From e7ea30d59a22857e7a2992ef7bd099b8f88127f7 Mon Sep 17 00:00:00 2001 From: Ben Woodcroft Date: Tue, 8 Aug 2017 09:19:22 +1000 Subject: [PATCH 01/61] ruby: Replace with ruby-2.4.1. * gnu/packages/ruby.scm (ruby-2.4.1): New variable. (ruby)[replacement]: New field. --- gnu/packages/ruby.scm | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) diff --git a/gnu/packages/ruby.scm b/gnu/packages/ruby.scm index 414b38c4fe..78ec9cdf36 100644 --- a/gnu/packages/ruby.scm +++ b/gnu/packages/ruby.scm @@ -49,6 +49,7 @@ (define-public ruby (package (name "ruby") + (replacement ruby-2.4.1) (version "2.4.0") (source (origin @@ -102,6 +103,26 @@ a focus on simplicity and productivity.") (home-page "https://ruby-lang.org") (license license:ruby))) +(define-public ruby-2.4.1 + (package + (inherit ruby) + (name "ruby") + (version "2.4.1") + (source + (origin + (method url-fetch) + (uri (string-append "http://cache.ruby-lang.org/pub/ruby/" + (version-major+minor version) + "/ruby-" version ".tar.xz")) + (sha256 + (base32 + "0m763zf2v0jhrha3cx21g4dif6vc9gm714invs8h3sg35ncskj2g")) + (modules '((guix build utils))) + (snippet `(begin + ;; Remove bundled libffi + (delete-file-recursively "ext/fiddle/libffi-3.2.1") + #t)))))) + (define-public ruby-2.3 (package (inherit ruby) From 5071f17b29ab40c44c329668550b85bc606cee02 Mon Sep 17 00:00:00 2001 From: Ben Woodcroft Date: Sun, 6 Aug 2017 16:41:05 +1000 Subject: [PATCH 02/61] gnu: ruby-tdiff: Update to 0.3.3-1.b662a604. * gnu/packages/ruby.scm: Update to 0.3.3-1.b662a604 --- gnu/packages/ruby.scm | 43 ++++++++++++++++++++++++------------------- 1 file changed, 24 insertions(+), 19 deletions(-) diff --git a/gnu/packages/ruby.scm b/gnu/packages/ruby.scm index 78ec9cdf36..4c8a6f2e5c 100644 --- a/gnu/packages/ruby.scm +++ b/gnu/packages/ruby.scm @@ -2878,26 +2878,31 @@ including comments and whitespace.") (license license:expat))) (define-public ruby-tdiff - (package - (name "ruby-tdiff") - (version "0.3.3") - (source (origin - (method url-fetch) - (uri (rubygems-uri "tdiff" version)) - (sha256 - (base32 - "0k41jbvn8qq4mgrixnhlk742b971d136i8wpbcv2cczvi22xpc86")))) - (build-system ruby-build-system) - (native-inputs - `(("ruby-rspec-2" ,ruby-rspec-2) - ("ruby-yard" ,ruby-yard) - ("ruby-rubygems-tasks" ,ruby-rubygems-tasks))) - (synopsis "Calculate the differences between two tree-like structures") - (description - "This library provides functions to calculate the differences between two + ;; Use a newer than released snapshot so that rspec-2 is not required. + (let ((commit "b662a6048f08abc45c1a834e5f34dd1c662935e2")) + (package + (name "ruby-tdiff") + (version (string-append "0.3.3-1." (string-take commit 8))) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/postmodern/tdiff.git") + (commit commit))) + (file-name (string-append name "-" version "-checkout")) + (sha256 + (base32 + "0n3gq8rx49f7ln6zqlshqfg2mgqyy30rsdjlnki5mv307ykc7ad4")))) + (build-system ruby-build-system) + (native-inputs + `(("ruby-rspec" ,ruby-rspec) + ("ruby-yard" ,ruby-yard) + ("ruby-rubygems-tasks" ,ruby-rubygems-tasks))) + (synopsis "Calculate the differences between two tree-like structures") + (description + "This library provides functions to calculate the differences between two tree-like structures. It is similar to Ruby's built-in @code{TSort} module.") - (home-page "https://github.com/postmodern/tdiff") - (license license:expat))) + (home-page "https://github.com/postmodern/tdiff") + (license license:expat)))) (define-public ruby-nokogiri-diff (package From 5b0c223ae3470d8f9433d6301eeb9eeaf9193b90 Mon Sep 17 00:00:00 2001 From: Ben Woodcroft Date: Sun, 6 Aug 2017 16:52:40 +1000 Subject: [PATCH 03/61] gnu: ruby-nokogiri-diff: Update to 0.2.0-1.a38491e4. * gnu/packages/ruby.scm (ruby-nokogiri-diff): Update to 0.2.0-1.a38491e4. --- gnu/packages/ruby.scm | 49 ++++++++++++++++++++++++------------------- 1 file changed, 27 insertions(+), 22 deletions(-) diff --git a/gnu/packages/ruby.scm b/gnu/packages/ruby.scm index 4c8a6f2e5c..29677dc025 100644 --- a/gnu/packages/ruby.scm +++ b/gnu/packages/ruby.scm @@ -2905,29 +2905,34 @@ tree-like structures. It is similar to Ruby's built-in @code{TSort} module.") (license license:expat)))) (define-public ruby-nokogiri-diff - (package - (name "ruby-nokogiri-diff") - (version "0.2.0") - (source (origin - (method url-fetch) - (uri (rubygems-uri "nokogiri-diff" version)) - (sha256 - (base32 - "0njr1s42war0bj1axb2psjvk49l74a8wzr799wckqqdcb6n51lc1")))) - (build-system ruby-build-system) - (propagated-inputs - `(("ruby-tdiff" ,ruby-tdiff) - ("ruby-nokogiri" ,ruby-nokogiri))) - (native-inputs - `(("ruby-rspec-2" ,ruby-rspec-2) - ("ruby-yard" ,ruby-yard) - ("ruby-rubygems-tasks" ,ruby-rubygems-tasks))) - (synopsis "Calculate the differences between two XML/HTML documents") - (description - "@code{Nokogiri::Diff} adds the ability to calculate the + ;; Use a newer than released snapshot so that rspec-2 is not required. + (let ((commit "a38491e4d8709b7406f2cae11a50226d927d06f5")) + (package + (name "ruby-nokogiri-diff") + (version (string-append "0.2.0-1." (string-take commit 8))) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/postmodern/nokogiri-diff.git") + (commit commit))) + (file-name (string-append name "-" version "-checkout")) + (sha256 + (base32 + "1ah2sfjh9n1p0ln2wkqzfl448ml7j4zfy6dhp1qgzq2m41php6rf")))) + (build-system ruby-build-system) + (propagated-inputs + `(("ruby-tdiff" ,ruby-tdiff) + ("ruby-nokogiri" ,ruby-nokogiri))) + (native-inputs + `(("ruby-rspec" ,ruby-rspec) + ("ruby-yard" ,ruby-yard) + ("ruby-rubygems-tasks" ,ruby-rubygems-tasks))) + (synopsis "Calculate the differences between two XML/HTML documents") + (description + "@code{Nokogiri::Diff} adds the ability to calculate the differences (added or removed nodes) between two XML/HTML documents.") - (home-page "https://github.com/postmodern/nokogiri-diff") - (license license:expat))) + (home-page "https://github.com/postmodern/nokogiri-diff") + (license license:expat)))) (define-public ruby-rack (package From 63755fcd65bc76240cf447aa4f6b282cff76ff57 Mon Sep 17 00:00:00 2001 From: Ben Woodcroft Date: Mon, 7 Aug 2017 18:39:44 +1000 Subject: [PATCH 04/61] gnu: ruby-puma: Update to 3.9.1. * gnu/packages/ruby.scm (ruby-puma): Update to 3.9.1. [source]: Remove patch. [arguments]: Disable tests. [native-inputs]: Remove field. * gnu/packages/patches/ruby-puma-ignore-broken-test.patch: Delete file. * gnu/local.mk (dist_patch_DATA): Remove it. --- gnu/local.mk | 1 - .../ruby-puma-ignore-broken-test.patch | 13 ----------- gnu/packages/ruby.scm | 23 ++++--------------- 3 files changed, 4 insertions(+), 33 deletions(-) delete mode 100644 gnu/packages/patches/ruby-puma-ignore-broken-test.patch diff --git a/gnu/local.mk b/gnu/local.mk index 8c00b00208..090ce77c76 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -1006,7 +1006,6 @@ dist_patch_DATA = \ %D%/packages/patches/rsem-makefile.patch \ %D%/packages/patches/ruby-concurrent-ignore-broken-test.patch \ %D%/packages/patches/ruby-concurrent-test-arm.patch \ - %D%/packages/patches/ruby-puma-ignore-broken-test.patch \ %D%/packages/patches/ruby-rack-ignore-failing-test.patch \ %D%/packages/patches/ruby-tzinfo-data-ignore-broken-test.patch\ %D%/packages/patches/rxvt-unicode-escape-sequences.patch \ diff --git a/gnu/packages/patches/ruby-puma-ignore-broken-test.patch b/gnu/packages/patches/ruby-puma-ignore-broken-test.patch deleted file mode 100644 index 8961ffa4ca..0000000000 --- a/gnu/packages/patches/ruby-puma-ignore-broken-test.patch +++ /dev/null @@ -1,13 +0,0 @@ -diff --git a/test/test_cli.rb b/test/test_cli.rb -index 9c515c6..6bd439f 100644 ---- a/test/test_cli.rb -+++ b/test/test_cli.rb -@@ -88,7 +88,7 @@ class TestCLI < Test::Unit::TestCase - s << "GET /stats HTTP/1.0\r\n\r\n" - body = s.read - -- assert_match(/\{ "workers": 2, "phase": 0, "booted_workers": 0, "old_workers": 0, "worker_status": \[\{ "pid": \d+, "index": 0, "phase": 0, "booted": false, "last_checkin": "[^"]+", "last_status": \{\} \},\{ "pid": \d+, "index": 1, "phase": 0, "booted": false, "last_checkin": "[^"]+", "last_status": \{\} \}\] \}/, body.split("\r\n").last) -+ #assert_match(/\{ "workers": 2, "phase": 0, "booted_workers": 0, "old_workers": 0, "worker_status": \[\{ "pid": \d+, "index": 0, "phase": 0, "booted": false, "last_checkin": "[^"]+", "last_status": \{\} \},\{ "pid": \d+, "index": 1, "phase": 0, "booted": false, "last_checkin": "[^"]+", "last_status": \{\} \}\] \}/, body.split("\r\n").last) - - # wait until the first status ping has come through - sleep 6 diff --git a/gnu/packages/ruby.scm b/gnu/packages/ruby.scm index 29677dc025..7d9d51f490 100644 --- a/gnu/packages/ruby.scm +++ b/gnu/packages/ruby.scm @@ -4029,7 +4029,7 @@ part of the Prawn PDF generator.") (define-public ruby-puma (package (name "ruby-puma") - (version "3.6.0") + (version "3.9.1") (source (origin (method url-fetch) @@ -4039,32 +4039,17 @@ part of the Prawn PDF generator.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "08aws79n9slcr50d9lwm011cp1pxvr1409c2jmyjxywvrc0a30v1")) - ;; Ignore broken tests reported upstream. - ;; https://github.com/puma/puma/issues/995 - ;; https://github.com/puma/puma/issues/1044 - (patches (search-patches "ruby-puma-ignore-broken-test.patch")))) + "03pifga841h17brh4vgia8i2ybh3cmsyg0dbybzdf6dq51wzcxdx")))) (build-system ruby-build-system) (arguments - `(#:phases + `(#:tests? #f ; Tests require an out-dated version of minitest. + #:phases (modify-phases %standard-phases - (add-after 'unpack 'delete-integration-tests - (lambda _ - ;; One broken test in this file cannot be easily removed in - ;; isolation, it probably causes race conditions. So we delete - ;; the entire file. - (delete-file "test/test_integration.rb") - #t)) (add-before 'build 'fix-gemspec (lambda _ (substitute* "puma.gemspec" (("git ls-files") "find * |sort")) #t))))) - (native-inputs - `(("ruby-hoe" ,ruby-hoe) - ("ruby-rake-compiler" ,ruby-rake-compiler) - ("ruby-hoe-git" ,ruby-hoe-git) - ("ruby-rack" ,ruby-rack))) (synopsis "Simple, concurrent HTTP server for Ruby/Rack") (description "Puma is a simple, fast, threaded, and highly concurrent HTTP 1.1 server From c36e27d504fa9c1529dd2768364b7747ff45f6de Mon Sep 17 00:00:00 2001 From: Mark H Weaver Date: Mon, 7 Aug 2017 21:30:47 -0400 Subject: [PATCH 05/61] gnu: linux-libre@4.1: Update to 4.1.43. * gnu/packages/linux.scm (linux-libre-4.1): Update to 4.1.43. --- 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 ed53b79ee9..dca3421ddf 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -386,8 +386,8 @@ It has been modified to remove all non-free binary blobs.") #:configuration-file kernel-config)) (define-public linux-libre-4.1 - (make-linux-libre "4.1.42" - "1g5jhn7cm6ixn7w8ciqm6qgxv7k1jg50v6k05hsvzvrqfpaxqlbz" + (make-linux-libre "4.1.43" + "0ycqmvczj7lm7czilnwpyp14n2lzilyx7m43rsq1qdm2m5rp4q2w" %intel-compatible-systems #:configuration-file kernel-config)) From c56b08b1e5c3a07fd6de43bd75cd21a81742af7c Mon Sep 17 00:00:00 2001 From: Mark H Weaver Date: Mon, 7 Aug 2017 21:31:36 -0400 Subject: [PATCH 06/61] gnu: linux-libre@4.4: Update to 4.4.80. * gnu/packages/linux.scm (linux-libre-4.4): Update to 4.4.80. --- 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 dca3421ddf..a4f4c0559b 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -380,8 +380,8 @@ It has been modified to remove all non-free binary blobs.") #:configuration-file kernel-config)) (define-public linux-libre-4.4 - (make-linux-libre "4.4.79" - "03x1nc2fxmh29sf2fbsqzmw8qrdzv5gakr9xrg1shxh31c6xr3xr" + (make-linux-libre "4.4.80" + "1s0d7lsapghgk6jh6igx2fhzj1f6nwmvhqrl2hdwf3dx14z93mp2" %intel-compatible-systems #:configuration-file kernel-config)) From 99ccc74725e023ffcb1d7b8fcf233725c7139566 Mon Sep 17 00:00:00 2001 From: Mark H Weaver Date: Mon, 7 Aug 2017 21:32:13 -0400 Subject: [PATCH 07/61] gnu: linux-libre@4.9: Update to 4.9.41. * gnu/packages/linux.scm (linux-libre-4.9): Update to 4.9.41. --- 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 a4f4c0559b..5a925284ed 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -374,8 +374,8 @@ It has been modified to remove all non-free binary blobs.") #:configuration-file kernel-config)) (define-public linux-libre-4.9 - (make-linux-libre "4.9.40" - "1qaqi2dcydyxw79yj9pa7yxf13ss4rng7bgg0i1dl63c3g7qjgcz" + (make-linux-libre "4.9.41" + "1mkx7rvcny8b0yjkzd8zc53d15h1w8y75m0x6jx0dz3r9y3k0nql" %intel-compatible-systems #:configuration-file kernel-config)) From 4f4134c26d69349a24aa4bbd525bb9367a951a9a Mon Sep 17 00:00:00 2001 From: Mark H Weaver Date: Mon, 7 Aug 2017 21:33:03 -0400 Subject: [PATCH 08/61] gnu: linux-libre: Update to 4.12.5. * gnu/packages/linux.scm (%linux-libre-version): Update to 4.12.5. (%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 5a925284ed..7edb5793fc 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -364,8 +364,8 @@ It has been modified to remove all non-free binary blobs.") (define %intel-compatible-systems '("x86_64-linux" "i686-linux")) -(define %linux-libre-version "4.12.4") -(define %linux-libre-hash "13c6ka4fhzi41bjlssbkz84hkag7knqpvfyp2jjhm3wm25r4lhw8") +(define %linux-libre-version "4.12.5") +(define %linux-libre-hash "0kybil1h07fwl9rb0rvmp0w356hi2v1azw603r18vh9x93i8b8xi") (define-public linux-libre (make-linux-libre %linux-libre-version From 7fae2063f8e118d50050dc3dde57941414bc2976 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Mon, 7 Aug 2017 16:26:31 +0200 Subject: [PATCH 09/61] =?UTF-8?q?gnu:=20sudo:=20Use=20=E2=80=98modify-phas?= =?UTF-8?q?es=E2=80=99=20syntax.?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/admin.scm (sudo)[arguments]: Use ‘modify-phases’. --- gnu/packages/admin.scm | 48 +++++++++++++++++++++--------------------- 1 file changed, 24 insertions(+), 24 deletions(-) diff --git a/gnu/packages/admin.scm b/gnu/packages/admin.scm index c4aa108f89..c0e5269f69 100644 --- a/gnu/packages/admin.scm +++ b/gnu/packages/admin.scm @@ -13,7 +13,7 @@ ;;; Copyright © 2016 Peter Feigl ;;; Copyright © 2016 John J. Foerch ;;; Copyright © 2016, 2017 ng0 -;;; Copyright © 2016 Tobias Geerinckx-Rice +;;; Copyright © 2016, 2017 Tobias Geerinckx-Rice ;;; Copyright © 2016 John Darrington ;;; Copyright © 2017 Ben Sturmfels ;;; Copyright © 2017 Ethan R. Jones @@ -849,29 +849,29 @@ system administrator.") ;; Avoid non-determinism; see . #:parallel-build? #f - #:phases (alist-cons-before - 'configure 'pre-configure - (lambda _ - (substitute* "src/sudo_usage.h.in" - ;; Do not capture 'configure' arguments since we would - ;; unduly retain references, and also because the - ;; CPPFLAGS above would close the string literal - ;; prematurely. - (("@CONFIGURE_ARGS@") "\"\"")) - (substitute* (find-files "." "Makefile\\.in") - (("-o [[:graph:]]+ -g [[:graph:]]+") - ;; Allow installation as non-root. - "") - (("^install: (.*)install-sudoers(.*)" _ before after) - ;; Don't try to create /etc/sudoers. - (string-append "install: " before after "\n")) - (("\\$\\(DESTDIR\\)\\$\\(rundir\\)") - ;; Don't try to create /run/sudo. - "$(TMPDIR)/dummy") - (("\\$\\(DESTDIR\\)\\$\\(vardir\\)") - ;; Don't try to create /var/db/sudo. - "$(TMPDIR)/dummy"))) - %standard-phases) + #:phases + (modify-phases %standard-phases + (add-before 'configure 'pre-configure + (lambda _ + (substitute* "src/sudo_usage.h.in" + ;; Do not capture 'configure' arguments since we would + ;; unduly retain references, and also because the + ;; CPPFLAGS above would close the string literal + ;; prematurely. + (("@CONFIGURE_ARGS@") "\"\"")) + (substitute* (find-files "." "Makefile\\.in") + (("-o [[:graph:]]+ -g [[:graph:]]+") + ;; Allow installation as non-root. + "") + (("^install: (.*)install-sudoers(.*)" _ before after) + ;; Don't try to create /etc/sudoers. + (string-append "install: " before after "\n")) + (("\\$\\(DESTDIR\\)\\$\\(rundir\\)") + ;; Don't try to create /run/sudo. + "$(TMPDIR)/dummy") + (("\\$\\(DESTDIR\\)\\$\\(vardir\\)") + ;; Don't try to create /var/db/sudo. + "$(TMPDIR)/dummy"))))) ;; XXX: The 'testsudoers' test series expects user 'root' to exist, but ;; the chroot's /etc/passwd doesn't have it. Turn off the tests. From d459524713623041a662443afbee3a8c73d9bf0a Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Tue, 8 Aug 2017 04:53:58 +0200 Subject: [PATCH 10/61] gnu: moreutils: Update to 0.61. * gnu/packages/moreutils.scm (moreutils): Update to 0.61. --- gnu/packages/moreutils.scm | 15 +++++++-------- 1 file changed, 7 insertions(+), 8 deletions(-) diff --git a/gnu/packages/moreutils.scm b/gnu/packages/moreutils.scm index b343a8db6d..03ffa8f992 100644 --- a/gnu/packages/moreutils.scm +++ b/gnu/packages/moreutils.scm @@ -1,7 +1,7 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2015 Taylan Ulrich Bayırlı/Kammer ;;; Copyright © 2016, 2017 Efraim Flashner -;;; Copyright © 2016 Tobias Geerinckx-Rice +;;; Copyright © 2016, 2017 Tobias Geerinckx-Rice ;;; ;;; This file is part of GNU Guix. ;;; @@ -30,21 +30,20 @@ (define-public moreutils (package (name "moreutils") - (version "0.60") + (version "0.61") (source (origin (method url-fetch) (uri (list (string-append - "mirror://debian/pool/main/m/moreutils/moreutils_" - version ".orig.tar.xz") - ;; The main Debian mirrors only hold the current packages. + "https://git.joeyh.name/index.cgi/moreutils.git/snapshot/" + name "-" version ".tar.gz") (string-append - "http://snapshot.debian.org/archive/debian-debug/20170109T210531Z" - "/pool/main/m/moreutils/moreutils_0.60.orig.tar.xz"))) + "http://drabczyk.org/" + name "-" version ".tar.gz"))) (sha256 (base32 - "1i8pphg5i5y4x1s1hz73gqhispgspr13bysmk9vh7l6jrfx1hbg4")))) + "12rhzy8hw8vljlf10b7ys9zky0p94fdvd6ihq8w8cnkia4rd6izb")))) (build-system gnu-build-system) ;; For building the manual pages. (native-inputs From 625761a5025131606bf40b22d056aa5a3912533c Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Mon, 7 Aug 2017 03:36:52 +0200 Subject: [PATCH 11/61] gnu: aspell-dict-en: Update to 2017.01.22-0. Add missing copyright line for 2016. * gnu/packages/aspell.scm (aspell-dict-en): Update to 2017.01.22-0. --- gnu/packages/aspell.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/gnu/packages/aspell.scm b/gnu/packages/aspell.scm index 509d428f64..3469c7a3ec 100644 --- a/gnu/packages/aspell.scm +++ b/gnu/packages/aspell.scm @@ -5,6 +5,7 @@ ;;; Copyright © 2016 Efraim Flashner ;;; Copyright © 2016 Christopher Andersson ;;; Copyright © 2016 Theodoros Foradis +;;; Copyright © 2016, 2017 Tobias Geerinckx-Rice ;;; ;;; This file is part of GNU Guix. ;;; @@ -123,10 +124,10 @@ dictionaries, including personal ones.") (define-public aspell-dict-en (aspell-dictionary "en" "English" - #:version "2016.11.20-0" + #:version "2017.01.22-0" #:sha256 (base32 - "1496jnhh2jvhkzcj0p4vy89bcs4g5wz6a76m33vw4dhchn5xm9jw"))) + "1qamzpw1fsnn5n9jpsnnnzqj1a0m0xvsikmkdp5a6pmb7sp3ziwk"))) (define-public aspell-dict-eo (aspell-dictionary "eo" "Esperanto" From fc3560fff11571d33c6d979bda4270ba2df2896f Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Tue, 8 Aug 2017 05:13:44 +0200 Subject: [PATCH 12/61] gnu: hunspell: Update home page. * gnu/packages/libreoffice.scm (hunspell)[home-page]: Update it. --- gnu/packages/libreoffice.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/libreoffice.scm b/gnu/packages/libreoffice.scm index f7775ff4a0..a6f2667cba 100644 --- a/gnu/packages/libreoffice.scm +++ b/gnu/packages/libreoffice.scm @@ -707,7 +707,7 @@ Zoner Draw version 4 and 5.") (build-system gnu-build-system) (inputs `(("perl" ,perl))) - (home-page "http://hunspell.sourceforge.net/") + (home-page "https://hunspell.github.io/") (synopsis "Spell checker") (description "Hunspell is a spell checker and morphological analyzer library and program designed for languages with rich morphology and complex From a40af5d0ad707906815ffdd48bd2aec89b4cc4e9 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Tue, 8 Aug 2017 05:12:53 +0200 Subject: [PATCH 13/61] gnu: hunspell: Update to 1.6.1. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/libreoffice.scm (hunspell): Update to 1.6.1. [native-inputs]: Add autoconf, automake, and libtool. [arguments]: Add ‘bootstrap’ phase. --- gnu/packages/libreoffice.scm | 15 +++++++++++++-- 1 file changed, 13 insertions(+), 2 deletions(-) diff --git a/gnu/packages/libreoffice.scm b/gnu/packages/libreoffice.scm index a6f2667cba..5faa8db7e5 100644 --- a/gnu/packages/libreoffice.scm +++ b/gnu/packages/libreoffice.scm @@ -4,6 +4,7 @@ ;;; Copyright © 2016 Efraim Flashner ;;; Copyright © 2017 Alex Griffin ;;; Copyright © 2017 Thomas Danckaert +;;; Copyright © 2017 Tobias Geerinckx-Rice ;;; ;;; This file is part of GNU Guix. ;;; @@ -695,18 +696,28 @@ Zoner Draw version 4 and 5.") (define-public hunspell (package (name "hunspell") - (version "1.5.4") + (version "1.6.1") (source (origin (method url-fetch) (uri (string-append "https://github.com/hunspell/hunspell/archive/v" version ".tar.gz")) (sha256 (base32 - "0ngwk18dwd8p5a5f20h2jlgrz9wbc1k189mmmprb2zmqwfi02b45")) + "0j9c20sj7bgd6f77193g1ihy8w905byk2gdhdc0r9dsh7irr7x9h")) (file-name (string-append name "-" version ".tar.gz")))) (build-system gnu-build-system) + (native-inputs + `(("autoconf" ,autoconf) + ("automake" ,automake) + ("libtool" ,libtool))) (inputs `(("perl" ,perl))) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'bootstrap + (lambda _ + (zero? (system* "autoreconf" "-vfi"))))))) (home-page "https://hunspell.github.io/") (synopsis "Spell checker") (description "Hunspell is a spell checker and morphological analyzer From b998781d241234fe5a5a41721afe4db5001bdc1f Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Mon, 7 Aug 2017 06:23:47 +0200 Subject: [PATCH 14/61] gnu: pciutils: Update to 3.5.5. * gnu/packages/pciutils.scm (pciutils): Update to 3.5.5. --- gnu/packages/pciutils.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/pciutils.scm b/gnu/packages/pciutils.scm index 7c9856468d..a3d85e8386 100644 --- a/gnu/packages/pciutils.scm +++ b/gnu/packages/pciutils.scm @@ -30,7 +30,7 @@ (define-public pciutils (package (name "pciutils") - (version "3.5.4") + (version "3.5.5") (source (origin (method url-fetch) (uri (string-append @@ -38,7 +38,7 @@ version ".tar.xz")) (sha256 (base32 - "0rpy7kkb2y89wmbcbfjjjxsk2x89v5xxhxib4vpl131ip5m3qab4")))) + "1x9rb5y82rzg8b67lh42yy9ag9xr7kzibz566lffd41g37xghqhx")))) (build-system gnu-build-system) (arguments '(#:phases From cc36165efa073842bab006c77d06dabcf90bc21e Mon Sep 17 00:00:00 2001 From: Ben Woodcroft Date: Tue, 8 Aug 2017 21:52:31 +1000 Subject: [PATCH 15/61] gnu: ruby-activesupport: Update to 5.1.3. * gnu/packages/ruby.scm (ruby-activesupport): Update to 5.1.3. --- gnu/packages/ruby.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/ruby.scm b/gnu/packages/ruby.scm index 7d9d51f490..02cc6e6fde 100644 --- a/gnu/packages/ruby.scm +++ b/gnu/packages/ruby.scm @@ -2565,14 +2565,14 @@ you about the changes.") (define-public ruby-activesupport (package (name "ruby-activesupport") - (version "5.0.0") + (version "5.1.3") (source (origin (method url-fetch) (uri (rubygems-uri "activesupport" version)) (sha256 (base32 - "0k7zhnz0aw1ym8phs10r85f91ja45vsd058fm9v0h2k0igw12cpf")))) + "16r18n6b1nlky0xx2lw8c1f15gr2vm34xz5g4byjcxf88m1s07xh")))) (build-system ruby-build-system) (arguments `(#:phases From b0a21b56db6c0e0db3cf5183509f860bae697712 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Tue, 8 Aug 2017 17:41:14 +0300 Subject: [PATCH 16/61] gnu: gegl: Fix building on aarch64. * gnu/packages/gimp.scm (gegl)[arguments]: Add '-lm' configure-flag. --- gnu/packages/gimp.scm | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/gnu/packages/gimp.scm b/gnu/packages/gimp.scm index 362e2047fa..40f39b29aa 100644 --- a/gnu/packages/gimp.scm +++ b/gnu/packages/gimp.scm @@ -1,7 +1,7 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2014, 2015 Ludovic Courtès ;;; Copyright © 2016 Ricardo Wurmus -;;; Copyright © 2016 Efraim Flashner +;;; Copyright © 2016, 2017 Efraim Flashner ;;; ;;; This file is part of GNU Guix. ;;; @@ -86,6 +86,7 @@ provided as well as the framework to add new color models and data types.") `(;; More than just the one test disabled below now fails; disable them ;; all according to the rationale given below. #:tests? #f + #:configure-flags '("LDFLAGS=-lm") #:phases (alist-cons-before 'build 'pre-build From 3616ff51b33b94c388413f9a2790cab7bbbe8e72 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Tue, 8 Aug 2017 17:43:05 +0300 Subject: [PATCH 17/61] gnu: gegl: Use 'modify-phases' syntax. * gnu/packages/gimp.scm (gegl)[arguments]: Use the 'modify-phases' syntax. --- gnu/packages/gimp.scm | 32 ++++++++++++++++---------------- 1 file changed, 16 insertions(+), 16 deletions(-) diff --git a/gnu/packages/gimp.scm b/gnu/packages/gimp.scm index 40f39b29aa..cf9038c0a6 100644 --- a/gnu/packages/gimp.scm +++ b/gnu/packages/gimp.scm @@ -83,27 +83,27 @@ provided as well as the framework to add new color models and data types.") (patches (search-patches "gegl-CVE-2012-4433.patch")))) (build-system gnu-build-system) (arguments - `(;; More than just the one test disabled below now fails; disable them + '(;; More than just the one test disabled below now fails; disable them ;; all according to the rationale given below. #:tests? #f #:configure-flags '("LDFLAGS=-lm") #:phases - (alist-cons-before - 'build 'pre-build - (lambda _ - ;; This test program seems to crash on exit. Specifically, whilst - ;; g_object_unreffing bufferA and bufferB - This seems to be a bug - ;; in the destructor. This is just a test program so will not have - ;; any wider effect, although might be hiding another problem. - ;; According to advice received on irc.gimp.org#gegl although 0.2.0 - ;; is the latest released version, any bug reports against it will - ;; be ignored. So we are on our own. - (substitute* "tools/img_cmp.c" - (("g_object_unref \\(buffer.\\);") "")) + (modify-phases %standard-phases + (add-before 'build 'pre-build + (lambda _ + ;; This test program seems to crash on exit. Specifically, whilst + ;; g_object_unreffing bufferA and bufferB - This seems to be a bug + ;; in the destructor. This is just a test program so will not have + ;; any wider effect, although might be hiding another problem. + ;; According to advice received on irc.gimp.org#gegl although 0.2.0 + ;; is the latest released version, any bug reports against it will + ;; be ignored. So we are on our own. + (substitute* "tools/img_cmp.c" + (("g_object_unref \\(buffer.\\);") "")) - (substitute* "tests/compositions/Makefile" - (("/bin/sh") (which "sh")))) - %standard-phases))) + (substitute* "tests/compositions/Makefile" + (("/bin/sh") (which "sh"))) + #t))))) (inputs `(("babl" ,babl) ("glib" ,glib) From 65831c6425bf9e82c665f2fe4d0803a483f888a1 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Tue, 8 Aug 2017 18:37:55 +0300 Subject: [PATCH 18/61] gnu: babl: Update to 0.1.28. * gnu/packages/gimp.scm (babl): Update to 0.1.28. --- 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 cf9038c0a6..13d2a68dba 100644 --- a/gnu/packages/gimp.scm +++ b/gnu/packages/gimp.scm @@ -43,7 +43,7 @@ (define-public babl (package (name "babl") - (version "0.1.18") + (version "0.1.28") (source (origin (method url-fetch) (uri (list (string-append "https://download.gimp.org/pub/babl/" @@ -54,7 +54,7 @@ version ".tar.bz2"))) (sha256 (base32 - "1ygvnq22pf0zvf3bj7h67vvbpz7b8hhjvrr79ribws7sr5dljfj8")))) + "00w6xfcv960c98qvxv81gcbj8l1jiab9sggmdl77m19awwiyvwv3")))) (build-system gnu-build-system) (home-page "http://gegl.org/babl/") (synopsis "Image pixel format conversion library") From dc7b3e56337ee9d8dcd8fe7d5cab71ef536d024f Mon Sep 17 00:00:00 2001 From: Christopher Baines Date: Sat, 5 Aug 2017 22:16:47 +0100 Subject: [PATCH 19/61] services: herd: Fix matching ok responses from shepherd service. Previously the match expression case for a successful response (where error is #f) required that the result component contained a list with a single element. As far as I see when looking at the responses from the shepherd, this is not normally the case. Therefore, to avoid treating successful responses as errors, make the match requirement more permissive, accepting any value. * gnu/services/herd.scm (invoke-action): Change match condition for ok responses. --- gnu/services/herd.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/services/herd.scm b/gnu/services/herd.scm index f8d60a4802..49400aba47 100644 --- a/gnu/services/herd.scm +++ b/gnu/services/herd.scm @@ -146,7 +146,7 @@ result. Otherwise return #f." (force-output sock) (match (read sock) - (('reply ('version 0 _ ...) ('result (result)) ('error #f) + (('reply ('version 0 _ ...) ('result result) ('error #f) ('messages messages)) (for-each display-message messages) (cont result)) From 0642838b2e9ab2bd988dccb64b9e1130006347bf Mon Sep 17 00:00:00 2001 From: Christopher Baines Date: Sat, 5 Aug 2017 22:24:18 +0100 Subject: [PATCH 20/61] services: herd: Add a stop-service procedure. * gnu/services/herd.scm (stop-service): New procedure. --- gnu/services/herd.scm | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/gnu/services/herd.scm b/gnu/services/herd.scm index 49400aba47..e16d51b9d0 100644 --- a/gnu/services/herd.scm +++ b/gnu/services/herd.scm @@ -49,7 +49,8 @@ unload-services unload-service load-services - start-service)) + start-service + stop-service)) ;;; Commentary: ;;; @@ -222,6 +223,10 @@ returns a shepherd object." (with-shepherd-action name ('start) result result)) +(define (stop-service name) + (with-shepherd-action name ('stop) result + result)) + ;; Local Variables: ;; eval: (put 'alist-let* 'scheme-indent-function 2) ;; eval: (put 'with-shepherd 'scheme-indent-function 1) From 9bb47d7df855e81c70923f26934c4a75d8140df5 Mon Sep 17 00:00:00 2001 From: Christopher Baines Date: Fri, 28 Jul 2017 14:52:45 +0100 Subject: [PATCH 21/61] gnu: 0ad: Update to 0.0.22-alpha. * gnu/packages/games.scm (0ad-data, 0ad): Update to 0.0.22-alpha. --- gnu/packages/games.scm | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/gnu/packages/games.scm b/gnu/packages/games.scm index 408b3b46d0..9f32e9f8e5 100644 --- a/gnu/packages/games.scm +++ b/gnu/packages/games.scm @@ -4384,7 +4384,7 @@ fight against their plot and save his fellow rabbits from slavery.") (define-public 0ad-data (package (name "0ad-data") - (version "0.0.21-alpha") + (version "0.0.22-alpha") (source (origin (method url-fetch) @@ -4393,7 +4393,7 @@ fight against their plot and save his fellow rabbits from slavery.") (file-name (string-append name "-" version ".tar.xz")) (sha256 (base32 - "15xadyrpvq27lm9p1ny7bcmmv56m16h3xadbkdx69gfkzxc3razk")) + "0vknk9ay9h2p34r7mym2g066f3s3c5d5vmap0ckcs5b86h5cscjc")) (modules '((guix build utils))) (snippet #~(begin @@ -4438,7 +4438,7 @@ fight against their plot and save his fellow rabbits from slavery.") (define-public 0ad (package (name "0ad") - (version "0.0.21-alpha") + (version "0.0.22-alpha") (source (origin (method url-fetch) @@ -4447,7 +4447,7 @@ fight against their plot and save his fellow rabbits from slavery.") (file-name (string-append name "-" version ".tar.xz")) (sha256 (base32 - "1kw3hqnr737ipx4f03khz3hvsh3ha7r8iy9njppk2faa53j27gln")) + "1cgmr4g5g9wv36v7ylbrvqhsjwgcsdgbqwc8zlqmnayk9zgkdpgx")) ;; A snippet here would cause a build failure because of timestamps ;; reset. See https://bugs.gnu.org/26734. )) From f032d0be9c3e87116efdcfe2226030b13e794e7a Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Wed, 9 Aug 2017 00:49:35 +0200 Subject: [PATCH 22/61] gnu: Use HTTPS for gnome.org and subdomains. * gnu/packages/fonts.scm (font-bitstream-vera)[home-page]: Use HTTPS. * gnu/packages/glib.scm (glib)[home-page]: Likewise. * gnu/packages/gnome.scm (gcr, libgnome-keyring, gnome-keyring, evince) (gnome-icon-theme, libgsf, gnome-mime-data, vala, vte, python2-rsvg) (glib-networking, gnome-settings-daemon, libchamplain, grilo, grilo-plugins) (gjs, zenity, mutter, network-manager, network-manager-applet, gdm) [home-page]: Likewise. * gnu/packages/gtk.scm (gtk-engines, murrine)[home-page]: Likewise. --- gnu/packages/fonts.scm | 2 +- gnu/packages/glib.scm | 2 +- gnu/packages/gnome.scm | 42 +++++++++++++++++++++--------------------- gnu/packages/gtk.scm | 4 ++-- 4 files changed, 25 insertions(+), 25 deletions(-) diff --git a/gnu/packages/fonts.scm b/gnu/packages/fonts.scm index e421b2c6ab..b01d39c7e2 100644 --- a/gnu/packages/fonts.scm +++ b/gnu/packages/fonts.scm @@ -140,7 +140,7 @@ provide serif, sans and monospaced variants.") (base32 "1p3qs51x5327gnk71yq8cvmxc6wgx79sqxfvxcv80cdvgggjfnyv")))) (build-system font-build-system) - (home-page "http://www.gnome.org/fonts/") + (home-page "https://www.gnome.org/fonts/") (synopsis "Bitstream Vera sans-serif typeface") (description "Vera is a sans-serif typeface from Bitstream, Inc. This package provides the TrueType (TTF) files.") diff --git a/gnu/packages/glib.scm b/gnu/packages/glib.scm index fcd1daf5e8..8425b10e02 100644 --- a/gnu/packages/glib.scm +++ b/gnu/packages/glib.scm @@ -283,7 +283,7 @@ shared NFS home directories.") "GLib provides data structure handling for C, portability wrappers, and interfaces for such runtime functionality as an event loop, threads, dynamic loading, and an object system.") - (home-page "http://developer.gnome.org/glib/") + (home-page "https://developer.gnome.org/glib/") (license license:lgpl2.0+))) ; some files are under lgpl2.1+ (define gobject-introspection diff --git a/gnu/packages/gnome.scm b/gnu/packages/gnome.scm index d9d3fe7939..5e852d1a61 100644 --- a/gnu/packages/gnome.scm +++ b/gnu/packages/gnome.scm @@ -578,7 +578,7 @@ and keep up to date translations of documentation.") `(("p11-kit" ,p11-kit) ("glib" ,glib) ("gtk+" ,gtk+))) - (home-page "http://www.gnome.org") + (home-page "https://www.gnome.org") (synopsis "Libraries for displaying certificates and accessing key stores") (description "The GCR package contains libraries used for displaying certificates and @@ -609,7 +609,7 @@ GNOME Desktop.") (propagated-inputs ;; Referred to in .h files and .pc. `(("glib" ,glib))) - (home-page "http://www.gnome.org") + (home-page "https://www.gnome.org") (synopsis "Accessing passwords from the GNOME keyring") (description "Client library to access passwords from the GNOME keyring.") @@ -673,7 +673,7 @@ GNOME Desktop.") ("libxslt" ,libxslt) ;for documentation ("docbook-xml" ,docbook-xml-4.2) ("docbook-xsl" ,docbook-xsl))) - (home-page "http://www.gnome.org") + (home-page "https://www.gnome.org") (synopsis "Daemon to store passwords and encryption keys") (description "gnome-keyring is a program that keeps passwords and other secrets for @@ -744,7 +744,7 @@ forgotten when the session ends.") ("pkg-config" ,pkg-config) ("xmllint" ,libxml2))) (home-page - "http://www.gnome.org/projects/evince/") + "https://www.gnome.org/projects/evince/") (synopsis "GNOME's document viewer") (description "Evince is a document viewer for multiple document formats. It @@ -843,7 +843,7 @@ GNOME and KDE desktops to the icon names proposed in the specification.") `(("icon-naming-utils" ,icon-naming-utils) ("intltool" ,intltool) ("pkg-config" ,pkg-config))) - (home-page "http://art.gnome.org/") + (home-page "https://art.gnome.org/") (synopsis "GNOME icon theme") (description @@ -1142,7 +1142,7 @@ XML/CSS rendering engine.") `(("gdk-pixbuf" ,gdk-pixbuf) ("glib" ,glib) ("libxml2" ,libxml2))) - (home-page "http://www.gnome.org/projects/libgsf") + (home-page "https://www.gnome.org/projects/libgsf") (synopsis "GNOME's Structured File Library") (description "Libgsf aims to provide an efficient extensible I/O abstraction for @@ -1366,7 +1366,7 @@ is intended for user preferences; not arbitrary data storage.") (native-inputs `(("perl" ,perl) ("intltool" ,intltool))) - (home-page "http://www.gnome.org") + (home-page "https://www.gnome.org") (synopsis "Base MIME and Application database for GNOME") (description "GNOME Mime Data is a module which contains the base MIME and Application database for GNOME. The data stored by this module is @@ -1984,7 +1984,7 @@ passwords in the GNOME keyring.") ("gobject-introspection" ,gobject-introspection))) ; for gir tests (propagated-inputs `(("glib" ,glib))) ; required by libvala-0.26.pc - (home-page "http://live.gnome.org/Vala/") + (home-page "https://live.gnome.org/Vala/") (synopsis "Compiler for the GObject type system") (description "Vala is a programming language that aims to bring modern programming @@ -2018,7 +2018,7 @@ libraries written in C.") `(("gtk+" ,gtk+) ;required by vte-2.91.pc ("gnutls" ,gnutls) ;ditto ("pcre2" ,pcre2))) ;ditto - (home-page "http://www.gnome.org/") + (home-page "https://www.gnome.org/") (synopsis "Virtual Terminal Emulator") (description "VTE is a library (libvte) implementing a terminal emulator widget for @@ -2288,7 +2288,7 @@ indicators etc).") `(("python" ,python-2) ("python2-pygtk" ,python2-pygtk) ("librsvg" ,librsvg))) - (home-page "http://www.gnome.org") + (home-page "https://www.gnome.org") (synopsis "Python bindings to librsvg") (description "This packages provides Python bindings to librsvg, the SVG rendering @@ -2339,7 +2339,7 @@ library.") ("gnutls" ,gnutls) ("gsettings-desktop-schemas" ,gsettings-desktop-schemas) ("p11-kit" ,p11-kit))) - (home-page "http://www.gnome.org") + (home-page "https://www.gnome.org") (synopsis "Network-related GIO modules") (description "This package contains various network related extensions for the GIO @@ -2961,7 +2961,7 @@ services for numerous locations.") ("librsvg" ,librsvg) ("xf86-input-wacom" ,xf86-input-wacom) ("network-manager" ,network-manager))) - (home-page "http://www.gnome.org") + (home-page "https://www.gnome.org") (synopsis "GNOME settings daemon") (description "This package contains the daemon responsible for setting the various @@ -3284,7 +3284,7 @@ GL based interactive canvas library.") ("cairo" ,cairo) ("gtk+3" ,gtk+) ("glib" ,glib))) - (home-page "http://projects.gnome.org/libchamplain/") + (home-page "https://projects.gnome.org/libchamplain/") (synopsis "C library providing a ClutterActor to display maps") (description "libchamplain is a C library providing a ClutterActor to display maps. @@ -3453,7 +3453,7 @@ as possible!") (variable "GRL_PLUGIN_PATH") (files (list (string-append "lib/grilo-" (version-major+minor version))))))) - (home-page "http://live.gnome.org/Grilo") + (home-page "https://live.gnome.org/Grilo") (synopsis "Framework for discovering and browsing media") (description "Grilo is a framework focused on making media discovery and browsing easy @@ -3506,7 +3506,7 @@ for application developers.") ;; with: "assertion failed: (source)". Outside of the build container, ;; most tests succeed. #:tests? #f)) - (home-page "http://live.gnome.org/Grilo") + (home-page "https://live.gnome.org/Grilo") (synopsis "Plugins for the Grilo media discovery library") (description "Grilo is a framework focused on making media discovery and browsing easy @@ -4505,7 +4505,7 @@ configuration program to choose applications starting on login.") `(("gtk+" ,gtk+) ("readline" ,readline))) (synopsis "Javascript bindings for GNOME") - (home-page "http://live.gnome.org/Gjs") + (home-page "https://live.gnome.org/Gjs") (description "Gjs is a javascript binding for GNOME. It's mainly based on spidermonkey javascript engine and the GObject introspection framework.") @@ -4592,7 +4592,7 @@ powerful general purpose text editor.") `(("libnotify" ,libnotify) ("webkitgtk" ,webkitgtk))) (synopsis "Display graphical dialog boxes from shell scripts") - (home-page "http://www.gnome.org") + (home-page "https://www.gnome.org") (description "Zenity is a rewrite of gdialog, the GNOME port of dialog which allows you to display dialog boxes from the commandline and shell scripts.") @@ -4690,7 +4690,7 @@ to display dialog boxes from the commandline and shell scripts.") ("xkeyboard-config" ,xkeyboard-config) ("zenity" ,zenity))) (synopsis "Window and compositing manager") - (home-page "http://www.gnome.org") + (home-page "https://www.gnome.org") (description "Mutter is a window and compositing manager that displays and manages your desktop via OpenGL. Mutter combines a sophisticated display engine using the @@ -4975,7 +4975,7 @@ users.") ("util-linux" ,util-linux) ("elogind" ,elogind))) (synopsis "Network connection manager") - (home-page "http://www.gnome.org/projects/NetworkManager/") + (home-page "https://www.gnome.org/projects/NetworkManager/") (description "NetworkManager is a system network service that manages your network devices and connections, attempting to keep active network connectivity when @@ -5038,7 +5038,7 @@ services.") ("jansson" ,jansson) ; for team support ("modem-manager" ,modem-manager))) (synopsis "Applet for managing network connections") - (home-page "http://www.gnome.org/projects/NetworkManager/") + (home-page "https://www.gnome.org/projects/NetworkManager/") (description "This package contains a systray applet for NetworkManager. It displays the available networks and allows users to easily switch between them.") @@ -5139,7 +5139,7 @@ libxml2.") ("libcanberra" ,libcanberra) ("linux-pam" ,linux-pam))) (synopsis "Display manager for GNOME") - (home-page "http://wiki.gnome.org/Projects/GDM/") + (home-page "https://wiki.gnome.org/Projects/GDM/") (description "GNOME Display Manager is a system service that is responsible for providing graphical log-ins and managing local and remote displays.") diff --git a/gnu/packages/gtk.scm b/gnu/packages/gtk.scm index b2aa6ecff5..e942f51719 100644 --- a/gnu/packages/gtk.scm +++ b/gnu/packages/gtk.scm @@ -1355,7 +1355,7 @@ can also be used to document application code.") (inputs ;; Don't propagate GTK+ to reduce "profile pollution". `(("gtk+" ,gtk+-2))) ; required by gtk-engines-2.pc - (home-page "http://live.gnome.org/GnomeArt") + (home-page "https://live.gnome.org/GnomeArt") (synopsis "Theming engines for GTK+ 2.x") (description "This package contains the standard GTK+ 2.x theming engines including @@ -1385,7 +1385,7 @@ Redmond95 and ThinIce.") ("intltool" ,intltool))) (propagated-inputs `(("gtk+" ,gtk+-2))) - (home-page "http://live.gnome.org/GnomeArt") + (home-page "https://live.gnome.org/GnomeArt") (synopsis "Cairo-based theming engine for GTK+ 2.x") (description "Murrine is a cairo-based GTK+ theming engine. It is named after the From e2bf423ab4b2a8f9c1d7fee1f66d8107e23a210d Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Tue, 8 Aug 2017 23:12:35 +0200 Subject: [PATCH 23/61] gnu: brasero: Update to 3.12.2. * gnu/packages/gnome.scm (brasero): Update to 3.12.2. --- gnu/packages/gnome.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/gnome.scm b/gnu/packages/gnome.scm index 5e852d1a61..9d3f35229f 100644 --- a/gnu/packages/gnome.scm +++ b/gnu/packages/gnome.scm @@ -141,7 +141,7 @@ (define-public brasero (package (name "brasero") - (version "3.12.1") + (version "3.12.2") (source (origin (method url-fetch) (uri (string-append "mirror://gnome/sources/" name "/" @@ -149,7 +149,7 @@ name "-" version ".tar.xz")) (sha256 (base32 - "09vi2hyhl0bz7imv3ky6h7x5m3d546n968wcghydwrkvwm9ylpls")))) + "0h90y674j26rvjahb8cc0w79zx477rb6zaqcj26wzvq8kmpic8k8")))) (build-system glib-or-gtk-build-system) (arguments `(#:configure-flags (list @@ -165,7 +165,7 @@ (lambda* (#:key inputs #:allow-other-keys) (substitute* "plugins/growisofs/burn-growisofs.c" (("\"growisofs") (string-append "\"" (which "growisofs")))) - #t ))))) + #t))))) (propagated-inputs `(("hicolor-icon-theme" ,hicolor-icon-theme))) (native-inputs From 9099bedfeae4ecfdbba967fece4f0850973e02f5 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Tue, 8 Aug 2017 23:50:34 +0200 Subject: [PATCH 24/61] gnu: gnumeric: Update to 1.12.35. * gnu/packages/gnome.scm (gnumeric): Update to 1.12.35. --- gnu/packages/gnome.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/gnome.scm b/gnu/packages/gnome.scm index 9d3f35229f..c3963d556b 100644 --- a/gnu/packages/gnome.scm +++ b/gnu/packages/gnome.scm @@ -1821,7 +1821,7 @@ Hints specification (EWMH).") (define-public gnumeric (package (name "gnumeric") - (version "1.12.34") + (version "1.12.35") (source (origin (method url-fetch) (uri (string-append "mirror://gnome/sources/" name "/" @@ -1829,7 +1829,7 @@ Hints specification (EWMH).") name "-" version ".tar.xz")) (sha256 (base32 - "09f7h4lvwzyl0amd3axapwbsrnrvvpwxyhs540jlrv425n0j0j8b")))) + "02kcq2af16m9mlzgkbdzswhw0nl6zf01dmvsfq3shy1mab7f7cbp")))) (build-system glib-or-gtk-build-system) (arguments `(;; The gnumeric developers don't worry much about failing tests. From a801ae4cae3f2260e4a8cb3c3f342efdead31cb5 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Tue, 8 Aug 2017 23:43:13 +0200 Subject: [PATCH 25/61] gnu: gspell: Order inputs alphabetically. * gnu/packages/gnome.scm (gspell)[inputs, native-inputs]: Re-order. --- gnu/packages/gnome.scm | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/gnu/packages/gnome.scm b/gnu/packages/gnome.scm index c3963d556b..95c9246d41 100644 --- a/gnu/packages/gnome.scm +++ b/gnu/packages/gnome.scm @@ -6454,17 +6454,17 @@ that support the Assistive Technology Service Provider Interface (AT-SPI).") #t))))) (inputs `(("enchant" ,enchant) - ("iso-codes" ,iso-codes) ("gtk+" ,gtk+) - ("glib" ,glib))) + ("glib" ,glib) + ("iso-codes" ,iso-codes))) (native-inputs `(("glib" ,glib "bin") ("pkg-config" ,pkg-config) ("xmllint" ,libxml2) ;; For tests. - ("xorg-server" ,xorg-server) - ("aspell-dict-en" ,aspell-dict-en))) + ("aspell-dict-en" ,aspell-dict-en) + ("xorg-server" ,xorg-server))) (home-page "https://wiki.gnome.org/Projects/gspell") (synopsis "GNOME's alternative spell checker") (description From eccd35be3d2afe276a7fb5be6ac8646c84fe5db5 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Wed, 9 Aug 2017 00:05:17 +0200 Subject: [PATCH 26/61] gnu: gspell: Propagate enchant dependency. * gnu/packages/gnome.scm (gspell)[inputs]: Move enchant from here... [propagated-inputs]: ...to here. --- gnu/packages/gnome.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/gnu/packages/gnome.scm b/gnu/packages/gnome.scm index 95c9246d41..6e8bb90f78 100644 --- a/gnu/packages/gnome.scm +++ b/gnu/packages/gnome.scm @@ -6453,8 +6453,7 @@ that support the Assistive Technology Service Provider Interface (AT-SPI).") "/lib/aspell")) #t))))) (inputs - `(("enchant" ,enchant) - ("gtk+" ,gtk+) + `(("gtk+" ,gtk+) ("glib" ,glib) ("iso-codes" ,iso-codes))) (native-inputs @@ -6465,6 +6464,8 @@ that support the Assistive Technology Service Provider Interface (AT-SPI).") ;; For tests. ("aspell-dict-en" ,aspell-dict-en) ("xorg-server" ,xorg-server))) + (propagated-inputs + `(("enchant" ,enchant))) ; enchant.pc is required by gspell-1.pc (home-page "https://wiki.gnome.org/Projects/gspell") (synopsis "GNOME's alternative spell checker") (description From e3705bb6ea64dec48eff76a81cfa04cbf134962f Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Wed, 9 Aug 2017 00:09:13 +0200 Subject: [PATCH 27/61] gnu: gedit: Update to 3.22.1. * gnu/packages/gnome.scm (gedit): Update to 3.22.1. --- gnu/packages/gnome.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/gnome.scm b/gnu/packages/gnome.scm index 6e8bb90f78..deac8b4ddb 100644 --- a/gnu/packages/gnome.scm +++ b/gnu/packages/gnome.scm @@ -4514,7 +4514,7 @@ javascript engine and the GObject introspection framework.") (define-public gedit (package (name "gedit") - (version "3.22.0") + (version "3.22.1") (source (origin (method url-fetch) (uri (string-append "mirror://gnome/sources/" name "/" @@ -4522,7 +4522,7 @@ javascript engine and the GObject introspection framework.") name "-" version ".tar.xz")) (sha256 (base32 - "0i9z5d31vibb3dd329gwvyga38zq5k1a2glcdq7m93ycbl5mlfq6")))) + "0as9r5zvnyrxh699q6jnd0p9ddqy5qamfbxggpdjzagzixhw6yxa")))) (build-system glib-or-gtk-build-system) (arguments `(#:configure-flags '("--disable-spell") ; XXX: gspell not packaged yet From 0d2df50caf3076f99884f0d773f2208202962bd7 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Wed, 9 Aug 2017 00:11:35 +0200 Subject: [PATCH 28/61] gnu: gedit: Support gspell. * gnu/packages/gnome.scm (gedit)[arguments]: Remove #:configure-flags. [inputs]: Add gspell. --- gnu/packages/gnome.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/gnome.scm b/gnu/packages/gnome.scm index deac8b4ddb..60017df5c8 100644 --- a/gnu/packages/gnome.scm +++ b/gnu/packages/gnome.scm @@ -4525,8 +4525,7 @@ javascript engine and the GObject introspection framework.") "0as9r5zvnyrxh699q6jnd0p9ddqy5qamfbxggpdjzagzixhw6yxa")))) (build-system glib-or-gtk-build-system) (arguments - `(#:configure-flags '("--disable-spell") ; XXX: gspell not packaged yet - #:phases + `(#:phases (modify-phases %standard-phases (add-after 'install 'wrap-gedit @@ -4552,6 +4551,7 @@ javascript engine and the GObject introspection framework.") ("pkg-config" ,pkg-config))) (inputs `(("glib" ,glib) + ("gspell" ,gspell) ("gtk+" ,gtk+) ("gtksourceview" ,gtksourceview) ("libpeas" ,libpeas) From a51fc34c2881a2610e308cd972b283eddf07fe73 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Wed, 9 Aug 2017 00:13:42 +0200 Subject: [PATCH 29/61] gnu: mutter: Update to 3.24.4. * gnu/packages/gnome.scm (mutter): Update to 3.24.4. --- gnu/packages/gnome.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/gnome.scm b/gnu/packages/gnome.scm index 60017df5c8..b19d14ff80 100644 --- a/gnu/packages/gnome.scm +++ b/gnu/packages/gnome.scm @@ -4601,7 +4601,7 @@ to display dialog boxes from the commandline and shell scripts.") (define-public mutter (package (name "mutter") - (version "3.24.2") + (version "3.24.4") (source (origin (method url-fetch) (uri (string-append "mirror://gnome/sources/" name "/" @@ -4609,7 +4609,7 @@ to display dialog boxes from the commandline and shell scripts.") name "-" version ".tar.xz")) (sha256 (base32 - "043q3384vwrkjdfhbwn9pwdml6z0g0ad0cj2fjnjzg6402i67071")))) + "1slspy5krbqfvnma72lvdnxjf8ag2cvxssa8bvi7y3xxy7xv603k")))) ;; NOTE: Since version 3.21.x, mutter now bundles and exports forked ;; versions of cogl and clutter. As a result, many of the inputs, ;; propagated-inputs, and configure flags used in cogl and clutter are From 666901b29807a255d3eaa6226ee5be60ef7e9f2f Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Wed, 9 Aug 2017 01:11:07 +0200 Subject: [PATCH 30/61] gnu: gnome-online-accounts: Update to 3.24.2. * gnu/packages/gnome.scm (gnome-online-accounts): Update to 3.24.2. --- gnu/packages/gnome.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/gnome.scm b/gnu/packages/gnome.scm index b19d14ff80..11d787a830 100644 --- a/gnu/packages/gnome.scm +++ b/gnu/packages/gnome.scm @@ -4701,7 +4701,7 @@ window manager.") (define-public gnome-online-accounts (package (name "gnome-online-accounts") - (version "3.24.1") + (version "3.24.2") (source (origin (method url-fetch) (uri (string-append "mirror://gnome/sources/" name "/" @@ -4709,7 +4709,7 @@ window manager.") name "-" version ".tar.xz")) (sha256 (base32 - "0lgniqmkr6ffdw3kcqd34lvp969j2q2qzcy30zkzl5c09r7anc0a")))) + "1fmgywfcvlb5sa0slxxlg80gafiaal8vnq6h5lcybqa12lnxa2mp")))) (build-system glib-or-gtk-build-system) (native-inputs `(("glib:bin" ,glib "bin") ; for glib-compile-schemas, etc. From c762011e4033378f47c226135df9aa52adfa20c4 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Wed, 9 Aug 2017 01:20:11 +0200 Subject: [PATCH 31/61] gnu: tracker: Update to 1.12.2. * gnu/packages/gnome.scm (tracker): Update to 1.12.2. --- gnu/packages/gnome.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/gnome.scm b/gnu/packages/gnome.scm index 11d787a830..d5b65b4bec 100644 --- a/gnu/packages/gnome.scm +++ b/gnu/packages/gnome.scm @@ -5432,7 +5432,7 @@ easy, safe, and automatic.") (define-public tracker (package (name "tracker") - (version "1.12.0") + (version "1.12.2") (source (origin (method url-fetch) (uri (string-append "mirror://gnome/sources/" name "/" @@ -5440,7 +5440,7 @@ easy, safe, and automatic.") name "-" version ".tar.xz")) (sha256 (base32 - "0vsrzzkcfvmylhpk1ww6xdx8z9sgjs0gn74gz82qngjyq3c3s6c3")))) + "1zdzh8l5ahi906i40i4pqw2cs1hwrl6l9a7fp344a3idk3pl5szb")))) (build-system glib-or-gtk-build-system) (native-inputs `(("gnome-common" ,gnome-common) From 026051953d5357a6619b17a8672569dfe180ba1b Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Wed, 9 Aug 2017 00:32:45 +0200 Subject: [PATCH 32/61] gnu: epiphany: Update to 3.24.3. * gnu/packages/gnome.scm (epiphany): Update to 3.24.3. --- gnu/packages/gnome.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/gnome.scm b/gnu/packages/gnome.scm index d5b65b4bec..ed4def65b5 100644 --- a/gnu/packages/gnome.scm +++ b/gnu/packages/gnome.scm @@ -4028,7 +4028,7 @@ a secret password store, an adblocker, and a modern UI.") (define-public epiphany (package (name "epiphany") - (version "3.24.2") + (version "3.24.3") (source (origin (method url-fetch) (uri (string-append "mirror://gnome/sources/" name "/" @@ -4036,7 +4036,7 @@ a secret password store, an adblocker, and a modern UI.") name "-" version ".tar.xz")) (sha256 (base32 - "13f5h7mbxdyjf93jp46hiaxsrngpr6frgf69d8iza7arc060vg2s")))) + "0m51cclpnb7lxk8w526rriyb2bi3aj17fbcvikhkg7qd65v1dxgy")))) (build-system glib-or-gtk-build-system) (arguments ;; FIXME: tests run under Xvfb, but fail with: From 41a46a5035b52401fc2fa36d07614d060becaddb Mon Sep 17 00:00:00 2001 From: Eric Bavier Date: Tue, 8 Aug 2017 00:19:05 -0500 Subject: [PATCH 33/61] gnu: petsc: Update to 3.7.6. * gnu/packages/maths.scm (petsc): Update to 3.7.6. --- gnu/packages/maths.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index e204588dd5..55b559e442 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -2,7 +2,7 @@ ;;; Copyright © 2013, 2014, 2015, 2016 Andreas Enge ;;; Copyright © 2013 Nikita Karetnikov ;;; Copyright © 2014, 2016, 2017 John Darrington -;;; Copyright © 2014, 2015, 2016 Eric Bavier +;;; Copyright © 2014, 2015, 2016, 2017 Eric Bavier ;;; Copyright © 2014 Federico Beffa ;;; Copyright © 2014 Mathieu Lirzin ;;; Copyright © 2015, 2016, 2017 Ricardo Wurmus @@ -1216,7 +1216,7 @@ September 2004}") (define-public petsc (package (name "petsc") - (version "3.7.2") + (version "3.7.6") (source (origin (method url-fetch) @@ -1224,7 +1224,7 @@ September 2004}") (uri (string-append "http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/" "petsc-lite-" version ".tar.gz")) (sha256 - (base32 "0jfrq6rd4zagw1iimz05m2w91k0jvz3qbik1lk8pqcxw3rvdqk5d")))) + (base32 "1y3f5jjq0v5b62i3sabp4kp5mgfyp3vnk0dxhwkrhpypax77nzxh")))) (build-system gnu-build-system) (native-inputs `(("python" ,python-2) From baeaf8821d24cce25b1ecf4a58496ec59545a2d5 Mon Sep 17 00:00:00 2001 From: Eric Bavier Date: Tue, 8 Aug 2017 00:19:51 -0500 Subject: [PATCH 34/61] gnu: slepc: Update to 3.7.4. * gnu/packages/maths.scm (slepc): Update to 3.7.4. [source]: Use direct source link. Remove 'file-name' field. --- gnu/packages/maths.scm | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 55b559e442..54db44b3df 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -1342,16 +1342,15 @@ scientific applications modeled by partial differential equations.") (define-public slepc (package (name "slepc") - (version "3.7.1") + (version "3.7.4") (source (origin (method url-fetch) - (uri (string-append "http://slepc.upv.es/download/download.php?" - "filename=slepc-" version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) + (uri (string-append "http://slepc.upv.es/download/distrib/slepc-" + version ".tar.gz")) (sha256 (base32 - "1hijlmrvxvfqslnx8yydzw5xqbsn1yy02g32w0hln1z3cgr1c0k7")))) + "12pbl8yd6r8k9xjlr1qw25rs0k1acgic7hw1s6l6bhiv9s285drg")))) (build-system gnu-build-system) (native-inputs `(("python" ,python-2))) From 9731c412e9ef2fad66181460e768b01cb3c600da Mon Sep 17 00:00:00 2001 From: Eric Bavier Date: Tue, 8 Aug 2017 00:21:20 -0500 Subject: [PATCH 35/61] gnu: petsc, slepc: Use 'parallel-job-count'. * gnu/packages/maths.scm (petsc, slepc)[arguments]: Set #:make-flags to override default unlimited '-j'. (petsc)[arguments]: Scrub build machine cores from installed files in 'clean-local-references' phase. --- gnu/packages/maths.scm | 12 +++++++++++- 1 file changed, 11 insertions(+), 1 deletion(-) diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 54db44b3df..cc9a9a40a8 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -1247,6 +1247,10 @@ September 2004}") (assoc-ref %build-inputs "superlu") "/include") ,(string-append "--with-superlu-lib=" (assoc-ref %build-inputs "superlu") "/lib/libsuperlu.a")) + #:make-flags + ;; Honor (parallel-job-count) for build. Do not use --with-make-np, + ;; whose value is dumped to $out/lib/petsc/conf/petscvariables. + (list (format #f "MAKE_NP=~a" (parallel-job-count))) #:phases (modify-phases %standard-phases (replace 'configure @@ -1261,13 +1265,17 @@ September 2004}") (format #t "configure flags: ~s~%" flags) (zero? (apply system* "./configure" flags))))) (add-after 'configure 'clean-local-references - (lambda* (#:key inputs outputs #:allow-other-keys) + (lambda* (#:key outputs #:allow-other-keys) (let ((out (assoc-ref outputs "out"))) (substitute* (find-files "." "^petsc(conf|machineinfo).h$") ;; Prevent build directory from leaking into compiled code (((getcwd)) out) ;; Scrub timestamp for reproducibility ((".*Libraries compiled on.*") "")) + (substitute* (find-files "." "petscvariables") + ;; Do not expose build machine characteristics, set to defaults. + (("MAKE_NP = [:digit:]+") "MAKE_NP = 2") + (("NPMAX = [:digit:]+") "NPMAX = 2")) #t))) (add-after 'install 'clean-install ;; Try to keep installed files from leaking build directory names. @@ -1364,6 +1372,8 @@ scientific applications modeled by partial differential equations.") #:configure-flags `(,(string-append "--with-arpack-dir=" (assoc-ref %build-inputs "arpack") "/lib")) + #:make-flags ;honor (parallel-job-count) + `(,(format #f "MAKE_NP=~a" (parallel-job-count))) #:phases (modify-phases %standard-phases (replace 'configure From 2509522c4f4be4491418e65b764862a05444f460 Mon Sep 17 00:00:00 2001 From: Eric Bavier Date: Tue, 8 Aug 2017 20:00:09 -0500 Subject: [PATCH 36/61] gnu: suitesparse: Use modify-phases. * gnu/packages/maths.scm (suitesparse)[arguments]: Use modify-phases. --- gnu/packages/maths.scm | 17 ++++++++--------- 1 file changed, 8 insertions(+), 9 deletions(-) diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index cc9a9a40a8..5f2697e13c 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -2448,15 +2448,14 @@ Fresnel integrals, and similar related functions as well.") (string-append "INSTALL_INCLUDE=" (assoc-ref %outputs "out") "/include")) #:phases - (alist-cons-before - 'install 'prepare-out - ;; README.txt states that the target directories must exist prior to - ;; running "make install". - (lambda _ - (mkdir-p (string-append (assoc-ref %outputs "out") "/lib")) - (mkdir-p (string-append (assoc-ref %outputs "out") "/include"))) - ;; no configure script - (alist-delete 'configure %standard-phases)))) + (modify-phases %standard-phases + (delete 'configure) ;no configure script + (add-before 'install 'prepare-out + ;; README.txt states that the target directories must exist prior to + ;; running "make install". + (lambda _ + (mkdir-p (string-append (assoc-ref %outputs "out") "/lib")) + (mkdir-p (string-append (assoc-ref %outputs "out") "/include"))))))) (inputs `(("tbb" ,tbb) ("lapack" ,lapack))) From bd5b5ac0c5721d85c8031f85df8a02b245170018 Mon Sep 17 00:00:00 2001 From: Eric Bavier Date: Tue, 8 Aug 2017 21:43:15 -0500 Subject: [PATCH 37/61] gnu: suitesparse: Update to 4.5.5. * gnu/packages/maths.scm (suitesparse): Update to 4.5.5. [source]: Add 'modules' and 'snippet' field to remove bundled source. [arguments]: Remove 'prepare-out' phase. Adjust #:make-flags for metis. Make build parallel, since it now appears to be safe. [inputs]: Add metis. --- gnu/packages/maths.scm | 27 +++++++++++++-------------- 1 file changed, 13 insertions(+), 14 deletions(-) diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 5f2697e13c..78c77b6813 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -2424,7 +2424,7 @@ Fresnel integrals, and similar related functions as well.") (define-public suitesparse (package (name "suitesparse") - (version "4.4.3") + (version "4.5.5") (source (origin (method url-fetch) @@ -2433,32 +2433,31 @@ Fresnel integrals, and similar related functions as well.") version ".tar.gz")) (sha256 (base32 - "100hdzr0mf4mzlwnqpmwpfw4pymgsf9n3g0ywb1yps2nk1zbkdy5")))) + "1dnr6pmjzc2qmbkmb4shigx1l74ilf6abn7svyd6brxgvph8vadr")) + (modules '((guix build utils))) + (snippet + ;; Remove bundled metis source + '(delete-file-recursively "metis-5.1.0")))) (build-system gnu-build-system) (arguments - '(#:parallel-build? #f ;cholmod build fails otherwise - #:tests? #f ;no "check" target + '(#:tests? #f ;no "check" target #:make-flags (list "CC=gcc" "BLAS=-lblas" "TBB=-ltbb" - "CHOLMOD_CONFIG=-DNPARTITION" ;required when METIS is not used + "MY_METIS_LIB=-lmetis" (string-append "INSTALL_LIB=" (assoc-ref %outputs "out") "/lib") (string-append "INSTALL_INCLUDE=" - (assoc-ref %outputs "out") "/include")) + (assoc-ref %outputs "out") "/include") + "library") #:phases (modify-phases %standard-phases - (delete 'configure) ;no configure script - (add-before 'install 'prepare-out - ;; README.txt states that the target directories must exist prior to - ;; running "make install". - (lambda _ - (mkdir-p (string-append (assoc-ref %outputs "out") "/lib")) - (mkdir-p (string-append (assoc-ref %outputs "out") "/include"))))))) + (delete 'configure)))) ;no configure script (inputs `(("tbb" ,tbb) - ("lapack" ,lapack))) + ("lapack" ,lapack) + ("metis" ,metis))) (home-page "http://faculty.cse.tamu.edu/davis/suitesparse.html") (synopsis "Suite of sparse matrix software") (description From 05cca6ce90407f19619a097815c53e5bd90d7780 Mon Sep 17 00:00:00 2001 From: Eric Bavier Date: Tue, 8 Aug 2017 21:46:19 -0500 Subject: [PATCH 38/61] gnu: stress-make: Patch default shell. * gnu/packages/debug.scm (stress-make)[arguments]: Add 'set-default-shell phase. --- gnu/packages/debug.scm | 36 +++++++++++++++++++++--------------- 1 file changed, 21 insertions(+), 15 deletions(-) diff --git a/gnu/packages/debug.scm b/gnu/packages/debug.scm index 34c1061418..bde06f35b9 100644 --- a/gnu/packages/debug.scm +++ b/gnu/packages/debug.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2014, 2015, 2016 Eric Bavier +;;; Copyright © 2014, 2015, 2016, 2017 Eric Bavier ;;; ;;; This file is part of GNU Guix. ;;; @@ -287,20 +287,26 @@ down the road.") ;; not accept a directory name instead. To let the gnu-build-system's ;; patch-* phases work properly, we unpack the source first, then ;; repack before the configure phase. - `(#:configure-flags '("--with-make-tar=./make.tar.xz") - #:phases - (modify-phases %standard-phases - (add-after 'unpack 'unpack-make - (lambda* (#:key inputs #:allow-other-keys) - (zero? (system* "tar" "xf" (assoc-ref inputs "make-source"))))) - (add-before 'configure 'repack-make - (lambda _ - (zero? (system* "tar" "cJf" "./make.tar.xz" - (string-append "make-" - ,(package-version gnu-make)))))) - (add-before 'configure 'bootstrap - (lambda _ - (zero? (system* "autoreconf" "-vfi"))))))) + (let ((make-dir (string-append "make-" (package-version gnu-make)))) + `(#:configure-flags '("--with-make-tar=./make.tar.xz") + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'unpack-make + (lambda* (#:key inputs #:allow-other-keys) + (zero? (system* "tar" "xf" (assoc-ref inputs "make-source"))))) + (add-after 'unpack-make 'set-default-shell + (lambda _ + ;; Taken mostly directly from (@ (gnu packages base) gnu-make) + (substitute* (string-append ,make-dir "/job.c") + (("default_shell = .*$") + (format #f "default_shell = \"~a\";\n" + (which "sh")))))) + (add-before 'configure 'repack-make + (lambda _ + (zero? (system* "tar" "cJf" "./make.tar.xz" ,make-dir)))) + (add-before 'configure 'bootstrap + (lambda _ + (zero? (system* "autoreconf" "-vfi")))))))) (home-page "https://github.com/losalamos/stress-make") (synopsis "Expose race conditions in Makefiles") (description From d84b09e937e7c5529d124744c84574a0637c3410 Mon Sep 17 00:00:00 2001 From: Eric Bavier Date: Wed, 9 Aug 2017 01:08:10 -0500 Subject: [PATCH 39/61] gnu: dealii: Update to 8.5.0. * gnu/packages/maths.scm (dealii): Update to 8.5.0. [arguments]: Delete 'hint-example-prefix phase, which would need adjusting for this version. Users can use e.g. 'export DEAL_II_DIR=$GUIX_ENVIRONMENT'. Adjust configuration flags. --- gnu/packages/maths.scm | 23 ++++++----------------- 1 file changed, 6 insertions(+), 17 deletions(-) diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 78c77b6813..6597191805 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -2693,7 +2693,7 @@ revised simplex and the branch-and-bound methods.") (define-public dealii (package (name "dealii") - (version "8.4.1") + (version "8.5.0") (source (origin (method url-fetch) @@ -2701,7 +2701,7 @@ revised simplex and the branch-and-bound methods.") "download/v" version "/dealii-" version ".tar.gz")) (sha256 (base32 - "1bdksvvyp1rj37df1ndh8j3x9nzpc3sazw8nd0hzvnlw0qnyk800")) + "0yfpy4zh8j7hmqakw17zdlmvfdcmhwgs66wcb716plc4y7v3z4g6")) (modules '((guix build utils))) (snippet ;; Remove bundled sources: UMFPACK, TBB, muParser, and boost @@ -2720,21 +2720,10 @@ revised simplex and the branch-and-bound methods.") ("suitesparse" ,suitesparse))) ;for UMFPACK (arguments `(#:build-type "DebugRelease" ;only supports Release, Debug, or DebugRelease - #:configure-flags '("-DCOMPAT_FILES=OFF") ;Follow new directory structure - #:phases (modify-phases %standard-phases - (add-after - 'install 'hint-example-prefix - ;; Set Cmake hints in examples so that they can find this - ;; deal.II when configuring. - (lambda* (#:key outputs #:allow-other-keys) - (let* ((out (assoc-ref %outputs "out")) - (exmpl (string-append out "/share/doc" - "/dealii/examples"))) - (substitute* (find-files exmpl "CMakeLists.txt") - (("([[:space:]]*HINTS.*)\n" _ line) - (string-append line " $ENV{HOME}/.guix-profile " - out "\n"))) - #t)))))) + #:configure-flags + ;; Work around a bug in libsuitesparseconfig linking + ;; see https://github.com/dealii/dealii/issues/4745 + '("-DCMAKE_POSITION_INDEPENDENT_CODE:BOOL=ON"))) (home-page "https://www.dealii.org") (synopsis "Finite element library") (description From c608fe8cf3988fff0e352f0cf563a060f79b4fb4 Mon Sep 17 00:00:00 2001 From: Manolis Ragkousis Date: Sat, 5 Aug 2017 18:56:29 +0300 Subject: [PATCH 40/61] gnu: Add ois. * gnu/packages/game-development.scm (ois): New variable. --- gnu/packages/game-development.scm | 41 +++++++++++++++++++++++++++++++ 1 file changed, 41 insertions(+) diff --git a/gnu/packages/game-development.scm b/gnu/packages/game-development.scm index efd8f6d034..c98c15e462 100644 --- a/gnu/packages/game-development.scm +++ b/gnu/packages/game-development.scm @@ -35,6 +35,7 @@ #:use-module (guix build-system gnu) #:use-module (guix build-system python) #:use-module (gnu packages) + #:use-module (gnu packages autotools) #:use-module (gnu packages boost) #:use-module (gnu packages curl) #:use-module (gnu packages databases) @@ -45,6 +46,7 @@ #:use-module (gnu packages glib) #:use-module (gnu packages gnunet) #:use-module (gnu packages guile) + #:use-module (gnu packages m4) #:use-module (gnu packages multiprecision) #:use-module (gnu packages music) #:use-module (gnu packages ncurses) @@ -893,3 +895,42 @@ suitable for pixel art, game graphics, and generally any detailed graphics painted with a mouse.") (home-page "http://pulkomandy.tk/projects/GrafX2") (license license:gpl2))) ; GPLv2 only + +(define-public ois + (package + (name "ois") + (version "1.3") + (source + (origin + ;; Development has moved to github and there are no recent tarball + ;; releases. + (method git-fetch) + (uri (git-reference + (url "https://github.com/wgois/OIS.git") + (commit "bb75ccc1aabc1c547195579963601ff6080ca2f2"))) + (file-name (string-append name "-" version)) + (sha256 + (base32 + "0w0pamjc3vj0jr718hysrw8x076fq6n9rd6wcb36sn2jd0lqvi98")))) + (build-system gnu-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'bootstrap + (lambda _ (zero? (system* "sh" "bootstrap"))))))) + (native-inputs + `(("autoconf" ,autoconf) + ("automake" ,automake) + ("libtool" ,libtool) + ("m4" ,m4) + ("pkg-config" ,pkg-config))) + (inputs + `(("libxaw" ,libxaw))) + (synopsis "Object Oriented Input System") + (description + "Cross Platform Object Oriented Input Lib System is a cross platform, +simple solution for using all kinds of Input Devices (Keyboards, Mice, +Joysticks, etc) and feedback devices (e.g. force feedback). Meant to be very +robust and compatible with many systems and operating systems.") + (home-page "https://github.com/wgois/OIS") + (license license:zlib))) From 2d5bf32b8aaf3fd60d9412898f269d990d5e3bde Mon Sep 17 00:00:00 2001 From: Manolis Ragkousis Date: Sun, 6 Aug 2017 17:07:17 +0300 Subject: [PATCH 41/61] gnu: googletest: Build shared libraries. * gnu/packages/check.scm (googletest)[arguments]: Pass "-DBUILD_SHARED_LIBS=ON" in #:configure-flags. --- gnu/packages/check.scm | 2 ++ 1 file changed, 2 insertions(+) diff --git a/gnu/packages/check.scm b/gnu/packages/check.scm index 2ab5c01359..ddfcf1750f 100644 --- a/gnu/packages/check.scm +++ b/gnu/packages/check.scm @@ -213,6 +213,8 @@ normally do not detect. The goal is to detect only real errors in the code (base32 "1n5p1m2m3fjrjdj752lf92f9wq3pl5cbsfrb49jqbg52ghkz99jq")))) (build-system cmake-build-system) + (arguments + `(#:configure-flags '("-DBUILD_SHARED_LIBS=ON"))) (native-inputs `(("python-2" ,python-2))) (home-page "https://github.com/google/googletest/") From ea77385c4c672aabc866c466ac8132b645510a6b Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Wed, 9 Aug 2017 14:08:23 +0300 Subject: [PATCH 42/61] gnu: viewnior: Don't build icon-theme.cache. * gnu/packages/image-viewers.scm (viewnior)[arguments]: Add phase to disable building the icon-theme.cache. --- gnu/packages/image-viewers.scm | 10 ++++++++-- 1 file changed, 8 insertions(+), 2 deletions(-) diff --git a/gnu/packages/image-viewers.scm b/gnu/packages/image-viewers.scm index 644780b5e9..b8a8af9280 100644 --- a/gnu/packages/image-viewers.scm +++ b/gnu/packages/image-viewers.scm @@ -2,7 +2,7 @@ ;;; Copyright © 2013, 2017 Ludovic Courtès ;;; Copyright © 2014 Ian Denhardt ;;; Copyright © 2015, 2016 Alex Kost -;;; Copyright © 2016 Efraim Flashner +;;; Copyright © 2016, 2017 Efraim Flashner ;;; Copyright © 2017 Alex Griffin ;;; Copyright © 2017 ng0 ;;; Copyright © 2017 Mathieu Othacehe @@ -214,7 +214,13 @@ it and customize it for your needs.") (modify-phases %standard-phases (add-after 'unpack 'autogen (lambda _ - (zero? (system* "sh" "autogen.sh"))))))) + (zero? (system* "sh" "autogen.sh")))) + (add-before 'install 'skip-gtk-update-icon-cache + (lambda _ + ;; Don't create 'icon-theme.cache' + (substitute* (find-files "data" "^Makefile$") + (("gtk-update-icon-cache") (which "true"))) + #t))))) (native-inputs `(("automake" ,automake) ("autoconf" ,autoconf) From e57fffad90a87d8ac38e4ac44ac5b5eb2d7bd191 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 4 Aug 2017 15:32:53 +0200 Subject: [PATCH 43/61] gnu: Add igraph. * gnu/packages/graph.scm: New file. * gnu/local.mk (GNU_SYSTEM_MODULES): Add it. --- gnu/local.mk | 1 + gnu/packages/graph.scm | 62 ++++++++++++++++++++++++++++++++++++++++++ 2 files changed, 63 insertions(+) create mode 100644 gnu/packages/graph.scm diff --git a/gnu/local.mk b/gnu/local.mk index 090ce77c76..3d79d5d22d 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -184,6 +184,7 @@ GNU_SYSTEM_MODULES = \ %D%/packages/gperf.scm \ %D%/packages/gprolog.scm \ %D%/packages/gps.scm \ + %D%/packages/graph.scm \ %D%/packages/graphics.scm \ %D%/packages/graphviz.scm \ %D%/packages/groff.scm \ diff --git a/gnu/packages/graph.scm b/gnu/packages/graph.scm new file mode 100644 index 0000000000..54b0962b68 --- /dev/null +++ b/gnu/packages/graph.scm @@ -0,0 +1,62 @@ +;;; GNU Guix --- Functional package management for GNU +;;; Copyright © 2017 Ricardo Wurmus +;;; +;;; This file is part of GNU Guix. +;;; +;;; GNU Guix is free software; you can redistribute it and/or modify it +;;; under the terms of the GNU General Public License as published by +;;; the Free Software Foundation; either version 3 of the License, or (at +;;; your option) any later version. +;;; +;;; GNU Guix is distributed in the hope that it will be useful, but +;;; WITHOUT ANY WARRANTY; without even the implied warranty of +;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +;;; GNU General Public License for more details. +;;; +;;; You should have received a copy of the GNU General Public License +;;; along with GNU Guix. If not, see . + +(define-module (gnu packages graph) + #:use-module (guix download) + #:use-module (guix packages) + #:use-module (guix build-system gnu) + #:use-module ((guix licenses) #:prefix license:) + #:use-module (gnu packages) + #:use-module (gnu packages compression) + #:use-module (gnu packages maths) + #:use-module (gnu packages multiprecision) + #:use-module (gnu packages xml)) + +(define-public igraph + (package + (name "igraph") + (version "0.7.1") + (source + (origin + (method url-fetch) + (uri (string-append "http://igraph.org/nightly/get/c/igraph-" + version ".tar.gz")) + (sha256 + (base32 + "1pxh8sdlirgvbvsw8v65h6prn7hlm45bfsl1yfcgd6rn4w706y6r")))) + (build-system gnu-build-system) + (arguments + `(#:configure-flags + (list "--with-external-glpk" + "--with-external-blas" + "--with-external-lapack"))) + (inputs + `(("gmp" ,gmp) + ("glpk" ,glpk) + ("libxml2" ,libxml2) + ("lapack" ,lapack) + ("openblas" ,openblas) + ("zlib" ,zlib))) + (home-page "http://igraph.org") + (synopsis "Network analysis and visualization") + (description + "This package provides a library for the analysis of networks and graphs. +It can handle large graphs very well and provides functions for generating +random and regular graphs, graph visualization, centrality methods and much +more.") + (license license:gpl2+))) From 31476df32e1d5194f4f7085bba487681cc250e38 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 4 Aug 2017 15:33:28 +0200 Subject: [PATCH 44/61] gnu: Add python-igraph. * gnu/packages/graph.scm (python-igraph): New variable. --- gnu/packages/graph.scm | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) diff --git a/gnu/packages/graph.scm b/gnu/packages/graph.scm index 54b0962b68..b379bfdd03 100644 --- a/gnu/packages/graph.scm +++ b/gnu/packages/graph.scm @@ -20,11 +20,13 @@ #:use-module (guix download) #:use-module (guix packages) #:use-module (guix build-system gnu) + #:use-module (guix build-system python) #:use-module ((guix licenses) #:prefix license:) #:use-module (gnu packages) #:use-module (gnu packages compression) #:use-module (gnu packages maths) #:use-module (gnu packages multiprecision) + #:use-module (gnu packages pkg-config) #:use-module (gnu packages xml)) (define-public igraph @@ -60,3 +62,23 @@ It can handle large graphs very well and provides functions for generating random and regular graphs, graph visualization, centrality methods and much more.") (license license:gpl2+))) + +(define-public python-igraph + (package (inherit igraph) + (name "python-igraph") + (version "0.7.1.post6") + (source + (origin + (method url-fetch) + (uri (pypi-uri "python-igraph" version)) + (sha256 + (base32 + "0xp61zz710qlzhmzbfr65d5flvsi8zf2xy78s6rsszh719wl5sm5")))) + (build-system python-build-system) + (arguments '()) + (inputs + `(("igraph" ,igraph))) + (native-inputs + `(("pkg-config" ,pkg-config))) + (home-page "http://pypi.python.org/pypi/python-igraph") + (synopsis "Python bindings for the igraph network analysis library"))) From 1738138cb3a48ed2f55c59c8d7c6ce12a4c4dcb3 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 4 Aug 2017 15:44:33 +0200 Subject: [PATCH 45/61] gnu: r-igraph: Move to (gnu packages graph). * gnu/packages/statistics.scm (r-igraph): Move from here... * gnu/packages/graph.scm (r-igraph): ...to here. --- gnu/packages/graph.scm | 34 ++++++++++++++++++++++++++++++++++ gnu/packages/statistics.scm | 31 ------------------------------- 2 files changed, 34 insertions(+), 31 deletions(-) diff --git a/gnu/packages/graph.scm b/gnu/packages/graph.scm index b379bfdd03..683bfeec66 100644 --- a/gnu/packages/graph.scm +++ b/gnu/packages/graph.scm @@ -21,12 +21,15 @@ #:use-module (guix packages) #:use-module (guix build-system gnu) #:use-module (guix build-system python) + #:use-module (guix build-system r) #:use-module ((guix licenses) #:prefix license:) #:use-module (gnu packages) + #:use-module (gnu packages gcc) #:use-module (gnu packages compression) #:use-module (gnu packages maths) #:use-module (gnu packages multiprecision) #:use-module (gnu packages pkg-config) + #:use-module (gnu packages statistics) #:use-module (gnu packages xml)) (define-public igraph @@ -82,3 +85,34 @@ more.") `(("pkg-config" ,pkg-config))) (home-page "http://pypi.python.org/pypi/python-igraph") (synopsis "Python bindings for the igraph network analysis library"))) + +(define-public r-igraph + (package + (name "r-igraph") + (version "1.1.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "igraph" version)) + (sha256 + (base32 + "1v26wyk52snh8z6m5p7yqwcd9dbqifhm57j112i9x53ppi0npcc9")))) + (build-system r-build-system) + (native-inputs + `(("gfortran" ,gfortran))) + (inputs + `(("gmp" ,gmp) + ("libxml2" ,libxml2))) + (propagated-inputs + `(("r-irlba" ,r-irlba) + ("r-magrittr" ,r-magrittr) + ("r-matrix" ,r-matrix) + ("r-pkgconfig" ,r-pkgconfig))) + (home-page "http://igraph.org") + (synopsis "Network analysis and visualization") + (description + "This package provides routines for simple graphs and network analysis. +It can handle large graphs very well and provides functions for generating +random and regular graphs, graph visualization, centrality methods and much +more.") + (license license:gpl2+))) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 55a8a2a483..6d5cbb43a3 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -3280,37 +3280,6 @@ optimized in C++, and the main interface function provides an easy way of performing parallel computations on multicore machines.") (license license:gpl2+))) -(define-public r-igraph - (package - (name "r-igraph") - (version "1.1.2") - (source - (origin - (method url-fetch) - (uri (cran-uri "igraph" version)) - (sha256 - (base32 - "1v26wyk52snh8z6m5p7yqwcd9dbqifhm57j112i9x53ppi0npcc9")))) - (build-system r-build-system) - (native-inputs - `(("gfortran" ,gfortran))) - (inputs - `(("gmp" ,gmp) - ("libxml2" ,libxml2))) - (propagated-inputs - `(("r-irlba" ,r-irlba) - ("r-magrittr" ,r-magrittr) - ("r-matrix" ,r-matrix) - ("r-pkgconfig" ,r-pkgconfig))) - (home-page "http://igraph.org") - (synopsis "Network analysis and visualization") - (description - "This package provides routines for simple graphs and network analysis. -It can handle large graphs very well and provides functions for generating -random and regular graphs, graph visualization, centrality methods and much -more.") - (license license:gpl2+))) - (define-public r-r-methodss3 (package (name "r-r-methodss3") From 18f5d2a70a8fb99e7435c47efcbe12602b6b415e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Aug 2017 15:43:35 +0200 Subject: [PATCH 46/61] gnu: Add reference to (gnu packages graph). This is a follow-up to 1738138cb3a48ed2f55c59c8d7c6ce12a4c4dcb3. --- gnu/packages/bioinformatics.scm | 1 + 1 file changed, 1 insertion(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index c08297d7b6..02b338be6e 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -60,6 +60,7 @@ #:use-module (gnu packages gd) #:use-module (gnu packages gtk) #:use-module (gnu packages glib) + #:use-module (gnu packages graph) #:use-module (gnu packages groff) #:use-module (gnu packages guile) #:use-module (gnu packages haskell) From 448052b713ba7016490de02cea7b6acf2211006f Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Wed, 9 Aug 2017 16:15:50 +0200 Subject: [PATCH 47/61] gnu: libgdata: Disable failing tests. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/gnome.scm (libgdata)[arguments]: Add ‘disable-failing-tests’ phase. --- gnu/packages/gnome.scm | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/gnu/packages/gnome.scm b/gnu/packages/gnome.scm index ed4def65b5..d7c29dc990 100644 --- a/gnu/packages/gnome.scm +++ b/gnu/packages/gnome.scm @@ -345,6 +345,13 @@ formats like PNG, SVG, PDF and EPS.") ;; The ca-certificates.crt is not available in the build ;; environment. (setenv "SSL_CERT_FILE" "/dev/null") + #t)) + (add-before 'check 'disable-failing-tests + (lambda _ + ;; The PicasaWeb API tests fail with gnome-online-accounts@3.24.2. + ;; They have been removed in libgdata 0.17.6, so just do the same. + (substitute* "gdata/tests/Makefile" + (("picasaweb\\$\\(EXEEXT\\) ") "")) #t))))) (native-inputs `(("glib:bin" ,glib "bin") From a4afc536f9853d74e78e3f895ad600900af86280 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Wed, 9 Aug 2017 16:45:32 +0200 Subject: [PATCH 48/61] gnu: virt-manager: Update to 1.4.2. * gnu/packages/virtualization.scm (virt-manager): Update to 1.4.2. --- gnu/packages/virtualization.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/virtualization.scm b/gnu/packages/virtualization.scm index 628396e52c..49998120d2 100644 --- a/gnu/packages/virtualization.scm +++ b/gnu/packages/virtualization.scm @@ -478,7 +478,7 @@ virtualization library.") (define-public virt-manager (package (name "virt-manager") - (version "1.4.1") + (version "1.4.2") (source (origin (method url-fetch) (uri (string-append "https://virt-manager.org/download/sources" @@ -486,7 +486,7 @@ virtualization library.") version ".tar.gz")) (sha256 (base32 - "0i1rkxz730vw1nqghrp189jhhp53pw81k0h71hhxmyqlkyclkig6")))) + "0x6mnqw8bng3r69pvmnq9q6yyhicxg22yz62b6dzbb4z16xl1r23")))) (build-system python-build-system) (arguments `(#:python ,python-2 From 28e12d6c81cef2aca7f792f3c99037a649faa9b0 Mon Sep 17 00:00:00 2001 From: ng0 Date: Wed, 9 Aug 2017 15:58:43 +0000 Subject: [PATCH 49/61] gnu: gnurl: Update to 7.55.0. * gnu/packages/gnunet.scm (gnurl): Update to 7.55.0. Signed-off-by: Tobias Geerinckx-Rice --- gnu/packages/gnunet.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/gnunet.scm b/gnu/packages/gnunet.scm index 9ca2d9502b..497afaf668 100644 --- a/gnu/packages/gnunet.scm +++ b/gnu/packages/gnunet.scm @@ -5,7 +5,7 @@ ;;; Copyright © 2015 Efraim Flashner ;;; Copyright © 2016 Ricardo Wurmus ;;; Copyright © 2016 Mark H Weaver -;;; Copyright © 2016, 2017 ng0 +;;; Copyright © 2016, 2017 ng0 ;;; ;;; This file is part of GNU Guix. ;;; @@ -186,14 +186,14 @@ and support for SSL3 and TLS.") (define-public gnurl (package (name "gnurl") - (version "7.54.1") + (version "7.55.0") (source (origin (method url-fetch) (uri (string-append "https://gnunet.org/sites/default/files/" name "-" version ".tar.bz2")) (sha256 (base32 - "0szbj352h95sgc9kbx9wzkgjksmg3g5k6cvlc7hz3wrbdh5gb0a4")))) + "0i9bik76rbyag3mbxbk8j383iaxs5v7lmjkn4v36ascl6bdks6vn")))) (build-system gnu-build-system) (outputs '("out" "doc")) ; 1.5 MiB of man3 pages From 12025fb9b0a55c11aca9d6f36b24f71e17dca128 Mon Sep 17 00:00:00 2001 From: Mark H Weaver Date: Mon, 24 Jul 2017 22:50:47 -0400 Subject: [PATCH 50/61] gnu: icecat: Rename patches to reflect CVE assignments. Document that our existing patches include fixes for CVE-2017-7753, CVE-2017-7784, CVE-2017-7786, CVE-2017-7787, CVE-2017-7791, CVE-2017-7792, CVE-2017-7798, CVE-2017-7798, CVE-2017-7800, CVE-2017-7801, and 17 out of 23 changesets for CVE-2017-7779. * gnu/packages/gnuzilla.scm (icecat)[source]: Rename patches to reflect CVE assignments. --- gnu/packages/gnuzilla.scm | 56 +++++++++++++++++++-------------------- 1 file changed, 28 insertions(+), 28 deletions(-) diff --git a/gnu/packages/gnuzilla.scm b/gnu/packages/gnuzilla.scm index 0fb25d8432..036e106cbc 100644 --- a/gnu/packages/gnuzilla.scm +++ b/gnu/packages/gnuzilla.scm @@ -509,52 +509,52 @@ standards.") (mozilla-patch "icecat-CVE-2017-5470-pt20.patch" "38273203b827" "12p9r4spdp09d6ic9sqspvdr50lmc1p86ydz2fxdifb1f95njhx0") (mozilla-patch "icecat-bug-1357022.patch" "5bd51bc3f587" "0z5drxpfjvb7s43qgcr404h8ckchgakwwwi4nxpx2i653w22a743") (mozilla-patch "icecat-bug-1318845.patch" "512efd480dac" "13cmqap795ayh6gh3b5bc6002pz0wp92qngs7fh5qqklc7a0gkzv") - (mozilla-patch "icecat-bug-1371586.patch" "d0c92199b9ed" "0qmsm7d4h6ysx3an247kpx9qpksfms7hrjgpdrghdbxla1hc4nc9") + (mozilla-patch "icecat-CVE-2017-7798-pt1.patch" "d0c92199b9ed" "0qmsm7d4h6ysx3an247kpx9qpksfms7hrjgpdrghdbxla1hc4nc9") (mozilla-patch "icecat-bug-1364513.patch" "88e9c2137640" "1mh4l745q1wlabn9sz47n0vy3h7c66fcay2b9dwa16iqwvh3lpiw") (mozilla-patch "icecat-bug-1366203.patch" "08dd87b6bb8f" "15bfwfwwd978mlcpk1d6m7506k8c2y402md7wzf6piabxl5kk6cf") - (mozilla-patch "icecat-bug-1368576.patch" "5a51a9ef8149" "0j0f9j0pryv3ik4bizhv8s6rr4dl1mjm01c23msayr0vbnpcagcs") - (mozilla-patch "icecat-bug-1369913.patch" "f47eaebc0c5c" "1b52xm3awpigasaz0hk5b13l7v4ry9vrawf571lzy2wwhphs4nxx") - (mozilla-patch "icecat-bug-1371424.patch" "40ce248a8c15" "1b722fiifr999ga0991cg5mlhidcnvf3zx2aiq5zjaabqn0f4dzk") - (mozilla-patch "icecat-bug-1372112.patch" "0c8359ac6718" "1w0v2p5jnhzvcsx8h1bglwjhp5y5bg1g8pzpvjw7pg1wlq2frccr") - (mozilla-patch "icecat-bug-1354443-pt1.patch" "8c27a68ee87e" "0kn05q8nvp26w5rnj8r0byw89h2awmwn04l9l3xv2i5w2a7zmjzf") - (mozilla-patch "icecat-bug-1354443-pt2.patch" "b2ee0c5466da" "0jgwsppq0606lwg5jk9q69lqa14q3j7h3c7q6mxbz7zqrcg7d0zg") - (mozilla-patch "icecat-bug-1354443-pt3.patch" "25f6ec16e501" "1yqd5ndwgd8x2pj9k2bnaq3rb1g7wikq0ii7l4dm6bqwabi2rdsg") - (mozilla-patch "icecat-bug-1354443-pt4.patch" "30443b4f758e" "0riszl3xnpfq5ffywygrc12nsvx0ffd36d5rf4vp87r8lj3fr55r") - (mozilla-patch "icecat-bug-1354443-pt5.patch" "1b934ab92c59" "114cvfzfxgkwwd4zpnrmm2kx6m94k0b3xcraba9aawwwhdxj6a1d") - (mozilla-patch "icecat-bug-1354443-pt6.patch" "830a345dc0e7" "01riivv033w3mr8b2myaw38rz2za1bdlhybny737ly68hhc67xdz") - (mozilla-patch "icecat-bug-1365189.patch" "5c26df489768" "1fdw4zbn0ilfghanxky4y7qcmkpkks2q1aqkzv26dnhhrr8350a1") - (mozilla-patch "icecat-bug-1365875.patch" "f21e4d78a0a8" "0szsc3zm3wgrw8pxm0rz54whkrc14yy4d8vwmxgqsdns43qjgkpk") - (mozilla-patch "icecat-bug-1346590.patch" "f19b6c6a0c6c" "0wkr010qnh4127z1j7fp45sqdk2da9x7j2k405r0x5bgqdd09qzp") - (mozilla-patch "icecat-bug-1376087.patch" "8353a3fa4106" "0kzs8pl6spjwgdsmiw702zvbvz73ng9zf184clsfr82l8kmggbgw") - (mozilla-patch "icecat-bug-1371889.patch" "b38fed9a9772" "14vzsldlv4hjpxgnl6fjjbzhgcwsmd52v06cgmv0a7y3lnggj3hp") - (mozilla-patch "icecat-bug-1322896.patch" "c254d3cc826c" "0pixwr18qik87c8qf4irg6hdffd8rbwpng73jxg05h7s827nfw3g") - (mozilla-patch "icecat-bug-1368652.patch" "6356dbf20658" "0a0hsxkik7ysfa48w8k21lidaabwpmxi1d3214r5zqkqqfhn9qjm") + (mozilla-patch "icecat-CVE-2017-7779-pt01.patch" "5a51a9ef8149" "0j0f9j0pryv3ik4bizhv8s6rr4dl1mjm01c23msayr0vbnpcagcs") + (mozilla-patch "icecat-CVE-2017-7779-pt02.patch" "f47eaebc0c5c" "1b52xm3awpigasaz0hk5b13l7v4ry9vrawf571lzy2wwhphs4nxx") + (mozilla-patch "icecat-CVE-2017-7779-pt03.patch" "40ce248a8c15" "1b722fiifr999ga0991cg5mlhidcnvf3zx2aiq5zjaabqn0f4dzk") + (mozilla-patch "icecat-CVE-2017-7798-pt2.patch" "0c8359ac6718" "1w0v2p5jnhzvcsx8h1bglwjhp5y5bg1g8pzpvjw7pg1wlq2frccr") + (mozilla-patch "icecat-CVE-2017-7779-pt04.patch" "8c27a68ee87e" "0kn05q8nvp26w5rnj8r0byw89h2awmwn04l9l3xv2i5w2a7zmjzf") + (mozilla-patch "icecat-CVE-2017-7779-pt05.patch" "b2ee0c5466da" "0jgwsppq0606lwg5jk9q69lqa14q3j7h3c7q6mxbz7zqrcg7d0zg") + (mozilla-patch "icecat-CVE-2017-7779-pt06.patch" "25f6ec16e501" "1yqd5ndwgd8x2pj9k2bnaq3rb1g7wikq0ii7l4dm6bqwabi2rdsg") + (mozilla-patch "icecat-CVE-2017-7779-pt07.patch" "30443b4f758e" "0riszl3xnpfq5ffywygrc12nsvx0ffd36d5rf4vp87r8lj3fr55r") + (mozilla-patch "icecat-CVE-2017-7779-pt08.patch" "1b934ab92c59" "114cvfzfxgkwwd4zpnrmm2kx6m94k0b3xcraba9aawwwhdxj6a1d") + (mozilla-patch "icecat-CVE-2017-7779-pt09.patch" "830a345dc0e7" "01riivv033w3mr8b2myaw38rz2za1bdlhybny737ly68hhc67xdz") + (mozilla-patch "icecat-CVE-2017-7786.patch" "5c26df489768" "1fdw4zbn0ilfghanxky4y7qcmkpkks2q1aqkzv26dnhhrr8350a1") + (mozilla-patch "icecat-CVE-2017-7791.patch" "f21e4d78a0a8" "0szsc3zm3wgrw8pxm0rz54whkrc14yy4d8vwmxgqsdns43qjgkpk") + (mozilla-patch "icecat-CVE-2017-7779-pt10.patch" "f19b6c6a0c6c" "0wkr010qnh4127z1j7fp45sqdk2da9x7j2k405r0x5bgqdd09qzp") + (mozilla-patch "icecat-CVE-2017-7784.patch" "8353a3fa4106" "0kzs8pl6spjwgdsmiw702zvbvz73ng9zf184clsfr82l8kmggbgw") + (mozilla-patch "icecat-bug-1371889.patch" "b38fed9a9772" "14vzsldlv4hjpxgnl6fjjbzhgcwsmd52v06cgmv0a7y3lnggj3hp"); XXX backed out upstream + (mozilla-patch "icecat-CVE-2017-7787.patch" "c254d3cc826c" "0pixwr18qik87c8qf4irg6hdffd8rbwpng73jxg05h7s827nfw3g") + (mozilla-patch "icecat-CVE-2017-7792.patch" "6356dbf20658" "0a0hsxkik7ysfa48w8k21lidaabwpmxi1d3214r5zqkqqfhn9qjm") (mozilla-patch "icecat-bug-1358073.patch" "8d6e685d061b" "0430gwg7zzbg0q9w2m04s5ljh47bc8x1gxvmkzbn23bh1wy4d4sq") (mozilla-patch "icecat-bug-1370869.patch" "3b8fde840188" "0vkymvzkfpzpg86npa5vpvvf564k18hkfdz8857rl0z4dp4rybzx") - (mozilla-patch "icecat-bug-1369994.patch" "267b649087ff" "04wzazdm0kvbfcgmlhx8qs1ibqn8sbvqdsd237rja5wpr761xxf1") + (mozilla-patch "icecat-CVE-2017-7779-pt11.patch" "267b649087ff" "04wzazdm0kvbfcgmlhx8qs1ibqn8sbvqdsd237rja5wpr761xxf1") (mozilla-patch "icecat-bug-1354796.patch" "69d1a9de76b9" "1q0p4kf8pvnkwwff3lz526pjj15a25pf724awblkcnzamwbib5ns") (mozilla-patch "icecat-bug-1363027.patch" "c5eaa2d51b9f" "1xyj5n1vqhscc369q6wxibs2igbilaiwyc0q9cq64j2qx8q0yqah") (mozilla-patch "icecat-bug-1364189.patch" "852a7781259e" "12y344p54avz5mrqirq14zp4csx8ydilnjv9nsw48kpa9y0l5xsg") (mozilla-patch "icecat-bug-1342417.patch" "37ccdc5fff2b" "1acywg8girplbs7wjrjbvkximhiyizddmnkkq1ldd0l3qbx9nihc") - (mozilla-patch "icecat-bug-1362924-pt1.patch" "057ed884ecb0" "1m49bqkq5lzc2j59wgwy0gbzvqj50p9lfn7cbc2n01v6d7m8rc2j") - (mozilla-patch "icecat-bug-1362924-pt2.patch" "dd7ed649b82f" "1fama1l2vx4p6ahhrsrpysfbk9nh5gwbi4pdnclpyxd42idsdqxs") - (mozilla-patch "icecat-bug-1353312.patch" "731958f7ff4d" "0l3i3mkb6rslnjag3caf4xyhjzxn91wfs0g6dbika4sxnhfs5d4i") + (mozilla-patch "icecat-CVE-2017-7779-pt12.patch" "057ed884ecb0" "1m49bqkq5lzc2j59wgwy0gbzvqj50p9lfn7cbc2n01v6d7m8rc2j") + (mozilla-patch "icecat-CVE-2017-7779-pt13.patch" "dd7ed649b82f" "1fama1l2vx4p6ahhrsrpysfbk9nh5gwbi4pdnclpyxd42idsdqxs") + (mozilla-patch "icecat-CVE-2017-7753.patch" "731958f7ff4d" "0l3i3mkb6rslnjag3caf4xyhjzxn91wfs0g6dbika4sxnhfs5d4i") (mozilla-patch "icecat-bug-1364870.patch" "de8deecbcb02" "048ic1vk7fd7wxqjgjqlnb7kv03ynaa4wkrk0ka8m39pkjh3yyxj") (mozilla-patch "icecat-bug-1365333.patch" "e3d13b270f45" "0jr8hpxpmfgrbh09xd9nj597cdnc6kl6gs5nir4zlzbbn8kp3429") (mozilla-patch "icecat-bug-1372063.patch" "58a144bf9677" "12y8vikbzcfcfiidjdq67dvdhhvylx68wdgnypsafrd1q8dx9jza") (mozilla-patch "icecat-bug-1373970.patch" "8321ef71adb5" "1wk8kq9n2vhqlinvvw01avv3c7qj0k3qnn7dj0whnl08a5yrqhpl") (mozilla-patch "icecat-bug-1338646.patch" "322c18d011af" "1yqb7zmjz211ryb98pjj7axbj6bwkj63rmfyifsybdy3zpb4nf48") - (mozilla-patch "icecat-bug-1371283.patch" "f9bc084fbb8a" "1ssml15yzx9s0wraq4n0xvq5bw7j8xq0p2y39h8j3f1c448n0j50") + (mozilla-patch "icecat-CVE-2017-7779-pt14.patch" "f9bc084fbb8a" "1ssml15yzx9s0wraq4n0xvq5bw7j8xq0p2y39h8j3f1c448n0j50") (mozilla-patch "icecat-bug-1359477.patch" "9b70b5b852e4" "0z2bi7w46g7mm8msav8vz28mgvnv21z3a5876n9gpw317gns4d6a") - (mozilla-patch "icecat-bug-1366903.patch" "6785c2a852da" "0p9jr171qi59scr5lrj6g0mv8mgm1i1wglr3jd16xywb0ymynnn5") - (mozilla-patch "icecat-bug-1368105.patch" "11c8e23f0fd7" "0zcikv6dn7biii4gspv2kfvma5hc76hk86jahm3zl2zlkk8ikfm9") + (mozilla-patch "icecat-CVE-2017-7779-pt15.patch" "6785c2a852da" "0p9jr171qi59scr5lrj6g0mv8mgm1i1wglr3jd16xywb0ymynnn5") + (mozilla-patch "icecat-CVE-2017-7779-pt16.patch" "11c8e23f0fd7" "0zcikv6dn7biii4gspv2kfvma5hc76hk86jahm3zl2zlkk8ikfm9") (mozilla-patch "icecat-bug-1355168.patch" "f45ba43512ad" "0p28q5acns5zjj7ks2x5lrmwzzps741507sq31xvrpzan5yav37x") (mozilla-patch "icecat-bug-1308820.patch" "e9a10fac6aae" "1s2zaka6ik1rmylamyh38vsqnqlblbqdhjpp0cv08fjb9flh5sbw") (mozilla-patch "icecat-bug-1305036.patch" "c42a348f2ed0" "1pz7qbdv9xvyd1dy7g9h047c0gmrgp5qdy2360qjk6879n74h1zb") (mozilla-patch "icecat-bug-1342913.patch" "f02db36497d2" "0g1kg418l1cibh5k1sjqj2vs2jcblpbn7b06qazk2kzcg70vf5gv") - (mozilla-patch "icecat-bug-1374047.patch" "0a44ed156da5" "1y8z1czm7f91p9bpd32b9k43nl0b9g4fzwv4w0khby9y38xgvcbs") - (mozilla-patch "icecat-bug-1371259.patch" "0a86729d653e" "0wyh7qskjwq9274d25p2ajylaab5mj5h8by58rz9lxsz06zrnz9f") - (mozilla-patch "icecat-bug-1378826.patch" "98ff43fb228a" "0ih0nsmk8rzdrajzlnryqiqb71jg7v4p71hfla2hrlvn41r3709m"))) + (mozilla-patch "icecat-CVE-2017-7800.patch" "0a44ed156da5" "1y8z1czm7f91p9bpd32b9k43nl0b9g4fzwv4w0khby9y38xgvcbs") + (mozilla-patch "icecat-CVE-2017-7801.patch" "0a86729d653e" "0wyh7qskjwq9274d25p2ajylaab5mj5h8by58rz9lxsz06zrnz9f") + (mozilla-patch "icecat-CVE-2017-7779-pt17.patch" "98ff43fb228a" "0ih0nsmk8rzdrajzlnryqiqb71jg7v4p71hfla2hrlvn41r3709m"))) (modules '((guix build utils))) (snippet '(begin From ea0277abcddc89ecdaea4cd928421604663b4ebd Mon Sep 17 00:00:00 2001 From: Mark H Weaver Date: Wed, 9 Aug 2017 03:39:10 -0400 Subject: [PATCH 51/61] gnu: icecat: Add more fixes from upstream mozilla-esr52. * gnu/packages/gnuzilla.scm (icecat)[source]: Add fixes for CVE-2017-7802, CVE-2017-7803, CVE-2017-7807, and the remaining 6 out of 23 changesets for CVE-2017-7779. --- gnu/packages/gnuzilla.scm | 36 +++++++++++++++++++++++++++++++++++- 1 file changed, 35 insertions(+), 1 deletion(-) diff --git a/gnu/packages/gnuzilla.scm b/gnu/packages/gnuzilla.scm index 036e106cbc..1daaa79c73 100644 --- a/gnu/packages/gnuzilla.scm +++ b/gnu/packages/gnuzilla.scm @@ -554,7 +554,41 @@ standards.") (mozilla-patch "icecat-bug-1342913.patch" "f02db36497d2" "0g1kg418l1cibh5k1sjqj2vs2jcblpbn7b06qazk2kzcg70vf5gv") (mozilla-patch "icecat-CVE-2017-7800.patch" "0a44ed156da5" "1y8z1czm7f91p9bpd32b9k43nl0b9g4fzwv4w0khby9y38xgvcbs") (mozilla-patch "icecat-CVE-2017-7801.patch" "0a86729d653e" "0wyh7qskjwq9274d25p2ajylaab5mj5h8by58rz9lxsz06zrnz9f") - (mozilla-patch "icecat-CVE-2017-7779-pt17.patch" "98ff43fb228a" "0ih0nsmk8rzdrajzlnryqiqb71jg7v4p71hfla2hrlvn41r3709m"))) + (mozilla-patch "icecat-CVE-2017-7779-pt17.patch" "98ff43fb228a" "0ih0nsmk8rzdrajzlnryqiqb71jg7v4p71hfla2hrlvn41r3709m") + (mozilla-patch "icecat-CVE-2017-7802.patch" "09f62bfc5800" "07q18qzxja1cywihr5vhhws328zghrwc6ldx8kcsawia1r1i5gp7") + (mozilla-patch "icecat-bug-1321803-pt1.patch" "cfb75012cfbd" "1bwwfm1vhr7ddsvmi1cinwdq6f4nd71fkd9lbnlhmh4ix63gz2yl") + (mozilla-patch "icecat-bug-1321803-pt2.patch" "0f3f951461d7" "1rp1cj4c0dkhd4pda88kx499h7ycw3037yh2khff78y61ckg2a85") + (mozilla-patch "icecat-bug-1321803-pt3.patch" "b654a39db998" "1v79mh8lrnn7q40c8zj24byrqyw3x8fwcw25w90wqajnbf0ixskx") + (mozilla-patch "icecat-bug-1334338.patch" "1be1fe3c9622" "1mhd9nyp8map76hgwrhm1k955fz8y5iszdvvgrv3z1r1h77k0nz0") + (mozilla-patch "icecat-bug-1379538.patch" "8fa66bc91b07" "1l44rwkdrv9y41nfb9h3fkykk3ci7xclp6rfwbbzm4293l00adrd") + (mozilla-patch "icecat-CVE-2017-7779-pt18.patch" "7c095249ef8a" "05dbvxlmh7jljjmis540nfgk2nn968prmxrm96674avn33989sqy") + (mozilla-patch "icecat-bug-1073952.patch" "06db7fb30689" "19qf9lrwy48fjzz3wpjfxsgqab68dnlci8jrwsljhpy6787xwxg2") + (mozilla-patch "icecat-CVE-2017-7803.patch" "c52d8ce8d5df" "03l9hk278b9mw75rxpn2ay1slyz21axa2l7dfxwkvj5vdn7ykdbj") + (mozilla-patch "icecat-CVE-2017-7779-pt19.patch" "d68c9edf056f" "0zfz0l9m675n4vvm87n8g3bdhhysla4qnywli5kwjy4krj9kq6qa") + (mozilla-patch "icecat-CVE-2017-7779-pt20.patch" "5dd82ab194b9" "10mdzwxibnmqs7y5arf8sjnva31i5vhbprlc63n74h8gh8k5kdlp") + (mozilla-patch "icecat-CVE-2017-7779-pt21.patch" "8fc70b2b57a8" "0yszfmb47x3rrzn5wncv112c1b7xw11j62adx4f7950fdj7zqr32") + (mozilla-patch "icecat-bug-1379444.patch" "47dd26630291" "0r2rc634sr4a5mfc53p1wx8d0zm6dsxiw2vzc7l89mac0d0cmi5n") + (mozilla-patch "icecat-bug-1372467.patch" "0f906e04a41d" "0f2zdpnb23yg3v5f1ha24cmagcwa01kf2xz1l2lcws4ss1w5b4a9") + (mozilla-patch "icecat-bug-1372383.patch" "56349462ff47" "17gc7kf0i367c1yh2w1701k8snvdm04nznc3q3yxdl3wxkh3c3sb") + (mozilla-patch "icecat-CVE-2017-7779-pt22.patch" "7b79969a18ee" "0ixycxbjh0wmihrhzpyjbkcnvwwrzs3ffb0lymzvqnr90yxvxhyy") + (mozilla-patch "icecat-CVE-2017-7779-pt23.patch" "f0ab032fd674" "04wc4i94cfj2vcawrv7hgbb70fkxggi7s6srk3i184686rczzpyw") + (mozilla-patch "icecat-bug-1308908.patch" "48a89721d076" "01gvdzy6whp2dqmjvx49f4mvl75dhjgr8dvx71pg4sx3xmdbkzyq") + (mozilla-patch "icecat-bug-1347667.patch" "ef1d17821945" "0s6gaarnvnibgf9x0xqcymaqc63lnbh9fm2g33i8cpp1xjhmywcv") + (mozilla-patch "icecat-bug-1367128-pt1.patch" "5a0f69630b03" "1vqbwmy58qxwfaisq0dxvvbsd5w5i4yb691i78gw1dv7kgf523qy") + (mozilla-patch "icecat-bug-1367128-pt2.patch" "7db52eca97b2" "081p8izjxscylfs090c9mzlmfvpdfvg1qsf5rik30hvifcpxp6lq") + (mozilla-patch "icecat-bug-1367128-pt3.patch" "c448439eb5dc" "18gp7mg3zh9dxi1300mcm0zk67nlmvp5q50gnyc1v2sv0gs6fdfb") + (mozilla-patch "icecat-bug-1377016.patch" "319a986ae1f4" "1dlmrklkpx42c72pblpw1fi91dhqarqyl3ldnd4943x2hsy3am8k") + (mozilla-patch "icecat-bug-1342433.patch" "09f5bd33efb8" "0dky981ggyc0237mbbyy1chndk0aznkhw00d3lrafiyxsyk6vg3z") + (mozilla-patch "icecat-bug-1359058-pt1.patch" "7ccb26caa02f" "1q97f4qbwjnz6f3g5dcy2v0av9jgbaplaz9pnm5yqdc250f5bhjz") + (mozilla-patch "icecat-bug-1359058-pt2.patch" "a93c1a40f0d8" "0gafbwv2npdjqh41fpvzmzdw3kcw1b41gm3jg9biwqxxwnvqqmfj") + (mozilla-patch "icecat-bug-1382303-pt1.patch" "688c9284fb12" "1rqimwkh8krihabsx7x2awvxls8n9dm2bmbl133fnkp2sjya979w") + (mozilla-patch "icecat-bug-1382303-pt2.patch" "7f969ba7b6e8" "036n1yrmmb6gydxcgyps89g63kj1w2rihk1zsmk7yw3crln226ai") + (mozilla-patch "icecat-bug-1382303-pt3.patch" "7e7b4f104462" "0wkw72qqyql528hvssrqyq72f5csfxa5fgv5s903csh97vawfl7i") + (mozilla-patch "icecat-bug-1383000.patch" "ce65d0641c07" "08bxn3b8rgjhkvdndc7mrd0k1715wbpa5qaxhslxlgj6lpkgk0b1") + (mozilla-patch "icecat-CVE-2017-7807.patch" "a86c77d533ee" "0mzfxpyk4484dk3j1sgplakx39ya0jnp3plxvcmvlc47ry60yq93") + (mozilla-patch "icecat-bug-1346620.patch" "d71000abc9bf" "10d632nq5zbhndrsx2vpkl7jprlnas361n1yh9s9szn8k4mj01rf") + (mozilla-patch "icecat-bug-1381016.patch" "c74486f87dc3" "1l938a2lhrlqfhmgrpypx13v6jw08528m4gnllr2h5sk2x65czip") + (mozilla-patch "icecat-bug-1371657.patch" "20a1a6ad46d5" "17yn5dpymrymgdywah403fzw0p2y9bjkccg0h4d221i3pwns4bcz"))) (modules '((guix build utils))) (snippet '(begin From c3317cd9fbbe58e4763ce1794314d9d4410468fe Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Aug 2017 18:09:33 +0200 Subject: [PATCH 52/61] gnu: r-ggbeeswarm: Update to 0.6.0. * gnu/packages/statistics.scm (r-ggbeeswarm): Update to 0.6.0. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 6d5cbb43a3..3769a195cd 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -4186,13 +4186,13 @@ representation of R code.") (define-public r-ggbeeswarm (package (name "r-ggbeeswarm") - (version "0.5.3") + (version "0.6.0") (source (origin (method url-fetch) (uri (cran-uri "ggbeeswarm" version)) (sha256 (base32 - "1jgp55rvmzc4agcrlsjn8m5lk85di9c4wj94xzikqkql4lvq3qpd")))) + "0crk29p5vi1r3a988kms4y7r0iqwgwzsikgvh18r9wbzyr98bb5v")))) (build-system r-build-system) (propagated-inputs `(("r-beeswarm" ,r-beeswarm) From 0ecd0658394ea0df7ee51f0633f5a8d011617c14 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Aug 2017 18:09:55 +0200 Subject: [PATCH 53/61] gnu: r-gdtools: Update to 0.1.5. * gnu/packages/statistics.scm (r-gdtools): Update to 0.1.5. --- 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 3769a195cd..3daaa6a8b2 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -1031,14 +1031,14 @@ aesthetic attributes.") (define-public r-gdtools (package (name "r-gdtools") - (version "0.1.4") + (version "0.1.5") (source (origin (method url-fetch) (uri (cran-uri "gdtools" version)) (sha256 (base32 - "0l8c4bh6765x9s6rw3mfm1bgicdzdngir1kxh9pxx4sidrdndcip")))) + "09y9x09gri33ghhrvjjnj5k5rk0kdpsk3wq02cln8gmywd6728vk")))) (build-system r-build-system) (native-inputs `(("r-rcpp" ,r-rcpp) From 23841b257343398bba23f6f5ae0df8a90c7cf604 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Aug 2017 18:12:03 +0200 Subject: [PATCH 54/61] gnu: Add r-pcapp. * gnu/packages/statistics.scm (r-pcapp): New variable. --- gnu/packages/statistics.scm | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 3daaa6a8b2..88cb462a74 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -4601,6 +4601,28 @@ can be efficiently implemented directly in the R language.") regression methodology including model selections and multivariate statistics.") (license license:gpl2+))) +(define-public r-pcapp + (package + (name "r-pcapp") + (version "1.9-72") + (source + (origin + (method url-fetch) + (uri (cran-uri "pcaPP" version)) + (sha256 + (base32 + "0i2822bv86dpqmk3q17x61nsp3gjjnn4nr8191rwvbiib7xhpgaq")))) + (properties `((upstream-name . "pcaPP"))) + (build-system r-build-system) + (propagated-inputs + `(("r-mvtnorm" ,r-mvtnorm))) + (home-page "http://cran.r-project.org/web/packages/pcaPP") + (synopsis "Robust PCA by projection pursuit") + (description + "This package provides functions for robust @dfn{principal component +analysis} (PCA) by projection pursuit.") + (license license:gpl3+))) + (define-public r-trimcluster (package (name "r-trimcluster") From 0bae5fd6a703ff82aad3d749da0209aac6a9c1fb Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Aug 2017 18:12:20 +0200 Subject: [PATCH 55/61] gnu: Add r-rrcov. * gnu/packages/statistics.scm (r-rrcov): New variable. --- gnu/packages/statistics.scm | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 88cb462a74..4c04832fff 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -4623,6 +4623,33 @@ regression methodology including model selections and multivariate statistics.") analysis} (PCA) by projection pursuit.") (license license:gpl3+))) +(define-public r-rrcov + (package + (name "r-rrcov") + (version "1.4-3") + (source + (origin + (method url-fetch) + (uri (cran-uri "rrcov" version)) + (sha256 + (base32 + "0kagqggi634mvrhd67ia7mpjrj5v6w2wq0z3kyppg5xkvzh335nq")))) + (build-system r-build-system) + (propagated-inputs + `(("r-cluster" ,r-cluster) + ("r-lattice" ,r-lattice) + ("r-mvtnorm" ,r-mvtnorm) + ("r-pcapp" ,r-pcapp) + ("r-robustbase" ,r-robustbase))) + (native-inputs + `(("gfortran" ,gfortran))) + (home-page "http://cran.r-project.org/web/packages/rrcov") + (synopsis "Scalable robust estimators with high breakdown Point") + (description + "This package provides an implementation of robust location and scatter +estimation and robust multivariate analysis with high breakdown point.") + (license license:gpl2+))) + (define-public r-trimcluster (package (name "r-trimcluster") From 5d0afe88497d81ac378c59890c1f517e6fc22bb2 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Aug 2017 18:12:39 +0200 Subject: [PATCH 56/61] gnu: Add r-fit-models. * gnu/packages/statistics.scm (r-fit-models): New variable. --- gnu/packages/statistics.scm | 28 ++++++++++++++++++++++++++++ 1 file changed, 28 insertions(+) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 4c04832fff..fae5d8d8d1 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -4650,6 +4650,34 @@ analysis} (PCA) by projection pursuit.") estimation and robust multivariate analysis with high breakdown point.") (license license:gpl2+))) +(define-public r-fit-models + (package + (name "r-fit-models") + (version "0.5-14") + (source + (origin + (method url-fetch) + (uri (cran-uri "fit.models" version)) + (sha256 + (base32 + "0vjbzmx0ambm6yzidb4vbgmhclwzwv2iz2cwl54ccdkvx4cx3fck")))) + (properties `((upstream-name . "fit.models"))) + (build-system r-build-system) + (propagated-inputs + `(("r-lattice" ,r-lattice))) + (home-page "http://cran.r-project.org/web/packages/fit.models") + (synopsis "Compare fitted models") + (description + "The @code{fit.models} function and its associated methods (coefficients, print, +summary, plot, etc.) were originally provided in the @code{robust} package to +compare robustly and classically fitted model objects. The aim of the +@code{fit.models} package is to separate this fitted model object comparison +functionality from the robust package and to extend it to support fitting +methods (e.g., classical, robust, Bayesian, regularized, etc.) more +generally.") + ;; Any version of the GPL + (license (list license:gpl2+ license:gpl3+)))) + (define-public r-trimcluster (package (name "r-trimcluster") From c5f744a68d3f357d63a87fcc349e0d9b343d4f0a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Aug 2017 18:12:55 +0200 Subject: [PATCH 57/61] gnu: Add r-robust. * gnu/packages/statistics.scm (r-robust): New variable. --- gnu/packages/statistics.scm | 28 ++++++++++++++++++++++++++++ 1 file changed, 28 insertions(+) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index fae5d8d8d1..bdee8e59c7 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -4678,6 +4678,34 @@ generally.") ;; Any version of the GPL (license (list license:gpl2+ license:gpl3+)))) +(define-public r-robust + (package + (name "r-robust") + (version "0.4-18") + (source + (origin + (method url-fetch) + (uri (cran-uri "robust" version)) + (sha256 + (base32 + "1b7qh1aff500nd6dh4y2ipmjgdiq8991shflb63pc39vpc0ny6g4")))) + (build-system r-build-system) + (propagated-inputs + `(("r-fit-models" ,r-fit-models) + ("r-lattice" ,r-lattice) + ("r-mass" ,r-mass) + ("r-robustbase" ,r-robustbase) + ("r-rrcov" ,r-rrcov))) + (native-inputs + `(("gfortran" ,gfortran))) + (home-page "http://cran.r-project.org/web/packages/robust") + (synopsis "Port of the S+ \"Robust Library\"") + (description + "This package is a port of the S+ \"Robust Library\". It provides +methods for robust statistics, notably for robust regression and robust +multivariate analysis.") + (license license:gpl2))) + (define-public r-trimcluster (package (name "r-trimcluster") From 1b22ecdac453504b2fcd84994f6909267fdc66e2 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 9 Aug 2017 18:13:10 +0200 Subject: [PATCH 58/61] gnu: r-wgcna: Update to 1.61. * gnu/packages/bioinformatics.scm (r-wgcna): Update to 1.61. [propagated-inputs]: Add r-rcpp, r-robust, r-survival. --- gnu/packages/bioinformatics.scm | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 02b338be6e..92c64cffa0 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8067,14 +8067,14 @@ in SNV base substitution data.") (define-public r-wgcna (package (name "r-wgcna") - (version "1.60") + (version "1.61") (source (origin (method url-fetch) (uri (cran-uri "WGCNA" version)) (sha256 (base32 - "16mxhwzhh5q48wmz1iba2r21cp0n0v8g11am4pi52iv6g0663ixl")))) + "1vrc2k33a196hrrl7k0z534fp96vv0shmigcr65ny1q0v6lq0h6i")))) (properties `((upstream-name . "WGCNA"))) (build-system r-build-system) (propagated-inputs @@ -8086,6 +8086,9 @@ in SNV base substitution data.") ("r-go-db" ,r-go-db) ("r-hmisc" ,r-hmisc) ("r-impute" ,r-impute) + ("r-rcpp" ,r-rcpp) + ("r-robust" ,r-robust) + ("r-survival" ,r-survival) ("r-matrixstats" ,r-matrixstats) ("r-preprocesscore" ,r-preprocesscore))) (home-page From 10756b9ed17a3646be2306e332741fba479e797e Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Wed, 9 Aug 2017 14:41:13 -0400 Subject: [PATCH 59/61] gnu: gnupg: Update to 2.1.23. * gnu/packages/gnupg.scm (gnupg): Update to 2.1.23. [arguments]: Remove 'enable-gpg2-is-gpg' from #:configure-flags, since it is now the default. --- gnu/packages/gnupg.scm | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/gnu/packages/gnupg.scm b/gnu/packages/gnupg.scm index a9d8679a29..5a9d6ac637 100644 --- a/gnu/packages/gnupg.scm +++ b/gnu/packages/gnupg.scm @@ -228,14 +228,14 @@ compatible to GNU Pth.") (define-public gnupg (package (name "gnupg") - (version "2.1.22") + (version "2.1.23") (source (origin (method url-fetch) (uri (string-append "mirror://gnupg/gnupg/gnupg-" version ".tar.bz2")) (sha256 (base32 - "1msazgy1q1pp7y2xr46z0il4pfzmzgzkp7v0hv5cz4hvkspnywa6")))) + "0xqd5nm4j3w9lwk35vg57gl2i8bfkmx7d24i44gkbscm2lwpci59")))) (build-system gnu-build-system) (native-inputs `(("pkg-config" ,pkg-config))) @@ -254,8 +254,7 @@ compatible to GNU Pth.") ("sqlite" ,sqlite) ("zlib" ,zlib))) (arguments - `(#:configure-flags '("--enable-gpg2-is-gpg" - ;; Otherwise, the test suite looks for the `gpg` + `(#:configure-flags '(;; Otherwise, the test suite looks for the `gpg` ;; executable in its installation directory in ;; /gnu/store before it has been installed. "--enable-gnupg-builddir-envvar") From df851f5a91bb2ea272d0b997ac862c7a58c40721 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Wed, 9 Aug 2017 15:53:24 -0400 Subject: [PATCH 60/61] download: Add the canonical GnuPG download site. * guix/download.scm (%mirrors): Add https://gnupg.org. --- guix/download.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/guix/download.scm b/guix/download.scm index d7590d4110..bf818e3cdf 100644 --- a/guix/download.scm +++ b/guix/download.scm @@ -67,12 +67,13 @@ ,@(map (cut string-append <> "/gcc") gnu-mirrors)) (gnupg "http://gd.tuwien.ac.at/privacy/gnupg/" + "http://artfiles.org/gnupg.org" + "http://www.crysys.hu/" + "https://gnupg.org/ftp/gcrypt/" "ftp://mirrors.dotsrc.org/gcrypt/" "ftp://mirror.cict.fr/gnupg/" - "http://artfiles.org/gnupg.org" "ftp://ftp.franken.de/pub/crypt/mirror/ftp.gnupg.org/gcrypt/" "ftp://ftp.freenet.de/pub/ftp.gnupg.org/gcrypt/" - "http://www.crysys.hu/" "ftp://ftp.hi.is/pub/mirrors/gnupg/" "ftp://ftp.heanet.ie/mirrors/ftp.gnupg.org/gcrypt/" "ftp://ftp.bit.nl/mirror/gnupg/" From ae7f246cf1c7e20ebf4025024bb10361938abaa2 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Wed, 9 Aug 2017 16:52:22 -0400 Subject: [PATCH 61/61] gnu: python-nbformat: Update to 4.3.0. * gnu/packages/python.scm (python-nbformat, python2-nbformat): Update to 4.3.0. --- gnu/packages/python.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 79c6eca00f..af320dfc0d 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -7981,14 +7981,14 @@ Debian-related files, such as: (define-public python-nbformat (package (name "python-nbformat") - (version "4.1.0") + (version "4.3.0") (source (origin (method url-fetch) (uri (pypi-uri "nbformat" version)) (sha256 (base32 - "0mq8iki3d4mnx7wy05phss7x98mds4fqydin8lcagidp1knw1xnv")))) + "12s7j4qja8b5bs1kyw5dzmrqbjxxj8wk52cyasbiqbv7fblcrssz")))) (build-system python-build-system) (arguments `(#:tests? #f)) ; no test target (propagated-inputs