f6e031ab36
* gnu/packages/julia.scm (julia): Update to 1.5.3. (libuv-julia): Update to 1fcc6d66f9df74189c74d3d390f02202bb7db953. (julia-patch): Update version. No change to patches.
482 lines
20 KiB
Scheme
482 lines
20 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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;;; Copyright © 2020 Tim Howes <timhowes@lavabit.com>
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;;; Copyright © 2020 Tobias Geerinckx-Rice <me@tobias.gr>
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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 "1fcc6d66f9df74189c74d3d390f02202bb7db953")
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(revision "2"))
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;; When upgrading Julia, also upgrade this. Get the commit from
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;; https://github.com/JuliaLang/julia/blob/v1.5.2/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")
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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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"040l7f1hk7xyza11sry5cj4fhw05na949865axqqhxnifdvnmfji"))))
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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 ".patch"))
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(define (julia-patch name sha)
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(let ((version "1.5.3"))
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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-9)
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(name "llvm-julia")
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(source (origin
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(inherit (package-source llvm-9))
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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-D27629-AArch64-large_model_6.0.1"
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"1qrshmlqvnasdyc158vfn3hnbigqph3lsq7acb9w8lwkpnnm2j4z")
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'("llvm8-D34078-vectorize-fdiv"
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"19spqc3xsazn1xs9gpcgv9ldadfkv49rmc5khl7sf1dlmhgi4602")
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'("llvm-7.0-D44650"
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"1h55kkmkiisfj6sk956if2bcj9s0v6n5czn8dxb870vp5nccj3ir")
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'("llvm9-D50010-VNCoercion-ni"
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"1s1d3sjsiq4vxg7ncy5cz56zgy5vcq6ls3iqaiqkvr23wyryqmdx")
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'("llvm-exegesis-mingw"
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"0ph1cj1j7arvf1xq2xcr7qf9g0cpdl14fincgr67vpi520zvd3vp")
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'("llvm-test-plugin-mingw"
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"12z738cnahbf6n381im7i0hxp1m6k9hrnfjlmq9sac46nxly9gnj")
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'("llvm7-revert-D44485"
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"0f59kq3p3mpwsbmskypbi4zn01l6ig0x7v2rjp08k2r8z8m6fa8n")
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'("llvm-8.0-D66657-codegen-degenerate"
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"1n1ddx19h90bbpimdyd9dh8fsm6gb93xxyqm4ljkxa1k3cx2vm72")
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'("llvm-8.0-D71495-vectorize-freduce"
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"1zff08wvji9lnpskk4b3p5zyjsy5hhy23ynxjqlj9dw7jvvfrf0p")
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'("llvm-D75072-SCEV-add-type"
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"029a3fywsm233vf48mscina24idd50dc75wr70lmimrhwnw27p0z")
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'("llvm-9.0-D65174-limit-merge-stores"
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"04bff1mnblfj9mxfdwr1qdnw3i3szmp60gnhxwas5y68qg33z6j0")
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'("llvm9-D71443-PPC-MC-redef-symbol"
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"1c93nv7rgc9jg5mqrnvv08xib1789qvlql94fwggh18mp3b9hbgy")
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'("llvm-9.0-D78196"
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"08a43hyg7yyqjq2vmfsmppf34xcz60wq6y9zw5fdyhw2h1mcnmns")
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'("llvm-julia-tsan-custom-as"
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"0awh40kf6lm4wn1nsjd1bmhfwq7rqj811szanp2xkpspykw9hg9s")
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'("llvm-9.0-D85499"
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"0vxlr35srvbvihlgrxq15v6dylp90vgi0qahj22j01jgqmdasjkm"))))
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(patch-flags '("-p1"))))
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(arguments
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(substitute-keyword-arguments (package-arguments llvm-9)
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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 libwhich
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(package
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(name "libwhich")
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(version "1.1.0")
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(source
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(origin
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(method git-fetch)
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(uri (git-reference
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(url "https://github.com/vtjnash/libwhich")
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;; fixes linux-vdso.so related tests
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(commit "87cffe10080c98e7b5786c5166e420bf1ada1d41")))
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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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"1bpa0fcqpa3ai3hm8mz0p13bf76fsq53wsfcx5qw302zh22108xr"))))
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(arguments
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`(#:make-flags
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(list (string-append "CC=" ,(cc-for-target)))
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#:phases
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(modify-phases %standard-phases
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(delete 'configure)
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(add-before 'check 'set-ld-library-path
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(lambda* (#:key native-inputs inputs #:allow-other-keys)
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(setenv "LD_LIBRARY_PATH"
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(string-append (assoc-ref (or native-inputs inputs) "zlib")
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"/lib"))))
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(replace 'install
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(lambda* (#:key outputs #:allow-other-keys)
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(let ((out (assoc-ref outputs "out")))
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(install-file "libwhich" (string-append out "/bin")))
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#t)))))
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(native-inputs
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;; used for tests
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`(("zlib" ,zlib)))
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(build-system gnu-build-system)
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(home-page "https://github.com/vtjnash/libwhich")
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(synopsis "Like @code{which}, for dynamic libraries")
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(description "@code{libwhich} is like @code{which}, but for dynamic
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libraries. It is also a bit like @code{ldd} and @code{otool -L}.")
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(license license:expat)))
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(define-public julia
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(package
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(name "julia")
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(version "1.5.3")
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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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"1zmim82x9kkdcgn0cdi01hmzi59zbszy1sqlygb86xq4hc1n66dy"))
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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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;; 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-after 'unpack 'use-system-libwhich
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(lambda* (#:key inputs #:allow-other-keys)
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;; don't build it
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(substitute* "deps/Makefile"
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(("DEP_LIBS \\+= libwhich") ""))
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;; call our version
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(substitute* "base/Makefile"
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(("\\$\\$\\(build_depsbindir\\)/libwhich")
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(string-append (assoc-ref inputs "libwhich") "/bin/libwhich")))
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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-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\",\"precompile\",
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\"client\",\"stacktraces\"]),
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testnames)"))
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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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;; Dates has a similar bug:
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;; https://github.com/JuliaLang/julia/issues/34655
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(substitute* "stdlib/Dates/test/io.jl"
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(("\"Dates.Date") "\"Date")
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(("\"Dates.Time") "\"Time"))
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;; Upstream bug I found when packaging
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;; https://github.com/JuliaLang/julia/issues/35785
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(substitute* "test/file.jl"
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(("@test dirname\\(t\\) == d") "@test_broken dirname(t) == d"))
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;; Deprecation test fails with --depwarn=no
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;; https://github.com/JuliaLang/julia/issues/37673
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(substitute* "test/Makefile"
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(("./runtests.jl") "--depwarn=error ./runtests.jl"))
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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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;; 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")
|
|
"/include")
|
|
"USE_SYSTEM_LLVM=1"
|
|
"LLVM_VER=9.0.1"
|
|
|
|
"USE_LLVM_SHLIB=1"
|
|
"USE_SYSTEM_LIBUNWIND=1"
|
|
"USE_SYSTEM_LIBUV=1"
|
|
(string-append "LIBUV="
|
|
(assoc-ref %build-inputs "libuv")
|
|
"/lib/libuv.so")
|
|
(string-append "LIBUV_INC="
|
|
(assoc-ref %build-inputs "libuv")
|
|
"/include")
|
|
"USE_SYSTEM_PATCHELF=1"
|
|
"USE_SYSTEM_PCRE=1"
|
|
"USE_SYSTEM_OPENLIBM=1"
|
|
"USE_SYSTEM_MBEDTLS=1"
|
|
"USE_SYSTEM_LIBSSH2=1"
|
|
"USE_SYSTEM_GMP=1"
|
|
"USE_SYSTEM_MPFR=1"
|
|
"USE_SYSTEM_ARPACK=1"
|
|
"USE_SYSTEM_LIBGIT2=1"
|
|
"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" ,libgit2-0.28)
|
|
("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
|
|
("libwhich" ,libwhich)
|
|
("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)))
|