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-rw-r--r--gnu/packages/audio.scm27
-rw-r--r--gnu/packages/bioinformatics.scm59
-rw-r--r--gnu/packages/commencement.scm1
-rw-r--r--gnu/packages/gcc.scm26
-rw-r--r--gnu/packages/gnome.scm10
-rw-r--r--gnu/packages/llvm.scm51
-rw-r--r--gnu/packages/patches/clang-libc-search-path.patch19
-rw-r--r--gnu/packages/patches/guile-linux-syscalls.patch22
-rw-r--r--gnu/packages/ruby.scm33
-rw-r--r--gnu/packages/video.scm4
10 files changed, 234 insertions, 18 deletions
diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm
index f6881883bb..6dd4bd7ffe 100644
--- a/gnu/packages/audio.scm
+++ b/gnu/packages/audio.scm
@@ -1034,6 +1034,33 @@ buffers, and audio capture.")
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")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 12c9175ed3..8dfaff3e00 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -780,6 +780,65 @@ analysis (from RNA-Seq), transcription factor binding quantification in
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")
diff --git a/gnu/packages/commencement.scm b/gnu/packages/commencement.scm
index db91bec5da..ebf770bfa7 100644
--- a/gnu/packages/commencement.scm
+++ b/gnu/packages/commencement.scm
@@ -518,6 +518,7 @@ exec ~a/bin/~a-~a -B~a/lib -Wl,-dynamic-linker -Wl,~a/~a \"$@\"~%"
(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++")
diff --git a/gnu/packages/gcc.scm b/gnu/packages/gcc.scm
index beb007e95b..c370fe8212 100644
--- a/gnu/packages/gcc.scm
+++ b/gnu/packages/gcc.scm
@@ -345,6 +345,32 @@ Go. It also includes runtime support libraries for these languages.")
'("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)
diff --git a/gnu/packages/gnome.scm b/gnu/packages/gnome.scm
index 30f834a168..f7a6465eb6 100644
--- a/gnu/packages/gnome.scm
+++ b/gnu/packages/gnome.scm
@@ -2402,15 +2402,17 @@ settings, themes, mouse settings, and startup of other daemons.")
(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
diff --git a/gnu/packages/llvm.scm b/gnu/packages/llvm.scm
index 6cf1fdab0a..47710e69fc 100644
--- a/gnu/packages/llvm.scm
+++ b/gnu/packages/llvm.scm
@@ -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 @@
#: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 @@ tools as well as libraries with equivalent functionality.")
(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 @@ tools as well as libraries with equivalent functionality.")
(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
diff --git a/gnu/packages/patches/clang-libc-search-path.patch b/gnu/packages/patches/clang-libc-search-path.patch
new file mode 100644
index 0000000000..327336ac09
--- /dev/null
+++ b/gnu/packages/patches/clang-libc-search-path.patch
@@ -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 {
diff --git a/gnu/packages/patches/guile-linux-syscalls.patch b/gnu/packages/patches/guile-linux-syscalls.patch
index 25a5e90e35..ac74d021d7 100644
--- a/gnu/packages/patches/guile-linux-syscalls.patch
+++ b/gnu/packages/patches/guile-linux-syscalls.patch
@@ -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
diff --git a/gnu/packages/ruby.scm b/gnu/packages/ruby.scm
index ff30c4988a..af87cf551f 100644
--- a/gnu/packages/ruby.scm
+++ b/gnu/packages/ruby.scm
@@ -88,6 +88,39 @@ a focus on simplicity and productivity.")
(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")
diff --git a/gnu/packages/video.scm b/gnu/packages/video.scm
index b923e47444..c118b2fe50 100644
--- a/gnu/packages/video.scm
+++ b/gnu/packages/video.scm
@@ -296,14 +296,14 @@ standards (MPEG-2, MPEG-4 ASP/H.263, MPEG-4 AVC/H.264, and VC-1/VMW3).")
(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)
generated by cgit v1.2.3 (git 2.45.0) at 2024-12-13 22:59:42 +0000