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1e96e6ac8b
* gnu/packages/julia.scm (libuv-julia): Upgrade to 2.0.0-1.35b1504. (libunwind-julia): New variable. (llvm-patch): Rename to ... (julia-patch): ... this. Update to 1.3.1. (llvm-julia): Adjust patch-set based on above change. Adjust indent. (julia): Update to 1.3.1. [source]: Add patch. [arguments]: Adjust custom 'prepare-deps (llvm-patch): Rename to ... (julia-patch): ... this. Update to 1.3.1. (llvm-julia): Adjust patch-set based on above change. (julia): Upgrade to 1.3.1. [arguments]: Adjust custom 'prepare-deps phase based on changed inputs. Remove most of 'hardcode-soname-map. Adjust 'fix-include-and-link-paths. Add new 'fix-precompile phase. Adjust custom 'disable-broken-tests phase. Add new 'make-wrapper phase. Adjust make-flags. [inputs]: Add p7zip, mbedtls-apache, curl libssh2. Remove openspecfun, fftw, fftwf, python2-virtualenv, rmath. Replace libunwind with libunwind-julia, custom suitesparse with system suitesparse, custom dsfmt with system dsfmt. [native-search-paths]: Add JULIA_DEPOT_PATH. * gnu/packages/patches/julia-SOURCE_DATE_EPOCH-mtime.patch: New file. * gnu/local.mk (dist_patch_DATA): Register it. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
475 lines
21 KiB
Scheme
475 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, 2020 Efraim Flashner <efraim@flashner.co.il>
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;;; Copyright © 2020 Nicolò Balzarotti <nicolo@nixo.xyz>
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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 curl)
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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 ssh)
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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 "35b1504507a7a4168caae3d78db54d1121b121e1")
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(revision "1"))
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;; When upgrading Julia, also upgrade this. Get the commit from
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;; https://github.com/JuliaLang/julia/blob/v1.3.1/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 (git-version "2.0.0" revision commit))
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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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"0dn3v6fdp1z382pqg3nhjzk60l61ky9b65mfgaj29fv2da95rwjs"))))
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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-julia
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;; The Julia projects requires their patched version.
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;; Get from https://github.com/JuliaLang/julia/tree/master/deps/patches
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(package
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(inherit libunwind)
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(name "libunwind-julia")
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(version "1.3.1")
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(source
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(origin
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(method url-fetch)
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(uri (string-append "mirror://savannah/libunwind/libunwind-"
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version ".tar.gz"))
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(sha256
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(base32
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"1y0l08k6ak1mqbfj6accf9s5686kljwgsl4vcqpxzk5n74wpm6a3"))
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(patches
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(list
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(julia-patch "libunwind-prefer-extbl"
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"0lr4dafw8qyfh8sw8hhbwkql1dlhqv8px7k81y2l20hhxfgnh2m1")
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(julia-patch "libunwind-static-arm"
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"1jk3bmiw61ypcchqkk1fyg5wh8wpggk574wxyfyaic870zh3lhgq")))))
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(home-page "https://github.com/JuliaLang/tree/master/deps/")))
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(define (julia-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 (julia-patch name sha)
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(let ((version "1.3.1"))
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(origin (method url-fetch)
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(uri (julia-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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(inherit (package-source llvm-6))
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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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(map (match-lambda
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((name hash)
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(julia-patch name hash)))
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(list
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'("llvm-6.0-D44650"
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"1336q4vqayr94wdcnlmcxh90mjdh34dzw9x2cbiqjnx9b1j8fxyb")
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'("llvm-6.0-DISABLE_ABI_CHECKS"
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"014fawd1ba7yckalypfld22zgic87x9nx3cim42zrwygywd36pyg")
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'("llvm-6.0-NVPTX-addrspaces"
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"1qdi2zmrjsrj0h84zv2vyly2hjcn4f67mfy0s1q353g4v4jkscqc")
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'("llvm-6.0.0_D27296-libssp"
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"0s5hi2r1j63i8m6ig1346crx2aiv9f7rgb3mg80kw1wx5y7pdpfh")
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'("llvm-D27629-AArch64-large_model_6.0.1"
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"1qrshmlqvnasdyc158vfn3hnbigqph3lsq7acb9w8lwkpnnm2j4z")
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'("llvm-D34078-vectorize-fdiv"
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"1696hg84a0jxcnggvqsc2cdp271hf9a44p4qsd078qm1mfawkaay")
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'("llvm-D42262-jumpthreading-not-i1"
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"1c8w210gwidbnkkw8anp17dk5pnxws2fl3mb2qxh7y9wzfpixgaq")
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'("llvm-D44892-Perf-integration"
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"0r37jd0ssh2k1pndkfd5blgpg9z90im4vlzprhb0n0wwz45g4b05")
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'("llvm-D46460"
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"1miqgswdc0qvbaf4571c2xkxyp9ais06b1bcpa83sq22vr4hbsfb")
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'("llvm-D49832-SCEVPred"
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"0v5c88hgqj6dymv3j86ca5mhpqab5fbnrvjiw1nvnrnya9l4dlbn")
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'("llvm-D50010-VNCoercion-ni"
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"0iblb3q1xixwrb12jpb89h3ywmqmzdp6aqp416j4ncwakyjhhfkp")
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'("llvm-D50167-scev-umin"
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"1f2rakcnnyhr7w10k7gqg0k0491pyvx5ijplivw557f714ys3q6v")
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'("llvm-OProfile-line-num"
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"1jvbbmwyags0xfwamb13qrf3rgcz9i1r03m9lava7swag8xb78c7")
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'("llvm-PPC-addrspaces"
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"1f23nhsxh2s3jskbgs7da9nwg3s1hrkbk5aahl08x41wi3mny01p")
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'("llvm-rL323946-LSRTy"
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"10cz3vy1yw0w643z7xx021wa4kymx9fcm3bjg61s6vzdqd6d9fns")
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'("llvm-rL326967-aligned-load"
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"04jxnv32yj5x17hqhi8g2p8rhgp38gmjzr871w7z8s44pq10v9v4")
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'("llvm-rL327898"
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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 "1.3.1")
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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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"1nwkmr9j55g1zkxdchnid1h022s0is52vx23niksshgvh793g41x"))
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(patches
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(search-patches "julia-SOURCE_DATE_EPOCH-mtime.patch"))))
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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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;; no USE_SYSTEM_{OBJCONV/LIBWHICH} option
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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 "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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;; 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" "curl" "dsfmt"
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"gmp" "lapack"
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"libssh2" "libgit2"
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"mbedtls" "mpfr"
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"openblas" "openlibm" "pcre2"
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"suitesparse"))
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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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(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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#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\\)\\$\\(EXE\\): \\$\\(OBJS\\) \\$\\(LIBFILES_release\\)")
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"$(BUILDDIR)/$(EXENAME)$(EXE): $(OBJS) $(LLT_release)")
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(("\\$\\(BUILDDIR\\)/\\$\\(EXENAME\\)-debug$(EXE): \\$\\(DOBJS\\) \\$\\(LIBFILES_debug\\)")
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"$(BUILDDIR)/$(EXENAME)-debug\\$\\(EXE\\): $(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-before 'build 'fix-precompile
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(lambda _
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(substitute* "base/loading.jl"
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(("something(Base.active_project(), \"\")") "\"\""))
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#t))
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(add-before 'check 'disable-broken-tests
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(lambda _
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(substitute* "test/choosetests.jl"
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(("tests = testnames")
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;; Those failings are not deterministic. They depends on the
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;; running order. I think it depends on the number of
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;; runners, disabling it for now
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;; https://github.com/JuliaLang/julia/issues/34330
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"tests = filter(e->!in(e,[\"backtrace\",\"exceptions\",
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\"stress\",\"precompile\",
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\"client\",\"stacktraces\"]),
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testnames)"))
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;; When HOME is not set, julia calls uv_os_homedir, which in
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;; turns call getpwuid_r. Add the HOME env variable to the
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;; external julia call to fix this
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(substitute* "test/cmdlineargs.jl"
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(("\"JULIA_PROJECT\"") "\"HOME\"=>\"/tmp\", \"JULIA_PROJECT\""))
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;; Marking the test as broken as it's a known bug:
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;; https://github.com/JuliaLang/julia/issues/32377
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(substitute* "stdlib/REPL/test/replcompletions.jl"
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(("@test count") "@test_broken count"))
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#t))
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(add-after 'install 'make-wrapper
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(lambda* (#:key inputs outputs #:allow-other-keys)
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(let* ((out (assoc-ref outputs "out"))
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(bin (string-append out "/bin"))
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(program "julia"))
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(with-directory-excursion bin
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(wrap-program program
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`("JULIA_LOAD_PATH" ":" prefix
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("" "$JULIA_LOAD_PATH")))
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(wrap-program program
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`("JULIA_DEPOT_PATH" ":" prefix
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("" "$JULIA_DEPOT_PATH"))))
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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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;; list of "USE_SYSTEM_*" is here:
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;; https://github.com/JuliaLang/julia/blob/v1.3.1/Make.inc
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"USE_SYSTEM_DSFMT=1"
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"USE_SYSTEM_P7ZIP=1"
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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_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")
|
|
"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"
|
|
(string-append "LIBUV="
|
|
(assoc-ref %build-inputs "libuv")
|
|
"/lib/libuv.so")
|
|
(string-append "LIBUV_INC="
|
|
(assoc-ref %build-inputs "libuv")
|
|
"/include")
|
|
"USE_SYSTEM_ZLIB=1")))
|
|
(inputs
|
|
`(("llvm" ,llvm-julia)
|
|
("p7zip" ,p7zip)
|
|
;; 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-julia)
|
|
("openlibm" ,openlibm)
|
|
("mbedtls" ,mbedtls-apache)
|
|
("curl" ,curl)
|
|
("libgit2" ,libgit2)
|
|
("libssh2" ,libssh2)
|
|
("fortran" ,gfortran)
|
|
("libuv" ,libuv-julia)
|
|
("pcre2" ,pcre2)
|
|
("utf8proc" ,utf8proc)
|
|
("mpfr" ,mpfr)
|
|
("wget" ,wget)
|
|
("which" ,which)
|
|
("zlib" ,zlib)
|
|
("gmp" ,gmp)
|
|
("suitesparse" ,suitesparse)
|
|
;; Find dependencies versions here:
|
|
;; https://raw.githubusercontent.com/JuliaLang/julia/v1.3.0/deps/Versions.make
|
|
("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" ,dsfmt)))
|
|
(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/")))
|
|
(search-path-specification
|
|
(variable "JULIA_DEPOT_PATH")
|
|
(files (list "share/julia/")))))
|
|
;; 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)))
|