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-rw-r--r--gnu/packages/julia.scm142
1 files changed, 84 insertions, 58 deletions
diff --git a/gnu/packages/julia.scm b/gnu/packages/julia.scm
index e3cefb4330..a6664a54c2 100644
--- a/gnu/packages/julia.scm
+++ b/gnu/packages/julia.scm
@@ -40,16 +40,17 @@
#: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 @@
(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 @@
(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 @@
version "/julia-" version ".tar.gz"))
(sha256
(base32
- "09gc6yf3v4in0qwhrbgjrjgvblp941di0mli4zax22mvf4dzc7s4"))))
+ "0bhickil88lalp9jdj1kmf4is70zinhx8ha9rng0g3z50r4a2qmv"))))
(build-system gnu-build-system)
(arguments
`(#:test-target "test"
@@ -86,6 +99,9 @@
(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 $ORIGIN to refer to each other, but (guix build
;; gremlin) doesn't support it yet, so skip this phase.
@@ -96,24 +112,33 @@
(delete 'configure)
(add-after 'unpack 'prepare-deps
(lambda* (#:key inputs #:allow-other-keys)
- (copy-file (assoc-ref inputs "rmath-julia")
- "deps/Rmath-julia-0.1.tar.gz")
+ (mkdir "deps/srccache")
(copy-file (assoc-ref inputs "dsfmt")
- "deps/dsfmt-2.2.3.tar.gz")
+ "deps/srccache/dsfmt-2.2.3.tar.gz")
(copy-file (assoc-ref inputs "objconv")
- "deps/objconv.zip")
+ "deps/srccache/objconv.zip")
(copy-file (assoc-ref inputs "suitesparse")
- "deps/SuiteSparse-4.4.2.tar.gz")
- (copy-file (assoc-ref inputs "virtualenv")
- "deps/virtualenv-1.11.6.tar.gz")
+ "deps/srccache/SuiteSparse-4.4.5.tar.gz")
+ (copy-file (string-append (assoc-ref inputs "virtualenv")
+ "/bin/virtualenv")
+ "julia-env")
+ #t))
+ (add-after 'unpack 'fix-llvm-flag
+ (lambda _
+ (substitute* "src/Makefile"
+ (("-lLLVM-\\$\\(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 @@
("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 @@
(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 @@
(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 @@
"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 @@
;; "/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 @@
"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 @@
("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 @@
"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)))