399 lines
17 KiB
Scheme
399 lines
17 KiB
Scheme
;;; GNU Guix --- Functional package management for GNU
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;;; Copyright © 2015, 2016, 2017 Ricardo Wurmus <rekado@elephly.net>
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;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il>
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;;;
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;;; This file is part of GNU Guix.
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;;;
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;;; GNU Guix is free software; you can redistribute it and/or modify it
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;;; under the terms of the GNU General Public License as published by
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;;; the Free Software Foundation; either version 3 of the License, or (at
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;;; your option) any later version.
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;;;
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;;; GNU Guix is distributed in the hope that it will be useful, but
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;;; WITHOUT ANY WARRANTY; without even the implied warranty of
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;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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;;; GNU General Public License for more details.
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;;;
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;;; You should have received a copy of the GNU General Public License
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;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
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(define-module (gnu packages julia)
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#:use-module ((guix licenses) #:prefix license:)
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#:use-module (guix packages)
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#:use-module (guix download)
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#:use-module (guix utils)
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#:use-module (guix git-download)
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#:use-module (guix build-system gnu)
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#:use-module (gnu packages)
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#:use-module (gnu packages algebra)
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#:use-module (gnu packages base)
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#:use-module (gnu packages compression)
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#:use-module (gnu packages elf)
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#:use-module (gnu packages gcc)
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#:use-module (gnu packages llvm)
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#:use-module (gnu packages libevent)
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#:use-module (gnu packages libunwind)
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#:use-module (gnu packages maths)
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#:use-module (gnu packages multiprecision) ; mpfr
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#:use-module (gnu packages pcre)
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#:use-module (gnu packages perl)
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#:use-module (gnu packages pkg-config)
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#:use-module (gnu packages python)
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#:use-module (gnu packages python-xyz)
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#:use-module (gnu packages textutils)
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#:use-module (gnu packages tls)
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#:use-module (gnu packages version-control)
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#:use-module (gnu packages wget)
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#:use-module (ice-9 match))
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(define libuv-julia
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(let ((commit "52d72a52cc7ccd570929990f010ed16e2ec604c8")
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(revision "5"))
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(package (inherit libuv)
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(name "libuv-julia")
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(version (string-append "1.9.0-" revision "." (string-take commit 8)))
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(source (origin
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(method git-fetch)
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(uri (git-reference
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(url "https://github.com/JuliaLang/libuv.git")
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(commit commit)))
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(file-name (string-append name "-" version "-checkout"))
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(sha256
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(base32
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"1daxh6ci6q7znxxajr3bm16dd53ragm0d681wf4kzg542qnjq3lh"))))
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(build-system gnu-build-system)
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(arguments
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(substitute-keyword-arguments (package-arguments libuv)
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((#:phases phases)
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`(modify-phases ,phases
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(delete 'autogen)))))
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(home-page "https://github.com/JuliaLang/libuv"))))
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(define libunwind-for-julia
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(package
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(inherit libunwind)
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(version "1.1-julia2")
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(source (origin
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(method url-fetch)
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(uri (string-append "https://s3.amazonaws.com/julialang/src/"
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"libunwind-" version ".tar.gz"))
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(sha256
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(base32
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"0499x7sg2v18a6cry6l8y713cgmic0adnjph8i0xr1db9p7n8qyv"))))))
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(define-public julia
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(package
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(name "julia")
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(version "0.6.0")
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(source (origin
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(method url-fetch)
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(uri (string-append
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"https://github.com/JuliaLang/julia/releases/download/v"
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version "/julia-" version ".tar.gz"))
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(sha256
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(base32
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"0rd6lcc9sic10q1j3c6f9qr901i1c4554m93n2sz5b3mh37byqhw"))))
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(build-system gnu-build-system)
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(arguments
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`(#:test-target "test"
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#:modules ((ice-9 match)
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(guix build gnu-build-system)
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(guix build utils))
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;; Do not strip binaries to keep support for full backtraces.
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;; See https://github.com/JuliaLang/julia/issues/17831
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#:strip-binaries? #f
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;; The DSOs use $ORIGIN to refer to each other, but (guix build
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;; gremlin) doesn't support it yet, so skip this phase.
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#:validate-runpath? #f
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#:phases
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(modify-phases %standard-phases
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(delete 'configure)
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(add-after 'unpack 'prepare-deps
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(lambda* (#:key inputs #:allow-other-keys)
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(mkdir "deps/srccache")
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(copy-file (assoc-ref inputs "dsfmt")
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"deps/srccache/dsfmt-2.2.3.tar.gz")
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(copy-file (assoc-ref inputs "objconv")
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"deps/srccache/objconv.zip")
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(copy-file (assoc-ref inputs "suitesparse")
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"deps/srccache/SuiteSparse-4.4.5.tar.gz")
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(copy-file (string-append (assoc-ref inputs "virtualenv")
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"/bin/virtualenv")
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"julia-env")
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(copy-file (assoc-ref inputs "unicode-data")
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"doc/UnicodeData.txt")
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#t))
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;; FIXME: Building the documentation requires Julia packages that
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;; would be downloaded from the Internet. We should build them in a
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;; separate build phase.
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(add-after 'unpack 'disable-documentation
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(lambda _
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(substitute* "Makefile"
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(("(install: .*) \\$\\(BUILDROOT\\)/doc/_build/html/en/index.html" _ line)
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(string-append line "\n"))
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(("src ui doc deps")
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"src ui deps"))
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#t))
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(add-before 'check 'set-home
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;; Some tests require a home directory to be set.
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(lambda _ (setenv "HOME" "/tmp") #t))
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(add-after 'unpack 'hardcode-soname-map
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;; ./src/runtime_ccall.cpp creates a map from library names to paths
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;; using the output of "/sbin/ldconfig -p". Since ldconfig is not
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;; used in Guix, we patch runtime_ccall.cpp to contain a static map.
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(lambda* (#:key inputs #:allow-other-keys)
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(use-modules (ice-9 match))
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(substitute* "src/runtime_ccall.cpp"
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;; Patch out invocations of '/sbin/ldconfig' to avoid getting
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;; error messages about missing '/sbin/ldconfig' on Guix System.
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(("popen\\(.*ldconfig.*\\);")
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"NULL;\n")
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;; Populate 'sonameMap'.
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(("jl_read_sonames.*;")
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(string-join
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(map (match-lambda
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((input libname soname)
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(string-append
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"sonameMap[\"" libname "\"] = "
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"\"" (assoc-ref inputs input) "/lib/" soname "\";")))
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'(("libc" "libc" "libc.so.6")
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("pcre2" "libpcre2-8" "libpcre2-8.so")
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("mpfr" "libmpfr" "libmpfr.so")
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("openblas" "libblas" "libopenblas.so")
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("arpack-ng" "libarpack" "libarpack.so")
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("lapack" "liblapack" "liblapack.so")
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("libgit2" "libgit2" "libgit2.so")
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("gmp" "libgmp" "libgmp.so")
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("openlibm" "libopenlibm" "libopenlibm.so")
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("openspecfun" "libopenspecfun" "libopenspecfun.so")
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("fftw" "libfftw3" "libfftw3_threads.so")
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("fftwf" "libfftw3f" "libfftw3f_threads.so"))))))
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(substitute* "base/fft/FFTW.jl"
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(("const libfftw = Base.libfftw_name")
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(string-append "const libfftw = \""
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(assoc-ref inputs "fftw") "/lib/libfftw3_threads.so"
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"\""))
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(("const libfftwf = Base.libfftwf_name")
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(string-append "const libfftwf = \""
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(assoc-ref inputs "fftwf") "/lib/libfftw3f_threads.so"
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"\"")))
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(substitute* "base/math.jl"
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(("const libm = Base.libm_name")
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(string-append "const libm = \""
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(assoc-ref inputs "openlibm")
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"/lib/libopenlibm.so"
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"\""))
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(("const openspecfun = \"libopenspecfun\"")
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(string-append "const openspecfun = \""
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(assoc-ref inputs "openspecfun")
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"/lib/libopenspecfun.so"
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"\"")))
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(substitute* "base/pcre.jl"
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(("const PCRE_LIB = \"libpcre2-8\"")
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(string-append "const PCRE_LIB = \""
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(assoc-ref inputs "pcre2")
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"/lib/libpcre2-8.so" "\"")))
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#t))
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(add-before 'build 'fix-include-and-link-paths
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(lambda* (#:key inputs #:allow-other-keys)
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;; LIBUTF8PROC is a linker flag, not a build target. It is
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;; included in the LIBFILES_* variable which is used as a
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;; collection of build targets and a list of libraries to link
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;; against.
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(substitute* "src/flisp/Makefile"
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(("\\$\\(BUILDDIR\\)/\\$\\(EXENAME\\): \\$\\(OBJS\\) \\$\\(LIBFILES_release\\)")
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"$(BUILDDIR)/$(EXENAME): $(OBJS) $(LLT_release)")
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(("\\$\\(BUILDDIR\\)/\\$\\(EXENAME\\)-debug: \\$\\(DOBJS\\) \\$\\(LIBFILES_debug\\)")
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"$(BUILDDIR)/$(EXENAME)-debug: $(DOBJS) $(LLT_debug)"))
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;; The REPL must be linked with libuv.
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(substitute* "ui/Makefile"
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(("JLDFLAGS \\+= ")
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(string-append "JLDFLAGS += "
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(assoc-ref %build-inputs "libuv")
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"/lib/libuv.so ")))
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(substitute* "base/Makefile"
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(("\\$\\(build_includedir\\)/uv-errno.h")
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(string-append (assoc-ref inputs "libuv")
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"/include/uv-errno.h")))
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#t))
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(add-before 'build 'replace-default-shell
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(lambda _
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(substitute* "base/client.jl"
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(("/bin/sh") (which "sh")))
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#t))
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(add-after 'unpack 'hardcode-paths
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(lambda _
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(substitute* "base/interactiveutil.jl"
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(("`which") (string-append "`" (which "which")))
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(("`wget") (string-append "`" (which "wget"))))
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#t))
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(add-before 'check 'disable-broken-tests
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(lambda _
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;; Adjust expected error messages to match what current libgit2
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;; provides.
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(substitute* "test/libgit2.jl"
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(("Invalid Content-Type") "invalid Content-Type")
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(("Failed to resolve path") "failed to resolve path"))
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(substitute* "test/choosetests.jl"
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;; These tests fail, probably because some of the input
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;; binaries have been stripped and thus backtraces don't look
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;; as expected.
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(("\"backtrace\",") "")
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(("\"compile\",") "")
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(("\"replutil\",") "")
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(("\"cmdlineargs\",") "")
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;; FIXME: This test fails with the following error:
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;; Error in testset file:
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;; Test Failed
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;; Expression: download("ba\0d", "good")
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;; Expected: ArgumentError
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;; Thrown: Base.UVError
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(("\"file\",") ""))
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#t)))
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#:make-flags
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(list
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(string-append "prefix=" (assoc-ref %outputs "out"))
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;; Passing the MARCH flag is necessary to build binary substitutes for
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;; the supported architectures.
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,(match (or (%current-target-system)
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(%current-system))
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("x86_64-linux" "MARCH=x86-64")
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("i686-linux" "MARCH=pentium4")
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("aarch64-linux" "MARCH=armv8-a")
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;; Prevent errors when querying this package on unsupported
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;; platforms, e.g. when running "guix package --search="
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(_ "MARCH=UNSUPPORTED"))
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"CONFIG_SHELL=bash" ;needed to build bundled libraries
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"USE_SYSTEM_DSFMT=0" ;not packaged for Guix and upstream has no
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;build system for a shared library.
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"USE_SYSTEM_LAPACK=1"
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"USE_SYSTEM_BLAS=1"
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"USE_BLAS64=0" ;needed when USE_SYSTEM_BLAS=1
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"USE_SYSTEM_FFTW=1"
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"LIBFFTWNAME=libfftw3"
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"LIBFFTWFNAME=libfftw3f"
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;; TODO: Suitesparse does not install shared libraries, so we cannot
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;; use the suitesparse package.
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;; "USE_SYSTEM_SUITESPARSE=1"
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;; (string-append "SUITESPARSE_INC=-I "
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;; (assoc-ref %build-inputs "suitesparse")
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;; "/include")
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"USE_GPL_LIBS=1" ;proudly
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"USE_SYSTEM_UTF8PROC=1"
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(string-append "UTF8PROC_INC="
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(assoc-ref %build-inputs "utf8proc")
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"/include")
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"USE_SYSTEM_LLVM=1"
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"USE_LLVM_SHLIB=0" ; FIXME: fails when set to 1
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"USE_SYSTEM_LIBUNWIND=1"
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"USE_SYSTEM_LIBUV=1"
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(string-append "LIBUV="
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(assoc-ref %build-inputs "libuv")
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"/lib/libuv.so")
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(string-append "LIBUV_INC="
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(assoc-ref %build-inputs "libuv")
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"/include")
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"USE_SYSTEM_PATCHELF=1"
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"USE_SYSTEM_PCRE=1"
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"USE_SYSTEM_OPENLIBM=1"
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"USE_SYSTEM_GMP=1"
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"USE_SYSTEM_MPFR=1"
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"USE_SYSTEM_ARPACK=1"
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"USE_SYSTEM_LIBGIT2=1"
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"USE_SYSTEM_OPENSPECFUN=1")))
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(inputs
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`(("llvm" ,llvm-3.9.1)
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;; The bundled version is 3.3.0 so stick to that version. With other
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;; versions, we get test failures in 'linalg/arnoldi' as described in
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;; <https://bugs.gnu.org/30282>.
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("arpack-ng" ,arpack-ng-3.3.0)
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("coreutils" ,coreutils) ;for bindings to "mkdir" and the like
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("lapack" ,lapack)
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("openblas" ,openblas) ;Julia does not build with Atlas
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("libunwind" ,libunwind-for-julia)
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("openlibm" ,openlibm)
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("openspecfun" ,openspecfun)
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("libgit2" ,libgit2)
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("fftw" ,fftw)
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("fftwf" ,fftwf)
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("fortran" ,gfortran)
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("libuv" ,libuv-julia)
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("pcre2" ,pcre2)
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("utf8proc" ,utf8proc)
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("mpfr" ,mpfr)
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("wget" ,wget)
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("which" ,which)
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("zlib" ,zlib)
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("gmp" ,gmp)
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("virtualenv" ,python2-virtualenv)
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;; FIXME: The following inputs are downloaded from upstream to allow us
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;; to use the lightweight Julia release tarball. Ideally, these inputs
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;; would eventually be replaced with proper Guix packages.
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;; TODO: run "make -f contrib/repackage_system_suitesparse4.make" to copy static lib
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("suitesparse"
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,(origin
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(method url-fetch)
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(uri "http://faculty.cse.tamu.edu/davis/SuiteSparse/SuiteSparse-4.4.5.tar.gz")
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(sha256
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(base32
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"1jcbxb8jx5wlcixzf6n5dca2rcfx6mlcms1k2rl5gp67ay3bix43"))))
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("objconv"
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,(origin
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(method url-fetch)
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;; No versioned URL, see <https://www.agner.org/optimize/> for updates.
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(uri "https://www.agner.org/optimize/objconv.zip")
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(file-name "objconv-2018-10-07.zip")
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(sha256
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(base32
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"0wp6ld9vk11f4nnkn56627zmlv9k5vafi99qa3yyn1pgcd61zcfs"))))
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("dsfmt"
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,(origin
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(method url-fetch)
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(uri (string-append
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"http://www.math.sci.hiroshima-u.ac.jp/~m-mat/MT/"
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"SFMT/dSFMT-src-2.2.3.tar.gz"))
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(sha256
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(base32
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"03kaqbjbi6viz0n33dk5jlf6ayxqlsq4804n7kwkndiga9s4hd42"))))))
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(native-inputs
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`(("openssl" ,openssl)
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("perl" ,perl)
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("patchelf" ,patchelf)
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("pkg-config" ,pkg-config)
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("python" ,python-2)
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("unicode-data"
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,(origin
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(method url-fetch)
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(uri "http://www.unicode.org/Public/9.0.0/ucd/UnicodeData.txt")
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(sha256
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(base32
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"13zfannnr6sa6s27ggvcvzmh133ndi38pfyxsssvjmw2s8ac9pv8"))))))
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;; Julia is not officially released for ARM and MIPS.
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;; See https://github.com/JuliaLang/julia/issues/10639
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(supported-systems '("i686-linux" "x86_64-linux" "aarch64-linux"))
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(home-page "https://julialang.org/")
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(synopsis "High-performance dynamic language for technical computing")
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(description
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"Julia is a high-level, high-performance dynamic programming language for
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technical computing, with syntax that is familiar to users of other technical
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computing environments. It provides a sophisticated compiler, distributed
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parallel execution, numerical accuracy, and an extensive mathematical function
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library.")
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(license license:expat)))
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