From 9495cf9a804e63b7173a78c22b9c91991b9520a6 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Fri, 13 May 2016 23:22:53 -0400 Subject: [PATCH 001/171] 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 @@ security, and applying best practice development processes.") (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 @@ security, and applying best practice development processes.") (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 @@ security, and applying best practice development processes.") (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 @@ will be issuing browser-trusted certificates for free.") (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") From 247783685beb6bc683a987d09cd2cfa398cf1e54 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Sat, 14 May 2016 01:35:04 -0400 Subject: [PATCH 002/171] 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 @@ security, and applying best practice development processes.") (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 From 6d461b21f0c3ce88feb44d2610950d5c5cf6157d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Thu, 12 May 2016 14:25:30 +0200 Subject: [PATCH 003/171] 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 @@ as well as the classic centralized workflow.") ;; 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") From 52e1defe02446b5f5d52f31ca17dddd13fa6353e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Sat, 14 May 2016 15:50:25 +0200 Subject: [PATCH 004/171] 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 @@ the Nix package manager.") ;; ;; 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) From 6e94a574787895cd74edd4ecca3fa347ed457330 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Sat, 14 May 2016 16:47:12 +0200 Subject: [PATCH 005/171] 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 @@ needed." (_ #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?) From c22a475725b99463de6e163a212c9398116c8aa0 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Sat, 14 May 2016 16:56:21 +0200 Subject: [PATCH 006/171] 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 @@ 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))) From cd436bf05a8344acf4462f3602e7d360821a902a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Sat, 14 May 2016 17:37:47 +0200 Subject: [PATCH 007/171] 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 @@ Return a list of URIs." (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 @@ on success." 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 @@ ;; '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 @@ in the store." %load-path))) #~#t) - (use-modules (guix build download)) + (use-modules (guix build download) + (guix base32)) - (url-fetch (call-with-input-string (getenv "guix download url") - read) - #$output - #:mirrors (call-with-input-file #$%mirror-file read)))) + (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) + + ;; 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 @@ in the store." #: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") From 8a7680a759c3eb549378310ac53a9f5032423dac Mon Sep 17 00:00:00 2001 From: Jan Nieuwenhuizen Date: Sat, 14 May 2016 10:13:21 +0200 Subject: [PATCH 008/171] 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 @@ XBINUTILS and the cross tool chain." ;; 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) From e6a905070ad4a5f6c726e94e04b4a60b324a0dfc Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=E5=AE=8B=E6=96=87=E6=AD=A6?= Date: Sun, 15 May 2016 14:09:17 +0800 Subject: [PATCH 009/171] 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 @@ point numbers.") (define-public wxmaxima (package (name "wxmaxima") - (version "15.04.0") + (version "16.04.2") (source (origin (method url-fetch) @@ -1596,7 +1596,7 @@ point numbers.") version "/" name "-" version ".tar.gz")) (sha256 (base32 - "1fm47ah4aw5qdjqhkz67w5fwhy8yfffa5z896crp0d3hk2bh4180")))) + "1fpqzk1921isiqrpgpf433ldq41924qs9sy99fl1zn5661b2l73n")))) (build-system gnu-build-system) (inputs `(("wxwidgets" ,wxwidgets) From e91fd7f591cfc41412095876a3beeff286074852 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=E5=AE=8B=E6=96=87=E6=AD=A6?= Date: Sun, 15 May 2016 18:24:15 +0800 Subject: [PATCH 010/171] 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 @@ archive on a per-file basis.") (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))) From 277a7d82b84c0b9ae86a9466479c34548209b0bf Mon Sep 17 00:00:00 2001 From: Jan Nieuwenhuizen Date: Sun, 3 Apr 2016 12:56:11 +0200 Subject: [PATCH 011/171] 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 @@ database is translated at Transifex.") ("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") From 9365ee1c464b1a4bda5325b9c5a16f9c09029d2a Mon Sep 17 00:00:00 2001 From: Jan Nieuwenhuizen Date: Sun, 3 Apr 2016 12:52:37 +0200 Subject: [PATCH 012/171] 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 +++++++++++++++ .../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 @@ specified duration and save it as a GIF encoded animated image file.") "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 From d8f3795622c892abd0ac023e40166ad4cd53646a Mon Sep 17 00:00:00 2001 From: David Thompson Date: Sun, 15 May 2016 18:32:36 -0400 Subject: [PATCH 013/171] 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 @@ match, cannon keep, and grave-itation pit.") (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 @@ match, cannon keep, and grave-itation pit.") (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 @@ match, cannon keep, and grave-itation pit.") (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 @@ match, cannon keep, and grave-itation pit.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "1xzrvsg0fpbj5p4pz6lls11m3ab4y2bnjlsm4gnw68x9006ffznp")))) + "0m3hhk5icx4y4gd970z7ya2013fq4vvqbjljmck62ik03baf8g90")))) (build-system cmake-build-system) (arguments '(#:configure-flags From b7ab191ddd73f1e74294c98bb2f6a9697ea8a556 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Thu, 17 Mar 2016 03:58:01 -0400 Subject: [PATCH 014/171] 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."))))) From 74dd0e483137ccdd3ed19e094811719ec69cf838 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sat, 14 May 2016 22:03:14 +0300 Subject: [PATCH 015/171] 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 @@ "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/"))) From 90cd0e138dc92101b1d832c490d868d85bb4184d Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sat, 14 May 2016 22:14:57 +0300 Subject: [PATCH 016/171] 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-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 From 3f61f926b9a7229becd8de8a48973b17e2784f98 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Thu, 12 May 2016 16:04:52 +0300 Subject: [PATCH 017/171] 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 @@ freedesktop.org project.") (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))) From 5c6fdaa9e15a91485e4d5f8d43d2918ec2b42d94 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Thu, 12 May 2016 16:22:20 +0300 Subject: [PATCH 018/171] 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 @@ applications, X servers (rootless or fullscreen) or other display servers.") (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 @@ applications, X servers (rootless or fullscreen) or other display servers.") name "-" version ".tar.bz2")) (sha256 (base32 - "01vcd1mfn2s0iiq2cjyzgvnxx6kcq9cwra1iipijhs0vwvjx0yhf")))) + "0jcrv3w8m415cq8xi886hcxfqbrn5dczxbzybx9bhf3dbqsyv6nq")))) (build-system gnu-build-system) (arguments `(#:configure-flags (list (string-append "--with-boost=" From 9c0c77f833b64e5ce46d1b53a4fbbd0b0cb1d0c2 Mon Sep 17 00:00:00 2001 From: Kei Yamashita Date: Tue, 10 May 2016 18:15:54 -0400 Subject: [PATCH 019/171] 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 @@ #: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 @@ Redmond95 and ThinIce.") "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+))) From 66056126ea15e7186636dcd31b1edf093ed9c72d Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Thu, 12 May 2016 16:36:00 +0300 Subject: [PATCH 020/171] 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 @@ interfaces, based on the useradd, usermod and userdel commands.") (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 @@ interfaces, based on the useradd, usermod and userdel commands.") 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 @@ interfaces, based on the useradd, usermod and userdel commands.") (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.") From 1fb8e074f1801d7ace96f8a3758ae391a151d802 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Thu, 12 May 2016 16:38:47 +0300 Subject: [PATCH 021/171] 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 @@ which speak the Mobile Interface Broadband Model (MBIM) protocol.") (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 @@ which speak the Mobile Interface Broadband Model (MBIM) protocol.") name "-" version ".tar.xz")) (sha256 (base32 - "19w2zkm5xl6i3vm1xhjjclks4awas17gfbb2k5y66gwnkiykjfnj")))) + "0h009bzss4bal47nk21lyp4s3mmlcivhhaaj7r9229qvx85bi0v2")))) (build-system gnu-build-system) (native-inputs `(("glib:bin" ,glib "bin") ; for glib-mkenums From a2ccaa0d790004c1c303a4421f7494ef73b65bd5 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Thu, 12 May 2016 18:48:35 +0300 Subject: [PATCH 022/171] 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-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) From 2b193389d243c469e159d0ab5dfc86b5867db05d Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Thu, 12 May 2016 20:50:52 +0300 Subject: [PATCH 023/171] 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-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 @@ 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 From e9eb24b1b25101439dbbafce3aa9ec0ce2e67c1a Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Thu, 12 May 2016 21:09:08 +0300 Subject: [PATCH 024/171] 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 @@ applications.") (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 From 30897c60a4bb54936c228daf46e26377306da280 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Thu, 12 May 2016 21:38:56 +0300 Subject: [PATCH 025/171] 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 @@ MPEG-2 and audio over Linux IEEE 1394.") (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 @@ MPEG-2 and audio over Linux IEEE 1394.") 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 - From 2f9e312a39618461b2efce0020e306fc3c112950 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Thu, 12 May 2016 22:01:44 +0300 Subject: [PATCH 026/171] 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 @@ configuration and monitoring interfaces.") (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 @@ configuration and monitoring interfaces.") `(#: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 From 9a12ca7771fdd88e45bb0b7de246bdf14b005f4f Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Thu, 12 May 2016 22:08:36 +0300 Subject: [PATCH 027/171] 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 @@ compliance.") (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 @@ compliance.") "wireless-regdb-" version ".tar.xz")) (sha256 (base32 - "0czi83k311fp27z42hxjm8vi88fsbc23mhavv96lkb4pmari0jjc")) + "07n6gcwfbddz3awbdflv3dhxjszsqq2lrdwih0a0ahcliac4qry9")) ;; We're building 'regulatory.bin' by ourselves. (snippet '(delete-file "regulatory.bin")))) From ec374039e428cd7ef82e36f6fa1fc28f1972a9ea Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Fri, 13 May 2016 08:13:27 +0300 Subject: [PATCH 028/171] 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 @@ as a drop-in replacement of MySQL.") (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 From 6747a852c5fb670039ca9f44808fff26754157f1 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Fri, 13 May 2016 08:27:38 +0300 Subject: [PATCH 029/171] 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 @@ is in the public domain.") (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 From 3fef0a2fa1160927bc323d7712eca28453591c07 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Fri, 13 May 2016 08:56:00 +0300 Subject: [PATCH 030/171] 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 @@ valid SQL query.") (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 From b4370be9deca08f8347fbb0e2fc07edb1d18acd4 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Wed, 11 May 2016 02:25:22 -0400 Subject: [PATCH 031/171] 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 @@ responses, rather than doing any computation.") (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 @@ responses, rather than doing any computation.") (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))) From 66395a6157e573450c691f4fe8fecec4dee8d5f7 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Mon, 16 May 2016 10:18:16 +0300 Subject: [PATCH 032/171] 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 @@ script files.") ("glu" ,glu) ("libx11" ,libx11) ("libxext" ,libxext))) + (inputs + `(("fontconfig" ,fontconfig) + ("libxft" ,libxft))) (arguments `(#:configure-flags `("-DENABLE_METIS:BOOL=OFF" "-DENABLE_BUILD_SHARED:BOOL=ON" From 6b287c5c35fc95f5bae7df8107ae6639d67344b8 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Mon, 16 May 2016 12:10:49 +0300 Subject: [PATCH 033/171] 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 @@ (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 From fd02719c7b7acb1ba4a268418a1f1f6879c5238d Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Mon, 16 May 2016 12:31:25 +0300 Subject: [PATCH 034/171] 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-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) From 284539ce86a0073ad65880ddf3f3fd7af981b8e7 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Mon, 16 May 2016 12:59:40 +0300 Subject: [PATCH 035/171] 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 @@ and XMP metadata of images in various formats.") (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 @@ and XMP metadata of images in various formats.") (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 From bf512da1e42ffb5599199f22c5c5e4cc3dc8111e Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Mon, 16 May 2016 14:07:47 +0300 Subject: [PATCH 036/171] 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 @@ more modular, simple, and flexible.") (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")))) From 3a66217ff25250d9bad4039471d5407bf1b23dcf Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Mon, 16 May 2016 14:12:54 +0300 Subject: [PATCH 037/171] 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 @@ (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 @@ (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 From d03f944614a86b447d9f7469526c95afbd012089 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Mon, 16 May 2016 14:18:21 +0300 Subject: [PATCH 038/171] 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 @@ See http://minikanren.org/ for more on miniKanren generally.") (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) From a83e60466223b96b0553bc83e727ece26b1aa744 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Mon, 16 May 2016 14:28:53 +0300 Subject: [PATCH 039/171] 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 @@ particular, reads spanning multiple exons.") (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 @@ particular, reads spanning multiple exons.") "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 From 44877dcc66ee5bb38101e32a32b11069e02813f1 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Mon, 16 May 2016 14:31:06 +0300 Subject: [PATCH 040/171] 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 @@ (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 @@ (("/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 From 002528bca512c2f45a7880e09be7c655bba7d2b0 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 15 May 2016 13:08:20 +0200 Subject: [PATCH 041/171] 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 @@ visual effects work for film.") "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 @@ visual effects work for film.") `(("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 @@ visual effects work for film.") ("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 From 81b98756a3164e6b0024b64ea5c90bbb615de12a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 14 May 2016 11:27:12 +0200 Subject: [PATCH 042/171] 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 @@ system calls, important for the performance of databases and other advanced 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") From 8226c2717c9bf5730683ff70a4ffa801d3ac0617 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 5 May 2016 14:37:52 +0200 Subject: [PATCH 043/171] 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 @@ (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 @@ ("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 From 7d0c3c8d018a4aff4ce42f863ce81242555ab119 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Mon, 16 May 2016 17:36:58 +0300 Subject: [PATCH 044/171] 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 @@ datetime module, available in Python 2.3+.") (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 @@ datetime module, available in Python 2.3+.") `(("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 @@ structures designed to make working with structured (tabular, 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 From 99404fff9f8be0478191dfd5a4ebbb5822527172 Mon Sep 17 00:00:00 2001 From: Alex Kost Date: Sun, 8 May 2016 11:24:19 +0300 Subject: [PATCH 045/171] 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 @@ repository and Maildir/IMAP as LOCAL repository.") ("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 From 789bda83d2f356a55a2c65ff1b4ffe3431fc11b3 Mon Sep 17 00:00:00 2001 From: Alex Kost Date: Sun, 8 May 2016 12:23:37 +0300 Subject: [PATCH 046/171] 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 @@ repository and Maildir/IMAP as LOCAL repository.") (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 From 704f2196688e2b257501e47657f728b7b6fa9c6a Mon Sep 17 00:00:00 2001 From: Alex Kost Date: Sun, 8 May 2016 12:27:50 +0300 Subject: [PATCH 047/171] 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 @@ repository and Maildir/IMAP as LOCAL repository.") ("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 @@ repository and Maildir/IMAP as LOCAL repository.") (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") From 47c96a577d82034d5a7b0d1062faf4ad0dd097d3 Mon Sep 17 00:00:00 2001 From: Alex Kost Date: Sun, 8 May 2016 12:29:11 +0300 Subject: [PATCH 048/171] 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 @@ can read the same mailbox from multiple computers. It supports IMAP as REMOTE 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 @@ repository and Maildir/IMAP as LOCAL repository.") (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) From 80ed14d38f098f25f87efb01288cd6df8b307b7b Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Wed, 4 May 2016 00:43:36 +0200 Subject: [PATCH 049/171] 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 @@ #: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 @@ colors, styles, options and details.") `(("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 @@ colors, styles, options and details.") ("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 @@ colors, styles, options and details.") (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 From f17a54475656f16867767ecfd512552e5f547cf1 Mon Sep 17 00:00:00 2001 From: Alex Griffin Date: Sat, 7 May 2016 12:16:39 -0500 Subject: [PATCH 050/171] 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 @@ #: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 @@ name comes from: \"The antidote against people who send Microsoft Word files 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))) From d3699b311b01b09d37640ed613fa6094059ed72f Mon Sep 17 00:00:00 2001 From: Alex Griffin Date: Sat, 7 May 2016 12:20:47 -0500 Subject: [PATCH 051/171] 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 @@ #: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 @@ collectively by the network. Bitcoin Core is the reference implementation 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/* From 8bfd602bb00ba7bed8f0108f4cea5ac92b772b7e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 29 Apr 2016 22:12:24 +0200 Subject: [PATCH 052/171] 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 @@ port if PORT is a TLS session record 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) From 8a0ac5bd558a2cf662f15d3670d2f39716df3337 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Mon, 16 May 2016 19:19:04 +0300 Subject: [PATCH 053/171] 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-public tmux (package (name "tmux") - (version "2.1") + (version "2.2") (source (origin (method url-fetch) (uri (string-append @@ -36,7 +37,7 @@ version "/tmux-" version ".tar.gz")) (sha256 (base32 - "0xk1mylsb08sf0w597mdgj9s6hxxjvjvjd6bngpjvvxwyixlwmii")))) + "1r0riry5vw604hc21087ffbkqgr6j4ia1rrsivz2k6grchdm8a5w")))) (build-system gnu-build-system) (inputs `(("libevent" ,libevent) From b6c2f7dafd6dcb5a461753955dec0bfdbfec161c Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Mon, 16 May 2016 19:31:23 +0300 Subject: [PATCH 054/171] 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 @@ command."))) (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 @@ command."))) (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "1c5jx0pcpz83x7s36jimfz5bj0vy7vwpchq9p4sgdqxy8gwr6rhw")))) + "1ppyfwxc276d2p2pwbzlmvs2bkgng425rl8k2rf9nsq66jxqq6b0")))) (build-system cmake-build-system) (arguments `(#:phases From af3ac1f5f7ae93b392c8e7b907c9c8cc4c7d4911 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Mon, 16 May 2016 14:27:48 -0400 Subject: [PATCH 055/171] 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-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") From 9583e07caea25ddec367e462151805ef8d86a445 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 6 May 2016 14:54:33 +0200 Subject: [PATCH 056/171] 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 @@ package definition." (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/")) From dbfeba52091801e37e5c959427ab35535da21f6f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 10 May 2016 11:43:43 +0200 Subject: [PATCH 057/171] 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 @@ barplots or heatmaps.") (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) From a936bf59ea12b91a448fb83fbae1dd75b59f543f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 10 May 2016 11:45:29 +0200 Subject: [PATCH 058/171] 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 @@ packages.") (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) From 3654a61146ce2e2fbf46a1d96015d904437eb963 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 10 May 2016 11:46:15 +0200 Subject: [PATCH 059/171] 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 @@ abnormal copy number.") (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) From 952ff8c86205ef9963f45228ff1b12f4cb29fa02 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 10 May 2016 11:47:03 +0200 Subject: [PATCH 060/171] 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 @@ S4Vectors package itself.") (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) From d1ab3d8fa5c2c93124d12b8a54742312e8cd550d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 10 May 2016 11:47:44 +0200 Subject: [PATCH 061/171] 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 @@ possible.") (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) From 052ee32b2452e87886097bbd0994554dffb40941 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 10 May 2016 11:48:30 +0200 Subject: [PATCH 062/171] 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 @@ names in their natural, rather than lexicographic, order.") (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 From e782ca3e97f020d504371b790739ddabd4a3443e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 10 May 2016 11:49:19 +0200 Subject: [PATCH 063/171] 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 @@ coding changes and predict coding outcomes.") (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) From 828980cad661f1c511fd8bcd58fe5c627f211481 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 10 May 2016 11:49:57 +0200 Subject: [PATCH 064/171] 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 @@ coding changes and predict coding outcomes.") (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) From 4466a02c9fc7a8487d63301335e1a3c966d1635e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 10 May 2016 11:50:35 +0200 Subject: [PATCH 065/171] 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 @@ manipulating genomic intervals and variables defined along a genome.") (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) From c4a4e17938da258b052c684b747dfa8953074222 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 10 May 2016 11:51:18 +0200 Subject: [PATCH 066/171] 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 @@ on Bioconductor or which replace R functions.") (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) From 63cea37234e010689b967e1370b885915b7328bb Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 10 May 2016 11:51:53 +0200 Subject: [PATCH 067/171] 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 @@ annotation data packages using SQLite data storage.") (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) From 6a2a0de1ab52dbdccbbbc52e38f0f4dc41ad0e10 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 10 May 2016 11:52:32 +0200 Subject: [PATCH 068/171] 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 @@ powerful online queries from gene annotation to database mining.") (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) From 2477d9773ac9408172d75a0d146a169bba0ae96c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 10 May 2016 11:53:48 +0200 Subject: [PATCH 069/171] 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 @@ objects.") (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) From b4c5a0db22033503eb07e5c03abf89234e061444 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 10 May 2016 11:54:43 +0200 Subject: [PATCH 070/171] 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 @@ biological sequences or sets of sequences.") (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) From d848ed7cf2d6fb9b1a3fe1db414ff571398ae9e2 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 10 May 2016 11:57:39 +0200 Subject: [PATCH 071/171] 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 @@ files.") (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) From 3cd551ea7b9dfab3cd0dbdcc8f74f5140876c8cc Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 10 May 2016 11:59:33 +0200 Subject: [PATCH 072/171] 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 @@ samples.") (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) From d23fbf1eb93f34378bb64e3d62f3e314527e2a03 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 10 May 2016 12:00:12 +0200 Subject: [PATCH 073/171] 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 @@ alignments.") (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 From c12b0a5a30c890da53839915146bc72d9f4426a8 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 10 May 2016 12:00:42 +0200 Subject: [PATCH 074/171] 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 @@ as well as query and modify the browser state, such as the current viewport.") (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) From 0c56023557ebebcef662dddddef5843947bab656 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 10 May 2016 12:01:09 +0200 Subject: [PATCH 075/171] 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 @@ information about the latest version of the Gene Ontologies.") (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))) From e48e88c2174389cf4f1d39c119fb817addd131d4 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 10 May 2016 12:01:42 +0200 Subject: [PATCH 076/171] 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 @@ information about the latest version of the Gene Ontologies.") (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 @@ information about the latest version of the Gene Ontologies.") ("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") From 5190ed1751ac0fb5dd034825ef1af98ac9dba6f3 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 10 May 2016 12:02:26 +0200 Subject: [PATCH 077/171] 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 @@ dependencies between GO terms can be implemented and applied.") (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) From d1bff89d2670edb971fefb953517c1b7ea25c6f0 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 10 May 2016 12:02:48 +0200 Subject: [PATCH 078/171] 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 @@ genome data packages and support for efficient SNP representation.") (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) From 7555817c2b37e7be2f251b3c1b144d073755c452 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 10 May 2016 12:03:08 +0200 Subject: [PATCH 079/171] 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 @@ microarray data, using nearest neighbor averaging.") (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) From 8adc3b628de10e18cef849ad24b714b460ac4ae2 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 10 May 2016 12:03:32 +0200 Subject: [PATCH 080/171] 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 @@ reference point and sorted by a user defined feature.") (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) From 1f5786a918ea7811c1060acc7d98f8609a37e59d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 10 May 2016 12:03:58 +0200 Subject: [PATCH 081/171] 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 @@ annotations for the genome of the model mouse Mus musculus.") (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") From a0fe3aeecfa830adfaad5a444ed763012218cc3f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 10 May 2016 12:04:18 +0200 Subject: [PATCH 082/171] 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 @@ Biostrings objects.") (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 From 96101b67186191b38325406acc8a688f51b9f7d8 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 10 May 2016 12:04:39 +0200 Subject: [PATCH 083/171] 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 @@ two-dimensional genome scans.") (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) From 9916ae15bb7622fb75f819d561cbc2c4257d0acd Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 10 May 2016 14:18:44 +0200 Subject: [PATCH 084/171] 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 @@ s-expression corresponding to that package, or #f on failure." (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." From 11e4c1fd104884999a84633baea1d2e298d2e334 Mon Sep 17 00:00:00 2001 From: Christopher Allan Webber Date: Fri, 29 Apr 2016 17:53:50 -0500 Subject: [PATCH 085/171] 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 @@ implementation, Emacs and, ultimately, the schemer, giving them access to live 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") From cb307c0833742299f28abc236b5a9530f7349493 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Tue, 17 May 2016 09:03:39 +0300 Subject: [PATCH 086/171] 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-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. From 4f04243405706a52b73c1acca883abfc030ce4d4 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Mon, 16 May 2016 22:45:37 +0200 Subject: [PATCH 087/171] 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 @@ identifiers in the MIT-Scheme documentation.") (gexp->derivation (or name (basename url)) #~(begin (mkdir #$output) - (setenv "PATH" - (string-append #$gzip "/bin")) (chdir #$output) (copy-file #$drv (basename #$url)))))) From a9e41d2faf979e1b39e2d587b940a89e071804c2 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Mon, 16 May 2016 22:48:16 +0200 Subject: [PATCH 088/171] 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 @@ identifiers in the MIT-Scheme documentation.") (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 From 122395f9fc42de7dbe2643b437ca4e484adb8ba0 Mon Sep 17 00:00:00 2001 From: Ben Woodcroft Date: Tue, 17 May 2016 21:07:00 +1000 Subject: [PATCH 089/171] 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 @@ identify enrichments with functional annotations of the genome.") (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 @@ identify enrichments with functional annotations of the genome.") (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 From daaeed765aebae138b4af1d3861eace0368fe2a6 Mon Sep 17 00:00:00 2001 From: Ben Woodcroft Date: Tue, 17 May 2016 21:36:46 +1000 Subject: [PATCH 090/171] 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 @@ data in the form of VCF files.") (define-public vsearch (package (name "vsearch") - (version "1.10.0") + (version "1.11.1") (source (origin (method url-fetch) @@ -3820,7 +3820,7 @@ data in the form of VCF files.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "1i3bad7gnn2y3a1yfixzshd99xdkjc8w5bxzgifpysc6jiljwvb5")) + "1pdvm3znjgq3zryy240yj9gc0bf1z31k6vf9jxrxgdgkvzgw85c7")) (modules '((guix build utils))) (snippet '(begin From 849485f5a05badf502e28c673e546b4660c4ca46 Mon Sep 17 00:00:00 2001 From: Ben Woodcroft Date: Tue, 17 May 2016 21:45:49 +1000 Subject: [PATCH 091/171] 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 @@ of these reads to align data quickly through a hash-based indexing scheme.") (define-public sortmerna (package (name "sortmerna") - (version "2.1") + (version "2.1b") (source (origin (method url-fetch) @@ -3559,7 +3559,7 @@ of these reads to align data quickly through a hash-based indexing scheme.") (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 @@ of these reads to align data quickly through a hash-based indexing scheme.") (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 From f99f3f24ef604f44023379da4b375c80e6844be1 Mon Sep 17 00:00:00 2001 From: Federico Beffa Date: Tue, 17 May 2016 13:51:34 +0200 Subject: [PATCH 092/171] 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 @@ identifiers in the MIT-Scheme documentation.") (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 From 787afdd0f1ce1d4aa7500d858f2635462b444699 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Tue, 17 May 2016 13:36:44 +0200 Subject: [PATCH 093/171] 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 @@ Run IMPORTER with ARGS.\n")) (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))))) From 149590380adb240e0993931b4f72e6f285b24483 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Tue, 17 May 2016 13:41:07 +0200 Subject: [PATCH 094/171] 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* (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 @@ (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 @@ Run IMPORTER with ARGS.\n")) (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 @@ no update is needed or known." #: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 From aa8fff0cebd8390c2faf733da79d9a1499458261 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Tue, 17 May 2016 13:50:10 +0200 Subject: [PATCH 095/171] 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 @@ store directory (/gnu/store)." 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 From 1c29f3ef8452860c4301d7ae57c89ac5956d1663 Mon Sep 17 00:00:00 2001 From: Federico Beffa Date: Tue, 17 May 2016 14:13:56 +0200 Subject: [PATCH 096/171] 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. From 99effc8faa43d478371eb06aee5df8ae1383c51a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Tue, 17 May 2016 18:04:13 +0200 Subject: [PATCH 097/171] 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 @@ standards.") 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 @@ then goes on to load the rest of the operating system. As a multiboot 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 @@ be determined." ((? 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 @@ from ~s: ~a (~s)~%") (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." From bbb5d8aeea213f32e51ae18407aa8941f18a010b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Tue, 17 May 2016 18:07:08 +0200 Subject: [PATCH 098/171] 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 @@ formats. GD is commonly used to generate charts, graphics, thumbnails, and 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 From fb2b0f5c87321f5aab0dc13130ef92a76040fbe3 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Tue, 17 May 2016 00:20:17 -0400 Subject: [PATCH 099/171] 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 @@ "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; + }; From 9576cc72dc4f2973551c72951e64e5bf6240ff6b Mon Sep 17 00:00:00 2001 From: humanitiesNerd Date: Tue, 17 May 2016 10:54:13 +0200 Subject: [PATCH 100/171] 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 @@ to recognize a name like \"RFC 1234\". This package enhances ffap so 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+))) + + From ad42be838811118f983d51d4560d158a729ebf1b Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Tue, 17 May 2016 14:31:09 -0400 Subject: [PATCH 101/171] 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 @@ more.") (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") From f1876bfc7a7dcb9516fff1b2c82f3c52b16c2ab5 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Thu, 17 Mar 2016 03:59:31 -0400 Subject: [PATCH 102/171] 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 @@ 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."))))) From dbd40ac19df16bb2ef0387c5fcbe8103b6b64840 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Wed, 18 May 2016 10:52:41 +0300 Subject: [PATCH 103/171] 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 @@ doing practical, real world data analysis in Python.") (package (inherit base) (native-inputs `(("python2-setuptools" ,python2-setuptools) - ,@(package-inputs base)))))) + ,@(package-native-inputs base)))))) (define-public python-tzlocal (package From e62ffce538649f97da702fc1080fa06668df10e7 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 26 Apr 2016 16:08:47 +0200 Subject: [PATCH 104/171] 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 @@ two-dimensional genome scans.") 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") From 7c544991dcee6cf8f79484f12a8249ede38d2dd2 Mon Sep 17 00:00:00 2001 From: Ben Woodcroft Date: Wed, 18 May 2016 21:21:09 +1000 Subject: [PATCH 105/171] 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 @@ identify enrichments with functional annotations of the genome.") "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") From 614f39271e580e99df5ce46f1482580c673791b0 Mon Sep 17 00:00:00 2001 From: Manolis Ragkousis Date: Wed, 18 May 2016 15:14:39 +0300 Subject: [PATCH 106/171] 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-public gnumach-headers (package (name "gnumach-headers") - (version "1.6") + (version "1.7") (source (origin (method url-fetch) @@ -40,7 +40,7 @@ version ".tar.gz")) (sha256 (base32 - "1m7xwsrv6x6gk9xi5phs104rdn9q3lr63p348vyv0dzd6r3zyncb")))) + "1vd0bykshf6ilr55792b5lf6yd5ywlkp1wqz00dcsx7fq3rfadz2")))) (build-system gnu-build-system) (arguments `(#:phases (alist-replace From eb3be3a79163fa57b09c1fb2c3f20d7f3e26186b Mon Sep 17 00:00:00 2001 From: Manolis Ragkousis Date: Wed, 18 May 2016 15:15:05 +0300 Subject: [PATCH 107/171] 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 mig (package (name "mig") - (version "1.6") + (version "1.7") (source (origin (method url-fetch) @@ -74,7 +74,7 @@ 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) From 0affdfb80554833648efab5f9e348c4a9698955b Mon Sep 17 00:00:00 2001 From: Manolis Ragkousis Date: Wed, 18 May 2016 15:15:41 +0300 Subject: [PATCH 108/171] 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 @@ communication.") (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 From bd9fe0f03b461bf33852d4cdb654459d5587aca0 Mon Sep 17 00:00:00 2001 From: Ben Woodcroft Date: Mon, 25 Apr 2016 13:03:17 +1000 Subject: [PATCH 109/171] 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 @@ #: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 @@ easily construct JSON objects in C, output them as JSON formatted strings and 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") From 65e46ca0ede8e7a150215f6bfd9ea756c8239085 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Wed, 18 May 2016 18:06:47 +0300 Subject: [PATCH 110/171] 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 @@ contain over 620 classes.") (define-public qtkeychain (package (name "qtkeychain") - (version "0.5.0") + (version "0.6.2") (source (origin (method url-fetch) @@ -513,7 +513,7 @@ contain over 620 classes.") "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))) From 64851f4a23f133901f5086dcd5ae4d4c0687164c Mon Sep 17 00:00:00 2001 From: Kei Yamashita Date: Tue, 17 May 2016 18:52:16 -0400 Subject: [PATCH 111/171] 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 @@ interface. It is fast, feature rich, easy to configure, and easy to use.") 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 From 91231156ce321058d82e6272135a4457e004f438 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Wed, 18 May 2016 21:59:38 +0200 Subject: [PATCH 112/171] 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 @@ pre-configured) fan level. It requires a working @code{thinkpad_acpi} or any 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+))) From b7b27a8f28746a488eeee489c71053059dc5a8dc Mon Sep 17 00:00:00 2001 From: Kei Yamashita Date: Tue, 17 May 2016 20:36:17 -0400 Subject: [PATCH 113/171] 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 @@ #: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 @@ #: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 @@ online as well as original implementations of various other algorithms.") (define-public octave (package (name "octave") - (version "4.0.0") + (version "4.0.2") (source (origin (method url-fetch) @@ -591,7 +594,7 @@ online as well as original implementations of various other algorithms.") version ".tar.gz")) (sha256 (base32 - "101jr9yck798586jz4vkjcgk36zksmxf1pxrzvipgn2xgyay0zjc")))) + "1hdxap3j88rpqjimnfhinym6z73wdi5dfa6fv85c13r1dk9qzk9r")))) (build-system gnu-build-system) (inputs `(("lapack" ,lapack) @@ -602,6 +605,7 @@ online as well as original implementations of various other algorithms.") ("arpack" ,arpack-ng) ("curl" ,curl) ("pcre" ,pcre) + ("cyrus-sasl" ,cyrus-sasl) ("fltk" ,fltk) ("fontconfig" ,fontconfig) ("freetype" ,freetype) @@ -609,6 +613,7 @@ online as well as original implementations of various other algorithms.") ("libxft" ,libxft) ("mesa" ,mesa) ("glu" ,glu) + ("openssl" ,openssl) ("zlib" ,zlib))) (native-inputs `(("gfortran" ,gfortran) @@ -626,9 +631,10 @@ online as well as original implementations of various other algorithms.") ("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 From 21f05134fc35edf5a15baf4fdb2e62905f3848e9 Mon Sep 17 00:00:00 2001 From: Kei Kebreau Date: Wed, 18 May 2016 09:58:47 -0400 Subject: [PATCH 114/171] 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. ;;; From 5c447e280e1a4aa6ce7c4611c8393708e08197fa Mon Sep 17 00:00:00 2001 From: humanitiesNerd Date: Tue, 17 May 2016 23:07:06 +0200 Subject: [PATCH 115/171] 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 @@ number.") 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+))) From 3fdb2a84be4c30d6f78510d0fc787766d8809340 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Thu, 19 May 2016 13:01:55 +0300 Subject: [PATCH 116/171] 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 @@ error-resilience, a Java-viewer for j2k-images, ...") (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 From 44c5f0258d3c91694e6c24dcc6701eb2949fd5d8 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Thu, 19 May 2016 13:06:49 +0300 Subject: [PATCH 117/171] 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 @@ error-resilience, a Java-viewer for j2k-images, ...") (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 @@ error-resilience, a Java-viewer for j2k-images, ...") ("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 From 0947698c42fb10b8802679cbc58f9a42a2d91043 Mon Sep 17 00:00:00 2001 From: Ben Woodcroft Date: Wed, 18 May 2016 21:47:35 +1000 Subject: [PATCH 118/171] 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 @@ directly from R. Once uploaded to a plotly account, plotly graphs (and the 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 From 39b3033731283b81ae36f022c6476634ab1d0455 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Thu, 19 May 2016 11:47:27 +0200 Subject: [PATCH 119/171] 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 @@ in finite element programs.") ;; ("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 From 458480235b85ce31db5485251f94415cfdddeff0 Mon Sep 17 00:00:00 2001 From: Hartmut Goebel Date: Sun, 15 May 2016 11:51:54 +0200 Subject: [PATCH 120/171] 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 @@ #: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 @@ packages; exception-based error handling; and very high level dynamic 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 @@ data types.") (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.) From 9684e30b9b597b93ae9c797ba8f3b40eff893ebe Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Thu, 19 May 2016 14:50:22 +0200 Subject: [PATCH 121/171] 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 @@ in finite element programs.") #: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") From 119b83989dd9edd1e8ba6cd379d159d024cbc61d Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Wed, 18 May 2016 13:26:17 -0400 Subject: [PATCH 122/171] 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 + .../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-public expat (package (name "expat") + (replacement expat/fixed) (version "2.1.0") (source (origin (method url-fetch) @@ -62,6 +64,15 @@ stream-oriented parser in which an application registers handlers for 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") From 0e40755d35fc0ec1e598796af2ba3e72cbd59af5 Mon Sep 17 00:00:00 2001 From: Jelle Licht Date: Tue, 17 May 2016 06:40:01 -0700 Subject: [PATCH 123/171] 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-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 @@ 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") From 0fc4a8afbad8783d4d0eb5ef50d57eb884afc8e1 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Thu, 19 May 2016 21:04:22 -0400 Subject: [PATCH 124/171] 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 @@ and copy/paste text in the console and in xterm.") (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 @@ and copy/paste text in the console and in xterm.") "btrfs-progs-v" version ".tar.xz")) (sha256 (base32 - "1znf2zhb56zbmdjk3lq107678xwsqwc5gczspypmc5i31qnppy7f")))) + "1lzbw275xgv69v4z8hmsf3jnip38116hxhkpv0madk8wv049drz6")))) (build-system gnu-build-system) (arguments '(#:test-target "test" From 186ed873375b9c9c20345a46d55c8663976f7bbf Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 20 May 2016 14:38:22 +0200 Subject: [PATCH 125/171] 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 @@ possible.") (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) From 679e670b36a649276b55d62a6979624aebc26a3a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 20 May 2016 14:38:52 +0200 Subject: [PATCH 126/171] 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 @@ names in their natural, rather than lexicographic, order.") (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 From 73af676feb5dabea719e9071ea734f9e8303f7f7 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 20 May 2016 14:39:24 +0200 Subject: [PATCH 127/171] 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 @@ on Bioconductor or which replace R functions.") (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) From d7420566a98933c56ee5cff0b6c5c6a1f2773a84 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 20 May 2016 14:39:53 +0200 Subject: [PATCH 128/171] 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 @@ powerful online queries from gene annotation to database mining.") (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) From 192e1ea8d15d076b29e55734d49f215f2f2f550a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 20 May 2016 14:40:25 +0200 Subject: [PATCH 129/171] 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 @@ files.") (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) From 8ede249e0ad349238e0347f8001d76039b86729f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 20 May 2016 14:41:12 +0200 Subject: [PATCH 130/171] 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 @@ as well as query and modify the browser state, such as the current viewport.") (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) From eb1a5b65c0a22a35c65357ca2106ce521179ad06 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 20 May 2016 14:45:40 +0200 Subject: [PATCH 131/171] 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 @@ Munsell colour system.") (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") From a76b3f69144684bc90bc86fc0c343e52cad14c0b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 20 May 2016 14:46:11 +0200 Subject: [PATCH 132/171] 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 @@ evaluation (NSE) in R.") (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") From 9a0ccf43cc82d5f77f1f3bc87f37ed0b2c9e68b3 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 20 May 2016 14:46:39 +0200 Subject: [PATCH 133/171] 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 @@ R/DBMS implementations.") (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") From 84e5368719a860964b54f5edb5dc387c2bd2dac9 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 20 May 2016 14:47:11 +0200 Subject: [PATCH 134/171] 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 @@ for template use among CRAN packages.") (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))) From df25b0048ad05fc42de7f20f2299802f94e4e2c8 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 20 May 2016 14:47:34 +0200 Subject: [PATCH 135/171] 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 @@ adapted for other output formats, such as HTML or LaTeX.") (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") From d5130e6345a3e9fd0af471b5e1c09bdd07322e97 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 20 May 2016 14:48:35 +0200 Subject: [PATCH 136/171] 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 @@ There is also a Shiny app as a user interface in this package.") (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") From 1b206aeb00717dba24de1f3b8af06bc054f77135 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 20 May 2016 14:49:07 +0200 Subject: [PATCH 137/171] 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 @@ emitter (http://pyyaml.org/wiki/LibYAML) for R.") (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) From 383f6337a001f5ffab1189e03aa3ad1a5bfaf8ae Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 20 May 2016 14:49:54 +0200 Subject: [PATCH 138/171] 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 @@ R packages that praise their users.") (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) From c1e2c9d41aecdab073a7407ceb75440823e7fc73 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 20 May 2016 14:50:54 +0200 Subject: [PATCH 139/171] 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 @@ collation, and NAMESPACE files.") (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))) From 3624ad71501cb7924003f4b8bcf9b08e7c9f4ff6 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 20 May 2016 14:51:26 +0200 Subject: [PATCH 140/171] 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 @@ functions make it easy to control additional request components.") (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 From 133f27b06af28dc99ba14cc53f301259392faa5c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 20 May 2016 14:51:58 +0200 Subject: [PATCH 141/171] 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 @@ informative error messages when it's not available.") (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) From 2f7ac060ff464f4bacd0d4a18fd9a82426220e74 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 20 May 2016 14:52:32 +0200 Subject: [PATCH 142/171] 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 @@ disk (or a connection).") (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") From f0c56a241140d279035d01555bfc12bc8378d782 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 20 May 2016 14:53:44 +0200 Subject: [PATCH 143/171] 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 @@ encoder/decoder, round-off-error-free sum and cumsum, etc.") (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 From b8f6a97ebd7f41a26d1ae8ae9d6e93c9dc4c6390 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 20 May 2016 14:54:25 +0200 Subject: [PATCH 144/171] 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 @@ persistent (on the file system).") (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 From 95513f284f35ba8d4ccff924de248ab03586d500 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 20 May 2016 14:56:16 +0200 Subject: [PATCH 145/171] 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 @@ t-probabilities, quantiles, random deviates and densities.") (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 From c969453e1c4cdbaa6bd1d35d788ee40b0df87920 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 20 May 2016 14:56:50 +0200 Subject: [PATCH 146/171] 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 @@ It uses and relies on grid graphics and formal (S4) classes and methods.") (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) From f6225d135c88f70d29729f9a6b593dd8b7141d45 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 20 May 2016 14:57:25 +0200 Subject: [PATCH 147/171] 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 @@ particularly easy to create complete web applications using httpuv alone.") (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") From 7740f5812889d398353fef98d871799334c3ac74 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 20 May 2016 14:58:57 +0200 Subject: [PATCH 148/171] 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 @@ reference point and sorted by a user defined feature.") (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) From 945eef85c511c11cf0d54ad3ec6e3745917260b7 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 20 May 2016 15:08:53 +0200 Subject: [PATCH 149/171] 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 @@ full text searching.") (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 From 813efdded15d9382ee8e71287367963f5dc7fd26 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 20 May 2016 15:09:36 +0200 Subject: [PATCH 150/171] 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 @@ associated functions (eg. contiguous and non-contiguous submatrix views).") (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 @@ well as additional utilities such as panel and axis annotation functions.") (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 From 2d69c1616d974f45ecdc4977d4501d0ae1dcd634 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 16 May 2016 20:10:55 +0200 Subject: [PATCH 151/171] 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 @@ as the 'native-search-paths' field." (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 From 8b196ad208e844e2829e49382811dff327bd297d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 16 May 2016 20:11:19 +0200 Subject: [PATCH 152/171] 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 @@ as the 'native-search-paths' field." (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 From a5948c0d41d7850c93f3128461ad3e87089e52a3 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 16 May 2016 20:11:42 +0200 Subject: [PATCH 153/171] 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 @@ as the 'native-search-paths' field." (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 From 987a1183344a716a65d13796dca9013a0c2bcf66 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 16 May 2016 20:12:08 +0200 Subject: [PATCH 154/171] 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 @@ as the 'native-search-paths' field." (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 From 932f2b70a6a5eee15b1508d7aae7f8a7fdb0e23a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 10 May 2016 15:50:28 +0200 Subject: [PATCH 155/171] 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 @@ 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 @@ repack them. This is necessary to ensure that archives are reproducible." (define %standard-phases (modify-phases gnu:%standard-phases + (replace 'unpack unpack) (replace 'configure configure) (replace 'build build) (replace 'check check) From 4483a1185d413f206d4f35b3eacf6f9d893ae3da Mon Sep 17 00:00:00 2001 From: Mark H Weaver Date: Fri, 20 May 2016 18:15:51 -0400 Subject: [PATCH 156/171] 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 @@ It has been modified to remove all non-free binary blobs.") (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)) From 3c9a7185e4ee81295838bb31f0d437da64dbd390 Mon Sep 17 00:00:00 2001 From: Mark H Weaver Date: Fri, 20 May 2016 18:17:12 -0400 Subject: [PATCH 157/171] 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 @@ for SYSTEM and optionally VARIANT, or #f if there is no such configuration." (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 @@ for SYSTEM and optionally VARIANT, or #f if there is no such configuration." (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) From 3cabdead6fbe080d9466bb3130a2b36dd4b07090 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Thu, 19 May 2016 23:24:50 +0200 Subject: [PATCH 158/171] 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 @@ Emit a Graphviz (dot) representation of the dependencies of PACKAGE...\n")) (_ #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 From 97507ebedc8e1265c2ed354e50a218fb9ee6087b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Thu, 19 May 2016 23:27:48 +0200 Subject: [PATCH 159/171] 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 @@ download with a fixed hash (aka. `fetchurl')." #t) (_ #f))) +(define (derivation-input." + (string." @@ -190,6 +195,30 @@ the store." (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 @@ that form." (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 @@ derivation at FILE." (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 @@ (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" From a773c3142dd168e1c4480614d3f5fd9d003954cd Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Fri, 20 May 2016 17:07:23 +0200 Subject: [PATCH 160/171] 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 @@ (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 @@ #: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 @@ name." ;; 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 @@ Dependencies may include packages, origin, and file names." (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 @@ Dependencies may include packages, origin, and file names." (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 @@ GNU-BUILD-SYSTEM have zero dependencies." (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 @@ a plain store file." (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 @@ substitutes." (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 @@ Emit a Graphviz (dot) representation of the dependencies of PACKAGE...\n")) (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 @@ Emit a Graphviz (dot) representation of the dependencies of PACKAGE...\n")) (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" From 30d4bc0434aa5d438c2d433f39c80e1f4a25bcac Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Fri, 20 May 2016 17:18:58 +0200 Subject: [PATCH 161/171] 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 @@ the cache STR originates form." (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. From cf8b312d1872aec1f38a179eeb981d79bf7faa03 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Fri, 20 May 2016 22:11:56 +0200 Subject: [PATCH 162/171] 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 @@ file name pairs." (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 @@ file name pairs." (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 @@ (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.")) From ece6864bd04fc2f9ff86fd4ac9cb0712dd71c094 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Fri, 20 May 2016 22:14:46 +0200 Subject: [PATCH 163/171] 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 @@ writing the result to OUTPUT." (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 @@ file name pairs." (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 @@ (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) From 28dee3d28271c284efadaf1de40dbd7535e36072 Mon Sep 17 00:00:00 2001 From: Mathieu Lirzin Date: Thu, 12 May 2016 23:15:37 +0200 Subject: [PATCH 164/171] 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 From a56be436d0253c96d0ff766092e3f94432033187 Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Thu, 19 May 2016 10:26:45 +0200 Subject: [PATCH 165/171] 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 @@ #: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 @@ Desktop. It is designed to be as simple as possible and has some unique 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") From b9b447be64fcde6ebb5811ee82a6f029b873ab18 Mon Sep 17 00:00:00 2001 From: Jan Nieuwenhuizen Date: Thu, 19 May 2016 23:50:09 +0200 Subject: [PATCH 166/171] 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 @@ #: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 @@ #: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 @@ procedures, embedded in the programming language Scheme, and intended to 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)))) From 548994142f52c168454ee725227aef6a975cb880 Mon Sep 17 00:00:00 2001 From: Matthew Jordan Date: Thu, 19 May 2016 14:10:40 -0400 Subject: [PATCH 167/171] 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/")))) From 3c47489766bbf3d381b63d4eda63b2aff2f35d0f Mon Sep 17 00:00:00 2001 From: Kei Yamashita Date: Sat, 14 May 2016 21:27:08 -0400 Subject: [PATCH 168/171] 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 @@ specified duration and save it as a GIF encoded animated image file.") 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") From 88bb4197c419d6095cc4061bac1ee0f96bf939b1 Mon Sep 17 00:00:00 2001 From: Lukas Gradl Date: Sat, 21 May 2016 18:19:42 -0500 Subject: [PATCH 169/171] 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 @@ respectively.") (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))) From 13913c52d5bf75d8c5bee4fdc0fa7ce70f0588f7 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Wed, 18 May 2016 23:16:51 -0400 Subject: [PATCH 170/171] 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-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") From 624d4e2e6ba402c374a340869306eec65a808a20 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sun, 22 May 2016 16:58:21 +0300 Subject: [PATCH 171/171] 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-public gnu-pw-mgr (package (name "gnu-pw-mgr") - (version "1.6") + (version "2.0") (source (origin (method url-fetch) @@ -37,7 +38,7 @@ version ".tar.xz")) (sha256 (base32 - "141wfm4w420ygrl7qvrc84drzv34jym0d2bxqcgi7n1vimql0slp")))) + "19qvg37snfa8s06q5crx25m1r1n4l0wvfpkbdxz17q7whp0plrl6")))) (build-system gnu-build-system) (native-inputs `(("which" ,which)