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Merge branch 'master' into core-updates

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This commit is contained in:
Mark H Weaver 2015-06-21 14:30:22 -04:00
commit bf76d98789
17 changed files with 297 additions and 39 deletions
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5
emacs/guix-pcomplete.el
View file

@ -254,7 +254,8 @@ group - the argument.")
"Complete argument for guix COMMAND."
(cond
((member command
'("archive" "build" "environment" "lint" "refresh"))
'("archive" "build" "edit" "environment" "lint" "refresh"
"size"))
(while t
(pcomplete-here (guix-pcomplete-all-packages))))
(t (pcomplete-here* (pcomplete-entries)))))
@ -302,7 +303,7 @@ INPUT is the current partially completed string."
((option? "-m" "--manifest")
(complete* (pcomplete-entries)))))
((and (command? "archive" "build")
((and (command? "archive" "build" "size")
(option? "-s" "--system"))
(complete* guix-pcomplete-systems))

1
gnu-system.am
View file

@ -394,6 +394,7 @@ dist_patch_DATA = \
gnu/packages/patches/calibre-no-updates-dialog.patch \
gnu/packages/patches/cdparanoia-fpic.patch \
gnu/packages/patches/chmlib-inttypes.patch \
gnu/packages/patches/clang-libc-search-path.patch \
gnu/packages/patches/clucene-pkgconfig.patch \
gnu/packages/patches/cmake-fix-tests.patch \
gnu/packages/patches/coreutils-dummy-man.patch \

9
gnu/build/file-systems.scm
View file

@ -286,16 +286,13 @@ (define* (mount-file-system spec #:key (root "/root"))
(when check?
(check-file-system source type))
(mkdir-p mount-point)
(mount source mount-point type flags
(if options
(string->pointer options)
%null-pointer))
(mount source mount-point type flags options)
;; For read-only bind mounts, an extra remount is needed, as per
;; <http://lwn.net/Articles/281157/>, which still applies to Linux 4.0.
(when (and (= MS_BIND (logand flags MS_BIND))
(= MS_RDONLY (logand flags MS_RDONLY)))
(mount source mount-point type (logior MS_BIND MS_REMOUNT MS_RDONLY)
%null-pointer))))))
(let ((flags (logior MS_BIND MS_REMOUNT MS_RDONLY)))
(mount source mount-point type flags #f)))))))
;;; file-systems.scm ends here

27
gnu/packages/audio.scm
View file

@ -1034,6 +1034,33 @@ (define-public patchage
and ALSA.")
(license license:gpl3+)))
(define-public raul
(package
(name "raul")
(version "0.8.0")
(source (origin
(method url-fetch)
(uri (string-append "http://download.drobilla.net/raul-"
version ".tar.bz2"))
(sha256
(base32
"09ms40xc1x6qli6lxkwn5ibqh62nl9w7dq0b6jh1q2zvnrxwsd8b"))))
(build-system waf-build-system)
(arguments
`(#:python ,python-2
#:tests? #f)) ; no check target
(inputs
`(("glib" ,glib)
("boost" ,boost)))
(native-inputs
`(("pkg-config" ,pkg-config)))
(home-page "http://drobilla.net/software/raul/")
(synopsis "Real-time audio utility library")
(description
"Raul (Real-time Audio Utility Library) is a C++ utility library primarily
aimed at audio/musical applications.")
(license license:gpl2+)))
(define-public rubberband
(package
(name "rubberband")

59
gnu/packages/bioinformatics.scm
View file

@ -780,6 +780,65 @@ (define-public express
ChIP-Seq, and analysis of metagenomic data.")
(license license:artistic2.0)))
(define-public fasttree
(package
(name "fasttree")
(version "2.1.8")
(source (origin
(method url-fetch)
(uri (string-append
"http://www.microbesonline.org/fasttree/FastTree-"
version ".c"))
(sha256
(base32
"0dzqc9vr9iiiw21y159xfjl2z90vw0y7r4x6456pcaxiy5hd2wmi"))))
(build-system gnu-build-system)
(arguments
`(#:tests? #f ; no "check" target
#:phases
(modify-phases %standard-phases
(delete 'unpack)
(delete 'configure)
(replace 'build
(lambda* (#:key source #:allow-other-keys)
(and (zero? (system* "gcc"
"-O3"
"-finline-functions"
"-funroll-loops"
"-Wall"
"-o"
"FastTree"
source
"-lm"))
(zero? (system* "gcc"
"-DOPENMP"
"-fopenmp"
"-O3"
"-finline-functions"
"-funroll-loops"
"-Wall"
"-o"
"FastTreeMP"
source
"-lm")))))
(replace 'install
(lambda* (#:key outputs #:allow-other-keys)
(let ((bin (string-append (assoc-ref outputs "out")
"/bin")))
(mkdir-p bin)
(copy-file "FastTree"
(string-append bin "/FastTree"))
(copy-file "FastTreeMP"
(string-append bin "/FastTreeMP"))
#t))))))
(home-page "http://www.microbesonline.org/fasttree")
(synopsis "Infers approximately-maximum-likelihood phylogenetic trees")
(description
"FastTree can handle alignments with up to a million of sequences in a
reasonable amount of time and memory. For large alignments, FastTree is
100-1,000 times faster than PhyML 3.0 or RAxML 7.")
(license license:gpl2+)))
(define-public fastx-toolkit
(package
(name "fastx-toolkit")

1
gnu/packages/commencement.scm
View file

@ -518,6 +518,7 @@ (define binutils-final
(define libstdc++
;; Intermediate libstdc++ that will allow us to build the final GCC
;; (remember that GCC-BOOT0 cannot build libstdc++.)
;; TODO: Write in terms of 'make-libstdc++'.
(package-with-bootstrap-guile
(package (inherit gcc-4.9)
(name "libstdc++")

26
gnu/packages/gcc.scm
View file

@ -345,6 +345,32 @@ (define-public gcc-5.1
'("gcc-arm-link-spec-fix.patch"
"gcc-5.0-libvtv-runpath.patch")))))))
(define-public (make-libstdc++ gcc)
"Return a libstdc++ package based on GCC. The primary use case is when
using compilers other than GCC."
(package
(inherit gcc)
(name "libstdc++")
(arguments
`(#:out-of-source? #t
#:phases (alist-cons-before
'configure 'chdir
(lambda _
(chdir "libstdc++-v3"))
%standard-phases)
#:configure-flags `("--disable-libstdcxx-pch"
,(string-append "--with-gxx-include-dir="
(assoc-ref %outputs "out")
"/include"))))
(outputs '("out" "debug"))
(inputs '())
(native-inputs '())
(propagated-inputs '())
(synopsis "GNU C++ standard library")))
(define-public libstdc++-4.9
(make-libstdc++ gcc-4.9))
(define* (custom-gcc gcc name languages #:key (separate-lib-output? #t))
"Return a custom version of GCC that supports LANGUAGES."
(package (inherit gcc)

10
gnu/packages/gnome.scm
View file

@ -2402,15 +2402,17 @@ (define-public totem-pl-parser
(native-inputs
`(("intltool" ,intltool)
("glib" ,glib "bin")
("gobject-introspection" ,gobject-introspection)
("pkg-config" ,pkg-config)))
(inputs
(propagated-inputs
`(("glib" ,glib)
("gmime" ,gmime)
("libarchive" ,libarchive)
("libxml2" ,libxml2)))
(inputs
`(("libarchive" ,libarchive)
("libgcrypt" ,libgcrypt)
("nettle" ,nettle)
("libsoup" ,libsoup)
("libxml2" ,libxml2)))
("libsoup" ,libsoup)))
(home-page "https://projects.gnome.org/totem")
(synopsis "Library to parse and save media playlists for GNOME")
(description "Totem-pl-parser is a GObjects-based library to parse and save

51
gnu/packages/llvm.scm
View file

@ -1,6 +1,7 @@
;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2014 Eric Bavier <bavier@member.fsf.org>
;;; Copyright © 2015 Mark H Weaver <mhw@netris.org>
;;; Copyright © 2015 Ludovic Courtès <ludo@gnu.org>
;;;
;;; This file is part of GNU Guix.
;;;
@ -25,6 +26,8 @@ (define-module (gnu packages llvm)
#:use-module (guix build-system gnu)
#:use-module (guix build-system cmake)
#:use-module (gnu packages)
#:use-module (gnu packages gcc)
#:use-module (gnu packages bootstrap) ;glibc-dynamic-linker
#:use-module (gnu packages perl)
#:use-module (gnu packages python)
#:use-module (gnu packages xml))
@ -84,7 +87,8 @@ (define (clang-from-llvm llvm hash)
(method url-fetch)
(uri (string-append "http://llvm.org/releases/"
version "/cfe-" version ".src.tar.xz"))
(sha256 (base32 hash))))
(sha256 (base32 hash))
(patches (list (search-patch "clang-libc-search-path.patch")))))
;; Using cmake allows us to treat llvm as an external library. There
;; doesn't seem to be any way to do this with clang's autotools-based
;; build system.
@ -92,10 +96,53 @@ (define (clang-from-llvm llvm hash)
(native-inputs (package-native-inputs llvm))
(inputs
`(("libxml2" ,libxml2)
("gcc-lib" ,gcc-4.9 "lib")
,@(package-inputs llvm)))
(propagated-inputs
`(("llvm" ,llvm)))
(arguments `(#:configure-flags '("-DCLANG_INCLUDE_TESTS=True")))
(arguments
`(#:configure-flags
(list "-DCLANG_INCLUDE_TESTS=True"
;; Find libgcc_s, crtbegin.o, and crtend.o.
(string-append "-DGCC_INSTALL_PREFIX="
(assoc-ref %build-inputs "gcc-lib"))
;; Use a sane default include directory.
(string-append "-DC_INCLUDE_DIRS="
(assoc-ref %build-inputs "libc")
"/include"))
;; Don't use '-g' during the build to save space.
#:build-type "Release"
#:phases (modify-phases %standard-phases
(add-after
'unpack 'set-glibc-file-names
(lambda* (#:key inputs #:allow-other-keys)
(let ((libc (assoc-ref inputs "libc")))
;; Patch the 'getLinuxDynamicLinker' function to that
;; it uses the right dynamic linker file name.
(substitute* "lib/Driver/Tools.cpp"
(("/lib64/ld-linux-x86-64.so.2")
(string-append libc
,(glibc-dynamic-linker))))
;; Same for libc's libdir, to allow crt1.o & co. to be
;; found.
(substitute* "lib/Driver/ToolChains.cpp"
(("@GLIBC_LIBDIR@")
(string-append libc "/lib")))))))))
;; Clang supports the same environment variables as GCC.
(native-search-paths
(list (search-path-specification
(variable "CPATH")
(files '("include")))
(search-path-specification
(variable "LIBRARY_PATH")
(files '("lib" "lib64")))))
(home-page "http://clang.llvm.org")
(synopsis "C language family frontend for LLVM")
(description

19
gnu/packages/patches/clang-libc-search-path.patch Normal file
View file

@ -0,0 +1,19 @@
Clang attempts to guess file names based on the OS and distro (yes!),
but unfortunately, that doesn't work for us.
This patch makes it easy to insert libc's $libdir so that Clang passes the
correct absolute file name of crt1.o etc. to 'ld'.
--- cfe-3.6.0.src/lib/Driver/ToolChains.cpp 2015-02-18 22:03:07.000000000 +0100
+++ cfe-3.6.0.src/lib/Driver/ToolChains.cpp 2015-06-19 16:37:20.459701044 +0200
@@ -3085,6 +3085,10 @@ Linux::Linux(const Driver &D, const llvm
addPathIfExists(SysRoot + "/lib", Paths);
addPathIfExists(SysRoot + "/usr/lib", Paths);
+
+ // Add libc's lib/ directory to the search path, so that crt1.o, crti.o,
+ // and friends can be found.
+ addPathIfExists("@GLIBC_LIBDIR@", Paths);
}
bool Linux::HasNativeLLVMSupport() const {

22
gnu/packages/patches/guile-linux-syscalls.patch
View file

@ -3,11 +3,9 @@ This patch adds bindings to Linux syscalls for which glibc has symbols.
Using the FFI would have been nice, but that's not an option when using
a statically-linked Guile in an initrd that doesn't have libc.so around.
diff --git a/libguile/posix.c b/libguile/posix.c
index 324f21b..cbee94d 100644
--- a/libguile/posix.c
+++ b/libguile/posix.c
@@ -2245,6 +2245,263 @@ scm_init_popen (void)
--- guile-2.0.11/libguile/posix.c.orig 2014-02-28 15:01:27.000000000 -0500
+++ guile-2.0.11/libguile/posix.c 2015-06-21 14:28:23.624251038 -0400
@@ -2245,6 +2245,269 @@
}
#endif
@ -26,15 +24,18 @@ index 324f21b..cbee94d 100644
+#define FUNC_NAME s_scm_mount
+{
+ int err;
+ char *c_source, *c_target, *c_type;
+ char *c_source, *c_target, *c_type, *c_data;
+ unsigned long c_flags;
+ void *c_data;
+
+ c_source = scm_to_locale_string (source);
+ c_target = scm_to_locale_string (target);
+ c_type = scm_to_locale_string (type);
+ c_flags = SCM_UNBNDP (flags) ? 0 : scm_to_ulong (flags);
+ c_data = SCM_UNBNDP (data) ? NULL : scm_to_pointer (data);
+
+ if (SCM_UNBNDP (data) || scm_is_false (data))
+ c_data = NULL;
+ else
+ c_data = scm_to_locale_string (data);
+
+ err = mount (c_source, c_target, c_type, c_flags, c_data);
+ if (err != 0)
@ -44,6 +45,9 @@ index 324f21b..cbee94d 100644
+ free (c_target);
+ free (c_type);
+
+ if (c_data != NULL)
+ free (c_data);
+
+ if (err != 0)
+ {
+ errno = err;
@ -271,5 +275,3 @@ index 324f21b..cbee94d 100644
void
scm_init_posix ()
{
--
2.4.1

33
gnu/packages/ruby.scm
View file

@ -88,6 +88,39 @@ (define-public ruby
(home-page "https://ruby-lang.org")
(license license:ruby)))
(define-public ruby-2.1
(package (inherit ruby)
(version "2.1.6")
(source
(origin
(method url-fetch)
(uri (string-append "http://cache.ruby-lang.org/pub/ruby/"
(version-major+minor version)
"/ruby-" version ".tar.bz2"))
(sha256
(base32
"1sbcmbhadcxk0509svwxbm2vvgmpf3xjxr1397bgp9x46nz36lkv"))))
(arguments
`(#:test-target "test"
#:parallel-tests? #f
#:phases
(alist-cons-before
'configure 'replace-bin-sh
(lambda _
(substitute* '("Makefile.in"
"ext/pty/pty.c"
"io.c"
"lib/mkmf.rb"
"process.c")
(("/bin/sh") (which "sh"))))
%standard-phases)))
(native-search-paths
(list (search-path-specification
(variable "GEM_PATH")
(files (list (string-append "lib/ruby/gems/"
(version-major+minor version)
".0"))))))))
(define-public ruby-1.8
(package (inherit ruby)
(version "1.8.7-p374")

4
gnu/packages/video.scm
View file

@ -296,14 +296,14 @@ (define-public libva
(define-public ffmpeg
(package
(name "ffmpeg")
(version "2.7")
(version "2.7.1")
(source (origin
(method url-fetch)
(uri (string-append "http://www.ffmpeg.org/releases/ffmpeg-"
version ".tar.bz2"))
(sha256
(base32
"0jl43b63b20db3yia5xxp0hh8zwdbirk5k9p1d7416nq1b5ckfx8"))))
"087pyx1wxvniq3wgj6z80wrb7ampwwsmwndmr7lymzhm4iyvj1vy"))))
(build-system gnu-build-system)
(inputs
`(("fontconfig" ,fontconfig)

27
gnu/system/file-systems.scm
View file

@ -39,6 +39,7 @@ (define-module (gnu system file-systems)
%pseudo-terminal-file-system
%devtmpfs-file-system
%immutable-store
%control-groups
%base-file-systems
@ -152,13 +153,31 @@ (define %immutable-store
(check? #f)
(flags '(read-only bind-mount))))
(define %control-groups
(cons (file-system
(device "cgroup")
(mount-point "/sys/fs/cgroup")
(type "tmpfs")
(check? #f))
(map (lambda (subsystem)
(file-system
(device "cgroup")
(mount-point (string-append "/sys/fs/cgroup/" subsystem))
(type "cgroup")
(check? #f)
(options subsystem)
(create-mount-point? #t)))
'("cpuset" "cpu" "cpuacct" "memory" "devices" "freezer"
"blkio" "perf_event" "hugetlb"))))
(define %base-file-systems
;; List of basic file systems to be mounted. Note that /proc and /sys are
;; currently mounted by the initrd.
(list %devtmpfs-file-system
%pseudo-terminal-file-system
%shared-memory-file-system
%immutable-store))
(append (list %devtmpfs-file-system
%pseudo-terminal-file-system
%shared-memory-file-system
%immutable-store)
%control-groups))

8
guix/gexp.scm
View file

@ -157,7 +157,7 @@ (define-record-type <local-file>
(recursive? local-file-recursive?)) ;Boolean
(define* (local-file file #:optional (name (basename file))
#:key (recursive? #t))
#:key recursive?)
"Return an object representing local file FILE to add to the store; this
object can be used in a gexp. FILE will be added to the store under NAME--by
default the base name of FILE.
@ -167,7 +167,11 @@ (define* (local-file file #:optional (name (basename file))
permission bits are kept.
This is the declarative counterpart of the 'interned-file' monadic procedure."
(%local-file file name recursive?))
;; Canonicalize FILE so that if it's a symlink, it is resolved. Failing to
;; do that, when RECURSIVE? is #t, we could end up creating a dangling
;; symlink in the store, and when RECURSIVE? is #f 'add-to-store' would just
;; throw an error, both of which are inconvenient.
(%local-file (canonicalize-path file) name recursive?))
(define-gexp-compiler (local-file-compiler (file local-file?) system target)
;; "Compile" FILE by adding it to the store.

11
guix/store.scm
View file

@ -610,11 +610,12 @@ (define add-to-store
store-path)))
(lambda (server basename recursive? hash-algo file-name)
"Add the contents of FILE-NAME under BASENAME to the store. When
RECURSIVE? is true and FILE-NAME designates a directory, the contents of
FILE-NAME are added recursively; if FILE-NAME designates a flat file and
RECURSIVE? is true, its contents are added, and its permission bits are
kept. HASH-ALGO must be a string such as \"sha256\"."
(let* ((st (stat file-name #f))
RECURSIVE? is false, FILE-NAME must designate a regular file--not a directory
nor a symlink. When RECURSIVE? is true and FILE-NAME designates a directory,
the contents of FILE-NAME are added recursively; if FILE-NAME designates a
flat file and RECURSIVE? is true, its contents are added, and its permission
bits are kept. HASH-ALGO must be a string such as \"sha256\"."
(let* ((st (false-if-exception (lstat file-name)))
(args `(,st ,basename ,recursive? ,hash-algo))
(cache (nix-server-add-to-store-cache server)))
(or (and st (hash-ref cache args))

23
tests/gexp.scm
View file

@ -101,7 +101,7 @@ (define-syntax-rule (test-assertm name exp)
(let* ((file (search-path %load-path "guix.scm"))
(local (local-file file))
(exp (gexp (display (ungexp local))))
(intd (add-to-store %store (basename file) #t
(intd (add-to-store %store (basename file) #f
"sha256" file)))
(and (gexp? exp)
(match (gexp-inputs exp)
@ -109,6 +109,25 @@ (define-syntax-rule (test-assertm name exp)
(eq? x local)))
(equal? `(display ,intd) (gexp->sexp* exp)))))
(test-assert "one local file, symlink"
(let ((file (search-path %load-path "guix.scm"))
(link (tmpnam)))
(dynamic-wind
(const #t)
(lambda ()
(symlink (canonicalize-path file) link)
(let* ((local (local-file link "my-file" #:recursive? #f))
(exp (gexp (display (ungexp local))))
(intd (add-to-store %store "my-file" #f
"sha256" file)))
(and (gexp? exp)
(match (gexp-inputs exp)
(((x "out"))
(eq? x local)))
(equal? `(display ,intd) (gexp->sexp* exp)))))
(lambda ()
(false-if-exception (delete-file link))))))
(test-assert "one plain file"
(let* ((file (plain-file "hi" "Hello, world!"))
(exp (gexp (display (ungexp file))))
@ -360,7 +379,7 @@ (define (match-input thing)
(test-assertm "gexp->derivation, local-file"
(mlet* %store-monad ((file -> (search-path %load-path "guix.scm"))
(intd (interned-file file))
(intd (interned-file file #:recursive? #f))
(local -> (local-file file))
(exp -> (gexp (begin
(stat (ungexp local))