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guix/gnu/packages/julia.scm
Ricardo Wurmus d70f5139da
gnu: julia: Update to 0.5.0. 
* gnu/packages/julia.scm (libuv-julia): Update to commit
8d5131b6c1595920dd30644cd1435b4f344b46c8.
(libunwind-for-julia): New variable.
(julia): Update to 0.5.0.
[arguments]: Disable stripping of binaries; modify "prepare-deps" phase;
add "fix-llvm-flag" phase; add "set-home" phase; adjust
"hardcode-soname-map" phase; remove fix for "double-conversion" from
"fix-include-and-link-paths" phase; enable "repl" and "replcompletions"
tests; disable "backtrace", "compile", "replutil", and "cmdlineargs"
tests; remove USE_SYSTEM_RMATH flag; remove USE_SYSTEM_GRISU flag.
[inputs]: Replace "llvm-3.5" with "llvm"; replace "libunwind" with
"libunwind-for-julia"; remove "double-conversion"; remove "rmath-julia";
update "suitesparse" origin; replace "virtualenv" origin with
"python2-virtualenv".
[native-inputs]: Add "openssl".
2016-10-01 21:36:36 +02:00

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;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2015, 2016 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il>
;;;
;;; 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 <http://www.gnu.org/licenses/>.
(define-module (gnu packages julia)
#:use-module ((guix licenses) #:prefix license:)
#:use-module (guix packages)
#:use-module (guix download)
#:use-module (guix utils)
#:use-module (guix git-download)
#:use-module (guix build-system gnu)
#:use-module (gnu packages)
#:use-module (gnu packages algebra)
#:use-module (gnu packages base)
#:use-module (gnu packages compression)
#:use-module (gnu packages elf)
#:use-module (gnu packages gcc)
#:use-module (gnu packages llvm)
#:use-module (gnu packages libevent)
#:use-module (gnu packages libunwind)
#:use-module (gnu packages maths)
#:use-module (gnu packages multiprecision) ; mpfr
#:use-module (gnu packages pcre)
#:use-module (gnu packages perl)
#:use-module (gnu packages pkg-config)
#:use-module (gnu packages python)
#:use-module (gnu packages textutils)
#:use-module (gnu packages tls)
#:use-module (gnu packages version-control)
#:use-module (gnu packages wget)
#:use-module (ice-9 match))
(define libuv-julia
(let ((commit "8d5131b6c1595920dd30644cd1435b4f344b46c8")
(revision "4"))
(package (inherit libuv)
(name "libuv-julia")
(version (string-append "1.9.0-" revision "." (string-take commit 8)))
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/JuliaLang/libuv.git")
(commit commit)))
(file-name (string-append name "-" version "-checkout"))
(sha256
(base32
"1fq0vhiprdryw8iisxxwyld3xdr5za6y8458p22ff56al98h22fv"))))
(build-system gnu-build-system)
(arguments
(substitute-keyword-arguments (package-arguments libuv)
((#:phases phases)
`(modify-phases ,phases
(delete 'autogen)))))
(home-page "https://github.com/JuliaLang/libuv"))))
(define libunwind-for-julia
(package
(inherit libunwind)
(version "1.1-julia2")
(source (origin
(method url-fetch)
(uri (string-append "https://s3.amazonaws.com/julialang/src/"
"libunwind-" version ".tar.gz"))
(sha256
(base32
"0499x7sg2v18a6cry6l8y713cgmic0adnjph8i0xr1db9p7n8qyv"))))))
(define-public julia
(package
(name "julia")
(version "0.5.0")
(source (origin
(method url-fetch)
(uri (string-append
"https://github.com/JuliaLang/julia/releases/download/v"
version "/julia-" version ".tar.gz"))
(sha256
(base32
"0bhickil88lalp9jdj1kmf4is70zinhx8ha9rng0g3z50r4a2qmv"))))
(build-system gnu-build-system)
(arguments
`(#:test-target "test"
#:modules ((ice-9 match)
(guix build gnu-build-system)
(guix build utils))
;; Do not strip binaries to keep support for full backtraces.
;; See https://github.com/JuliaLang/julia/issues/17831
#:strip-binaries? #f
;; The DSOs use $ORIGIN to refer to each other, but (guix build
;; gremlin) doesn't support it yet, so skip this phase.
#:validate-runpath? #f
#:phases
(modify-phases %standard-phases
(delete 'configure)
(add-after 'unpack 'prepare-deps
(lambda* (#:key inputs #:allow-other-keys)
(mkdir "deps/srccache")
(copy-file (assoc-ref inputs "dsfmt")
"deps/srccache/dsfmt-2.2.3.tar.gz")
(copy-file (assoc-ref inputs "objconv")
"deps/srccache/objconv.zip")
(copy-file (assoc-ref inputs "suitesparse")
"deps/srccache/SuiteSparse-4.4.5.tar.gz")
(copy-file (string-append (assoc-ref inputs "virtualenv")
"/bin/virtualenv")
"julia-env")
#t))
(add-after 'unpack 'fix-llvm-flag
(lambda _
(substitute* "src/Makefile"
(("-lLLVM-\\$\\(shell \\$\\(LLVM_CONFIG_HOST\\) --version\\)")
"$(shell $(LLVM_CONFIG_HOST) --libs)"))
#t))
(add-before 'check 'set-home
;; Some tests require a home directory to be set.
(lambda _ (setenv "HOME" "/tmp") #t))
(add-after 'unpack 'hardcode-soname-map
;; ./src/runtime_ccall.cpp creates a map from library names to paths
;; using the output of "/sbin/ldconfig -p". Since ldconfig is not
;; used in Guix, we patch runtime_ccall.cpp to contain a static map.
(lambda* (#:key inputs #:allow-other-keys)
(use-modules (ice-9 match))
(substitute* "src/runtime_ccall.cpp"
(("jl_read_sonames.*;")
(string-join
(map (match-lambda
((input libname soname)
(string-append
"sonameMap[\"" libname "\"] = "
"\"" (assoc-ref inputs input) "/lib/" soname "\";")))
'(("libc" "libc" "libc.so.6")
("pcre2" "libpcre2-8" "libpcre2-8.so")
("mpfr" "libmpfr" "libmpfr.so")
("openblas" "libblas" "libopenblas.so")
("arpack-ng" "libarpack" "libarpack.so")
("lapack" "liblapack" "liblapack.so")
("libgit2" "libgit2" "libgit2.so")
("gmp" "libgmp" "libgmp.so")
("openlibm" "libopenlibm" "libopenlibm.so")
("openspecfun" "libopenspecfun" "libopenspecfun.so")
("fftw" "libfftw3" "libfftw3.so")
("fftwf" "libfftw3f" "libfftw3f.so"))))))
(substitute* "base/fft/FFTW.jl"
(("const libfftw = Base.libfftw_name")
(string-append "const libfftw = \""
(assoc-ref inputs "fftw") "/lib/libfftw3.so"
"\""))
(("const libfftwf = Base.libfftwf_name")
(string-append "const libfftwf = \""
(assoc-ref inputs "fftwf") "/lib/libfftw3f.so"
"\"")))
(substitute* "base/math.jl"
(("const libm = Base.libm_name")
(string-append "const libm = \""
(assoc-ref inputs "openlibm")
"/lib/libopenlibm.so"
"\""))
(("const openspecfun = \"libopenspecfun\"")
(string-append "const openspecfun = \""
(assoc-ref inputs "openspecfun")
"/lib/libopenspecfun.so"
"\"")))
(substitute* "base/pcre.jl"
(("const PCRE_LIB = \"libpcre2-8\"")
(string-append "const PCRE_LIB = \""
(assoc-ref inputs "pcre2")
"/lib/libpcre2-8.so" "\"")))
#t))
(add-before 'build 'fix-include-and-link-paths
(lambda* (#:key inputs #:allow-other-keys)
;; LIBUTF8PROC is a linker flag, not a build target. It is
;; included in the LIBFILES_* variable which is used as a
;; collection of build targets and a list of libraries to link
;; against.
(substitute* "src/flisp/Makefile"
(("\\$\\(BUILDDIR\\)/\\$\\(EXENAME\\): \\$\\(OBJS\\) \\$\\(LIBFILES_release\\)")
"$(BUILDDIR)/$(EXENAME): $(OBJS) $(LLT_release)")
(("\\$\\(BUILDDIR\\)/\\$\\(EXENAME\\)-debug: \\$\\(DOBJS\\) \\$\\(LIBFILES_debug\\)")
"$(BUILDDIR)/$(EXENAME)-debug: $(DOBJS) $(LLT_debug)"))
;; The REPL must be linked with libuv.
(substitute* "ui/Makefile"
(("JLDFLAGS \\+= ")
(string-append "JLDFLAGS += "
(assoc-ref %build-inputs "libuv")
"/lib/libuv.so ")))
(substitute* "base/Makefile"
(("\\$\\(build_includedir\\)/uv-errno.h")
(string-append (assoc-ref inputs "libuv")
"/include/uv-errno.h")))
#t))
(add-before 'build 'replace-default-shell
(lambda _
(substitute* "base/client.jl"
(("/bin/sh") (which "sh")))
#t))
(add-after 'unpack 'hardcode-paths
(lambda _
(substitute* "base/interactiveutil.jl"
(("`which") (string-append "`" (which "which")))
(("`wget") (string-append "`" (which "wget"))))
#t))
(add-before 'check 'disable-broken-tests
(lambda _
(substitute* "test/choosetests.jl"
;; These tests fail, probably because some of the input
;; binaries have been stripped and thus backtraces don't look
;; as expected.
(("\"backtrace\",") "")
(("\"compile\",") "")
(("\"replutil\",") "")
(("\"cmdlineargs\",") ""))
#t)))
#:make-flags
(list
(string-append "prefix=" (assoc-ref %outputs "out"))
;; Passing the MARCH flag is necessary to build binary substitutes for
;; the supported architectures.
,(match (or (%current-target-system)
(%current-system))
("x86_64-linux" "MARCH=x86-64")
("i686-linux" "MARCH=pentium4")
;; Prevent errors when querying this package on unsupported
;; platforms, e.g. when running "guix package --search="
(_ "MARCH=UNSUPPORTED"))
"CONFIG_SHELL=bash" ;needed to build bundled libraries
"USE_SYSTEM_DSFMT=0" ;not packaged for Guix and upstream has no
;build system for a shared library.
"USE_SYSTEM_LAPACK=1"
"USE_SYSTEM_BLAS=1"
"USE_BLAS64=0" ;needed when USE_SYSTEM_BLAS=1
"USE_SYSTEM_FFTW=1"
"LIBFFTWNAME=libfftw3"
"LIBFFTWFNAME=libfftw3f"
;; TODO: Suitesparse does not install shared libraries, so we cannot
;; use the suitesparse package.
;; "USE_SYSTEM_SUITESPARSE=1"
;; (string-append "SUITESPARSE_INC=-I "
;; (assoc-ref %build-inputs "suitesparse")
;; "/include")
"USE_GPL_LIBS=1" ;proudly
"USE_SYSTEM_UTF8PROC=1"
(string-append "UTF8PROC_INC="
(assoc-ref %build-inputs "utf8proc")
"/include")
"USE_SYSTEM_LLVM=1"
"USE_SYSTEM_LIBUNWIND=1"
"USE_SYSTEM_LIBUV=1"
(string-append "LIBUV="
(assoc-ref %build-inputs "libuv")
"/lib/libuv.so")
(string-append "LIBUV_INC="
(assoc-ref %build-inputs "libuv")
"/include")
"USE_SYSTEM_PATCHELF=1"
"USE_SYSTEM_PCRE=1"
"USE_SYSTEM_OPENLIBM=1"
"USE_SYSTEM_GMP=1"
"USE_SYSTEM_MPFR=1"
"USE_SYSTEM_ARPACK=1"
"USE_SYSTEM_LIBGIT2=1"
"USE_SYSTEM_OPENSPECFUN=1")))
(inputs
`(("llvm" ,llvm)
("arpack-ng" ,arpack-ng)
("coreutils" ,coreutils) ;for bindings to "mkdir" and the like
("lapack" ,lapack)
("openblas" ,openblas) ;Julia does not build with Atlas
("libunwind" ,libunwind-for-julia)
("openlibm" ,openlibm)
("openspecfun" ,openspecfun)
("libgit2" ,libgit2)
("fftw" ,fftw)
("fftwf" ,fftwf)
("fortran" ,gfortran)
("libuv" ,libuv-julia)
("pcre2" ,pcre2)
("utf8proc" ,utf8proc)
("mpfr" ,mpfr)
("wget" ,wget)
("which" ,which)
("zlib" ,zlib)
("gmp" ,gmp)
("virtualenv" ,python2-virtualenv)
;; FIXME: The following inputs are downloaded from upstream to allow us
;; to use the lightweight Julia release tarball. Ideally, these inputs
;; would eventually be replaced with proper Guix packages.
;; TODO: run "make -f contrib/repackage_system_suitesparse4.make" to copy static lib
("suitesparse"
,(origin
(method url-fetch)
(uri "http://faculty.cse.tamu.edu/davis/SuiteSparse/SuiteSparse-4.4.5.tar.gz")
(sha256
(base32
"1jcbxb8jx5wlcixzf6n5dca2rcfx6mlcms1k2rl5gp67ay3bix43"))))
("objconv"
,(origin
(method url-fetch)
(uri "http://www.agner.org/optimize/objconv.zip")
(sha256
(base32
"1fi7qa2sd9vb35dvkgripjf0fayzg2qmff215f8agfqfiwd1g8qs"))))
("dsfmt"
,(origin
(method url-fetch)
(uri (string-append
"http://www.math.sci.hiroshima-u.ac.jp/~m-mat/MT/"
"SFMT/dSFMT-src-2.2.3.tar.gz"))
(sha256
(base32
"03kaqbjbi6viz0n33dk5jlf6ayxqlsq4804n7kwkndiga9s4hd42"))))))
(native-inputs
`(("openssl" ,openssl)
("perl" ,perl)
("patchelf" ,patchelf)
("pkg-config" ,pkg-config)
("python" ,python-2)))
;; Julia is not officially released for ARM and MIPS.
;; See https://github.com/JuliaLang/julia/issues/10639
(supported-systems '("i686-linux" "x86_64-linux"))
(home-page "http://julialang.org/")
(synopsis "High-performance dynamic language for technical computing")
(description
"Julia is a high-level, high-performance dynamic programming language for
technical computing, with syntax that is familiar to users of other technical
computing environments. It provides a sophisticated compiler, distributed
parallel execution, numerical accuracy, and an extensive mathematical function
library.")
(license license:expat)))
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