diff options
| -rw-r--r-- | gnu/packages/julia.scm | 142 |
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))) |