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01/02: Merge branch 'master' into core-updates
|
From: |
Ludovic Courtès |
|
Subject: |
01/02: Merge branch 'master' into core-updates |
|
Date: |
Wed, 13 Jan 2016 17:19:50 +0000 |
civodul pushed a commit to branch core-updates
in repository guix.
commit 8c986ab12034d67db836a881f57c69754d8073ae
Merge: 203795a 7a2eed3
Author: Ludovic Courtès <address@hidden>
Date: Wed Jan 13 17:50:17 2016 +0100
Merge branch 'master' into core-updates
.gitignore | 3 +
Makefile.am | 45 +-
build-aux/hydra/guix.scm | 28 +-
configure.ac | 5 +-
daemon.am | 6 +-
doc.am | 16 +-
doc/guix.texi | 91 +++-
doc/images/bootstrap-packages.dot | 105 +++
emacs/guix-command.el | 1 +
emacs/guix-emacs.el | 21 +-
emacs/guix-init.el | 13 -
emacs/guix-main.scm | 1 +
emacs/guix-pcomplete.el | 7 +-
emacs/guix-ui-package.el | 19 +-
gnu-system.am | 17 +-
gnu/build/linux-boot.scm | 3 +-
gnu/build/linux-modules.scm | 2 +-
gnu/packages/admin.scm | 13 +-
gnu/packages/algebra.scm | 6 +-
gnu/packages/audio.scm | 24 +-
gnu/packages/bdw-gc.scm | 2 +-
gnu/packages/bioinformatics.scm | 692 ++++++++++++++++++--
gnu/packages/boost.scm | 56 +-
gnu/packages/code.scm | 28 +-
gnu/packages/commencement.scm | 5 +-
gnu/packages/ebook.scm | 6 +-
gnu/packages/emacs.scm | 45 +-
gnu/packages/gnome.scm | 4 +-
gnu/packages/gnuzilla.scm | 9 +-
gnu/packages/graphics.scm | 3 +-
gnu/packages/gtk.scm | 18 +-
gnu/packages/java.scm | 127 ++--
gnu/packages/julia.scm | 129 +++-
gnu/packages/kodi.scm | 2 +-
gnu/packages/ldc.scm | 118 ++++
gnu/packages/libreoffice.scm | 15 +-
gnu/packages/linux-libre-i686.conf | 220 +++++--
gnu/packages/linux-libre-x86_64.conf | 252 +++++---
gnu/packages/linux.scm | 12 +-
gnu/packages/man.scm | 15 +-
gnu/packages/maths.scm | 14 +-
gnu/packages/package-management.scm | 6 +-
gnu/packages/patches/asymptote-gsl2.patch | 33 +
.../patches/bedtools-32bit-compilation.patch | 171 -----
gnu/packages/patches/boost-mips-avoid-m32.patch | 15 -
gnu/packages/patches/csound-header-ordering.patch | 20 +
.../patches/gtk2-respect-GUIX_GTK2_PATH.patch | 46 ++
.../patches/gtk3-respect-GUIX_GTK3_PATH.patch | 38 ++
.../patches/julia-0.3.10-fix-empty-array.patch | 13 -
gnu/packages/patches/ldc-disable-tests.patch | 90 +++
.../patches/libcmis-fix-test-onedrive.patch | 35 +
gnu/packages/patches/nss-pkgconfig.patch | 27 +-
gnu/packages/patches/openimageio-boost-1.60.patch | 47 ++
gnu/packages/patches/sudo-CVE-2015-5602.patch | 372 +++++++++++
.../patches/w3m-disable-sslv2-and-sslv3.patch | 24 +
.../patches/w3m-disable-weak-ciphers.patch | 24 +
gnu/packages/patches/w3m-fix-compile.patch | 15 -
.../patches/w3m-force-ssl_verify_server-on.patch | 24 +
gnu/packages/patches/w3m-libgc.patch | 28 +
gnu/packages/plotutils.scm | 71 ++-
gnu/packages/ruby.scm | 42 ++-
gnu/packages/samba.scm | 8 +-
gnu/packages/skribilo.scm | 9 +-
gnu/packages/statistics.scm | 450 +++++++++++++-
gnu/packages/texlive.scm | 119 ++--
gnu/packages/textutils.scm | 46 +-
gnu/packages/video.scm | 6 +-
gnu/packages/w3m.scm | 7 +-
gnu/packages/webkit.scm | 6 +-
gnu/packages/xml.scm | 25 +
gnu/packages/xorg.scm | 5 +-
gnu/services.scm | 69 ++-
gnu/system.scm | 8 +-
guix/build-system/gnu.scm | 16 +-
guix/build-system/python.scm | 9 +-
guix/build/git.scm | 43 +-
guix/build/pull.scm | 149 ++---
guix/build/ruby-build-system.scm | 19 +-
guix/http-client.scm | 26 +-
guix/import/cran.scm | 46 +-
guix/monad-repl.scm | 22 +-
guix/scripts/lint.scm | 13 +-
guix/scripts/package.scm | 33 +-
guix/ui.scm | 4 +-
guix/utils.scm | 42 ++-
m4/guix.m4 | 27 +-
tests/guix-package.sh | 20 +-
tests/utils.scm | 10 +-
88 files changed, 3582 insertions(+), 994 deletions(-)
diff --cc gnu/packages/bdw-gc.scm
index 0a483ef,f4bbc64..992a11b
--- a/gnu/packages/bdw-gc.scm
+++ b/gnu/packages/bdw-gc.scm
@@@ -1,5 -1,5 +1,5 @@@
;;; GNU Guix --- Functional package management for GNU
--;;; Copyright © 2012, 2013, 2014 Ludovic Courtès <address@hidden>
++;;; Copyright © 2012, 2013, 2014, 2016 Ludovic Courtès <address@hidden>
;;; Copyright © 2014 Mark H Weaver <address@hidden>
;;;
;;; This file is part of GNU Guix.
diff --cc gnu/packages/commencement.scm
index d758913,73b27a2..1928360
--- a/gnu/packages/commencement.scm
+++ b/gnu/packages/commencement.scm
@@@ -452,18 -424,18 +452,19 @@@ exec ~a/bin/~a-~a -B~a/lib -Wl,-dynamic
glibc-final-with-bootstrap-bash
(car (assoc-ref %boot1-inputs "bash"))))
(bash (package (inherit static-bash)
- (native-inputs `(("bison" ,bison-boot1)))
(arguments
`(#:guile ,%bootstrap-guile
- ,@(package-arguments static-bash))))))
- (package-with-bootstrap-guile
- (package-with-explicit-inputs bash
- `(("gcc" ,gcc)
- ("libc" ,glibc-final-with-bootstrap-bash)
- ,@(fold alist-delete %boot1-inputs
- '("gcc" "libc")))
- (current-source-location)
- #:guile %bootstrap-guile))))
+ ,@(package-arguments static-bash)))))
+ (inputs `(("gcc" ,gcc)
+ ("libc" ,glibc-final-with-bootstrap-bash)
+ ,@(fold alist-delete %boot1-inputs
+ '("gcc" "libc")))))
+ (package
+ (inherit (package-with-bootstrap-guile
+ (package-with-explicit-inputs bash inputs
- (current-source-location))))
++ (current-source-location)
++ #:guile %bootstrap-guile)))
+ (native-inputs `(("bison" ,bison-boot1))))))
(define gettext-boot0
;; A minimal gettext used during bootstrap.
diff --cc gnu/packages/emacs.scm
index 947c7e2,e82ffd3..ba7bd49
--- a/gnu/packages/emacs.scm
+++ b/gnu/packages/emacs.scm
@@@ -70,18 -70,23 +70,24 @@@
(sha256
(base32
"0kn3rzm91qiswi0cql89kbv6mqn27rwsyjfb8xmwy9m5s8fxfiyx"))
- (patches (list (search-patch "emacs-exec-path.patch")))))
+ (patches (list (search-patch "emacs-exec-path.patch")
+ (search-patch "emacs-source-date-epoch.patch")))))
(build-system glib-or-gtk-build-system)
(arguments
- '(#:phases (alist-cons-before
- 'configure 'fix-/bin/pwd
- (lambda _
- ;; Use `pwd', not `/bin/pwd'.
- (substitute* (find-files "." "^Makefile\\.in$")
- (("/bin/pwd")
- "pwd")))
- %standard-phases)))
+ '(#:phases (modify-phases %standard-phases
+ (add-before 'configure 'fix-/bin/pwd
+ (lambda _
+ ;; Use `pwd', not `/bin/pwd'.
+ (substitute* (find-files "." "^Makefile\\.in$")
+ (("/bin/pwd")
+ "pwd"))))
+ (add-after 'install 'remove-info.info
+ (lambda* (#:key outputs #:allow-other-keys)
+ ;; Remove 'info.info', which is provided by Texinfo.
+ (let ((out (assoc-ref outputs "out")))
+ (delete-file
+ (string-append out "/share/info/info.info.gz"))
+ #t))))))
(inputs
`(("gnutls" ,gnutls)
("ncurses" ,ncurses)
diff --cc gnu/packages/plotutils.scm
index 6166226,09a2d4f..e9a2471
--- a/gnu/packages/plotutils.scm
+++ b/gnu/packages/plotutils.scm
@@@ -1,5 -1,6 +1,6 @@@
;;; GNU Guix --- Functional package management for GNU
--;;; Copyright © 2013, 2014, 2015 Ludovic Courtès <address@hidden>
++;;; Copyright © 2013, 2014, 2015, 2016 Ludovic Courtès <address@hidden>
+ ;;; Copyright © 2015 Eric Bavier <address@hidden>
;;;
;;; This file is part of GNU Guix.
;;;
@@@ -156,3 -167,61 +167,61 @@@ just-in-time graph generation, handles
basic statistical capabilities. It allows significant user control over
colors, styles, options and details.")
(license license:gpl2+)))
+
+ (define-public asymptote
+ (package
+ (name "asymptote")
+ (version "2.35")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append "mirror://sourceforge/asymptote/"
+ version "/asymptote-" version ".src.tgz"))
+ (sha256
+ (base32
+ "11f28vxw0ybhvl7vxmqcdwvw7y6gz55ykw9ybgzb2px6lsvgag7z"))
+ (patches (list (search-patch "asymptote-gsl2.patch")))))
+ (build-system gnu-build-system)
+ ;; Note: The 'asy' binary retains a reference to docdir for use with its
+ ;; "help" command in interactive mode, so adding a "doc" output is not
+ ;; currently useful.
+ (native-inputs
+ `(("gs" ,ghostscript) ;For tests
+ ("texinfo" ,texinfo) ;For generating documentation
+ ("texlive" ,texlive) ;For tests and documentation
+ ("perl" ,perl)))
+ (inputs
+ `(("fftw" ,fftw)
+ ("freeglut" ,freeglut)
+ ("gsl" ,gsl)
- ("libgc" ,libgc-for-c++)
++ ("libgc" ,libgc)
+ ("python" ,python-2)
+ ("readline" ,readline)
+ ("zlib" ,zlib)))
+ (arguments
+ `(#:configure-flags
+ (list (string-append "--enable-gc=" (assoc-ref %build-inputs "libgc"))
+ (string-append "--with-latex="
+ (assoc-ref %outputs "out")
+ "/share/texmf/tex/latex")
+ (string-append "--with-context="
+ (assoc-ref %outputs "out")
+ "/share/texmf/tex/context/third"))
+ #:phases (modify-phases %standard-phases
+ (add-before 'build 'patch-pdf-viewer
+ (lambda _
+ ;; Default to a free pdf viewer
+ (substitute* "settings.cc"
+ (("defaultPDFViewer=\"acroread\"")
+ "defaultPDFViewer=\"gv\"")))))))
+ (home-page "http://asymptote.sourceforge.net";)
+ (synopsis "Script-based vector graphics language")
+ (description
+ "Asymptote is a powerful descriptive vector graphics language for
+ technical drawing, inspired by MetaPost but with an improved C++-like syntax.
+ Asymptote provides for figures the same high-quality level of typesetting that
+ LaTeX does for scientific text.")
+ ;; Most source files do not contain license statements, but the README
+ ;; contains: "All source files in the Asymptote project, unless explicitly
+ ;; noted otherwise, are released under version 3 (or later) of the GNU
+ ;; Lesser General Public License"
+ (license license:lgpl3+)))
diff --cc gnu/packages/ruby.scm
index 2977f94,577be18..fd36f8d
--- a/gnu/packages/ruby.scm
+++ b/gnu/packages/ruby.scm
@@@ -100,28 -95,9 +100,28 @@@ a focus on simplicity and productivity.
(home-page "https://ruby-lang.org";)
(license license:ruby)))
+(define-public ruby-2.2
+ (package (inherit ruby)
+ (version "2.2.4")
+ (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
+ "0g3ps4q3iz7wj9m45n8xyxzw8nh29ljdqb87b0f6i0p3853gz2yj"))
+ (modules '((guix build utils)))
+ (snippet `(begin
+ ;; Remove bundled libffi
+ (delete-file-recursively
+ (string-append "ext/fiddle/libffi-3.2.1"))
+ #t))))))
+
(define-public ruby-2.1
(package (inherit ruby)
- (version "2.1.6")
+ (version "2.1.8")
(source
(origin
(method url-fetch)