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gnu: julia: Update to 0.5.0.

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* gnu/packages/julia.scm (libuv-julia): Update to commit
8d5131b6c1595920dd30644cd1435b4f344b46c8.
(libunwind-for-julia): New variable.
(julia): Update to 0.5.0.
[arguments]: Disable stripping of binaries; modify "prepare-deps" phase;
add "fix-llvm-flag" phase; add "set-home" phase; adjust
"hardcode-soname-map" phase; remove fix for "double-conversion" from
"fix-include-and-link-paths" phase; enable "repl" and "replcompletions"
tests; disable "backtrace", "compile", "replutil", and "cmdlineargs"
tests; remove USE_SYSTEM_RMATH flag; remove USE_SYSTEM_GRISU flag.
[inputs]: Replace "llvm-3.5" with "llvm"; replace "libunwind" with
"libunwind-for-julia"; remove "double-conversion"; remove "rmath-julia";
update "suitesparse" origin; replace "virtualenv" origin with
"python2-virtualenv".
[native-inputs]: Add "openssl".
This commit is contained in:
Ricardo Wurmus 2016-09-24 14:16:21 +02:00
parent 9b72ce60fb
commit d70f5139da
No known key found for this signature in database
GPG key ID: 197A5888235FACAC
1 changed files with 84 additions and 58 deletions
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142
gnu/packages/julia.scm
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@ -40,16 +40,17 @@ (define-module (gnu packages julia)
#:use-module (gnu packages pkg-config)
#:use-module (gnu packages python)
#:use-module (gnu packages textutils)
#:use-module (gnu packages tls)
#:use-module (gnu packages version-control)
#:use-module (gnu packages wget)
#:use-module (ice-9 match))
(define libuv-julia
(let ((commit "efb40768b7c7bd9f173a7868f74b92b1c5a61a0e")
(revision "3"))
(let ((commit "8d5131b6c1595920dd30644cd1435b4f344b46c8")
(revision "4"))
(package (inherit libuv)
(name "libuv-julia")
(version (string-append "0.11.26." revision "-" (string-take commit 8)))
(version (string-append "1.9.0-" revision "." (string-take commit 8)))
(source (origin
(method git-fetch)
(uri (git-reference
@ -58,7 +59,7 @@ (define libuv-julia
(file-name (string-append name "-" version "-checkout"))
(sha256
(base32
"16k6pm2jl0ymz5j4ldxn94imdimahqqfd2izgr3zf1vwyyay77w3"))))
"1fq0vhiprdryw8iisxxwyld3xdr5za6y8458p22ff56al98h22fv"))))
(build-system gnu-build-system)
(arguments
(substitute-keyword-arguments (package-arguments libuv)
@ -67,10 +68,22 @@ (define libuv-julia
(delete 'autogen)))))
(home-page "https://github.com/JuliaLang/libuv"))))
(define libunwind-for-julia
(package
(inherit libunwind)
(version "1.1-julia2")
(source (origin
(method url-fetch)
(uri (string-append "https://s3.amazonaws.com/julialang/src/"
"libunwind-" version ".tar.gz"))
(sha256
(base32
"0499x7sg2v18a6cry6l8y713cgmic0adnjph8i0xr1db9p7n8qyv"))))))
(define-public julia
(package
(name "julia")
(version "0.4.5")
(version "0.5.0")
(source (origin
(method url-fetch)
(uri (string-append
@ -78,7 +91,7 @@ (define-public julia
version "/julia-" version ".tar.gz"))
(sha256
(base32
"09gc6yf3v4in0qwhrbgjrjgvblp941di0mli4zax22mvf4dzc7s4"))))
"0bhickil88lalp9jdj1kmf4is70zinhx8ha9rng0g3z50r4a2qmv"))))
(build-system gnu-build-system)
(arguments
`(#:test-target "test"
@ -86,6 +99,9 @@ (define-public julia
(guix build gnu-build-system)
(guix build utils))
;; Do not strip binaries to keep support for full backtraces.
;; See https://github.com/JuliaLang/julia/issues/17831
#:strip-binaries? #f
;; The DSOs use $ORIGIN to refer to each other, but (guix build
;; gremlin) doesn't support it yet, so skip this phase.
@ -96,24 +112,33 @@ (define-public julia
(delete 'configure)
(add-after 'unpack 'prepare-deps
(lambda* (#:key inputs #:allow-other-keys)
(copy-file (assoc-ref inputs "rmath-julia")
"deps/Rmath-julia-0.1.tar.gz")
(mkdir "deps/srccache")
(copy-file (assoc-ref inputs "dsfmt")
"deps/dsfmt-2.2.3.tar.gz")
"deps/srccache/dsfmt-2.2.3.tar.gz")
(copy-file (assoc-ref inputs "objconv")
"deps/objconv.zip")
"deps/srccache/objconv.zip")
(copy-file (assoc-ref inputs "suitesparse")
"deps/SuiteSparse-4.4.2.tar.gz")
(copy-file (assoc-ref inputs "virtualenv")
"deps/virtualenv-1.11.6.tar.gz")
"deps/srccache/SuiteSparse-4.4.5.tar.gz")
(copy-file (string-append (assoc-ref inputs "virtualenv")
"/bin/virtualenv")
"julia-env")
#t))
(add-after 'unpack 'fix-llvm-flag
(lambda _
(substitute* "src/Makefile"
(("-lLLVM-\\$\\(shell \\$\\(LLVM_CONFIG_HOST\\) --version\\)")
"$(shell $(LLVM_CONFIG_HOST) --libs)"))
#t))
(add-before 'check 'set-home
;; Some tests require a home directory to be set.
(lambda _ (setenv "HOME" "/tmp") #t))
(add-after 'unpack 'hardcode-soname-map
;; ./src/ccall.cpp creates a map from library names to paths using the
;; output of "/sbin/ldconfig -p". Since ldconfig is not used in Guix,
;; we patch ccall.cpp to contain a static map.
;; ./src/runtime_ccall.cpp creates a map from library names to paths
;; using the output of "/sbin/ldconfig -p". Since ldconfig is not
;; used in Guix, we patch runtime_ccall.cpp to contain a static map.
(lambda* (#:key inputs #:allow-other-keys)
(use-modules (ice-9 match))
(substitute* "src/ccall.cpp"
(substitute* "src/runtime_ccall.cpp"
(("jl_read_sonames.*;")
(string-join
(map (match-lambda
@ -133,6 +158,31 @@ (define-public julia
("openspecfun" "libopenspecfun" "libopenspecfun.so")
("fftw" "libfftw3" "libfftw3.so")
("fftwf" "libfftw3f" "libfftw3f.so"))))))
(substitute* "base/fft/FFTW.jl"
(("const libfftw = Base.libfftw_name")
(string-append "const libfftw = \""
(assoc-ref inputs "fftw") "/lib/libfftw3.so"
"\""))
(("const libfftwf = Base.libfftwf_name")
(string-append "const libfftwf = \""
(assoc-ref inputs "fftwf") "/lib/libfftw3f.so"
"\"")))
(substitute* "base/math.jl"
(("const libm = Base.libm_name")
(string-append "const libm = \""
(assoc-ref inputs "openlibm")
"/lib/libopenlibm.so"
"\""))
(("const openspecfun = \"libopenspecfun\"")
(string-append "const openspecfun = \""
(assoc-ref inputs "openspecfun")
"/lib/libopenspecfun.so"
"\"")))
(substitute* "base/pcre.jl"
(("const PCRE_LIB = \"libpcre2-8\"")
(string-append "const PCRE_LIB = \""
(assoc-ref inputs "pcre2")
"/lib/libpcre2-8.so" "\"")))
#t))
(add-before 'build 'fix-include-and-link-paths
(lambda* (#:key inputs #:allow-other-keys)
@ -153,10 +203,6 @@ (define-public julia
(assoc-ref %build-inputs "libuv")
"/lib/libuv.so ")))
(substitute* "deps/Makefile"
(("/usr/include/double-conversion")
(string-append (assoc-ref %build-inputs "double-conversion")
"/include/double-conversion")))
(substitute* "base/Makefile"
(("\\$\\(build_includedir\\)/uv-errno.h")
(string-append (assoc-ref inputs "libuv")
@ -176,15 +222,13 @@ (define-public julia
(add-before 'check 'disable-broken-tests
(lambda _
(substitute* "test/choosetests.jl"
;; These tests time out. See
;; https://github.com/JuliaLang/julia/issues/14374 for ongoing
;; discussion.
(("\"replcompletions\",") "")
(("\"repl\",") ""))
(substitute* "test/repl.jl"
;; This test fails because we cannot escape the build
;; directory.
(("@test pwd\\(\\) == homedir\\(\\)") "#"))
;; These tests fail, probably because some of the input
;; binaries have been stripped and thus backtraces don't look
;; as expected.
(("\"backtrace\",") "")
(("\"compile\",") "")
(("\"replutil\",") "")
(("\"cmdlineargs\",") ""))
#t)))
#:make-flags
(list
@ -203,9 +247,6 @@ (define-public julia
"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_RMATH=0" ;Julia uses a bundled version of R's math
;library, patched to use the DSFMT RNG.
"USE_SYSTEM_LAPACK=1"
"USE_SYSTEM_BLAS=1"
"USE_BLAS64=0" ;needed when USE_SYSTEM_BLAS=1
@ -222,7 +263,6 @@ (define-public julia
;; "/include")
"USE_GPL_LIBS=1" ;proudly
"USE_SYSTEM_GRISU=1" ;for double-conversion
"USE_SYSTEM_UTF8PROC=1"
(string-append "UTF8PROC_INC="
(assoc-ref %build-inputs "utf8proc")
@ -245,15 +285,14 @@ (define-public julia
"USE_SYSTEM_LIBGIT2=1"
"USE_SYSTEM_OPENSPECFUN=1")))
(inputs
`(("llvm" ,llvm-3.5)
`(("llvm" ,llvm)
("arpack-ng" ,arpack-ng)
("coreutils" ,coreutils) ;for bindings to "mkdir" and the like
("lapack" ,lapack)
("openblas" ,openblas) ;Julia does not build with Atlas
("libunwind" ,libunwind)
("libunwind" ,libunwind-for-julia)
("openlibm" ,openlibm)
("openspecfun" ,openspecfun)
("double-conversion" ,double-conversion)
("libgit2" ,libgit2)
("fftw" ,fftw)
("fftwf" ,fftwf)
@ -266,24 +305,19 @@ (define-public julia
("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.
("rmath-julia"
,(origin
(method url-fetch)
(uri "https://api.github.com/repos/JuliaLang/Rmath-julia/tarball/v0.1")
(file-name "rmath-julia-0.1.tar.gz")
(sha256
(base32
"0ai5dhjc43zcvangz123ryxmlbm51s21rg13bllwyn98w67arhb4"))))
;; TODO: run "make -f contrib/repackage_system_suitesparse4.make" to copy static lib
("suitesparse"
,(origin
(method url-fetch)
(uri "http://faculty.cse.tamu.edu/davis/SuiteSparse/SuiteSparse-4.4.2.tar.gz")
(uri "http://faculty.cse.tamu.edu/davis/SuiteSparse/SuiteSparse-4.4.5.tar.gz")
(sha256
(base32
"1dg0qsv07n71nbn9cgcvn73933rgy1jnxw5bfqkwfq3bidk44cqc"))))
"1jcbxb8jx5wlcixzf6n5dca2rcfx6mlcms1k2rl5gp67ay3bix43"))))
("objconv"
,(origin
(method url-fetch)
@ -299,18 +333,10 @@ (define-public julia
"SFMT/dSFMT-src-2.2.3.tar.gz"))
(sha256
(base32
"03kaqbjbi6viz0n33dk5jlf6ayxqlsq4804n7kwkndiga9s4hd42"))))
("virtualenv"
,(origin
(method url-fetch)
(uri (string-append "https://pypi.python.org/packages/24/cc/"
"a3cdf0a49ffcaef483b7e2511476aa520cf7260c199a6928fda6c43ba916/"
"virtualenv-1.11.6.tar.gz"))
(sha256
(base32
"1xq4prmg25n9cz5zcvbqx68lmc3kl39by582vd8pzs9f3qalqyiy"))))))
"03kaqbjbi6viz0n33dk5jlf6ayxqlsq4804n7kwkndiga9s4hd42"))))))
(native-inputs
`(("perl" ,perl)
`(("openssl" ,openssl)
("perl" ,perl)
("patchelf" ,patchelf)
("pkg-config" ,pkg-config)
("python" ,python-2)))