11d73fb412
* gnu/packages/julia.scm (julia)[native-search-paths]: Add specification for JULIA_LOAD_PATH. Signed-off-by: Julien Lepiller <julien@lepiller.eu>
500 lines
21 KiB
Scheme
500 lines
21 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 "26dbe5672c33fc885462c509fe2a9b36f35866fd")
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(revision "6"))
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;; When upgrading Julia, also upgrade this.
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;; Get the commit from https://github.com/JuliaLang/julia/blob/v1.1.1/deps/libuv.version
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(package
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(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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"17pn2xmqaramilx897s9grs966i5246gi6sric5alch4g9j4685n"))))
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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 (llvm-patch-url version name)
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(string-append "https://raw.githubusercontent.com/JuliaLang/julia/v" version
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"/deps/patches/" name))
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(define (llvm-patch name sha)
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(let ((version "1.1.1"))
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(origin (method url-fetch)
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(uri (llvm-patch-url version name))
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(sha256 (base32 sha))
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(file-name name))))
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(define llvm-julia
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(package
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(inherit llvm-6)
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(name "llvm-julia")
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(source (origin
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(method url-fetch)
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(uri "http://releases.llvm.org/6.0.1/llvm-6.0.1.src.tar.xz")
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(sha256
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(base32
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"1qpls3vk85lydi5b4axl0809fv932qgsqgdgrk098567z4jc7mmn"))
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;; Those patches are inside the Julia source repo.
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;; They are _not_ Julia specific (https://github.com/julialang/julia#llvm)
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;; but they are required to build Julia.
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;; Discussion: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=919628
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(patches
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(list
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(llvm-patch "llvm-6.0-D44650.patch"
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"1336q4vqayr94wdcnlmcxh90mjdh34dzw9x2cbiqjnx9b1j8fxyb")
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(llvm-patch "llvm-6.0-DISABLE_ABI_CHECKS.patch"
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"014fawd1ba7yckalypfld22zgic87x9nx3cim42zrwygywd36pyg")
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(llvm-patch "llvm-6.0-NVPTX-addrspaces.patch"
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"1qdi2zmrjsrj0h84zv2vyly2hjcn4f67mfy0s1q353g4v4jkscqc")
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(llvm-patch "llvm-6.0.0_D27296-libssp.patch"
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"0s5hi2r1j63i8m6ig1346crx2aiv9f7rgb3mg80kw1wx5y7pdpfh")
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(llvm-patch "llvm-D27629-AArch64-large_model_6.0.1.patch"
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"1qrshmlqvnasdyc158vfn3hnbigqph3lsq7acb9w8lwkpnnm2j4z")
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(llvm-patch "llvm-D34078-vectorize-fdiv.patch"
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"1696hg84a0jxcnggvqsc2cdp271hf9a44p4qsd078qm1mfawkaay")
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(llvm-patch "llvm-D42262-jumpthreading-not-i1.patch"
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"1c8w210gwidbnkkw8anp17dk5pnxws2fl3mb2qxh7y9wzfpixgaq")
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(llvm-patch "llvm-D44892-Perf-integration.patch"
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"0r37jd0ssh2k1pndkfd5blgpg9z90im4vlzprhb0n0wwz45g4b05")
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(llvm-patch "llvm-D46460.patch"
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"1miqgswdc0qvbaf4571c2xkxyp9ais06b1bcpa83sq22vr4hbsfb")
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(llvm-patch "llvm-D49832-SCEVPred.patch"
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"0v5c88hgqj6dymv3j86ca5mhpqab5fbnrvjiw1nvnrnya9l4dlbn")
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(llvm-patch "llvm-D50010-VNCoercion-ni.patch"
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"0iblb3q1xixwrb12jpb89h3ywmqmzdp6aqp416j4ncwakyjhhfkp")
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(llvm-patch "llvm-D50167-scev-umin.patch"
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"1f2rakcnnyhr7w10k7gqg0k0491pyvx5ijplivw557f714ys3q6v")
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(llvm-patch "llvm-OProfile-line-num.patch"
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"1jvbbmwyags0xfwamb13qrf3rgcz9i1r03m9lava7swag8xb78c7")
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(llvm-patch "llvm-PPC-addrspaces.patch"
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"1f23nhsxh2s3jskbgs7da9nwg3s1hrkbk5aahl08x41wi3mny01p")
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(llvm-patch "llvm-rL323946-LSRTy.patch"
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"10cz3vy1yw0w643z7xx021wa4kymx9fcm3bjg61s6vzdqd6d9fns")
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(llvm-patch "llvm-rL326967-aligned-load.patch"
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"04jxnv32yj5x17hqhi8g2p8rhgp38gmjzr871w7z8s44pq10v9v4")
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(llvm-patch "llvm-rL327898.patch"
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"15ah49gbsll23z28kpyahi5vl0fh3fkxcgd1zmxxdcl96s3x8bnq")))))
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(arguments
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(substitute-keyword-arguments (package-arguments llvm-6)
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((#:configure-flags flags)
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`(list ;; Taken from NixOS. Only way I could get libLLVM-6.0.so
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"-DCMAKE_BUILD_TYPE=Release"
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;; Build a native compiler and the NVPTX backend (NVIDIA) since
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;; Julia insists on it, nothing more. This reduces build times and
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;; disk usage.
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,(string-append "-DLLVM_TARGETS_TO_BUILD=" (system->llvm-target))
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"-DLLVM_EXPERIMENTAL_TARGETS_TO_BUILD=NVPTX"
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"-DLLVM_INSTALL_UTILS=ON"
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"-DLLVM_BUILD_TESTS=ON"
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"-DLLVM_ENABLE_FFI=ON"
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"-DLLVM_ENABLE_RTTI=ON"
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;; "-DLLVM_HOST_TRIPLE=${stdenv.hostPlatform.config}"
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;; "-DLLVM_DEFAULT_TARGET_TRIPLE=${stdenv.hostPlatform.config}"
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;; "-DLLVM_EXPERIMENTAL_TARGETS_TO_BUILD=WebAssembly"
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"-DLLVM_ENABLE_DUMP=ON"
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"-DLLVM_LINK_LLVM_DYLIB=ON"))))))
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(define-public julia
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(package
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(name "julia")
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(version "1.1.1")
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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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"0hk983mywimclgnjc41zmlppm5kfdz2aj85ky07p49ilcqxi998f"))))
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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 "libwhich")
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(string-append "deps/srccache/libwhich-"
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"81e9723c0273d78493dc8c8ed570f68d9ce7e89e"
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".tar.gz"))
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(copy-file (assoc-ref inputs "rmath")
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"deps/srccache/Rmath-julia-0.1.tar.gz")
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;; needed by libwhich
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(setenv "LD_LIBRARY_PATH"
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(string-join (map (lambda (pkg)
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(string-append (assoc-ref inputs pkg)
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"/lib"))
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'("arpack-ng" "fftw" "gmp" "lapack"
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"libgit2" "mpfr" "openblas" "openlibm"
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"openspecfun" "pcre2"))
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":"))
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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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("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/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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#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* "stdlib/InteractiveUtils/src/InteractiveUtils.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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(define (touch file-name)
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(call-with-output-file file-name (const #t)))
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;; FIXME: All git tests works except this one. But *THIS* "fix"
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;; is not working, so right now I'm disabling all libgit2.jl tests
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;; (substitute* "stdlib/LibGit2/test/libgit2.jl"
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;; (("!LibGit2.use_http_path(cfg, github_cred)") "true")
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;; (("LibGit2.use_http_path(cfg, mygit_cred)") "true"))
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(map (lambda (test)
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(delete-file test)
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(touch test))
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'("stdlib/Sockets/test/runtests.jl"
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"stdlib/Distributed/test/runtests.jl"
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;; FIXME: see above
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"stdlib/LibGit2/test/libgit2.jl"))
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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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(("\"cmdlineargs\",") ""))
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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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(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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"LIBBLAS=-lopenblas"
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"LIBBLASNAME=libopenblas"
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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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"LLVM_VER=6.0.1"
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"USE_LLVM_SHLIB=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_ZLIB=1"
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"USE_SYSTEM_OPENSPECFUN=1")))
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(inputs
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`(("llvm" ,llvm-julia)
|
|
|
|
;; The bundled version is 3.3.0 so stick to that version. With other
|
|
;; versions, we get test failures in 'linalg/arnoldi' as described in
|
|
;; <https://bugs.gnu.org/30282>.
|
|
("arpack-ng" ,arpack-ng-3.3.0)
|
|
|
|
("coreutils" ,coreutils) ;for bindings to "mkdir" and the like
|
|
("lapack" ,lapack)
|
|
("openblas" ,openblas) ;Julia does not build with Atlas
|
|
("libunwind" ,libunwind)
|
|
("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
|
|
;; Find dependency versions here:
|
|
;; https://raw.githubusercontent.com/JuliaLang/julia/77a2c1e245c85812dc1c7687540beedecc52758f/deps/Versions.make
|
|
("rmath"
|
|
,(origin
|
|
(method git-fetch)
|
|
(uri (git-reference
|
|
(url "https://github.com/JuliaLang/Rmath-julia")
|
|
(commit "v0.1")))
|
|
(file-name "rmath-julia-0.1-checkout")
|
|
(sha256
|
|
(base32
|
|
"1zkpy0cg5zivq40zbhbdgj9128fqzs2j94wkwih8nc6xaj3gp9p6"))))
|
|
("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)
|
|
;; No versioned URL, see <https://www.agner.org/optimize/> for updates.
|
|
(uri "https://www.agner.org/optimize/objconv.zip")
|
|
(file-name "objconv-2018-10-07.zip")
|
|
(sha256
|
|
(base32
|
|
"0wp6ld9vk11f4nnkn56627zmlv9k5vafi99qa3yyn1pgcd61zcfs"))))
|
|
("libwhich"
|
|
,(let ((commit "81e9723c0273d78493dc8c8ed570f68d9ce7e89e"))
|
|
(origin
|
|
;; Note: We use a /tarball URL, but that's because Julia's build
|
|
;; system checks the hash of that tarball; thus we can't use
|
|
;; 'git-fetch'.
|
|
(method url-fetch)
|
|
(uri (string-append
|
|
"https://api.github.com/repos/vtjnash/libwhich/tarball/"
|
|
commit))
|
|
(file-name (string-append "libwhich-" (string-take commit 7)
|
|
".tar.gz"))
|
|
(sha256
|
|
(base32
|
|
"1p7zg31kpmpbmh1znrk1xrbd074agx13b9q4dcw8n2zrwwdlbz3b")))))
|
|
("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)))
|
|
(native-search-paths
|
|
(list (search-path-specification
|
|
(variable "JULIA_LOAD_PATH")
|
|
(files (list "share/julia/packages/")))))
|
|
;; Julia is not officially released for ARM and MIPS.
|
|
;; See https://github.com/JuliaLang/julia/issues/10639
|
|
(supported-systems '("i686-linux" "x86_64-linux" "aarch64-linux"))
|
|
(home-page "https://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)))
|