + (source (origin + (method url-fetch) + (uri (string-append "https://libbsd.freedesktop.org/releases/" + "libbsd-" version ".tar.xz")) + (sha256 + (base32 + "1a1l7afchlvvj2zfi7ajcg26bbkh5i98y2v5h9j5p1px9m7n6jwk")))) + (build-system gnu-build-system) + (synopsis "Utility functions from BSD systems") + (description "This library provides useful functions commonly found on BSD +systems, and lacking on others like GNU systems, thus making it easier to port +projects with strong BSD origins, without needing to embed the same code over +and over again on each project.") + (home-page "https://libbsd.freedesktop.org/wiki/") + ;; This package is a collection of third-party functions that were + ;; originally released under various non-copyleft licenses. + (license (list bsd-2 bsd-3 bsd-4 expat isc public-domain + (non-copyleft "file://COPYING" + "See COPYING in the distribution."))))) -- cgit v1.2.3 From 74dd0e483137ccdd3ed19e094811719ec69cf838 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sat, 14 May 2016 22:03:14 +0300 Subject: gnu: libidn: Update license. * gnu/packages/libidn.scm (libidn)[license]: Change the license to gpl2+ gpl3+ lgpl3+ fdl1.3+. --- gnu/packages/libidn.scm | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/gnu/packages/libidn.scm b/gnu/packages/libidn.scm index 382e14f0cc..053565c909 100644 --- a/gnu/packages/libidn.scm +++ b/gnu/packages/libidn.scm @@ -1,5 +1,6 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2012 Andreas Enge +;;; Copyright © 2016 Efraim Flashner ;;; ;;; This file is part of GNU Guix. ;;; @@ -40,5 +41,7 @@ (define-public libidn "libidn is a library implementing of the Stringprep, Punycode and IDNA specifications. These are used to encode and decode internationalized domain names. It includes native C, C# and Java libraries.") - (license lgpl2.1+) + ;; The C code is dual-licensed gpl2+ lgpl3+, the manual is fdl1.3+, + ;; the command line tool is gpl3+. + (license (list gpl2+ gpl3+ lgpl3+ fdl1.3+)) (home-page "http://www.gnu.org/software/libidn/"))) -- cgit v1.2.3 From 90cd0e138dc92101b1d832c490d868d85bb4184d Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sat, 14 May 2016 22:14:57 +0300 Subject: gnu: owncloud-client: Update to 2.2.0. * gnu/packages/owncloud.scm (owncloud-client): Update to 2.2.0. --- gnu/packages/owncloud.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/owncloud.scm b/gnu/packages/owncloud.scm index e75426e579..954e689f7d 100644 --- a/gnu/packages/owncloud.scm +++ b/gnu/packages/owncloud.scm @@ -34,14 +34,14 @@ (define-module (gnu packages owncloud) (define-public owncloud-client (package (name "owncloud-client") - (version "2.1.1") + (version "2.2.0") (source (origin (method url-fetch) (uri (string-append "https://download.owncloud.com/desktop/stable/" "owncloudclient-" version ".tar.xz")) (sha256 - (base32 "1jxi439qff4acvyvszjprj42kvzhlz255wv8g4p3jrf55svzwz2f")))) + (base32 "1ak7hq13hl7qndm3zz7hdfvw6930kmhjh27s1427g784vxcqb23q")))) (build-system cmake-build-system) (arguments `(#:phases -- cgit v1.2.3 From 3f61f926b9a7229becd8de8a48973b17e2784f98 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Thu, 12 May 2016 16:04:52 +0300 Subject: gnu: libinput: Update to 1.3.0. * gnu/packages/freedesktop.scm (libinput): Update to 1.3.0. --- gnu/packages/freedesktop.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/freedesktop.scm b/gnu/packages/freedesktop.scm index a610776096..acaeb43b41 100644 --- a/gnu/packages/freedesktop.scm +++ b/gnu/packages/freedesktop.scm @@ -82,14 +82,14 @@ (define-public xdg-utils (define-public libinput (package (name "libinput") - (version "1.2.0") + (version "1.3.0") (source (origin (method url-fetch) (uri (string-append "https://freedesktop.org/software/libinput/" name "-" version ".tar.xz")) (sha256 (base32 - "0b3f67xsy1s84cvzw22mjfkbcv6pj4p4yns4h3m0fmb7zqbvjm0p")))) + "1sn1s1bz06fa49izqkqf519sjclsvhf42i6slzx1w5hx4vxpb2lr")))) (build-system gnu-build-system) (native-inputs `(("pkg-config" ,pkg-config))) -- cgit v1.2.3 From 5c6fdaa9e15a91485e4d5f8d43d2918ec2b42d94 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Thu, 12 May 2016 16:22:20 +0300 Subject: gnu: exempi: Update to 2.3.0. * gnu/packages/freedesktop.scm (exempi): Update to 2.3.0. --- gnu/packages/freedesktop.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/freedesktop.scm b/gnu/packages/freedesktop.scm index acaeb43b41..722087484b 100644 --- a/gnu/packages/freedesktop.scm +++ b/gnu/packages/freedesktop.scm @@ -288,7 +288,7 @@ (define-public wayland (define-public exempi (package (name "exempi") - (version "2.2.2") + (version "2.3.0") (source (origin (method url-fetch) (uri (string-append @@ -296,7 +296,7 @@ (define-public exempi name "-" version ".tar.bz2")) (sha256 (base32 - "01vcd1mfn2s0iiq2cjyzgvnxx6kcq9cwra1iipijhs0vwvjx0yhf")))) + "0jcrv3w8m415cq8xi886hcxfqbrn5dczxbzybx9bhf3dbqsyv6nq")))) (build-system gnu-build-system) (arguments `(#:configure-flags (list (string-append "--with-boost=" -- cgit v1.2.3 From 9c0c77f833b64e5ce46d1b53a4fbbd0b0cb1d0c2 Mon Sep 17 00:00:00 2001 From: Kei Yamashita Date: Tue, 10 May 2016 18:15:54 -0400 Subject: gnu: Add gtkspell3. * gnu/packages/gtk.scm (gtkspell3): New variable. Signed-off-by: Efraim Flashner --- gnu/packages/gtk.scm | 29 +++++++++++++++++++++++++++++ 1 file changed, 29 insertions(+) diff --git a/gnu/packages/gtk.scm b/gnu/packages/gtk.scm index 7e81a81986..8abf16ef36 100644 --- a/gnu/packages/gtk.scm +++ b/gnu/packages/gtk.scm @@ -10,6 +10,7 @@ ;;; Copyright © 2015 David Hashe ;;; Copyright © 2016 Efraim Flashner ;;; Copyright © 2016 Fabian Harfert +;;; Copyright © 2016 Kei Yamashita ;;; ;;; This file is part of GNU Guix. ;;; @@ -41,6 +42,7 @@ (define-module (gnu packages gtk) #:use-module (gnu packages check) #:use-module (gnu packages compression) #:use-module (gnu packages docbook) + #:use-module (gnu packages enchant) #:use-module (gnu packages fontutils) #:use-module (gnu packages gettext) #:use-module (gnu packages ghostscript) @@ -1244,3 +1246,30 @@ (define-public murrine "Murrine is a cairo-based GTK+ theming engine. It is named after the glass artworks done by Venicians glass blowers.") (license license:gpl2+))) + +(define-public gtkspell3 + (package + (name "gtkspell3") + (version "3.0.8") + (source (origin + (method url-fetch) + (uri (string-append "mirror://sourceforge/gtkspell/" + version "/" name "-" version ".tar.gz")) + (sha256 + (base32 + "1zrz5pz4ryvcssk898liynmy2wyxgj95ak7mp2jv7x62yzihq6h1")))) + (build-system gnu-build-system) + (native-inputs + `(("intltool" ,intltool) + ("pkg-config" ,pkg-config))) + (inputs + `(("enchant" ,enchant) + ("gobject-introspection" ,gobject-introspection) + ("gtk+" ,gtk+) + ("pango" ,pango))) + (home-page "http://gtkspell.sourceforge.net") + (synopsis "Spell-checking addon for GTK's TextView widget") + (description + "GtkSpell provides word-processor-style highlighting and replacement of +misspelled words in a GtkTextView widget.") + (license license:gpl2+))) -- cgit v1.2.3 From 66056126ea15e7186636dcd31b1edf093ed9c72d Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Thu, 12 May 2016 16:36:00 +0300 Subject: gnu: libmbim: Update to 1.12.4. * gnu/packages/freedesktop.scm (libmbim): Update to 1.12.4. [home-page]: Use https. --- gnu/packages/freedesktop.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/freedesktop.scm b/gnu/packages/freedesktop.scm index 722087484b..c273f2aa90 100644 --- a/gnu/packages/freedesktop.scm +++ b/gnu/packages/freedesktop.scm @@ -448,7 +448,7 @@ (define-public accountsservice (define-public libmbim (package (name "libmbim") - (version "1.12.2") + (version "1.12.4") (source (origin (method url-fetch) (uri (string-append @@ -456,7 +456,7 @@ (define-public libmbim name "-" version ".tar.xz")) (sha256 (base32 - "0abv0h9c3kbw4bq1b9270sg189jcjj3x3wa91bj836ynwg9m34wl")))) + "0flpgzsqpjgybjkx4smbb4rjxf2w1xgd1v9gmz61rvl89qasznbv")))) (build-system gnu-build-system) (native-inputs `(("glib:bin" ,glib "bin") ; for glib-mkenums @@ -467,7 +467,7 @@ (define-public libmbim (inputs `(("libgudev" ,libgudev))) (synopsis "Library to communicate with MBIM-powered modems") - (home-page "http://www.freedesktop.org/wiki/Software/libmbim/") + (home-page "https://www.freedesktop.org/wiki/Software/libmbim/") (description "Libmbim is a GLib-based library for talking to WWAN modems and devices which speak the Mobile Interface Broadband Model (MBIM) protocol.") -- cgit v1.2.3 From 1fb8e074f1801d7ace96f8a3758ae391a151d802 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Thu, 12 May 2016 16:38:47 +0300 Subject: gnu: libqmi: Update to 1.14.2. * gnu/packages/freedesktop.scm (libqmi): Update to 1.14.2. --- gnu/packages/freedesktop.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/freedesktop.scm b/gnu/packages/freedesktop.scm index c273f2aa90..9bd080c7f9 100644 --- a/gnu/packages/freedesktop.scm +++ b/gnu/packages/freedesktop.scm @@ -479,7 +479,7 @@ (define-public libmbim (define-public libqmi (package (name "libqmi") - (version "1.12.8") + (version "1.14.2") (source (origin (method url-fetch) (uri (string-append @@ -487,7 +487,7 @@ (define-public libqmi name "-" version ".tar.xz")) (sha256 (base32 - "19w2zkm5xl6i3vm1xhjjclks4awas17gfbb2k5y66gwnkiykjfnj")))) + "0h009bzss4bal47nk21lyp4s3mmlcivhhaaj7r9229qvx85bi0v2")))) (build-system gnu-build-system) (native-inputs `(("glib:bin" ,glib "bin") ; for glib-mkenums -- cgit v1.2.3 From a2ccaa0d790004c1c303a4421f7494ef73b65bd5 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Thu, 12 May 2016 18:48:35 +0300 Subject: gnu: qemu: Update to 2.6.0. * gnu/packages/qemu.scm (qemu): Update to 2.6.0. [arguments]: Re-enable parallel tests. --- gnu/packages/qemu.scm | 9 +++------ 1 file changed, 3 insertions(+), 6 deletions(-) diff --git a/gnu/packages/qemu.scm b/gnu/packages/qemu.scm index 9e3fbf462c..6dd6ce4d76 100644 --- a/gnu/packages/qemu.scm +++ b/gnu/packages/qemu.scm @@ -55,20 +55,17 @@ (define (qemu-patch commit file-name sha256) (define-public qemu (package (name "qemu") - (version "2.5.1.1") + (version "2.6.0") (source (origin (method url-fetch) (uri (string-append "http://wiki.qemu-project.org/download/qemu-" version ".tar.bz2")) (sha256 (base32 - "1rpgr1v6gnsdb4bcxwn1krsz4d4h9xgvlg6ark648nkn8dp99n98")))) + "1v1lhhd6m59hqgmiz100g779rjq70pik5v4b3g936ci73djlmb69")))) (build-system gnu-build-system) (arguments - '(;; FIXME: On x86_64, the test 'check-qtest-x86_64' sometimes fails when - ;; parallel builds are enabled. - #:parallel-tests? #f - #:phases (alist-replace + '(#:phases (alist-replace 'configure (lambda* (#:key inputs outputs (configure-flags '()) #:allow-other-keys) -- cgit v1.2.3 From 2b193389d243c469e159d0ab5dfc86b5867db05d Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Thu, 12 May 2016 20:50:52 +0300 Subject: gnu: libical: Update to 2.0.0. * gnu/packages/calendar.scm (libical): Update to 2.0.0. [arguments]: Add configure-flag to add "/lib64" to the rpath. --- gnu/packages/calendar.scm | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/gnu/packages/calendar.scm b/gnu/packages/calendar.scm index 5ddd358607..ff57ba10b3 100644 --- a/gnu/packages/calendar.scm +++ b/gnu/packages/calendar.scm @@ -2,6 +2,7 @@ ;;; Copyright © 2015 David Thompson ;;; Copyright © 2015, 2016 Leo Famulari ;;; Copyright © 2016 Kei Yamashita +;;; Copyright © 2016 Efraim Flashner ;;; ;;; This file is part of GNU Guix. ;;; @@ -37,7 +38,7 @@ (define-module (gnu packages calendar) (define-public libical (package (name "libical") - (version "1.0.1") + (version "2.0.0") (source (origin (method url-fetch) (uri (string-append @@ -45,10 +46,14 @@ (define-public libical version "/libical-" version ".tar.gz")) (sha256 (base32 - "14lmjj63zyx88rf1z71l0v9ms4c2vpdhmixksjjxgywp5p2f7708")))) + "1njn2kr0rrjqv5g3hdhpdzrhankyj4fl1bgn76z3g4n1b7vi2k35")))) (build-system cmake-build-system) (arguments '(#:tests? #f ; test suite appears broken + #:configure-flags + (list (string-append "-DCMAKE_INSTALL_RPATH=" + (assoc-ref %outputs "out") "/lib:" + (assoc-ref %outputs "out") "/lib64")) #:phases (modify-phases %standard-phases (add-before 'configure 'patch-paths -- cgit v1.2.3 From e9eb24b1b25101439dbbafce3aa9ec0ce2e67c1a Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Thu, 12 May 2016 21:09:08 +0300 Subject: gnu: bluez: Update to 5.39. * gnu/packages/linux.scm (bluez): Update to 5.39. [source]: Use kernel mirror. --- gnu/packages/linux.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 192221de80..3462d287b5 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -2390,15 +2390,15 @@ (define-public libaio (define-public bluez (package (name "bluez") - (version "5.36") + (version "5.39") (source (origin (method url-fetch) (uri (string-append - "https://www.kernel.org/pub/linux/bluetooth/bluez-" + "mirror://kernel.org/linux/bluetooth/bluez-" version ".tar.xz")) (sha256 (base32 - "1wkqwmi5krr37mxcqqlp5m2xnw7vw70v3ww7j09vvlskxcdflhx3")))) + "0fsrf9rdmrdyx0vmcpfji4imjsvliawyy5sjb6b64myka28vrl91")))) (build-system gnu-build-system) (arguments '(#:configure-flags -- cgit v1.2.3 From 30897c60a4bb54936c228daf46e26377306da280 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Thu, 12 May 2016 21:38:56 +0300 Subject: gnu: mdadm: Update to 3.4. * gnu/packages/linux.scm (mdadm): Update to 3.4. [source]: Remove patch. * gnu/packages/patches/mdadm-gcc-4.9-fix.patch: Delete file. * gnu/local.mk (dist_patch_DATA): Remove it. --- gnu/local.mk | 1 - gnu/packages/linux.scm | 5 ++-- gnu/packages/patches/mdadm-gcc-4.9-fix.patch | 38 ---------------------------- 3 files changed, 2 insertions(+), 42 deletions(-) delete mode 100644 gnu/packages/patches/mdadm-gcc-4.9-fix.patch diff --git a/gnu/local.mk b/gnu/local.mk index 229785b2db..f366be40b4 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -620,7 +620,6 @@ dist_patch_DATA = \ gnu/packages/patches/matplotlib-setupext-tk.patch \ gnu/packages/patches/maxima-defsystem-mkdir.patch \ gnu/packages/patches/mcron-install.patch \ - gnu/packages/patches/mdadm-gcc-4.9-fix.patch \ gnu/packages/patches/mhash-keygen-test-segfault.patch \ gnu/packages/patches/mit-krb5-CVE-2015-8629.patch \ gnu/packages/patches/mit-krb5-CVE-2015-8630.patch \ diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 3462d287b5..48f7499453 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -2318,7 +2318,7 @@ (define-public libiec61883 (define-public mdadm (package (name "mdadm") - (version "3.3.2") + (version "3.4") (source (origin (method url-fetch) (uri (string-append @@ -2326,8 +2326,7 @@ (define-public mdadm version ".tar.xz")) (sha256 (base32 - "132vdvh3myjgcjn6i9w90ck16ddjxjcszklzkyvr4f5ifqd7wfhg")) - (patches (search-patches "mdadm-gcc-4.9-fix.patch")))) + "0248v9f28mrbwabl94ck22gfim29sqhkf70wrpfi52nk4x3bxl17")))) (build-system gnu-build-system) (inputs `(("udev" ,eudev))) diff --git a/gnu/packages/patches/mdadm-gcc-4.9-fix.patch b/gnu/packages/patches/mdadm-gcc-4.9-fix.patch deleted file mode 100644 index 222fd0ea32..0000000000 --- a/gnu/packages/patches/mdadm-gcc-4.9-fix.patch +++ /dev/null @@ -1,38 +0,0 @@ -From 68641cdb646eaa15099c1d6cfff1eaa5dd2ac841 Mon Sep 17 00:00:00 2001 -From: Jes Sorensen -Date: Tue, 24 Feb 2015 16:00:40 -0500 -Subject: [PATCH] write_super_imsm_spares(): C statements are terminated by ; - -Signed-off-by: Jes Sorensen -Signed-off-by: NeilBrown ---- - super-intel.c | 12 ++++++------ - 1 file changed, 6 insertions(+), 6 deletions(-) - -diff --git a/super-intel.c b/super-intel.c -index 819e0da..7f75b53 100644 ---- a/super-intel.c -+++ b/super-intel.c -@@ -5115,13 +5115,13 @@ static int write_super_imsm_spares(struct intel_super *super, int doclose) - __u32 sum; - struct dl *d; - -- spare->mpb_size = __cpu_to_le32(sizeof(struct imsm_super)), -- spare->generation_num = __cpu_to_le32(1UL), -+ spare->mpb_size = __cpu_to_le32(sizeof(struct imsm_super)); -+ spare->generation_num = __cpu_to_le32(1UL); - spare->attributes = MPB_ATTRIB_CHECKSUM_VERIFY; -- spare->num_disks = 1, -- spare->num_raid_devs = 0, -- spare->cache_size = mpb->cache_size, -- spare->pwr_cycle_count = __cpu_to_le32(1), -+ spare->num_disks = 1; -+ spare->num_raid_devs = 0; -+ spare->cache_size = mpb->cache_size; -+ spare->pwr_cycle_count = __cpu_to_le32(1); - - snprintf((char *) spare->sig, MAX_SIGNATURE_LENGTH, - MPB_SIGNATURE MPB_VERSION_RAID0); --- -2.4.3 - -- cgit v1.2.3 From 2f9e312a39618461b2efce0020e306fc3c112950 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Thu, 12 May 2016 22:01:44 +0300 Subject: gnu: iw: Update to 4.3. * gnu/packages/linux.scm (iw): Update to 4.3. [source]: Use kernel mirror. [home-page]: Update to new home-page. --- gnu/packages/linux.scm | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 48f7499453..84deae706f 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -1168,15 +1168,15 @@ (define-public libnl (define-public iw (package (name "iw") - (version "3.17") + (version "4.3") (source (origin (method url-fetch) (uri (string-append - "https://www.kernel.org/pub/software/network/iw/iw-" + "mirror://kernel.org/software/network/iw/iw-" version ".tar.xz")) (sha256 (base32 - "14zsapqhivk0ws5z21y1ys2c2czi05mzk7bl2yb7qxcfrnsjx9j8")))) + "085jyvrxzarvn5jl0fk618jjxy50nqx7ifngszc4jxk6a4ddibd6")))) (build-system gnu-build-system) (native-inputs `(("pkg-config" ,pkg-config))) (inputs `(("libnl" ,libnl))) @@ -1184,11 +1184,11 @@ (define-public iw `(#:make-flags (list (string-append "PREFIX=" (assoc-ref %outputs "out")) "CC=gcc") #:phases (alist-delete 'configure %standard-phases))) - (home-page "http://wireless.kernel.org/en/users/Documentation/iw") + (home-page "https://wireless.wiki.kernel.org/") (synopsis "Tool for configuring wireless devices") (description "iw is a new nl80211 based CLI configuration utility for wireless -devices. It replaces 'iwconfig', which is deprecated.") +devices. It replaces @code{iwconfig}, which is deprecated.") (license license:isc))) (define-public powertop -- cgit v1.2.3 From 9a12ca7771fdd88e45bb0b7de246bdf14b005f4f Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Thu, 12 May 2016 22:08:36 +0300 Subject: gnu: wireless-regdb: Update to 2016.05.02. * gnu/packages/linux.scm (wireless-regdb): Update to 2016.05.02. --- gnu/packages/linux.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 84deae706f..d489e7292b 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -1813,7 +1813,7 @@ (define-public crda (define-public wireless-regdb (package (name "wireless-regdb") - (version "2015.04.06") + (version "2016.05.02") (source (origin (method url-fetch) (uri (string-append @@ -1821,7 +1821,7 @@ (define-public wireless-regdb "wireless-regdb-" version ".tar.xz")) (sha256 (base32 - "0czi83k311fp27z42hxjm8vi88fsbc23mhavv96lkb4pmari0jjc")) + "07n6gcwfbddz3awbdflv3dhxjszsqq2lrdwih0a0ahcliac4qry9")) ;; We're building 'regulatory.bin' by ourselves. (snippet '(delete-file "regulatory.bin")))) -- cgit v1.2.3 From ec374039e428cd7ef82e36f6fa1fc28f1972a9ea Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Fri, 13 May 2016 08:13:27 +0300 Subject: gnu: postgresql: Update to 9.5.3. * gnu/packages/databases.scm (postgresql): Update to 9.5.3. --- gnu/packages/databases.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm index a8998d803d..1e39ea004b 100644 --- a/gnu/packages/databases.scm +++ b/gnu/packages/databases.scm @@ -327,14 +327,14 @@ (define-public mariadb (define-public postgresql (package (name "postgresql") - (version "9.5.2") + (version "9.5.3") (source (origin (method url-fetch) (uri (string-append "https://ftp.postgresql.org/pub/source/v" version "/postgresql-" version ".tar.bz2")) (sha256 (base32 - "0hbwwhh0pz0a6vf8j5bskiq7gmz9rwc9ywcqyhg5asshckj35lgq")))) + "1d500d2qsdzysnis6qi84xchnz5xh8kx8sjfmkbsijwaqlfw11bk")))) (build-system gnu-build-system) (arguments `(#:phases -- cgit v1.2.3 From 6747a852c5fb670039ca9f44808fff26754157f1 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Fri, 13 May 2016 08:27:38 +0300 Subject: gnu: tdb: Update to 1.3.9. * gnu/packages/databases.scm (tdb): Update to 1.3.9. --- gnu/packages/databases.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm index 1e39ea004b..f411d12367 100644 --- a/gnu/packages/databases.scm +++ b/gnu/packages/databases.scm @@ -455,14 +455,14 @@ (define-public sqlite (define-public tdb (package (name "tdb") - (version "1.3.8") + (version "1.3.9") (source (origin (method url-fetch) (uri (string-append "https://www.samba.org/ftp/tdb/tdb-" version ".tar.gz")) (sha256 (base32 - "1cg6gmpgn36dd4bsp3j9k3hyrm87d8hdigqyyqxw5jga4w2aq186")))) + "1ll4q17scax1arg12faj8p25jq1f7q9irc3pwla0ziymwqkgf0bi")))) (build-system gnu-build-system) (arguments '(#:phases (alist-replace -- cgit v1.2.3 From 3fef0a2fa1160927bc323d7712eca28453591c07 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Fri, 13 May 2016 08:56:00 +0300 Subject: gnu: unixodbc: Update to 2.3.4. * gnu/packages/databases.scm (unixodbc): Update to 2.3.4. --- gnu/packages/databases.scm | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm index f411d12367..57181f6e5f 100644 --- a/gnu/packages/databases.scm +++ b/gnu/packages/databases.scm @@ -817,14 +817,15 @@ (define-public perl-sql-tokenizer (define-public unixodbc (package (name "unixodbc") - (version "2.3.2") + (version "2.3.4") (source (origin (method url-fetch) (uri (string-append - "ftp://ftp.unixodbc.org/pub/unixODBC/unixODBC-" version ".tar.gz")) + "ftp://ftp.unixodbc.org/pub/unixODBC/unixODBC-" + version ".tar.gz")) (sha256 - (base32 "16jw5fq7wgfky6ak1h2j2pqx99jivsdl4q8aq6immpr55xs5jd4w")))) + (base32 "0f8y88rcc2akjvjv5y66yx7k0ms9h1s0vbcfy25j93didflhj59f")))) (build-system gnu-build-system) (synopsis "Data source abstraction library") (description "Unixodbc is a library providing an API with which to access -- cgit v1.2.3 From b4370be9deca08f8347fbb0e2fc07edb1d18acd4 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Wed, 11 May 2016 02:25:22 -0400 Subject: gnu: python-cryptography, python-cryptography-vectors: Update to 1.3.2. * gnu/packages/python.scm (python-cryptography): Update to 1.3.2. (python-cryptography-vectors): Update to 1.3.2. --- gnu/packages/python.scm | 22 ++++++++++++++-------- 1 file changed, 14 insertions(+), 8 deletions(-) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 7593fc71ac..c6643a6dd6 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -5837,16 +5837,18 @@ (define-public python2-pretend (define-public python-cryptography-vectors (package (name "python-cryptography-vectors") - (version "1.3.1") + (version "1.3.2") (source (origin (method url-fetch) - (uri (string-append "https://pypi.python.org/packages/source/c/" - "cryptography-vectors/cryptography_vectors-" - version ".tar.gz")) + (uri (string-append + "https://pypi.python.org/packages/" + "3f/fd/" + "5883a7fdfcdf6edec55c58605be99d8c36ce97a9b729763ea9cf30e761b7" + "/cryptography_vectors-" version ".tar.gz")) (sha256 (base32 - "1144l3ypz3bngxd59lb4y74xa401w92lhvvjgxzglmvbh8wzkcbb")))) + "0ss682bpgzdfy2vam8yhhrx7p5gnw89ydlvaswqp52za8sd8nsh0")))) (build-system python-build-system) (native-inputs `(("python-setuptools" ,python-setuptools))) @@ -5863,14 +5865,18 @@ (define-public python2-cryptography-vectors (define-public python-cryptography (package (name "python-cryptography") - (version "1.3.1") + (version "1.3.2") (source (origin (method url-fetch) - (uri (pypi-uri "cryptography" version)) + (uri (string-append + "https://pypi.python.org/packages/" + "04/da/" + "35f9a1d34dab5d777f65fb87731288f338ab0ae46a525ffdf0405b573dd0" + "/cryptography-" version ".tar.gz")) (sha256 (base32 - "1qjkrpfvxcyd0kal3zpm5y7f9p3y77ixn9jw8f4dqpgrw1sn3cxl")))) + "121067qdbzd0ir0nxjdf0kgai7qlsc9yh2xhrj4cavcn4y4gmapv")))) (build-system python-build-system) (inputs `(("openssl" ,openssl))) -- cgit v1.2.3 From 66395a6157e573450c691f4fe8fecec4dee8d5f7 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Mon, 16 May 2016 10:18:16 +0300 Subject: gnu: gmsh: Add missing inputs. * gnu/packages/maths.scm (gmsh)[inputs]: Add fontconfig, libxft. --- gnu/packages/maths.scm | 3 +++ 1 file changed, 3 insertions(+) diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 73104a3487..a7941187d1 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -664,6 +664,9 @@ (define-public gmsh ("glu" ,glu) ("libx11" ,libx11) ("libxext" ,libxext))) + (inputs + `(("fontconfig" ,fontconfig) + ("libxft" ,libxft))) (arguments `(#:configure-flags `("-DENABLE_METIS:BOOL=OFF" "-DENABLE_BUILD_SHARED:BOOL=ON" -- cgit v1.2.3 From 6b287c5c35fc95f5bae7df8107ae6639d67344b8 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Mon, 16 May 2016 12:10:49 +0300 Subject: download: Update debian mirrors. * guix/download.scm (mirrors)[debian]: Add Debian's archive to the Debian mirror list. --- guix/download.scm | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/guix/download.scm b/guix/download.scm index ff0bef3c1f..67c55aff33 100644 --- a/guix/download.scm +++ b/guix/download.scm @@ -202,7 +202,8 @@ (define %mirrors (debian "http://ftp.de.debian.org/debian/" "http://ftp.fr.debian.org/debian/" - "http://ftp.debian.org/debian/")))) + "http://ftp.debian.org/debian/" + "http://archive.debian.org/debian/")))) (define %mirror-file ;; Copy of the list of mirrors to a file. This allows us to keep a single -- cgit v1.2.3 From fd02719c7b7acb1ba4a268418a1f1f6879c5238d Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Mon, 16 May 2016 12:31:25 +0300 Subject: gnu: fvwm: Update to 2.6.6. * gnu/packages/fvwm.scm (fvwm): Update to 2.6.6. [source]: Change download location to Github. --- gnu/packages/fvwm.scm | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/gnu/packages/fvwm.scm b/gnu/packages/fvwm.scm index b994fbf6b6..933820e5fa 100644 --- a/gnu/packages/fvwm.scm +++ b/gnu/packages/fvwm.scm @@ -1,5 +1,6 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2015 Sou Bunnbu +;;; Copyright © 2016 Efraim Flashner ;;; ;;; This file is part of GNU Guix. ;;; @@ -33,15 +34,16 @@ (define-module (gnu packages fvwm) (define-public fvwm (package (name "fvwm") - (version "2.6.5") + (version "2.6.6") (source (origin (method url-fetch) (uri (string-append - "ftp://ftp.fvwm.org/pub/fvwm/version-2/fvwm-" - version ".tar.bz2")) + "https://github.com/fvwmorg/fvwm/releases/download/" + "version-" (string-join (string-split version #\.) "_") + "/" name "-" version ".tar.gz")) (sha256 (base32 - "1ks8igvmzm0m0sra05k8xzc8vkqy3gv1qskl6davw1irqnarjm11")))) + "0b6w0vk6cpqaz0ws3vl4by0mycv33r42a0m806j2h8avy9ghipn5")))) (build-system gnu-build-system) (native-inputs `(("perl" ,perl) -- cgit v1.2.3 From 284539ce86a0073ad65880ddf3f3fd7af981b8e7 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Mon, 16 May 2016 12:59:40 +0300 Subject: gnu: geeqie: Update source location. * gnu/packages/geeqie.scm (geeqie)[source]: Download from Github. [home-page]: Project has moved to new url. --- gnu/packages/geeqie.scm | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/gnu/packages/geeqie.scm b/gnu/packages/geeqie.scm index 9cc8f74255..7ea75aa3a0 100644 --- a/gnu/packages/geeqie.scm +++ b/gnu/packages/geeqie.scm @@ -1,5 +1,6 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2013 Ludovic Courtès +;;; Copyright © 2016 Efraim Flashner ;;; ;;; This file is part of GNU Guix. ;;; @@ -63,8 +64,9 @@ (define-public geeqie (version "1.1") (source (origin (method url-fetch) - (uri (string-append "mirror://sourceforge/geeqie/geeqie-" - version ".tar.gz")) + (uri (string-append "https://github.com/BestImageViewer/geeqie/" + "archive/" version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 "1kzy39z9505xkayyx7rjj2wda76xy3ch1s5z35zn8yli54ffhi2m")))) @@ -78,7 +80,7 @@ (define-public geeqie (native-inputs `(("intltool" ,intltool) ("pkg-config" ,pkg-config))) - (home-page "http://geeqie.sourceforge.net") + (home-page "http://www.geeqie.org/") (synopsis "Lightweight GTK+ based image viewer") (description "Geeqie is a lightweight GTK+ based image viewer for Unix like operating -- cgit v1.2.3 From bf512da1e42ffb5599199f22c5c5e4cc3dc8111e Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Mon, 16 May 2016 14:07:47 +0300 Subject: gnu: giblib: Add mirror for source. * gnu/packages/image.scm (giblib)[source]: Add a download mirror from slackbuilds. --- gnu/packages/image.scm | 10 +++++++--- 1 file changed, 7 insertions(+), 3 deletions(-) diff --git a/gnu/packages/image.scm b/gnu/packages/image.scm index 264a8c88ac..2d7d1060d5 100644 --- a/gnu/packages/image.scm +++ b/gnu/packages/image.scm @@ -501,9 +501,13 @@ (define-public giblib (version "1.2.4") (source (origin (method url-fetch) - (uri (string-append - "http://linuxbrit.co.uk/downloads/giblib-" - version ".tar.gz")) + (uri (list + (string-append + "http://linuxbrit.co.uk/downloads/giblib-" + version ".tar.gz") + (string-append + "https://sourceforge.net/projects/slackbuildsdirectlinks/" + "files/giblib/giblib-" version ".tar.gz"))) (sha256 (base32 "1b4bmbmj52glq0s898lppkpzxlprq9aav49r06j2wx4dv3212rhp")))) -- cgit v1.2.3 From 3a66217ff25250d9bad4039471d5407bf1b23dcf Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Mon, 16 May 2016 14:12:54 +0300 Subject: gnu: gkrellm: Update urls. * gnu/packages/gkrellm.scm (gkrellm)[source]: Download from new site. [home-page]: Update to new site. --- gnu/packages/gkrellm.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/gnu/packages/gkrellm.scm b/gnu/packages/gkrellm.scm index 31bca00889..ed83186ae8 100644 --- a/gnu/packages/gkrellm.scm +++ b/gnu/packages/gkrellm.scm @@ -1,5 +1,6 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2013 Andreas Enge +;;; Copyright © 2016 Efraim Flashner ;;; ;;; This file is part of GNU Guix. ;;; @@ -33,7 +34,7 @@ (define-public gkrellm (source (origin (method url-fetch) - (uri (string-append "http://members.dslextreme.com/users/billw/gkrellm/gkrellm-" + (uri (string-append "http://gkrellm.srcbox.net/releases/gkrellm-" version ".tar.bz2")) (sha256 (base32 @@ -57,7 +58,7 @@ (define-public gkrellm (list (string-append "INSTALLROOT=" out) "CC=gcc" "X11_LIBS = -lX11 -lSM -lICE -lgmodule-2.0")))) - (home-page "http://members.dslextreme.com/users/billw/gkrellm/gkrellm.html") + (home-page "http://gkrellm.srcbox.net/") (synopsis "System monitors") (description "GKrellM is a single process stack of system monitors which supports -- cgit v1.2.3 From d03f944614a86b447d9f7469526c95afbd012089 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Mon, 16 May 2016 14:18:21 +0300 Subject: gnu: guile-irregex: Update to 0.9.4. * gnu/packages/guile.scm (guile-irregex): Update to 0.9.4. --- gnu/packages/guile.scm | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/gnu/packages/guile.scm b/gnu/packages/guile.scm index cf79d4e255..74e58c44af 100644 --- a/gnu/packages/guile.scm +++ b/gnu/packages/guile.scm @@ -565,16 +565,15 @@ (define-public guile-minikanren (define-public guile-irregex (package (name "guile-irregex") - (version "0.9.3") + (version "0.9.4") (source (origin (method url-fetch) (uri (string-append "http://synthcode.com/scheme/irregex/irregex-" - version - ".tar.gz")) + version ".tar.gz")) (sha256 (base32 - "1b8jl7bycyl2ssp6sb1j24pp9hvqyxm85ki9bmwd50glyyjs5zay")))) + "0cmaqvqvyarcnnsyrl2p6vwyv1r3k1q7qw8p9zrlnz1vpbj7vb90")))) (build-system gnu-build-system) (arguments `(#:modules ((guix build utils) -- cgit v1.2.3 From a83e60466223b96b0553bc83e727ece26b1aa744 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Mon, 16 May 2016 14:28:53 +0300 Subject: gnu: hmmer: Update urls. * gnu/packages/bioinformatics.scm (hmmer)[source]: Project has moved to eddylab, with their downloads. [home-page]: Update to new homepage. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index c7bf03bcbc..6a2611e203 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -2094,7 +2094,7 @@ (define-public hmmer (source (origin (method url-fetch) (uri (string-append - "http://selab.janelia.org/software/hmmer" + "http://eddylab.org/software/hmmer" (version-prefix version 1) "/" version "/hmmer-" version ".tar.gz")) (sha256 @@ -2102,7 +2102,7 @@ (define-public hmmer "0djmgc0pfli0jilfx8hql1axhwhqxqb8rxg2r5rg07aw73sfs5nx")))) (build-system gnu-build-system) (native-inputs `(("perl" ,perl))) - (home-page "http://hmmer.janelia.org") + (home-page "http://hmmer.org/") (synopsis "Biosequence analysis using profile hidden Markov models") (description "HMMER is used for searching sequence databases for homologs of protein -- cgit v1.2.3 From 44877dcc66ee5bb38101e32a32b11069e02813f1 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Mon, 16 May 2016 14:31:06 +0300 Subject: gnu: hugs: Update urls. * gnu/packages/hugs.scm (hugs)[source]: Update url. [home-page]: Use https. --- gnu/packages/hugs.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/gnu/packages/hugs.scm b/gnu/packages/hugs.scm index 36be5aee4a..2dcc61f4de 100644 --- a/gnu/packages/hugs.scm +++ b/gnu/packages/hugs.scm @@ -1,5 +1,6 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2013 Nikita Karetnikov +;;; Copyright © 2016 Efraim Flashner ;;; ;;; This file is part of GNU Guix. ;;; @@ -29,7 +30,7 @@ (define-public hugs (source (origin (method url-fetch) - (uri (string-append "http://cvs.haskell.org/Hugs/downloads/2006-09/" + (uri (string-append "https://www.haskell.org/hugs/downloads/2006-09/" name "98-plus-" version ".tar.gz")) (sha256 (base32 @@ -67,7 +68,7 @@ (define-public hugs (("/bin/cp") (which "cp")))) %standard-phases) #:tests? #f)) ; no test target - (home-page "http://haskell.org/hugs") + (home-page "https://www.haskell.org/hugs/") (synopsis "Functional programming system based on Haskell 98") (description "Hugs 98 is an interpreter and programming environment for developing -- cgit v1.2.3 From 002528bca512c2f45a7880e09be7c655bba7d2b0 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 May 2016 13:08:20 +0200 Subject: gnu: rapicorn: Fix tests. * gnu/packages/graphics.scm (rapicorn)[arguments]: Add build phases "fix-tests" and "pre-check". Generalize "replace-/bin/ls" phase to "replace-fhs-paths". [propagated-inputs]: Add python2-enum34. [native-inputs]: Add xorg-server. --- gnu/packages/graphics.scm | 31 ++++++++++++++++++++++++------- 1 file changed, 24 insertions(+), 7 deletions(-) diff --git a/gnu/packages/graphics.scm b/gnu/packages/graphics.scm index d08542fd4a..ca99cd0302 100644 --- a/gnu/packages/graphics.scm +++ b/gnu/packages/graphics.scm @@ -295,15 +295,30 @@ (define-public rapicorn "1y51yjrpsihas1jy905m9p3r8iiyhq6bwi2690c564i5dnix1f9d")))) (build-system gnu-build-system) (arguments - `(;; FIXME: At least "testrcore1" fails. - #:tests? #f - #:phases + `(#:phases (modify-phases %standard-phases - (add-after 'unpack 'replace-/bin/ls + (add-after 'unpack 'fix-tests + (lambda _ + ;; Our grep does not support perl regular expressions. + (substitute* "taptool.sh" + (("grep -P") "grep -E")) + ;; Disable path tests because we cannot access /bin or /sbin. + (substitute* "rcore/tests/multitest.cc" + (("TCMP \\(Path::equals \\(\"/bin\"") "//")) + #t)) + (add-before 'check 'pre-check + (lambda _ + ;; The test suite requires a running X server (with DISPLAY + ;; number 99 or higher). + (system "Xvfb :99 &") + (setenv "DISPLAY" ":99") + #t)) + (add-after 'unpack 'replace-fhs-paths (lambda _ (substitute* (cons "Makefile.decl" (find-files "." "^Makefile\\.in$")) - (("/bin/ls") (which "ls"))) + (("/bin/ls") (which "ls")) + (("/usr/bin/env") (which "env"))) #t))))) ;; These libraries are listed in the "Required" section of the pkg-config ;; file. @@ -311,7 +326,8 @@ (define-public rapicorn `(("librsvg" ,librsvg) ("cairo" ,cairo) ("pango" ,pango) - ("libxml2" ,libxml2))) + ("libxml2" ,libxml2) + ("python2-enum34" ,python2-enum34))) (inputs `(("gdk-pixbuf" ,gdk-pixbuf) ("libpng" ,libpng-1.2) @@ -326,7 +342,8 @@ (define-public rapicorn ("doxygen" ,doxygen) ("graphviz" ,graphviz) ("intltool" ,intltool) - ("pkg-config" ,pkg-config))) + ("pkg-config" ,pkg-config) + ("xvfb" ,xorg-server))) (home-page "http://rapicorn.org") (synopsis "Toolkit for rapid development of user interfaces") (description -- cgit v1.2.3 From 81b98756a3164e6b0024b64ea5c90bbb615de12a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 14 May 2016 11:27:12 +0200 Subject: gnu: Add SBC. * gnu/packages/linux.scm (sbc): New variable. --- gnu/packages/linux.scm | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index d489e7292b..97514c7b8e 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -12,6 +12,7 @@ ;;; Copyright © 2016 Raymond Nicholson ;;; Copyright © 2016 Mathieu Lirzin ;;; Copyright © 2016 Nicolas Goaziou +;;; Copyright © 2016 Ricardo Wurmus ;;; ;;; This file is part of GNU Guix. ;;; @@ -2386,6 +2387,29 @@ (define-public libaio applications.") (license license:lgpl2.1+))) +(define-public sbc + (package + (name "sbc") + (version "1.3") + (source (origin + (method url-fetch) + (uri (string-append "https://www.kernel.org/pub/linux/bluetooth/" + name "-" version ".tar.xz")) + (sha256 + (base32 + "02ckd2z51z0h85qgv7x8vv8ybp5czm9if1z78411j53gaz7j4476")))) + (build-system gnu-build-system) + (inputs + `(("libsndfile" ,libsndfile))) + (native-inputs + `(("pkg-config" ,pkg-config))) + (home-page "https://www.kernel.org/pub/linux/bluetooth/") + (synopsis "Bluetooth subband audio codec") + (description + "The SBC is a digital audio encoder and decoder used to transfer data to +Bluetooth audio output devices like headphones or loudspeakers.") + (license license:gpl2+))) + (define-public bluez (package (name "bluez") -- cgit v1.2.3 From 8226c2717c9bf5730683ff70a4ffa801d3ac0617 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 5 May 2016 14:37:52 +0200 Subject: gnu:: java-swt: Use ant-build-system. * gnu/packages/java.scm (java-swt): Use ant-build-system. [native-inputs]: Remove JDK. --- gnu/packages/java.scm | 74 +++++++++++++++++++++++---------------------------- 1 file changed, 33 insertions(+), 41 deletions(-) diff --git a/gnu/packages/java.scm b/gnu/packages/java.scm index e715798691..ff785efad6 100644 --- a/gnu/packages/java.scm +++ b/gnu/packages/java.scm @@ -66,48 +66,41 @@ (define-public java-swt (sha256 (base32 "03mhzraikcs4fsz7d3h5af9pw1bbcfd6dglsvbk2ciwimy9zj30q")))) - (build-system gnu-build-system) + (build-system ant-build-system) (arguments - `(#:make-flags '("-f" "make_linux.mak") + `(#:jar-name "swt.jar" #:tests? #f ; no "check" target #:phases - (alist-replace - 'unpack - (lambda _ - (and (mkdir "swt") - (zero? (system* "unzip" (assoc-ref %build-inputs "source") "-d" "swt")) - (chdir "swt") - (mkdir "src") - (zero? (system* "unzip" "src.zip" "-d" "src")) - (chdir "src"))) - (alist-replace - 'build - (lambda* (#:key inputs outputs #:allow-other-keys) - (let ((lib (string-append (assoc-ref outputs "out") "/lib"))) - (setenv "JAVA_HOME" (assoc-ref inputs "jdk")) - - ;; Build shared libraries. Users of SWT have to set the system - ;; property swt.library.path to the "lib" directory of this - ;; package output. - (mkdir-p lib) - (setenv "OUTPUT_DIR" lib) - (zero? (system* "bash" "build.sh")) - - ;; build jar - (mkdir "build") - (for-each (lambda (file) - (format #t "Compiling ~s\n" file) - (system* "javac" "-d" "build" file)) - (find-files "." "\\.java")) - (zero? (system* "jar" "cvf" "swt.jar" "-C" "build" ".")))) - (alist-cons-after - 'install 'install-java-files - (lambda* (#:key outputs #:allow-other-keys) - (let ((java (string-append (assoc-ref outputs "out") - "/share/java"))) - (install-file "swt.jar" java) - #t)) - (alist-delete 'configure %standard-phases)))))) + (modify-phases %standard-phases + (replace 'unpack + (lambda* (#:key source #:allow-other-keys) + (and (mkdir "swt") + (zero? (system* "unzip" source "-d" "swt")) + (chdir "swt") + (mkdir "src") + (zero? (system* "unzip" "src.zip" "-d" "src"))))) + ;; The classpath contains invalid icecat jars. Since we don't need + ;; anything other than the JDK on the classpath, we can simply unset + ;; it. + (add-after 'configure 'unset-classpath + (lambda _ (unsetenv "CLASSPATH") #t)) + (add-before 'build 'build-native + (lambda* (#:key inputs outputs #:allow-other-keys) + (let ((lib (string-append (assoc-ref outputs "out") "/lib"))) + ;; Build shared libraries. Users of SWT have to set the system + ;; property swt.library.path to the "lib" directory of this + ;; package output. + (mkdir-p lib) + (setenv "OUTPUT_DIR" lib) + (with-directory-excursion "src" + (zero? (system* "bash" "build.sh")))))) + (add-after 'install 'install-native + (lambda* (#:key outputs #:allow-other-keys) + (let ((lib (string-append (assoc-ref outputs "out") "/lib"))) + (for-each (lambda (file) + (install-file file lib)) + (find-files "." "\\.so$")) + #t)))))) (inputs `(("xulrunner" ,icecat) ("gtk" ,gtk+-2) @@ -117,8 +110,7 @@ (define-public java-swt ("glu" ,glu))) (native-inputs `(("pkg-config" ,pkg-config) - ("unzip" ,unzip) - ("jdk" ,icedtea "jdk"))) + ("unzip" ,unzip))) (home-page "https://www.eclipse.org/swt/") (synopsis "Widget toolkit for Java") (description -- cgit v1.2.3 From 7d0c3c8d018a4aff4ce42f863ce81242555ab119 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Mon, 16 May 2016 17:36:58 +0300 Subject: gnu: python-pandas: Update to 0.18.1. * gnu/packages/python.scm (python-pandas): Update to 0.18.1. [native-inputs]: Remove python-setuptools. [properties]: Define python2-pandas. (python2-pandas)[native-inputs]: Add python2-setuptools. * gnu/packages/patches/python-pandas-fix-tslib-test-failure.patch: Delete file. * gnu/local.mk (dist_patch_DATA): Remove it. --- gnu/local.mk | 1 - .../python-pandas-fix-tslib-test-failure.patch | 141 --------------------- gnu/packages/python.scm | 28 ++-- 3 files changed, 14 insertions(+), 156 deletions(-) delete mode 100644 gnu/packages/patches/python-pandas-fix-tslib-test-failure.patch diff --git a/gnu/local.mk b/gnu/local.mk index f366be40b4..f64adebb41 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -705,7 +705,6 @@ dist_patch_DATA = \ gnu/packages/patches/python-paste-remove-website-test.patch \ gnu/packages/patches/python-paste-remove-timing-test.patch \ gnu/packages/patches/python2-pygobject-2-gi-info-type-error-domain.patch \ - gnu/packages/patches/python-pandas-fix-tslib-test-failure.patch \ gnu/packages/patches/qt4-ldflags.patch \ gnu/packages/patches/ratpoison-shell.patch \ gnu/packages/patches/readline-link-ncurses.patch \ diff --git a/gnu/packages/patches/python-pandas-fix-tslib-test-failure.patch b/gnu/packages/patches/python-pandas-fix-tslib-test-failure.patch deleted file mode 100644 index 62d6a38086..0000000000 --- a/gnu/packages/patches/python-pandas-fix-tslib-test-failure.patch +++ /dev/null @@ -1,141 +0,0 @@ -This patch is required to fix a test failure when python-dateutil version -2.5.2 or later is used. It is derived from the following commits: - -80ef4e06526b9b60cf24268454c9456585a790a3 -845ff974af6f7c3b3067cce8a7149b771c2be87 - -diff --git a/pandas/tseries/tests/test_tslib.py b/pandas/tseries/tests/test_tslib.py -index f0d5bf7..863bc6f 100644 ---- a/pandas/tseries/tests/test_tslib.py -+++ b/pandas/tseries/tests/test_tslib.py -@@ -474,6 +474,11 @@ def test_does_not_convert_mixed_integer(self): - good_date_string)) - - def test_parsers(self): -+ -+ # https://github.com/dateutil/dateutil/issues/217 -+ import dateutil -+ yearfirst = dateutil.__version__ >= LooseVersion('2.5.0') -+ - cases = {'2011-01-01': datetime.datetime(2011, 1, 1), - '2Q2005': datetime.datetime(2005, 4, 1), - '2Q05': datetime.datetime(2005, 4, 1), -@@ -527,20 +532,26 @@ def test_parsers(self): - } - - for date_str, expected in compat.iteritems(cases): -- result1, _, _ = tools.parse_time_string(date_str) -- result2 = to_datetime(date_str) -- result3 = to_datetime([date_str]) -- result4 = to_datetime(np.array([date_str], dtype=object)) -- result5 = Timestamp(date_str) -- result6 = DatetimeIndex([date_str])[0] -- result7 = date_range(date_str, freq='S', periods=1) -+ result1, _, _ = tools.parse_time_string(date_str, -+ yearfirst=yearfirst) -+ result2 = to_datetime(date_str, yearfirst=yearfirst) -+ result3 = to_datetime([date_str], yearfirst=yearfirst) -+ result4 = to_datetime(np.array([date_str], dtype=object), -+ yearfirst=yearfirst) -+ result6 = DatetimeIndex([date_str], yearfirst=yearfirst)[0] - self.assertEqual(result1, expected) - self.assertEqual(result2, expected) - self.assertEqual(result3, expected) - self.assertEqual(result4, expected) -- self.assertEqual(result5, expected) - self.assertEqual(result6, expected) -- self.assertEqual(result7, expected) -+ -+ # these really need to have yearfist, but we don't support -+ if not yearfirst: -+ result5 = Timestamp(date_str) -+ self.assertEqual(result5, expected) -+ result7 = date_range(date_str, freq='S', periods=1, -+ yearfirst=yearfirst) -+ self.assertEqual(result7, expected) - - # NaT - result1, _, _ = tools.parse_time_string('NaT') -@@ -589,23 +589,62 @@ def test_parsers_quarter_invalid(self): - self.assertRaises(ValueError, tools.parse_time_string, case) - - def test_parsers_dayfirst_yearfirst(self): -+ -+ # https://github.com/dateutil/dateutil/issues/217 -+ # this issue was closed -+ import dateutil -+ is_compat_version = dateutil.__version__ >= LooseVersion('2.5.2') -+ if is_compat_version: -+ dayfirst_yearfirst1 = datetime.datetime(2010, 12, 11) -+ dayfirst_yearfirst2 = datetime.datetime(2020, 12, 21) -+ else: -+ dayfirst_yearfirst1 = datetime.datetime(2010, 11, 12) -+ dayfirst_yearfirst2 = datetime.datetime(2020, 12, 21) -+ - # str : dayfirst, yearfirst, expected -- cases = {'10-11-12': [(False, False, datetime.datetime(2012, 10, 11)), -- (True, False, datetime.datetime(2012, 11, 10)), -- (False, True, datetime.datetime(2010, 11, 12)), -- (True, True, datetime.datetime(2010, 11, 12))], -- '20/12/21': [(False, False, datetime.datetime(2021, 12, 20)), -- (True, False, datetime.datetime(2021, 12, 20)), -- (False, True, datetime.datetime(2020, 12, 21)), -- (True, True, datetime.datetime(2020, 12, 21))]} -+ cases = {'10-11-12': [(False, False, False, -+ datetime.datetime(2012, 10, 11)), -+ (True, False, False, -+ datetime.datetime(2012, 11, 10)), -+ (False, True, False, -+ datetime.datetime(2010, 11, 12)), -+ (True, True, False, dayfirst_yearfirst1)], -+ '20/12/21': [(False, False, False, -+ datetime.datetime(2021, 12, 20)), -+ (True, False, False, -+ datetime.datetime(2021, 12, 20)), -+ (False, True, False, -+ datetime.datetime(2020, 12, 21)), -+ (True, True, True, dayfirst_yearfirst2)]} - - tm._skip_if_no_dateutil() - from dateutil.parser import parse - for date_str, values in compat.iteritems(cases): -- for dayfirst, yearfirst, expected in values: -- result1, _, _ = tools.parse_time_string(date_str, -- dayfirst=dayfirst, -- yearfirst=yearfirst) -+ for dayfirst, yearfirst, is_compat, expected in values: -+ -+ f = lambda x: tools.parse_time_string(x, -+ dayfirst=dayfirst, -+ yearfirst=yearfirst) -+ -+ # we now have an invalid parse -+ if is_compat and is_compat_version: -+ self.assertRaises(tslib.DateParseError, f, date_str) -+ -+ def f(date_str): -+ return to_datetime(date_str, dayfirst=dayfirst, -+ yearfirst=yearfirst) -+ -+ self.assertRaises(ValueError, f, date_str) -+ -+ def f(date_str): -+ return DatetimeIndex([date_str], dayfirst=dayfirst, -+ yearfirst=yearfirst)[0] -+ -+ self.assertRaises(ValueError, f, date_str) -+ -+ continue -+ -+ result1, _, _ = f(date_str) - - result2 = to_datetime(date_str, dayfirst=dayfirst, - yearfirst=yearfirst) -@@ -614,7 +653,6 @@ def test_parsers_dayfirst_yearfirst(self): - yearfirst=yearfirst)[0] - - # Timestamp doesn't support dayfirst and yearfirst -- - self.assertEqual(result1, expected) - self.assertEqual(result2, expected) - self.assertEqual(result3, expected) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index c6643a6dd6..6eb244356b 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -983,15 +983,16 @@ (define-public python2-parsedatetime (define-public python-pandas (package (name "python-pandas") - (version "0.18.0") + (version "0.18.1") (source (origin (method url-fetch) - (uri (pypi-uri "pandas" version)) + (uri (string-append + "https://pypi.python.org/packages/11/09/" + "e66eb844daba8680ddff26335d5b4fead77f60f957678243549a8dd4830d/" + "pandas-" version ".tar.gz")) (sha256 - (base32 "050qw0ap5bhyv5flp78x3lcq1dlminl3xaj6kbrm0jqmx0672xf9")) - (patches (search-patches - "python-pandas-fix-tslib-test-failure.patch")))) + (base32 "1ckpxrvvjj6zxmn68icd9hib8qcpx9b35f6izxnr25br5ilq7r6j")))) (build-system python-build-system) (propagated-inputs `(("python-numpy" ,python-numpy))) @@ -999,8 +1000,7 @@ (define-public python-pandas `(("python-pytz" ,python-pytz) ("python-dateutil" ,python-dateutil-2))) (native-inputs - `(("python-nose" ,python-nose) - ("python-setuptools" ,python-setuptools))) + `(("python-nose" ,python-nose))) (home-page "http://pandas.pydata.org") (synopsis "Data structures for data analysis, time series, and statistics") (description @@ -1009,15 +1009,15 @@ (define-public python-pandas multidimensional, potentially heterogeneous) and time series data both easy and intuitive. It aims to be the fundamental high-level building block for doing practical, real world data analysis in Python.") - (license bsd-3))) + (license bsd-3) + (properties `((python2-variant . ,(delay python2-pandas)))))) (define-public python2-pandas - (let ((pandas (package-with-python2 python-pandas))) - (package (inherit pandas) - (propagated-inputs - `(("python2-numpy" ,python2-numpy) - ,@(alist-delete "python-numpy" - (package-propagated-inputs pandas))))))) + (let ((base (package-with-python2 (strip-python2-variant python-pandas)))) + (package + (inherit base) + (native-inputs `(("python2-setuptools" ,python2-setuptools) + ,@(package-inputs base)))))) (define-public python-tzlocal (package -- cgit v1.2.3 From 99404fff9f8be0478191dfd5a4ebbb5822527172 Mon Sep 17 00:00:00 2001 From: Alex Kost Date: Sun, 8 May 2016 11:24:19 +0300 Subject: gnu: mu: Use 'modify-phases'. * gnu/packages/mail.scm (mu): Use 'modify-phases'. --- gnu/packages/mail.scm | 25 +++++++++++++------------ 1 file changed, 13 insertions(+), 12 deletions(-) diff --git a/gnu/packages/mail.scm b/gnu/packages/mail.scm index b127419d7b..a2af7c7f97 100644 --- a/gnu/packages/mail.scm +++ b/gnu/packages/mail.scm @@ -13,6 +13,7 @@ ;;; Copyright © 2016 Al McElrath ;;; Copyright © 2016 Leo Famulari ;;; Copyright © 2016 Lukas Gradl +;;; Copyright © 2016 Alex Kost ;;; ;;; This file is part of GNU Guix. ;;; @@ -364,18 +365,18 @@ (define-public mu ("gmime" ,gmime) ("tzdata" ,tzdata))) ;for mu/test/test-mu-query.c (arguments - '(#:phases (alist-cons-after - 'unpack 'autoreconf - (lambda _ - (zero? (system* "autoreconf" "-vi"))) - (alist-cons-before - 'check 'check-tz-setup - (lambda* (#:key inputs #:allow-other-keys) - ;; For mu/test/test-mu-query.c - (setenv "TZDIR" - (string-append (assoc-ref inputs "tzdata") - "/share/zoneinfo"))) - %standard-phases)))) + '(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'autoreconf + (lambda _ + (zero? (system* "autoreconf" "-vi")))) + (add-before 'check 'check-tz-setup + (lambda* (#:key inputs #:allow-other-keys) + ;; For mu/test/test-mu-query.c + (setenv "TZDIR" + (string-append (assoc-ref inputs "tzdata") + "/share/zoneinfo")) + #t))))) (home-page "http://www.djcbsoftware.nl/code/mu/") (synopsis "Quickly find emails") (description -- cgit v1.2.3 From 789bda83d2f356a55a2c65ff1b4ffe3431fc11b3 Mon Sep 17 00:00:00 2001 From: Alex Kost Date: Sun, 8 May 2016 12:23:37 +0300 Subject: gnu: mu: Install emacs files in a proper place. * gnu/packages/mail.scm (mu)[arguments]: Add 'patch-configure.ac' phase to avoid adding "mu4e" sub-directory to 'lispdir' variable. --- gnu/packages/mail.scm | 11 ++++++++++- 1 file changed, 10 insertions(+), 1 deletion(-) diff --git a/gnu/packages/mail.scm b/gnu/packages/mail.scm index a2af7c7f97..526e63829d 100644 --- a/gnu/packages/mail.scm +++ b/gnu/packages/mail.scm @@ -367,7 +367,16 @@ (define-public mu (arguments '(#:phases (modify-phases %standard-phases - (add-after 'unpack 'autoreconf + (add-after 'unpack 'patch-configure.ac + ;; By default, elisp code goes to "share/emacs/site-lisp/mu4e", + ;; so our Emacs package can't find it. Setting "--with-lispdir" + ;; configure flag doesn't help because "mu4e" will be added to + ;; the lispdir anyway, so we have to modify "configure.ac". + (lambda _ + (substitute* "configure.ac" + (("^ +lispdir=.*") "")) + #t)) + (add-after 'patch-configure.ac 'autoreconf (lambda _ (zero? (system* "autoreconf" "-vi")))) (add-before 'check 'check-tz-setup -- cgit v1.2.3 From 704f2196688e2b257501e47657f728b7b6fa9c6a Mon Sep 17 00:00:00 2001 From: Alex Kost Date: Sun, 8 May 2016 12:27:50 +0300 Subject: gnu: mu: Install emacs autoloads. * gnu/packages/mail.scm (mu)[arguments]: Add 'install-emacs-autoloads' phase. Use appropriate modules and imported-modules. --- gnu/packages/mail.scm | 14 +++++++++++++- 1 file changed, 13 insertions(+), 1 deletion(-) diff --git a/gnu/packages/mail.scm b/gnu/packages/mail.scm index 526e63829d..76efceacd2 100644 --- a/gnu/packages/mail.scm +++ b/gnu/packages/mail.scm @@ -365,7 +365,12 @@ (define-public mu ("gmime" ,gmime) ("tzdata" ,tzdata))) ;for mu/test/test-mu-query.c (arguments - '(#:phases + `(#: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 (add-after 'unpack 'patch-configure.ac ;; By default, elisp code goes to "share/emacs/site-lisp/mu4e", @@ -385,6 +390,13 @@ (define-public mu (setenv "TZDIR" (string-append (assoc-ref inputs "tzdata") "/share/zoneinfo")) + #t)) + (add-after 'install 'install-emacs-autoloads + (lambda* (#:key outputs #:allow-other-keys) + (emacs-generate-autoloads + "mu4e" + (string-append (assoc-ref outputs "out") + "/share/emacs/site-lisp")) #t))))) (home-page "http://www.djcbsoftware.nl/code/mu/") (synopsis "Quickly find emails") -- cgit v1.2.3 From 47c96a577d82034d5a7b0d1062faf4ad0dd097d3 Mon Sep 17 00:00:00 2001 From: Alex Kost Date: Sun, 8 May 2016 12:29:11 +0300 Subject: gnu: mu: Update to 0.9.16. * gnu/packages/mail.scm (%mu-gtester-patch): Remove. (mu): Update to 0.9.16. [source]: Remove 'patches'. --- gnu/packages/mail.scm | 14 ++------------ 1 file changed, 2 insertions(+), 12 deletions(-) diff --git a/gnu/packages/mail.scm b/gnu/packages/mail.scm index 76efceacd2..e86afb2f2d 100644 --- a/gnu/packages/mail.scm +++ b/gnu/packages/mail.scm @@ -326,19 +326,10 @@ (define-public offlineimap repository and Maildir/IMAP as LOCAL repository.") (license gpl2+))) -(define %mu-gtester-patch - ;; Ensure tests have unique names, to placate GLib 2.6's gtester. - (origin - (method url-fetch) - (uri "https://github.com/djcb/mu/commit/b44039ed.patch") - (sha256 - (base32 - "165hryqqhx3wah8a4f5jaq465azx1pm9r4jid7880pys9gd88qlv")))) - (define-public mu (package (name "mu") - (version "0.9.13") + (version "0.9.16") (source (origin (method url-fetch) (uri (string-append "https://github.com/djcb/mu/archive/v" @@ -346,8 +337,7 @@ (define-public mu (file-name (string-append "mu-" version ".tar.gz")) (sha256 (base32 - "0wj33pma8xgjvn2akk7khzbycwn4c9sshxvzdph9dnpy7gyqxj51")) - (patches (list %mu-gtester-patch)))) + "0p7hqri1r1x6750x138cc29mh81kdav2dcim26y58s8an206h25g")))) (build-system gnu-build-system) (native-inputs `(("pkg-config" ,pkg-config) -- cgit v1.2.3 From 80ed14d38f098f25f87efb01288cd6df8b307b7b Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Wed, 4 May 2016 00:43:36 +0200 Subject: gnu: asymptote: Install Emacs data. * gnu/packages/plotutils.scm (asymptote)[arguments]: Add a phase to install Emacs-Lisp files in an appropriate place. Signed-off-by: Alex Kost --- gnu/packages/plotutils.scm | 27 +++++++++++++++++++++++---- 1 file changed, 23 insertions(+), 4 deletions(-) diff --git a/gnu/packages/plotutils.scm b/gnu/packages/plotutils.scm index 3fdd539835..ef61239cab 100644 --- a/gnu/packages/plotutils.scm +++ b/gnu/packages/plotutils.scm @@ -25,6 +25,7 @@ (define-module (gnu packages plotutils) #:use-module (guix build-system gnu) #:use-module (gnu packages algebra) #:use-module (gnu packages bdw-gc) + #:use-module (gnu packages emacs) #:use-module (gnu packages xorg) #:use-module (gnu packages image) #:use-module (gnu packages ghostscript) @@ -188,6 +189,7 @@ (define-public asymptote `(("gs" ,ghostscript) ;For tests ("texinfo" ,texinfo) ;For generating documentation ("texlive" ,texlive) ;For tests and documentation + ("emacs" ,emacs-no-x) ("perl" ,perl))) (inputs `(("fftw" ,fftw) @@ -198,7 +200,13 @@ (define-public asymptote ("readline" ,readline) ("zlib" ,zlib))) (arguments - `(#:configure-flags + `(#:modules ((guix build emacs-utils) + (guix build gnu-build-system) + (guix build utils) + (srfi srfi-26)) + #:imported-modules (,@%gnu-build-system-modules + (guix build emacs-utils)) + #:configure-flags (list (string-append "--enable-gc=" (assoc-ref %build-inputs "libgc")) (string-append "--with-latex=" (assoc-ref %outputs "out") @@ -210,15 +218,26 @@ (define-public asymptote (modify-phases %standard-phases (add-before 'build 'patch-pdf-viewer (lambda _ - ;; Default to a free pdf viewer + ;; Default to a free pdf viewer. (substitute* "settings.cc" (("defaultPDFViewer=\"acroread\"") - "defaultPDFViewer=\"gv\"")))) + "defaultPDFViewer=\"gv\"")) + #t)) (add-before 'check 'set-HOME ;; Some tests require write access to $HOME, otherwise leading to ;; "failed to create directory /homeless-shelter/.asy" error. (lambda _ - (setenv "HOME" "/tmp")))))) + (setenv "HOME" "/tmp") + #t)) + (add-after 'install 'install-Emacs-data + (lambda* (#:key outputs #:allow-other-keys) + ;; Install related Emacs libraries into an appropriate location. + (let* ((out (assoc-ref outputs "out")) + (lisp-dir (string-append out "/share/emacs/site-lisp"))) + (for-each (cut install-file <> lisp-dir) + (find-files "." "\\.el$")) + (emacs-generate-autoloads ,name lisp-dir)) + #t))))) (home-page "http://asymptote.sourceforge.net") (synopsis "Script-based vector graphics language") (description -- cgit v1.2.3 From f17a54475656f16867767ecfd512552e5f547cf1 Mon Sep 17 00:00:00 2001 From: Alex Griffin Date: Sat, 7 May 2016 12:16:39 -0500 Subject: gnu: Add utfcpp. * gnu/packages/textutils.scm (utfcpp): New variable. Signed-off-by: Alex Kost --- gnu/packages/textutils.scm | 44 +++++++++++++++++++++++++++++++++++++++++++- 1 file changed, 43 insertions(+), 1 deletion(-) diff --git a/gnu/packages/textutils.scm b/gnu/packages/textutils.scm index f6735a43e0..080c95ba1c 100644 --- a/gnu/packages/textutils.scm +++ b/gnu/packages/textutils.scm @@ -4,6 +4,7 @@ ;;; Copyright © 2015, 2016 Ben Woodcroft ;;; Copyright © 2015 Roel Janssen ;;; Copyright © 2016 Jelle Licht +;;; Copyright © 2016 Alex Griffin ;;; ;;; This file is part of GNU Guix. ;;; @@ -27,8 +28,10 @@ (define-module (gnu packages textutils) #:use-module (guix git-download) #:use-module (guix build-system gnu) #:use-module (guix build-system cmake) + #:use-module (guix build-system trivial) #:use-module (gnu packages autotools) - #:use-module (gnu packages python)) + #:use-module (gnu packages python) + #:use-module (gnu packages zip)) (define-public recode (package @@ -328,3 +331,42 @@ (define-public antiword to everybody, because they believe that everybody runs Windows and therefore runs Word\".") (license license:gpl2+))) + +(define-public utfcpp + (package + (name "utfcpp") + (version "2.3.4") + (source (origin + (method url-fetch) + (uri + (string-append + "mirror://sourceforge/project/utfcpp/utf8cpp_2x/Release%20" + version "/utf8_v" + (string-map (lambda (x) (if (eq? x #\.) #\_ x)) version) + ".zip")) + (file-name (string-append name "-" version ".zip")) + (sha256 + (base32 + "1vqhs0aipcvvdrwcs7h3jsryg6mgbmc4s34n5cm6d36q4nxwwwrk")))) + (build-system trivial-build-system) + (arguments + `(#:modules ((guix build utils)) + #:builder + (begin + (use-modules (guix build utils)) + (let ((source (assoc-ref %build-inputs "source")) + (out (assoc-ref %outputs "out")) + (unzip (string-append (assoc-ref %build-inputs "unzip") + "/bin/unzip"))) + (mkdir-p out) + (with-directory-excursion out + (system* unzip source) + (mkdir-p "share/doc") + (rename-file "doc" "share/doc/utfcpp") + (rename-file "source" "include")))))) + (native-inputs `(("unzip" ,unzip))) + (home-page "https://github.com/nemtrif/utfcpp") + (synopsis "Portable C++ library for handling UTF-8") + (description "UTF8-CPP is a C++ library for handling UTF-8 encoded text +in a portable way.") + (license license:boost1.0))) -- cgit v1.2.3 From d3699b311b01b09d37640ed613fa6094059ed72f Mon Sep 17 00:00:00 2001 From: Alex Griffin Date: Sat, 7 May 2016 12:20:47 -0500 Subject: gnu: Add ledger. * gnu/packages/finance.scm (ledger): New variable. Co-authored-by: Alex Kost --- gnu/packages/finance.scm | 106 +++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 106 insertions(+) diff --git a/gnu/packages/finance.scm b/gnu/packages/finance.scm index e9487d4207..b511d2c951 100644 --- a/gnu/packages/finance.scm +++ b/gnu/packages/finance.scm @@ -1,6 +1,7 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2015 Andreas Enge ;;; Copyright © 2016 Efraim Flashner +;;; Copyright © 2016 Alex Griffin ;;; ;;; This file is part of GNU Guix. ;;; @@ -23,13 +24,21 @@ (define-module (gnu packages finance) #:use-module (guix download) #:use-module (guix build utils) #:use-module (guix build-system gnu) + #:use-module (guix build-system cmake) + #:use-module (gnu packages base) #:use-module (gnu packages boost) #:use-module (gnu packages databases) + #:use-module (gnu packages emacs) + #:use-module (gnu packages groff) + #:use-module (gnu packages libedit) #:use-module (gnu packages linux) + #:use-module (gnu packages multiprecision) #:use-module (gnu packages pkg-config) #:use-module (gnu packages protobuf) #:use-module (gnu packages python) #:use-module (gnu packages qt) + #:use-module (gnu packages texinfo) + #:use-module (gnu packages textutils) #:use-module (gnu packages tls) #:use-module (gnu packages upnp)) @@ -81,3 +90,100 @@ (define-public bitcoin-core of the bitcoin protocol. This package provides the Bitcoin Core command line client and a client based on Qt.") (license license:expat))) + +(define-public ledger + (package + (name "ledger") + (version "3.1.1") + (source (origin + (method url-fetch) + (uri (string-append + "https://github.com/ledger/ledger/archive/v" + version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "12jlv3gsjhrja25q9hrwh73cdacd2l3c2yyn8qnijav9mdhnbw4h")))) + (build-system cmake-build-system) + (arguments + `(#:modules ((guix build cmake-build-system) + (guix build utils) + (guix build emacs-utils)) + #:imported-modules (,@%cmake-build-system-modules + (guix build emacs-utils)) + #:configure-flags + `("-DBUILD_DOCS:BOOL=ON" + "-DBUILD_WEB_DOCS:BOOL=ON" + "-DBUILD_EMACSLISP:BOOL=ON" + "-DUSE_PYTHON:BOOL=ON" + "-DCMAKE_INSTALL_LIBDIR:PATH=lib" + ,(string-append "-DUTFCPP_INCLUDE_DIR:PATH=" + (assoc-ref %build-inputs "utfcpp") + "/include")) + #:phases + (modify-phases %standard-phases + (add-before 'configure 'install-examples + (lambda* (#:key outputs #:allow-other-keys) + (let ((examples (string-append (assoc-ref outputs "out") + "/share/doc/ledger/examples"))) + (install-file "test/input/sample.dat" examples) + (install-file "test/input/demo.ledger" examples)) + #t)) + (add-after 'build 'build-doc + (lambda _ (zero? (system* "make" "doc")))) + (add-before 'check 'check-setup + ;; One test fails if it can't set the timezone. + (lambda* (#:key inputs #:allow-other-keys) + (setenv "TZDIR" + (string-append (assoc-ref inputs "tzdata") + "/share/zoneinfo")) + #t)) + (add-after 'install 'relocate-elisp + (lambda* (#:key outputs #:allow-other-keys) + (let* ((site-dir (string-append (assoc-ref outputs "out") + "/share/emacs/site-lisp")) + (guix-dir (string-append site-dir "/guix.d")) + (orig-dir (string-append site-dir "/ledger-mode")) + (dest-dir (string-append guix-dir "/ledger-mode"))) + (mkdir-p guix-dir) + (rename-file orig-dir dest-dir) + (emacs-generate-autoloads ,name dest-dir)) + #t))))) + (inputs + `(("boost" ,boost) + ("gmp" ,gmp) + ("libedit" ,libedit) + ("mpfr" ,mpfr) + ("python" ,python-2) + ("tzdata" ,tzdata) + ("utfcpp" ,utfcpp))) + (native-inputs + `(("emacs" ,emacs-no-x) + ("groff" ,groff) + ("texinfo" ,texinfo))) + (home-page "http://ledger-cli.org/") + (synopsis "Command-line double-entry accounting program") + (description + "Ledger is a powerful, double-entry accounting system that is +accessed from the UNIX command-line. This may put off some users, since +there is no flashy UI, but for those who want unparalleled reporting +access to their data there are few alternatives. + +Ledger uses text files for input. It reads the files and generates +reports; there is no other database or stored state. To use Ledger, +you create a file of your account names and transactions, run from the +command line with some options to specify input and requested reports, and +get output. The output is generally plain text, though you could generate +a graph or html instead. Ledger is simple in concept, surprisingly rich +in ability, and easy to use.") + ;; There are some extra licenses in files which do not presently get + ;; installed when you build this package. Different versions of the GPL + ;; are used in the contrib and python subdirectories. The bundled version + ;; of utfcpp is under the Boost 1.0 license. Also the file + ;; `tools/update_copyright_year` has an Expat license. + (license (list license:bsd-3 + license:asl2.0 ; src/strptime.cc + (license:non-copyleft + "file://src/wcwidth.cc" + "See src/wcwidth.cc in the distribution.") + license:gpl2+)))) ; lisp/* -- cgit v1.2.3 From 8bfd602bb00ba7bed8f0108f4cea5ac92b772b7e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 29 Apr 2016 22:12:24 +0200 Subject: build: Accept dates with space-padded hour field. * guix/build/download.scm: Replace "parse-rfc-822-date" from the (web http) module. --- guix/build/download.scm | 79 +++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 79 insertions(+) diff --git a/guix/build/download.scm b/guix/build/download.scm index 824e1c354a..7741726c41 100644 --- a/guix/build/download.scm +++ b/guix/build/download.scm @@ -426,6 +426,85 @@ (define (close-connection port) (module-define! (resolve-module '(web client)) 'shutdown (const #f)) + +;; XXX: Work around , fixed in Guile commit +;; 16050431f29d56f80c4a8253506fc851b8441840. Guile's date validation +;; procedure rejects dates in which the hour is not padded with a zero but +;; with whitespace. +(begin + (define-syntax string-match? + (lambda (x) + (syntax-case x () + ((_ str pat) (string? (syntax->datum #'pat)) + (let ((p (syntax->datum #'pat))) + #`(let ((s str)) + (and + (= (string-length s) #,(string-length p)) + #,@(let lp ((i 0) (tests '())) + (if (< i (string-length p)) + (let ((c (string-ref p i))) + (lp (1+ i) + (case c + ((#\.) ; Whatever. + tests) + ((#\d) ; Digit. + (cons #`(char-numeric? (string-ref s #,i)) + tests)) + ((#\a) ; Alphabetic. + (cons #`(char-alphabetic? (string-ref s #,i)) + tests)) + (else ; Literal. + (cons #`(eqv? (string-ref s #,i) #,c) + tests))))) + tests))))))))) + + (define (parse-rfc-822-date str space zone-offset) + (let ((parse-non-negative-integer (@@ (web http) parse-non-negative-integer)) + (parse-month (@@ (web http) parse-month)) + (bad-header (@@ (web http) bad-header))) + ;; We could verify the day of the week but we don't. + (cond ((string-match? (substring str 0 space) "aaa, dd aaa dddd dd:dd:dd") + (let ((date (parse-non-negative-integer str 5 7)) + (month (parse-month str 8 11)) + (year (parse-non-negative-integer str 12 16)) + (hour (parse-non-negative-integer str 17 19)) + (minute (parse-non-negative-integer str 20 22)) + (second (parse-non-negative-integer str 23 25))) + (make-date 0 second minute hour date month year zone-offset))) + ((string-match? (substring str 0 space) "aaa, d aaa dddd dd:dd:dd") + (let ((date (parse-non-negative-integer str 5 6)) + (month (parse-month str 7 10)) + (year (parse-non-negative-integer str 11 15)) + (hour (parse-non-negative-integer str 16 18)) + (minute (parse-non-negative-integer str 19 21)) + (second (parse-non-negative-integer str 22 24))) + (make-date 0 second minute hour date month year zone-offset))) + + ;; The next two clauses match dates that have a space instead of + ;; a leading zero for hours, like " 8:49:37". + ((string-match? (substring str 0 space) "aaa, dd aaa dddd d:dd:dd") + (let ((date (parse-non-negative-integer str 5 7)) + (month (parse-month str 8 11)) + (year (parse-non-negative-integer str 12 16)) + (hour (parse-non-negative-integer str 18 19)) + (minute (parse-non-negative-integer str 20 22)) + (second (parse-non-negative-integer str 23 25))) + (make-date 0 second minute hour date month year zone-offset))) + ((string-match? (substring str 0 space) "aaa, d aaa dddd d:dd:dd") + (let ((date (parse-non-negative-integer str 5 6)) + (month (parse-month str 7 10)) + (year (parse-non-negative-integer str 11 15)) + (hour (parse-non-negative-integer str 17 18)) + (minute (parse-non-negative-integer str 19 21)) + (second (parse-non-negative-integer str 22 24))) + (make-date 0 second minute hour date month year zone-offset))) + + (else + (bad-header 'date str) ; prevent tail call + #f)))) + (module-set! (resolve-module '(web http)) + 'parse-rfc-822-date parse-rfc-822-date)) + ;; XXX: Work around , present in Guile ;; up to 2.0.11. (unless (or (> (string->number (major-version)) 2) -- cgit v1.2.3 From 8a0ac5bd558a2cf662f15d3670d2f39716df3337 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Mon, 16 May 2016 19:19:04 +0300 Subject: gnu: tmux: Update to 2.2. * gnu/packages/tmux.scm (tmux): Update to 2.2. --- gnu/packages/tmux.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/gnu/packages/tmux.scm b/gnu/packages/tmux.scm index 48d50ccafc..d89fc16844 100644 --- a/gnu/packages/tmux.scm +++ b/gnu/packages/tmux.scm @@ -1,5 +1,6 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2013 Cyril Roelandt +;;; Copyright © 2016 Efraim Flashner ;;; ;;; This file is part of GNU Guix. ;;; @@ -28,7 +29,7 @@ (define-module (gnu packages tmux) (define-public tmux (package (name "tmux") - (version "2.1") + (version "2.2") (source (origin (method url-fetch) (uri (string-append @@ -36,7 +37,7 @@ (define-public tmux version "/tmux-" version ".tar.gz")) (sha256 (base32 - "0xk1mylsb08sf0w597mdgj9s6hxxjvjvjd6bngpjvvxwyixlwmii")))) + "1r0riry5vw604hc21087ffbkqgr6j4ia1rrsivz2k6grchdm8a5w")))) (build-system gnu-build-system) (inputs `(("libevent" ,libevent) -- cgit v1.2.3 From b6c2f7dafd6dcb5a461753955dec0bfdbfec161c Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Mon, 16 May 2016 19:31:23 +0300 Subject: gnu: libgit2: Update to 0.24.1. * gnu/packages/version-control.scm (libgit2): Update to 0.24.1. --- gnu/packages/version-control.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/version-control.scm b/gnu/packages/version-control.scm index d47b3e86d2..db3e9f1768 100644 --- a/gnu/packages/version-control.scm +++ b/gnu/packages/version-control.scm @@ -324,7 +324,7 @@ (define-public git-manpages (define-public libgit2 (package (name "libgit2") - (version "0.24.0") + (version "0.24.1") (source (origin (method url-fetch) (uri (string-append "https://github.com/libgit2/libgit2/" @@ -332,7 +332,7 @@ (define-public libgit2 (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "1c5jx0pcpz83x7s36jimfz5bj0vy7vwpchq9p4sgdqxy8gwr6rhw")))) + "1ppyfwxc276d2p2pwbzlmvs2bkgng425rl8k2rf9nsq66jxqq6b0")))) (build-system cmake-build-system) (arguments `(#:phases -- cgit v1.2.3 From af3ac1f5f7ae93b392c8e7b907c9c8cc4c7d4911 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Mon, 16 May 2016 14:27:48 -0400 Subject: gnu: imagemagick: Update to 6.9.4-1. * gnu/packages/imagemagick.scm (imagemagick): Update to 6.9.4-1. --- gnu/packages/imagemagick.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/imagemagick.scm b/gnu/packages/imagemagick.scm index 095f662376..fb5f9339b2 100644 --- a/gnu/packages/imagemagick.scm +++ b/gnu/packages/imagemagick.scm @@ -40,14 +40,14 @@ (define-module (gnu packages imagemagick) (define-public imagemagick (package (name "imagemagick") - (version "6.9.3-10") + (version "6.9.4-1") (source (origin (method url-fetch) (uri (string-append "mirror://imagemagick/ImageMagick-" version ".tar.xz")) (sha256 (base32 - "0sik2jl1cywnpr5xm28mjhs1l8kxry65f3v2kqzp0cczhwf04gz3")))) + "0fvb9i7kai5ashaiaxqr1cikyyp5w1zczdq28l9nypfd77wgx81f")))) (build-system gnu-build-system) (arguments `(#:configure-flags '("--with-frozenpaths") -- cgit v1.2.3 From 9583e07caea25ddec367e462151805ef8d86a445 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 6 May 2016 14:54:33 +0200 Subject: import cran: Use URL for Bioconductor 3.3. * guix/import/cran.scm (%bioconductor-svn-url): Update to release URL for version 3.3. --- guix/import/cran.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/guix/import/cran.scm b/guix/import/cran.scm index 69485bc88d..6f2ceedeba 100644 --- a/guix/import/cran.scm +++ b/guix/import/cran.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2015 Ricardo Wurmus +;;; Copyright © 2015, 2016 Ricardo Wurmus ;;; Copyright © 2015, 2016 Ludovic Courtès ;;; ;;; This file is part of GNU Guix. @@ -111,11 +111,11 @@ (define* (maybe-inputs package-inputs #:optional (type 'inputs)) (define %cran-url "http://cran.r-project.org/web/packages/") (define %bioconductor-url "http://bioconductor.org/packages/") -;; The latest Bioconductor release is 3.2. Bioconductor packages should be +;; The latest Bioconductor release is 3.3. Bioconductor packages should be ;; updated together. (define %bioconductor-svn-url (string-append "https://readonly:readonly@" - "hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/" + "hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/" "madman/Rpacks/")) -- cgit v1.2.3 From dbfeba52091801e37e5c959427ab35535da21f6f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 10 May 2016 11:43:43 +0200 Subject: gnu: r-biocgenerics: Update to 0.18.0. * gnu/packages/bioinformatics.scm (r-biocgenerics): Update to 0.18.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 6a2611e203..64797bb666 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -4018,13 +4018,13 @@ (define-public r-acsnminer (define-public r-biocgenerics (package (name "r-biocgenerics") - (version "0.16.1") + (version "0.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocGenerics" version)) (sha256 (base32 - "0f16ryy5f012hvksrwlmm33bcl7lw97i2jvhbnwfwl03j4w7nhc1")))) + "1jjp48vbph09w5bmc7368gjjywsa1lmzfybpiwlypr60b51vlkp6")))) (properties `((upstream-name . "BiocGenerics"))) (build-system r-build-system) -- cgit v1.2.3 From a936bf59ea12b91a448fb83fbae1dd75b59f543f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 10 May 2016 11:45:29 +0200 Subject: gnu: r-dnacopy: Update to 1.46.0. * gnu/packages/bioinformatics.scm (r-dnacopy): Update to 1.46.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 64797bb666..5ab3106896 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -4038,13 +4038,13 @@ (define-public r-biocgenerics (define-public r-dnacopy (package (name "r-dnacopy") - (version "1.44.0") + (version "1.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DNAcopy" version)) (sha256 (base32 - "1c1px4rbr36xx929hp59k7ca9k5ab66qmn8k63fk13278ncm6h66")))) + "0vwv2mndfjpcjp4sybg75abc7xnx8zyw8zjk717k6xh8c33ymcip")))) (properties `((upstream-name . "DNAcopy"))) (build-system r-build-system) -- cgit v1.2.3 From 3654a61146ce2e2fbf46a1d96015d904437eb963 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 10 May 2016 11:46:15 +0200 Subject: gnu: r-s4vectors: Update to 0.10.0. * gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.10.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 5ab3106896..795051f2e7 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -4060,13 +4060,13 @@ (define-public r-dnacopy (define-public r-s4vectors (package (name "r-s4vectors") - (version "0.8.11") + (version "0.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "S4Vectors" version)) (sha256 (base32 - "12iibcs63m9iy7f45wgjcqsna2dnqwckphk682389grshz0g4x66")))) + "1mi6lf6pnb9l657igy0vj4yz03yawbr2jhk22l757fzbjc7n9q3b")))) (properties `((upstream-name . "S4Vectors"))) (build-system r-build-system) -- cgit v1.2.3 From 952ff8c86205ef9963f45228ff1b12f4cb29fa02 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 10 May 2016 11:47:03 +0200 Subject: gnu: r-iranges: Update to 2.6.0. * gnu/packages/bioinformatics (r-iranges): Update to 2.6.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 795051f2e7..c49455b370 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -4087,13 +4087,13 @@ (define-public r-s4vectors (define-public r-iranges (package (name "r-iranges") - (version "2.4.8") + (version "2.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "IRanges" version)) (sha256 (base32 - "0hi5k1j5jm4xrg1l506g279qw1xkvp1gg1zgsjzpbng4vx4k4iyl")))) + "0dz7z0pk8hq79mcgylw920999s08h6j8xrl31rdxhssmi7l8v6vy")))) (properties `((upstream-name . "IRanges"))) (build-system r-build-system) -- cgit v1.2.3 From d1ab3d8fa5c2c93124d12b8a54742312e8cd550d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 10 May 2016 11:47:44 +0200 Subject: gnu: r-genomeinfodb: Update to 1.8.0. * gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.8.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index c49455b370..a41ef525d7 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -4116,13 +4116,13 @@ (define-public r-iranges (define-public r-genomeinfodb (package (name "r-genomeinfodb") - (version "1.6.3") + (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomeInfoDb" version)) (sha256 (base32 - "1ggp005n2rlkad00ilzn95y4rd484yr1chdhnd6fwg45rbi94d63")))) + "0fcfzw3d0rxlc320bvz0vlxg26fa1278abhjmknb815046g7fn3s")))) (properties `((upstream-name . "GenomeInfoDb"))) (build-system r-build-system) -- cgit v1.2.3 From 052ee32b2452e87886097bbd0994554dffb40941 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 10 May 2016 11:48:30 +0200 Subject: gnu: r-variantannotation: Update to 1.18.0. * gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.18.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index a41ef525d7..e402bb4758 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -4142,13 +4142,13 @@ (define-public r-genomeinfodb (define-public r-variantannotation (package (name "r-variantannotation") - (version "1.16.4") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "VariantAnnotation" version)) (sha256 (base32 - "1z42j3p9b8h725inq8n0230llsdbav3gwcxy1nliypzfkxbzahsb")))) + "1mjm5kav0mjymcj3ha1jnw9snym39w5vc2zkl25dpg78nl00nwar")))) (properties `((upstream-name . "VariantAnnotation"))) (inputs -- cgit v1.2.3 From e782ca3e97f020d504371b790739ddabd4a3443e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 10 May 2016 11:49:19 +0200 Subject: gnu: r-xvector: Update to 0.12.0. * gnu/packages/bioinformatics.scm (r-xvector): Update to 0.12.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index e402bb4758..5564e9c882 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -4174,13 +4174,13 @@ (define-public r-variantannotation (define-public r-xvector (package (name "r-xvector") - (version "0.10.0") + (version "0.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "XVector" version)) (sha256 (base32 - "0havwyr6xqk7w0rmbwfj9jq1djz7wzdz7w39adhklwzwz9l4ih3a")))) + "0c9cqjcxxks3an4wiq167h2grxlfyazajn7bmxhbk42zifp8vmqp")))) (properties `((upstream-name . "XVector"))) (build-system r-build-system) -- cgit v1.2.3 From 828980cad661f1c511fd8bcd58fe5c627f211481 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 10 May 2016 11:49:57 +0200 Subject: gnu: r-genomicranges: Update to 1.24.0. * gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.24.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 5564e9c882..79ccfcd018 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -4210,13 +4210,13 @@ (define-public r-xvector (define-public r-genomicranges (package (name "r-genomicranges") - (version "1.22.4") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicRanges" version)) (sha256 (base32 - "02df5683nrpn9d10ws8jz9b55nr9055hh882xp2i154xdddir0k0")))) + "1iyzg1npl3rnnslwq3h759vf0xhshnn5v801rnlj6bnxzhn9yaqh")))) (properties `((upstream-name . "GenomicRanges"))) (build-system r-build-system) -- cgit v1.2.3 From 4466a02c9fc7a8487d63301335e1a3c966d1635e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 10 May 2016 11:50:35 +0200 Subject: gnu: r-biobase: Update to 2.32.0. * gnu/packages/bioinformatics.scm (r-biobase): Update to 2.32.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 79ccfcd018..a062be62a9 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -4237,13 +4237,13 @@ (define-public r-genomicranges (define-public r-biobase (package (name "r-biobase") - (version "2.30.0") + (version "2.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Biobase" version)) (sha256 (base32 - "1qasjpq3kw8h7qw8cin3bjvv1256hqr1mm24fq3v0ymxzlb66szi")))) + "0q4icv9n5rc2qfkv6k1wjhmfcpzcyr8f45m2z3xharbdv912kl1i")))) (properties `((upstream-name . "Biobase"))) (build-system r-build-system) -- cgit v1.2.3 From c4a4e17938da258b052c684b747dfa8953074222 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 10 May 2016 11:51:18 +0200 Subject: gnu: r-annotationdbi: Update to 1.34.0. * gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.34.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index a062be62a9..b2d4d6b233 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -4259,13 +4259,13 @@ (define-public r-biobase (define-public r-annotationdbi (package (name "r-annotationdbi") - (version "1.32.3") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationDbi" version)) (sha256 (base32 - "1v6x62hgys5827yg2xayjrd9xawbayzm6wy0q4vxh1s6yxc9bklj")))) + "0ri766402q3r4fdgibhb7ij7r73g6gdsj1g6iimm4mcinipfixwj")))) (properties `((upstream-name . "AnnotationDbi"))) (build-system r-build-system) -- cgit v1.2.3 From 63cea37234e010689b967e1370b885915b7328bb Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 10 May 2016 11:51:53 +0200 Subject: gnu: r-biomart: Update to 2.28.0. * gnu/packages/bioinformatics.scm (r-biomart): Update to 2.28.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index b2d4d6b233..d82a79459d 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -4286,13 +4286,13 @@ (define-public r-annotationdbi (define-public r-biomart (package (name "r-biomart") - (version "2.26.1") + (version "2.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biomaRt" version)) (sha256 (base32 - "1s709055abj2gd35g6nnk5d2ai5ii09iir270l2xika6pi62gj3f")))) + "1g0w6an9hkflgyhvq6pmrs92s93qarv23v636b9a4bz771wjvm5v")))) (properties `((upstream-name . "biomaRt"))) (build-system r-build-system) -- cgit v1.2.3 From 6a2a0de1ab52dbdccbbbc52e38f0f4dc41ad0e10 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 10 May 2016 11:52:32 +0200 Subject: gnu: r-biocparallel: Update to 1.6.0. * gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.6.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index d82a79459d..e6cf6a87bc 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -4316,13 +4316,13 @@ (define-public r-biomart (define-public r-biocparallel (package (name "r-biocparallel") - (version "1.4.3") + (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocParallel" version)) (sha256 (base32 - "1f5mndx66vampcsq0n66afg6x851crl0h3nyv2nyp9bsgzj9cdzq")))) + "0yhjihbggs3mn4z43s3fsf70brzjvbilm9ljz1z326xwmk7j40ys")))) (properties `((upstream-name . "BiocParallel"))) (build-system r-build-system) -- cgit v1.2.3 From 2477d9773ac9408172d75a0d146a169bba0ae96c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 10 May 2016 11:53:48 +0200 Subject: gnu: r-biostrings: Update to 2.40.0. * gnu/packages/bioinformatics.scm (r-biostrings): Update to 2.40.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index e6cf6a87bc..cd7d4605df 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -4340,13 +4340,13 @@ (define-public r-biocparallel (define-public r-biostrings (package (name "r-biostrings") - (version "2.38.4") + (version "2.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Biostrings" version)) (sha256 (base32 - "0cjd7i4bdwabzb02gm753aji5xaihkj5ak8nb0d32cclxbj0hp33")))) + "03gyhiz14xy51nzg0glihk1rv19pq4p1aa3y5g23bzcshs67ggj9")))) (properties `((upstream-name . "Biostrings"))) (build-system r-build-system) -- cgit v1.2.3 From b4c5a0db22033503eb07e5c03abf89234e061444 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 10 May 2016 11:54:43 +0200 Subject: gnu: r-rsamtools: Update to 1.24.0. * gnu/packages/bioinformatics.scm (r-rsamtools): Update to 1.24.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index cd7d4605df..f3d78c78d9 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -4366,13 +4366,13 @@ (define-public r-biostrings (define-public r-rsamtools (package (name "r-rsamtools") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rsamtools" version)) (sha256 (base32 - "1yc3nzzms3igjwr4l9yd3wdac95glcs08b4cfp7disyly0wcskjd")))) + "0w0drs8cpk8nlazq64ag7nm1w5jd1m8riialivm01hz5zcra7scb")))) (properties `((upstream-name . "Rsamtools"))) (build-system r-build-system) -- cgit v1.2.3 From d848ed7cf2d6fb9b1a3fe1db414ff571398ae9e2 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 10 May 2016 11:57:39 +0200 Subject: gnu: r-summarizedexperiment: Update to 1.2.0. * gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to 1.2.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index f3d78c78d9..bb01f2e218 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -4410,13 +4410,13 @@ (define-public r-rsamtools (define-public r-summarizedexperiment (package (name "r-summarizedexperiment") - (version "1.0.2") + (version "1.2.0") (source (origin (method url-fetch) (uri (bioconductor-uri "SummarizedExperiment" version)) (sha256 (base32 - "1gpmh1mi70m5k5qnyjs1h0qn8ajrzalzic7k3762xchxsmmdvxn4")))) + "1pfbw2dlifa7m7gxpazb6z517kw3p5a3khslykcy7gml5xsf2ch8")))) (properties `((upstream-name . "SummarizedExperiment"))) (build-system r-build-system) -- cgit v1.2.3 From 3cd551ea7b9dfab3cd0dbdcc8f74f5140876c8cc Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 10 May 2016 11:59:33 +0200 Subject: gnu: r-genomicalignments: Update to 1.8.0. * gnu/packages/bioinformatics.scm (r-genomicalignments): Update to 1.8.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index bb01f2e218..7270275c6a 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -4439,13 +4439,13 @@ (define-public r-summarizedexperiment (define-public r-genomicalignments (package (name "r-genomicalignments") - (version "1.6.3") + (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicAlignments" version)) (sha256 (base32 - "02b9j1pfd39bkvb623k5k0ziq9rpw093hifqw65vb954dwj29jhd")))) + "1y4qgqxq8dax9swgl59m6i7ggjpqrjllgx87b9vwls3z0nf1i6xj")))) (properties `((upstream-name . "GenomicAlignments"))) (build-system r-build-system) -- cgit v1.2.3 From d23fbf1eb93f34378bb64e3d62f3e314527e2a03 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 10 May 2016 12:00:12 +0200 Subject: gnu: r-rtracklayer: Update to 1.32.0. * gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.32.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 7270275c6a..72f794ca02 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -4472,13 +4472,13 @@ (define-public r-genomicalignments (define-public r-rtracklayer (package (name "r-rtracklayer") - (version "1.30.4") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "rtracklayer" version)) (sha256 (base32 - "0knjnwywh9k726mq28s3sy013zhw6d6nfa8hfw670720nq18i2p0")))) + "0nrwk1g8b1ymvbgnqniimbvwfq13r01va9rx3b03xj4hpywzy5nv")))) (build-system r-build-system) (arguments `(#:phases -- cgit v1.2.3 From c12b0a5a30c890da53839915146bc72d9f4426a8 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 10 May 2016 12:00:42 +0200 Subject: gnu: r-genomicfeatures: Update to 1.24.0. * gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.24.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 72f794ca02..56e80c8002 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -4517,13 +4517,13 @@ (define-public r-rtracklayer (define-public r-genomicfeatures (package (name "r-genomicfeatures") - (version "1.22.13") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicFeatures" version)) (sha256 (base32 - "0n3rkj66la6wizgcsf2rmwcsyfxz9kv5zak337lmk1raqfnancz4")))) + "1rfqxq6brrfzdajxd6ydbfaag0529d1cpjihvagmf8124prx2b2f")))) (properties `((upstream-name . "GenomicFeatures"))) (build-system r-build-system) -- cgit v1.2.3 From 0c56023557ebebcef662dddddef5843947bab656 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 10 May 2016 12:01:09 +0200 Subject: gnu: r-graph: Update to 1.50.0. * gnu/packages/bioinformatics.scm (r-graph): Update to 1.50.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 56e80c8002..080787a8f9 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -4582,13 +4582,13 @@ (define-public r-go-db (define-public r-graph (package (name "r-graph") - (version "1.48.0") + (version "1.50.0") (source (origin (method url-fetch) (uri (bioconductor-uri "graph" version)) (sha256 (base32 - "16w75rji3kv24gfv44w66y1a2y75ax26rl470y3ypna0ndc3rrcd")))) + "0ys5s19m5r30rlr0fnx2h0z2qw7n2xrad4l2yfb1bbrk8dwyf4pi")))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics))) -- cgit v1.2.3 From e48e88c2174389cf4f1d39c119fb817addd131d4 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 10 May 2016 12:01:42 +0200 Subject: gnu: r-topgo: Update to 2.24.0. * gnu/packages/bioinformatics.scm (r-topgo): Update to 2.24.0. [propagated-inputs]: Add r-matrixstats. --- gnu/packages/bioinformatics.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 080787a8f9..8958487701 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -4601,13 +4601,13 @@ (define-public r-graph (define-public r-topgo (package (name "r-topgo") - (version "2.22.0") + (version "2.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "topGO" version)) (sha256 (base32 - "029j9nb39b8l9xlzsp83pmjr8ap247aia387yzaa1yyw8klapdaf")))) + "1p4vsl32qhjw15yv9ym01ni63gjg73jaghlf17wc4zfn3iaz2zar")))) (properties `((upstream-name . "topGO"))) (build-system r-build-system) @@ -4616,6 +4616,7 @@ (define-public r-topgo ("r-biobase" ,r-biobase) ("r-biocgenerics" ,r-biocgenerics) ("r-go-db" ,r-go-db) + ("r-matrixstats" ,r-matrixstats) ("r-graph" ,r-graph) ("r-sparsem" ,r-sparsem))) (home-page "http://bioconductor.org/packages/topGO") -- cgit v1.2.3 From 5190ed1751ac0fb5dd034825ef1af98ac9dba6f3 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 10 May 2016 12:02:26 +0200 Subject: gnu: r-bsgenome: Update to 1.40.0. * gnu/packages/bioinformatics.scm (r-bsgenome): Update to 1.40.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 8958487701..e4a3711cdc 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -4632,13 +4632,13 @@ (define-public r-topgo (define-public r-bsgenome (package (name "r-bsgenome") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BSgenome" version)) (sha256 (base32 - "130w0m6q8kkca7gyz1aqj5jjhalwvwi6rk2yvbjrnj4gpnncyrd2")))) + "08g3w47ysbmgj4hclb0x2wsn7pi9cnm3xkkfk4shgrka2g23qz44")))) (properties `((upstream-name . "BSgenome"))) (build-system r-build-system) -- cgit v1.2.3 From d1bff89d2670edb971fefb953517c1b7ea25c6f0 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 10 May 2016 12:02:48 +0200 Subject: gnu: r-impute: Update to 1.46.0. * gnu/packages/bioinformatics.scm (r-impute): Update to 1.46.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index e4a3711cdc..b8a1e7dcd6 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -4662,13 +4662,13 @@ (define-public r-bsgenome (define-public r-impute (package (name "r-impute") - (version "1.44.0") + (version "1.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "impute" version)) (sha256 (base32 - "0y4x5jk7gsf4xn56jrkdcdnxpcfll4h6ivncd7n4snmzixldvmvw")))) + "0v9ibgv8kp8il52miz7b7z65mv6irqxylx6lfzkxgvxd970dgrz0")))) (inputs `(("gfortran" ,gfortran))) (build-system r-build-system) -- cgit v1.2.3 From 7555817c2b37e7be2f251b3c1b144d073755c452 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 10 May 2016 12:03:08 +0200 Subject: gnu: r-seqpattern: Update to 1.4.0. * gnu/packages/bioinformatics.scm (r-seqpattern): Update to 1.4.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index b8a1e7dcd6..cd2928cf1f 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -4682,13 +4682,13 @@ (define-public r-impute (define-public r-seqpattern (package (name "r-seqpattern") - (version "1.2.0") + (version "1.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "seqPattern" version)) (sha256 (base32 - "0p9zj6bic7sa0hb2bjm988kkk5n9r1kvlbqkzvy702f642n0j53i")))) + "1dj9hfnbdj11yjxwd8jmxrdkj7n6gmaaj6244g2psgarhjcp4wfb")))) (properties `((upstream-name . "seqPattern"))) (build-system r-build-system) -- cgit v1.2.3 From 8adc3b628de10e18cef849ad24b714b460ac4ae2 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 10 May 2016 12:03:32 +0200 Subject: gnu: r-genomation: Update to 1.4.0. * gnu/packages/bioinformatics.scm (r-genomation): Update to 1.4.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index cd2928cf1f..936321e58c 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -4708,13 +4708,13 @@ (define-public r-seqpattern (define-public r-genomation (package (name "r-genomation") - (version "1.2.2") + (version "1.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "genomation" version)) (sha256 (base32 - "0kvzwc21zsh2c8d34yn935ncn38bfkpzmknycd8h7b0521x20mi9")))) + "16q1qkl6cwwj5hqhxpfgbz0y27hwz3h8zkjxpbyvjy1q0894sdjl")))) (build-system r-build-system) (propagated-inputs `(("r-biostrings" ,r-biostrings) -- cgit v1.2.3 From 1f5786a918ea7811c1060acc7d98f8609a37e59d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 10 May 2016 12:03:58 +0200 Subject: gnu: r-seqlogo: Update to 1.38.0. * gnu/packages/bioinformatics.scm (r-seqlogo): Update to 1.38.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 936321e58c..a102a0cf87 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -4855,14 +4855,14 @@ (define-public r-org-mm-eg-db (define-public r-seqlogo (package (name "r-seqlogo") - (version "1.36.0") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "seqLogo" version)) (sha256 (base32 - "0kn1a1nf2j4v9c09vjkz9bmxlln7yhg87bnyrdsxy1m55x56rn5k")))) + "01jddx62nhi3r7czbh9hxy0wwpazbc9ax1fgagfxl6p4kx9xz9rb")))) (properties `((upstream-name . "seqLogo"))) (build-system r-build-system) (home-page "http://bioconductor.org/packages/seqLogo") -- cgit v1.2.3 From a0fe3aeecfa830adfaad5a444ed763012218cc3f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 10 May 2016 12:04:18 +0200 Subject: gnu: r-motifrg: Update to 1.16.0. * gnu/packages/bioinformatics.scm (r-motifrg): Update to 1.16.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index a102a0cf87..4284686433 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -5002,14 +5002,14 @@ (define-public r-bsgenome-dmelanogaster-ucsc-dm3 (define-public r-motifrg (package (name "r-motifrg") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "motifRG" version)) (sha256 (base32 - "1v9zm5629k2lcqbbgw8bwflvbircyxkfavbkvmbd212kgwcng8vn")))) + "1ds22paqc0923y6z1fy0arw0wxvvmglfvfgarhywv1qywhq68mbq")))) (properties `((upstream-name . "motifRG"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 96101b67186191b38325406acc8a688f51b9f7d8 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 10 May 2016 12:04:39 +0200 Subject: gnu: r-zlibbioc: Update to 1.18.0. * gnu/packages/bioinformatics.scm (r-zlibbioc): Update to 1.18.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 4284686433..aa16d39861 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -5054,13 +5054,13 @@ (define-public r-qtl (define-public r-zlibbioc (package (name "r-zlibbioc") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "zlibbioc" version)) (sha256 (base32 - "01wc26ndg4jsn1wyrl6zzq636gxaip5fci0xapym4lh9wryc4wnw")))) + "0m8l7zpx1l3qsk73k3ibkxxzzff938x3qhnwki1ymf3cnsg8cb36")))) (properties `((upstream-name . "zlibbioc"))) (build-system r-build-system) -- cgit v1.2.3 From 9916ae15bb7622fb75f819d561cbc2c4257d0acd Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 10 May 2016 14:18:44 +0200 Subject: import cran: latest-bioconductor-release: Wrap Bioconductor URL in list. * guix/import/cran.scm (latest-bioconductor-release): Wrap Bioconductor URL in list in the "urls" field of the "upstream-source" value. --- guix/import/cran.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/guix/import/cran.scm b/guix/import/cran.scm index 6f2ceedeba..f9369414cd 100644 --- a/guix/import/cran.scm +++ b/guix/import/cran.scm @@ -267,7 +267,7 @@ (define meta (upstream-source (package (package-name package)) (version version) - (urls (bioconductor-uri upstream-name version)))))) + (urls (list (bioconductor-uri upstream-name version))))))) (define (cran-package? package) "Return true if PACKAGE is an R package from CRAN." -- cgit v1.2.3 From 11e4c1fd104884999a84633baea1d2e298d2e334 Mon Sep 17 00:00:00 2001 From: Christopher Allan Webber Date: Fri, 29 Apr 2016 17:53:50 -0500 Subject: gnu: Add geiser-next. Also, I previously committed to this repository in 2015; add self to copyright headers for that year too. * gnu/packages/emacs.scm (geiser-next): New variable. --- gnu/packages/emacs.scm | 31 +++++++++++++++++++++++++++++++ 1 file changed, 31 insertions(+) diff --git a/gnu/packages/emacs.scm b/gnu/packages/emacs.scm index 11010b2a47..f0c1555f7d 100644 --- a/gnu/packages/emacs.scm +++ b/gnu/packages/emacs.scm @@ -7,6 +7,7 @@ ;;; Copyright © 2015, 2016 Ricardo Wurmus ;;; Copyright © 2016 Nils Gillmann ;;; Copyright © 2016 Chris Marusich +;;; Copyright © 2015, 2016 Christopher Allan Webber ;;; ;;; This file is part of GNU Guix. ;;; @@ -260,6 +261,36 @@ (define-public geiser metadata.") (license license:bsd-3))) +(define-public geiser-next + ;; Geiser's upcoming version supports guile-next, and 0.8.1 does not. + ;; When the next Geiser release comes out, we can remove this. + (let ((commit "2e335695fc1a4a0b520b50deb761b958194cbec4")) + (package + (inherit geiser) + (name "geiser-next") + (version (string-append "0.8.1-1" + (string-take commit 7))) + (source (origin + (method git-fetch) + (uri (git-reference + (url "git://git.sv.gnu.org/geiser.git") + (commit commit))) + (sha256 + (base32 + "00rmpn8zncq1fiah5m12l26z0s28bh7ql63kxdvksqdgfrisnmgf")))) + (native-inputs + `(("autoconf" ,autoconf) + ("automake" ,automake) + ("texinfo" ,texinfo) + ,@(package-native-inputs geiser))) + (arguments + (substitute-keyword-arguments (package-arguments geiser) + ((#:phases phases) + `(modify-phases ,phases + (add-after 'unpack 'autogen + (lambda _ + (zero? (system* "sh" "autogen.sh"))))))))))) + (define-public paredit (package (name "paredit") -- cgit v1.2.3 From cb307c0833742299f28abc236b5a9530f7349493 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Tue, 17 May 2016 09:03:39 +0300 Subject: gnu: cflow: Update to 1.5. * gnu/packages/code.scm (cflow): Update to 1.5. --- gnu/packages/code.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/code.scm b/gnu/packages/code.scm index af671d5780..7e8a361967 100644 --- a/gnu/packages/code.scm +++ b/gnu/packages/code.scm @@ -43,14 +43,14 @@ (define-module (gnu packages code) (define-public cflow (package (name "cflow") - (version "1.4") + (version "1.5") (source (origin (method url-fetch) (uri (string-append "mirror://gnu/cflow/cflow-" version ".tar.bz2")) (sha256 (base32 - "1jkbq97ajcf834z68hbn3xfhiz921zhn39gklml1racf0kb3jzh3")))) + "0yq33k5ap1zpnja64n89iai4zh018ffr72wki5a6mzczd880mr3g")))) (build-system gnu-build-system) ;; Needed to have cflow-mode.el installed. -- cgit v1.2.3 From 4f04243405706a52b73c1acca883abfc030ce4d4 Mon Sep 17 00:00:00 2001 From: Ludovic Courtès Date: Mon, 16 May 2016 22:45:37 +0200 Subject: gnu: 'uncompressed-file-fetch' no longer depends on gzip. * gnu/packages/emacs.scm (uncompressed-file-fetch): Remove dependency on GZIP. --- gnu/packages/emacs.scm | 2 -- 1 file changed, 2 deletions(-) diff --git a/gnu/packages/emacs.scm b/gnu/packages/emacs.scm index f0c1555f7d..860ef11d29 100644 --- a/gnu/packages/emacs.scm +++ b/gnu/packages/emacs.scm @@ -1403,8 +1403,6 @@ (define* (uncompressed-file-fetch url hash-algo hash (gexp->derivation (or name (basename url)) #~(begin (mkdir #$output) - (setenv "PATH" - (string-append #$gzip "/bin")) (chdir #$output) (copy-file #$drv (basename #$url)))))) -- cgit v1.2.3 From a9e41d2faf979e1b39e2d587b940a89e071804c2 Mon Sep 17 00:00:00 2001 From: Ludovic Courtès Date: Mon, 16 May 2016 22:48:16 +0200 Subject: gnu: emacs-constants: Factorize home-page in source URL. * gnu/packages/emacs.scm (emacs-constants): Move 'home-page' above. Use it in 'uri'. --- gnu/packages/emacs.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/emacs.scm b/gnu/packages/emacs.scm index 860ef11d29..5fbbc033b7 100644 --- a/gnu/packages/emacs.scm +++ b/gnu/packages/emacs.scm @@ -1410,17 +1410,17 @@ (define-public emacs-constants (package (name "emacs-constants") (version "2.2") + (home-page "https://staff.fnwi.uva.nl/c.dominik/Tools/constants") (source (origin (file-name (string-append name "-" version ".el")) (method uncompressed-file-fetch) - (uri "https://staff.fnwi.uva.nl/c.dominik/Tools/constants/constants.el") + (uri (string-append home-page "/constants.el")) ;FIXME: unversioned URI (patches (search-patches "emacs-constants-lisp-like.patch")) (sha256 (base32 "14q094aphsjhq8gklv7i5a7byl0ygz63cv3n6b5p8ji2jy0mnnw3")))) (build-system emacs-build-system) - (home-page "https://staff.fnwi.uva.nl/c.dominik/Tools/constants") (synopsis "Enter definition of constants into an Emacs buffer") (description "This package provides functions for inserting the definition of natural -- cgit v1.2.3 From 122395f9fc42de7dbe2643b437ca4e484adb8ba0 Mon Sep 17 00:00:00 2001 From: Ben Woodcroft Date: Tue, 17 May 2016 21:07:00 +1000 Subject: gnu: diamond: Update to 0.8.1. * gnu/packages/bioinformatics.scm (diamond): Update to 0.8.1. [source]: Remove 'snippet'. [build-system]: Use cmake-build-system. [arguments]: Remove modifications to phases. [native-inputs]: Remove field. [inputs]: Remove 'boost'. --- gnu/packages/bioinformatics.scm | 31 +++++-------------------------- 1 file changed, 5 insertions(+), 26 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index aa16d39861..f882185936 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1482,7 +1482,7 @@ (define-public deeptools (define-public diamond (package (name "diamond") - (version "0.7.9") + (version "0.8.1") (source (origin (method url-fetch) (uri (string-append @@ -1491,33 +1491,12 @@ (define-public diamond (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "0hfkcfv9f76h5brbyw9fyvmc0l9cmbsxrcdqk0fa9xv82zj47p15")) - (snippet '(begin - (delete-file "bin/diamond") - #t)))) - (build-system gnu-build-system) + "1dqancz32c2l7w1b2vkvh5zqa2jnf99j1c41djnx1l8pxn044zdc")))) + (build-system cmake-build-system) (arguments - '(#:tests? #f ;no "check" target - #:phases - (modify-phases %standard-phases - (add-after 'unpack 'enter-source-dir - (lambda _ - (chdir "src") - #t)) - (delete 'configure) - (replace 'install - (lambda* (#:key outputs #:allow-other-keys) - (let ((bin (string-append (assoc-ref outputs "out") - "/bin"))) - (mkdir-p bin) - (copy-file "../bin/diamond" - (string-append bin "/diamond")) - #t)))))) - (native-inputs - `(("bc" ,bc))) + '(#:tests? #f)) ; no "check" target (inputs - `(("boost" ,boost) - ("zlib" ,zlib))) + `(("zlib" ,zlib))) (home-page "https://github.com/bbuchfink/diamond") (synopsis "Accelerated BLAST compatible local sequence aligner") (description -- cgit v1.2.3 From daaeed765aebae138b4af1d3861eace0368fe2a6 Mon Sep 17 00:00:00 2001 From: Ben Woodcroft Date: Tue, 17 May 2016 21:36:46 +1000 Subject: gnu: vsearch: Update to 1.11.1. * gnu/packages/bioinformatics.scm (vsearch): Update to 1.11.1. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index f882185936..7aa1853256 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -3810,7 +3810,7 @@ (define-public vcftools (define-public vsearch (package (name "vsearch") - (version "1.10.0") + (version "1.11.1") (source (origin (method url-fetch) @@ -3820,7 +3820,7 @@ (define-public vsearch (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "1i3bad7gnn2y3a1yfixzshd99xdkjc8w5bxzgifpysc6jiljwvb5")) + "1pdvm3znjgq3zryy240yj9gc0bf1z31k6vf9jxrxgdgkvzgw85c7")) (modules '((guix build utils))) (snippet '(begin -- cgit v1.2.3 From 849485f5a05badf502e28c673e546b4660c4ca46 Mon Sep 17 00:00:00 2001 From: Ben Woodcroft Date: Tue, 17 May 2016 21:45:49 +1000 Subject: gnu: sortmerna: Update to 2.1b. * gnu/packages/bioinformatics.scm (sortmerna): Update to 2.1b. [inputs]: New field. --- gnu/packages/bioinformatics.scm | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 7aa1853256..60cf6b7007 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -3549,7 +3549,7 @@ (define-public snap-aligner (define-public sortmerna (package (name "sortmerna") - (version "2.1") + (version "2.1b") (source (origin (method url-fetch) @@ -3559,7 +3559,7 @@ (define-public sortmerna (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "1mc5cf1c7xh0h7xb11vh7gqgzx0qvrfa606cb8ixlfg3f2av58s4")))) + "1ghaghvd82af9j5adavxh77g7hm247d1r69m3fbi6f1jdivj5ldk")))) (build-system gnu-build-system) (outputs '("out" ;for binaries "db")) ;for sequence databases @@ -3579,6 +3579,8 @@ (define-public sortmerna (install-file file share)) (find-files "rRNA_databases" ".*fasta")) #t)))))) + (inputs + `(("zlib" ,zlib))) (home-page "http://bioinfo.lifl.fr/RNA/sortmerna") (synopsis "Biological sequence analysis tool for NGS reads") (description -- cgit v1.2.3 From f99f3f24ef604f44023379da4b375c80e6844be1 Mon Sep 17 00:00:00 2001 From: Federico Beffa Date: Tue, 17 May 2016 13:51:34 +0200 Subject: gnu: emacs-constants: Update to 2.6. * gnu/packages/emacs.scm (emacs-constants): Change to versioned repository and update to 2.6. --- gnu/packages/emacs.scm | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/gnu/packages/emacs.scm b/gnu/packages/emacs.scm index 5fbbc033b7..8ba645e57a 100644 --- a/gnu/packages/emacs.scm +++ b/gnu/packages/emacs.scm @@ -1409,17 +1409,17 @@ (define* (uncompressed-file-fetch url hash-algo hash (define-public emacs-constants (package (name "emacs-constants") - (version "2.2") + (version "2.6") (home-page "https://staff.fnwi.uva.nl/c.dominik/Tools/constants") (source (origin (file-name (string-append name "-" version ".el")) - (method uncompressed-file-fetch) - (uri (string-append home-page "/constants.el")) ;FIXME: unversioned URI - (patches (search-patches "emacs-constants-lisp-like.patch")) + (method url-fetch) + (uri (string-append "https://github.com/fedeinthemix/emacs-constants" + "/archive/v" version ".tar.gz")) (sha256 (base32 - "14q094aphsjhq8gklv7i5a7byl0ygz63cv3n6b5p8ji2jy0mnnw3")))) + "0pnrpmmxq8mh5h2hbrp5vcym0j0fh6dv3s7c5ccn18wllhzg9g7n")))) (build-system emacs-build-system) (synopsis "Enter definition of constants into an Emacs buffer") (description -- cgit v1.2.3 From 787afdd0f1ce1d4aa7500d858f2635462b444699 Mon Sep 17 00:00:00 2001 From: Ludovic Courtès Date: Tue, 17 May 2016 13:36:44 +0200 Subject: import: Exit with non-zero when an unknown importer is asked. * guix/scripts/import.scm (guix-import): Use 'leave' instead of 'format' when IMPORTER is unknown. --- guix/scripts/import.scm | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/guix/scripts/import.scm b/guix/scripts/import.scm index 7b29794e8f..cf8fc073b2 100644 --- a/guix/scripts/import.scm +++ b/guix/scripts/import.scm @@ -109,5 +109,4 @@ (define (guix-import . args) (if (member importer importers) (let ((expr (apply (resolve-importer importer) args))) (pretty-print expr (newline-rewriting-port (current-output-port)))) - (format (current-error-port) - (_ "guix import: invalid importer~%")))))) + (leave (_ "~a: invalid importer~%") importer))))) -- cgit v1.2.3 From 149590380adb240e0993931b4f72e6f285b24483 Mon Sep 17 00:00:00 2001 From: Ludovic Courtès Date: Tue, 17 May 2016 13:41:07 +0200 Subject: import: Gracefully report import failures. Previously, something like 'guix import gnu which' would spit out a backtrace if, say, the 'which' tarball could not be authenticated. * guix/upstream.scm (download-tarball): Mention failure modes in docstring. * guix/import/gnu.scm (gnu-package->sexp): Return #f when 'download-tarball' returns #f. * guix/scripts/import.scm (guix-import): Call 'leave' when IMPORTER does not return a (package ...) sexp. --- guix/import/gnu.scm | 48 ++++++++++++++++++++++++++---------------------- guix/scripts/import.scm | 8 ++++++-- guix/upstream.scm | 5 +++-- 3 files changed, 35 insertions(+), 26 deletions(-) diff --git a/guix/import/gnu.scm b/guix/import/gnu.scm index 834f0ae5cf..2cfb46beb9 100644 --- a/guix/import/gnu.scm +++ b/guix/import/gnu.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2014, 2015 Ludovic Courtès +;;; Copyright © 2014, 2015, 2016 Ludovic Courtès ;;; ;;; This file is part of GNU Guix. ;;; @@ -55,8 +55,8 @@ (define (preferred-archive-type release) (define* (gnu-package->sexp package release #:key (key-download 'interactive)) "Return the 'package' sexp for the RELEASE (a ) of PACKAGE (a -). Use KEY-DOWNLOAD as the OpenPGP key download policy (see -'download-tarball' for details.)" +), or #f upon failure. Use KEY-DOWNLOAD as the OpenPGP key +download policy (see 'download-tarball' for details.)" (define name (gnu-package-name package)) @@ -79,25 +79,29 @@ (define sig-url (find (cute string-suffix? (string-append archive-type ".sig") <>) (upstream-source-signature-urls release))) - (let ((tarball (with-store store - (download-tarball store url sig-url - #:key-download key-download)))) - `(package - (name ,name) - (version ,(upstream-source-version release)) - (source (origin - (method url-fetch) - (uri (string-append ,url-base version - ,(string-append ".tar." archive-type))) - (sha256 - (base32 - ,(bytevector->nix-base32-string (file-sha256 tarball)))))) - (build-system gnu-build-system) - (synopsis ,(gnu-package-doc-summary package)) - (description ,(gnu-package-doc-description package)) - (home-page ,(match (gnu-package-doc-urls package) - ((head . tail) (qualified-url head)))) - (license find-by-yourself!)))) + (with-store store + (match (download-tarball store url sig-url + #:key-download key-download) + ((? string? tarball) + `(package + (name ,name) + (version ,(upstream-source-version release)) + (source (origin + (method url-fetch) + (uri (string-append ,url-base version + ,(string-append ".tar." archive-type))) + (sha256 + (base32 + ,(bytevector->nix-base32-string + (file-sha256 tarball)))))) + (build-system gnu-build-system) + (synopsis ,(gnu-package-doc-summary package)) + (description ,(gnu-package-doc-description package)) + (home-page ,(match (gnu-package-doc-urls package) + ((head . tail) (qualified-url head)))) + (license find-by-yourself!))) + (#f ;failure to download or authenticate the tarball + #f)))) (define* (gnu->guix-package name #:key (key-download 'interactive)) diff --git a/guix/scripts/import.scm b/guix/scripts/import.scm index cf8fc073b2..e54744feca 100644 --- a/guix/scripts/import.scm +++ b/guix/scripts/import.scm @@ -107,6 +107,10 @@ (define (guix-import . args) (show-version-and-exit "guix import")) ((importer args ...) (if (member importer importers) - (let ((expr (apply (resolve-importer importer) args))) - (pretty-print expr (newline-rewriting-port (current-output-port)))) + (match (apply (resolve-importer importer) args) + ((and expr ('package _ ...)) + (pretty-print expr (newline-rewriting-port + (current-output-port)))) + (x + (leave (_ "'~a' import failed~%") importer))) (leave (_ "~a: invalid importer~%") importer))))) diff --git a/guix/upstream.scm b/guix/upstream.scm index 167c9ff89a..18157376d2 100644 --- a/guix/upstream.scm +++ b/guix/upstream.scm @@ -143,8 +143,9 @@ (define* (download-tarball store url signature-url #:key (key-download 'interactive)) "Download the tarball at URL to the store; check its OpenPGP signature at SIGNATURE-URL, unless SIGNATURE-URL is false. On success, return the tarball -file name. KEY-DOWNLOAD specifies a download policy for missing OpenPGP keys; -allowed values: 'interactive' (default), 'always', and 'never'." +file name; return #f on failure (network failure or authentication failure). +KEY-DOWNLOAD specifies a download policy for missing OpenPGP keys; allowed +values: 'interactive' (default), 'always', and 'never'." (let ((tarball (download-to-store store url))) (if (not signature-url) tarball -- cgit v1.2.3 From aa8fff0cebd8390c2faf733da79d9a1499458261 Mon Sep 17 00:00:00 2001 From: Ludovic Courtès Date: Tue, 17 May 2016 13:50:10 +0200 Subject: store: Clarify 'query-path-hash' docstring. * guix/store.scm (query-path-hash): Clarify docstring. --- guix/store.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/guix/store.scm b/guix/store.scm index f352a99cbd..4d89f4a413 100644 --- a/guix/store.scm +++ b/guix/store.scm @@ -615,7 +615,7 @@ (define-operation (valid-path? (string path)) boolean) (define-operation (query-path-hash (store-path path)) - "Return the SHA256 hash of PATH as a bytevector." + "Return the SHA256 hash of the nar serialization of PATH as a bytevector." base16) (define hash-part->path -- cgit v1.2.3 From 1c29f3ef8452860c4301d7ae57c89ac5956d1663 Mon Sep 17 00:00:00 2001 From: Federico Beffa Date: Tue, 17 May 2016 14:13:56 +0200 Subject: gnu: emacs-constants: Remove old patch. * gnu/packages/patches/emacs-constants-lisp-like.patch: Remove it. * gnu/local.mk (dist_patch_DATA): Remove entry for above patch. --- gnu/local.mk | 1 - .../patches/emacs-constants-lisp-like.patch | 81 ---------------------- 2 files changed, 82 deletions(-) delete mode 100644 gnu/packages/patches/emacs-constants-lisp-like.patch diff --git a/gnu/local.mk b/gnu/local.mk index f64adebb41..4bbded90eb 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -466,7 +466,6 @@ dist_patch_DATA = \ gnu/packages/patches/duplicity-test_selection-tmp.patch \ gnu/packages/patches/elfutils-tests-ptrace.patch \ gnu/packages/patches/einstein-build.patch \ - gnu/packages/patches/emacs-constants-lisp-like.patch \ gnu/packages/patches/emacs-exec-path.patch \ gnu/packages/patches/emacs-scheme-complete-scheme-r5rs-info.patch \ gnu/packages/patches/emacs-source-date-epoch.patch \ diff --git a/gnu/packages/patches/emacs-constants-lisp-like.patch b/gnu/packages/patches/emacs-constants-lisp-like.patch deleted file mode 100644 index 5ec37f3adf..0000000000 --- a/gnu/packages/patches/emacs-constants-lisp-like.patch +++ /dev/null @@ -1,81 +0,0 @@ -Add Scheme support - ---- constants/constants.el.orig 2015-12-26 17:44:31.734520833 +0100 -+++ constants/constants.el 2015-12-30 17:41:28.402871263 +0100 -@@ -684,6 +684,33 @@ - - (eval-when-compile (defvar ctable)) - -+(defun constants-is-lisp-like (mode) -+ (save-match-data -+ (string-match "\\(lisp\\|scheme\\)" (symbol-name mode)))) -+ -+(defun constants-is-set-like () -+ (save-excursion -+ (condition-case nil -+ (save-match-data -+ (progn (up-list -1) -+ (or (looking-at "(set[qf!]?\\>") (looking-at "(define\\>")))) -+ (error nil)))) ; return value nil means use default -+ -+;;;###autoload -+(defun constants-lisp-like-function () -+ "Check context for constants insertion." -+ (if (constants-is-set-like) -+ '(emacs-lisp-mode "%n %v%t; %d %u" "e" "(* %p %v)") -+ '(emacs-lisp-mode "(%n %v)%t; %d %u" "e" "(* %p %v)"))) -+ -+;;;###autoload -+(mapc (lambda (mode-hook) -+ (add-hook mode-hook -+ (lambda () -+ (setq constants-language-function -+ 'constants-lisp-like-function)))) -+ '(scheme-mode-hook emacs-lisp-mode-hook lisp-mode-hook)) -+ - ;;;###autoload - (defun constants-insert (&optional unit-system names) - "Insert one or more natural constant definitions in source code. -@@ -826,8 +853,9 @@ - (funcall process-func ins)) - ;; Here comes the insertion stuff for source code editing modes. - ;; First make sure we start a new line -- (if (string-match -- "\\S-" (buffer-substring (point-at-bol) (point-at-eol))) -+ (if (and (string-match -+ "\\S-" (buffer-substring (point-at-bol) (point-at-eol))) -+ (not (constants-is-lisp-like mode))) - ;; non-empty line, insert after this line - (progn - (end-of-line 1) -@@ -841,13 +869,24 @@ - (if (string-match "\\(.*\\)%t\\(.*\\)" line) - (let ((comment-column 42)) - (insert (match-string 1 line)) -- (indent-to comment-column) -- (insert (match-string 2 line))) -+ (if (and (constants-is-lisp-like mode) -+ (or (constants-is-set-like) -+ (null clist))) -+ (save-excursion -+ (progn -+ (move-to-column comment-column t) -+ (insert (match-string 2 line)) -+ ;; insert a newline such that paredit's M-) can mode -+ ;; the closing parentheses to the next line. -+ (newline-and-indent))) -+ (progn -+ (indent-to comment-column) -+ (insert (match-string 2 line))))) - (insert line))) -- (if constants-indent-code -- (newline-and-indent) -- (newline)))))) -- -+ (unless (and (constants-is-lisp-like mode) (null clist)) -+ (if constants-indent-code -+ (newline-and-indent) -+ (newline))))))) - ;;;###autoload - (defun constants-get (&optional const message) - "Return the value of CONST as defined in the constants package. -- cgit v1.2.3 From 99effc8faa43d478371eb06aee5df8ae1383c51a Mon Sep 17 00:00:00 2001 From: Ludovic Courtès Date: Tue, 17 May 2016 18:04:13 +0200 Subject: lint: Honor 'cpe-name' and 'cpe-version' package properties. * guix/scripts/lint.scm (package-name->cpe-name): Remove. (package-vulnerabilities): Honor 'cpe-name' and 'cpe-version' properties. * gnu/packages/grub.scm (grub)[properties]: New field. * gnu/packages/gnuzilla.scm (icecat)[properties]: Add 'cpe-name' and 'cpe-version'. * doc/guix.texi (Invoking guix lint): Mention 'cpe-name'. --- doc/guix.texi | 13 +++++++++++++ gnu/packages/gnuzilla.scm | 6 +++++- gnu/packages/grub.scm | 5 +++-- guix/scripts/lint.scm | 21 +++++++++------------ 4 files changed, 30 insertions(+), 15 deletions(-) diff --git a/doc/guix.texi b/doc/guix.texi index 0e63ecadfd..3f0106be02 100644 --- a/doc/guix.texi +++ b/doc/guix.texi @@ -4961,6 +4961,19 @@ To view information about a particular vulnerability, visit pages such as: where @code{CVE-YYYY-ABCD} is the CVE identifier---e.g., @code{CVE-2015-7554}. +Package developers can specify in package recipes the +@uref{https://nvd.nist.gov/cpe.cfm,Common Platform Enumeration (CPE)} +name and version of the package when they differ from the name that Guix +uses, as in this example: + +@example +(package + (name "grub") + ;; @dots{} + ;; CPE calls this package "grub2". + (properties '((cpe-name . "grub2")))) +@end example + @item formatting Warn about obvious source code formatting issues: trailing white space, use of tabulations, etc. diff --git a/gnu/packages/gnuzilla.scm b/gnu/packages/gnuzilla.scm index df1075c370..7e52534b8f 100644 --- a/gnu/packages/gnuzilla.scm +++ b/gnu/packages/gnuzilla.scm @@ -517,4 +517,8 @@ (define-public icecat software, which does not recommend non-free plugins and addons. It also features built-in privacy-protecting features.") (license license:mpl2.0) ;and others, see toolkit/content/license.html - (properties '((ftp-directory . "/gnu/gnuzilla"))))) + (properties + `((ftp-directory . "/gnu/gnuzilla") + (cpe-name . "firefox_esr") + (cpe-version . ,(string-drop-right version + (string-length "-gnu1"))))))) diff --git a/gnu/packages/grub.scm b/gnu/packages/grub.scm index 5fc7ee8386..ec2feebbf4 100644 --- a/gnu/packages/grub.scm +++ b/gnu/packages/grub.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2013, 2014, 2015 Ludovic Courtès +;;; Copyright © 2013, 2014, 2015, 2016 Ludovic Courtès ;;; Copyright © 2015 Mark H Weaver ;;; Copyright © 2015 Leo Famulari ;;; @@ -132,4 +132,5 @@ (define-public grub bootloader, GRUB handles the presence of multiple operating systems installed on the same computer; upon booting the computer, the user is presented with a menu to select one of the installed operating systems.") - (license gpl3+))) + (license gpl3+) + (properties '((cpe-name . "grub2"))))) diff --git a/guix/scripts/lint.scm b/guix/scripts/lint.scm index 06001d3eae..b4fdb6f905 100644 --- a/guix/scripts/lint.scm +++ b/guix/scripts/lint.scm @@ -600,15 +600,6 @@ (define (patch-file-name patch) ((? origin?) (and=> (origin-actual-file-name patch) basename)))) -(define (package-name->cpe-name name) - "Do a basic conversion of NAME, a Guix package name, to the corresponding -Common Platform Enumeration (CPE) name." - (match name - ("icecat" "firefox") ;or "firefox_esr" - ("grub" "grub2") - ;; TODO: Add more. - (_ name))) - (define (current-vulnerabilities*) "Like 'current-vulnerabilities', but return the empty list upon networking or HTTP errors. This allows network-less operation and makes problems with @@ -635,9 +626,15 @@ (define package-vulnerabilities (current-vulnerabilities*))))) (lambda (package) "Return a list of vulnerabilities affecting PACKAGE." - ((force lookup) - (package-name->cpe-name (package-name package)) - (package-version package))))) + ;; First we retrieve the Common Platform Enumeration (CPE) name and + ;; version for PACKAGE, then we can pass them to LOOKUP. + (let ((name (or (assoc-ref (package-properties package) + 'cpe-name) + (package-name package))) + (version (or (assoc-ref (package-properties package) + 'cpe-version) + (package-version package)))) + ((force lookup) name version))))) (define (check-vulnerabilities package) "Check for known vulnerabilities for PACKAGE." -- cgit v1.2.3 From bbb5d8aeea213f32e51ae18407aa8941f18a010b Mon Sep 17 00:00:00 2001 From: Ludovic Courtès Date: Tue, 17 May 2016 18:07:08 +0200 Subject: gnu: gd: Specify 'cpe-name'. * gnu/packages/gd.scm (gd)[properties]: New field. --- gnu/packages/gd.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/gnu/packages/gd.scm b/gnu/packages/gd.scm index 6ae5579b9c..769e7cecf2 100644 --- a/gnu/packages/gd.scm +++ b/gnu/packages/gd.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2013 Ludovic Courtès +;;; Copyright © 2013, 2016 Ludovic Courtès ;;; Copyright © 2015 Mark H Weaver ;;; Copyright © 2015 Eric Bavier ;;; @@ -69,7 +69,8 @@ (define-public gd most anything else, on the fly. While not restricted to use on the web, the most common applications of GD involve website development.") (license (non-copyleft "file://COPYING" - "See COPYING file in the distribution.")))) + "See COPYING file in the distribution.")) + (properties '((cpe-name . "libgd"))))) (define-public perl-gd (package -- cgit v1.2.3 From fb2b0f5c87321f5aab0dc13130ef92a76040fbe3 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Tue, 17 May 2016 00:20:17 -0400 Subject: gnu: gd: Fix-CVE-2016-3074. * gnu/packages/patches/gd-CVE-2016-3074.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/gd.scm (gd)[source]: Use it. --- gnu/local.mk | 1 + gnu/packages/gd.scm | 4 +++- gnu/packages/patches/gd-CVE-2016-3074.patch | 36 +++++++++++++++++++++++++++++ 3 files changed, 40 insertions(+), 1 deletion(-) create mode 100644 gnu/packages/patches/gd-CVE-2016-3074.patch diff --git a/gnu/local.mk b/gnu/local.mk index 4bbded90eb..0e461b3209 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -494,6 +494,7 @@ dist_patch_DATA = \ gnu/packages/patches/gcc-cross-environment-variables.patch \ gnu/packages/patches/gcc-libvtv-runpath.patch \ gnu/packages/patches/gcc-5.0-libvtv-runpath.patch \ + gnu/packages/patches/gd-CVE-2016-3074.patch \ gnu/packages/patches/geoclue-config.patch \ gnu/packages/patches/ghostscript-CVE-2015-3228.patch \ gnu/packages/patches/ghostscript-runpath.patch \ diff --git a/gnu/packages/gd.scm b/gnu/packages/gd.scm index 769e7cecf2..e52a030f86 100644 --- a/gnu/packages/gd.scm +++ b/gnu/packages/gd.scm @@ -2,6 +2,7 @@ ;;; Copyright © 2013, 2016 Ludovic Courtès ;;; Copyright © 2015 Mark H Weaver ;;; Copyright © 2015 Eric Bavier +;;; Copyright © 2016 Leo Famulari ;;; ;;; This file is part of GNU Guix. ;;; @@ -48,7 +49,8 @@ (define-public gd "libgd-" version ".tar.xz")) (sha256 (base32 - "11djy9flzxczphigqgp7fbbblbq35gqwwhn9xfcckawlapa1xnls")))) + "11djy9flzxczphigqgp7fbbblbq35gqwwhn9xfcckawlapa1xnls")) + (patches (search-patches "gd-CVE-2016-3074.patch")))) (build-system gnu-build-system) (native-inputs `(("pkg-config" ,pkg-config))) diff --git a/gnu/packages/patches/gd-CVE-2016-3074.patch b/gnu/packages/patches/gd-CVE-2016-3074.patch new file mode 100644 index 0000000000..a90c51d77b --- /dev/null +++ b/gnu/packages/patches/gd-CVE-2016-3074.patch @@ -0,0 +1,36 @@ +Adapted from upstream commit 2bb97f407c1145c850416a3bfbcc8cf124e68a19 +(gd2: handle corrupt images better (CVE-2016-3074)). + +This patch omits the upstream changes to '.gitignore', and the test +added in files 'tests/Makefile.am', 'tests/gd2/gd2_read_corrupt.c', and +'tests/gd2/invalid_neg_size.gd2'. + +We omit the test because its input data, +'tests/gd2/invalid_neg_size.gd2', is provided as a binary Git diff, +which is not supported by `patch`. + +https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2016-3074 +https://github.com/libgd/libgd/commit/2bb97f407c1145c850416a3bfbcc8cf124e68a19 +--- + .gitignore | 1 + + src/gd_gd2.c | 2 ++ + tests/Makefile.am | 3 ++- + tests/gd2/gd2_read_corrupt.c | 25 +++++++++++++++++++++++++ + tests/gd2/invalid_neg_size.gd2 | Bin 0 -> 1676 bytes + 5 files changed, 30 insertions(+), 1 deletion(-) + create mode 100644 tests/gd2/gd2_read_corrupt.c + create mode 100644 tests/gd2/invalid_neg_size.gd2 + +diff --git a/src/gd_gd2.c b/src/gd_gd2.c +index 6f28461..a50b33d 100644 +--- a/src/gd_gd2.c ++++ b/src/gd_gd2.c +@@ -165,6 +165,8 @@ _gd2GetHeader (gdIOCtxPtr in, int *sx, int *sy, + if (gdGetInt (&cidx[i].size, in) != 1) { + goto fail2; + }; ++ if (cidx[i].offset < 0 || cidx[i].size < 0) ++ goto fail2; + }; + *chunkIdx = cidx; + }; -- cgit v1.2.3 From 9576cc72dc4f2973551c72951e64e5bf6240ff6b Mon Sep 17 00:00:00 2001 From: humanitiesNerd Date: Tue, 17 May 2016 10:54:13 +0200 Subject: gnu: Add emacs-zenburn-theme. * gnu/packages/emacs.scm (emacs-zenburn-theme): New variable. Signed-off-by: Alex Kost --- gnu/packages/emacs.scm | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) diff --git a/gnu/packages/emacs.scm b/gnu/packages/emacs.scm index 8ba645e57a..32ed72218b 100644 --- a/gnu/packages/emacs.scm +++ b/gnu/packages/emacs.scm @@ -8,6 +8,7 @@ ;;; Copyright © 2016 Nils Gillmann ;;; Copyright © 2016 Chris Marusich ;;; Copyright © 2015, 2016 Christopher Allan Webber +;;; Copyright © 2016 humanitiesNerd ;;; ;;; This file is part of GNU Guix. ;;; @@ -1588,3 +1589,26 @@ (define-public emacs-ffap-rfc-space that it correctly finds RFCs even when a space appears before the number.") (license license:gpl3+))) + +(define-public emacs-zenburn-theme + (package + (name "emacs-zenburn-theme") + (version "2.4") + (source (origin + (method url-fetch) + (uri (string-append + "https://github.com/bbatsov/zenburn-emacs/archive/v" + version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "0lyi84bm8sa7vj40n6zg6rlbsmi53mi1y9xn6gkjj29s5zbcnlg7")))) + (build-system emacs-build-system) + (home-page "http://github.com/bbatsov/zenburn-emacs") + (synopsis "Low contrast color theme for Emacs") + (description + "Zenburn theme is a port of the popular Vim Zenburn theme for Emacs. +It is built on top of the custom theme support in Emacs 24 or later.") + (license license:gpl3+))) + + -- cgit v1.2.3 From ad42be838811118f983d51d4560d158a729ebf1b Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Tue, 17 May 2016 14:31:09 -0400 Subject: gnu: libndp: Update to 1.6 [fixes CVE-2016-3698]. * gnu/packages/networking.scm (libndp): Update to 1.6. --- gnu/packages/networking.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/networking.scm b/gnu/packages/networking.scm index 306a3a0218..ffad1db2f2 100644 --- a/gnu/packages/networking.scm +++ b/gnu/packages/networking.scm @@ -138,14 +138,14 @@ (define-public zeromq (define-public libndp (package (name "libndp") - (version "1.5") + (version "1.6") (source (origin (method url-fetch) (uri (string-append "http://libndp.org/files/" name "-" version ".tar.gz")) (sha256 (base32 - "15f743hjc7yy2sv3hzvfc27s1gny4mh5aww59vn195fff2midwgs")))) + "03mczwrxqbp54msafxzzyhaazkvjdwm2kipjkrb5xg8kw22glz8c")))) (build-system gnu-build-system) (home-page "http://libndp.org/") (synopsis "Library for Neighbor Discovery Protocol") -- cgit v1.2.3 From f1876bfc7a7dcb9516fff1b2c82f3c52b16c2ab5 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Thu, 17 Mar 2016 03:59:31 -0400 Subject: gnu: Add signify. * gnu/packages/crypto.scm (signify): New variable. --- gnu/packages/crypto.scm | 42 ++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 42 insertions(+) diff --git a/gnu/packages/crypto.scm b/gnu/packages/crypto.scm index a8d675be4c..08eb146cf7 100644 --- a/gnu/packages/crypto.scm +++ b/gnu/packages/crypto.scm @@ -1,6 +1,7 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2014 David Thompson ;;; Copyright © 2015 Ricardo Wurmus +;;; Copyright © 2016 Leo Famulari ;;; ;;; This file is part of GNU Guix. ;;; @@ -19,6 +20,8 @@ (define-module (gnu packages crypto) #:use-module (gnu packages) + #:use-module (gnu packages pkg-config) + #:use-module (gnu packages libbsd) #:use-module (guix licenses) #:use-module (guix packages) #:use-module (guix download) @@ -46,3 +49,42 @@ (define-public libsodium communication, encryption, decryption, signatures, etc.") (license isc) (home-page "http://libsodium.org"))) + +(define-public signify + (package + (name "signify") + (version "17") + (source (origin + (method url-fetch) + (uri (string-append "https://github.com/aperezdc/signify/" + "archive/v" version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "0kfv2k1fqck31vwlnicavb0h541ilad9zd7j8zz8x2kx36wwqpr7")))) + (build-system gnu-build-system) + ;; TODO Build with libwaive (described in README.md), to implement something + ;; like OpenBSD's pledge(). + (arguments + `(#:tests? #f ; no test suite + #:make-flags + (list "CC=gcc" + (string-append "PREFIX=" (assoc-ref %outputs "out"))) + #:phases + (modify-phases %standard-phases + (delete 'configure)))) + (native-inputs + `(("pkg-config" ,pkg-config))) + (inputs + `(("libbsd" ,libbsd))) + (synopsis "Create and verify cryptographic signatures") + (description "The signify utility creates and verifies cryptographic +signatures using the elliptic curve Ed25519. This is a Linux port of the +OpenBSD tool of the same name.") + (home-page "https://github.com/aperezdc/signify") + ;; This package includes third-party code that was originally released under + ;; various non-copyleft licenses. See the source files for clarification. + (license (list bsd-3 bsd-4 expat isc public-domain + (non-copyleft "file://base64.c" + "See base64.c in the distribution for + the license from IBM."))))) -- cgit v1.2.3 From dbd40ac19df16bb2ef0387c5fcbe8103b6b64840 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Wed, 18 May 2016 10:52:41 +0300 Subject: gnu: python2-pandas: Fix native-inputs. * gnu/packages/python.scm (python2-pandas)[native-inputs]: Use python2- versions of python-panda's native-inputs, not of inputs. --- gnu/packages/python.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 6eb244356b..1929f83a16 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -1017,7 +1017,7 @@ (define-public python2-pandas (package (inherit base) (native-inputs `(("python2-setuptools" ,python2-setuptools) - ,@(package-inputs base)))))) + ,@(package-native-inputs base)))))) (define-public python-tzlocal (package -- cgit v1.2.3 From e62ffce538649f97da702fc1080fa06668df10e7 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 26 Apr 2016 16:08:47 +0200 Subject: gnu: Add Piranha. * gnu/packages/bioinformatics.scm (piranha): New variable. --- gnu/packages/bioinformatics.scm | 64 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 64 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 60cf6b7007..1f7972870c 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -5051,6 +5051,70 @@ (define-public r-zlibbioc libraries for systems that do not have these available via other means.") (license license:artistic2.0))) +(define-public piranha + (package + (name "piranha") + (version "1.1.3") + (source (origin + (method url-fetch) + (uri (string-append "https://github.com/smithlabcode/piranha" + "/archive/svn/tags/piranha-" + version ".tar.gz")) + (sha256 + (base32 + "1lczxff01n4139w7xwqamlb36g9hgrcy93gh03nqszhwb8ivsrqd")))) + (build-system gnu-build-system) + (arguments + `(#:test-target "test" + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'copy-smithlab-cpp + (lambda* (#:key inputs #:allow-other-keys) + (mkdir "src/smithlab_cpp") + (for-each (lambda (file) + (install-file file "./src/smithlab_cpp/")) + (find-files (assoc-ref inputs "smithlab-cpp"))) + #t)) + (add-after 'install 'install-to-store + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (bin (string-append out "/bin"))) + (mkdir-p bin) + (for-each (lambda (file) + (install-file file bin)) + (find-files "bin" ".*"))) + #t))) + #:configure-flags + (list (string-append "--with-bam_tools_headers=" + (assoc-ref %build-inputs "bamtools") "/include/bamtools") + (string-append "--with-bam_tools_library=" + (assoc-ref %build-inputs "bamtools") "/lib/bamtools")))) + (inputs + `(("bamtools" ,bamtools) + ("samtools" ,samtools-0.1) + ("gsl" ,gsl) + ("smithlab-cpp" + ,(let ((commit "3723e2d")) + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/smithlabcode/smithlab_cpp.git") + (commit commit))) + (file-name (string-append "smithlab_cpp-" commit "-checkout")) + (sha256 + (base32 + "0l4gvbwslw5ngziskja41c00x1r06l3yidv7y0xw9djibhykzy0g"))))))) + (native-inputs + `(("python" ,python-2))) + (home-page "https://github.com/smithlabcode/piranha") + (synopsis "Peak-caller for CLIP-seq and RIP-seq data") + (description + "Piranha is a peak-caller for genomic data produced by CLIP-seq and +RIP-seq experiments. It takes input in BED or BAM format and identifies +regions of statistically significant read enrichment. Additional covariates +may optionally be provided to further inform the peak-calling process.") + (license license:gpl3+))) + (define-public pepr (package (name "pepr") -- cgit v1.2.3 From 7c544991dcee6cf8f79484f12a8249ede38d2dd2 Mon Sep 17 00:00:00 2001 From: Ben Woodcroft Date: Wed, 18 May 2016 21:21:09 +1000 Subject: gnu: diamond: Do not specify target architecture. * gnu/packages/bioinformatics.scm (diamond)[arguments]: Do not specify target architecture. --- gnu/packages/bioinformatics.scm | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 1f7972870c..8cec840c6c 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1494,7 +1494,13 @@ (define-public diamond "1dqancz32c2l7w1b2vkvh5zqa2jnf99j1c41djnx1l8pxn044zdc")))) (build-system cmake-build-system) (arguments - '(#:tests? #f)) ; no "check" target + '(#:tests? #f ; no "check" target + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'remove-native-compilation + (lambda _ + (substitute* "CMakeLists.txt" (("-march=native") "")) + #t))))) (inputs `(("zlib" ,zlib))) (home-page "https://github.com/bbuchfink/diamond") -- cgit v1.2.3 From 614f39271e580e99df5ce46f1482580c673791b0 Mon Sep 17 00:00:00 2001 From: Manolis Ragkousis Date: Wed, 18 May 2016 15:14:39 +0300 Subject: gnu: gnumach-headers: Update to 1.7. * gnu/packages/hurd.scm (gnumach-headers): Update to version 1.7. --- gnu/packages/hurd.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/hurd.scm b/gnu/packages/hurd.scm index ff29aee489..4fb0869399 100644 --- a/gnu/packages/hurd.scm +++ b/gnu/packages/hurd.scm @@ -32,7 +32,7 @@ (define-module (gnu packages hurd) (define-public gnumach-headers (package (name "gnumach-headers") - (version "1.6") + (version "1.7") (source (origin (method url-fetch) @@ -40,7 +40,7 @@ (define-public gnumach-headers version ".tar.gz")) (sha256 (base32 - "1m7xwsrv6x6gk9xi5phs104rdn9q3lr63p348vyv0dzd6r3zyncb")))) + "1vd0bykshf6ilr55792b5lf6yd5ywlkp1wqz00dcsx7fq3rfadz2")))) (build-system gnu-build-system) (arguments `(#:phases (alist-replace -- cgit v1.2.3 From eb3be3a79163fa57b09c1fb2c3f20d7f3e26186b Mon Sep 17 00:00:00 2001 From: Manolis Ragkousis Date: Wed, 18 May 2016 15:15:05 +0300 Subject: gnu: mig: Update to 1.7. * gnu/packages/hurd.scm (mig): Update to version 1.7. --- gnu/packages/hurd.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/hurd.scm b/gnu/packages/hurd.scm index 4fb0869399..360e3a65ee 100644 --- a/gnu/packages/hurd.scm +++ b/gnu/packages/hurd.scm @@ -66,7 +66,7 @@ (define-public gnumach-headers (define-public mig (package (name "mig") - (version "1.6") + (version "1.7") (source (origin (method url-fetch) @@ -74,7 +74,7 @@ (define-public mig version ".tar.gz")) (sha256 (base32 - "1i9qd6j5g8wsv9k9n6vpdqflyw0284wyayb2s2h7pp4yyi2jsksk")))) + "1hxqd8p14pgamgavmbmziswvd1zvwqx7lgc9qga805q9jrs93q2b")))) (build-system gnu-build-system) ;; Flex is needed both at build and run time. (inputs `(("gnumach-headers" ,gnumach-headers) -- cgit v1.2.3 From 0affdfb80554833648efab5f9e348c4a9698955b Mon Sep 17 00:00:00 2001 From: Manolis Ragkousis Date: Wed, 18 May 2016 15:15:41 +0300 Subject: gnu: hurd-headers: Update to 0.8. * gnu/packages/hurd.scm (hurd-headers): Update to version 0.8. --- gnu/packages/hurd.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/hurd.scm b/gnu/packages/hurd.scm index 360e3a65ee..7a0a158899 100644 --- a/gnu/packages/hurd.scm +++ b/gnu/packages/hurd.scm @@ -97,14 +97,14 @@ (define-public mig (define-public hurd-headers (package (name "hurd-headers") - (version "0.7") + (version "0.8") (source (origin (method url-fetch) (uri (string-append "mirror://gnu/hurd/hurd-" version ".tar.gz")) (sha256 (base32 - "1q2pyc16vb5plqi8hlwnnc9jk8zlifm91cavz6x7vhbwy0nh2yvh")))) + "1pbc4aqgzxvkgivw80ghp3w755cl0fwxmg357vq7chimj64jk78d")))) (build-system gnu-build-system) (native-inputs `(;; Autoconf shouldn't be necessary but there seems to be a bug in the -- cgit v1.2.3 From bd9fe0f03b461bf33852d4cdb654459d5587aca0 Mon Sep 17 00:00:00 2001 From: Ben Woodcroft Date: Mon, 25 Apr 2016 13:03:17 +1000 Subject: gnu: Add krona-tools. * gnu/packages/web.scm (krona-tools): New variable. --- gnu/packages/web.scm | 96 ++++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 96 insertions(+) diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm index 5df4765d3c..bd30da2533 100644 --- a/gnu/packages/web.scm +++ b/gnu/packages/web.scm @@ -11,6 +11,7 @@ ;;; Copyright © 2016 Jelle Licht ;;; Copyright © 2016 Efraim Flashner ;;; Copyright © 2016 Rene Saavedra +;;; Copyright © 2016 Ben Woodcroft ;;; ;;; This file is part of GNU Guix. ;;; @@ -56,6 +57,7 @@ (define-module (gnu packages web) #:use-module (gnu packages icu4c) #:use-module (gnu packages lua) #:use-module (gnu packages base) + #:use-module (gnu packages perl) #:use-module (gnu packages python) #:use-module (gnu packages pcre) #:use-module (gnu packages pkg-config) @@ -274,6 +276,100 @@ (define-public json-c parse JSON formatted strings back into the C representation of JSON objects.") (license l:x11))) +(define-public krona-tools + (package + (name "krona-tools") + (version "2.6.1") + (source (origin + (method url-fetch) + (uri (string-append + "https://github.com/marbl/Krona/releases/download/v" + version "/KronaTools-" version ".tar")) + (sha256 + (base32 + "1fj5mf6wbwz7v74n2safbw7fpw32fik19vf0wdbc2srn82i8fiwz")))) + (build-system perl-build-system) + (arguments + `(#:tests? #f ; no tests + #:phases + (modify-phases %standard-phases + ;; There is no configure or build steps. + (delete 'configure) + (replace 'build + ;; Remove 'use lib' statements from scripts as PERL5LIB is set + ;; correctly during installation. + (lambda _ + (for-each + (lambda (executable) + (display executable)(display "\n") + (substitute* executable + (("use lib \\(`ktGetLibPath`\\);") ""))) + (find-files "scripts/" ".*")) + #t)) + ;; Install script "install.pl" expects the build directory to remain + ;; after installation, creating symlinks etc., so re-implement it + ;; here. + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let ((bin (string-append (assoc-ref outputs "out") "/bin")) + (perl (string-append (assoc-ref outputs "out") + "/lib/perl5/site_perl")) + (share (string-append + (assoc-ref outputs "out") "/share/krona-tools"))) + (mkdir-p bin) + (for-each + (lambda (script) + (let* ((executable (string-append "scripts/" script ".pl"))) + ;; Prefix executables with 'kt' as install script does. + (copy-file executable (string-append bin "/kt" script)))) + '("ClassifyBLAST" + "GetContigMagnitudes" + "GetTaxIDFromGI" + "ImportBLAST" + "ImportDiskUsage" + "ImportEC" + "ImportFCP" + "ImportGalaxy" + "ImportKrona" + "ImportMETAREP-BLAST" + "ImportMETAREP-EC" + "ImportMGRAST" + "ImportPhymmBL" + "ImportRDP" + "ImportRDPComparison" + "ImportTaxonomy" + "ImportText" + "ImportXML")) + (mkdir-p share) + (copy-recursively "data" (string-append share "/data")) + (copy-recursively "img" (string-append share "/img")) + (copy-recursively "taxonomy" (string-append share "/taxonomy")) + (substitute* '("lib/KronaTools.pm") + (("taxonomyDir = \".libPath/../taxonomy\"") + (string-append "taxonomyDir = \"" share "/taxonomy\""))) + (install-file "lib/KronaTools.pm" perl)))) + (add-after 'install 'wrap-program + (lambda* (#:key inputs outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (path (getenv "PERL5LIB"))) + (for-each + (lambda (executable) + (wrap-program executable + `("PERL5LIB" ":" prefix + (,(string-append out "/lib/perl5/site_perl"))))) + (find-files (string-append out "/bin/") ".*")))))))) + (inputs + `(("perl" ,perl))) + (home-page "https://github.com/marbl/Krona/wiki") + (synopsis "Hierarchical data exploration with zoomable HTML5 pie charts") + (description + "Krona is a flexible tool for exploring the relative proportions of +hierarchical data, such as metagenomic classifications, using a radial, +space-filling display. It is implemented using HTML5 and JavaScript, allowing +charts to be explored locally or served over the Internet, requiring only a +current version of any major web browser.") + (license l:bsd-3))) + (define-public rapidjson (package (name "rapidjson") -- cgit v1.2.3 From 65e46ca0ede8e7a150215f6bfd9ea756c8239085 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Wed, 18 May 2016 18:06:47 +0300 Subject: gnu: qtkeychain: Update to 0.6.2. * gnu/packages/qt.scm (qtkeychain): Update to 0.6.2. --- gnu/packages/qt.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/qt.scm b/gnu/packages/qt.scm index 097ec06d2a..47720384c2 100644 --- a/gnu/packages/qt.scm +++ b/gnu/packages/qt.scm @@ -2,7 +2,7 @@ ;;; Copyright © 2013, 2014, 2015 Andreas Enge ;;; Copyright © 2015 Sou Bunnbu ;;; Copyright © 2015 Ludovic Courtès -;;; Copyright © 2015 Efraim Flashner +;;; Copyright © 2015, 2016 Efraim Flashner ;;; ;;; This file is part of GNU Guix. ;;; @@ -505,7 +505,7 @@ (define-public python-pyqt-4 (define-public qtkeychain (package (name "qtkeychain") - (version "0.5.0") + (version "0.6.2") (source (origin (method url-fetch) @@ -513,7 +513,7 @@ (define-public qtkeychain "archive/v" version ".tar.gz")) (file-name (string-append name "-" version ".tar.gz")) (sha256 - (base32 "055mkd4pz6cyff4cw0784wjc1w92m8x223sxi96ph15fr3lplbg6")))) + (base32 "0g76pa786mg0fxy52hrljw09dvi6kffk2ms42lxapvpy6j94a4xf")))) (build-system cmake-build-system) (inputs `(("qt" ,qt))) -- cgit v1.2.3 From 64851f4a23f133901f5086dcd5ae4d4c0687164c Mon Sep 17 00:00:00 2001 From: Kei Yamashita Date: Tue, 17 May 2016 18:52:16 -0400 Subject: gnu: wmbattery: Fix UPower-related memory leak. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/gnustep.scm (wmbattery)[source](snippet): New field. Signed-off-by: Ludovic Courtès --- gnu/packages/gnustep.scm | 12 ++++++++++-- 1 file changed, 10 insertions(+), 2 deletions(-) diff --git a/gnu/packages/gnustep.scm b/gnu/packages/gnustep.scm index 31fca5b504..30574fca18 100644 --- a/gnu/packages/gnustep.scm +++ b/gnu/packages/gnustep.scm @@ -1,6 +1,6 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2014 Ludovic Courtès -;;; Copyright © 2016 Kei Yamashita +;;; Copyright © 2016 Kei Kebreau ;;; ;;; This file is part of GNU Guix. ;;; @@ -101,7 +101,15 @@ (define-public wmbattery version ".orig.tar.gz")) (sha256 (base32 - "0hi6bivv3xd2k68w08krndfl68wdx7nmc2wjzsmcd4q3qgwgyk44")))) + "0hi6bivv3xd2k68w08krndfl68wdx7nmc2wjzsmcd4q3qgwgyk44")) + (modules '((guix build utils))) + (snippet + ;; Fix memory leak: + ;; . + '(substitute* "upower.c" + (("up = up_client_new\\(\\);") + (string-append "if (!up)\n" + " up = up_client_new();")))))) (build-system gnu-build-system) (arguments `(#:tests? #f ; no "check" target -- cgit v1.2.3 From 91231156ce321058d82e6272135a4457e004f438 Mon Sep 17 00:00:00 2001 From: Ludovic Courtès Date: Wed, 18 May 2016 21:59:38 +0200 Subject: gnu: Add ntfs-3g. * gnu/packages/linux.scm (ntfs-3g): New variable. --- gnu/packages/linux.scm | 35 +++++++++++++++++++++++++++++++++++ 1 file changed, 35 insertions(+) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 97514c7b8e..ba8dce09e7 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -2671,3 +2671,38 @@ (define-public thinkfan other @code{hwmon} driver that enables temperature reading and fan control from userspace.") (license license:gpl3+))) + +(define-public ntfs-3g + (package + (name "ntfs-3g") + (version "2016.2.22") + (source (origin + (method url-fetch) + (uri (string-append "https://tuxera.com/opensource/" + "ntfs-3g_ntfsprogs-" version ".tgz")) + (sha256 + (base32 + "180y5y09h30ryf2vim8j30a2npwz1iv9ly5yjmh3wjdkwh2jrdyp")) + (modules '((guix build utils))) + (snippet + ;; Install under $prefix. + '(substitute* '("src/Makefile.in" "ntfsprogs/Makefile.in") + (("/sbin") + "@sbindir@"))))) + (build-system gnu-build-system) + (inputs `(("util-linux" ,util-linux) + ("fuse" ,fuse))) ;libuuid + (native-inputs `(("pkg-config" ,pkg-config))) + (arguments + '(#:configure-flags (list "--exec-prefix=${prefix}" + "--with-fuse=external" ;use our own FUSE + "--enable-mount-helper" + "--enable-posix-acls" + "--enable-xattr-mappings"))) + (home-page "http://www.tuxera.com/community/open-source-ntfs-3g/") + (synopsis "Read-write access to NTFS file systems") + (description + "NTFS-3G provides read-write access to NTFS file systems, which are +commonly found on Microsoft Windows. It is implemented as a FUSE file system. +The package provides additional NTFS tools.") + (license license:gpl2+))) -- cgit v1.2.3 From b7b27a8f28746a488eeee489c71053059dc5a8dc Mon Sep 17 00:00:00 2001 From: Kei Yamashita Date: Tue, 17 May 2016 20:36:17 -0400 Subject: gnu: octave: Update to 4.0.2. * gnu/packages/maths.scm (octave): Update to 4.0.2. [inputs]: Added cyrus-sasl, openssl. Signed-off-by: Efraim Flashner --- gnu/packages/maths.scm | 16 +++++++++++----- 1 file changed, 11 insertions(+), 5 deletions(-) diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index a7941187d1..2926c1c4c9 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -11,6 +11,7 @@ ;;; Copyright © 2015, 2016 Efraim Flashner ;;; Copyright © 2015 Fabian Harfert ;;; Copyright © 2016 Roel Janssen +;;; Copyright © 2016 Kei Kebreau ;;; ;;; This file is part of GNU Guix. ;;; @@ -46,6 +47,7 @@ (define-module (gnu packages maths) #:use-module (gnu packages cmake) #:use-module (gnu packages compression) #:use-module (gnu packages curl) + #:use-module (gnu packages cyrus-sasl) #:use-module (gnu packages documentation) #:use-module (gnu packages elf) #:use-module (gnu packages flex) @@ -79,6 +81,7 @@ (define-module (gnu packages maths) #:use-module (gnu packages tcl) #:use-module (gnu packages texinfo) #:use-module (gnu packages texlive) + #:use-module (gnu packages tls) #:use-module (gnu packages wxwidgets) #:use-module (gnu packages xml) #:use-module (gnu packages zip) @@ -583,7 +586,7 @@ (define-public nlopt (define-public octave (package (name "octave") - (version "4.0.0") + (version "4.0.2") (source (origin (method url-fetch) @@ -591,7 +594,7 @@ (define-public octave version ".tar.gz")) (sha256 (base32 - "101jr9yck798586jz4vkjcgk36zksmxf1pxrzvipgn2xgyay0zjc")))) + "1hdxap3j88rpqjimnfhinym6z73wdi5dfa6fv85c13r1dk9qzk9r")))) (build-system gnu-build-system) (inputs `(("lapack" ,lapack) @@ -602,6 +605,7 @@ (define-public octave ("arpack" ,arpack-ng) ("curl" ,curl) ("pcre" ,pcre) + ("cyrus-sasl" ,cyrus-sasl) ("fltk" ,fltk) ("fontconfig" ,fontconfig) ("freetype" ,freetype) @@ -609,6 +613,7 @@ (define-public octave ("libxft" ,libxft) ("mesa" ,mesa) ("glu" ,glu) + ("openssl" ,openssl) ("zlib" ,zlib))) (native-inputs `(("gfortran" ,gfortran) @@ -626,9 +631,10 @@ (define-public octave ("ghostscript" ,ghostscript) ("gnuplot" ,gnuplot))) (arguments - `(#:configure-flags (list (string-append "--with-shell=" - (assoc-ref %build-inputs "bash") - "/bin/sh")))) + `(#:configure-flags + (list (string-append "--with-shell=" + (assoc-ref %build-inputs "bash") + "/bin/sh")))) (home-page "http://www.gnu.org/software/octave/") (synopsis "High-level language for numerical computation") (description "GNU Octave is a high-level interpreted language that is -- cgit v1.2.3 From 21f05134fc35edf5a15baf4fdb2e62905f3848e9 Mon Sep 17 00:00:00 2001 From: Kei Kebreau Date: Wed, 18 May 2016 09:58:47 -0400 Subject: Update name for Kei Kebreau. * .mailmap: Add Kei Kebreau. * gnu/local.mk: Replace "Kei Yamashita" with "Kei Kebreau". * gnu/packages/calendar.scm: Likewise. * gnu/packages/dillo.scm: Likewise. * gnu/packages/fltk.scm: Likewise. * gnu/packages/game-development.scm: Likewise. * gnu/packages/games.scm: Likewise. * gnu/packages/gnome.scm: Likewise. * gnu/packages/gtk.scm: Likewise. * gnu/packages/music.scm: Likewise. * gnu/packages/xfce.scm: Likewise. Signed-off-by: Alex Kost --- .mailmap | 1 + gnu/local.mk | 2 +- gnu/packages/calendar.scm | 2 +- gnu/packages/dillo.scm | 2 +- gnu/packages/fltk.scm | 2 +- gnu/packages/game-development.scm | 2 +- gnu/packages/games.scm | 2 +- gnu/packages/gnome.scm | 2 +- gnu/packages/gtk.scm | 2 +- gnu/packages/music.scm | 2 +- gnu/packages/xfce.scm | 2 +- 11 files changed, 11 insertions(+), 10 deletions(-) diff --git a/.mailmap b/.mailmap index 8f61e0efae..21841c1a0a 100644 --- a/.mailmap +++ b/.mailmap @@ -24,6 +24,7 @@ Joshua Grant Joshua Grant Joshua Grant Joshua Grant +Kei Kebreau Leo Famulari Ludovic Courtès Mathieu Lirzin diff --git a/gnu/local.mk b/gnu/local.mk index 0e461b3209..3fa27925ec 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -4,7 +4,7 @@ # Copyright © 2016 Mathieu Lirzin # Copyright © 2013, 2014, 2015, 2016 Mark H Weaver # Copyright © 2016 Chris Marusich -# Copyright © 2016 Kei Yamashita +# Copyright © 2016 Kei Kebreau # # This file is part of GNU Guix. # diff --git a/gnu/packages/calendar.scm b/gnu/packages/calendar.scm index ff57ba10b3..3b5aba72c8 100644 --- a/gnu/packages/calendar.scm +++ b/gnu/packages/calendar.scm @@ -1,7 +1,7 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2015 David Thompson ;;; Copyright © 2015, 2016 Leo Famulari -;;; Copyright © 2016 Kei Yamashita +;;; Copyright © 2016 Kei Kebreau ;;; Copyright © 2016 Efraim Flashner ;;; ;;; This file is part of GNU Guix. diff --git a/gnu/packages/dillo.scm b/gnu/packages/dillo.scm index 0fd84d9177..6e0c4d17a9 100644 --- a/gnu/packages/dillo.scm +++ b/gnu/packages/dillo.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2016 Kei Yamashita +;;; Copyright © 2016 Kei Kebreau ;;; ;;; This file is part of GNU Guix. ;;; diff --git a/gnu/packages/fltk.scm b/gnu/packages/fltk.scm index bc6b4ab5e6..27d2f62ca7 100644 --- a/gnu/packages/fltk.scm +++ b/gnu/packages/fltk.scm @@ -2,7 +2,7 @@ ;;; Copyright © 2014 John Darrington ;;; Copyright © 2015 Eric Bavier ;;; Copyright © 2015 Ricardo Wurmus -;;; Copyright © 2016 Kei Yamashita +;;; Copyright © 2016 Kei Kebreau ;;; ;;; This file is part of GNU Guix. ;;; diff --git a/gnu/packages/game-development.scm b/gnu/packages/game-development.scm index f6b3c0bbb7..56617bb895 100644 --- a/gnu/packages/game-development.scm +++ b/gnu/packages/game-development.scm @@ -6,7 +6,7 @@ ;;; Copyright © 2015 Alex Kost ;;; Copyright © 2015, 2016 David Thompson ;;; Copyright © 2016 Efraim Flashner -;;; Copyright © 2016 Kei Yamashita +;;; Copyright © 2016 Kei Kebreau ;;; ;;; This file is part of GNU Guix. ;;; diff --git a/gnu/packages/games.scm b/gnu/packages/games.scm index 1af40e9409..fc16862471 100644 --- a/gnu/packages/games.scm +++ b/gnu/packages/games.scm @@ -18,7 +18,7 @@ ;;; Copyright © 2016 Manolis Fragkiskos Ragkousis ;;; Copyright © 2016 Nils Gillmann ;;; Copyright © 2016 Albin Söderqvist -;;; Copyright © 2016 Kei Yamashita +;;; Copyright © 2016 Kei Kebreau ;;; Copyright © 2016 Alex Griffin ;;; ;;; This file is part of GNU Guix. diff --git a/gnu/packages/gnome.scm b/gnu/packages/gnome.scm index 8963e3fca6..c42dfc26e0 100644 --- a/gnu/packages/gnome.scm +++ b/gnu/packages/gnome.scm @@ -15,7 +15,7 @@ ;;; Copyright © 2016 Rene Saavedra ;;; Copyright © 2016 Jochem Raat ;;; Copyright © 2016 Rene Saavedra -;;; Copyright © 2016 Kei Yamashita +;;; Copyright © 2016 Kei Kebreau ;;; Copyright © 2016 Jan Nieuwenhuizen ;;; ;;; This file is part of GNU Guix. diff --git a/gnu/packages/gtk.scm b/gnu/packages/gtk.scm index 8abf16ef36..1fe52a4b83 100644 --- a/gnu/packages/gtk.scm +++ b/gnu/packages/gtk.scm @@ -10,7 +10,7 @@ ;;; Copyright © 2015 David Hashe ;;; Copyright © 2016 Efraim Flashner ;;; Copyright © 2016 Fabian Harfert -;;; Copyright © 2016 Kei Yamashita +;;; Copyright © 2016 Kei Kebreau ;;; ;;; This file is part of GNU Guix. ;;; diff --git a/gnu/packages/music.scm b/gnu/packages/music.scm index 39e261df8c..f2787ee2d1 100644 --- a/gnu/packages/music.scm +++ b/gnu/packages/music.scm @@ -5,7 +5,7 @@ ;;; Copyright © 2016 Al McElrath ;;; Copyright © 2016 Efraim Flashner ;;; Copyright © 2016 Leo Famulari -;;; Copyright © 2016 Kei Yamashita +;;; Copyright © 2016 Kei Kebreau ;;; ;;; This file is part of GNU Guix. ;;; diff --git a/gnu/packages/xfce.scm b/gnu/packages/xfce.scm index c164c66a18..c201f03ab5 100644 --- a/gnu/packages/xfce.scm +++ b/gnu/packages/xfce.scm @@ -3,7 +3,7 @@ ;;; Copyright © 2014, 2015 Mark H Weaver ;;; Copyright © 2016 Andreas Enge ;;; Copyright © 2016 Florian Paul Schmidt -;;; Copyright © 2016 Kei Yamashita +;;; Copyright © 2016 Kei Kebreau ;;; ;;; This file is part of GNU Guix. ;;; -- cgit v1.2.3 From 5c447e280e1a4aa6ce7c4611c8393708e08197fa Mon Sep 17 00:00:00 2001 From: humanitiesNerd Date: Tue, 17 May 2016 23:07:06 +0200 Subject: gnu: Add emacs-smartparens. * gnu/packages/emacs.scm (emacs-smartparens): New variable. Signed-off-by: Alex Kost --- gnu/packages/emacs.scm | 29 ++++++++++++++++++++++++++++- 1 file changed, 28 insertions(+), 1 deletion(-) diff --git a/gnu/packages/emacs.scm b/gnu/packages/emacs.scm index 32ed72218b..18898e9c29 100644 --- a/gnu/packages/emacs.scm +++ b/gnu/packages/emacs.scm @@ -1611,4 +1611,31 @@ (define-public emacs-zenburn-theme It is built on top of the custom theme support in Emacs 24 or later.") (license license:gpl3+))) - +(define-public emacs-smartparens + (package + (name "emacs-smartparens") + (version "1.7.1") + (source (origin + (method url-fetch) + (uri (string-append + "https://github.com/Fuco1/smartparens/archive/" + version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "1b47ppkzsj8j8a2p0bmvq05rhm2d2lsm3wlc0sg542r4zr6nji8s")))) + (build-system emacs-build-system) + (propagated-inputs `(("emacs-dash" ,emacs-dash))) + (home-page "https://github.com/Fuco1/smartparens") + (synopsis "Paredit-like insertion, wrapping and navigation with user +defined pairs") + (description + "Smartparens is a minor mode for Emacs that deals with parens pairs +and tries to be smart about it. It started as a unification effort to +combine functionality of several existing packages in a single, +compatible and extensible way to deal with parentheses, delimiters, tags +and the like. Some of these packages include autopair, textmate, +wrap-region, electric-pair-mode, paredit and others. With the basic +features found in other packages it also brings many improvements as +well as completely new features.") + (license license:gpl3+))) -- cgit v1.2.3 From 3fdb2a84be4c30d6f78510d0fc787766d8809340 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Thu, 19 May 2016 13:01:55 +0300 Subject: gnu: giflib: Update to 5.1.4 [fixes CVE-2015-7555, CVE-2016-3977]. * gnu/packages/image.scm (giflib): Update to 5.1.4. --- gnu/packages/image.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/image.scm b/gnu/packages/image.scm index 2d7d1060d5..b8251f89e1 100644 --- a/gnu/packages/image.scm +++ b/gnu/packages/image.scm @@ -392,14 +392,14 @@ (define-public openjpeg-1 (define-public giflib (package (name "giflib") - (version "5.1.1") + (version "5.1.4") (source (origin (method url-fetch) (uri (string-append "mirror://sourceforge/giflib/giflib-" (first (string-split version #\.)) ".x/giflib-" version ".tar.bz2")) (sha256 - (base32 "1z1gzq16sdya8xnl5qjc07634kkwj5m0n3bvvj4v9j11xfn1841r")))) + (base32 "1md83dip8rf29y40cm5r7nn19705f54iraz6545zhwa6y8zyq9yz")))) (build-system gnu-build-system) (outputs '("bin" ; utility programs "out")) ; library -- cgit v1.2.3 From 44c5f0258d3c91694e6c24dcc6701eb2949fd5d8 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Thu, 19 May 2016 13:06:49 +0300 Subject: gnu: giflib: Use 'modify-phases'. * gnu/packages/image.scm (giflib)[arguments]: Use 'modify-phases'. --- gnu/packages/image.scm | 42 +++++++++++++++++++++--------------------- 1 file changed, 21 insertions(+), 21 deletions(-) diff --git a/gnu/packages/image.scm b/gnu/packages/image.scm index b8251f89e1..3651e97f3e 100644 --- a/gnu/packages/image.scm +++ b/gnu/packages/image.scm @@ -399,7 +399,8 @@ (define-public giflib (first (string-split version #\.)) ".x/giflib-" version ".tar.bz2")) (sha256 - (base32 "1md83dip8rf29y40cm5r7nn19705f54iraz6545zhwa6y8zyq9yz")))) + (base32 + "1md83dip8rf29y40cm5r7nn19705f54iraz6545zhwa6y8zyq9yz")))) (build-system gnu-build-system) (outputs '("bin" ; utility programs "out")) ; library @@ -408,26 +409,25 @@ (define-public giflib ("libsm" ,libsm) ("perl" ,perl))) (arguments - `(#:phases (alist-cons-after - 'unpack 'disable-html-doc-gen - (lambda _ - (substitute* "doc/Makefile.in" - (("^all: allhtml manpages") ""))) - (alist-cons-after - 'install 'install-manpages - (lambda* (#:key outputs #:allow-other-keys) - (let* ((bin (assoc-ref outputs "bin")) - (man1dir (string-append bin "/share/man/man1"))) - (mkdir-p man1dir) - (for-each (lambda (file) - (let ((base (basename file))) - (format #t "installing `~a' to `~a'~%" - base man1dir) - (copy-file file - (string-append - man1dir "/" base)))) - (find-files "doc" "\\.1")))) - %standard-phases)))) + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'disable-html-doc-gen + (lambda _ + (substitute* "doc/Makefile.in" + (("^all: allhtml manpages") "")))) + (add-after 'install 'install-manpages + (lambda* (#:key outputs #:allow-other-keys) + (let* ((bin (assoc-ref outputs "bin")) + (man1dir (string-append bin "/share/man/man1"))) + (mkdir-p man1dir) + (for-each (lambda (file) + (let ((base (basename file))) + (format #t "installing `~a' to `~a'~%" + base man1dir) + (copy-file file + (string-append + man1dir "/" base)))) + (find-files "doc" "\\.1")))))))) (synopsis "Tools and library for working with GIF images") (description "GIFLIB is a library for reading and writing GIF images. It is API and -- cgit v1.2.3 From 0947698c42fb10b8802679cbc58f9a42a2d91043 Mon Sep 17 00:00:00 2001 From: Ben Woodcroft Date: Wed, 18 May 2016 21:47:35 +1000 Subject: gnu: Add r-biased-urn. * gnu/packages/statistics.scm (r-biased-urn): New variable. --- gnu/packages/statistics.scm | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 7b3483206f..58f5c9d644 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -5,6 +5,7 @@ ;;; Copyright © 2016 Efraim Flashner ;;; Copyright © 2016 Pjotr Prins ;;; Copyright © 2016 Roel Janssen +;;; Copyright © 2016 Ben Woodcroft ;;; ;;; This file is part of GNU Guix. ;;; @@ -2593,6 +2594,28 @@ (define-public r-plotly data behind them) can be viewed and modified in a web browser.") (license license:x11))) +(define-public r-biased-urn + (package + (name "r-biased-urn") + (version "1.07") + (source + (origin + (method url-fetch) + (uri (cran-uri "BiasedUrn" version)) + (sha256 + (base32 + "13i2lgfnjhlbbm2yxfc2l5hswqw6x03pwba5csjmirv8kpjw4xr3")))) + (properties `((upstream-name . "BiasedUrn"))) + (build-system r-build-system) + (home-page "http://www.agner.org/random/") + (synopsis "Biased urn model distributions") + (description + "This package provides statistical models of biased sampling in the form +of univariate and multivariate noncentral hypergeometric distributions, +including Wallenius' noncentral hypergeometric distribution and Fisher's +noncentral hypergeometric distribution (also called extended hypergeometric +distribution).") + (license license:gpl3+))) (define-public r-ztable (package -- cgit v1.2.3 From 39b3033731283b81ae36f022c6476634ab1d0455 Mon Sep 17 00:00:00 2001 From: Ludovic Courtès Date: Thu, 19 May 2016 11:47:27 +0200 Subject: gnu: flann: Strip .mex file. * gnu/packages/maths.scm (flann)[arguments]: Add #:strip-directories. --- gnu/packages/maths.scm | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 2926c1c4c9..da7bfa6b76 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -12,6 +12,7 @@ ;;; Copyright © 2015 Fabian Harfert ;;; Copyright © 2016 Roel Janssen ;;; Copyright © 2016 Kei Kebreau +;;; Copyright © 2016 Ludovic Courtès ;;; ;;; This file is part of GNU Guix. ;;; @@ -2208,7 +2209,12 @@ (define-public flann ;; ("python2-numpy" ,python2-numpy) ; only required for the tests ("zlib" ,zlib))) (arguments - `(#:tests? #f)) ; The test data are downloaded from the Internet. + `(;; The 'share/flann/octave' contains a .mex file, which is an ELF file + ;; taken 46 MiB unstripped, and 6 MiB stripped. + #:strip-directories '("lib" "lib64" "libexec" + "bin" "sbin" "share/flann/octave") + + #:tests? #f)) ; The test data are downloaded from the Internet. (home-page "http://www.cs.ubc.ca/research/flann/") (synopsis "Library for approximate nearest neighbors computation") (description "FLANN is a library for performing fast approximate -- cgit v1.2.3 From 458480235b85ce31db5485251f94415cfdddeff0 Mon Sep 17 00:00:00 2001 From: Hartmut Goebel Date: Sun, 15 May 2016 11:51:54 +0200 Subject: gnu: python: Add 'python' variables for different major/minor versions. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/python.scm (python-2): Rename variable to... (python-2.7): ...this. (python-2): Refer to "python-2.7". (python): Rename variable to... (python-3.4): ...this. (python-3): Refer to "python-3.4". (python): Refer to "python-3". Signed-off-by: Ludovic Courtès --- gnu/packages/python.scm | 13 +++++++++++-- 1 file changed, 11 insertions(+), 2 deletions(-) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 1929f83a16..37c8594a37 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -90,7 +90,7 @@ (define-module (gnu packages python) #:use-module (guix build-system trivial) #:use-module (srfi srfi-1)) -(define-public python-2 +(define-public python-2.7 (package (name "python") (version "2.7.10") @@ -262,7 +262,10 @@ (define-public python-2 data types.") (license psfl))) -(define-public python +;; Current 2.x version. +(define-public python-2 python-2.7) + +(define-public python-3.4 (package (inherit python-2) (version "3.4.3") (source (origin @@ -288,6 +291,12 @@ (define-public python (version-major+minor version) "/site-packages")))))))) +;; Current 3.x version. +(define-public python-3 python-3.4) + +;; Current major version. +(define-public python python-3) + ;; Minimal variants of Python, mostly used to break the cycle between Tk and ;; Python (Tk -> libxcb -> Python.) -- cgit v1.2.3 From 9684e30b9b597b93ae9c797ba8f3b40eff893ebe Mon Sep 17 00:00:00 2001 From: Ludovic Courtès Date: Thu, 19 May 2016 14:50:22 +0200 Subject: gnu: flann: Do not install .a files. * gnu/packages/maths.scm (flann)[arguments]: Add #:phases. --- gnu/packages/maths.scm | 11 +++++++++++ 1 file changed, 11 insertions(+) diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index da7bfa6b76..95240af962 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -2214,6 +2214,17 @@ (define-public flann #:strip-directories '("lib" "lib64" "libexec" "bin" "sbin" "share/flann/octave") + ;; Save 12 MiB by not installing .a files. Passing + ;; '-DBUILD_STATIC_LIBS=OFF' has no effect. + #:phases (modify-phases %standard-phases + (add-after 'install 'remove-static-libraries + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (lib (string-append out "/lib"))) + (for-each delete-file + (find-files lib "\\.a$")) + #t)))) + #:tests? #f)) ; The test data are downloaded from the Internet. (home-page "http://www.cs.ubc.ca/research/flann/") (synopsis "Library for approximate nearest neighbors computation") -- cgit v1.2.3 From 119b83989dd9edd1e8ba6cd379d159d024cbc61d Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Wed, 18 May 2016 13:26:17 -0400 Subject: gnu: expat: Fix CVE-2016-0718. Improve fix for CVE-2015-1283. * gnu/packages/patches/expat-CVE-2015-1283-refix.patch, gnu/packages/patches/expat-CVE-2016-0718.patch: New files. * gnu/local.mk (dist_patch_DATA): Add them. * gnu/packages/xml.scm (expat)[replacement]: New field. (expat/fixed): New variable. [source]: Use new patches. --- gnu/local.mk | 2 + .../patches/expat-CVE-2015-1283-refix.patch | 42 ++ gnu/packages/patches/expat-CVE-2016-0718.patch | 761 +++++++++++++++++++++ gnu/packages/xml.scm | 11 + 4 files changed, 816 insertions(+) create mode 100644 gnu/packages/patches/expat-CVE-2015-1283-refix.patch create mode 100644 gnu/packages/patches/expat-CVE-2016-0718.patch diff --git a/gnu/local.mk b/gnu/local.mk index 3fa27925ec..5655a05bcf 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -472,6 +472,8 @@ dist_patch_DATA = \ gnu/packages/patches/eudev-rules-directory.patch \ gnu/packages/patches/evilwm-lost-focus-bug.patch \ gnu/packages/patches/expat-CVE-2015-1283.patch \ + gnu/packages/patches/expat-CVE-2015-1283-refix.patch \ + gnu/packages/patches/expat-CVE-2016-0718.patch \ gnu/packages/patches/fastcap-mulGlobal.patch \ gnu/packages/patches/fastcap-mulSetup.patch \ gnu/packages/patches/fasthenry-spAllocate.patch \ diff --git a/gnu/packages/patches/expat-CVE-2015-1283-refix.patch b/gnu/packages/patches/expat-CVE-2015-1283-refix.patch new file mode 100644 index 0000000000..af5e3bcc3e --- /dev/null +++ b/gnu/packages/patches/expat-CVE-2015-1283-refix.patch @@ -0,0 +1,42 @@ +Update previous fix for CVE-2015-1283 to not rely on undefined behavior. + +Copied from Debian, as found in Debian package version 2.1.0-6+deb8u2. + +https://sources.debian.net/src/expat/2.1.0-6%2Bdeb8u2/debian/patches/CVE-2015-1283-refix.patch/ + +From 29a11774d8ebbafe8418b4a5ffb4cc1160b194a1 Mon Sep 17 00:00:00 2001 +From: Pascal Cuoq +Date: Sun, 15 May 2016 09:05:46 +0200 +Subject: [PATCH] Avoid relying on undefined behavior in CVE-2015-1283 fix. + +--- + expat/lib/xmlparse.c | 6 ++++-- + 1 file changed, 4 insertions(+), 2 deletions(-) + +diff --git a/lib/xmlparse.c b/lib/xmlparse.c +index 13e080d..cdb12ef 100644 +--- a/lib/xmlparse.c ++++ b/lib/xmlparse.c +@@ -1695,7 +1695,8 @@ XML_GetBuffer(XML_Parser parser, int len + } + + if (len > bufferLim - bufferEnd) { +- int neededSize = len + (int)(bufferEnd - bufferPtr); ++ /* Do not invoke signed arithmetic overflow: */ ++ int neededSize = (int) ((unsigned)len + (unsigned)(bufferEnd - bufferPtr)); + /* BEGIN MOZILLA CHANGE (sanity check neededSize) */ + if (neededSize < 0) { + errorCode = XML_ERROR_NO_MEMORY; +@@ -1729,7 +1730,8 @@ XML_GetBuffer(XML_Parser parser, int len + if (bufferSize == 0) + bufferSize = INIT_BUFFER_SIZE; + do { +- bufferSize *= 2; ++ /* Do not invoke signed arithmetic overflow: */ ++ bufferSize = (int) (2U * (unsigned) bufferSize); + /* BEGIN MOZILLA CHANGE (prevent infinite loop on overflow) */ + } while (bufferSize < neededSize && bufferSize > 0); + /* END MOZILLA CHANGE */ +-- +2.8.2 + diff --git a/gnu/packages/patches/expat-CVE-2016-0718.patch b/gnu/packages/patches/expat-CVE-2016-0718.patch new file mode 100644 index 0000000000..22436c20cc --- /dev/null +++ b/gnu/packages/patches/expat-CVE-2016-0718.patch @@ -0,0 +1,761 @@ +Fix CVE-2016-0718. + +Copied from Debian, as found in Debian package version 2.1.0-6+deb8u2. + +https://sources.debian.net/src/expat/2.1.0-6%2Bdeb8u2/debian/patches/CVE-2016-0718-v2-2-1.patch/ + +From cdfcb1b5c95e93b00ae9e9d25708b4a3bee72c15 Mon Sep 17 00:00:00 2001 +From: Sebastian Pipping +Date: Mon, 2 May 2016 00:02:44 +0200 +Subject: [PATCH] Address CVE-2016-0718 (/patch/ version 2.2.1) + +* Out of bounds memory access when doing text conversion on malformed input +* Integer overflow related to memory allocation + +Reported by Gustavo Grieco + +Patch credits go to +* Christian Heimes +* Karl Waclawek +* Gustavo Grieco +* Sebastian Pipping +* Pascal Cuoq +--- + expat/lib/xmlparse.c | 34 +++++++++----- + expat/lib/xmltok.c | 115 +++++++++++++++++++++++++++++++++++------------- + expat/lib/xmltok.h | 10 ++++- + expat/lib/xmltok_impl.c | 62 +++++++++++++------------- + 4 files changed, 146 insertions(+), 75 deletions(-) + +diff --git a/lib/xmlparse.c b/lib/xmlparse.c +index e308c79..13e080d 100644 +--- a/lib/xmlparse.c ++++ b/lib/xmlparse.c +@@ -2436,11 +2436,11 @@ doContent(XML_Parser parser, + for (;;) { + int bufSize; + int convLen; +- XmlConvert(enc, ++ const enum XML_Convert_Result convert_res = XmlConvert(enc, + &fromPtr, rawNameEnd, + (ICHAR **)&toPtr, (ICHAR *)tag->bufEnd - 1); + convLen = (int)(toPtr - (XML_Char *)tag->buf); +- if (fromPtr == rawNameEnd) { ++ if ((convert_res == XML_CONVERT_COMPLETED) || (convert_res == XML_CONVERT_INPUT_INCOMPLETE)) { + tag->name.strLen = convLen; + break; + } +@@ -2661,11 +2661,11 @@ doContent(XML_Parser parser, + if (MUST_CONVERT(enc, s)) { + for (;;) { + ICHAR *dataPtr = (ICHAR *)dataBuf; +- XmlConvert(enc, &s, next, &dataPtr, (ICHAR *)dataBufEnd); ++ const enum XML_Convert_Result convert_res = XmlConvert(enc, &s, next, &dataPtr, (ICHAR *)dataBufEnd); + *eventEndPP = s; + charDataHandler(handlerArg, dataBuf, + (int)(dataPtr - (ICHAR *)dataBuf)); +- if (s == next) ++ if ((convert_res == XML_CONVERT_COMPLETED) || (convert_res == XML_CONVERT_INPUT_INCOMPLETE)) + break; + *eventPP = s; + } +@@ -3269,11 +3269,11 @@ doCdataSection(XML_Parser parser, + if (MUST_CONVERT(enc, s)) { + for (;;) { + ICHAR *dataPtr = (ICHAR *)dataBuf; +- XmlConvert(enc, &s, next, &dataPtr, (ICHAR *)dataBufEnd); ++ const enum XML_Convert_Result convert_res = XmlConvert(enc, &s, next, &dataPtr, (ICHAR *)dataBufEnd); + *eventEndPP = next; + charDataHandler(handlerArg, dataBuf, + (int)(dataPtr - (ICHAR *)dataBuf)); +- if (s == next) ++ if ((convert_res == XML_CONVERT_COMPLETED) || (convert_res == XML_CONVERT_INPUT_INCOMPLETE)) + break; + *eventPP = s; + } +@@ -5350,6 +5350,7 @@ reportDefault(XML_Parser parser, const ENCODING *enc, + const char *s, const char *end) + { + if (MUST_CONVERT(enc, s)) { ++ enum XML_Convert_Result convert_res; + const char **eventPP; + const char **eventEndPP; + if (enc == encoding) { +@@ -5362,11 +5363,11 @@ reportDefault(XML_Parser parser, const ENCODING *enc, + } + do { + ICHAR *dataPtr = (ICHAR *)dataBuf; +- XmlConvert(enc, &s, end, &dataPtr, (ICHAR *)dataBufEnd); ++ convert_res = XmlConvert(enc, &s, end, &dataPtr, (ICHAR *)dataBufEnd); + *eventEndPP = s; + defaultHandler(handlerArg, dataBuf, (int)(dataPtr - (ICHAR *)dataBuf)); + *eventPP = s; +- } while (s != end); ++ } while ((convert_res != XML_CONVERT_COMPLETED) && (convert_res != XML_CONVERT_INPUT_INCOMPLETE)); + } + else + defaultHandler(handlerArg, (XML_Char *)s, (int)((XML_Char *)end - (XML_Char *)s)); +@@ -6169,8 +6170,8 @@ poolAppend(STRING_POOL *pool, const ENCODING *enc, + if (!pool->ptr && !poolGrow(pool)) + return NULL; + for (;;) { +- XmlConvert(enc, &ptr, end, (ICHAR **)&(pool->ptr), (ICHAR *)pool->end); +- if (ptr == end) ++ const enum XML_Convert_Result convert_res = XmlConvert(enc, &ptr, end, (ICHAR **)&(pool->ptr), (ICHAR *)pool->end); ++ if ((convert_res == XML_CONVERT_COMPLETED) || (convert_res == XML_CONVERT_INPUT_INCOMPLETE)) + break; + if (!poolGrow(pool)) + return NULL; +@@ -6254,8 +6255,13 @@ poolGrow(STRING_POOL *pool) + } + } + if (pool->blocks && pool->start == pool->blocks->s) { +- int blockSize = (int)(pool->end - pool->start)*2; +- BLOCK *temp = (BLOCK *) ++ BLOCK *temp; ++ int blockSize = (int)((unsigned)(pool->end - pool->start)*2U); ++ ++ if (blockSize < 0) ++ return XML_FALSE; ++ ++ temp = (BLOCK *) + pool->mem->realloc_fcn(pool->blocks, + (offsetof(BLOCK, s) + + blockSize * sizeof(XML_Char))); +@@ -6270,6 +6276,10 @@ poolGrow(STRING_POOL *pool) + else { + BLOCK *tem; + int blockSize = (int)(pool->end - pool->start); ++ ++ if (blockSize < 0) ++ return XML_FALSE; ++ + if (blockSize < INIT_BLOCK_SIZE) + blockSize = INIT_BLOCK_SIZE; + else +diff --git a/lib/xmltok.c b/lib/xmltok.c +index bf09dfc..cb98ce1 100644 +--- a/lib/xmltok.c ++++ b/lib/xmltok.c +@@ -318,39 +318,55 @@ enum { /* UTF8_cvalN is value of masked first byte of N byte sequence */ + UTF8_cval4 = 0xf0 + }; + +-static void PTRCALL ++static enum XML_Convert_Result PTRCALL + utf8_toUtf8(const ENCODING *enc, + const char **fromP, const char *fromLim, + char **toP, const char *toLim) + { ++ enum XML_Convert_Result res = XML_CONVERT_COMPLETED; + char *to; + const char *from; + if (fromLim - *fromP > toLim - *toP) { + /* Avoid copying partial characters. */ ++ res = XML_CONVERT_OUTPUT_EXHAUSTED; + for (fromLim = *fromP + (toLim - *toP); fromLim > *fromP; fromLim--) + if (((unsigned char)fromLim[-1] & 0xc0) != 0x80) + break; + } +- for (to = *toP, from = *fromP; from != fromLim; from++, to++) ++ for (to = *toP, from = *fromP; (from < fromLim) && (to < toLim); from++, to++) + *to = *from; + *fromP = from; + *toP = to; ++ ++ if ((to == toLim) && (from < fromLim)) ++ return XML_CONVERT_OUTPUT_EXHAUSTED; ++ else ++ return res; + } + +-static void PTRCALL ++static enum XML_Convert_Result PTRCALL + utf8_toUtf16(const ENCODING *enc, + const char **fromP, const char *fromLim, + unsigned short **toP, const unsigned short *toLim) + { ++ enum XML_Convert_Result res = XML_CONVERT_COMPLETED; + unsigned short *to = *toP; + const char *from = *fromP; +- while (from != fromLim && to != toLim) { ++ while (from < fromLim && to < toLim) { + switch (((struct normal_encoding *)enc)->type[(unsigned char)*from]) { + case BT_LEAD2: ++ if (fromLim - from < 2) { ++ res = XML_CONVERT_INPUT_INCOMPLETE; ++ break; ++ } + *to++ = (unsigned short)(((from[0] & 0x1f) << 6) | (from[1] & 0x3f)); + from += 2; + break; + case BT_LEAD3: ++ if (fromLim - from < 3) { ++ res = XML_CONVERT_INPUT_INCOMPLETE; ++ break; ++ } + *to++ = (unsigned short)(((from[0] & 0xf) << 12) + | ((from[1] & 0x3f) << 6) | (from[2] & 0x3f)); + from += 3; +@@ -358,8 +374,14 @@ utf8_toUtf16(const ENCODING *enc, + case BT_LEAD4: + { + unsigned long n; +- if (to + 1 == toLim) ++ if (toLim - to < 2) { ++ res = XML_CONVERT_OUTPUT_EXHAUSTED; + goto after; ++ } ++ if (fromLim - from < 4) { ++ res = XML_CONVERT_INPUT_INCOMPLETE; ++ goto after; ++ } + n = ((from[0] & 0x7) << 18) | ((from[1] & 0x3f) << 12) + | ((from[2] & 0x3f) << 6) | (from[3] & 0x3f); + n -= 0x10000; +@@ -377,6 +399,7 @@ utf8_toUtf16(const ENCODING *enc, + after: + *fromP = from; + *toP = to; ++ return res; + } + + #ifdef XML_NS +@@ -425,7 +448,7 @@ static const struct normal_encoding internal_utf8_encoding = { + STANDARD_VTABLE(sb_) NORMAL_VTABLE(utf8_) + }; + +-static void PTRCALL ++static enum XML_Convert_Result PTRCALL + latin1_toUtf8(const ENCODING *enc, + const char **fromP, const char *fromLim, + char **toP, const char *toLim) +@@ -433,30 +456,35 @@ latin1_toUtf8(const ENCODING *enc, + for (;;) { + unsigned char c; + if (*fromP == fromLim) +- break; ++ return XML_CONVERT_COMPLETED; + c = (unsigned char)**fromP; + if (c & 0x80) { + if (toLim - *toP < 2) +- break; ++ return XML_CONVERT_OUTPUT_EXHAUSTED; + *(*toP)++ = (char)((c >> 6) | UTF8_cval2); + *(*toP)++ = (char)((c & 0x3f) | 0x80); + (*fromP)++; + } + else { + if (*toP == toLim) +- break; ++ return XML_CONVERT_OUTPUT_EXHAUSTED; + *(*toP)++ = *(*fromP)++; + } + } + } + +-static void PTRCALL ++static enum XML_Convert_Result PTRCALL + latin1_toUtf16(const ENCODING *enc, + const char **fromP, const char *fromLim, + unsigned short **toP, const unsigned short *toLim) + { +- while (*fromP != fromLim && *toP != toLim) ++ while (*fromP < fromLim && *toP < toLim) + *(*toP)++ = (unsigned char)*(*fromP)++; ++ ++ if ((*toP == toLim) && (*fromP < fromLim)) ++ return XML_CONVERT_OUTPUT_EXHAUSTED; ++ else ++ return XML_CONVERT_COMPLETED; + } + + #ifdef XML_NS +@@ -483,13 +511,18 @@ static const struct normal_encoding latin1_encoding = { + STANDARD_VTABLE(sb_) + }; + +-static void PTRCALL ++static enum XML_Convert_Result PTRCALL + ascii_toUtf8(const ENCODING *enc, + const char **fromP, const char *fromLim, + char **toP, const char *toLim) + { +- while (*fromP != fromLim && *toP != toLim) ++ while (*fromP < fromLim && *toP < toLim) + *(*toP)++ = *(*fromP)++; ++ ++ if ((*toP == toLim) && (*fromP < fromLim)) ++ return XML_CONVERT_OUTPUT_EXHAUSTED; ++ else ++ return XML_CONVERT_COMPLETED; + } + + #ifdef XML_NS +@@ -536,13 +569,14 @@ unicode_byte_type(char hi, char lo) + } + + #define DEFINE_UTF16_TO_UTF8(E) \ +-static void PTRCALL \ ++static enum XML_Convert_Result PTRCALL \ + E ## toUtf8(const ENCODING *enc, \ + const char **fromP, const char *fromLim, \ + char **toP, const char *toLim) \ + { \ +- const char *from; \ +- for (from = *fromP; from != fromLim; from += 2) { \ ++ const char *from = *fromP; \ ++ fromLim = from + (((fromLim - from) >> 1) << 1); /* shrink to even */ \ ++ for (; from < fromLim; from += 2) { \ + int plane; \ + unsigned char lo2; \ + unsigned char lo = GET_LO(from); \ +@@ -552,7 +586,7 @@ E ## toUtf8(const ENCODING *enc, \ + if (lo < 0x80) { \ + if (*toP == toLim) { \ + *fromP = from; \ +- return; \ ++ return XML_CONVERT_OUTPUT_EXHAUSTED; \ + } \ + *(*toP)++ = lo; \ + break; \ +@@ -562,7 +596,7 @@ E ## toUtf8(const ENCODING *enc, \ + case 0x4: case 0x5: case 0x6: case 0x7: \ + if (toLim - *toP < 2) { \ + *fromP = from; \ +- return; \ ++ return XML_CONVERT_OUTPUT_EXHAUSTED; \ + } \ + *(*toP)++ = ((lo >> 6) | (hi << 2) | UTF8_cval2); \ + *(*toP)++ = ((lo & 0x3f) | 0x80); \ +@@ -570,7 +604,7 @@ E ## toUtf8(const ENCODING *enc, \ + default: \ + if (toLim - *toP < 3) { \ + *fromP = from; \ +- return; \ ++ return XML_CONVERT_OUTPUT_EXHAUSTED; \ + } \ + /* 16 bits divided 4, 6, 6 amongst 3 bytes */ \ + *(*toP)++ = ((hi >> 4) | UTF8_cval3); \ +@@ -580,7 +614,11 @@ E ## toUtf8(const ENCODING *enc, \ + case 0xD8: case 0xD9: case 0xDA: case 0xDB: \ + if (toLim - *toP < 4) { \ + *fromP = from; \ +- return; \ ++ return XML_CONVERT_OUTPUT_EXHAUSTED; \ ++ } \ ++ if (fromLim - from < 4) { \ ++ *fromP = from; \ ++ return XML_CONVERT_INPUT_INCOMPLETE; \ + } \ + plane = (((hi & 0x3) << 2) | ((lo >> 6) & 0x3)) + 1; \ + *(*toP)++ = ((plane >> 2) | UTF8_cval4); \ +@@ -596,20 +634,32 @@ E ## toUtf8(const ENCODING *enc, \ + } \ + } \ + *fromP = from; \ ++ if (from < fromLim) \ ++ return XML_CONVERT_INPUT_INCOMPLETE; \ ++ else \ ++ return XML_CONVERT_COMPLETED; \ + } + + #define DEFINE_UTF16_TO_UTF16(E) \ +-static void PTRCALL \ ++static enum XML_Convert_Result PTRCALL \ + E ## toUtf16(const ENCODING *enc, \ + const char **fromP, const char *fromLim, \ + unsigned short **toP, const unsigned short *toLim) \ + { \ ++ enum XML_Convert_Result res = XML_CONVERT_COMPLETED; \ ++ fromLim = *fromP + (((fromLim - *fromP) >> 1) << 1); /* shrink to even */ \ + /* Avoid copying first half only of surrogate */ \ + if (fromLim - *fromP > ((toLim - *toP) << 1) \ +- && (GET_HI(fromLim - 2) & 0xF8) == 0xD8) \ ++ && (GET_HI(fromLim - 2) & 0xF8) == 0xD8) { \ + fromLim -= 2; \ +- for (; *fromP != fromLim && *toP != toLim; *fromP += 2) \ ++ res = XML_CONVERT_INPUT_INCOMPLETE; \ ++ } \ ++ for (; *fromP < fromLim && *toP < toLim; *fromP += 2) \ + *(*toP)++ = (GET_HI(*fromP) << 8) | GET_LO(*fromP); \ ++ if ((*toP == toLim) && (*fromP < fromLim)) \ ++ return XML_CONVERT_OUTPUT_EXHAUSTED; \ ++ else \ ++ return res; \ + } + + #define SET2(ptr, ch) \ +@@ -1288,7 +1338,7 @@ unknown_isInvalid(const ENCODING *enc, const char *p) + return (c & ~0xFFFF) || checkCharRefNumber(c) < 0; + } + +-static void PTRCALL ++static enum XML_Convert_Result PTRCALL + unknown_toUtf8(const ENCODING *enc, + const char **fromP, const char *fromLim, + char **toP, const char *toLim) +@@ -1299,21 +1349,21 @@ unknown_toUtf8(const ENCODING *enc, + const char *utf8; + int n; + if (*fromP == fromLim) +- break; ++ return XML_CONVERT_COMPLETED; + utf8 = uenc->utf8[(unsigned char)**fromP]; + n = *utf8++; + if (n == 0) { + int c = uenc->convert(uenc->userData, *fromP); + n = XmlUtf8Encode(c, buf); + if (n > toLim - *toP) +- break; ++ return XML_CONVERT_OUTPUT_EXHAUSTED; + utf8 = buf; + *fromP += (AS_NORMAL_ENCODING(enc)->type[(unsigned char)**fromP] + - (BT_LEAD2 - 2)); + } + else { + if (n > toLim - *toP) +- break; ++ return XML_CONVERT_OUTPUT_EXHAUSTED; + (*fromP)++; + } + do { +@@ -1322,13 +1372,13 @@ unknown_toUtf8(const ENCODING *enc, + } + } + +-static void PTRCALL ++static enum XML_Convert_Result PTRCALL + unknown_toUtf16(const ENCODING *enc, + const char **fromP, const char *fromLim, + unsigned short **toP, const unsigned short *toLim) + { + const struct unknown_encoding *uenc = AS_UNKNOWN_ENCODING(enc); +- while (*fromP != fromLim && *toP != toLim) { ++ while (*fromP < fromLim && *toP < toLim) { + unsigned short c = uenc->utf16[(unsigned char)**fromP]; + if (c == 0) { + c = (unsigned short) +@@ -1340,6 +1390,11 @@ unknown_toUtf16(const ENCODING *enc, + (*fromP)++; + *(*toP)++ = c; + } ++ ++ if ((*toP == toLim) && (*fromP < fromLim)) ++ return XML_CONVERT_OUTPUT_EXHAUSTED; ++ else ++ return XML_CONVERT_COMPLETED; + } + + ENCODING * +@@ -1503,7 +1558,7 @@ initScan(const ENCODING * const *encodingTable, + { + const ENCODING **encPtr; + +- if (ptr == end) ++ if (ptr >= end) + return XML_TOK_NONE; + encPtr = enc->encPtr; + if (ptr + 1 == end) { +diff --git a/lib/xmltok.h b/lib/xmltok.h +index ca867aa..752007e 100644 +--- a/lib/xmltok.h ++++ b/lib/xmltok.h +@@ -130,6 +130,12 @@ typedef int (PTRCALL *SCANNER)(const ENCODING *, + const char *, + const char **); + ++enum XML_Convert_Result { ++ XML_CONVERT_COMPLETED = 0, ++ XML_CONVERT_INPUT_INCOMPLETE = 1, ++ XML_CONVERT_OUTPUT_EXHAUSTED = 2 /* and therefore potentially input remaining as well */ ++}; ++ + struct encoding { + SCANNER scanners[XML_N_STATES]; + SCANNER literalScanners[XML_N_LITERAL_TYPES]; +@@ -158,12 +164,12 @@ struct encoding { + const char *ptr, + const char *end, + const char **badPtr); +- void (PTRCALL *utf8Convert)(const ENCODING *enc, ++ enum XML_Convert_Result (PTRCALL *utf8Convert)(const ENCODING *enc, + const char **fromP, + const char *fromLim, + char **toP, + const char *toLim); +- void (PTRCALL *utf16Convert)(const ENCODING *enc, ++ enum XML_Convert_Result (PTRCALL *utf16Convert)(const ENCODING *enc, + const char **fromP, + const char *fromLim, + unsigned short **toP, +diff --git a/lib/xmltok_impl.c b/lib/xmltok_impl.c +index 9c2895b..6c5a3ba 100644 +--- a/lib/xmltok_impl.c ++++ b/lib/xmltok_impl.c +@@ -93,13 +93,13 @@ static int PTRCALL + PREFIX(scanComment)(const ENCODING *enc, const char *ptr, + const char *end, const char **nextTokPtr) + { +- if (ptr != end) { ++ if (ptr < end) { + if (!CHAR_MATCHES(enc, ptr, ASCII_MINUS)) { + *nextTokPtr = ptr; + return XML_TOK_INVALID; + } + ptr += MINBPC(enc); +- while (ptr != end) { ++ while (ptr < end) { + switch (BYTE_TYPE(enc, ptr)) { + INVALID_CASES(ptr, nextTokPtr) + case BT_MINUS: +@@ -147,7 +147,7 @@ PREFIX(scanDecl)(const ENCODING *enc, const char *ptr, + *nextTokPtr = ptr; + return XML_TOK_INVALID; + } +- while (ptr != end) { ++ while (ptr < end) { + switch (BYTE_TYPE(enc, ptr)) { + case BT_PERCNT: + if (ptr + MINBPC(enc) == end) +@@ -233,7 +233,7 @@ PREFIX(scanPi)(const ENCODING *enc, const char *ptr, + *nextTokPtr = ptr; + return XML_TOK_INVALID; + } +- while (ptr != end) { ++ while (ptr < end) { + switch (BYTE_TYPE(enc, ptr)) { + CHECK_NAME_CASES(enc, ptr, end, nextTokPtr) + case BT_S: case BT_CR: case BT_LF: +@@ -242,7 +242,7 @@ PREFIX(scanPi)(const ENCODING *enc, const char *ptr, + return XML_TOK_INVALID; + } + ptr += MINBPC(enc); +- while (ptr != end) { ++ while (ptr < end) { + switch (BYTE_TYPE(enc, ptr)) { + INVALID_CASES(ptr, nextTokPtr) + case BT_QUEST: +@@ -305,7 +305,7 @@ static int PTRCALL + PREFIX(cdataSectionTok)(const ENCODING *enc, const char *ptr, + const char *end, const char **nextTokPtr) + { +- if (ptr == end) ++ if (ptr >= end) + return XML_TOK_NONE; + if (MINBPC(enc) > 1) { + size_t n = end - ptr; +@@ -348,7 +348,7 @@ PREFIX(cdataSectionTok)(const ENCODING *enc, const char *ptr, + ptr += MINBPC(enc); + break; + } +- while (ptr != end) { ++ while (ptr < end) { + switch (BYTE_TYPE(enc, ptr)) { + #define LEAD_CASE(n) \ + case BT_LEAD ## n: \ +@@ -391,11 +391,11 @@ PREFIX(scanEndTag)(const ENCODING *enc, const char *ptr, + *nextTokPtr = ptr; + return XML_TOK_INVALID; + } +- while (ptr != end) { ++ while (ptr < end) { + switch (BYTE_TYPE(enc, ptr)) { + CHECK_NAME_CASES(enc, ptr, end, nextTokPtr) + case BT_S: case BT_CR: case BT_LF: +- for (ptr += MINBPC(enc); ptr != end; ptr += MINBPC(enc)) { ++ for (ptr += MINBPC(enc); ptr < end; ptr += MINBPC(enc)) { + switch (BYTE_TYPE(enc, ptr)) { + case BT_S: case BT_CR: case BT_LF: + break; +@@ -432,7 +432,7 @@ static int PTRCALL + PREFIX(scanHexCharRef)(const ENCODING *enc, const char *ptr, + const char *end, const char **nextTokPtr) + { +- if (ptr != end) { ++ if (ptr < end) { + switch (BYTE_TYPE(enc, ptr)) { + case BT_DIGIT: + case BT_HEX: +@@ -441,7 +441,7 @@ PREFIX(scanHexCharRef)(const ENCODING *enc, const char *ptr, + *nextTokPtr = ptr; + return XML_TOK_INVALID; + } +- for (ptr += MINBPC(enc); ptr != end; ptr += MINBPC(enc)) { ++ for (ptr += MINBPC(enc); ptr < end; ptr += MINBPC(enc)) { + switch (BYTE_TYPE(enc, ptr)) { + case BT_DIGIT: + case BT_HEX: +@@ -464,7 +464,7 @@ static int PTRCALL + PREFIX(scanCharRef)(const ENCODING *enc, const char *ptr, + const char *end, const char **nextTokPtr) + { +- if (ptr != end) { ++ if (ptr < end) { + if (CHAR_MATCHES(enc, ptr, ASCII_x)) + return PREFIX(scanHexCharRef)(enc, ptr + MINBPC(enc), end, nextTokPtr); + switch (BYTE_TYPE(enc, ptr)) { +@@ -474,7 +474,7 @@ PREFIX(scanCharRef)(const ENCODING *enc, const char *ptr, + *nextTokPtr = ptr; + return XML_TOK_INVALID; + } +- for (ptr += MINBPC(enc); ptr != end; ptr += MINBPC(enc)) { ++ for (ptr += MINBPC(enc); ptr < end; ptr += MINBPC(enc)) { + switch (BYTE_TYPE(enc, ptr)) { + case BT_DIGIT: + break; +@@ -506,7 +506,7 @@ PREFIX(scanRef)(const ENCODING *enc, const char *ptr, const char *end, + *nextTokPtr = ptr; + return XML_TOK_INVALID; + } +- while (ptr != end) { ++ while (ptr < end) { + switch (BYTE_TYPE(enc, ptr)) { + CHECK_NAME_CASES(enc, ptr, end, nextTokPtr) + case BT_SEMI: +@@ -529,7 +529,7 @@ PREFIX(scanAtts)(const ENCODING *enc, const char *ptr, const char *end, + #ifdef XML_NS + int hadColon = 0; + #endif +- while (ptr != end) { ++ while (ptr < end) { + switch (BYTE_TYPE(enc, ptr)) { + CHECK_NAME_CASES(enc, ptr, end, nextTokPtr) + #ifdef XML_NS +@@ -716,7 +716,7 @@ PREFIX(scanLt)(const ENCODING *enc, const char *ptr, const char *end, + hadColon = 0; + #endif + /* we have a start-tag */ +- while (ptr != end) { ++ while (ptr < end) { + switch (BYTE_TYPE(enc, ptr)) { + CHECK_NAME_CASES(enc, ptr, end, nextTokPtr) + #ifdef XML_NS +@@ -740,7 +740,7 @@ PREFIX(scanLt)(const ENCODING *enc, const char *ptr, const char *end, + case BT_S: case BT_CR: case BT_LF: + { + ptr += MINBPC(enc); +- while (ptr != end) { ++ while (ptr < end) { + switch (BYTE_TYPE(enc, ptr)) { + CHECK_NMSTRT_CASES(enc, ptr, end, nextTokPtr) + case BT_GT: +@@ -785,7 +785,7 @@ static int PTRCALL + PREFIX(contentTok)(const ENCODING *enc, const char *ptr, const char *end, + const char **nextTokPtr) + { +- if (ptr == end) ++ if (ptr >= end) + return XML_TOK_NONE; + if (MINBPC(enc) > 1) { + size_t n = end - ptr; +@@ -832,7 +832,7 @@ PREFIX(contentTok)(const ENCODING *enc, const char *ptr, const char *end, + ptr += MINBPC(enc); + break; + } +- while (ptr != end) { ++ while (ptr < end) { + switch (BYTE_TYPE(enc, ptr)) { + #define LEAD_CASE(n) \ + case BT_LEAD ## n: \ +@@ -895,7 +895,7 @@ PREFIX(scanPercent)(const ENCODING *enc, const char *ptr, const char *end, + *nextTokPtr = ptr; + return XML_TOK_INVALID; + } +- while (ptr != end) { ++ while (ptr < end) { + switch (BYTE_TYPE(enc, ptr)) { + CHECK_NAME_CASES(enc, ptr, end, nextTokPtr) + case BT_SEMI: +@@ -921,7 +921,7 @@ PREFIX(scanPoundName)(const ENCODING *enc, const char *ptr, const char *end, + *nextTokPtr = ptr; + return XML_TOK_INVALID; + } +- while (ptr != end) { ++ while (ptr < end) { + switch (BYTE_TYPE(enc, ptr)) { + CHECK_NAME_CASES(enc, ptr, end, nextTokPtr) + case BT_CR: case BT_LF: case BT_S: +@@ -941,7 +941,7 @@ PREFIX(scanLit)(int open, const ENCODING *enc, + const char *ptr, const char *end, + const char **nextTokPtr) + { +- while (ptr != end) { ++ while (ptr < end) { + int t = BYTE_TYPE(enc, ptr); + switch (t) { + INVALID_CASES(ptr, nextTokPtr) +@@ -973,7 +973,7 @@ PREFIX(prologTok)(const ENCODING *enc, const char *ptr, const char *end, + const char **nextTokPtr) + { + int tok; +- if (ptr == end) ++ if (ptr >= end) + return XML_TOK_NONE; + if (MINBPC(enc) > 1) { + size_t n = end - ptr; +@@ -1141,7 +1141,7 @@ PREFIX(prologTok)(const ENCODING *enc, const char *ptr, const char *end, + *nextTokPtr = ptr; + return XML_TOK_INVALID; + } +- while (ptr != end) { ++ while (ptr < end) { + switch (BYTE_TYPE(enc, ptr)) { + CHECK_NAME_CASES(enc, ptr, end, nextTokPtr) + case BT_GT: case BT_RPAR: case BT_COMMA: +@@ -1204,10 +1204,10 @@ PREFIX(attributeValueTok)(const ENCODING *enc, const char *ptr, + const char *end, const char **nextTokPtr) + { + const char *start; +- if (ptr == end) ++ if (ptr >= end) + return XML_TOK_NONE; + start = ptr; +- while (ptr != end) { ++ while (ptr < end) { + switch (BYTE_TYPE(enc, ptr)) { + #define LEAD_CASE(n) \ + case BT_LEAD ## n: ptr += n; break; +@@ -1262,10 +1262,10 @@ PREFIX(entityValueTok)(const ENCODING *enc, const char *ptr, + const char *end, const char **nextTokPtr) + { + const char *start; +- if (ptr == end) ++ if (ptr >= end) + return XML_TOK_NONE; + start = ptr; +- while (ptr != end) { ++ while (ptr < end) { + switch (BYTE_TYPE(enc, ptr)) { + #define LEAD_CASE(n) \ + case BT_LEAD ## n: ptr += n; break; +@@ -1326,7 +1326,7 @@ PREFIX(ignoreSectionTok)(const ENCODING *enc, const char *ptr, + end = ptr + n; + } + } +- while (ptr != end) { ++ while (ptr < end) { + switch (BYTE_TYPE(enc, ptr)) { + INVALID_CASES(ptr, nextTokPtr) + case BT_LT: +@@ -1373,7 +1373,7 @@ PREFIX(isPublicId)(const ENCODING *enc, const char *ptr, const char *end, + { + ptr += MINBPC(enc); + end -= MINBPC(enc); +- for (; ptr != end; ptr += MINBPC(enc)) { ++ for (; ptr < end; ptr += MINBPC(enc)) { + switch (BYTE_TYPE(enc, ptr)) { + case BT_DIGIT: + case BT_HEX: +@@ -1760,7 +1760,7 @@ PREFIX(updatePosition)(const ENCODING *enc, + case BT_CR: + pos->lineNumber++; + ptr += MINBPC(enc); +- if (ptr != end && BYTE_TYPE(enc, ptr) == BT_LF) ++ if (ptr < end && BYTE_TYPE(enc, ptr) == BT_LF) + ptr += MINBPC(enc); + pos->columnNumber = (XML_Size)-1; + break; +-- +2.8.2 + diff --git a/gnu/packages/xml.scm b/gnu/packages/xml.scm index e1f111e329..9eaf71aefa 100644 --- a/gnu/packages/xml.scm +++ b/gnu/packages/xml.scm @@ -7,6 +7,7 @@ ;;; Copyright © 2015 Mark H Weaver ;;; Copyright © 2015 Efraim Flashner ;;; Copyright © 2015 Raimon Grau +;;; Copyright © 2016 Leo Famulari ;;; ;;; This file is part of GNU Guix. ;;; @@ -44,6 +45,7 @@ (define-module (gnu packages xml) (define-public expat (package (name "expat") + (replacement expat/fixed) (version "2.1.0") (source (origin (method url-fetch) @@ -62,6 +64,15 @@ (define-public expat things the parser might find in the XML document (like start tags).") (license license:expat))) +(define expat/fixed + (package + (inherit expat) + (source (origin + (inherit (package-source expat)) + (patches (search-patches "expat-CVE-2015-1283.patch" + "expat-CVE-2015-1283-refix.patch" + "expat-CVE-2016-0718.patch")))))) + (define-public libxml2 (package (name "libxml2") -- cgit v1.2.3 From 0e40755d35fc0ec1e598796af2ba3e72cbd59af5 Mon Sep 17 00:00:00 2001 From: Jelle Licht Date: Tue, 17 May 2016 06:40:01 -0700 Subject: gnu: jemalloc: Update to 4.2.0. * gnu/packages/jemalloc.scm (jemalloc): Update to 4.2.0. Signed-off-by: Efraim Flashner --- gnu/packages/jemalloc.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/jemalloc.scm b/gnu/packages/jemalloc.scm index 52d43e8bd3..e82bcd84c8 100644 --- a/gnu/packages/jemalloc.scm +++ b/gnu/packages/jemalloc.scm @@ -27,7 +27,7 @@ (define-module (gnu packages jemalloc) (define-public jemalloc (package (name "jemalloc") - (version "4.1.0") + (version "4.2.0") (source (origin (method url-fetch) (uri (string-append @@ -35,7 +35,7 @@ (define-public jemalloc name "-" version ".tar.bz2")) (sha256 (base32 - "13pc6gcs5d6ws63jv83vslrb1vlqdnf1dg43awkb9bbj9xqnvl7s")))) + "1jvasihaizawz44j02bri47bd905flns03nkigipys81p6pds5mj")))) (build-system gnu-build-system) (home-page "http://www.canonware.com/jemalloc/") (synopsis "General-purpose scalable concurrent malloc implementation") -- cgit v1.2.3 From 0fc4a8afbad8783d4d0eb5ef50d57eb884afc8e1 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Thu, 19 May 2016 21:04:22 -0400 Subject: gnu: btrfs-progs: Update to 4.5.3. * gnu/packages/linux.scm (btrfs-progs): Update to 4.5.3. --- gnu/packages/linux.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index ba8dce09e7..08936f60d3 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -2551,7 +2551,7 @@ (define-public gpm (define-public btrfs-progs (package (name "btrfs-progs") - (version "4.5.1") + (version "4.5.3") (source (origin (method url-fetch) (uri (string-append "mirror://kernel.org/linux/kernel/" @@ -2559,7 +2559,7 @@ (define-public btrfs-progs "btrfs-progs-v" version ".tar.xz")) (sha256 (base32 - "1znf2zhb56zbmdjk3lq107678xwsqwc5gczspypmc5i31qnppy7f")))) + "1lzbw275xgv69v4z8hmsf3jnip38116hxhkpv0madk8wv049drz6")))) (build-system gnu-build-system) (arguments '(#:test-target "test" -- cgit v1.2.3 From 186ed873375b9c9c20345a46d55c8663976f7bbf Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 20 May 2016 14:38:22 +0200 Subject: gnu: r-genomeinfodb: Update to 1.8.1. * gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.8.1. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 8cec840c6c..643f006985 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -4103,13 +4103,13 @@ (define-public r-iranges (define-public r-genomeinfodb (package (name "r-genomeinfodb") - (version "1.8.0") + (version "1.8.1") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomeInfoDb" version)) (sha256 (base32 - "0fcfzw3d0rxlc320bvz0vlxg26fa1278abhjmknb815046g7fn3s")))) + "0k4s6z5qj53zkfnyrmcbn3l2nzgm56bhv58rv321j22qa56cpz7d")))) (properties `((upstream-name . "GenomeInfoDb"))) (build-system r-build-system) -- cgit v1.2.3 From 679e670b36a649276b55d62a6979624aebc26a3a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 20 May 2016 14:38:52 +0200 Subject: gnu: r-variantannotation: Update to 1.18.1. * gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.18.1. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 643f006985..f946d17f46 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -4129,13 +4129,13 @@ (define-public r-genomeinfodb (define-public r-variantannotation (package (name "r-variantannotation") - (version "1.18.0") + (version "1.18.1") (source (origin (method url-fetch) (uri (bioconductor-uri "VariantAnnotation" version)) (sha256 (base32 - "1mjm5kav0mjymcj3ha1jnw9snym39w5vc2zkl25dpg78nl00nwar")))) + "1jdpdnp7l81xfprba2ykfnj6i64fd84vxaax0wvrz6qahxvnjzyw")))) (properties `((upstream-name . "VariantAnnotation"))) (inputs -- cgit v1.2.3 From 73af676feb5dabea719e9071ea734f9e8303f7f7 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 20 May 2016 14:39:24 +0200 Subject: gnu: r-annotationdbi: Update to 1.34.2. * gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.34.2. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index f946d17f46..b1164bd94e 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -4246,13 +4246,13 @@ (define-public r-biobase (define-public r-annotationdbi (package (name "r-annotationdbi") - (version "1.34.0") + (version "1.34.2") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationDbi" version)) (sha256 (base32 - "0ri766402q3r4fdgibhb7ij7r73g6gdsj1g6iimm4mcinipfixwj")))) + "0nw6c23098gkjlwlrra4rh1m65azczb31qr01pq81cn5gya1zkr4")))) (properties `((upstream-name . "AnnotationDbi"))) (build-system r-build-system) -- cgit v1.2.3 From d7420566a98933c56ee5cff0b6c5c6a1f2773a84 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 20 May 2016 14:39:53 +0200 Subject: gnu: r-biocparallel: Update to 1.6.2. * gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.6.2. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index b1164bd94e..70ce98acc0 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -4303,13 +4303,13 @@ (define-public r-biomart (define-public r-biocparallel (package (name "r-biocparallel") - (version "1.6.0") + (version "1.6.2") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocParallel" version)) (sha256 (base32 - "0yhjihbggs3mn4z43s3fsf70brzjvbilm9ljz1z326xwmk7j40ys")))) + "0ki5xvb3cwjmlsx81gr8ylk1qy3imlj2dd04mzpvl28x42ay4dqj")))) (properties `((upstream-name . "BiocParallel"))) (build-system r-build-system) -- cgit v1.2.3 From 192e1ea8d15d076b29e55734d49f215f2f2f550a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 20 May 2016 14:40:25 +0200 Subject: gnu: r-summarizedexperiment: Update to 1.2.2. * gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to 1.2.2. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 70ce98acc0..dfdce41ccc 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -4397,13 +4397,13 @@ (define-public r-rsamtools (define-public r-summarizedexperiment (package (name "r-summarizedexperiment") - (version "1.2.0") + (version "1.2.2") (source (origin (method url-fetch) (uri (bioconductor-uri "SummarizedExperiment" version)) (sha256 (base32 - "1pfbw2dlifa7m7gxpazb6z517kw3p5a3khslykcy7gml5xsf2ch8")))) + "1c81acgw3a0ha5fgapfh9xq8yhryqqf8k259n2dz0mgz1k2d9klg")))) (properties `((upstream-name . "SummarizedExperiment"))) (build-system r-build-system) -- cgit v1.2.3 From 8ede249e0ad349238e0347f8001d76039b86729f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 20 May 2016 14:41:12 +0200 Subject: gnu: r-genomicfeatures: Update to 1.24.2. * gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.24.2. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index dfdce41ccc..446a1385c5 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -4504,13 +4504,13 @@ (define-public r-rtracklayer (define-public r-genomicfeatures (package (name "r-genomicfeatures") - (version "1.24.0") + (version "1.24.2") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicFeatures" version)) (sha256 (base32 - "1rfqxq6brrfzdajxd6ydbfaag0529d1cpjihvagmf8124prx2b2f")))) + "0ga5a7w8jnnq2k0kc07mshl6cggmbhzh42pzvhnilgl4x3kpbysl")))) (properties `((upstream-name . "GenomicFeatures"))) (build-system r-build-system) -- cgit v1.2.3 From eb1a5b65c0a22a35c65357ca2106ce521179ad06 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 20 May 2016 14:45:40 +0200 Subject: gnu: r-rcpp: Update to 0.12.5. * gnu/packages/statistics.scm (r-rcpp): Update to 0.12.5. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 58f5c9d644..93133650b9 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -357,13 +357,13 @@ (define-public r-munsell (define-public r-rcpp (package (name "r-rcpp") - (version "0.12.4") + (version "0.12.5") (source (origin (method url-fetch) (uri (cran-uri "Rcpp" version)) (sha256 - (base32 "1lyhyaxrnb5w4igi3l1p378s4jblcnrv6h7h5ym42ljm54mm44w3")))) + (base32 "1vw0zbd6zhqixqg7h8ahn1dr1hb492365x419nrp2lhvr60r8i0k")))) (build-system r-build-system) (home-page "http://www.rcpp.org") (synopsis "Seamless R and C++ Integration") -- cgit v1.2.3 From a76b3f69144684bc90bc86fc0c343e52cad14c0b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 20 May 2016 14:46:11 +0200 Subject: gnu: r-dbi: Update to 0.4-1. * gnu/packages/statistics.scm (r-dbi): Update to 0.4-1. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 93133650b9..0594ca7ca2 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -605,13 +605,13 @@ (define-public r-lazyeval (define-public r-dbi (package (name "r-dbi") - (version "0.3.1") + (version "0.4-1") (source (origin (method url-fetch) (uri (cran-uri "DBI" version)) (sha256 (base32 - "0xj5baxwnhl23rd5nskhjvranrwrc68f3xlyrklglipi41bm69hw")))) + "13n6ibmrma42qmq17qgkyjsc0ciwqf17sd7lw7w26pwpyjd4mwgg")))) (build-system r-build-system) (home-page "https://github.com/rstats-db/DBI") (synopsis "R database interface") -- cgit v1.2.3 From 9a0ccf43cc82d5f77f1f3bc87f37ed0b2c9e68b3 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 20 May 2016 14:46:39 +0200 Subject: gnu: r-bh: Update to 1.60.0-2. * gnu/packages/statistics.scm (r-bh): Update to 1.60.0-2. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 0594ca7ca2..0fdae81b34 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -625,13 +625,13 @@ (define-public r-dbi (define-public r-bh (package (name "r-bh") - (version "1.60.0-1") + (version "1.60.0-2") (source (origin (method url-fetch) (uri (cran-uri "BH" version)) (sha256 (base32 - "08gc3b0irgvpjl59irdxs8jhlbky4yp4fvs3zi4pq0wdwj43cfsk")))) + "136497fng9bcvrf8favpj8inz96pxdwp1rrb2k00sxjxjbgawhg4")))) (build-system r-build-system) (home-page "https://github.com/eddelbuettel/bh") (synopsis "R package providing subset of Boost headers") -- cgit v1.2.3 From 84e5368719a860964b54f5edb5dc387c2bd2dac9 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 20 May 2016 14:47:11 +0200 Subject: gnu: r-evaluate: Update to 0.9. * gnu/packages/statistics.scm (r-evaluate): Update to 0.9. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 0fdae81b34..ab0f3b4085 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -643,13 +643,13 @@ (define-public r-bh (define-public r-evaluate (package (name "r-evaluate") - (version "0.8.3") + (version "0.9") (source (origin (method url-fetch) (uri (cran-uri "evaluate" version)) (sha256 (base32 - "08d6164m9wqf9qq6yh1s9a0qxwqzqpsq7312hilzy79gxf9gixzr")))) + "1bn6bympg9prr8d16g1g530bddii8i04hf4i2bkw0yf4dsfqq4g8")))) (build-system r-build-system) (propagated-inputs `(("r-stringr" ,r-stringr))) -- cgit v1.2.3 From df25b0048ad05fc42de7f20f2299802f94e4e2c8 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 20 May 2016 14:47:34 +0200 Subject: gnu: r-formatr: Update to 1.4. * gnu/packages/statistics.scm (r-formatr): Update to 1.4. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index ab0f3b4085..6fd989f168 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -665,13 +665,13 @@ (define-public r-evaluate (define-public r-formatr (package (name "r-formatr") - (version "1.3") + (version "1.4") (source (origin (method url-fetch) (uri (cran-uri "formatR" version)) (sha256 (base32 - "09fsd0z6nhksc1h921h8q28f87hr6d1q8d6dmpxphjylb9r5xmj4")))) + "1fvynq0fj1r9grg9vvfdh5fl2riv6qki9f2rfpyvbvqq3xxpmi3f")))) (build-system r-build-system) (home-page "http://yihui.name/formatR") (synopsis "Format R code automatically") -- cgit v1.2.3 From d5130e6345a3e9fd0af471b5e1c09bdd07322e97 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 20 May 2016 14:48:35 +0200 Subject: gnu: r-highr: Update to 0.6. * gnu/packages/statistics.scm (r-highr): Update to 0.6. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 6fd989f168..0ce18be618 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -685,13 +685,13 @@ (define-public r-formatr (define-public r-highr (package (name "r-highr") - (version "0.5.1") + (version "0.6") (source (origin (method url-fetch) (uri (cran-uri "highr" version)) (sha256 (base32 - "11hyawzhaw3ph5y5xphi7alx6df1d0i6wh0a2n5m4sxxhdrzswnb")))) + "0n9v44dxdy5fhkdmpbpa2p78whyd9z3rhhy42ipdz5m5vsr55qa3")))) (build-system r-build-system) (home-page "https://github.com/yihui/highr") (synopsis "Syntax highlighting for R source code") -- cgit v1.2.3 From 1b206aeb00717dba24de1f3b8af06bc054f77135 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 20 May 2016 14:49:07 +0200 Subject: gnu: r-knitr: Update to 1.13. * gnu/packages/statistics.scm (r-knitr): Update to 1.13. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 0ce18be618..b0ab03d1d7 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -766,13 +766,13 @@ (define-public r-yaml (define-public r-knitr (package (name "r-knitr") - (version "1.12.3") + (version "1.13") (source (origin (method url-fetch) (uri (cran-uri "knitr" version)) (sha256 (base32 - "1v3rzv6wq8mvpdrljsaqk4z3f8323jnv385js24wmn4fglqly6dz")))) + "0v69846myi4fbjp8wiik4295fhba67s3i6ccysghm6x031i2f26q")))) (build-system r-build-system) (propagated-inputs `(("r-evaluate" ,r-evaluate) -- cgit v1.2.3 From 383f6337a001f5ffab1189e03aa3ad1a5bfaf8ae Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 20 May 2016 14:49:54 +0200 Subject: gnu: r-testthat: Update to 1.0.2. * gnu/packages/statistics.scm (r-testthat): Update to 1.0.2. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index b0ab03d1d7..99aa499584 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -916,13 +916,13 @@ (define-public r-praise (define-public r-testthat (package (name "r-testthat") - (version "1.0.0") + (version "1.0.2") (source (origin (method url-fetch) (uri (cran-uri "testthat" version)) (sha256 (base32 - "1ci1y54kaz7g4di79fcibp0m0wkkxn2glchhs6v8jfg6374ka410")))) + "0pj1r01x4ny4capr83dfa19hi5i2sjjxky99schzip8zrq5dzxqf")))) (build-system r-build-system) (propagated-inputs `(("r-digest" ,r-digest) -- cgit v1.2.3 From c1e2c9d41aecdab073a7407ceb75440823e7fc73 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 20 May 2016 14:50:54 +0200 Subject: gnu: r-openssl: Update to 0.9.3. * gnu/packages/statistics.scm (r-openssl): Update to 0.9.3. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 99aa499584..ba1ae241dd 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -1396,14 +1396,14 @@ (define-public r-roxygen2 (define-public r-openssl (package (name "r-openssl") - (version "0.9.2") + (version "0.9.3") (source (origin (method url-fetch) (uri (cran-uri "openssl" version)) (sha256 (base32 - "1dbsaciz39zvsmcyxkmpfm5yxzrpw2iv2nb86525wn80q0cyv0cb")))) + "0ldqam7d9fyxwhr651ld6lsh05lg4v2y8ajxwzq9ywzjmfb3vlpz")))) (build-system r-build-system) (inputs `(("openssl" ,openssl))) -- cgit v1.2.3 From 3624ad71501cb7924003f4b8bcf9b08e7c9f4ff6 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 20 May 2016 14:51:26 +0200 Subject: gnu: r-git2r: Update to 0.15.0. * gnu/packages/statistics.scm (r-git2r): Update to 0.15.0. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index ba1ae241dd..2be25d9fc3 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -1453,13 +1453,13 @@ (define-public r-httr (define-public r-git2r (package (name "r-git2r") - (version "0.14.0") + (version "0.15.0") (source (origin (method url-fetch) (uri (cran-uri "git2r" version)) (sha256 (base32 - "0jkkrggffpflaaw0gn2hnm1wz83xs31amriim481g73zf30g2bpr")))) + "1rpdf85wy9fp456ypvbhl3p9whkb7kgl0n7rkqxd2bhvyzkvjak8")))) (build-system r-build-system) ;; This R package contains modified sources of libgit2. This modified ;; version of libgit2 is built as the package is built. Hence libgit2 is -- cgit v1.2.3 From 133f27b06af28dc99ba14cc53f301259392faa5c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 20 May 2016 14:51:58 +0200 Subject: gnu: r-devtools: Update to 1.11.1. * gnu/packages/statistics.scm (r-devtools): Update to 1.11.1. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 2be25d9fc3..45cfc6916d 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -1497,13 +1497,13 @@ (define-public r-rstudioapi (define-public r-devtools (package (name "r-devtools") - (version "1.11.0") + (version "1.11.1") (source (origin (method url-fetch) (uri (cran-uri "devtools" version)) (sha256 (base32 - "101j15d0f9107pnmdpdwqyvk2ncykq48336rl8lnqp6idiq8id2q")))) + "0ik3l3q62sspdph613f9ik5yz36s8q5nrc50dqgn3pxzvpwpdj2i")))) (build-system r-build-system) (propagated-inputs `(("r-curl" ,r-curl) -- cgit v1.2.3 From 2f7ac060ff464f4bacd0d4a18fd9a82426220e74 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 20 May 2016 14:52:32 +0200 Subject: gnu: r-plotrix: Update to 3.6-2. * gnu/packages/statistics.scm (r-plotrix): Update to 3.6-2. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 45cfc6916d..1cf8e6dd6b 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -1568,13 +1568,13 @@ (define-public r-readr (define-public r-plotrix (package (name "r-plotrix") - (version "3.6-1") + (version "3.6-2") (source (origin (method url-fetch) (uri (cran-uri "plotrix" version)) (sha256 (base32 - "1y8xnlpy4zba70af9lwj2sshvfdfcmfdh92wamyzj8z9gciailfr")))) + "1jn1k3skmlgyvpijj6vlcn5m2zgrsdh00g1fq8n5dqs1pkl1sqrw")))) (build-system r-build-system) (home-page "http://cran.r-project.org/web/packages/plotrix") (synopsis "Various plotting functions") -- cgit v1.2.3 From f0c56a241140d279035d01555bfc12bc8378d782 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 20 May 2016 14:53:44 +0200 Subject: gnu: r-rmarkdown: Update to 0.9.6. * gnu/packages/statistics.scm (r-rmarkdown): Update to 0.9.6. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 1cf8e6dd6b..468248a286 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -1731,14 +1731,14 @@ (define-public r-catools (define-public r-rmarkdown (package (name "r-rmarkdown") - (version "0.9.5") + (version "0.9.6") (source (origin (method url-fetch) (uri (cran-uri "rmarkdown" version)) (sha256 (base32 - "1zz98jxvw3lzva5kkj1n37gbhjwqd96gjs04y6h37pqy6qmkhk8c")))) + "09ajq5miqzz46q0i9svvbh93dbi7xbjn4702d6z3scdz272gx7l2")))) (properties `((upstream-name . "rmarkdown"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From b8f6a97ebd7f41a26d1ae8ae9d6e93c9dc4c6390 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 20 May 2016 14:54:25 +0200 Subject: gnu: r-r-rsp: Update to 0.30.0. * gnu/packages/statistics.scm (r-r-rsp): Update to 0.30.0. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 468248a286..1fcf0ea554 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -2412,13 +2412,13 @@ (define-public r-r-cache (define-public r-r-rsp (package (name "r-r-rsp") - (version "0.21.0") + (version "0.30.0") (source (origin (method url-fetch) (uri (cran-uri "R.rsp" version)) (sha256 (base32 - "0snc6ps75s3ci6sy8mil1wg2i9xmlr1ygh9n244y1brdvp43dfsw")))) + "1ssykygqkxzx9qblxhavxlf2z6r5bhk0s47yw1dllfiyc8zy7jv2")))) (properties `((upstream-name . "R.rsp"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 95513f284f35ba8d4ccff924de248ab03586d500 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 20 May 2016 14:56:16 +0200 Subject: gnu: r-matrixstats: Update to 0.50.2. * gnu/packages/statistics.scm (r-matrixstats): Update to 0.50.2. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 1fcf0ea554..7c0a23e9b7 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -2462,13 +2462,13 @@ (define-public r-mvtnorm (define-public r-matrixstats (package (name "r-matrixstats") - (version "0.50.1") + (version "0.50.2") (source (origin (method url-fetch) (uri (cran-uri "matrixStats" version)) (sha256 (base32 - "08l32abp7dfnsc49ca4hzznh934y60n5z01x5ga2ixky5961s57c")))) + "0zj27xxx9cyrq16rn4g3l0krqg68p8f2qp18w1w4i767j87amlbj")))) (properties `((upstream-name . "matrixStats"))) (build-system r-build-system) (native-inputs -- cgit v1.2.3 From c969453e1c4cdbaa6bd1d35d788ee40b0df87920 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 20 May 2016 14:56:50 +0200 Subject: gnu: r-plotly: Update to 3.6.0. * gnu/packages/statistics.scm (r-plotly): Update to 3.6.0. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 7c0a23e9b7..c7bd0028d0 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -2564,13 +2564,13 @@ (define-public r-hexbin (define-public r-plotly (package (name "r-plotly") - (version "3.4.13") + (version "3.6.0") (source (origin (method url-fetch) (uri (cran-uri "plotly" version)) (sha256 (base32 - "1pfl9w35iwin8a1hfwcihajyps2ngjbyrmvi61b9lspcdbk39lf8")))) + "15hvqa0sf4z6l6vvr614zjszfphwpv66zpc665iyiynq0pd1jv2c")))) (build-system r-build-system) (propagated-inputs `(("r-base64enc" ,r-base64enc) -- cgit v1.2.3 From f6225d135c88f70d29729f9a6b593dd8b7141d45 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 20 May 2016 14:57:25 +0200 Subject: gnu: r-jsonlite: Update to 0.9.20. * gnu/packages/web.scm (r-jsonlite): Update to 0.9.20. --- gnu/packages/web.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm index bd30da2533..c86e0f03fc 100644 --- a/gnu/packages/web.scm +++ b/gnu/packages/web.scm @@ -3060,13 +3060,13 @@ (define-public r-httpuv (define-public r-jsonlite (package (name "r-jsonlite") - (version "0.9.19") + (version "0.9.20") (source (origin (method url-fetch) (uri (cran-uri "jsonlite" version)) (sha256 (base32 - "1hbdraj3xv2l2gs9f205j8z054ycy0bfdvwdhvpa9qlji588sz7g")))) + "08b2gifd81yzj0h4k7pqp2cc2r5lwsg3sxnssi6c96rgqvl4702n")))) (build-system r-build-system) (home-page "http://arxiv.org/abs/1403.2805") (synopsis "Robust, high performance JSON parser and generator for R") -- cgit v1.2.3 From 7740f5812889d398353fef98d871799334c3ac74 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 20 May 2016 14:58:57 +0200 Subject: gnu: r-genomation: Update to 1.4.2. * gnu/packages/bioinformatics.scm (r-genomation): Update to 1.4.2. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 446a1385c5..d404ff839c 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -4695,13 +4695,13 @@ (define-public r-seqpattern (define-public r-genomation (package (name "r-genomation") - (version "1.4.0") + (version "1.4.2") (source (origin (method url-fetch) (uri (bioconductor-uri "genomation" version)) (sha256 (base32 - "16q1qkl6cwwj5hqhxpfgbz0y27hwz3h8zkjxpbyvjy1q0894sdjl")))) + "017hxh3yhizlsswd2vw8504arkckrcgq5zraiw67lldq9wzs5qzg")))) (build-system r-build-system) (propagated-inputs `(("r-biostrings" ,r-biostrings) -- cgit v1.2.3 From 945eef85c511c11cf0d54ad3ec6e3745917260b7 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 20 May 2016 15:08:53 +0200 Subject: gnu: armadillo: Update to 6.700.7. * gnu/packages/maths.scm (armadillo): Update to 6.700.7. --- gnu/packages/maths.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 95240af962..3fc06869c9 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -1641,14 +1641,14 @@ (define-public wxmaxima (define-public armadillo (package (name "armadillo") - (version "6.700.4") + (version "6.700.7") (source (origin (method url-fetch) (uri (string-append "mirror://sourceforge/arma/armadillo-" version ".tar.gz")) (sha256 (base32 - "0dsdjcps5l2nhg0455rrc708inffarzj7n435vj4sm9lxwf21wg9")))) + "0xbidcxrvbq33xf7iysg2nic2ai9a043psl33kiv6ifkk7p8hcra")))) (build-system cmake-build-system) (arguments `(#:tests? #f)) ;no test target (inputs -- cgit v1.2.3 From 813efdded15d9382ee8e71287367963f5dc7fd26 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 20 May 2016 15:09:36 +0200 Subject: gnu: r-rcpparmadillo: Update to 0.6.700.6.0. * gnu/packages/statistics.scm (r-rcpparmadillo): Update to 0.6.700.6.0. * gnu/packages/maths.scm (armadillo-for-rcpparmadillo): Update to 6.700.6. --- gnu/packages/maths.scm | 4 ++-- gnu/packages/statistics.scm | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 3fc06869c9..19ed44f2c9 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -1669,14 +1669,14 @@ (define-public armadillo (define-public armadillo-for-rcpparmadillo (package (inherit armadillo) - (version "6.700.3") + (version "6.700.6") (source (origin (method url-fetch) (uri (string-append "mirror://sourceforge/arma/armadillo-" version ".tar.gz")) (sha256 (base32 - "1vnhifa7d0aij3kv5bxf6m91d99h3y2fyj48jrx7jcvwyb1q5wwq")))))) + "1cdpjxb0fz5f28y5qrqgpw53s7qi8s2v3al9lfdldqxngb21vpx8")))))) (define-public muparser (package diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index c7bd0028d0..43f9042e9c 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -1647,13 +1647,13 @@ (define-public r-latticeextra (define-public r-rcpparmadillo (package (name "r-rcpparmadillo") - (version "0.6.700.3.0") + (version "0.6.700.6.0") (source (origin (method url-fetch) (uri (cran-uri "RcppArmadillo" version)) (sha256 (base32 - "1mc62b6my568ni18w4clgs6l6ggqrwzsm3lgx0c1prf4rap69s8w")) + "0x736cjg1pbvn8c6h91c88qmmz4pddvvqg88k9c9kwhn24fjrra0")) (modules '((guix build utils))) ;; Remove bundled armadillo sources (snippet -- cgit v1.2.3 From 2d69c1616d974f45ecdc4977d4501d0ae1dcd634 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 16 May 2016 20:10:55 +0200 Subject: gnu: Add gcc-objc-4.9. * gnu/packages/gcc.scm (gcc-objc-4.9): New variable. --- gnu/packages/gcc.scm | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/gnu/packages/gcc.scm b/gnu/packages/gcc.scm index 740ed51485..64035b3dfe 100644 --- a/gnu/packages/gcc.scm +++ b/gnu/packages/gcc.scm @@ -615,6 +615,15 @@ (define-public gcc-objc-4.8 (variable "LIBRARY_PATH") (files '("lib" "lib64")))))) +(define-public gcc-objc-4.9 + (custom-gcc gcc-4.9 "gcc-objc" '("objc") + (list (search-path-specification + (variable "OBJC_INCLUDE_PATH") + (files '("include"))) + (search-path-specification + (variable "LIBRARY_PATH") + (files '("lib" "lib64")))))) + (define-public gcc-objc++-4.8 (custom-gcc gcc-4.8 "gcc-objc++" '("obj-c++") (list (search-path-specification -- cgit v1.2.3 From 8b196ad208e844e2829e49382811dff327bd297d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 16 May 2016 20:11:19 +0200 Subject: gnu: Add default gcc-objc. * gnu/packages/gcc.scm (gcc-objc): New variable. --- gnu/packages/gcc.scm | 2 ++ 1 file changed, 2 insertions(+) diff --git a/gnu/packages/gcc.scm b/gnu/packages/gcc.scm index 64035b3dfe..d8b96c7dd0 100644 --- a/gnu/packages/gcc.scm +++ b/gnu/packages/gcc.scm @@ -624,6 +624,8 @@ (define-public gcc-objc-4.9 (variable "LIBRARY_PATH") (files '("lib" "lib64")))))) +(define-public gcc-objc gcc-objc-4.9) + (define-public gcc-objc++-4.8 (custom-gcc gcc-4.8 "gcc-objc++" '("obj-c++") (list (search-path-specification -- cgit v1.2.3 From a5948c0d41d7850c93f3128461ad3e87089e52a3 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 16 May 2016 20:11:42 +0200 Subject: gnu: Add gcc-objc++-4.9. * gnu/packages/gcc.scm (gcc-objc++-4.9): New variable. --- gnu/packages/gcc.scm | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/gnu/packages/gcc.scm b/gnu/packages/gcc.scm index d8b96c7dd0..53b6c54ec9 100644 --- a/gnu/packages/gcc.scm +++ b/gnu/packages/gcc.scm @@ -635,6 +635,15 @@ (define-public gcc-objc++-4.8 (variable "LIBRARY_PATH") (files '("lib" "lib64")))))) +(define-public gcc-objc++-4.9 + (custom-gcc gcc-4.9 "gcc-objc++" '("obj-c++") + (list (search-path-specification + (variable "OBJCPLUS_INCLUDE_PATH") + (files '("include"))) + (search-path-specification + (variable "LIBRARY_PATH") + (files '("lib" "lib64")))))) + (define (make-libstdc++-doc gcc) "Return a package with the libstdc++ documentation for GCC." (package -- cgit v1.2.3 From 987a1183344a716a65d13796dca9013a0c2bcf66 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 16 May 2016 20:12:08 +0200 Subject: gnu: Add default gcc-objc++. * gnu/packages/gcc.scm (gcc-objc++): New variable. --- gnu/packages/gcc.scm | 2 ++ 1 file changed, 2 insertions(+) diff --git a/gnu/packages/gcc.scm b/gnu/packages/gcc.scm index 53b6c54ec9..233a20bc86 100644 --- a/gnu/packages/gcc.scm +++ b/gnu/packages/gcc.scm @@ -644,6 +644,8 @@ (define-public gcc-objc++-4.9 (variable "LIBRARY_PATH") (files '("lib" "lib64")))))) +(define-public gcc-objc++ gcc-objc++-4.9) + (define (make-libstdc++-doc gcc) "Return a package with the libstdc++ documentation for GCC." (package -- cgit v1.2.3 From 932f2b70a6a5eee15b1508d7aae7f8a7fdb0e23a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 10 May 2016 15:50:28 +0200 Subject: ant-build-system: Add unpack phase. * guix/build/ant-build-system.scm (unpack): New procedure. (%standard-phases): Use it. --- guix/build/ant-build-system.scm | 12 ++++++++++++ 1 file changed, 12 insertions(+) diff --git a/guix/build/ant-build-system.scm b/guix/build/ant-build-system.scm index 27277af34b..6dc19ff2db 100644 --- a/guix/build/ant-build-system.scm +++ b/guix/build/ant-build-system.scm @@ -86,6 +86,17 @@ (define (generate-classpath inputs) (find-files dir "\\.*jar$"))) inputs)) ":")) +(define* (unpack #:key source #:allow-other-keys) + "Unpack the jar archive SOURCE. When SOURCE is not a jar archive fall back +to the default GNU unpack strategy." + (if (string-suffix? ".jar" source) + (begin + (mkdir "src") + (with-directory-excursion "src" + (zero? (system* "jar" "-xf" source)))) + ;; Use GNU unpack strategy for things that aren't jar archives. + ((assq-ref gnu:%standard-phases 'unpack) #:source source))) + (define* (configure #:key inputs outputs (jar-name #f) #:allow-other-keys) (when jar-name @@ -151,6 +162,7 @@ (define* (install #:key (make-flags '()) #:allow-other-keys) (define %standard-phases (modify-phases gnu:%standard-phases + (replace 'unpack unpack) (replace 'configure configure) (replace 'build build) (replace 'check check) -- cgit v1.2.3 From 4483a1185d413f206d4f35b3eacf6f9d893ae3da Mon Sep 17 00:00:00 2001 From: Mark H Weaver Date: Fri, 20 May 2016 18:15:51 -0400 Subject: gnu: linux-libre-4.4: Update to 4.4.11. * gnu/packages/linux.scm (linux-libre-4.4): Update to 4.4.11. --- gnu/packages/linux.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 08936f60d3..f0e6865706 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -340,13 +340,13 @@ (define-public linux-libre (define-public linux-libre-4.4 (package (inherit linux-libre) - (version "4.4.10") + (version "4.4.11") (source (origin (method url-fetch) (uri (linux-libre-urls version)) (sha256 (base32 - "1k7h632vgh3wlz44qqawy238f4mzn19bm9sz9zqq0ql6wwhkjdkj")))) + "17pb9w72vigdrhm8hnkdyw9kwc2l06nabzygpdkwbvf7fg3j03vc")))) (native-inputs (let ((conf (kernel-config (or (%current-target-system) (%current-system)) -- cgit v1.2.3 From 3c9a7185e4ee81295838bb31f0d437da64dbd390 Mon Sep 17 00:00:00 2001 From: Mark H Weaver Date: Fri, 20 May 2016 18:17:12 -0400 Subject: gnu: linux-libre: Update to 4.5.5. * gnu/packages/linux.scm (linux-libre): Update to 4.5.5. --- gnu/packages/linux.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index f0e6865706..5b1d2a9540 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -225,7 +225,7 @@ (define* (kernel-config system #:key variant) (search-path %load-path file))) (define-public linux-libre - (let* ((version "4.5.4") + (let* ((version "4.5.5") (build-phase '(lambda* (#:key system inputs #:allow-other-keys #:rest args) ;; Avoid introducing timestamps @@ -303,7 +303,7 @@ (define-public linux-libre (uri (linux-libre-urls version)) (sha256 (base32 - "0c587v03kz5whh82apva6gwqvczdi6djy29gk0gfd9dbkb2518b1")))) + "1zys74hfdi13yyk17x45hvvbx7m97wk7pala3cd8k93xbq8qnai0")))) (build-system gnu-build-system) (supported-systems '("x86_64-linux" "i686-linux")) (native-inputs `(("perl" ,perl) -- cgit v1.2.3 From 3cabdead6fbe080d9466bb3130a2b36dd4b07090 Mon Sep 17 00:00:00 2001 From: Ludovic Courtès Date: Thu, 19 May 2016 23:24:50 +0200 Subject: graph: Use absolute file name canonicalization. * guix/scripts/graph.scm (guix-graph): Wrap in 'with-fluids'. --- guix/scripts/graph.scm | 21 ++++++++++++--------- 1 file changed, 12 insertions(+), 9 deletions(-) diff --git a/guix/scripts/graph.scm b/guix/scripts/graph.scm index ba63780e2b..1623421196 100644 --- a/guix/scripts/graph.scm +++ b/guix/scripts/graph.scm @@ -356,15 +356,18 @@ (define (guix-graph . args) (_ #f)) opts))) (with-store store - (run-with-store store - ;; XXX: Since grafting can trigger unsolicited builds, disable it. - (mlet %store-monad ((_ (set-grafting #f)) - (nodes (mapm %store-monad - (node-type-convert type) - packages))) - (export-graph (concatenate nodes) - (current-output-port) - #:node-type type)))))) + ;; Ask for absolute file names so that .drv file names passed from the + ;; user to 'read-derivation' are absolute when it returns. + (with-fluids ((%file-port-name-canonicalization 'absolute)) + (run-with-store store + ;; XXX: Since grafting can trigger unsolicited builds, disable it. + (mlet %store-monad ((_ (set-grafting #f)) + (nodes (mapm %store-monad + (node-type-convert type) + packages))) + (export-graph (concatenate nodes) + (current-output-port) + #:node-type type))))))) #t) ;;; graph.scm ends here -- cgit v1.2.3 From 97507ebedc8e1265c2ed354e50a218fb9ee6087b Mon Sep 17 00:00:00 2001 From: Ludovic Courtès Date: Thu, 19 May 2016 23:27:48 +0200 Subject: derivations: 'derivation' sorts items in the resulting object. * guix/derivations.scm (derivation-inputderivation-input] [coalesce-duplicate-inputs]: New procedures. Sort OUTPUTS, INPUTS, and ENV-VARS. * tests/derivations.scm ("read-derivation vs. derivation"): New test. --- guix/derivations.scm | 133 +++++++++++++++++++++++++------------------------- tests/derivations.scm | 27 ++++++++++ 2 files changed, 94 insertions(+), 66 deletions(-) diff --git a/guix/derivations.scm b/guix/derivations.scm index d4f697477b..76593f373b 100644 --- a/guix/derivations.scm +++ b/guix/derivations.scm @@ -176,6 +176,11 @@ (define (fixed-output-derivation? drv) #t) (_ #f))) +(define (derivation-input." + (string." @@ -190,6 +195,30 @@ (define (valid-derivation-input? store input) (every (cut valid-path? store <>) (derivation-input-output-paths input))) +(define (coalesce-duplicate-inputs inputs) + "Return a list of inputs, such that when INPUTS contains the same DRV twice, +they are coalesced, with their sub-derivations merged. This is needed because +Nix itself keeps only one of them." + (fold (lambda (input result) + (match input + (($ path sub-drvs) + ;; XXX: quadratic + (match (find (match-lambda + (($ p s) + (string=? p path))) + result) + (#f + (cons input result)) + ((and dup ($ _ sub-drvs2)) + ;; Merge DUP with INPUT. + (let ((sub-drvs (delete-duplicates + (append sub-drvs sub-drvs2)))) + (cons (make-derivation-input path + (sort sub-drvs string path sub-drvs) - ;; XXX: quadratic - (match (find (match-lambda - (($ p s) - (string=? p path))) - result) - (#f - (cons input result)) - ((and dup ($ _ sub-drvs2)) - ;; Merge DUP with INPUT. - (let ((sub-drvs (delete-duplicates - (append sub-drvs sub-drvs2)))) - (cons (make-derivation-input path sub-drvs) - (delq dup result)))))))) - '() - inputs)) - (define (write-output output port) (match output ((name . ($ path hash-algo hash recursive?)) @@ -515,7 +521,7 @@ (define (write-input input port) (display "(" port) (write path port) (display "," port) - (write-string-list (sort sub-drvs string outputs inputs sources system builder args env-vars) (display "Derive(" port) - (write-list (sort outputs - (lambda (o1 o2) - (stringstring @@ -653,7 +644,10 @@ (define derivation-hash ; `hashDerivationModulo' in derivations.cc (let ((hash (derivation-path->base16-hash path))) (make-derivation-input hash sub-drvs)))) inputs)) - (drv (make-derivation outputs inputs sources + (drv (make-derivation outputs + (sort (coalesce-duplicate-inputs inputs) + derivation-inputderivation-input + (match-lambda + (((? derivation? drv)) + (make-derivation-input (derivation-file-name drv) '("out"))) + (((? derivation? drv) sub-drvs ...) + (make-derivation-input (derivation-file-name drv) sub-drvs)) + (((? direct-store-path? input)) + (make-derivation-input input '("out"))) + (((? direct-store-path? input) sub-drvs ...) + (make-derivation-input input sub-drvs)) + ((input . _) + (let ((path (add-to-store store (basename input) + #t "sha256" input))) + (make-derivation-input path '()))))) + + ;; Note: lists are sorted alphabetically, to conform with the behavior of + ;; C++ `std::map' in Nix itself. + (let* ((outputs (map (lambda (name) ;; Return outputs with an empty path. (cons name (make-derivation-output "" hash-algo hash recursive?))) - outputs)) - (inputs (map (match-lambda - (((? derivation? drv)) - (make-derivation-input (derivation-file-name drv) - '("out"))) - (((? derivation? drv) sub-drvs ...) - (make-derivation-input (derivation-file-name drv) - sub-drvs)) - (((? direct-store-path? input)) - (make-derivation-input input '("out"))) - (((? direct-store-path? input) sub-drvs ...) - (make-derivation-input input sub-drvs)) - ((input . _) - (let ((path (add-to-store store - (basename input) - #t "sha256" input))) - (make-derivation-input path '())))) - (delete-duplicates inputs))) - (env-vars (env-vars-with-empty-outputs (user+system-env-vars))) + (sort outputs stringderivation-input + (delete-duplicates inputs))) + derivation-inputstring drv) - (map derivation-input-path - inputs)))) + (map derivation-input-path inputs)))) (set-file-name drv file)))) (define* (map-derivation store drv mapping diff --git a/tests/derivations.scm b/tests/derivations.scm index cb7196e2a9..d8553b223e 100644 --- a/tests/derivations.scm +++ b/tests/derivations.scm @@ -367,6 +367,33 @@ (define prefix-len (string-length dir)) (and (eq? 'one (call-with-input-file one read)) (eq? 'two (call-with-input-file two read))))))) +(test-assert "read-derivation vs. derivation" + ;; Make sure 'derivation' and 'read-derivation' return objects that are + ;; identical. + (let* ((sources (unfold (cut >= <> 10) + (lambda (n) + (add-text-to-store %store + (format #f "input~a" n) + (random-text))) + 1+ + 0)) + (inputs (map (lambda (file) + (derivation %store "derivation-input" + %bash '() + #:inputs `((,%bash) (,file)))) + sources)) + (builder (add-text-to-store %store "builder.sh" + "echo one > $one ; echo two > $two" + '())) + (drv (derivation %store "derivation" + %bash `(,builder) + #:inputs `((,%bash) (,builder) + ,@(map list (append sources inputs))) + #:outputs '("two" "one"))) + (drv* (call-with-input-file (derivation-file-name drv) + read-derivation))) + (equal? drv* drv))) + (test-assert "multiple-output derivation, derivation-path->output-path" (let* ((builder (add-text-to-store %store "builder.sh" "echo one > $out ; echo two > $second" -- cgit v1.2.3 From a773c3142dd168e1c4480614d3f5fd9d003954cd Mon Sep 17 00:00:00 2001 From: Ludovic Courtès Date: Fri, 20 May 2016 17:07:23 +0200 Subject: graph: Allow store file names for 'derivation' and 'references' graphs. * guix/scripts/graph.scm (%derivation-node-type)[convert]: Add 'derivation-path?' and catch-all clauses. (%reference-node-type)[convert]: Add 'store-path?' and catch-all clauses. (assert-package, nodes-from-package): New procedures. (%package-node-type, %bag-node-type,%bag-with-origins-node-type) (%bag-emerged-node-type): Add 'convert' field (guix-graph): Rename 'packages' to 'items' and allow 'store-path?' arguments. * guix/graph.scm ()[convert]: Adjust comment. * doc/guix.texi (Invoking guix graph): Document it. --- doc/guix.texi | 14 +++++++++++ guix/graph.scm | 2 +- guix/scripts/graph.scm | 63 ++++++++++++++++++++++++++++++++++++++++---------- tests/guix-graph.sh | 18 ++++++++++++++- 4 files changed, 83 insertions(+), 14 deletions(-) diff --git a/doc/guix.texi b/doc/guix.texi index 3f0106be02..d88cc256d7 100644 --- a/doc/guix.texi +++ b/doc/guix.texi @@ -5161,6 +5161,12 @@ derivations (@pxref{Derivations}) and plain store items. Compared to the above representation, many additional nodes are visible, including build scripts, patches, Guile modules, etc. +For this type of graph, it is also possible to pass a @file{.drv} file +name instead of a package name, as in: + +@example +guix graph -t derivation `guix system build -d my-config.scm` +@end example @end table All the types above correspond to @emph{build-time dependencies}. The @@ -5173,6 +5179,14 @@ by @command{guix gc --references} (@pxref{Invoking guix gc}). If the given package output is not available in the store, @command{guix graph} attempts to obtain dependency information from substitutes. + +Here you can also pass a store file name instead of a package name. For +example, the command below produces the reference graph of your profile +(which can be big!): + +@example +guix graph -t references `readlink -f ~/.guix-profile` +@end example @end table The available options are the following: diff --git a/guix/graph.scm b/guix/graph.scm index 1a8f2d55b3..ad93403a1e 100644 --- a/guix/graph.scm +++ b/guix/graph.scm @@ -65,7 +65,7 @@ (define-record-type* node-type make-node-type (identifier node-type-identifier) ;node -> M identifier (label node-type-label) ;node -> string (edges node-type-edges) ;node -> M list of nodes - (convert node-type-convert ;package -> M list of nodes + (convert node-type-convert ;any -> M list of nodes (default (lift1 list %store-monad))) (name node-type-name) ;string (description node-type-description)) ;string diff --git a/guix/scripts/graph.scm b/guix/scripts/graph.scm index 1623421196..782fca5d63 100644 --- a/guix/scripts/graph.scm +++ b/guix/scripts/graph.scm @@ -33,6 +33,7 @@ (define-module (guix scripts graph) #:use-module (srfi srfi-1) #:use-module (srfi srfi-26) #:use-module (srfi srfi-34) + #:use-module (srfi srfi-35) #:use-module (srfi srfi-37) #:use-module (ice-9 match) #:export (%package-node-type @@ -70,11 +71,27 @@ (define (package-node-edges package) ;; Filter out origins and other non-package dependencies. (filter package? packages)))) +(define assert-package + (match-lambda + ((? package? package) + package) + (x + (raise + (condition + (&message + (message (format #f (_ "~a: invalid argument (package name expected)") + x)))))))) + +(define nodes-from-package + ;; The default conversion method. + (lift1 (compose list assert-package) %store-monad)) + (define %package-node-type ;; Type for the traversal of package nodes. (node-type (name "package") (description "the DAG of packages, excluding implicit inputs") + (convert nodes-from-package) ;; We use package addresses as unique identifiers. This generally works ;; well, but for generated package objects, we could end up with two @@ -131,6 +148,7 @@ (define %bag-node-type (node-type (name "bag") (description "the DAG of packages, including implicit inputs") + (convert nodes-from-package) (identifier bag-node-identifier) (label node-full-name) (edges (lift1 (compose (cut filter package? <>) bag-node-edges) @@ -140,6 +158,7 @@ (define %bag-with-origins-node-type (node-type (name "bag-with-origins") (description "the DAG of packages and origins, including implicit inputs") + (convert nodes-from-package) (identifier bag-node-identifier) (label node-full-name) (edges (lift1 (lambda (thing) @@ -170,6 +189,7 @@ (define %bag-emerged-node-type (node-type (name "bag-emerged") (description "same as 'bag', but without the bootstrap nodes") + (convert nodes-from-package) (identifier bag-node-identifier) (label node-full-name) (edges (lift1 (compose (cut filter package? <>) @@ -215,10 +235,19 @@ (define %derivation-node-type (node-type (name "derivation") (description "the DAG of derivations") - (convert (lambda (package) - (with-monad %store-monad - (>>= (package->derivation package) - (lift1 list %store-monad))))) + (convert (match-lambda + ((? package? package) + (with-monad %store-monad + (>>= (package->derivation package) + (lift1 list %store-monad)))) + ((? derivation-path? item) + (mbegin %store-monad + ((store-lift add-temp-root) item) + (return (list (file->derivation item))))) + (x + (raise + (condition (&message (message "unsupported argument for \ +derivation graph"))))))) (identifier (lift1 derivation-node-identifier %store-monad)) (label derivation-node-label) (edges (lift1 derivation-dependencies %store-monad)))) @@ -246,12 +275,20 @@ (define %reference-node-type (node-type (name "references") (description "the DAG of run-time dependencies (store references)") - (convert (lambda (package) - ;; Return the output file names of PACKAGE. - (mlet %store-monad ((drv (package->derivation package))) - (return (match (derivation->output-paths drv) - (((_ . file-names) ...) - file-names)))))) + (convert (match-lambda + ((? package? package) + ;; Return the output file names of PACKAGE. + (mlet %store-monad ((drv (package->derivation package))) + (return (match (derivation->output-paths drv) + (((_ . file-names) ...) + file-names))))) + ((? store-path? item) + (with-monad %store-monad + (return (list item)))) + (x + (raise + (condition (&message (message "unsupported argument for \ +reference graph"))))))) (identifier (lift1 identity %store-monad)) (label store-path-package-name) (edges references*))) @@ -348,7 +385,9 @@ (define (guix-graph . args) (alist-cons 'argument arg result)) %default-options)) (type (assoc-ref opts 'node-type)) - (packages (filter-map (match-lambda + (items (filter-map (match-lambda + (('argument . (? store-path? item)) + item) (('argument . spec) (specification->package spec)) (('expression . exp) @@ -364,7 +403,7 @@ (define (guix-graph . args) (mlet %store-monad ((_ (set-grafting #f)) (nodes (mapm %store-monad (node-type-convert type) - packages))) + items))) (export-graph (concatenate nodes) (current-output-port) #:node-type type))))))) diff --git a/tests/guix-graph.sh b/tests/guix-graph.sh index 4d5a755bc1..1ec99706fd 100644 --- a/tests/guix-graph.sh +++ b/tests/guix-graph.sh @@ -1,5 +1,5 @@ # GNU Guix --- Functional package management for GNU -# Copyright © 2015 Ludovic Courtès +# Copyright © 2015, 2016 Ludovic Courtès # # This file is part of GNU Guix. # @@ -20,6 +20,10 @@ # Test the 'guix graph' command-line utility. # +tmpfile1="t-guix-graph1-$$" +tmpfile2="t-guix-graph2-$$" +trap 'rm -f "$tmpfile1" "$tmpfile2"' EXIT + guix graph --version for package in guile-bootstrap coreutils python @@ -37,3 +41,15 @@ guix graph -e '(@ (gnu packages bootstrap) %bootstrap-guile)' \ | grep guile-bootstrap if guix graph -e +; then false; else true; fi + +# Try passing store file names. + +guix graph -t references guile-bootstrap > "$tmpfile1" +guix graph -t references `guix build guile-bootstrap` > "$tmpfile2" +cmp "$tmpfile1" "$tmpfile2" + +# XXX: Filter the file names in the graph to work around the fact that we get +# a mixture of relative and absolute file names. +guix graph -t derivation coreutils > "$tmpfile1" +guix graph -t derivation `guix build -d coreutils` > "$tmpfile2" +cmp "$tmpfile1" "$tmpfile2" -- cgit v1.2.3 From 30d4bc0434aa5d438c2d433f39c80e1f4a25bcac Mon Sep 17 00:00:00 2001 From: Ludovic Courtès Date: Fri, 20 May 2016 17:18:58 +0200 Subject: substitute: Gracefully handle invalid store file names. Before, something like: echo have /gnu/foo | ./test-env guix substitute --query would lead to an ugly backtrace. * guix/scripts/substitute.scm (narinfo-cache-file): Call 'leave' when 'store-hash-part' returns #f. --- guix/scripts/substitute.scm | 12 +++++++++--- 1 file changed, 9 insertions(+), 3 deletions(-) diff --git a/guix/scripts/substitute.scm b/guix/scripts/substitute.scm index d46d610347..5cdc55f2b2 100755 --- a/guix/scripts/substitute.scm +++ b/guix/scripts/substitute.scm @@ -440,9 +440,15 @@ (define (obsolete? date now ttl) (define (narinfo-cache-file cache-url path) "Return the name of the local file that contains an entry for PATH. The entry is stored in a sub-directory specific to CACHE-URL." - (string-append %narinfo-cache-directory "/" - (bytevector->base32-string (sha256 (string->utf8 cache-url))) - "/" (store-path-hash-part path))) + ;; The daemon does not sanitize its input, so PATH could be something like + ;; "/gnu/store/foo". Gracefully handle that. + (match (store-path-hash-part path) + (#f + (leave (_ "'~a' does not name a store item~%") path)) + ((? string? hash-part) + (string-append %narinfo-cache-directory "/" + (bytevector->base32-string (sha256 (string->utf8 cache-url))) + "/" hash-part)))) (define (cached-narinfo cache-url path) "Check locally if we have valid info about PATH coming from CACHE-URL. -- cgit v1.2.3 From cf8b312d1872aec1f38a179eeb981d79bf7faa03 Mon Sep 17 00:00:00 2001 From: Ludovic Courtès Date: Fri, 20 May 2016 22:11:56 +0200 Subject: grafts: Preserve empty directories when grafting. * guix/build/graft.scm (rewrite-directory)[rewrite-leaf]: Add case for 'directory. Pass #:directories? #t to 'find-files'. --- guix/build/graft.scm | 5 ++++- tests/grafts.scm | 24 ++++++++++++++++++++++++ 2 files changed, 28 insertions(+), 1 deletion(-) diff --git a/guix/build/graft.scm b/guix/build/graft.scm index b216e6c0d7..e9fce03181 100644 --- a/guix/build/graft.scm +++ b/guix/build/graft.scm @@ -115,6 +115,8 @@ (define (rewrite-leaf file) (replace-store-references input output mapping store) (chmod output (stat:perms stat)))))))) + ((directory) + (mkdir-p dest)) (else (error "unsupported file type" stat))))) @@ -124,6 +126,7 @@ (define (rewrite-leaf file) (umask #o022) (n-par-for-each (parallel-job-count) - rewrite-leaf (find-files directory))) + rewrite-leaf (find-files directory (const #t) + #:directories? #t))) ;;; graft.scm ends here diff --git a/tests/grafts.scm b/tests/grafts.scm index afed704cde..f8c9eced1d 100644 --- a/tests/grafts.scm +++ b/tests/grafts.scm @@ -127,6 +127,30 @@ (define %mkdir (list one two dep) (references %store dep))))))) +(test-assert "graft-derivation, preserve empty directories" + (run-with-store %store + (mlet* %store-monad ((fake (text-file "bash" "Fake bash.")) + (graft -> (graft + (origin %bash) + (replacement fake))) + (drv (gexp->derivation + "to-graft" + #~(begin + (use-modules (guix build utils)) + (mkdir-p (string-append #$output + "/a/b/c/d")) + (symlink #$%bash + (string-append #$output + "/bash"))) + #:modules '((guix build utils)))) + (grafted ((store-lift graft-derivation) drv + (list graft))) + (_ (built-derivations (list grafted))) + (out -> (derivation->output-path grafted))) + (return (and (string=? (readlink (string-append out "/bash")) + fake) + (file-is-directory? (string-append out "/a/b/c/d"))))))) + (test-assert "graft-derivation, no dependencies on grafted output" (run-with-store %store (mlet* %store-monad ((fake (text-file "bash" "Fake bash.")) -- cgit v1.2.3 From ece6864bd04fc2f9ff86fd4ac9cb0712dd71c094 Mon Sep 17 00:00:00 2001 From: Ludovic Courtès Date: Fri, 20 May 2016 22:14:46 +0200 Subject: grafts: Rename files whose name matches a graft. Fixes . Reported by Mark H Weaver . * guix/build/graft.scm (rename-matching-files): New procedure. (rewrite-directory): Use it. * tests/grafts.scm ("graft-derivation, renaming"): New test. --- guix/build/graft.scm | 25 ++++++++++++++++++++++++- tests/grafts.scm | 17 +++++++++++++++++ 2 files changed, 41 insertions(+), 1 deletion(-) diff --git a/guix/build/graft.scm b/guix/build/graft.scm index e9fce03181..b61982dd64 100644 --- a/guix/build/graft.scm +++ b/guix/build/graft.scm @@ -83,6 +83,28 @@ (define pattern (put-u8 output (char->integer char)) result))))) +(define (rename-matching-files directory mapping) + "Apply MAPPING to the names of all the files in DIRECTORY, where MAPPING is +a list of store file name pairs." + (let* ((mapping (map (match-lambda + ((source . target) + (cons (basename source) (basename target)))) + mapping)) + (matches (find-files directory + (lambda (file stat) + (assoc-ref mapping (basename file))) + #:directories? #t))) + + ;; XXX: This is not quite correct: if MAPPING contains "foo", and + ;; DIRECTORY contains "bar/foo/foo", we first rename "bar/foo" and then + ;; "bar/foo/foo" no longer exists so we fail. Oh well, surely that's good + ;; enough! + (for-each (lambda (file) + (let ((target (assoc-ref mapping (basename file)))) + (rename-file file + (string-append (dirname file) "/" target)))) + matches))) + (define* (rewrite-directory directory output mapping #:optional (store (%store-directory))) "Copy DIRECTORY to OUTPUT, replacing strings according to MAPPING, a list of @@ -127,6 +149,7 @@ (define (rewrite-leaf file) (n-par-for-each (parallel-job-count) rewrite-leaf (find-files directory (const #t) - #:directories? #t))) + #:directories? #t)) + (rename-matching-files output mapping)) ;;; graft.scm ends here diff --git a/tests/grafts.scm b/tests/grafts.scm index f8c9eced1d..8cd048552c 100644 --- a/tests/grafts.scm +++ b/tests/grafts.scm @@ -182,4 +182,21 @@ (define %mkdir (and (string=? (readlink one) repl) (string=? (readlink two) one)))))) +(test-assert "graft-derivation, renaming" ; + (let* ((build `(begin + (use-modules (guix build utils)) + (mkdir-p (string-append (assoc-ref %outputs "out") "/" + (assoc-ref %build-inputs "in"))))) + (orig (build-expression->derivation %store "thing-to-graft" build + #:modules '((guix build utils)) + #:inputs `(("in" ,%bash)))) + (repl (add-text-to-store %store "bash" "fake bash")) + (grafted (graft-derivation %store orig + (list (graft + (origin %bash) + (replacement repl)))))) + (and (build-derivations %store (list grafted)) + (let ((out (derivation->output-path grafted))) + (file-is-directory? (string-append out "/" repl)))))) + (test-end) -- cgit v1.2.3 From 28dee3d28271c284efadaf1de40dbd7535e36072 Mon Sep 17 00:00:00 2001 From: Mathieu Lirzin Date: Thu, 12 May 2016 23:15:37 +0200 Subject: build: Fix 'AM_V_at' typo. * Makefile.am (hydra-jobs.scm): Fix 'AM_V_at' typo. --- Makefile.am | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Makefile.am b/Makefile.am index dfd486b256..c2c571cf3b 100644 --- a/Makefile.am +++ b/Makefile.am @@ -509,7 +509,7 @@ hydra-jobs.scm: $(GOBJECTS) $(AM_V_GEN)$(top_builddir)/pre-inst-env "$(GUILE)" \ "$(top_srcdir)/build-aux/hydra/evaluate.scm" \ "$(top_srcdir)/build-aux/hydra/gnu-system.scm" > "$@.tmp" - $(AT_V_at)mv "$@.tmp" "$@" + $(AM_V_at)mv "$@.tmp" "$@" .PHONY: sync-descriptions gen-ChangeLog gen-AUTHORS clean-go make-go .PHONY: assert-no-store-file-names assert-binaries-available -- cgit v1.2.3 From a56be436d0253c96d0ff766092e3f94432033187 Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Thu, 19 May 2016 10:26:45 +0200 Subject: gnu: Add dia. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/gnome.scm (dia): New variable. Signed-off-by: Ludovic Courtès --- gnu/packages/gnome.scm | 51 ++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 51 insertions(+) diff --git a/gnu/packages/gnome.scm b/gnu/packages/gnome.scm index c42dfc26e0..8726d3d88b 100644 --- a/gnu/packages/gnome.scm +++ b/gnu/packages/gnome.scm @@ -17,6 +17,7 @@ ;;; Copyright © 2016 Rene Saavedra ;;; Copyright © 2016 Kei Kebreau ;;; Copyright © 2016 Jan Nieuwenhuizen +;;; Copyright © 2016 Roel Janssen ;;; ;;; This file is part of GNU Guix. ;;; @@ -59,6 +60,7 @@ (define-module (gnu packages gnome) #:use-module (gnu packages flex) #:use-module (gnu packages docbook) #:use-module (gnu packages enchant) + #:use-module (gnu packages fontutils) #:use-module (gnu packages game-development) #:use-module (gnu packages gettext) #:use-module (gnu packages glib) @@ -163,6 +165,55 @@ (define-public brasero features to enable users to create their discs easily and quickly.") (license license:gpl2+))) +(define-public dia + ;; This version from GNOME's repository includes fixes for compiling with + ;; recent versions of the build tools. The latest activity on the + ;; pre-GNOME version has been in 2014, while GNOME has continued applying + ;; fixes in 2016. + (let ((commit "fbc306168edab63db80b904956117cbbdc514ee4")) + (package + (name "dia") + (version (string-append "0.97.2-" (string-take commit 7))) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://git.gnome.org/browse/dia") + (commit commit))) + (file-name (string-append name "-" version "-checkout")) + (sha256 + (base32 + "1b4bba0k8ph4cwgw8xjglss0p6n111bpd5app67lrq79mp0ad06l")))) + (build-system gnu-build-system) + (inputs + `(("glib" ,glib "bin") + ("pango" ,pango) + ("gdk-pixbuf" ,gdk-pixbuf) + ("gtk+" ,gtk+-2) + ("libxml2" ,libxml2) + ("freetype" ,freetype) + ("libart-lgpl" ,libart-lgpl))) + (native-inputs + `(("intltool" ,intltool) + ("pkg-config" ,pkg-config) + ("automake" ,automake) + ("autoconf" ,autoconf) + ("libtool" ,libtool) + ("perl" ,perl) + ("python-wrapper" ,python-wrapper))) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-before 'configure 'run-autogen + (lambda _ + (system* "sh" "autogen.sh")))))) + (home-page "https://wiki.gnome.org/Apps/Dia") + (synopsis "Diagram creation for GNOME") + (description "Dia can be used to draw different types of diagrams, and +includes support for UML static structure diagrams (class diagrams), entity +relationship modeling, and network diagrams. The program supports various file +formats like PNG, SVG, PDF and EPS.") + (license license:gpl2+)))) + (define-public gnome-common (package (name "gnome-common") -- cgit v1.2.3 From b9b447be64fcde6ebb5811ee82a6f029b873ab18 Mon Sep 17 00:00:00 2001 From: Jan Nieuwenhuizen Date: Thu, 19 May 2016 23:50:09 +0200 Subject: gnu: Add sicp. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/scheme.scm (sicp): New variable. Co-authored-by: Ludovic Courtès --- gnu/packages/scheme.scm | 55 +++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 55 insertions(+) diff --git a/gnu/packages/scheme.scm b/gnu/packages/scheme.scm index 6cf75c2471..6f2ce9f51f 100644 --- a/gnu/packages/scheme.scm +++ b/gnu/packages/scheme.scm @@ -4,6 +4,7 @@ ;;; Copyright © 2015 Federico Beffa ;;; Copyright © 2016 Ricardo Wurmus ;;; Copyright © 2016 Efraim Flashner +;;; Copyright © 2016 Jan Nieuwenhuizen ;;; ;;; This file is part of GNU Guix. ;;; @@ -25,8 +26,10 @@ (define-module (gnu packages scheme) #:use-module (guix licenses) #:use-module (guix packages) #:use-module (guix download) + #:use-module (guix git-download) #:use-module (guix utils) #:use-module (guix build-system gnu) + #:use-module (guix build-system trivial) #:use-module (gnu packages m4) #:use-module (gnu packages multiprecision) #:use-module (gnu packages databases) @@ -34,6 +37,7 @@ (define-module (gnu packages scheme) #:use-module (gnu packages texinfo) #:use-module (gnu packages texlive) #:use-module (gnu packages base) + #:use-module (gnu packages compression) #:use-module (gnu packages pkg-config) #:use-module (gnu packages avahi) #:use-module (gnu packages libphidget) @@ -714,3 +718,54 @@ (define* (copy-files-to-directory files dir support teaching and research in mathematical physics and electrical engineering.") (license gpl2+)))) + +(define-public sicp + (let ((commit "5b52db566968d28a89fbbaf338d207f01cc81cac")) + (package + (name "sicp") + (version (string-append "20160220-1." (string-take commit 7))) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/sarabander/sicp") + (commit commit))) + (sha256 + (base32 + "10h6h7szwlfbshwh18bnl2hvyddj5i7106l79s145l0sjjv15cxb")) + (file-name (string-append name "-" version "-checkout")))) + (build-system trivial-build-system) + (native-inputs `(("gzip" ,gzip) + ("source" ,source) + ("texinfo" ,texinfo))) + (arguments + `(#:modules ((guix build utils) + (srfi srfi-1) + (srfi srfi-26)) + #:builder + (begin + (use-modules (guix build utils) + (srfi srfi-1) + (srfi srfi-26)) + (let ((gzip (assoc-ref %build-inputs "gzip")) + (source (assoc-ref %build-inputs "source")) + (texinfo (assoc-ref %build-inputs "texinfo")) + (info-dir (string-append %output "/share/info"))) + (setenv "PATH" (string-append gzip "/bin" + ":" texinfo "/bin")) + (mkdir-p info-dir) + (and (zero? + (system* "makeinfo" "--output" + (string-append info-dir "/sicp.info") + (string-append source "/sicp-pocket.texi"))) + (every zero? + (map (cut system* "gzip" "-9n" <>) + (find-files info-dir)))))))) + (home-page "http://sarabander.github.io/sicp") + (synopsis "Structure and Interpretation of Computer Programs") + (description "Structure and Interpretation of Computer Programs (SICP) is +a textbook aiming to teach the principles of computer programming. + +Using Scheme, a dialect of the Lisp programming language, the book explains +core computer science concepts such as abstraction in programming, +metalinguistic abstraction, recursion, interpreters, and modular programming.") + (license cc-by-sa4.0)))) -- cgit v1.2.3 From 548994142f52c168454ee725227aef6a975cb880 Mon Sep 17 00:00:00 2001 From: Matthew Jordan Date: Thu, 19 May 2016 14:10:40 -0400 Subject: gnu: Add envstore. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/package/shellutils.scm: New file. Signed-off-by: Ludovic Courtès --- gnu/local.mk | 1 + gnu/packages/shellutils.scm | 50 +++++++++++++++++++++++++++++++++++++++++++++ 2 files changed, 51 insertions(+) create mode 100644 gnu/packages/shellutils.scm diff --git a/gnu/local.mk b/gnu/local.mk index 5655a05bcf..c13090196e 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -304,6 +304,7 @@ GNU_SYSTEM_MODULES = \ gnu/packages/search.scm \ gnu/packages/serialization.scm \ gnu/packages/serveez.scm \ + gnu/packages/shellutils.scm \ gnu/packages/shishi.scm \ gnu/packages/skarnet.scm \ gnu/packages/skribilo.scm \ diff --git a/gnu/packages/shellutils.scm b/gnu/packages/shellutils.scm new file mode 100644 index 0000000000..8108b0465d --- /dev/null +++ b/gnu/packages/shellutils.scm @@ -0,0 +1,50 @@ +;;; GNU Guix --- Functional package management for GNU +;;; Copyright © 2016 Matthew Jordan +;;; +;;; 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 packages shellutils) + #:use-module (guix licenses) + #:use-module (guix packages) + #:use-module (guix download) + #:use-module (guix utils) + #:use-module (guix build-system gnu)) + +(define-public envstore + (package + (name "envstore") + (version "2.1") + (source + (origin + (method url-fetch) + (uri (string-append "https://finalrewind.org/projects/" + name "/" name "-" version ".tar.bz2")) + (sha256 + (base32 "1x97lxad80m5blhdfanl5v2qzjwcgbij2i23701bn8mpyxsrqszi")))) + (build-system gnu-build-system) + (arguments + `(#:test-target "test" + #:make-flags (list "CC=gcc" + (string-append "PREFIX=" (assoc-ref %outputs "out"))) + #:phases + (modify-phases %standard-phases + (delete 'configure)))) + (home-page "https://finalrewind.org/projects/envstore/") + (synopsis "Save and restore environment variables") + (description "Envstore is a program for sharing environment variables +between various shells or commands.") + (license + (non-copyleft "http://www.wtfpl.net/txt/copying/")))) -- cgit v1.2.3 From 3c47489766bbf3d381b63d4eda63b2aff2f35d0f Mon Sep 17 00:00:00 2001 From: Kei Yamashita Date: Sat, 14 May 2016 21:27:08 -0400 Subject: gnu: Add gnome-calendar. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/gnome.scm (gnome-calendar): New variable. Signed-off-by: Ludovic Courtès --- gnu/packages/gnome.scm | 28 ++++++++++++++++++++++++++++ 1 file changed, 28 insertions(+) diff --git a/gnu/packages/gnome.scm b/gnu/packages/gnome.scm index 8726d3d88b..c5d53d1e0a 100644 --- a/gnu/packages/gnome.scm +++ b/gnu/packages/gnome.scm @@ -5076,6 +5076,34 @@ (define-public libzapojit Microsoft SkyDrive and Hotmail, using their REST protocols.") (license license:lgpl2.1+))) +(define-public gnome-calendar + (package + (name "gnome-calendar") + (version "3.20.2") + (source (origin + (method url-fetch) + (uri (string-append "mirror://gnome/sources/" name "/" + (version-major+minor version) "/" + name "-" version ".tar.xz")) + (sha256 + (base32 + "1vny8fclwglapdyxd2g9fbwdlk5hhnb993k2hvq3rf0hcgswycpi")))) + (build-system glib-or-gtk-build-system) + (native-inputs + `(("intltool" ,intltool) + ("pkg-config" ,pkg-config))) + (inputs + `(("bdb" ,bdb) + ("desktop-file-utils" ,desktop-file-utils) + ("evolution-data-server" ,evolution-data-server) + ("gnome-online-accounts" ,gnome-online-accounts))) + (home-page "https://wiki.gnome.org/Apps/Calendar") + (synopsis "GNOME's calendar application") + (description + "GNOME Calendar is a simple calendar application designed to fit the GNOME +desktop. It supports multiple calendars, monthly view and yearly view.") + (license license:gpl3+))) + (define-public gnome-tweak-tool (package (name "gnome-tweak-tool") -- cgit v1.2.3 From 88bb4197c419d6095cc4061bac1ee0f96bf939b1 Mon Sep 17 00:00:00 2001 From: Lukas Gradl Date: Sat, 21 May 2016 18:19:42 -0500 Subject: gnu: Add python2-rope. * gnu/packages/python.scm (python2-rope): New variable. --- gnu/packages/python.scm | 28 ++++++++++++++++++++++++++++ 1 file changed, 28 insertions(+) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 37c8594a37..602da2d5ca 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -18,6 +18,7 @@ ;;; Copyright © 2015 Kyle Meyer ;;; Copyright © 2015, 2016 Chris Marusich ;;; Copyright © 2016 Danny Milosavljevic +;;; Copyright © 2016 Lukas Gradl ;;; ;;; This file is part of GNU Guix. ;;; @@ -8760,3 +8761,30 @@ (define-public python2-shedskin (description (string-append "This is an experimental compiler for a subset of Python. It generates C++ code and a Makefile.")) (license (list gpl3 bsd-3 license:expat)))) + +(define-public python2-rope + (package + (name "python2-rope") + (version "0.10.3") + (source + (origin + (method url-fetch) + (uri (pypi-uri "rope" version)) + (sha256 + (base32 + "18k5znhpwvrfck3yp0jmhd5j8r0f0s8bk1zh5yhs2cfgmfhbwigb")))) + (arguments + ;; Rope is currently python-2 only. + ;; https://github.com/python-rope/rope/issues/57 + `(#:python ,python-2)) + (build-system python-build-system) + (native-inputs + `(("python2-unittest2" ,python2-unittest2) + ("python2-setuptools" ,python2-setuptools))) + (home-page "https://github.com/python-rope/rope") + (synopsis "Refactoring library for Python") + (description "Rope is a refactoring library for Python. It facilitates +the renaming, moving and extracting of attributes, functions, modules, fields +and parameters in Python 2 source code. These refactorings can also be applied +to occurences in strings and comments.") + (license gpl2))) -- cgit v1.2.3 From 13913c52d5bf75d8c5bee4fdc0fa7ce70f0588f7 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Wed, 18 May 2016 23:16:51 -0400 Subject: gnu: imagemagick: Update to 6.9.4-4. * gnu/packages/imagemagick.scm (imagemagick): Update to 6.9.4-4. --- gnu/packages/imagemagick.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/imagemagick.scm b/gnu/packages/imagemagick.scm index fb5f9339b2..a7bbe0cce0 100644 --- a/gnu/packages/imagemagick.scm +++ b/gnu/packages/imagemagick.scm @@ -40,14 +40,14 @@ (define-module (gnu packages imagemagick) (define-public imagemagick (package (name "imagemagick") - (version "6.9.4-1") + (version "6.9.4-4") (source (origin (method url-fetch) (uri (string-append "mirror://imagemagick/ImageMagick-" version ".tar.xz")) (sha256 (base32 - "0fvb9i7kai5ashaiaxqr1cikyyp5w1zczdq28l9nypfd77wgx81f")))) + "005nnp0masv59yfcdip6qld86567zjbz59c9lkcqrxclm27vmx0p")))) (build-system gnu-build-system) (arguments `(#:configure-flags '("--with-frozenpaths") -- cgit v1.2.3 From 624d4e2e6ba402c374a340869306eec65a808a20 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sun, 22 May 2016 16:58:21 +0300 Subject: gnu: gnu-pw-mgr: Update to 2.0. * gnu/packages/gnu-pw-mgr.scm (gnu-pw-mgr): Update to 2.0. --- gnu/packages/gnu-pw-mgr.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/gnu/packages/gnu-pw-mgr.scm b/gnu/packages/gnu-pw-mgr.scm index 76329e8084..461f4f8cb7 100644 --- a/gnu/packages/gnu-pw-mgr.scm +++ b/gnu/packages/gnu-pw-mgr.scm @@ -1,6 +1,7 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2013 Eric Bavier ;;; Copyright © 2015 Mark H Weaver +;;; Copyright © 2016 Efraim Flashner ;;; ;;; This file is part of GNU Guix. ;;; @@ -29,7 +30,7 @@ (define-module (gnu packages gnu-pw-mgr) (define-public gnu-pw-mgr (package (name "gnu-pw-mgr") - (version "1.6") + (version "2.0") (source (origin (method url-fetch) @@ -37,7 +38,7 @@ (define-public gnu-pw-mgr version ".tar.xz")) (sha256 (base32 - "141wfm4w420ygrl7qvrc84drzv34jym0d2bxqcgi7n1vimql0slp")))) + "19qvg37snfa8s06q5crx25m1r1n4l0wvfpkbdxz17q7whp0plrl6")))) (build-system gnu-build-system) (native-inputs `(("which" ,which) -- cgit v1.2.3