From 86300e61b99994ccf03e240c9aa0e7e58120f83c Mon Sep 17 00:00:00 2001 From: Mark H Weaver Date: Mon, 18 Dec 2017 19:50:39 -0500 Subject: [PATCH 01/77] gnu: linux-libre@4.4: Update to 4.4.106. * gnu/packages/linux.scm (linux-libre-4.4): Update to 4.4.106. --- 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 75263a08e2..2ac828c84d 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -390,8 +390,8 @@ It has been modified to remove all non-free binary blobs.") #:configuration-file kernel-config)) (define-public linux-libre-4.4 - (make-linux-libre "4.4.105" - "177qvci7wfrc23vi11bnyayfivxf6d8hankgrzv26jr3z6j0rall" + (make-linux-libre "4.4.106" + "1dn67fl8lbckjxcra1d02fqjald71cxp4fq3bld4wc1r4saanqi7" %intel-compatible-systems #:configuration-file kernel-config)) From 48e1f444152363918195427f46cc26dbba30792a Mon Sep 17 00:00:00 2001 From: Mark H Weaver Date: Mon, 18 Dec 2017 19:51:22 -0500 Subject: [PATCH 02/77] gnu: linux-libre@4.9: Update to 4.9.70. * gnu/packages/linux.scm (linux-libre-4.9): Update to 4.9.70. --- 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 2ac828c84d..351490f470 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -384,8 +384,8 @@ It has been modified to remove all non-free binary blobs.") #:configuration-file kernel-config)) (define-public linux-libre-4.9 - (make-linux-libre "4.9.69" - "0xkqbh8fpx47appszjbxzljr6vr0wyk0fphlkynpcrmingk4b98j" + (make-linux-libre "4.9.70" + "1bwfk68zzwmznhf3zv858wpav2r43g7hg4wxcdyfamy8k38v0r43" %intel-compatible-systems #:configuration-file kernel-config)) From 7a6a08c945e64b844c8d7655d883b5c30d9092fb Mon Sep 17 00:00:00 2001 From: Mark H Weaver Date: Mon, 18 Dec 2017 19:52:02 -0500 Subject: [PATCH 03/77] gnu: linux-libre: Update to 4.14.7. * gnu/packages/linux.scm (%linux-libre-version): Update to 4.14.7. (%linux-libre-hash): Update hash. --- 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 351490f470..7ab2ba84d6 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -370,8 +370,8 @@ It has been modified to remove all non-free binary blobs.") (define %intel-compatible-systems '("x86_64-linux" "i686-linux")) (define %linux-compatible-systems '("x86_64-linux" "i686-linux" "armhf-linux")) -(define %linux-libre-version "4.14.6") -(define %linux-libre-hash "0q6dl2shkj5dkf0wgzgfyaq0axk97w05j618xi619y9xqph4ql79") +(define %linux-libre-version "4.14.7") +(define %linux-libre-hash "1hwmg4mqpm3n6qxcjl01fbl3pbbirw9727jzfc7gy6livifyibfi") ;; linux-libre configuration for armhf-linux is derived from Debian armmp. It ;; supports qemu "virt" machine and possibly a large number of ARM boards. From 4498cbd7ad16589a34e713669fa019d68d614cab Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Fri, 15 Dec 2017 22:50:04 -0500 Subject: [PATCH 04/77] gnu: GnuPG pinentry: Update to 1.1.0. * gnu/packages/gnupg.scm (pinentry-tty, pinentry-gtk2, pinentry-gnome3, pinentry-qt): Update to 1.1.0. --- gnu/packages/gnupg.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/gnupg.scm b/gnu/packages/gnupg.scm index 8a81e9f9e9..336cd8f741 100644 --- a/gnu/packages/gnupg.scm +++ b/gnu/packages/gnupg.scm @@ -727,14 +727,14 @@ including tools for signing keys, keyring analysis, and party preparation. (define-public pinentry-tty (package (name "pinentry-tty") - (version "1.0.0") + (version "1.1.0") (source (origin (method url-fetch) (uri (string-append "mirror://gnupg/pinentry/pinentry-" version ".tar.bz2")) (sha256 (base32 - "0ni7g4plq6x78p32al7m8h2zsakvg1rhfz0qbc3kdc7yq7nw4whn")))) + "0w35ypl960pczg5kp6km3dyr000m1hf0vpwwlh72jjkjza36c1v8")))) (build-system gnu-build-system) (arguments `(#:configure-flags '("--enable-pinentry-tty"))) From 4fad6598c60b48bf956096530c86f6920c72bd1c Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Tue, 19 Dec 2017 01:12:33 -0500 Subject: [PATCH 05/77] gnu: keepassxc: Update to 2.2.4. * gnu/packages/password-utils.scm (keepassxc): Update to 2.2.4. --- gnu/packages/password-utils.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/password-utils.scm b/gnu/packages/password-utils.scm index ffa152f279..6824210341 100644 --- a/gnu/packages/password-utils.scm +++ b/gnu/packages/password-utils.scm @@ -88,7 +88,7 @@ human.") (define-public keepassxc (package (name "keepassxc") - (version "2.2.2") + (version "2.2.4") (source (origin (method url-fetch) @@ -97,7 +97,7 @@ human.") version "-src.tar.xz")) (sha256 (base32 - "0wrl8kxb16wzdgfjj057yv18cfg0b8z8lxp1fl2q8fkdgr7phm9g")))) + "1pfkq1m5vb90kx67vyw70s1hc4ivjsvq2535vm6wdwwsncna6bz5")))) (build-system cmake-build-system) (arguments `(#:configure-flags From 4a408d847ea7e41e538ec54ee902bd1a3756eedb Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Tue, 19 Dec 2017 02:24:16 -0500 Subject: [PATCH 06/77] gnu: mpd: Update to 0.20.13. * gnu/packages/mpd.scm (mpd): Update to 0.20.13. --- gnu/packages/mpd.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/mpd.scm b/gnu/packages/mpd.scm index 74b53afce1..e6bc2b4e71 100644 --- a/gnu/packages/mpd.scm +++ b/gnu/packages/mpd.scm @@ -76,7 +76,7 @@ interfacing MPD in the C, C++ & Objective C languages.") (define-public mpd (package (name "mpd") - (version "0.20.12") + (version "0.20.13") (source (origin (method url-fetch) (uri @@ -85,7 +85,7 @@ interfacing MPD in the C, C++ & Objective C languages.") "/mpd-" version ".tar.xz")) (sha256 (base32 - "02gpfkki61c24hphaas9pb29wpvd0pbmwdqrpn8wi1gv103aqng1")))) + "0h7z90dnpwlyad4kfi1ja9v9vzqic0xg93iy4q0dwlhav0scbha6")))) (build-system gnu-build-system) (arguments `(#:phases From a1ac7bf361dd5d10dd84e4666a0c2d7b07970e25 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Tue, 19 Dec 2017 09:52:21 +0100 Subject: [PATCH 07/77] tests: Adjust php-fpm test to new nginx API. Fixes . Reported by Mark H Weaver . This is a followup to 8b223ceac4ff0781e95d69362875f87cff03f4d6. * gnu/tests/web.scm (%php-fpm-nginx-server-blocks): Turn 'listen' into a list. --- gnu/tests/web.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/tests/web.scm b/gnu/tests/web.scm index f1214fb5fd..336f25b3c7 100644 --- a/gnu/tests/web.scm +++ b/gnu/tests/web.scm @@ -154,7 +154,7 @@ echo(\"Computed by php:\".((string)(2+3))); (root "/srv") (locations (list (nginx-php-location))) - (listen "8042") + (listen '("8042")) (ssl-certificate #f) (ssl-certificate-key #f)))) From 28fc96cb1e45bdf754970edbeb619cffc9b720bd Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Tue, 19 Dec 2017 10:47:19 +0100 Subject: [PATCH 08/77] gnu: Update r-cowplot to 0.9.2. * gnu/packages/statistics.scm (r-cowplot): Update to 0.9.2. --- 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 80a1df9cfb..41740d6418 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -4394,14 +4394,14 @@ Farebrother's algorithm or Liu et al.'s algorithm.") (define-public r-cowplot (package (name "r-cowplot") - (version "0.9.1") + (version "0.9.2") (source (origin (method url-fetch) (uri (cran-uri "cowplot" version)) (sha256 (base32 - "0iq0wsi7467cj8hqml06whk3xsiv89x8dvm9ynwp411pzzbdjgwm")))) + "13yjw7yv7imyqiawqqp304hkp6x36iv6rf6gn03dwzwkj9zwx4lb")))) (build-system r-build-system) (propagated-inputs `(("r-ggplot2" ,r-ggplot2) From ba1ba9fcbd93eb2275d60b3bec0f44bd8b5786e5 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Tue, 19 Dec 2017 11:30:36 +0200 Subject: [PATCH 09/77] gnu: emulation-station: Add missing file-name field. * gnu/packages/games.scm (emulation-station)[source]: Add missing file-name field. --- gnu/packages/games.scm | 1 + 1 file changed, 1 insertion(+) diff --git a/gnu/packages/games.scm b/gnu/packages/games.scm index d8df3d532d..11b65a76fe 100644 --- a/gnu/packages/games.scm +++ b/gnu/packages/games.scm @@ -2509,6 +2509,7 @@ emulation community. It provides highly accurate emulation.") (uri (git-reference (url "https://github.com/Aloshi/EmulationStation.git") (commit commit))) ; no version tag + (file-name (string-append name "-" version "-checkout")) (sha256 (base32 "0cm0sq2wri2l9cvab1l0g02za59q7klj0h3p028vr96n6njj4w9v")))) From fb6ca493f1416761129a139b36d40c2153dd4af2 Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Tue, 19 Dec 2017 12:27:43 +0100 Subject: [PATCH 10/77] gnu: Update gwl to 0.1.1. * gnu/packages/package-management.scm (gwl): Update to 0.1.1. --- gnu/packages/package-management.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/package-management.scm b/gnu/packages/package-management.scm index dae6499b62..d96a4d1a1f 100644 --- a/gnu/packages/package-management.scm +++ b/gnu/packages/package-management.scm @@ -776,14 +776,14 @@ written entirely in Python."))) (define-public gwl (package (name "gwl") - (version "0.1.0") + (version "0.1.1") (source (origin (method url-fetch) (uri (string-append "https://www.guixwl.org/releases/gwl-" version ".tar.gz")) (sha256 (base32 - "1x4swwp7kmhd57j3scii5c4h8swkcvab2r6mz7wxwwbx300wcqpy")))) + "06pm967mq1wyggx7l0nfapw5s0k5qc5r9lawk2v3db868br779a7")))) (build-system gnu-build-system) (native-inputs `(("autoconf" ,autoconf) From b28e05d45e9d9485113ad1535b5572f4eab77da5 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 19 Dec 2017 08:34:45 +0100 Subject: [PATCH 11/77] gnu: antiword: Fix broken embedded directory name. * gnu/packages/textutils.scm (antiword)[arguments]: Replace "configure" phase to substitute reference to "/usr/share/antiword" with the actual directory in the store. --- gnu/packages/textutils.scm | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/gnu/packages/textutils.scm b/gnu/packages/textutils.scm index 674a3507d0..2fb1d1495e 100644 --- a/gnu/packages/textutils.scm +++ b/gnu/packages/textutils.scm @@ -388,7 +388,14 @@ regular expression object can be specified.") (assoc-ref %outputs "out") "/share/antiword")) #:phases (modify-phases %standard-phases - (delete 'configure) + (replace 'configure + (lambda* (#:key outputs #:allow-other-keys) + ;; Ensure that mapping files can be found in the actual package + ;; data directory. + (substitute* "antiword.h" + (("/usr/share/antiword") + (string-append (assoc-ref outputs "out") "/share/antiword"))) + #t)) (replace 'install (lambda* (#:key make-flags #:allow-other-keys) (zero? (apply system* "make" `("global_install" ,@make-flags)))))))) From 79b43bc3a158cc861fd246c41ad779d8b1312adb Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 19 Dec 2017 09:30:27 +0100 Subject: [PATCH 12/77] gnu: pcsc-lite: Update to 1.8.23. * gnu/packages/security-token.scm (pcsc-lite): Update to 1.8.23. [arguments]: Disable libsystemd check. --- gnu/packages/security-token.scm | 1 + 1 file changed, 1 insertion(+) diff --git a/gnu/packages/security-token.scm b/gnu/packages/security-token.scm index 7c6b957411..7ce531bb6d 100644 --- a/gnu/packages/security-token.scm +++ b/gnu/packages/security-token.scm @@ -5,6 +5,7 @@ ;;; Copyright © 2016 Marius Bakke ;;; Copyright © 2017 Thomas Danckaert ;;; Copyright © 2017 Tobias Geerinckx-Rice +;;; Copyright © 2017 Ricardo Wurmus ;;; ;;; This file is part of GNU Guix. ;;; From 21bc352664fcd1c32e88f363a9d1455e83e5cc2a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 18 Dec 2017 18:30:12 +0100 Subject: [PATCH 13/77] gnu: dino: Update to 0.0-3.f25fadde2. * gnu/packages/messaging.scm (dino): Update to 0.0-3.f25fadde2. --- gnu/packages/messaging.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/messaging.scm b/gnu/packages/messaging.scm index 1780536d05..880ce81b1e 100644 --- a/gnu/packages/messaging.scm +++ b/gnu/packages/messaging.scm @@ -568,8 +568,8 @@ end-to-end encryption support; XML console.") (define-public dino ;; The only release tarball is for version 0.0, but it is very old and fails ;; to build. - (let ((commit "2a514d0969f5c25d5e2d14421125a47df6b14974") - (revision "2")) + (let ((commit "f25fadde2d6c9492b9cafe2cddbcc7b966942e47") + (revision "3")) (package (name "dino") (version (string-append "0.0-" revision "." (string-take commit 9))) @@ -581,7 +581,7 @@ end-to-end encryption support; XML console.") (file-name (string-append name "-" version "-checkout")) (sha256 (base32 - "0v9fqikxvamdw7bxbwc4s01x0vf30vl77149y16krijaqnq6kzv0")))) + "1nhzrw3pbpybn9qclckk6z427vbgnqd0y1l63zd1rfw4zw099mzs")))) (build-system cmake-build-system) (arguments `(#:tests? #f ; there are no tests From f3b985fa61739910c87f2bb8541568204e29ed64 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 18 Dec 2017 17:58:38 +0100 Subject: [PATCH 14/77] gnu: python-nbxmpp: Update to 0.6.1. * gnu/packages/messaging.scm (python-nbxmpp): Update to 0.6.1. --- gnu/packages/messaging.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/messaging.scm b/gnu/packages/messaging.scm index 880ce81b1e..e549ad4f7c 100644 --- a/gnu/packages/messaging.scm +++ b/gnu/packages/messaging.scm @@ -493,14 +493,14 @@ simultaneously and therefore appear under the same nickname on IRC.") (define-public python-nbxmpp (package (name "python-nbxmpp") - (version "0.5.5") + (version "0.6.1") (source (origin (method url-fetch) (uri (pypi-uri "nbxmpp" version)) (sha256 (base32 - "1gnzrzrdl4nii1sc5x8p5iw2ya5sl70j3nn34abqsny51p2pzmv6")))) + "0qvkiscy42nhzhccszi049ws8cnhpxgc13g8naq1rsa5x9zy163c")))) (build-system python-build-system) (arguments `(#:tests? #f)) ; no tests From 0464dc1c1e6f32823eb82409a4b39d03fa983cc7 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 18 Dec 2017 17:52:01 +0100 Subject: [PATCH 15/77] gnu: gajim: Update to 0.16.9. * gnu/packages/messaging.scm (gajim): Update to 0.16.9. --- gnu/packages/messaging.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/messaging.scm b/gnu/packages/messaging.scm index e549ad4f7c..8b3bf5cf68 100644 --- a/gnu/packages/messaging.scm +++ b/gnu/packages/messaging.scm @@ -518,7 +518,7 @@ was initially a fork of xmpppy, but uses non-blocking sockets.") (define-public gajim (package (name "gajim") - (version "0.16.8") + (version "0.16.9") (source (origin (method url-fetch) (uri (string-append "https://gajim.org/downloads/" @@ -526,7 +526,7 @@ was initially a fork of xmpppy, but uses non-blocking sockets.") "/gajim-" version ".tar.bz2")) (sha256 (base32 - "0ckakdjg30fsyjsgyy2573x9nmjivdg76y049l86wns5axw8im26")))) + "0v08zdvpqaig0wxpxn1l8rsj3wr3fqvnagn8cnvch17vfqv9gcr1")))) (build-system gnu-build-system) (arguments `(#:phases From 7a070f020be4e0fa47259eb4d6d1dcfd940b570e Mon Sep 17 00:00:00 2001 From: nee Date: Thu, 7 Dec 2017 22:25:26 +0100 Subject: [PATCH 16/77] gnu: Add quakespasm. * gnu/packages/games.scm (quakespasm): New variable. Signed-off-by: Kei Kebreau --- gnu/packages/games.scm | 44 ++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 44 insertions(+) diff --git a/gnu/packages/games.scm b/gnu/packages/games.scm index 11b65a76fe..cc21a63f53 100644 --- a/gnu/packages/games.scm +++ b/gnu/packages/games.scm @@ -5140,3 +5140,47 @@ abilities and powers. With a modern graphical and customisable interface, intuitive mouse control, streamlined mechanics and deep, challenging combat, Tales of Maj’Eyal offers engaging roguelike gameplay for the 21st century.") (license license:gpl3+))) + +(define-public quakespasm + (package + (name "quakespasm") + (version "0.93.0") + (source + (origin + (method url-fetch) + (uri (string-append "mirror://sourceforge/quakespasm/Source/quakespasm-" + version ".tgz")) + (sha256 + (base32 + "0b2nz7w4za32pc34r62ql270z692qcjs2pm0i3svkxkvfammhdfq")))) + (arguments + `(#:tests? #f + #:make-flags '("CC=gcc" + "MP3LIB=mpg123" + "USE_CODEC_FLAC=1" + "USE_CODEC_MIKMOD=1" + "USE_SDL2=1" + "-CQuake") + #:phases (modify-phases %standard-phases + (delete 'configure) + (add-after 'unpack 'fix-makefile-paths + (lambda* (#:key outputs #:allow-other-keys) + (let ((out (assoc-ref outputs "out"))) + (mkdir-p (string-append out "/bin")) + (substitute* "Quake/Makefile" + (("/usr/local/games") + (string-append out "/bin"))) + #t)))))) + (build-system gnu-build-system) + (inputs `(("libmikmod" ,libmikmod) + ("libvorbis" ,libvorbis) + ("flac" ,flac) + ("mesa" ,mesa) + ("mpg123" ,mpg123) + ("sdl2" ,sdl2))) + (synopsis "First person shooter engine for Quake 1") + (description "Quakespasm is a modern engine for id software's Quake 1. +It includes support for 64 bit CPUs, custom music playback, a new sound driver, +some graphical niceities, and numerous bug-fixes and other improvements.") + (home-page "http://quakespasm.sourceforge.net/") + (license license:gpl2+))) From a8db968fa48ecb3dd219833a9e393a383d842215 Mon Sep 17 00:00:00 2001 From: Kei Kebreau Date: Tue, 19 Dec 2017 11:26:16 -0500 Subject: [PATCH 17/77] gnu: wxmaxima: Update to 17.10.1. * gnu/packages/maths.scm (wxmaxima): Update to 17.10.1. --- 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 5c7926a635..837e142f59 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -2489,7 +2489,7 @@ point numbers.") (define-public wxmaxima (package (name "wxmaxima") - (version "17.05.1") + (version "17.10.1") (source (origin (method url-fetch) @@ -2498,7 +2498,7 @@ point numbers.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "0dv0cy0cf46v0cbw32izscpkdmpxg1qhwq1f4cz46kkqd8k4yfbj")))) + "0qlzc31cqkwpfgrb9cif9bcnkj3rq487plg4rns7jxv6pq4609v1")))) (build-system gnu-build-system) (native-inputs `(("autoconf" ,autoconf) From 9a56cf2b5b4970843c215091ea9823a67e077310 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Wed, 13 Dec 2017 18:49:28 -0500 Subject: [PATCH 18/77] services: urandom-seed: Try using a HWRNG to seed the Linux CRNG at boot. * gnu/services/base.scm (urandom-seed-shepherd-service): Try to read from '/dev/hwrng' at boot, as a supplement to any saved random seed. * doc/guix.texi (Base Services): Document the new feature. --- doc/guix.texi | 4 +++- gnu/services/base.scm | 18 ++++++++++++++++++ 2 files changed, 21 insertions(+), 1 deletion(-) diff --git a/doc/guix.texi b/doc/guix.texi index 3bb29db960..6b6f8dedae 100644 --- a/doc/guix.texi +++ b/doc/guix.texi @@ -10025,7 +10025,9 @@ well as in the @var{groups} field of the @var{operating-system} record. @deffn {Scheme Procedure} urandom-seed-service Save some entropy in @var{%random-seed-file} to seed @file{/dev/urandom} -when rebooting. +when rebooting. It also tries to seed @file{/dev/urandom} from +@file{/dev/hwrng} while booting, if @file{/dev/hwrng} exists and is +readable. @end deffn @defvr {Scheme Variable} %random-seed-file diff --git a/gnu/services/base.scm b/gnu/services/base.scm index 5e08927af3..a3654fd4d3 100644 --- a/gnu/services/base.scm +++ b/gnu/services/base.scm @@ -516,6 +516,24 @@ stopped before 'kill' is called." (call-with-output-file "/dev/urandom" (lambda (urandom) (dump-port seed urandom)))))) + + ;; Try writing from /dev/hwrng into /dev/urandom. + ;; It seems that the file /dev/hwrng always exists, even + ;; when there is no hardware random number generator + ;; available. So, we handle a failed read or any other error + ;; reported by the operating system. + (let ((buf (catch 'system-error + (lambda () + (call-with-input-file "/dev/hwrng" + (lambda (hwrng) + (get-bytevector-n hwrng 512)))) + ;; Silence is golden... + (const #f)))) + (when buf + (call-with-output-file "/dev/urandom" + (lambda (urandom) + (put-bytevector urandom buf))))) + ;; Immediately refresh the seed in case the system doesn't ;; shut down cleanly. (call-with-input-file "/dev/urandom" From 68f1869cfca63ee361b2b036eb424f20a9da0d91 Mon Sep 17 00:00:00 2001 From: Danny Milosavljevic Date: Tue, 19 Dec 2017 10:45:15 +0100 Subject: [PATCH 19/77] gnu: xfce4-session: Disable (duplicate) Gtk+ icon cache generation. * gnu/packages/xfce.scm (xfce4-session)[arguments]: Add make-flags to disable Gtk+ icon cache generation. --- gnu/packages/xfce.scm | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/gnu/packages/xfce.scm b/gnu/packages/xfce.scm index 7668a1d380..bbe6ab4545 100644 --- a/gnu/packages/xfce.scm +++ b/gnu/packages/xfce.scm @@ -492,7 +492,10 @@ your system in categories, so you can quickly find and launch them.") (build-system gnu-build-system) (arguments '(#:configure-flags - (list (string-append "--with-xsession-prefix=" %output)))) + (list (string-append "--with-xsession-prefix=" %output)) + ;; Disable icon cache update. + #:make-flags + '("gtk_update_icon_cache=true"))) (native-inputs `(("pkg-config" ,pkg-config) ("intltool" ,intltool))) From 618f0582b49edb0a5f633c953b00fc93d03c077a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Tue, 19 Dec 2017 17:57:15 +0100 Subject: [PATCH 20/77] upstream: Reject bogus archive type guesses. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit This would crash 'guix refresh -u' with source URLs ending in "…/v1.2.3". * guix/upstream.scm (package-update): Be stricter when determining ARCHIVE-TYPE. --- guix/upstream.scm | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/guix/upstream.scm b/guix/upstream.scm index 0fe3308876..caaa0e44e4 100644 --- a/guix/upstream.scm +++ b/guix/upstream.scm @@ -278,7 +278,13 @@ and 'interactive' (default)." ((archive-type) (match (and=> (package-source package) origin-uri) ((? string? uri) - (file-extension (basename uri))) + (let ((type (file-extension (basename uri)))) + ;; Sometimes we have URLs such as + ;; "https://github.com/…/tarball/v0.1", in which case + ;; we must not consider "1" as the extension. + (and (or (string-contains type "z") + (string=? type "tar")) + type))) (_ "gz"))) ((url signature-url) From 8d11ef4470a6836b4312c8b2605c567221336fe4 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 19 Dec 2017 20:05:28 +0100 Subject: [PATCH 21/77] gnu: r-vegan: Update to 2.4-5. * gnu/packages/bioinformatics.scm (r-vegan): Update to 2.4-5. --- 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 cf026ab24e..b36c9f4d09 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -5857,14 +5857,14 @@ information as possible.") (define-public r-vegan (package (name "r-vegan") - (version "2.4-4") + (version "2.4-5") (source (origin (method url-fetch) (uri (cran-uri "vegan" version)) (sha256 (base32 - "1n57dzv2aid6iqd9fkqik401sidqanhzsawyak94qbiyh6dbd1x9")))) + "0cyyvn3xsjn24w590jn6z4xajafv7yzvj6c51vqi9q6m8v5831ya")))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran))) From 756ac7254c5addd7aaeacbf466a4a115f18b666d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 19 Dec 2017 20:05:42 +0100 Subject: [PATCH 22/77] gnu: r-dexseq: Update to 1.24.2. * gnu/packages/bioinformatics.scm (r-dexseq): 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 b36c9f4d09..77cb109060 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6025,14 +6025,14 @@ distribution.") (define-public r-dexseq (package (name "r-dexseq") - (version "1.24.1") + (version "1.24.2") (source (origin (method url-fetch) (uri (bioconductor-uri "DEXSeq" version)) (sha256 (base32 - "1hwckj4ijgpdchbakvh60nmcaz4fwd5yplhn0880z3dnlsrp8ik3")))) + "18nh8ynxirfwkmc4sawdxgl7w1sl9ny5zpv8zbhv9vi5vgb8pxmj")))) (properties `((upstream-name . "DEXSeq"))) (build-system r-build-system) (propagated-inputs From 7665fb39f594c1423b56c9eb86ee8e6ef1cde407 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 19 Dec 2017 20:06:00 +0100 Subject: [PATCH 23/77] gnu: r-biocstyle: Update to 2.6.1. * gnu/packages/bioinformatics.scm (r-biocstyle): Update to 2.6.1. --- 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 77cb109060..e221ba043a 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6703,13 +6703,13 @@ authoring books and technical documents with R Markdown.") (define-public r-biocstyle (package (name "r-biocstyle") - (version "2.6.0") + (version "2.6.1") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocStyle" version)) (sha256 (base32 - "05f2j9fx8s5gh4f8qkl6wcz32ghz04wxhqb3xxcn1bj24qd7x1x8")))) + "03pp04pkcq99kdv2spzr995h2cxsza7l6w3d4gp4112m06prcybm")))) (properties `((upstream-name . "BiocStyle"))) (build-system r-build-system) From ab0dd8ac10dac54240c0ee4a7c7dc52eff9389ad Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 19 Dec 2017 20:06:13 +0100 Subject: [PATCH 24/77] gnu: r-edger: Update to 3.20.2. * gnu/packages/bioinformatics.scm (r-edger): Update to 3.20.2. --- 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 e221ba043a..397d52945a 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6973,13 +6973,13 @@ names in their natural, rather than lexicographic, order.") (define-public r-edger (package (name "r-edger") - (version "3.20.1") + (version "3.20.2") (source (origin (method url-fetch) (uri (bioconductor-uri "edgeR" version)) (sha256 (base32 - "01qnxwr9rmz8r5ga3hvjk632365ga2aygx71mxkk7jiad2pjznsp")))) + "0j5s3i33qmld9l7gs1rzpv601zxyqz711x8mq35hml088c8s99w9")))) (properties `((upstream-name . "edgeR"))) (build-system r-build-system) (propagated-inputs From d41f678420bd1b8476727c070376d045918115b9 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 19 Dec 2017 20:06:25 +0100 Subject: [PATCH 25/77] gnu: r-limma: Update to 3.34.4. * gnu/packages/bioinformatics.scm (r-limma): Update to 3.34.4. --- 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 397d52945a..e5e76d0ee2 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7039,13 +7039,13 @@ coding changes and predict coding outcomes.") (define-public r-limma (package (name "r-limma") - (version "3.34.2") + (version "3.34.4") (source (origin (method url-fetch) (uri (bioconductor-uri "limma" version)) (sha256 (base32 - "1zyw01z9crm1jc86fva4pqxd9zxfsbsqwjq6ry39gag9pfb7pwcz")))) + "1vcxf9jg8xngxg5kb9bp8rw5sghpnkpj320iq309m2fp41ahsk3f")))) (build-system r-build-system) (home-page "http://bioinf.wehi.edu.au/limma") (synopsis "Package for linear models for microarray and RNA-seq data") From 28d25d037ea218f62df48daa533e977fef3d0268 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 19 Dec 2017 20:06:44 +0100 Subject: [PATCH 26/77] gnu: r-rtracklayer: Update to 1.38.2. * gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.38.2. --- 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 e5e76d0ee2..2613dd3294 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7393,13 +7393,13 @@ alignments.") (define-public r-rtracklayer (package (name "r-rtracklayer") - (version "1.38.0") + (version "1.38.2") (source (origin (method url-fetch) (uri (bioconductor-uri "rtracklayer" version)) (sha256 (base32 - "12al1ygzy9p4myxa1fd817m28x2fj6f863znk9bw3hp7knbi98dh")))) + "1sjn3976f1sqvrq6jq2hgc60ffxgfr3jlklaxfrk3xad5cv2kr2d")))) (build-system r-build-system) (arguments `(#:phases From 2ccd85019231293dccb8c48d8f692ce852beaa36 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 19 Dec 2017 20:07:03 +0100 Subject: [PATCH 27/77] gnu: r-gqtlstats: Update to 1.10.1. * gnu/packages/bioinformatics.scm (r-gqtlstats): Update to 1.10.1. --- 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 2613dd3294..fb8d8d2aca 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10168,14 +10168,14 @@ defining LD blocks.") (define-public r-gqtlstats (package (name "r-gqtlstats") - (version "1.10.0") + (version "1.10.1") (source (origin (method url-fetch) (uri (bioconductor-uri "gQTLstats" version)) (sha256 (base32 - "1cbdqawxzgna8rrgj3siph5sw4d2pb57qc0gn6ibfkhyk45f8gdv")))) + "0gvq1sf2zjbkk431x40z6wql3c1rpclnnwa2f1hvykb8mmw70kmq")))) (properties `((upstream-name . "gQTLstats"))) (build-system r-build-system) (propagated-inputs From 11e42209a85fcf6f17fe1f8e58abcbda01258395 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 19 Dec 2017 20:07:22 +0100 Subject: [PATCH 28/77] gnu: r-gviz: Update to 1.22.2. * gnu/packages/bioinformatics.scm (r-gviz): Update to 1.22.2. --- 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 fb8d8d2aca..7818bba5a1 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10222,14 +10222,14 @@ family of feature/genome hypotheses.") (define-public r-gviz (package (name "r-gviz") - (version "1.22.0") + (version "1.22.2") (source (origin (method url-fetch) (uri (bioconductor-uri "Gviz" version)) (sha256 (base32 - "1lrw65a8426wpxw975wjcaiacpp6fqa00nif1yxigyankbfs23c8")))) + "173n99mc95sij2vb8n3xd016x7mxhjs961q3l29xkg1lrnnm2sva")))) (properties `((upstream-name . "Gviz"))) (build-system r-build-system) (propagated-inputs From b9e8a5c594ae4d821f9a3d9dcf091f074aabcf64 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 19 Dec 2017 20:07:37 +0100 Subject: [PATCH 29/77] gnu: r-biomart: Update to 2.34.1. * gnu/packages/bioinformatics.scm (r-biomart): Update to 2.34.1. [propagated-inputs]: Add r-httr. --- 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 7818bba5a1..76c67acf7c 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7172,18 +7172,19 @@ annotation data packages using SQLite data storage.") (define-public r-biomart (package (name "r-biomart") - (version "2.34.0") + (version "2.34.1") (source (origin (method url-fetch) (uri (bioconductor-uri "biomaRt" version)) (sha256 (base32 - "1dn3ysf0vb3mmg2b3380g0j1ajf88x4rh7fddfp990h2xlnsy2cx")))) + "0jzv8b86vpvavwnzi5xf7y18xmn72zkabkn2kclg1mgl847cq13k")))) (properties `((upstream-name . "biomaRt"))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) + ("r-httr" ,r-httr) ("r-progress" ,r-progress) ("r-rcurl" ,r-rcurl) ("r-stringr" ,r-stringr) From f46a74e9f015d4c7cc300724958222ca1f0a17d9 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 19 Dec 2017 20:08:01 +0100 Subject: [PATCH 30/77] gnu: r-proxy: Update to 0.4-20. * gnu/packages/cran.scm (r-proxy): Update to 0.4-20. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index e7c9c6588a..aabedea481 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -541,14 +541,14 @@ plot networks.") (define-public r-proxy (package (name "r-proxy") - (version "0.4-19") + (version "0.4-20") (source (origin (method url-fetch) (uri (cran-uri "proxy" version)) (sha256 (base32 - "0ladwgi70jw2a3adgg2xadw8hz3mm6llsw428c1fcrl305sy49vb")))) + "15g6dacdmlbkcnimblscghl23aj732cn6qwbs583r4im9v5nvbla")))) (build-system r-build-system) (home-page "http://cran.r-project.org/web/packages/proxy") (synopsis "Distance and similarity measures") From 2960f9658f19637136c783d57ccd0b7598b0e934 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 19 Dec 2017 20:08:15 +0100 Subject: [PATCH 31/77] gnu: r-vcd: Update to 1.4-4. * gnu/packages/cran.scm (r-vcd): Update to 1.4-4. --- gnu/packages/cran.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index aabedea481..a52a4e928c 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -1620,14 +1620,14 @@ modeling for empirical income distributions.") (define-public r-vcd (package (name "r-vcd") - (version "1.4-3") + (version "1.4-4") (source (origin (method url-fetch) (uri (cran-uri "vcd" version)) (sha256 (base32 - "05azric2w8mrsdk7y0484cjygcgcmbp96q2v500wvn91fj98kkhp")))) + "1lp99h0wvsc61l1dgcqjxdrcgpgw88ak430cdsv43kmm43qssqd5")))) (build-system r-build-system) (propagated-inputs `(("r-colorspace" ,r-colorspace) From d0c1a402dbfb8be82a7d91bfc792d9c433ed35ea Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 19 Dec 2017 20:08:32 +0100 Subject: [PATCH 32/77] gnu: r-digest: Update to 0.6.13. * gnu/packages/statistics.scm (r-digest): Update to 0.6.13. --- 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 41740d6418..70fe46d050 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -703,13 +703,13 @@ effects of different types of color-blindness.") (define-public r-digest (package (name "r-digest") - (version "0.6.12") + (version "0.6.13") (source (origin (method url-fetch) (uri (cran-uri "digest" version)) (sha256 - (base32 "1awy9phxdvqnadby7rvwy2hkbrj210bqf4xvi27asdq028zlcyd4")))) + (base32 "1bsgl07bvf4nk6bn7n3l2ilvk4qvn3nk7yxp22miil7x405xdks6")))) (build-system r-build-system) ;; Vignettes require r-knitr, which requires r-digest, so we have to ;; disable them and the tests. From de3fd9253f1dce0a7a9de0571db0c9f7ffd753d5 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 19 Dec 2017 20:08:45 +0100 Subject: [PATCH 33/77] gnu: r-reshape2: Update to 1.4.3. * gnu/packages/statistics.scm (r-reshape2): Update to 1.4.3. --- 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 70fe46d050..1b8571ae4a 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -988,13 +988,13 @@ the input of another.") (define-public r-reshape2 (package (name "r-reshape2") - (version "1.4.2") + (version "1.4.3") (source (origin (method url-fetch) (uri (cran-uri "reshape2" version)) (sha256 - (base32 "0swvjmc9f8cvkrsz463cp6snd8bncbv6q8yrfrb4rgkr0dhq6dvd")))) + (base32 "03ki5ka1dj208fc0dclbm0b4xp9d769pah2j9cs34l776p4r9zwa")))) (build-system r-build-system) (propagated-inputs `(("r-plyr" ,r-plyr) From 1028f9ef11c5ca2e2531c219e53ffefabde8cc57 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 19 Dec 2017 20:09:12 +0100 Subject: [PATCH 34/77] gnu: r-yaml: Update to 2.1.16. * gnu/packages/statistics.scm (r-yaml): Update to 2.1.16. --- 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 1b8571ae4a..fda019cc50 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -1328,13 +1328,13 @@ syntax that can be converted to XHTML or other formats.") (define-public r-yaml (package (name "r-yaml") - (version "2.1.14") + (version "2.1.16") (source (origin (method url-fetch) (uri (cran-uri "yaml" version)) (sha256 (base32 - "0x88xicrf7vwp77xgan27mnpdljhpkn0pz5kphnwqi3ddy25k9a1")))) + "1xlsmqal607w6c9rx86061y1fwpbyd5lqp9bad5n7cc9a0blpnkm")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/yaml/") (synopsis "Methods to convert R data to YAML and back") From 069e3b5c095ac938cb56af89d2f1c1a97c07b433 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 19 Dec 2017 20:09:30 +0100 Subject: [PATCH 35/77] gnu: r-backports: Update to 1.1.2. * gnu/packages/statistics.scm (r-backports): Update to 1.1.2. --- 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 fda019cc50..dc6506fae5 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -2007,14 +2007,14 @@ limited to R.") (define-public r-backports (package (name "r-backports") - (version "1.1.1") + (version "1.1.2") (source (origin (method url-fetch) (uri (cran-uri "backports" version)) (sha256 (base32 - "15w8psmv203wzijrk4hvwaw3i4byh2m5s09yrkqwhfckhaj82kj9")))) + "0mml9h3xagi7144pyb3jj9zbh9qzns7izkhdg7df20v7bikr6nz8")))) (build-system r-build-system) (home-page "http://cran.r-project.org/web/packages/backports") (synopsis "Reimplementations of functions introduced since R 3.0.0") From 004e108aadce3017a0ec76ce56bb23fd0818dcbe Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 19 Dec 2017 20:09:46 +0100 Subject: [PATCH 36/77] gnu: r-git2r: Update to 0.20.0. * gnu/packages/statistics.scm (r-git2r): Update to 0.20.0. --- 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 dc6506fae5..a6089b90ce 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -2278,13 +2278,13 @@ functions make it easy to control additional request components.") (define-public r-git2r (package (name "r-git2r") - (version "0.19.0") + (version "0.20.0") (source (origin (method url-fetch) (uri (cran-uri "git2r" version)) (sha256 (base32 - "0ws6fbndmaafk2am4dwnz24qizxhld0yh54hgx0z6lzv3p1j209q")))) + "1pqggijvsalb5cc2pr5gwfj3s713s63f4xii1xrd0qagfgbgz846")))) (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 0300cacae1f9d65c6f962e7e8fe5125770927cc7 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 19 Dec 2017 20:10:00 +0100 Subject: [PATCH 37/77] gnu: r-plotrix: Update to 3.7. * gnu/packages/statistics.scm (r-plotrix): Update to 3.7. --- 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 a6089b90ce..f74e3812db 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -2415,13 +2415,13 @@ disk (or a connection).") (define-public r-plotrix (package (name "r-plotrix") - (version "3.6-6") + (version "3.7") (source (origin (method url-fetch) (uri (cran-uri "plotrix" version)) (sha256 (base32 - "07hywp3ym0gbpqdj3f4vhr0bhmynhby8vh6p1b9cm2hv26pzs9q4")))) + "0rw81n9p3d2i03b4pgcfj5blryc94f29bm9a4j9bnp5h8qjj6pry")))) (build-system r-build-system) (home-page "http://cran.r-project.org/web/packages/plotrix") (synopsis "Various plotting functions") From 102a271870c621aaa8f6f881e6f7ee72d0e8a1a1 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 19 Dec 2017 20:10:21 +0100 Subject: [PATCH 38/77] gnu: r-rcpparmadillo: Update to 0.8.300.1.0. * gnu/packages/statistics.scm (r-rcpparmadillo): Update to 0.8.300.1.0. --- 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 f74e3812db..70f80f6d24 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -2474,13 +2474,13 @@ well as additional utilities such as panel and axis annotation functions.") (define-public r-rcpparmadillo (package (name "r-rcpparmadillo") - (version "0.8.100.1.0") + (version "0.8.300.1.0") (source (origin (method url-fetch) (uri (cran-uri "RcppArmadillo" version)) (sha256 (base32 - "19sghlkslz6llcrjk5pd8c6dsb338jsi4dnwrbbrjkfq6jdr5jlp")))) + "0p6cbnwxgzigf7n5qhqvxdr3nd3pq3c2qq6pskqz7avzf813fy83")))) (properties `((upstream-name . "RcppArmadillo"))) (build-system r-build-system) (native-inputs From 0a1b447e2b94d054d9e4d3bfea95cb89c374bf13 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 19 Dec 2017 20:10:54 +0100 Subject: [PATCH 39/77] gnu: r-rprojroot: Update to 1.3-1. * gnu/packages/statistics.scm (r-rprojroot): Update to 1.3-1. --- 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 70f80f6d24..46f3df0792 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -2545,14 +2545,14 @@ encoder/decoder, round-off-error-free sum and cumsum, etc.") (define-public r-rprojroot (package (name "r-rprojroot") - (version "1.2") + (version "1.3-1") (source (origin (method url-fetch) (uri (cran-uri "rprojroot" version)) (sha256 (base32 - "1fgyxv1zv04sllcclzz089xl6hpdzac7xk61l0l4acb7rqsx5d18")))) + "1jigr2jh3hzy35h94im52yq81lyikw7nfvmbxij84a1b9c32r332")))) (build-system r-build-system) (propagated-inputs `(("r-backports" ,r-backports))) From 4a1945da162d06ff849cd362d66191c0e1d3f530 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 19 Dec 2017 20:11:08 +0100 Subject: [PATCH 40/77] gnu: r-segmented: Update to 0.5-3.0. * gnu/packages/statistics.scm (r-segmented): Update to 0.5-3.0. --- 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 46f3df0792..a02e10c4a4 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -2859,14 +2859,14 @@ statements.") (define-public r-segmented (package (name "r-segmented") - (version "0.5-2.2") + (version "0.5-3.0") (source (origin (method url-fetch) (uri (cran-uri "segmented" version)) (sha256 (base32 - "1wdjxkgqjqw5q2nywmgkf6y21lb0alhvaqg0m0dr2xyxf1ii79rs")))) + "0nrik5fyq59hwiwjcpbi4p5yfavgfjq6wyrynhkrbm4k6v1g1wlq")))) (build-system r-build-system) (home-page "http://cran.r-project.org/web/packages/segmented") (synopsis "Regression models with breakpoints estimation") From d2dc69b8be18d8261babeef3ad329594f1775585 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 19 Dec 2017 20:11:26 +0100 Subject: [PATCH 41/77] gnu: r-iterators: Update to 1.0.9. * gnu/packages/statistics.scm (r-iterators): Update to 1.0.9. --- 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 a02e10c4a4..4d1825def6 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -2923,14 +2923,14 @@ standard R subsetting and Kronecker products.") (define-public r-iterators (package (name "r-iterators") - (version "1.0.8") + (version "1.0.9") (source (origin (method url-fetch) (uri (cran-uri "iterators" version)) (sha256 (base32 - "1f057pabs7ss9h1n244can26qsi5n2k3salrdk0b0vkphlrs4kmf")))) + "16sycjq912ix52fjxjhcwiaqr0yj1v5iqmrvjljd3z857031w06y")))) (build-system r-build-system) (home-page "http://cran.r-project.org/web/packages/iterators") (synopsis "Iterator construct for R") From 83b0e1d53f4cea39902ace30c7163ecc1ee6a8cb Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 19 Dec 2017 20:11:41 +0100 Subject: [PATCH 42/77] gnu: r-registry: Update to 0.5. * gnu/packages/statistics.scm (r-registry): Update to 0.5. --- 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 4d1825def6..18beeefc5d 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -3144,14 +3144,14 @@ options and registries, vignette, unit test and bibtex related utilities.") (define-public r-registry (package (name "r-registry") - (version "0.3") + (version "0.5") (source (origin (method url-fetch) (uri (cran-uri "registry" version)) (sha256 (base32 - "0c7lscfxncwwd8zp46h2xfw9gw14dypqv6m2kx85xjhjh0xw99aq")))) + "1yqfl1g6vsl28zn8brzc39659k8lqsmfms7900j7p64ilydyb2sx")))) (build-system r-build-system) (home-page "http://cran.r-project.org/web/packages/registry") (synopsis "Infrastructure for R package registries") From f9f1291bc06cf223b1ca71a4b06435fe4c27faf3 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 19 Dec 2017 20:11:57 +0100 Subject: [PATCH 43/77] gnu: r-ade4: Update to 1.7-10. * gnu/packages/statistics.scm (r-ade4): Update to 1.7-10. [propagated-inputs]: Add r-mass. --- gnu/packages/statistics.scm | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 18beeefc5d..43c95de267 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -1898,15 +1898,17 @@ chain.") (define-public r-ade4 (package (name "r-ade4") - (version "1.7-8") + (version "1.7-10") (source (origin (method url-fetch) (uri (cran-uri "ade4" version)) (sha256 (base32 - "1a5p3wf8l9cp1bjp57b1pc5bqs39kw1v21i4waj9j18wawzlmpb6")))) + "0zk81x0yn30gbyc0jpzyw1nxd08ccihl6vyk0ijvj3aw3nr5flc6")))) (build-system r-build-system) + (propagated-inputs + `(("r-mass" ,r-mass))) (home-page "http://pbil.univ-lyon1.fr/ADE-4") (synopsis "Multivariate data analysis and graphical display") (description From 5378f38332b5730d34f8dbd5dab71a547b6dcf02 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 19 Dec 2017 20:12:25 +0100 Subject: [PATCH 44/77] gnu: r-curl: Update to 3.1. * gnu/packages/web.scm (r-curl): Update to 3.1. --- 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 514003755c..a1a21c5eb6 100644 --- a/gnu/packages/web.scm +++ b/gnu/packages/web.scm @@ -3907,13 +3907,13 @@ LaTeX.") (define-public r-curl (package (name "r-curl") - (version "3.0") + (version "3.1") (source (origin (method url-fetch) (uri (cran-uri "curl" version)) (sha256 (base32 - "01m52jz2q38yc32xbnmpm48hck2xj9fyhxq262p04y67gjpf7y3v")))) + "15fbjya2xrf2k9hhvg3frisrram4yk5wlfz67zj1z8ahpsb2a3r7")))) (build-system r-build-system) (arguments `(#:phases From 02cdb45f345da30a04c384b6763e9f9dc6503801 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 19 Dec 2017 20:12:46 +0100 Subject: [PATCH 45/77] gnu: Add r-truncnorm. * gnu/packages/cran.scm (r-truncnorm): New variable. --- gnu/packages/cran.scm | 20 ++++++++++++++++++++ 1 file changed, 20 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index a52a4e928c..eafc489deb 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -1444,6 +1444,26 @@ imputations.") ;; Any of these two versions. (license (list license:gpl2 license:gpl3)))) +(define-public r-truncnorm + (package + (name "r-truncnorm") + (version "1.0-7") + (source + (origin + (method url-fetch) + (uri (cran-uri "truncnorm" version)) + (sha256 + (base32 + "1qac05z50618y4bw1d7yznsli1bv82s0g8h37iacrjrdkv87bmy7")))) + (build-system r-build-system) + (home-page "http://cran.r-project.org/web/packages/truncnorm/") + (synopsis "Truncated normal distribution") + (description "This package provides functions for the truncated normal +distribution with mean equal to @code{mean} and standard deviation equal to +@code{sd}. It includes density, distribution, quantile, and expected value +functions, as well as a random generation function.") + (license license:gpl2))) + (define-public r-hardyweinberg (package (name "r-hardyweinberg") From cb8b4c119645f1889ec342bed4394fac52e0b741 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 19 Dec 2017 20:13:04 +0100 Subject: [PATCH 46/77] gnu: Add r-rsolnp. * gnu/packages/cran.scm (r-rsolnp): New variable. --- gnu/packages/cran.scm | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index eafc489deb..851eca1079 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -1464,6 +1464,29 @@ distribution with mean equal to @code{mean} and standard deviation equal to functions, as well as a random generation function.") (license license:gpl2))) +(define-public r-rsolnp + (package + (name "r-rsolnp") + (version "1.16") + (source + (origin + (method url-fetch) + (uri (cran-uri "Rsolnp" version)) + (sha256 + (base32 + "0w7nkj6igr0gi7r7jg950lsx7dj6aipgxi6vbjsf5f5yc9h7fhii")))) + (properties `((upstream-name . "Rsolnp"))) + (build-system r-build-system) + (propagated-inputs + `(("r-truncnorm" ,r-truncnorm))) + (home-page "http://cran.r-project.org/web/packages/Rsolnp/") + (synopsis "General non-linear optimization") + (description "The Rsolnp package implements a general non-linear augmented +Lagrange multiplier method solver, a @dfn{sequential quadratic +programming} (SQP) based solver).") + ;; Any version of the GPL. + (license license:gpl2+))) + (define-public r-hardyweinberg (package (name "r-hardyweinberg") From d03949449a1d5ec5042ffaf1e6a42354e1229e3c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 19 Dec 2017 20:13:16 +0100 Subject: [PATCH 47/77] gnu: r-hardyweinberg: Update to 1.5.9. * gnu/packages/cran.scm (r-hardyweinberg): Update to 1.5.9. [propagated-inputs]: Add r-rsolnp. --- gnu/packages/cran.scm | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 851eca1079..3a3fc31bd0 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -1490,19 +1490,20 @@ programming} (SQP) based solver).") (define-public r-hardyweinberg (package (name "r-hardyweinberg") - (version "1.5.8") + (version "1.5.9") (source (origin (method url-fetch) (uri (cran-uri "HardyWeinberg" version)) (sha256 (base32 - "0xbcchmzii0jv0ygr91n72r39j1axraxd2i607b56v4yd5d8sy4k")))) + "0qk3lly5qczn61rj0q9xzscppspvk238yjgr4p71pkzkjhiv40jz")))) (properties `((upstream-name . "HardyWeinberg"))) (build-system r-build-system) (propagated-inputs `(("r-mice" ,r-mice) - ("r-rcpp" ,r-rcpp))) + ("r-rcpp" ,r-rcpp) + ("r-rsolnp" ,r-rsolnp))) (home-page "https://cran.r-project.org/package=HardyWeinberg") (synopsis "Statistical tests and graphics for Hardy-Weinberg equilibrium") (description From 2976f304e2f926f6efbb436c3e4ba600d13ac939 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 19 Dec 2017 20:13:42 +0100 Subject: [PATCH 48/77] gnu: Add r-cli. * gnu/packages/cran.scm (r-cli): New variable. --- gnu/packages/cran.scm | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 3a3fc31bd0..9b80b68984 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -1817,3 +1817,25 @@ plots in @code{ggplot2}.") distributions over time or space. This package enables the creation of such plots in @code{ggplot2}.") (license license:gpl2))) + +(define-public r-cli + (package + (name "r-cli") + (version "1.0.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "cli" version)) + (sha256 + (base32 + "07as3dr7vwx02p3qgzlmxz1dlrd3x3lysrzp222ip9jcjpydp8wg")))) + (build-system r-build-system) + (propagated-inputs + `(("r-assertthat" ,r-assertthat) + ("r-crayon" ,r-crayon))) + (home-page "https://github.com/r-lib/cli#readme") + (synopsis "Helpers for developing command line interfaces") + (description "This package provides a suite of tools designed to build +attractive command line interfaces (CLIs). It includes tools for drawing +rules, boxes, trees, and Unicode symbols with ASCII alternatives.") + (license license:expat))) From aead9e1bc53b2908764ce2c4f27e1c6748f6abf0 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 19 Dec 2017 20:13:56 +0100 Subject: [PATCH 49/77] gnu: r-testthat: Update to 2.0.0. * gnu/packages/statistics.scm (r-testthat): Update to 2.0.0. [propagated-inputs]: Add r-cli, r-rlang, and r-withr. --- gnu/packages/statistics.scm | 11 +++++++---- 1 file changed, 7 insertions(+), 4 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 43c95de267..f92f6d3904 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -1502,20 +1502,23 @@ R packages that praise their users.") (define-public r-testthat (package (name "r-testthat") - (version "1.0.2") + (version "2.0.0") (source (origin (method url-fetch) (uri (cran-uri "testthat" version)) (sha256 (base32 - "0pj1r01x4ny4capr83dfa19hi5i2sjjxky99schzip8zrq5dzxqf")))) + "155l53kb69jga5d8c5nvdwqlvlgfmk4vzyyl4d0108j53jnlgh1v")))) (build-system r-build-system) (propagated-inputs - `(("r-digest" ,r-digest) + `(("r-cli" ,r-cli) ("r-crayon" ,r-crayon) + ("r-digest" ,r-digest) ("r-magrittr" ,r-magrittr) ("r-praise" ,r-praise) - ("r-r6" ,r-r6))) + ("r-r6" ,r-r6) + ("r-rlang" ,r-rlang) + ("r-withr" ,r-withr))) (home-page "https://github.com/hadley/testthat") (synopsis "Unit testing for R") (description From 57ae890fb3ae49878de9ef648d9c4dc397a99989 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 19 Dec 2017 20:14:27 +0100 Subject: [PATCH 50/77] gnu: r-htmltable: Update to 1.11.0. * gnu/packages/web.scm (r-htmltable): Update to 1.11.0. [propagated-inputs]: Add r-dplyr, r-htmltools, r-rstudioapi, and r-tidyr. --- gnu/packages/web.scm | 10 +++++++--- 1 file changed, 7 insertions(+), 3 deletions(-) diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm index a1a21c5eb6..6071caefdc 100644 --- a/gnu/packages/web.scm +++ b/gnu/packages/web.scm @@ -3876,22 +3876,26 @@ applications.") (define-public r-htmltable (package (name "r-htmltable") - (version "1.9") + (version "1.11.0") (source (origin (method url-fetch) (uri (cran-uri "htmlTable" version)) (sha256 (base32 - "0ciic1f4iczq14j81fg7kxibn65sy8z1zxkvk1yxnxxg6dzplj2v")))) + "0x0qrzx6igg5z8jh901d2a8g2idpm5f4frwp1m02910scifcrxwf")))) (properties `((upstream-name . "htmlTable"))) (build-system r-build-system) (propagated-inputs `(("r-checkmate" ,r-checkmate) + ("r-dplyr" ,r-dplyr) + ("r-htmltools" ,r-htmltools) ("r-htmlwidgets" ,r-htmlwidgets) ("r-knitr" ,r-knitr) ("r-magrittr" ,r-magrittr) - ("r-stringr" ,r-stringr))) + ("r-rstudioapi" ,r-rstudioapi) + ("r-stringr" ,r-stringr) + ("r-tidyr" ,r-tidyr))) (home-page "http://gforge.se/packages/") (synopsis "Advanced tables for Markdown/HTML") (description From 74c96b0b09929f74e82f31743d2a4aede6705431 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Tue, 19 Dec 2017 14:38:02 -0500 Subject: [PATCH 51/77] gnu: webkitgtk: Update to 2.18.4 [fixes CVE-2017-{7156,13856,13866,13870}]. * gnu/packages/webkit.scm (webkitgtk): Update to 2.18.4. --- gnu/packages/webkit.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/webkit.scm b/gnu/packages/webkit.scm index 89fe9102ed..e2d753aa3d 100644 --- a/gnu/packages/webkit.scm +++ b/gnu/packages/webkit.scm @@ -54,14 +54,14 @@ (define-public webkitgtk (package (name "webkitgtk") - (version "2.18.3") + (version "2.18.4") (source (origin (method url-fetch) (uri (string-append "https://www.webkitgtk.org/releases/" name "-" version ".tar.xz")) (sha256 (base32 - "17lgn7qwrwqxl1lgmq5icvzmna6aymx4c7al47rp0vvac7hj0m71")))) + "1f1j0r996l20cgkvbwpizn7d4yp58cy334b1pvn4kfb5c2dbpdl7")))) (build-system cmake-build-system) (arguments '(#:tests? #f ; no tests From afcbc348a31f576cc87a573ef7ba61b116ec760a Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Wed, 20 Dec 2017 01:20:47 -0500 Subject: [PATCH 52/77] gnu: babl: Update to 0.1.38. * gnu/packages/gimp.scm (babl): Update to 0.1.38. --- gnu/packages/gimp.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/gimp.scm b/gnu/packages/gimp.scm index c820818687..b0797453fa 100644 --- a/gnu/packages/gimp.scm +++ b/gnu/packages/gimp.scm @@ -43,7 +43,7 @@ (define-public babl (package (name "babl") - (version "0.1.30") + (version "0.1.38") (source (origin (method url-fetch) (uri (list (string-append "https://download.gimp.org/pub/babl/" @@ -54,7 +54,7 @@ version ".tar.bz2"))) (sha256 (base32 - "1k2k3phh9ybma2snw6hm8inx2dw1jq6cf7w2aqvi4rfr0rxjrha5")))) + "11pfbyzq20596p9sgwraxspg3djg1jzz6wvz4bapf0yyr97jiyd0")))) (build-system gnu-build-system) (home-page "http://gegl.org/babl/") (synopsis "Image pixel format conversion library") From 09a91adcf8fcb0520bccbb8ae5f0639f002472cd Mon Sep 17 00:00:00 2001 From: Rutger Helling Date: Wed, 20 Dec 2017 08:36:43 +0100 Subject: [PATCH 53/77] gnu: libressl: Update to 2.6.4. * gnu/packages/tls.scm (libressl): Update to 2.6.4. Signed-off-by: Leo Famulari --- gnu/packages/tls.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/tls.scm b/gnu/packages/tls.scm index 75d8c9497e..7d5c85a314 100644 --- a/gnu/packages/tls.scm +++ b/gnu/packages/tls.scm @@ -486,14 +486,14 @@ required structures.") (define-public libressl (package (name "libressl") - (version "2.6.3") + (version "2.6.4") (source (origin (method url-fetch) (uri (string-append "mirror://openbsd/LibreSSL/" name "-" version ".tar.gz")) (sha256 (base32 - "162wgzmg4zzqj5cxrsrmkfv1623dc4g8h3fsf1lvjw9i4sc6bbdf")))) + "07yi37a2ghsgj2b4w30q1s4d2inqnix7ika1m21y57p9z71212k3")))) (build-system gnu-build-system) (arguments ;; Do as if 'getentropy' was missing since older Linux kernels lack it From 8bc6956bbd28b749538d113a214a63a93039537f Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Sat, 2 Dec 2017 18:08:21 -0500 Subject: [PATCH 54/77] gnu: rng-tools: Update to 6.1. Rng-tools development appears to have moved to GitHub [0]: "NOTE: The rng-tools project hasn't seen updates in some time, but is still in active use. To facilitate ongoing development, the rng-tools project is moved to here: https://github.com/nhorman/rng-tools" [0] https://sourceforge.net/p/gkernel/wiki/Home/ * gnu/packages/linux.scm (rng-tools): Update to 6.1. [source]: Use new upstream URL and give a descriptive file-name. [arguments]: Add a 'bootstrap' phase. [native-inputs]: Add autoconf, automake, and pkg-config. [inputs]: Add sysfsutils. --- gnu/packages/linux.scm | 24 +++++++++++++++++++----- 1 file changed, 19 insertions(+), 5 deletions(-) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 7ab2ba84d6..2eb35c92f2 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -3490,16 +3490,30 @@ The following service daemons are also provided: (define-public rng-tools (package (name "rng-tools") - (version "5") + (version "6.1") (source (origin (method url-fetch) - (uri (string-append - "http://downloads.sourceforge.net/sourceforge/gkernel/" - "rng-tools-" version ".tar.gz")) + (uri (string-append "https://github.com/nhorman/rng-tools/" + "archive/v" version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "13h7lc8wl9khhvkr0i3bl5j9bapf8anhqis1lcnwxg1vc2v058b0")))) + "00ywsknjpc9jd9kfmz2syk9l0xkiiwyx5qhl5zvhhc69v6682i31")))) (build-system gnu-build-system) + (arguments + `(;; Avoid using OpenSSL, curl, and libxml2, reducing the closure by 166 MiB. + #:configure-flags '("--without-nistbeacon") + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'bootstrap + (lambda _ + (zero? (system* "sh" "autogen.sh"))))))) + (native-inputs + `(("autoconf" ,autoconf) + ("automake" ,automake) + ("pkg-config" ,pkg-config))) + (inputs + `(("libsysfs" ,sysfsutils))) (synopsis "Random number generator daemon") (description "Monitor a hardware random number generator, and supply entropy From 48a9654ad6a19a9e6b149b8473547404a61de9c3 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Wed, 20 Dec 2017 16:50:28 +0100 Subject: [PATCH 55/77] gnu: exim: Update to 4.90. * gnu/packages/mail.scm (exim): Update to 4.90. --- gnu/packages/mail.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/mail.scm b/gnu/packages/mail.scm index 0423dd7c56..6aedcf7c3a 100644 --- a/gnu/packages/mail.scm +++ b/gnu/packages/mail.scm @@ -1049,7 +1049,7 @@ delivery.") (define-public exim (package (name "exim") - (version "4.89.1") + (version "4.90") (source (origin (method url-fetch) @@ -1059,7 +1059,7 @@ delivery.") version ".tar.bz2"))) (sha256 (base32 - "133sjkcm9wlhpcxflr5v865varc1995bqa1y3vjs1w6zc34kp18w")))) + "1cmx2648zhpsc4pznky7qsqbjazd3wn4gpslbl30j56cv1m6rb3x")))) (build-system gnu-build-system) (inputs `(("bdb" ,bdb) From 5965b08307a61fa5472309ac4f7df86bc6037364 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Fri, 15 Dec 2017 22:56:47 -0500 Subject: [PATCH 56/77] gnu: libassuan: Update to 2.5.1. * gnu/packages/gnupg.scm (libassuan): Update to 2.5.1. --- gnu/packages/gnupg.scm | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/gnu/packages/gnupg.scm b/gnu/packages/gnupg.scm index 336cd8f741..4d93044195 100644 --- a/gnu/packages/gnupg.scm +++ b/gnu/packages/gnupg.scm @@ -140,7 +140,7 @@ generation.") (define-public libassuan (package (name "libassuan") - (version "2.4.4") + (version "2.5.1") (source (origin (method url-fetch) @@ -148,10 +148,11 @@ generation.") version ".tar.bz2")) (sha256 (base32 - "18bwffjkx9pn0lawbsn6zhd90i7xhjgpf9b0nl5xw9134w1a2scy")))) + "0jb4nb4nrjr949gd3lw8lh4v5d6qigxaq6xwy24w5apjnhvnrya7")))) (build-system gnu-build-system) (propagated-inputs - `(("libgpg-error" ,libgpg-error) ("pth" ,pth))) + `(("libgpg-error" ,libgpg-error) + ("pth" ,pth))) (home-page "https://gnupg.org") (synopsis "IPC library used by GnuPG and related software") From e6f63412c9abe6a3b4ddf0ce39735d1e2a65491d Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Wed, 20 Dec 2017 03:20:09 -0500 Subject: [PATCH 57/77] gnu: python-pygpgme: Use GnuPG 1 for the test suite. * gnu/packages/gnupg.scm (python-pygpgme, python2-pygpgme)[inputs]: Use gnupg-1 and make it a native-input. --- gnu/packages/gnupg.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/gnu/packages/gnupg.scm b/gnu/packages/gnupg.scm index 4d93044195..a9b097b212 100644 --- a/gnu/packages/gnupg.scm +++ b/gnu/packages/gnupg.scm @@ -492,9 +492,10 @@ distributed separately.") (lambda _ (zero? (system* "make" "check"))))))) (build-system python-build-system) + (native-inputs + `(("gnupg" ,gnupg-1))) (inputs - `(("gnupg" ,gnupg-2.0) - ("gpgme" ,gpgme))) + `(("gpgme" ,gpgme))) (home-page "https://launchpad.net/pygpgme") (synopsis "Python module for working with OpenPGP messages") (description From 0e06bec250f34dbab378b2c1e937af75db900bcc Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Wed, 20 Dec 2017 03:20:01 -0500 Subject: [PATCH 58/77] gnu: gpgme: Build with the latest GnuPG. * gnu/packages/gnupg.scm (gpgme)[inputs]: Use the latest gnupg package. [arguments]: Keep a reference to the gnupg package used for build. --- gnu/packages/gnupg.scm | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/gnu/packages/gnupg.scm b/gnu/packages/gnupg.scm index a9b097b212..7a791aecd2 100644 --- a/gnu/packages/gnupg.scm +++ b/gnu/packages/gnupg.scm @@ -385,10 +385,14 @@ libskba (working with X.509 certificates and CMS data).") ;; Needs to be propagated because gpgme.h includes gpg-error.h. `(("libgpg-error" ,libgpg-error))) (inputs - `(("gnupg" ,gnupg-2.0) + `(("gnupg" ,gnupg) ("libassuan" ,libassuan))) (arguments - `(#:phases + `(#:configure-flags + (list (string-append "--enable-fixed-path=" + (assoc-ref %build-inputs "gnupg") + "/bin")) + #:phases (modify-phases %standard-phases (add-after 'configure 'patch-cmake-file (lambda _ From 4305176096d192e09673b05e7a1049501607b809 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 20 Dec 2017 23:18:24 +0100 Subject: [PATCH 59/77] gnu: microscheme: Fix home page. * gnu/packages/avr.scm (microscheme)[home-page]: Use GitHub project page. Fixes . --- gnu/packages/avr.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/avr.scm b/gnu/packages/avr.scm index ecb7cd19a8..e9e93cbb9a 100644 --- a/gnu/packages/avr.scm +++ b/gnu/packages/avr.scm @@ -158,7 +158,7 @@ C++.") (native-inputs `(("unzip" ,unzip) ("xxd" ,xxd))) - (home-page "http://microscheme.org/") + (home-page "https://github.com/ryansuchocki/microscheme/") (synopsis "Scheme subset for Atmel microcontrollers") (description "Microscheme, or @code{(ms)} for short, is a functional programming From 770635e11df514d96da4583d2c21d3c4bb2292ff Mon Sep 17 00:00:00 2001 From: Mark H Weaver Date: Wed, 20 Dec 2017 18:27:08 -0500 Subject: [PATCH 60/77] gnu: linux-libre@4.4: Update to 4.4.107. * gnu/packages/linux.scm (linux-libre-4.4): Update to 4.4.107. --- 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 2eb35c92f2..ca7115ecac 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -390,8 +390,8 @@ It has been modified to remove all non-free binary blobs.") #:configuration-file kernel-config)) (define-public linux-libre-4.4 - (make-linux-libre "4.4.106" - "1dn67fl8lbckjxcra1d02fqjald71cxp4fq3bld4wc1r4saanqi7" + (make-linux-libre "4.4.107" + "0pfzv15c1qj7a77n8cdmsi77yhlbzv35y7qa03j0b96ajwjsclsp" %intel-compatible-systems #:configuration-file kernel-config)) From 0786e4bd12639a306a6f038e9f1f5dbb5d2ac4d9 Mon Sep 17 00:00:00 2001 From: Mark H Weaver Date: Wed, 20 Dec 2017 18:27:48 -0500 Subject: [PATCH 61/77] gnu: linux-libre@4.9: Update to 4.9.71. * gnu/packages/linux.scm (linux-libre-4.9): Update to 4.9.71. --- 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 ca7115ecac..8b94319dbb 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -384,8 +384,8 @@ It has been modified to remove all non-free binary blobs.") #:configuration-file kernel-config)) (define-public linux-libre-4.9 - (make-linux-libre "4.9.70" - "1bwfk68zzwmznhf3zv858wpav2r43g7hg4wxcdyfamy8k38v0r43" + (make-linux-libre "4.9.71" + "0z4m77zbndlqy43bgl1xhklpjilbvrhbfbcppc55z3f61qwjf0mc" %intel-compatible-systems #:configuration-file kernel-config)) From 66df43b9aeeba1779f4455d551fee900887a0779 Mon Sep 17 00:00:00 2001 From: Mark H Weaver Date: Wed, 20 Dec 2017 18:28:36 -0500 Subject: [PATCH 62/77] gnu: linux-libre: Update to 4.14.8. * gnu/packages/linux.scm (%linux-libre-version): Update to 4.14.8. (%linux-libre-hash): Update hash. --- 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 8b94319dbb..ae705f10cd 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -370,8 +370,8 @@ It has been modified to remove all non-free binary blobs.") (define %intel-compatible-systems '("x86_64-linux" "i686-linux")) (define %linux-compatible-systems '("x86_64-linux" "i686-linux" "armhf-linux")) -(define %linux-libre-version "4.14.7") -(define %linux-libre-hash "1hwmg4mqpm3n6qxcjl01fbl3pbbirw9727jzfc7gy6livifyibfi") +(define %linux-libre-version "4.14.8") +(define %linux-libre-hash "0y8nggpdgfqfx6dy5k39vj552k5mxamwjn6mldwrhs2aqpsrbwr3") ;; linux-libre configuration for armhf-linux is derived from Debian armmp. It ;; supports qemu "virt" machine and possibly a large number of ARM boards. From dacd8cf2e8ac4adc25f6e2306a30849295dbb291 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Wed, 20 Dec 2017 20:06:14 -0500 Subject: [PATCH 63/77] gnu: links: Fix-CVE-2017-11114. * gnu/packages/patches/links-CVE-2017-11114.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/web-browsers.scm (links)[source]: Use it. --- gnu/local.mk | 1 + .../patches/links-CVE-2017-11114.patch | 99 +++++++++++++++++++ gnu/packages/web-browsers.scm | 1 + 3 files changed, 101 insertions(+) create mode 100644 gnu/packages/patches/links-CVE-2017-11114.patch diff --git a/gnu/local.mk b/gnu/local.mk index efb91fd826..f583a61c66 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -855,6 +855,7 @@ dist_patch_DATA = \ %D%/packages/patches/lierolibre-newer-libconfig.patch \ %D%/packages/patches/lierolibre-remove-arch-warning.patch \ %D%/packages/patches/lierolibre-try-building-other-arch.patch \ + %D%/packages/patches/links-CVE-2017-11114.patch \ %D%/packages/patches/linux-pam-no-setfsuid.patch \ %D%/packages/patches/lirc-localstatedir.patch \ %D%/packages/patches/llvm-3.5-fix-clang-build-with-gcc5.patch \ diff --git a/gnu/packages/patches/links-CVE-2017-11114.patch b/gnu/packages/patches/links-CVE-2017-11114.patch new file mode 100644 index 0000000000..c5ac9884b5 --- /dev/null +++ b/gnu/packages/patches/links-CVE-2017-11114.patch @@ -0,0 +1,99 @@ +Fix CVE-2017-11114: + +https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2017-11114 +http://seclists.org/fulldisclosure/2017/Jul/76 + +Patch copied from Debian: + +https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=870299#12 + +Origin: upstream, commit: fee5dca79a93a37024e494b985386a5fe60bc1b7 +Origin: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=870299#12 +Author: Mikulas Patocka +Date: Wed Aug 2 20:13:29 2017 +0200 +Subject: Fix read out of memory in case of corrupted UTF-8 data + +--- + charsets.c | 37 +------------------------------------ + links.h | 9 ++++----- + 2 files changed, 5 insertions(+), 41 deletions(-) + +Index: links-2.14/charsets.c +=================================================================== +--- links-2.14.orig/charsets.c ++++ links-2.14/charsets.c +@@ -215,41 +215,6 @@ static struct conv_table *get_translatio + return utf_table; + } + +-unsigned short int utf8_2_uni_table[0x200] = { +- 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, +- 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, +- 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, +- 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, +- 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, +- 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, +- 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, +- 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, +- 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, +- 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, +- 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, +- 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, +- 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, +- 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, +- 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, +- 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, +- 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 128, 0, 0, 0, 192, 0, +- 0, 0, 256, 0, 0, 0, 320, 0, 0, 0, 384, 0, 0, 0, 448, 0, +- 0, 0, 512, 0, 0, 0, 576, 0, 0, 0, 640, 0, 0, 0, 704, 0, +- 0, 0, 768, 0, 0, 0, 832, 0, 0, 0, 896, 0, 0, 0, 960, 0, +- 0, 0, 1024, 0, 0, 0, 1088, 0, 0, 0, 1152, 0, 0, 0, 1216, 0, +- 0, 0, 1280, 0, 0, 0, 1344, 0, 0, 0, 1408, 0, 0, 0, 1472, 0, +- 0, 0, 1536, 0, 0, 0, 1600, 0, 0, 0, 1664, 0, 0, 0, 1728, 0, +- 0, 0, 1792, 0, 0, 0, 1856, 0, 0, 0, 1920, 0, 0, 0, 1984, 0, +- 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, +- 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, +- 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, +- 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, +- 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, +- 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, +- 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, +- 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, +-}; +- + unsigned char utf_8_1[256] = { + 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, + 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, +@@ -269,7 +234,7 @@ unsigned char utf_8_1[256] = { + 3, 3, 3, 3, 3, 3, 3, 3, 2, 2, 2, 2, 1, 1, 6, 6, + }; + +-static_const unsigned min_utf_8[9] = { ++static_const unsigned min_utf_8[8] = { + 0, 0x4000000, 0x200000, 0x10000, 0x800, 0x80, 0x100, 0x1, + }; + +Index: links-2.14/links.h +=================================================================== +--- links-2.14.orig/links.h ++++ links-2.14/links.h +@@ -3906,15 +3906,14 @@ unsigned char *cp_strchr(int charset, un + void init_charset(void); + + unsigned get_utf_8(unsigned char **p); +-extern unsigned short int utf8_2_uni_table[0x200]; + #define GET_UTF_8(s, c) \ + do { \ + if ((unsigned char)(s)[0] < 0x80) \ + (c) = (s)++[0]; \ +- else if (((c) = utf8_2_uni_table[((unsigned char)(s)[0] << 2) + \ +- ((unsigned char)(s)[1] >> 6) - 0x200])) \ +- (c) += (unsigned char)(s)[1] & 0x3f, (s) += 2; \ +- else \ ++ else if ((unsigned char)(s)[0] >= 0xc2 && (unsigned char)(s)[0] < 0xe0 &&\ ++ ((unsigned char)(s)[1] & 0xc0) == 0x80) { \ ++ (c) = (unsigned char)(s)[0] * 0x40 + (unsigned char)(s)[1], (c) -= 0x3080, (s) += 2;\ ++ } else \ + (c) = get_utf_8(&(s)); \ + } while (0) + #define FWD_UTF_8(s) \ diff --git a/gnu/packages/web-browsers.scm b/gnu/packages/web-browsers.scm index 385147c379..95d2878835 100644 --- a/gnu/packages/web-browsers.scm +++ b/gnu/packages/web-browsers.scm @@ -83,6 +83,7 @@ older or slower computers and embedded systems.") (method url-fetch) (uri (string-append "http://links.twibright.com/download/" name "-" version ".tar.bz2")) + (patches (search-patches "links-CVE-2017-11114.patch")) (sha256 (base32 "1f24y83wa1vzzjq5kp857gjqdpnmf8pb29yw7fam0m8wxxw0c3gp")))) From fa79a908bb06f0c54b34334da57909b048f14995 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Wed, 20 Dec 2017 17:17:02 +0100 Subject: [PATCH 64/77] gnu: Add perl-test-requiresinternet. * gnu/packages/perl-check.scm (perl-test-requiresinternet): New public variable. --- gnu/packages/perl-check.scm | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) diff --git a/gnu/packages/perl-check.scm b/gnu/packages/perl-check.scm index b1d1f08150..5df2940bd6 100644 --- a/gnu/packages/perl-check.scm +++ b/gnu/packages/perl-check.scm @@ -869,6 +869,30 @@ checks for pod coverage of all appropriate files.") If this fails, then rather than failing tests this skips all tests.") (license perl-license))) +(define-public perl-test-requiresinternet + (package + (name "perl-test-requiresinternet") + (version "0.05") + (source + (origin + (method url-fetch) + (uri (string-append + "mirror://cpan/authors/id/M/MA/MALLEN/Test-RequiresInternet-" + version + ".tar.gz")) + (sha256 + (base32 + "0gl33vpj9bb78pzyijp884b66sbw6jkh1ci0xki8rmf03hmb79xv")))) + (build-system perl-build-system) + (home-page "http://search.cpan.org/dist/Test-RequiresInternet/") + (synopsis "Easily test network connectivity when running tests") + (description + "This Perl module is intended to easily test network connectivity to +non-local Internet resources before functional tests begin. If the sockets +cannot connect to the specified hosts and ports, the exception is caught and +reported, and the tests skipped.") + (license perl-license))) + (define-public perl-test-script (package (name "perl-test-script") From 91213c384b62bc422896d39005efa922e4fa75f2 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Thu, 21 Dec 2017 02:40:30 +0100 Subject: [PATCH 65/77] gnu: weechat: Update to 2.0.1. * gnu/packages/irc.scm (weechat): Update to 2.0.1. --- gnu/packages/irc.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/irc.scm b/gnu/packages/irc.scm index fbcc0b6f1b..0e0813c1cb 100644 --- a/gnu/packages/irc.scm +++ b/gnu/packages/irc.scm @@ -153,14 +153,14 @@ SILC and ICB protocols via plugins.") (define-public weechat (package (name "weechat") - (version "2.0") + (version "2.0.1") (source (origin (method url-fetch) (uri (string-append "https://weechat.org/files/src/weechat-" version ".tar.xz")) (sha256 (base32 - "1ix2izrlr5jx5vl49kz9jbib7cq9mr6i7iyxkcz6xjfrryx2s5x9")) + "1l854dramvn9vfba7jpazkjwm4k4i5pshq58vjv6z2mxmcp5hhv9")) (patches (search-patches "weechat-python.patch")))) (build-system cmake-build-system) (native-inputs `(("gettext" ,gettext-minimal) From dab2542f845bf1b6b7761f1be6fc55b9259238fe Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Thu, 21 Dec 2017 01:53:48 -0500 Subject: [PATCH 66/77] gnu: mupdf: Update to 1.12.0 [fixes CVE-2017-15369]. * gnu/packages/pdf.scm (mupdf): Update to 1.12.0. [source]: Remove obsolete patches. [inputs]: Add freeglut. * gnu/packages/patches/mupdf-CVE-2017-14685.patch, gnu/packages/patches/mupdf-CVE-2017-14686.patch, gnu/packages/patches/mupdf-CVE-2017-14687.patch, gnu/packages/patches/mupdf-CVE-2017-15587.patch: Delete files. * gnu/local.mk (dist_patch_DATA): Remove them. * gnu/packages/patches/mupdf-build-with-openjpeg-2.1.patch: Update and rename to... * gnu/packages/patches/mupdf-build-with-latest-openjpeg.patch: ... new file. --- gnu/local.mk | 6 +- .../patches/mupdf-CVE-2017-14685.patch | 34 ----- .../patches/mupdf-CVE-2017-14686.patch | 34 ----- .../patches/mupdf-CVE-2017-14687.patch | 130 ------------------ .../patches/mupdf-CVE-2017-15587.patch | 25 ---- ...=> mupdf-build-with-latest-openjpeg.patch} | 8 +- gnu/packages/pdf.scm | 13 +- 7 files changed, 10 insertions(+), 240 deletions(-) delete mode 100644 gnu/packages/patches/mupdf-CVE-2017-14685.patch delete mode 100644 gnu/packages/patches/mupdf-CVE-2017-14686.patch delete mode 100644 gnu/packages/patches/mupdf-CVE-2017-14687.patch delete mode 100644 gnu/packages/patches/mupdf-CVE-2017-15587.patch rename gnu/packages/patches/{mupdf-build-with-openjpeg-2.1.patch => mupdf-build-with-latest-openjpeg.patch} (69%) diff --git a/gnu/local.mk b/gnu/local.mk index f583a61c66..8ffcc58005 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -897,11 +897,7 @@ dist_patch_DATA = \ %D%/packages/patches/mozjs38-tracelogger.patch \ %D%/packages/patches/mozjs38-version-detection.patch \ %D%/packages/patches/mumps-build-parallelism.patch \ - %D%/packages/patches/mupdf-build-with-openjpeg-2.1.patch \ - %D%/packages/patches/mupdf-CVE-2017-14685.patch \ - %D%/packages/patches/mupdf-CVE-2017-14686.patch \ - %D%/packages/patches/mupdf-CVE-2017-14687.patch \ - %D%/packages/patches/mupdf-CVE-2017-15587.patch \ + %D%/packages/patches/mupdf-build-with-latest-openjpeg.patch \ %D%/packages/patches/mupen64plus-ui-console-notice.patch \ %D%/packages/patches/mutt-store-references.patch \ %D%/packages/patches/ncurses-CVE-2017-10684-10685.patch \ diff --git a/gnu/packages/patches/mupdf-CVE-2017-14685.patch b/gnu/packages/patches/mupdf-CVE-2017-14685.patch deleted file mode 100644 index 3fcce5fedf..0000000000 --- a/gnu/packages/patches/mupdf-CVE-2017-14685.patch +++ /dev/null @@ -1,34 +0,0 @@ -Fix CVE-2017-14685: - -https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2017-14685 - -Patch copied from upstream source repository: - -https://git.ghostscript.com/?p=mupdf.git;h=ab1a420613dec93c686acbee2c165274e922f82a - -From ab1a420613dec93c686acbee2c165274e922f82a Mon Sep 17 00:00:00 2001 -From: Tor Andersson -Date: Tue, 19 Sep 2017 15:23:04 +0200 -Subject: [PATCH] Fix 698539: Don't use xps font if it could not be loaded. - -xps_load_links_in_glyphs did not cope with font loading failures. ---- - source/xps/xps-link.c | 2 ++ - 1 file changed, 2 insertions(+) - -diff --git a/source/xps/xps-link.c b/source/xps/xps-link.c -index c07e0d7..c26a8d9 100644 ---- a/source/xps/xps-link.c -+++ b/source/xps/xps-link.c -@@ -91,6 +91,8 @@ xps_load_links_in_glyphs(fz_context *ctx, xps_document *doc, const fz_matrix *ct - bidi_level = atoi(bidi_level_att); - - font = xps_lookup_font(ctx, doc, base_uri, font_uri_att, style_att); -+ if (!font) -+ return; - text = xps_parse_glyphs_imp(ctx, doc, &local_ctm, font, fz_atof(font_size_att), - fz_atof(origin_x_att), fz_atof(origin_y_att), - is_sideways, bidi_level, indices_att, unicode_att); --- -2.9.1 - diff --git a/gnu/packages/patches/mupdf-CVE-2017-14686.patch b/gnu/packages/patches/mupdf-CVE-2017-14686.patch deleted file mode 100644 index e462a6ffeb..0000000000 --- a/gnu/packages/patches/mupdf-CVE-2017-14686.patch +++ /dev/null @@ -1,34 +0,0 @@ -Fix CVE-2017-14686: - -https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2017-14686 - -Patch copied from upstream source repository: - -https://git.ghostscript.com/?p=mupdf.git;h=0f0fbc07d9be31f5e83ec5328d7311fdfd8328b1 - -From 0f0fbc07d9be31f5e83ec5328d7311fdfd8328b1 Mon Sep 17 00:00:00 2001 -From: Tor Andersson -Date: Tue, 19 Sep 2017 16:33:38 +0200 -Subject: [PATCH] Fix 698540: Check name, comment and meta size field signs. - ---- - source/fitz/unzip.c | 3 +++ - 1 file changed, 3 insertions(+) - -diff --git a/source/fitz/unzip.c b/source/fitz/unzip.c -index f2d4f32..0bcce0f 100644 ---- a/source/fitz/unzip.c -+++ b/source/fitz/unzip.c -@@ -141,6 +141,9 @@ static void read_zip_dir_imp(fz_context *ctx, fz_zip_archive *zip, int start_off - (void) fz_read_int32_le(ctx, file); /* ext file atts */ - offset = fz_read_int32_le(ctx, file); - -+ if (namesize < 0 || metasize < 0 || commentsize < 0) -+ fz_throw(ctx, FZ_ERROR_GENERIC, "invalid size in zip entry"); -+ - name = fz_malloc(ctx, namesize + 1); - n = fz_read(ctx, file, (unsigned char*)name, namesize); - if (n < (size_t)namesize) --- -2.9.1 - diff --git a/gnu/packages/patches/mupdf-CVE-2017-14687.patch b/gnu/packages/patches/mupdf-CVE-2017-14687.patch deleted file mode 100644 index cdc41df813..0000000000 --- a/gnu/packages/patches/mupdf-CVE-2017-14687.patch +++ /dev/null @@ -1,130 +0,0 @@ -Fix CVE-2017-14687: - -https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2017-14687 - -Patch copied from upstream source repository: - -https://git.ghostscript.com/?p=mupdf.git;h=2b16dbd8f73269cb15ca61ece75cf8d2d196ed28 - -From 2b16dbd8f73269cb15ca61ece75cf8d2d196ed28 Mon Sep 17 00:00:00 2001 -From: Tor Andersson -Date: Tue, 19 Sep 2017 17:17:12 +0200 -Subject: [PATCH] Fix 698558: Handle non-tags in tag name comparisons. - -Use fz_xml_is_tag instead of fz_xml_tag && !strcmp idiom. ---- - source/html/css-apply.c | 2 +- - source/svg/svg-run.c | 2 +- - source/xps/xps-common.c | 6 +++--- - source/xps/xps-glyphs.c | 2 +- - source/xps/xps-path.c | 4 ++-- - source/xps/xps-resource.c | 2 +- - 6 files changed, 9 insertions(+), 9 deletions(-) - -diff --git a/source/html/css-apply.c b/source/html/css-apply.c -index de55490..6a91df0 100644 ---- a/source/html/css-apply.c -+++ b/source/html/css-apply.c -@@ -328,7 +328,7 @@ match_selector(fz_css_selector *sel, fz_xml *node) - - if (sel->name) - { -- if (strcmp(sel->name, fz_xml_tag(node))) -+ if (!fz_xml_is_tag(node, sel->name)) - return 0; - } - -diff --git a/source/svg/svg-run.c b/source/svg/svg-run.c -index f974c67..5302c64 100644 ---- a/source/svg/svg-run.c -+++ b/source/svg/svg-run.c -@@ -1044,7 +1044,7 @@ svg_run_use(fz_context *ctx, fz_device *dev, svg_document *doc, fz_xml *root, co - fz_xml *linked = fz_tree_lookup(ctx, doc->idmap, xlink_href_att + 1); - if (linked) - { -- if (!strcmp(fz_xml_tag(linked), "symbol")) -+ if (fz_xml_is_tag(linked, "symbol")) - svg_run_use_symbol(ctx, dev, doc, root, linked, &local_state); - else - svg_run_element(ctx, dev, doc, linked, &local_state); -diff --git a/source/xps/xps-common.c b/source/xps/xps-common.c -index cc7fed9..f2f9b93 100644 ---- a/source/xps/xps-common.c -+++ b/source/xps/xps-common.c -@@ -47,7 +47,7 @@ xps_parse_brush(fz_context *ctx, xps_document *doc, const fz_matrix *ctm, const - else if (fz_xml_is_tag(node, "RadialGradientBrush")) - xps_parse_radial_gradient_brush(ctx, doc, ctm, area, base_uri, dict, node); - else -- fz_warn(ctx, "unknown brush tag: %s", fz_xml_tag(node)); -+ fz_warn(ctx, "unknown brush tag"); - } - - void -@@ -85,7 +85,7 @@ xps_begin_opacity(fz_context *ctx, xps_document *doc, const fz_matrix *ctm, cons - if (opacity_att) - opacity = fz_atof(opacity_att); - -- if (opacity_mask_tag && !strcmp(fz_xml_tag(opacity_mask_tag), "SolidColorBrush")) -+ if (fz_xml_is_tag(opacity_mask_tag, "SolidColorBrush")) - { - char *scb_opacity_att = fz_xml_att(opacity_mask_tag, "Opacity"); - char *scb_color_att = fz_xml_att(opacity_mask_tag, "Color"); -@@ -129,7 +129,7 @@ xps_end_opacity(fz_context *ctx, xps_document *doc, char *base_uri, xps_resource - - if (opacity_mask_tag) - { -- if (strcmp(fz_xml_tag(opacity_mask_tag), "SolidColorBrush")) -+ if (!fz_xml_is_tag(opacity_mask_tag, "SolidColorBrush")) - fz_pop_clip(ctx, dev); - } - } -diff --git a/source/xps/xps-glyphs.c b/source/xps/xps-glyphs.c -index 29dc5b3..5b26d78 100644 ---- a/source/xps/xps-glyphs.c -+++ b/source/xps/xps-glyphs.c -@@ -592,7 +592,7 @@ xps_parse_glyphs(fz_context *ctx, xps_document *doc, const fz_matrix *ctm, - - /* If it's a solid color brush fill/stroke do a simple fill */ - -- if (fill_tag && !strcmp(fz_xml_tag(fill_tag), "SolidColorBrush")) -+ if (fz_xml_is_tag(fill_tag, "SolidColorBrush")) - { - fill_opacity_att = fz_xml_att(fill_tag, "Opacity"); - fill_att = fz_xml_att(fill_tag, "Color"); -diff --git a/source/xps/xps-path.c b/source/xps/xps-path.c -index 6faeb0c..021d202 100644 ---- a/source/xps/xps-path.c -+++ b/source/xps/xps-path.c -@@ -879,14 +879,14 @@ xps_parse_path(fz_context *ctx, xps_document *doc, const fz_matrix *ctm, char *b - if (!data_att && !data_tag) - return; - -- if (fill_tag && !strcmp(fz_xml_tag(fill_tag), "SolidColorBrush")) -+ if (fz_xml_is_tag(fill_tag, "SolidColorBrush")) - { - fill_opacity_att = fz_xml_att(fill_tag, "Opacity"); - fill_att = fz_xml_att(fill_tag, "Color"); - fill_tag = NULL; - } - -- if (stroke_tag && !strcmp(fz_xml_tag(stroke_tag), "SolidColorBrush")) -+ if (fz_xml_is_tag(stroke_tag, "SolidColorBrush")) - { - stroke_opacity_att = fz_xml_att(stroke_tag, "Opacity"); - stroke_att = fz_xml_att(stroke_tag, "Color"); -diff --git a/source/xps/xps-resource.c b/source/xps/xps-resource.c -index c2292e6..8e81ab8 100644 ---- a/source/xps/xps-resource.c -+++ b/source/xps/xps-resource.c -@@ -84,7 +84,7 @@ xps_parse_remote_resource_dictionary(fz_context *ctx, xps_document *doc, char *b - if (!xml) - return NULL; - -- if (strcmp(fz_xml_tag(xml), "ResourceDictionary")) -+ if (!fz_xml_is_tag(xml, "ResourceDictionary")) - { - fz_drop_xml(ctx, xml); - fz_throw(ctx, FZ_ERROR_GENERIC, "expected ResourceDictionary element"); --- -2.9.1 - diff --git a/gnu/packages/patches/mupdf-CVE-2017-15587.patch b/gnu/packages/patches/mupdf-CVE-2017-15587.patch deleted file mode 100644 index 7d24666756..0000000000 --- a/gnu/packages/patches/mupdf-CVE-2017-15587.patch +++ /dev/null @@ -1,25 +0,0 @@ -Fix CVE-2017-15587. - -https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2017-15587 -https://nandynarwhals.org/CVE-2017-15587/ - -This patch is these two upstream commits squashed together: - - - -diff --git a/source/pdf/pdf-xref.c b/source/pdf/pdf-xref.c -index 66bd0ed8..89499e61 100644 ---- a/source/pdf/pdf-xref.c -+++ b/source/pdf/pdf-xref.c -@@ -924,7 +924,7 @@ pdf_read_new_xref_section(fz_context *ctx, pdf_document *doc, fz_stream *stm, fz - pdf_xref_entry *table; - int i, n; - -- if (i0 < 0 || i1 < 0) -+ if (i0 < 0 || i1 < 0 || i0 > INT_MAX - i1) - fz_throw(ctx, FZ_ERROR_GENERIC, "negative xref stream entry index"); - //if (i0 + i1 > pdf_xref_len(ctx, doc)) - // fz_throw(ctx, FZ_ERROR_GENERIC, "xref stream has too many entries"); --- -2.15.0 - diff --git a/gnu/packages/patches/mupdf-build-with-openjpeg-2.1.patch b/gnu/packages/patches/mupdf-build-with-latest-openjpeg.patch similarity index 69% rename from gnu/packages/patches/mupdf-build-with-openjpeg-2.1.patch rename to gnu/packages/patches/mupdf-build-with-latest-openjpeg.patch index 0b5b735ff3..d5c9c60242 100644 --- a/gnu/packages/patches/mupdf-build-with-openjpeg-2.1.patch +++ b/gnu/packages/patches/mupdf-build-with-latest-openjpeg.patch @@ -1,4 +1,4 @@ -Make it possible to build MuPDF with OpenJPEG 2.1, which is the latest +Make it possible to build MuPDF with OpenJPEG 2.3, which is the latest release series and contains many important bug fixes. Patch adapted from Debian: @@ -10,16 +10,16 @@ And related to this upstream commit: http://git.ghostscript.com/?p=mupdf.git;a=commit;h=f88bfe2e62dbadb96d4f52d7aa025f0a516078da diff --git a/source/fitz/load-jpx.c b/source/fitz/load-jpx.c -index 6b92e5c..72dea50 100644 +index 65699ba..ea84778 100644 --- a/source/fitz/load-jpx.c +++ b/source/fitz/load-jpx.c -@@ -444,11 +444,6 @@ +@@ -445,11 +445,6 @@ fz_load_jpx_info(fz_context *ctx, const unsigned char *data, size_t size, int *w #else /* HAVE_LURATECH */ -#define OPJ_STATIC -#define OPJ_HAVE_INTTYPES_H --#if !defined(_WIN32) && !defined(_WIN64) +-#if !defined(_MSC_VER) || _MSC_VER >= 1600 -#define OPJ_HAVE_STDINT_H -#endif #define USE_JPIP diff --git a/gnu/packages/pdf.scm b/gnu/packages/pdf.scm index 84b9261885..335d0b29dc 100644 --- a/gnu/packages/pdf.scm +++ b/gnu/packages/pdf.scm @@ -567,25 +567,22 @@ extracting content or merging files.") (define-public mupdf (package (name "mupdf") - (version "1.11") + (version "1.12.0") (source (origin (method url-fetch) (uri (string-append "https://mupdf.com/downloads/archive/" - name "-" version "-source.tar.gz")) + name "-" version "-source.tar.xz")) + (patches (search-patches "mupdf-build-with-latest-openjpeg.patch")) (sha256 (base32 - "02phamcchgsmvjnb3ir7r5sssvx9fcrscn297z73b82n1jl79510")) - (patches (search-patches "mupdf-build-with-openjpeg-2.1.patch" - "mupdf-CVE-2017-14685.patch" - "mupdf-CVE-2017-14686.patch" - "mupdf-CVE-2017-14687.patch" - "mupdf-CVE-2017-15587.patch")) + "0b9j0gqbc3jhmx87r6idcsh8lnb30840c3hyx6dk2gdjqqh3hysp")) (modules '((guix build utils))) (snippet '(delete-file-recursively "thirdparty")))) (build-system gnu-build-system) (inputs `(("curl" ,curl) + ("freeglut" ,freeglut) ("freetype" ,freetype) ("harfbuzz" ,harfbuzz) ("jbig2dec" ,jbig2dec) From 417f3d494f6b7febd086ae064e67646b7faee9ff Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Thu, 21 Dec 2017 09:02:46 +0200 Subject: [PATCH 67/77] gnu: xboing: Fix CVE-2004-0149. * gnu/packages/patches/xboing-CVE-2004-0149: New file. * gnu/packages/games.scm (xboing)[source]: Add patch. * gnu/local.mk (dist_patch_DATA): Register it. --- gnu/local.mk | 1 + gnu/packages/games.scm | 3 +- .../patches/xboing-CVE-2004-0149.patch | 134 ++++++++++++++++++ 3 files changed, 137 insertions(+), 1 deletion(-) create mode 100644 gnu/packages/patches/xboing-CVE-2004-0149.patch diff --git a/gnu/local.mk b/gnu/local.mk index 8ffcc58005..88e3c770aa 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -1141,6 +1141,7 @@ dist_patch_DATA = \ %D%/packages/patches/wpa-supplicant-fix-zeroed-keys.patch \ %D%/packages/patches/wpa-supplicant-fix-nonce-reuse.patch \ %D%/packages/patches/wpa-supplicant-krack-followups.patch \ + %D%/packages/patches/xboing-CVE-2004-0149.patch \ %D%/packages/patches/xcb-proto-python3-print.patch \ %D%/packages/patches/xcb-proto-python3-whitespace.patch \ %D%/packages/patches/xdotool-fix-makefile.patch \ diff --git a/gnu/packages/games.scm b/gnu/packages/games.scm index cc21a63f53..c494d0beba 100644 --- a/gnu/packages/games.scm +++ b/gnu/packages/games.scm @@ -1071,7 +1071,8 @@ Portable Game Notation.") (uri (string-append "http://www.techrescue.org/xboing/xboing" version ".tar.gz")) (sha256 - (base32 "16m2si8wmshxpifk861vhpqviqxgcg8bxj6wfw8hpnm4r2w9q0b7")))) + (base32 "16m2si8wmshxpifk861vhpqviqxgcg8bxj6wfw8hpnm4r2w9q0b7")) + (patches (search-patches "xboing-CVE-2004-0149.patch")))) (arguments `(#:tests? #f #:phases diff --git a/gnu/packages/patches/xboing-CVE-2004-0149.patch b/gnu/packages/patches/xboing-CVE-2004-0149.patch new file mode 100644 index 0000000000..b40146b434 --- /dev/null +++ b/gnu/packages/patches/xboing-CVE-2004-0149.patch @@ -0,0 +1,134 @@ +https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2004-0149 +https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=174924 +--- + demo.c | 2 +- + editor.c | 12 ++++++------ + file.c | 2 +- + highscore.c | 6 +++--- + misc.c | 2 +- + preview.c | 2 +- + 6 files changed, 13 insertions(+), 13 deletions(-) + +diff --git a/demo.c b/demo.c +index 9084e70..f4fc2cd 100644 +--- a/demo.c ++++ b/demo.c +@@ -154,7 +154,7 @@ static void DoBlocks(display, window) + + /* Construct the demo level filename */ + if ((str = getenv("XBOING_LEVELS_DIR")) != NULL) +- sprintf(levelPath, "%s/demo.data", str); ++ snprintf(levelPath, sizeof(levelPath),"%s/demo.data", str); + else + sprintf(levelPath, "%s/demo.data", LEVEL_INSTALL_DIR); + +diff --git a/editor.c b/editor.c +index f2bb9ed..66d0679 100644 +--- a/editor.c ++++ b/editor.c +@@ -213,7 +213,7 @@ static void DoLoadLevel(display, window) + + /* Construct the Edit level filename */ + if ((str = getenv("XBOING_LEVELS_DIR")) != NULL) +- sprintf(levelPath, "%s/editor.data", str); ++ snprintf(levelPath,sizeof(levelPath)-1, "%s/editor.data", str); + else + sprintf(levelPath, "%s/editor.data", LEVEL_INSTALL_DIR); + +@@ -958,8 +958,8 @@ static void LoadALevel(display) + if ((num > 0) && (num <= MAX_NUM_LEVELS)) + { + /* Construct the Edit level filename */ +- if ((str2 = getenv("XBOING_LEVELS_DIR")) != NULL) +- sprintf(levelPath, "%s/level%02ld.data", str2, (u_long) num); ++ if ((str2 = getenv("XBOING_LEVELS_DIR")) != NULL) ++ snprintf(levelPath, sizeof(levelPath)-1,"%s/level%02ld.data", str2, (u_long) num); + else + sprintf(levelPath, "%s/level%02ld.data", + LEVEL_INSTALL_DIR, (u_long) num); +@@ -1017,9 +1017,9 @@ static void SaveALevel(display) + num = atoi(str); + if ((num > 0) && (num <= MAX_NUM_LEVELS)) + { +- /* Construct the Edit level filename */ +- if ((str2 = getenv("XBOING_LEVELS_DIR")) != NULL) +- sprintf(levelPath, "%s/level%02ld.data", str2, (u_long) num); ++ /* Construct the Edit level filename */ ++ if ((str2 = getenv("XBOING_LEVELS_DIR")) != NULL) ++ snprintf(levelPath, sizeof(levelPath)-1,"%s/level%02ld.data", str2, (u_long) num); + else + sprintf(levelPath, "%s/level%02ld.data", + LEVEL_INSTALL_DIR, (u_long) num); +diff --git a/file.c b/file.c +index 4c043cd..99a0854 100644 +--- a/file.c ++++ b/file.c +@@ -139,7 +139,7 @@ void SetupStage(display, window) + + /* Construct the level filename */ + if ((str = getenv("XBOING_LEVELS_DIR")) != NULL) +- sprintf(levelPath, "%s/level%02ld.data", str, newLevel); ++ snprintf(levelPath,sizeof(levelPath), "%s/level%02ld.data", str, newLevel); + else + sprintf(levelPath, "%s/level%02ld.data", LEVEL_INSTALL_DIR, newLevel); + +diff --git a/highscore.c b/highscore.c +index f0db3e9..792273e 100644 +--- a/highscore.c ++++ b/highscore.c +@@ -1023,7 +1023,7 @@ int ReadHighScoreTable(type) + { + /* Use the environment variable if it exists */ + if ((str = getenv("XBOING_SCORE_FILE")) != NULL) +- strcpy(filename, str); ++ strncpy(filename, str, sizeof(filename)-1); + else + strcpy(filename, HIGH_SCORE_FILE); + } +@@ -1095,7 +1095,7 @@ int WriteHighScoreTable(type) + { + /* Use the environment variable if it exists */ + if ((str = getenv("XBOING_SCORE_FILE")) != NULL) +- strcpy(filename, str); ++ strncpy(filename, str, sizeof(filename)-1); + else + strcpy(filename, HIGH_SCORE_FILE); + } +@@ -1218,7 +1218,7 @@ static int LockUnlock(cmd) + + /* Use the environment variable if it exists */ + if ((str = getenv("XBOING_SCORE_FILE")) != NULL) +- strcpy(filename, str); ++ strncpy(filename, str, sizeof(filename)-1); + else + strcpy(filename, HIGH_SCORE_FILE); + +diff --git a/misc.c b/misc.c +index f3ab37e..7f3ddce 100644 +--- a/misc.c ++++ b/misc.c +@@ -427,7 +427,7 @@ char *GetHomeDir() + */ + + if ((ptr = getenv("HOME")) != NULL) +- (void) strcpy(dest, ptr); ++ (void) strncpy(dest, ptr,sizeof(dest)-1); + else + { + /* HOME variable is not present so get USER var */ +diff --git a/preview.c b/preview.c +index 41c1187..687f566 100644 +--- a/preview.c ++++ b/preview.c +@@ -139,7 +139,7 @@ static void DoLoadLevel(display, window) + + /* Construct the Preview level filename */ + if ((str = getenv("XBOING_LEVELS_DIR")) != NULL) +- sprintf(levelPath, "%s/level%02d.data", str, lnum); ++ snprintf(levelPath, sizeof(levelPath)-1, "%s/level%02d.data", str, lnum); + else + sprintf(levelPath, "%s/level%02d.data", LEVEL_INSTALL_DIR, lnum); + +-- +2.15.1 + From ce16d312c6fc4d23dcf45b73709712b56d6d2174 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Thu, 21 Dec 2017 02:55:44 -0500 Subject: [PATCH 68/77] gnu: libexif: Fix CVE-2017-7544. * gnu/packages/patches/libexif-CVE-2017-7544.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/photo.scm (feh)[source]: Use it. --- gnu/local.mk | 1 + .../patches/libexif-CVE-2017-7544.patch | 29 +++++++++++++++++++ gnu/packages/photo.scm | 2 ++ 3 files changed, 32 insertions(+) create mode 100644 gnu/packages/patches/libexif-CVE-2017-7544.patch diff --git a/gnu/local.mk b/gnu/local.mk index 88e3c770aa..dcb08c1caa 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -805,6 +805,7 @@ dist_patch_DATA = \ %D%/packages/patches/libevent-2.0-evbuffer-add-use-last-with-datap.patch \ %D%/packages/patches/libevent-2.1-dns-tests.patch \ %D%/packages/patches/libevent-2.1-skip-failing-test.patch \ + %D%/packages/patches/libexif-CVE-2017-7544.patch \ %D%/packages/patches/libgit2-0.25.1-mtime-0.patch \ %D%/packages/patches/libgdata-fix-tests.patch \ %D%/packages/patches/libgdata-glib-duplicate-tests.patch \ diff --git a/gnu/packages/patches/libexif-CVE-2017-7544.patch b/gnu/packages/patches/libexif-CVE-2017-7544.patch new file mode 100644 index 0000000000..c4ea373dc5 --- /dev/null +++ b/gnu/packages/patches/libexif-CVE-2017-7544.patch @@ -0,0 +1,29 @@ +Fix CVE-2017-7544: + +https://sourceforge.net/p/libexif/bugs/130/ +https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2017-7544 + +Patch copied from upstream bug tracker: + +https://sourceforge.net/p/libexif/bugs/130/#489a + +Index: libexif/exif-data.c +=================================================================== +RCS file: /cvsroot/libexif/libexif/libexif/exif-data.c,v +retrieving revision 1.131 +diff -u -r1.131 exif-data.c +--- a/libexif/exif-data.c 12 Jul 2012 17:28:26 -0000 1.131 ++++ b/libexif/exif-data.c 25 Jul 2017 21:34:06 -0000 +@@ -255,6 +255,12 @@ + exif_mnote_data_set_offset (data->priv->md, *ds - 6); + exif_mnote_data_save (data->priv->md, &e->data, &e->size); + e->components = e->size; ++ if (exif_format_get_size (e->format) != 1) { ++ /* e->format is taken from input code, ++ * but we need to make sure it is a 1 byte ++ * entity due to the multiplication below. */ ++ e->format = EXIF_FORMAT_UNDEFINED; ++ } + } + } + diff --git a/gnu/packages/photo.scm b/gnu/packages/photo.scm index 34a2180500..40f3a4e4c1 100644 --- a/gnu/packages/photo.scm +++ b/gnu/packages/photo.scm @@ -28,6 +28,7 @@ #:use-module ((guix licenses) #:prefix license:) #:use-module (guix packages) #:use-module (guix utils) + #:use-module (gnu packages) #:use-module (gnu packages algebra) #:use-module (gnu packages autotools) #:use-module (gnu packages base) @@ -89,6 +90,7 @@ cameras (CRW/CR2, NEF, RAF, DNG, and others).") (method url-fetch) (uri (string-append "mirror://sourceforge/libexif/libexif/" version "/libexif-" version ".tar.bz2")) + (patches (search-patches "libexif-CVE-2017-7544.patch")) (sha256 (base32 "06nlsibr3ylfwp28w8f5466l6drgrnydgxrm4jmxzrmk5svaxk8n")))) From c521c8f1a4cd50996d661c01f8ac6d4832d825f4 Mon Sep 17 00:00:00 2001 From: Konrad Hinsen Date: Tue, 19 Dec 2017 12:50:00 +0100 Subject: [PATCH 69/77] gnu: Add python-tempdir. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/python.scm (python-tempdir, python2-tempdir): New variables. Signed-off-by: Ludovic Courtès --- gnu/packages/python.scm | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 4baef43914..1ef54b7fd5 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -11974,3 +11974,30 @@ belong to tagged versions.") "BooleanOperations provides a Python library that enables boolean operations on paths.") (license license:expat))) + +(define-public python-tempdir + (package + (name "python-tempdir") + (version "0.7.1") + (source + (origin + (method url-fetch) + (uri (pypi-uri "tempdir" version)) + (sha256 + (base32 + "13msyyxqbicr111a294x7fsqbkl6a31fyrqflx3q7k547gnq15k8")))) + (build-system python-build-system) + (home-page "https://pypi.org/project/tempdir/") + (arguments + ;; the package has no tests + '(#:tests? #f)) + (synopsis "Python library for managing temporary directories") + (description + "This library manages temporary directories that are automatically +deleted with all their contents when they are no longer needed. It is +particularly convenient for use in tests.") + (license license:expat))) + +(define-public python2-tempdir + (package-with-python2 python-tempdir)) + From 2a0e3d163581f053138508b0d40a28e07dc37923 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Wed, 20 Dec 2017 19:39:59 -0500 Subject: [PATCH 70/77] gnu: libarchive: Fix CVE-2017-14502. * gnu/packages/patches/libarchive-CVE-2017-14502.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/backup.scm (libarchive-3.3.2)[source]: Use it. --- gnu/local.mk | 1 + gnu/packages/backup.scm | 3 +- .../patches/libarchive-CVE-2017-14502.patch | 40 +++++++++++++++++++ 3 files changed, 43 insertions(+), 1 deletion(-) create mode 100644 gnu/packages/patches/libarchive-CVE-2017-14502.patch diff --git a/gnu/local.mk b/gnu/local.mk index dcb08c1caa..32f24ab3b1 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -791,6 +791,7 @@ dist_patch_DATA = \ %D%/packages/patches/liba52-set-soname.patch \ %D%/packages/patches/liba52-use-mtune-not-mcpu.patch \ %D%/packages/patches/libarchive-CVE-2017-14166.patch \ + %D%/packages/patches/libarchive-CVE-2017-14502.patch \ %D%/packages/patches/libbase-fix-includes.patch \ %D%/packages/patches/libbase-use-own-logging.patch \ %D%/packages/patches/libbonobo-activation-test-race.patch \ diff --git a/gnu/packages/backup.scm b/gnu/packages/backup.scm index e634d6ab96..fab71d055a 100644 --- a/gnu/packages/backup.scm +++ b/gnu/packages/backup.scm @@ -253,7 +253,8 @@ random access nor for in-place modification.") (method url-fetch) (uri (string-append "http://libarchive.org/downloads/libarchive-" version ".tar.gz")) - (patches (search-patches "libarchive-CVE-2017-14166.patch")) + (patches (search-patches "libarchive-CVE-2017-14166.patch" + "libarchive-CVE-2017-14502.patch")) (sha256 (base32 "1km0mzfl6in7l5vz9kl09a88ajx562rw93ng9h2jqavrailvsbgd")))))) diff --git a/gnu/packages/patches/libarchive-CVE-2017-14502.patch b/gnu/packages/patches/libarchive-CVE-2017-14502.patch new file mode 100644 index 0000000000..8e0508afb5 --- /dev/null +++ b/gnu/packages/patches/libarchive-CVE-2017-14502.patch @@ -0,0 +1,40 @@ +Fix CVE-2017-14502: + +https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2017-14502 +https://bugs.chromium.org/p/oss-fuzz/issues/detail?id=573 + +Patch copied from upstream source repository: + +https://github.com/libarchive/libarchive/commit/5562545b5562f6d12a4ef991fae158bf4ccf92b6 + +From 5562545b5562f6d12a4ef991fae158bf4ccf92b6 Mon Sep 17 00:00:00 2001 +From: Joerg Sonnenberger +Date: Sat, 9 Sep 2017 17:47:32 +0200 +Subject: [PATCH] Avoid a read off-by-one error for UTF16 names in RAR + archives. + +Reported-By: OSS-Fuzz issue 573 +--- + libarchive/archive_read_support_format_rar.c | 6 +++++- + 1 file changed, 5 insertions(+), 1 deletion(-) + +diff --git a/libarchive/archive_read_support_format_rar.c b/libarchive/archive_read_support_format_rar.c +index cbb14c32..751de697 100644 +--- a/libarchive/archive_read_support_format_rar.c ++++ b/libarchive/archive_read_support_format_rar.c +@@ -1496,7 +1496,11 @@ read_header(struct archive_read *a, struct archive_entry *entry, + return (ARCHIVE_FATAL); + } + filename[filename_size++] = '\0'; +- filename[filename_size++] = '\0'; ++ /* ++ * Do not increment filename_size here as the computations below ++ * add the space for the terminating NUL explicitly. ++ */ ++ filename[filename_size] = '\0'; + + /* Decoded unicode form is UTF-16BE, so we have to update a string + * conversion object for it. */ +-- +2.15.1 + From 0c9c9526bb3fb665997b3b054f8b57ffdb559043 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Thu, 21 Dec 2017 02:12:55 -0500 Subject: [PATCH 71/77] gnu: libxslt: Fix CVE-2017-5029 and re-apply the fix for CVE-2016-4738. This is a followup to commit 2663c38826cd6c2ef0c5119f8072fac8e89b2e9b. * gnu/packages/xml.scm (libxslt)[replacement]: New field. (libxslt/fixed): New variable. * gnu/packages/patches/libxslt-CVE-2017-5029.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. --- gnu/local.mk | 1 + .../patches/libxslt-CVE-2017-5029.patch | 82 +++++++++++++++++++ gnu/packages/xml.scm | 15 +++- 3 files changed, 97 insertions(+), 1 deletion(-) create mode 100644 gnu/packages/patches/libxslt-CVE-2017-5029.patch diff --git a/gnu/local.mk b/gnu/local.mk index 32f24ab3b1..20b3c3e366 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -851,6 +851,7 @@ dist_patch_DATA = \ %D%/packages/patches/libxml2-CVE-2017-9049+CVE-2017-9050.patch \ %D%/packages/patches/libxslt-generated-ids.patch \ %D%/packages/patches/libxslt-CVE-2016-4738.patch \ + %D%/packages/patches/libxslt-CVE-2017-5029.patch \ %D%/packages/patches/libxt-guix-search-paths.patch \ %D%/packages/patches/lierolibre-check-unaligned-access.patch \ %D%/packages/patches/lierolibre-is-free-software.patch \ diff --git a/gnu/packages/patches/libxslt-CVE-2017-5029.patch b/gnu/packages/patches/libxslt-CVE-2017-5029.patch new file mode 100644 index 0000000000..cd86928b21 --- /dev/null +++ b/gnu/packages/patches/libxslt-CVE-2017-5029.patch @@ -0,0 +1,82 @@ +Fix CVE-2017-5029: + +https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2017-5029 + +Patch copied from upstream source repository: + +https://git.gnome.org/browse/libxslt/commit/?id=08ab2774b870de1c7b5a48693df75e8154addae5 + +From 08ab2774b870de1c7b5a48693df75e8154addae5 Mon Sep 17 00:00:00 2001 +From: Nick Wellnhofer +Date: Thu, 12 Jan 2017 15:39:52 +0100 +Subject: [PATCH] Check for integer overflow in xsltAddTextString + +Limit buffer size in xsltAddTextString to INT_MAX. The issue can be +exploited to trigger an out of bounds write on 64-bit systems. + +Originally reported to Chromium: + +https://crbug.com/676623 +--- + libxslt/transform.c | 25 ++++++++++++++++++++++--- + libxslt/xsltInternals.h | 4 ++-- + 2 files changed, 24 insertions(+), 5 deletions(-) + +diff --git a/libxslt/transform.c b/libxslt/transform.c +index 519133fc..02bff34a 100644 +--- a/libxslt/transform.c ++++ b/libxslt/transform.c +@@ -813,13 +813,32 @@ xsltAddTextString(xsltTransformContextPtr ctxt, xmlNodePtr target, + return(target); + + if (ctxt->lasttext == target->content) { ++ int minSize; + +- if (ctxt->lasttuse + len >= ctxt->lasttsize) { ++ /* Check for integer overflow accounting for NUL terminator. */ ++ if (len >= INT_MAX - ctxt->lasttuse) { ++ xsltTransformError(ctxt, NULL, target, ++ "xsltCopyText: text allocation failed\n"); ++ return(NULL); ++ } ++ minSize = ctxt->lasttuse + len + 1; ++ ++ if (ctxt->lasttsize < minSize) { + xmlChar *newbuf; + int size; ++ int extra; ++ ++ /* Double buffer size but increase by at least 100 bytes. */ ++ extra = minSize < 100 ? 100 : minSize; ++ ++ /* Check for integer overflow. */ ++ if (extra > INT_MAX - ctxt->lasttsize) { ++ size = INT_MAX; ++ } ++ else { ++ size = ctxt->lasttsize + extra; ++ } + +- size = ctxt->lasttsize + len + 100; +- size *= 2; + newbuf = (xmlChar *) xmlRealloc(target->content,size); + if (newbuf == NULL) { + xsltTransformError(ctxt, NULL, target, +diff --git a/libxslt/xsltInternals.h b/libxslt/xsltInternals.h +index 060b1783..5ad17719 100644 +--- a/libxslt/xsltInternals.h ++++ b/libxslt/xsltInternals.h +@@ -1754,8 +1754,8 @@ struct _xsltTransformContext { + * Speed optimization when coalescing text nodes + */ + const xmlChar *lasttext; /* last text node content */ +- unsigned int lasttsize; /* last text node size */ +- unsigned int lasttuse; /* last text node use */ ++ int lasttsize; /* last text node size */ ++ int lasttuse; /* last text node use */ + /* + * Per Context Debugging + */ +-- +2.15.1 + diff --git a/gnu/packages/xml.scm b/gnu/packages/xml.scm index 4f75de344c..344d7c347f 100644 --- a/gnu/packages/xml.scm +++ b/gnu/packages/xml.scm @@ -188,12 +188,16 @@ project (but it is usable outside of the Gnome platform).") (define-public libxslt (package (name "libxslt") + (replacement libxslt/fixed) (version "1.1.29") (source (origin (method url-fetch) (uri (string-append "ftp://xmlsoft.org/libxslt/libxslt-" version ".tar.gz")) - (patches (search-patches "libxslt-CVE-2016-4738.patch")) + ;; XXX Oops, the patches field is redefined below, which means the + ;; patch for CVE-2016-4738 was not used. Fixed in the definition of + ;; libxslt/fixed below. + ;(patches (search-patches "libxslt-CVE-2016-4738.patch")) (sha256 (base32 "1klh81xbm9ppzgqk339097i39b7fnpmlj8lzn8bpczl3aww6x5xm")) @@ -210,6 +214,15 @@ project (but it is usable outside of the Gnome platform).") based on libxml for XML parsing, tree manipulation and XPath support.") (license license:x11))) +(define libxslt/fixed + (package + (inherit libxslt) + (source (origin + (inherit (package-source libxslt)) + (patches (search-patches "libxslt-CVE-2016-4738.patch" + "libxslt-CVE-2017-5029.patch" + "libxslt-generated-ids.patch")))))) + (define-public perl-graph-readwrite (package (name "perl-graph-readwrite") From 806e891e85aff27ea87c4e60930d8c4ed7d5091f Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Wed, 20 Dec 2017 16:47:18 -0500 Subject: [PATCH 72/77] gnu: gnupg@2.0: Superseded by the latest GnuPG. The 2.0 series of GnuPG will stop receiving upstream support on 2017-12-31. From the release announcement of GnuPG 2.2.0: "This release marks the start of a new long term support series to replace the 2.0.x series which will reach end-of-life on 2017-12-31." https://lists.gnupg.org/pipermail/gnupg-announce/2017q3/000413.html * gnu/packages/gnupg.scm (gnupg-2.0)[properties]: New field. --- gnu/packages/gnupg.scm | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/gnu/packages/gnupg.scm b/gnu/packages/gnupg.scm index 7a791aecd2..247e907b15 100644 --- a/gnu/packages/gnupg.scm +++ b/gnu/packages/gnupg.scm @@ -341,7 +341,8 @@ libskba (working with X.509 certificates and CMS data).") ;; Keep the old name around to ease transition. (symlink "gpgv" "gpgv2") (symlink "gpg" "gpg2") - #t))))))))) + #t))))))) + (properties `((superseded . ,gnupg))))) (define-public gnupg-1 (package (inherit gnupg) From 5308f15b433c4562dcbe1938b08d045a2adabe7f Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Thu, 21 Dec 2017 15:03:02 +0100 Subject: [PATCH 73/77] gnu: zstd: Update to 1.3.3. * gnu/packages/compression.scm (zstd): Update to 1.3.3. --- gnu/packages/compression.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/compression.scm b/gnu/packages/compression.scm index 2710504917..9ddc76fe81 100644 --- a/gnu/packages/compression.scm +++ b/gnu/packages/compression.scm @@ -1593,7 +1593,7 @@ or junctions, and always follows hard links.") (define-public zstd (package (name "zstd") - (version "1.3.2") + (version "1.3.3") (source (origin (method url-fetch) (uri (string-append "https://github.com/facebook/zstd/archive/v" @@ -1601,7 +1601,7 @@ or junctions, and always follows hard links.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "12krs9k5f408kyn0d7dwxqyc67177mgd14783ay10rafqsim8l5c")))) + "0yr91gwi380632w9y7p6idl72svq0mq0jajvdii05pp77qalfz57")))) (build-system gnu-build-system) (arguments `(#:phases From f45e314e19c903d2686d11184ecc689ffb444c0a Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Thu, 21 Dec 2017 17:44:03 +0100 Subject: [PATCH 74/77] gnu: zstd: Disable unrelated format support. * gnu/packages/compression.scm (zstd)[arguments]: Add HAVE_LZMA=0 to --- gnu/packages/compression.scm | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/gnu/packages/compression.scm b/gnu/packages/compression.scm index 9ddc76fe81..5cdb14ba37 100644 --- a/gnu/packages/compression.scm +++ b/gnu/packages/compression.scm @@ -1609,7 +1609,13 @@ or junctions, and always follows hard links.") (delete 'configure)) ; no configure script #:make-flags (list "CC=gcc" - (string-append "PREFIX=" (assoc-ref %outputs "out"))) + (string-append "PREFIX=" (assoc-ref %outputs "out")) + ;; Skip auto-detection of, and creating a dependency on, the build + ;; environment's ‘xz’ for what amounts to a dubious feature anyway. + "HAVE_LZMA=0" + ;; Not currently detected, but be explicit & avoid surprises later. + "HAVE_LZ4=0" + "HAVE_ZLIB=0") #:test-target "test")) (home-page "http://zstd.net/") (synopsis "Zstandard real-time compression algorithm") From 00840ee004151c15c2207ea18efa153d49449435 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Thu, 21 Dec 2017 18:37:31 +0100 Subject: [PATCH 75/77] gnu: weechat: Run tests. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/irc.scm (weechat)[native-inputs]: Add cpputest. [arguments]: Add ‘-DENABLE_TESTS=ON’ to #:configure-flags. Add ‘disable-failing-tests’ phase to do just that. Run the others. --- gnu/packages/irc.scm | 40 +++++++++++++++++++++++++++++----------- 1 file changed, 29 insertions(+), 11 deletions(-) diff --git a/gnu/packages/irc.scm b/gnu/packages/irc.scm index 0e0813c1cb..ec329ade7e 100644 --- a/gnu/packages/irc.scm +++ b/gnu/packages/irc.scm @@ -163,8 +163,11 @@ SILC and ICB protocols via plugins.") "1l854dramvn9vfba7jpazkjwm4k4i5pshq58vjv6z2mxmcp5hhv9")) (patches (search-patches "weechat-python.patch")))) (build-system cmake-build-system) - (native-inputs `(("gettext" ,gettext-minimal) - ("pkg-config" ,pkg-config))) + (native-inputs + `(("gettext" ,gettext-minimal) + ("pkg-config" ,pkg-config) + ;; For tests. + ("cpputest" ,cpputest))) (inputs `(("ncurses" ,ncurses) ("libgcrypt" ,libgcrypt "out") ("zlib" ,zlib) @@ -177,15 +180,30 @@ SILC and ICB protocols via plugins.") ("perl" ,perl) ("tcl" ,tcl))) (arguments - `(#:tests? #f ; tests require cpputime - #:phases (modify-phases %standard-phases - (add-after 'install 'wrap - (lambda* (#:key inputs outputs #:allow-other-keys) - (let ((out (assoc-ref outputs "out")) - (py2 (assoc-ref inputs "python"))) - (wrap-program (string-append out "/bin/weechat") - `("PATH" ":" prefix (,(string-append py2 "/bin")))) - #t)))))) + `(#:configure-flags + (list "-DENABLE_TESTS=ON") ; ‘make test’ fails otherwise + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'disable-failing-tests + ;; For reasons best left to the imagination, CppUTest cannot skip + ;; more than one single test... Resort to manual patching instead. + ;; See . + (λ _ + ;; Don't test plugin support for languages we don't enable. + (substitute* "tests/unit/test-plugins.cpp" + ((".*\\$\\{plugin.name\\} == (javascript|php|ruby)" all) + (string-append "// SKIP" all))) + (substitute* "tests/scripts/test-scripts.cpp" + ((".*\\{ \"(jvascript|php|ruby)\", " all) ; sic + (string-append "// SKIP" all))) + #t)) + (add-after 'install 'wrap + (lambda* (#:key inputs outputs #:allow-other-keys) + (let ((out (assoc-ref outputs "out")) + (py2 (assoc-ref inputs "python"))) + (wrap-program (string-append out "/bin/weechat") + `("PATH" ":" prefix (,(string-append py2 "/bin")))) + #t)))))) (synopsis "Extensible chat client") (description "WeeChat (Wee Enhanced Environment for Chat) is an @dfn{Internet Relay Chat} (IRC) client, which is designed to be light and fast. From 382e5f19479db12052df6a15998410a3e01a8edb Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Thu, 21 Dec 2017 12:49:01 -0500 Subject: [PATCH 76/77] gnu: gnupg: Update to 2.2.4. * gnu/packages/gnupg.scm (gnupg): Update to 2.2.4. --- gnu/packages/gnupg.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/gnupg.scm b/gnu/packages/gnupg.scm index 247e907b15..0aa7dad0fa 100644 --- a/gnu/packages/gnupg.scm +++ b/gnu/packages/gnupg.scm @@ -226,14 +226,14 @@ compatible to GNU Pth.") (define-public gnupg (package (name "gnupg") - (version "2.2.3") + (version "2.2.4") (source (origin (method url-fetch) (uri (string-append "mirror://gnupg/gnupg/gnupg-" version ".tar.bz2")) (sha256 (base32 - "1d4482c4pbi0p1k8cc0f9c4q51k56v8navrbz5samxrrs42p3lyb")))) + "1v7j8v2ww1knknbrhw3svfrqkmf9ll58iq0dczbsdpqgg1j3w6j0")))) (build-system gnu-build-system) (native-inputs `(("pkg-config" ,pkg-config))) From 5dc0e0b055ce2ab12c40066cee34511cd7a5cf03 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Thu, 21 Dec 2017 13:22:29 -0500 Subject: [PATCH 77/77] gnu: imagemagick: Update to 6.9.9-27. * gnu/packages/imagemagick.scm (imagemagick): Update to 6.9.9-27. --- 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 ac9fca8600..29ce574197 100644 --- a/gnu/packages/imagemagick.scm +++ b/gnu/packages/imagemagick.scm @@ -46,14 +46,14 @@ ;; The 7 release series has an incompatible API, while the 6 series is still ;; maintained. Don't update to 7 until we've made sure that the ImageMagick ;; users are ready for the 7-series API. - (version "6.9.9-23") + (version "6.9.9-27") (source (origin (method url-fetch) (uri (string-append "mirror://imagemagick/ImageMagick-" version ".tar.xz")) (sha256 (base32 - "0cd6zcbcfvznf0i3q4xz1c4wm4cfplg4zc466lvlb1w8qbn25948")))) + "0z71az1bfar1r6mm3ijxbci0vb1ri66ypaals8wb17h1d85hkl17")))) (build-system gnu-build-system) (arguments `(#:configure-flags '("--with-frozenpaths" "--without-gcc-arch")