523 lines
16 KiB
Scheme
523 lines
16 KiB
Scheme
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(use-modules ((guix licenses)
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#:prefix license:))
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(use-modules
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(guix packages))
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(use-modules
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(guix download))
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(use-modules
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(guix utils))
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(use-modules
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(guix git-download))
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(use-modules
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(guix build-system gnu))
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(use-modules
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(gnu packages))
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(use-modules
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(gnu packages algebra))
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(use-modules
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(gnu packages base))
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(use-modules
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(gnu packages compression))
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(use-modules
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(gnu packages elf))
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(use-modules
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(gnu packages gcc))
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(use-modules
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(gnu packages llvm))
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(use-modules
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(gnu packages libevent))
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(use-modules
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(gnu packages libunwind))
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(use-modules
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(gnu packages maths))
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(use-modules
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(gnu packages multiprecision)) ; mpfr)
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(use-modules
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(gnu packages pcre))
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(use-modules
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(gnu packages perl))
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(use-modules
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(gnu packages pkg-config))
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(use-modules
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(gnu packages python))
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(use-modules
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(gnu packages python-xyz))
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(use-modules
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(gnu packages textutils))
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(use-modules
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(gnu packages tls))
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(use-modules
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(gnu packages version-control))
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(use-modules
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(gnu packages wget))
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(use-modules
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(ice-9 match))
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;; (define openblas-julia
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;; (package
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;; (inherit openblas)
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;; (name "openblas-julia")
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;; INTERFACE64=
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;; ))
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;; This works *BUT* we need to apply a lot of patches. Compiling this
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;; with julia applies the patches automatically
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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
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(origin
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(method url-fetch)
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(uri
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(string-append
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"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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(patches '("./llvm-6.0-D44650.patch"
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"./llvm-6.0-DISABLE_ABI_CHECKS.patch"
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"./llvm-6.0-NVPTX-addrspaces.patch"
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"./llvm-6.0.0_D27296-libssp.patch"
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"./llvm-D27629-AArch64-large_model_6.0.1.patch"
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"./llvm-D34078-vectorize-fdiv.patch"
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"./llvm-D42262-jumpthreading-not-i1.patch"
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"./llvm-D44892-Perf-integration.patch"
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"./llvm-D46460.patch"
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"./llvm-D49832-SCEVPred.patch"
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"./llvm-D50010-VNCoercion-ni.patch"
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"./llvm-D50167-scev-umin.patch"
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"./llvm-OProfile-line-num.patch"
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"./llvm-PPC-addrspaces.patch"
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"./llvm-rL323946-LSRTy.patch"
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"./llvm-rL326967-aligned-load.patch"
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"./llvm-rL327898.patch"
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))
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))
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(arguments
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(substitute-keyword-arguments
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(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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"-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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)))))
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(define libuv-julia
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(let
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((commit "2348256acf5759a544e5ca7935f638d2bc091d60"))
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(package
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(inherit libuv)
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(name "libuv-julia")
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(version commit)
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(source
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(origin
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(method url-fetch)
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(uri (string-append
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"https://api.github.com/repos/JuliaLang/libuv/tarball/"
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commit))
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(sha256
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(base32
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"1363f4vqayfcv5zqg07qmzjff56yhad74k16c22ian45lram8mv8"))))
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(build-system gnu-build-system)
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(arguments
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(substitute-keyword-arguments
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(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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(package
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(name "julia")
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(version "1.1.0")
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(source
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(origin
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(method url-fetch)
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(uri
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(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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"1bd6c5gqd7f2i837ay8iqi8h36smhcg0lq7f8c2axxaw8x6rcfmx"))))
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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
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((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*
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(#:key inputs #:allow-other-keys)
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(mkdir "deps/srccache")
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(copy-file
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(assoc-ref inputs "dsfmt")
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"deps/srccache/dsfmt-2.2.3.tar.gz")
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(copy-file
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(string-append
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(assoc-ref inputs "virtualenv")
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"/bin/virtualenv")
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"julia-env")
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(copy-file
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(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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(copy-file
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(assoc-ref inputs "objconv")
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"deps/srccache/objconv.zip")
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(copy-file
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(assoc-ref inputs "suitesparse")
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"deps/srccache/SuiteSparse-4.4.5.tar.gz")
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;; needed by libwhich
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(setenv "LD_LIBRARY_PATH"
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(string-join
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(map (lambda (pkg)
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(string-append (assoc-ref inputs pkg) "/lib"))
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(list
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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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":"))
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;; (copy-file
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;; (assoc-ref inputs "llvm")
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;; "deps/srccache/llvm-6.0.0.src.tar.xz")
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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 _
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(setenv "HOME" "/tmp")
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#t))
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(add-after 'unpack 'hardcode-soname-map
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;; ./src/runtime_ccall.cpp creates a map from library names to paths
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;; using the output of "/sbin/ldconfig -p". Since ldconfig is not
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;; used in Guix, we patch runtime_ccall.cpp to contain a static map.
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(lambda* (#:key inputs #:allow-other-keys)
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(use-modules (ice-9 match))
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(substitute* "src/runtime_ccall.cpp"
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;; Patch out invocations of '/sbin/ldconfig' to avoid getting
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;; error messages about missing '/sbin/ldconfig' on Guix System.
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(("popen\\(.*ldconfig.*\\);")
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"NULL;\n")
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;; Populate 'sonameMap'.
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(("jl_read_sonames.*;")
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(string-join
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(map (match-lambda
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((input libname soname)
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(string-append
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"sonameMap[\"" libname "\"] = "
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"\"" (assoc-ref inputs input) "/lib/" soname "\";")))
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'(("libc" "libc" "libc.so.6")
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("pcre2" "libpcre2-8" "libpcre2-8.so")
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("mpfr" "libmpfr" "libmpfr.so")
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("openblas" "libblas" "libopenblas.so")
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("arpack-ng" "libarpack" "libarpack.so")
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("lapack" "liblapack" "liblapack.so")
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("libgit2" "libgit2" "libgit2.so")
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("gmp" "libgmp" "libgmp.so")
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;; ("openlibm" "libopenlibm" "libopenlibm.so")
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("openspecfun" "libopenspecfun" "libopenspecfun.so")
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("fftw" "libfftw3" "libfftw3_threads.so")
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("fftwf" "libfftw3f" "libfftw3f_threads.so"))))))
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;; FIXME: NIXO
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;; (substitute* "base/fft/FFTW.jl"
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;; (("const libfftw = Base.libfftw_name")
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;; (string-append "const libfftw = \""
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;; (assoc-ref inputs "fftw") "/lib/libfftw3_threads.so"
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;; "\""))
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;; (("const libfftwf = Base.libfftwf_name")
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;; (string-append "const libfftwf = \""
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;; (assoc-ref inputs "fftwf") "/lib/libfftw3f_threads.so"
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;; "\"")))
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(substitute* "base/math.jl"
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(("const libm = Base.libm_name")
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(string-append "const libm = \""
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(assoc-ref inputs "openlibm")
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"/lib/libopenlibm.so"
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"\""))
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(("const openspecfun = \"libopenspecfun\"")
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(string-append "const openspecfun = \""
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(assoc-ref inputs "openspecfun")
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"/lib/libopenspecfun.so"
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"\"")))
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;; (substitute* "base/pcre.jl"
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;; (("const PCRE_LIB = \"libpcre2-8\"")
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;; (string-append "const PCRE_LIB = \""
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;; (assoc-ref inputs "pcre2")
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;; "/lib/libpcre2-8.so" "\"")))
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#t))
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(add-before 'build 'fix-include-and-link-paths
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(lambda*
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(#:key inputs #:allow-other-keys)
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|
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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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|
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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) $(LLT_debug)"))
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|
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;; The REPL must be linked with libuv.
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|
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(substitute* "ui/Makefile"
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(("JLDFLAGS \\+= ")
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|
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(string-append "JLDFLAGS += "
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|
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(assoc-ref %build-inputs "libuv")
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|
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"/lib/libuv.so ")))
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|
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(substitute* "base/Makefile"
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|
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(("\\$\\(build_includedir\\)/uv/errno.h")
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|
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(string-append
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(assoc-ref inputs "libuv")
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"/include/uv/errno.h")))
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#t))
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|
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(add-before 'build 'replace-default-shell
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|
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(lambda _
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(substitute* "base/client.jl"
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(("/bin/sh")
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||
|
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(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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|
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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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;; Don't know why FIXME
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;; (substitute* "stdlib/LibGit2/test/libgit2.jl"
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;; (("!LibGit2.use_http_path(cfg, github_cred)")
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;; "true")
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;; (("LibGit2.use_http_path(cfg, mygit_cred)")
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;; "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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"stdlib/LibGit2/test/libgit2.jl"
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))
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(substitute* "test/choosetests.jl"
|
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|
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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
|
||
|
|
;; as expected.
|
||
|
|
(("\"backtrace\",")
|
||
|
|
"")
|
||
|
|
(("\"cmdlineargs\",")
|
||
|
|
""))
|
||
|
|
#t)))
|
||
|
|
#:make-flags
|
||
|
|
(list
|
||
|
|
(string-append "prefix=" (assoc-ref %outputs "out"))
|
||
|
|
(string-append "PREFIX=" (assoc-ref %outputs "out"))
|
||
|
|
;; Passing the MARCH flag is necessary to build binary substitutes for
|
||
|
|
;; the supported architectures.
|
||
|
|
,(match
|
||
|
|
(or
|
||
|
|
(%current-target-system)
|
||
|
|
(%current-system))
|
||
|
|
("x86_64-linux" "MARCH=x86-64")
|
||
|
|
("i686-linux" "MARCH=pentium4")
|
||
|
|
("aarch64-linux" "MARCH=armv8-a")
|
||
|
|
;; Prevent errors when querying this package on unsupported
|
||
|
|
;; platforms, e.g. when running "guix package --search="
|
||
|
|
(_ "MARCH=UNSUPPORTED"))
|
||
|
|
"CONFIG_SHELL=bash" ;needed to build bundled libraries
|
||
|
|
"USE_SYSTEM_DSFMT=0" ;not packaged for Guix and upstream has no
|
||
|
|
;build system for a shared library.
|
||
|
|
"USE_SYSTEM_LAPACK=1"
|
||
|
|
"USE_SYSTEM_BLAS=1"
|
||
|
|
|
||
|
|
;; TODO: What about building blas with 64 support?
|
||
|
|
"USE_BLAS64=0" ;needed when USE_SYSTEM_BLAS=1
|
||
|
|
"LIBBLAS=-lopenblas"
|
||
|
|
"LIBBLASNAME=libopenblas"
|
||
|
|
|
||
|
|
"USE_SYSTEM_FFTW=1"
|
||
|
|
"LIBFFTWNAME=libfftw3"
|
||
|
|
"LIBFFTWFNAME=libfftw3f"
|
||
|
|
|
||
|
|
;; TODO: Suitesparse does not install shared libraries, so we cannot
|
||
|
|
;; use the suitesparse package.
|
||
|
|
;; "USE_SYSTEM_SUITESPARSE=1"
|
||
|
|
;; (string-append "SUITESPARSE_INC=-I "
|
||
|
|
;; (assoc-ref %build-inputs "suitesparse")
|
||
|
|
;; "/include")
|
||
|
|
|
||
|
|
"USE_GPL_LIBS=1" ;proudly
|
||
|
|
"USE_SYSTEM_UTF8PROC=1"
|
||
|
|
(string-append "UTF8PROC_INC="
|
||
|
|
(assoc-ref %build-inputs "utf8proc")
|
||
|
|
"/include")
|
||
|
|
"USE_SYSTEM_LLVM=1"
|
||
|
|
"LLVM_VER=6.0.1"
|
||
|
|
|
||
|
|
;; "LLVM_VER=6.0.0"
|
||
|
|
"USE_LLVM_SHLIB=1" ; FIXME: fails when set to 1
|
||
|
|
|
||
|
|
"USE_SYSTEM_LIBUNWIND=1"
|
||
|
|
"USE_SYSTEM_LIBUV=1"
|
||
|
|
(string-append "LIBUV="
|
||
|
|
(assoc-ref %build-inputs "libuv")
|
||
|
|
"/lib/libuv.so")
|
||
|
|
(string-append "LIBUV_INC="
|
||
|
|
(assoc-ref %build-inputs "libuv")
|
||
|
|
"/include")
|
||
|
|
"USE_SYSTEM_PATCHELF=1"
|
||
|
|
"USE_SYSTEM_PCRE=1"
|
||
|
|
"USE_SYSTEM_OPENLIBM=1"
|
||
|
|
|
||
|
|
"USE_SYSTEM_GMP=1"
|
||
|
|
"USE_SYSTEM_MPFR=1"
|
||
|
|
"USE_SYSTEM_ARPACK=1"
|
||
|
|
"USE_SYSTEM_LIBGIT2=1"
|
||
|
|
"USE_SYSTEM_ZLIB=1"
|
||
|
|
"USE_SYSTEM_OPENSPECFUN=1")))
|
||
|
|
(inputs
|
||
|
|
`( ("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)
|
||
|
|
("libuv", libuv-julia)
|
||
|
|
("libgit2" ,libgit2)
|
||
|
|
("fftw" ,fftw)
|
||
|
|
("fftwf" ,fftwf)
|
||
|
|
("fortran" ,gfortran)
|
||
|
|
("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
|
||
|
|
("rmath"
|
||
|
|
,(origin
|
||
|
|
(method url-fetch)
|
||
|
|
(uri "https://api.github.com/repos/JuliaLang/Rmath-julia/tarball/v0.1")
|
||
|
|
(sha256
|
||
|
|
(base32
|
||
|
|
"1qyps217175qhid46l8f5i1v8i82slgp23ia63x2hzxwfmx8617p"))))
|
||
|
|
("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"
|
||
|
|
,(origin
|
||
|
|
(method url-fetch)
|
||
|
|
(uri
|
||
|
|
(string-append
|
||
|
|
"https://api.github.com/repos/vtjnash/libwhich/tarball/"
|
||
|
|
"81e9723c0273d78493dc8c8ed570f68d9ce7e89e"))
|
||
|
|
(sha256
|
||
|
|
(base32
|
||
|
|
"1p7zg31kpmpbmh1znrk1xrbd074agx13b9q4dcw8n2zrwwdlbz3b"))))
|
||
|
|
;; ("llvm"
|
||
|
|
;; ,(origin
|
||
|
|
;; (method url-fetch)
|
||
|
|
;; (uri
|
||
|
|
;; (string-append
|
||
|
|
;; "http://releases.llvm.org/6.0.0/llvm-6.0.0.src.tar.xz"))
|
||
|
|
;; (sha256
|
||
|
|
;; (base32
|
||
|
|
;; "0224xvfg6h40y5lrbnb9qaq3grmdc5rg00xq03s1wxjfbf8krx8z"))))
|
||
|
|
;; ("cmake" ,cmake) ;; required to build llvm
|
||
|
|
("dsfmt"
|
||
|
|
,(origin
|
||
|
|
(method url-fetch)
|
||
|
|
(uri
|
||
|
|
(string-append
|
||
|
|
"http://www.math.sci.hiroshima-u.ac.jp/~m-mat/MT/"
|
||
|
|
"SFMT/dSFMT-src-2.2.3.tar.gz"))
|
||
|
|
(sha256
|
||
|
|
(base32
|
||
|
|
"03kaqbjbi6viz0n33dk5jlf6ayxqlsq4804n7kwkndiga9s4hd42"))))))
|
||
|
|
(native-inputs
|
||
|
|
`(("openssl" ,openssl)
|
||
|
|
("perl" ,perl)
|
||
|
|
("patchelf" ,patchelf)
|
||
|
|
("pkg-config" ,pkg-config)
|
||
|
|
("python" ,python-2)))
|
||
|
|
;; Julia is not officially released for ARM and MIPS.
|
||
|
|
;; See https://github.com/JuliaLang/julia/issues/10639
|
||
|
|
(supported-systems
|
||
|
|
'("i686-linux" "x86_64-linux" "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))
|
||
|
|
|