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gnu: julia: Upgrade to 1.3.1. 

* gnu/packages/julia.scm (libuv-julia): Upgrade to 2.0.0-1.35b1504.
(libunwind-julia): New variable.
(llvm-patch): Rename to ...
(julia-patch): ... this. Update to 1.3.1.
(llvm-julia): Adjust patch-set based on above change. Adjust indent.
(julia): Update to 1.3.1.
[source]: Add patch.
[arguments]: Adjust custom 'prepare-deps (llvm-patch): Rename to ...
(julia-patch): ... this. Update to 1.3.1.
(llvm-julia): Adjust patch-set based on above change.
(julia): Upgrade to 1.3.1.
[arguments]: Adjust custom 'prepare-deps phase based on changed inputs.
Remove most of 'hardcode-soname-map. Adjust 'fix-include-and-link-paths.
Add new 'fix-precompile phase. Adjust custom 'disable-broken-tests
phase. Add new 'make-wrapper phase. Adjust make-flags.
[inputs]: Add p7zip, mbedtls-apache, curl libssh2.
Remove openspecfun, fftw, fftwf, python2-virtualenv, rmath.
Replace libunwind with libunwind-julia, custom suitesparse with system
suitesparse, custom dsfmt with system dsfmt.
[native-search-paths]: Add JULIA_DEPOT_PATH.
* gnu/packages/patches/julia-SOURCE_DATE_EPOCH-mtime.patch: New file.
* gnu/local.mk (dist_patch_DATA): Register it.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
master
Nicolò Balzarotti 2020-04-02 11:55:20 +02:00 committed by Efraim Flashner
parent 46e8bc52c2
commit 1e96e6ac8b
No known key found for this signature in database
GPG Key ID: 41AAE7DCCA3D8351
3 changed files with 184 additions and 179 deletions
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2
gnu/local.mk
View File

@ -29,6 +29,7 @@
# Copyright © 2020 Brendan Tildesley <mail@brendan.scot> # Copyright © 2020 Brendan Tildesley <mail@brendan.scot>
# Copyright © 2020 Vincent Legoll <vincent.legoll@gmail.com> # Copyright © 2020 Vincent Legoll <vincent.legoll@gmail.com>
# Copyright © 2020 R Veera Kumar <vkor@vkten.in> # Copyright © 2020 R Veera Kumar <vkor@vkten.in>
# Copyright © 2020 Nicolò Balzarotti <nicolo@nixo.xyz
# #
# This file is part of GNU Guix. # This file is part of GNU Guix.
# #
@ -1065,6 +1066,7 @@ dist_patch_DATA = \
%D%/packages/patches/jfsutils-add-sysmacros.patch \ %D%/packages/patches/jfsutils-add-sysmacros.patch \
%D%/packages/patches/jfsutils-include-systypes.patch \ %D%/packages/patches/jfsutils-include-systypes.patch \
%D%/packages/patches/jsoncpp-fix-inverted-case.patch \ %D%/packages/patches/jsoncpp-fix-inverted-case.patch \
%D%/packages/patches/julia-SOURCE_DATE_EPOCH-mtime.patch \
%D%/packages/patches/kdbusaddons-kinit-file-name.patch \ %D%/packages/patches/kdbusaddons-kinit-file-name.patch \
%D%/packages/patches/libnftnl-dont-check-NFTNL_FLOWTABLE_SIZE.patch \ %D%/packages/patches/libnftnl-dont-check-NFTNL_FLOWTABLE_SIZE.patch \
%D%/packages/patches/libvirt-create-machine-cgroup.patch \ %D%/packages/patches/libvirt-create-machine-cgroup.patch \

333
gnu/packages/julia.scm
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@ -1,6 +1,7 @@
;;; GNU Guix --- Functional package management for GNU ;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2015, 2016, 2017 Ricardo Wurmus <rekado@elephly.net> ;;; Copyright © 2015, 2016, 2017 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il> ;;; Copyright © 2016, 2020 Efraim Flashner <efraim@flashner.co.il>
;;; Copyright © 2020 Nicolò Balzarotti <nicolo@nixo.xyz>
;;; ;;;
;;; This file is part of GNU Guix. ;;; This file is part of GNU Guix.
;;; ;;;
@ -28,6 +29,7 @@
#:use-module (gnu packages algebra) #:use-module (gnu packages algebra)
#:use-module (gnu packages base) #:use-module (gnu packages base)
#:use-module (gnu packages compression) #:use-module (gnu packages compression)
#:use-module (gnu packages curl)
#:use-module (gnu packages elf) #:use-module (gnu packages elf)
#:use-module (gnu packages gcc) #:use-module (gnu packages gcc)
#:use-module (gnu packages llvm) #:use-module (gnu packages llvm)
@ -41,20 +43,21 @@
#:use-module (gnu packages python) #:use-module (gnu packages python)
#:use-module (gnu packages python-xyz) #:use-module (gnu packages python-xyz)
#:use-module (gnu packages textutils) #:use-module (gnu packages textutils)
#:use-module (gnu packages ssh)
#:use-module (gnu packages tls) #:use-module (gnu packages tls)
#:use-module (gnu packages version-control) #:use-module (gnu packages version-control)
#:use-module (gnu packages wget) #:use-module (gnu packages wget)
#:use-module (ice-9 match)) #:use-module (ice-9 match))
(define libuv-julia (define libuv-julia
(let ((commit "26dbe5672c33fc885462c509fe2a9b36f35866fd") (let ((commit "35b1504507a7a4168caae3d78db54d1121b121e1")
(revision "6")) (revision "1"))
;; When upgrading Julia, also upgrade this. ;; When upgrading Julia, also upgrade this. Get the commit from
;; Get the commit from https://github.com/JuliaLang/julia/blob/v1.1.1/deps/libuv.version ;; https://github.com/JuliaLang/julia/blob/v1.3.1/deps/libuv.version
(package (package
(inherit libuv) (inherit libuv)
(name "libuv-julia") (name "libuv-julia")
(version (string-append "1.9.0-" revision "." (string-take commit 8))) (version (git-version "2.0.0" revision commit))
(source (origin (source (origin
(method git-fetch) (method git-fetch)
(uri (git-reference (uri (git-reference
@ -63,7 +66,7 @@
(file-name (string-append name "-" version "-checkout")) (file-name (string-append name "-" version "-checkout"))
(sha256 (sha256
(base32 (base32
"17pn2xmqaramilx897s9grs966i5246gi6sric5alch4g9j4685n")))) "0dn3v6fdp1z382pqg3nhjzk60l61ky9b65mfgaj29fv2da95rwjs"))))
(build-system gnu-build-system) (build-system gnu-build-system)
(arguments (arguments
(substitute-keyword-arguments (package-arguments libuv) (substitute-keyword-arguments (package-arguments libuv)
@ -72,14 +75,37 @@
(delete 'autogen))))) (delete 'autogen)))))
(home-page "https://github.com/JuliaLang/libuv")))) (home-page "https://github.com/JuliaLang/libuv"))))
(define (llvm-patch-url version name) (define libunwind-julia
;; The Julia projects requires their patched version.
;; Get from https://github.com/JuliaLang/julia/tree/master/deps/patches
(package
(inherit libunwind)
(name "libunwind-julia")
(version "1.3.1")
(source
(origin
(method url-fetch)
(uri (string-append "mirror://savannah/libunwind/libunwind-"
version ".tar.gz"))
(sha256
(base32
"1y0l08k6ak1mqbfj6accf9s5686kljwgsl4vcqpxzk5n74wpm6a3"))
(patches
(list
(julia-patch "libunwind-prefer-extbl"
"0lr4dafw8qyfh8sw8hhbwkql1dlhqv8px7k81y2l20hhxfgnh2m1")
(julia-patch "libunwind-static-arm"
"1jk3bmiw61ypcchqkk1fyg5wh8wpggk574wxyfyaic870zh3lhgq")))))
(home-page "https://github.com/JuliaLang/tree/master/deps/")))
(define (julia-patch-url version name)
(string-append "https://raw.githubusercontent.com/JuliaLang/julia/v" version (string-append "https://raw.githubusercontent.com/JuliaLang/julia/v" version
"/deps/patches/" name)) "/deps/patches/" name))
(define (llvm-patch name sha) (define (julia-patch name sha)
(let ((version "1.1.1")) (let ((version "1.3.1"))
(origin (method url-fetch) (origin (method url-fetch)
(uri (llvm-patch-url version name)) (uri (julia-patch-url version name))
(sha256 (base32 sha)) (sha256 (base32 sha))
(file-name name)))) (file-name name))))
@ -88,51 +114,50 @@
(inherit llvm-6) (inherit llvm-6)
(name "llvm-julia") (name "llvm-julia")
(source (origin (source (origin
(method url-fetch) (inherit (package-source llvm-6))
(uri "http://releases.llvm.org/6.0.1/llvm-6.0.1.src.tar.xz")
(sha256
(base32
"1qpls3vk85lydi5b4axl0809fv932qgsqgdgrk098567z4jc7mmn"))
;; Those patches are inside the Julia source repo. ;; Those patches are inside the Julia source repo.
;; They are _not_ Julia specific (https://github.com/julialang/julia#llvm) ;; They are _not_ Julia specific (https://github.com/julialang/julia#llvm)
;; but they are required to build Julia. ;; but they are required to build Julia.
;; Discussion: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=919628 ;; Discussion: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=919628
(patches (patches
(list (map (match-lambda
(llvm-patch "llvm-6.0-D44650.patch" ((name hash)
"1336q4vqayr94wdcnlmcxh90mjdh34dzw9x2cbiqjnx9b1j8fxyb") (julia-patch name hash)))
(llvm-patch "llvm-6.0-DISABLE_ABI_CHECKS.patch" (list
"014fawd1ba7yckalypfld22zgic87x9nx3cim42zrwygywd36pyg") '("llvm-6.0-D44650"
(llvm-patch "llvm-6.0-NVPTX-addrspaces.patch" "1336q4vqayr94wdcnlmcxh90mjdh34dzw9x2cbiqjnx9b1j8fxyb")
"1qdi2zmrjsrj0h84zv2vyly2hjcn4f67mfy0s1q353g4v4jkscqc") '("llvm-6.0-DISABLE_ABI_CHECKS"
(llvm-patch "llvm-6.0.0_D27296-libssp.patch" "014fawd1ba7yckalypfld22zgic87x9nx3cim42zrwygywd36pyg")
"0s5hi2r1j63i8m6ig1346crx2aiv9f7rgb3mg80kw1wx5y7pdpfh") '("llvm-6.0-NVPTX-addrspaces"
(llvm-patch "llvm-D27629-AArch64-large_model_6.0.1.patch" "1qdi2zmrjsrj0h84zv2vyly2hjcn4f67mfy0s1q353g4v4jkscqc")
"1qrshmlqvnasdyc158vfn3hnbigqph3lsq7acb9w8lwkpnnm2j4z") '("llvm-6.0.0_D27296-libssp"
(llvm-patch "llvm-D34078-vectorize-fdiv.patch" "0s5hi2r1j63i8m6ig1346crx2aiv9f7rgb3mg80kw1wx5y7pdpfh")
"1696hg84a0jxcnggvqsc2cdp271hf9a44p4qsd078qm1mfawkaay") '("llvm-D27629-AArch64-large_model_6.0.1"
(llvm-patch "llvm-D42262-jumpthreading-not-i1.patch" "1qrshmlqvnasdyc158vfn3hnbigqph3lsq7acb9w8lwkpnnm2j4z")
"1c8w210gwidbnkkw8anp17dk5pnxws2fl3mb2qxh7y9wzfpixgaq") '("llvm-D34078-vectorize-fdiv"
(llvm-patch "llvm-D44892-Perf-integration.patch" "1696hg84a0jxcnggvqsc2cdp271hf9a44p4qsd078qm1mfawkaay")
"0r37jd0ssh2k1pndkfd5blgpg9z90im4vlzprhb0n0wwz45g4b05") '("llvm-D42262-jumpthreading-not-i1"
(llvm-patch "llvm-D46460.patch" "1c8w210gwidbnkkw8anp17dk5pnxws2fl3mb2qxh7y9wzfpixgaq")
"1miqgswdc0qvbaf4571c2xkxyp9ais06b1bcpa83sq22vr4hbsfb") '("llvm-D44892-Perf-integration"
(llvm-patch "llvm-D49832-SCEVPred.patch" "0r37jd0ssh2k1pndkfd5blgpg9z90im4vlzprhb0n0wwz45g4b05")
"0v5c88hgqj6dymv3j86ca5mhpqab5fbnrvjiw1nvnrnya9l4dlbn") '("llvm-D46460"
(llvm-patch "llvm-D50010-VNCoercion-ni.patch" "1miqgswdc0qvbaf4571c2xkxyp9ais06b1bcpa83sq22vr4hbsfb")
"0iblb3q1xixwrb12jpb89h3ywmqmzdp6aqp416j4ncwakyjhhfkp") '("llvm-D49832-SCEVPred"
(llvm-patch "llvm-D50167-scev-umin.patch" "0v5c88hgqj6dymv3j86ca5mhpqab5fbnrvjiw1nvnrnya9l4dlbn")
"1f2rakcnnyhr7w10k7gqg0k0491pyvx5ijplivw557f714ys3q6v") '("llvm-D50010-VNCoercion-ni"
(llvm-patch "llvm-OProfile-line-num.patch" "0iblb3q1xixwrb12jpb89h3ywmqmzdp6aqp416j4ncwakyjhhfkp")
"1jvbbmwyags0xfwamb13qrf3rgcz9i1r03m9lava7swag8xb78c7") '("llvm-D50167-scev-umin"
(llvm-patch "llvm-PPC-addrspaces.patch" "1f2rakcnnyhr7w10k7gqg0k0491pyvx5ijplivw557f714ys3q6v")
"1f23nhsxh2s3jskbgs7da9nwg3s1hrkbk5aahl08x41wi3mny01p") '("llvm-OProfile-line-num"
(llvm-patch "llvm-rL323946-LSRTy.patch" "1jvbbmwyags0xfwamb13qrf3rgcz9i1r03m9lava7swag8xb78c7")
"10cz3vy1yw0w643z7xx021wa4kymx9fcm3bjg61s6vzdqd6d9fns") '("llvm-PPC-addrspaces"
(llvm-patch "llvm-rL326967-aligned-load.patch" "1f23nhsxh2s3jskbgs7da9nwg3s1hrkbk5aahl08x41wi3mny01p")
"04jxnv32yj5x17hqhi8g2p8rhgp38gmjzr871w7z8s44pq10v9v4") '("llvm-rL323946-LSRTy"
(llvm-patch "llvm-rL327898.patch" "10cz3vy1yw0w643z7xx021wa4kymx9fcm3bjg61s6vzdqd6d9fns")
"15ah49gbsll23z28kpyahi5vl0fh3fkxcgd1zmxxdcl96s3x8bnq"))))) '("llvm-rL326967-aligned-load"
"04jxnv32yj5x17hqhi8g2p8rhgp38gmjzr871w7z8s44pq10v9v4")
'("llvm-rL327898"
"15ah49gbsll23z28kpyahi5vl0fh3fkxcgd1zmxxdcl96s3x8bnq"))))))
(arguments (arguments
(substitute-keyword-arguments (package-arguments llvm-6) (substitute-keyword-arguments (package-arguments llvm-6)
((#:configure-flags flags) ((#:configure-flags flags)
@ -158,7 +183,7 @@
(define-public julia (define-public julia
(package (package
(name "julia") (name "julia")
(version "1.1.1") (version "1.3.1")
(source (origin (source (origin
(method url-fetch) (method url-fetch)
(uri (string-append (uri (string-append
@ -166,7 +191,9 @@
version "/julia-" version ".tar.gz")) version "/julia-" version ".tar.gz"))
(sha256 (sha256
(base32 (base32
"0hk983mywimclgnjc41zmlppm5kfdz2aj85ky07p49ilcqxi998f")))) "1nwkmr9j55g1zkxdchnid1h022s0is52vx23niksshgvh793g41x"))
(patches
(search-patches "julia-SOURCE_DATE_EPOCH-mtime.patch"))))
(build-system gnu-build-system) (build-system gnu-build-system)
(arguments (arguments
`(#:test-target "test" `(#:test-target "test"
@ -188,30 +215,25 @@
(add-after 'unpack 'prepare-deps (add-after 'unpack 'prepare-deps
(lambda* (#:key inputs #:allow-other-keys) (lambda* (#:key inputs #:allow-other-keys)
(mkdir "deps/srccache") (mkdir "deps/srccache")
(copy-file (assoc-ref inputs "dsfmt") ;; no USE_SYSTEM_{OBJCONV/LIBWHICH} option
"deps/srccache/dsfmt-2.2.3.tar.gz")
(copy-file (assoc-ref inputs "objconv") (copy-file (assoc-ref inputs "objconv")
"deps/srccache/objconv.zip") "deps/srccache/objconv.zip")
(copy-file (assoc-ref inputs "suitesparse")
"deps/srccache/SuiteSparse-4.4.5.tar.gz")
(copy-file (string-append (assoc-ref inputs "virtualenv")
"/bin/virtualenv")
"julia-env")
(copy-file (assoc-ref inputs "libwhich") (copy-file (assoc-ref inputs "libwhich")
(string-append "deps/srccache/libwhich-" (string-append "deps/srccache/libwhich-"
"81e9723c0273d78493dc8c8ed570f68d9ce7e89e" "81e9723c0273d78493dc8c8ed570f68d9ce7e89e"
".tar.gz")) ".tar.gz"))
(copy-file (assoc-ref inputs "rmath")
"deps/srccache/Rmath-julia-0.1.tar.gz")
;; needed by libwhich ;; needed by libwhich
(setenv "LD_LIBRARY_PATH" (setenv "LD_LIBRARY_PATH"
(string-join (map (lambda (pkg) (string-join (map (lambda (pkg)
(string-append (assoc-ref inputs pkg) (string-append (assoc-ref inputs pkg)
"/lib")) "/lib"))
'("arpack-ng" "fftw" "gmp" "lapack" '("arpack-ng" "curl" "dsfmt"
"libgit2" "mpfr" "openblas" "openlibm" "gmp" "lapack"
"openspecfun" "pcre2")) "libssh2" "libgit2"
"mbedtls" "mpfr"
"openblas" "openlibm" "pcre2"
"suitesparse"))
":")) ":"))
#t)) #t))
;; FIXME: Building the documentation requires Julia packages that ;; FIXME: Building the documentation requires Julia packages that
@ -233,42 +255,11 @@
;; using the output of "/sbin/ldconfig -p". Since ldconfig is not ;; using the output of "/sbin/ldconfig -p". Since ldconfig is not
;; used in Guix, we patch runtime_ccall.cpp to contain a static map. ;; used in Guix, we patch runtime_ccall.cpp to contain a static map.
(lambda* (#:key inputs #:allow-other-keys) (lambda* (#:key inputs #:allow-other-keys)
(use-modules (ice-9 match))
(substitute* "src/runtime_ccall.cpp"
;; Patch out invocations of '/sbin/ldconfig' to avoid getting
;; error messages about missing '/sbin/ldconfig' on Guix System.
(("popen\\(.*ldconfig.*\\);")
"NULL;\n")
;; Populate 'sonameMap'.
(("jl_read_sonames.*;")
(string-join
(map (match-lambda
((input libname soname)
(string-append
"sonameMap[\"" libname "\"] = "
"\"" (assoc-ref inputs input) "/lib/" soname "\";")))
'(("libc" "libc" "libc.so.6")
("pcre2" "libpcre2-8" "libpcre2-8.so")
("mpfr" "libmpfr" "libmpfr.so")
("openblas" "libblas" "libopenblas.so")
("arpack-ng" "libarpack" "libarpack.so")
("lapack" "liblapack" "liblapack.so")
("libgit2" "libgit2" "libgit2.so")
("gmp" "libgmp" "libgmp.so")
("openspecfun" "libopenspecfun" "libopenspecfun.so")
("fftw" "libfftw3" "libfftw3_threads.so")
("fftwf" "libfftw3f" "libfftw3f_threads.so"))))))
(substitute* "base/math.jl" (substitute* "base/math.jl"
(("const libm = Base.libm_name") (("const libm = Base.libm_name")
(string-append "const libm = \"" (string-append "const libm = \""
(assoc-ref inputs "openlibm") (assoc-ref inputs "openlibm")
"/lib/libopenlibm.so" "/lib/libopenlibm.so"
"\""))
(("const openspecfun = \"libopenspecfun\"")
(string-append "const openspecfun = \""
(assoc-ref inputs "openspecfun")
"/lib/libopenspecfun.so"
"\""))) "\"")))
#t)) #t))
(add-before 'build 'fix-include-and-link-paths (add-before 'build 'fix-include-and-link-paths
@ -278,10 +269,10 @@
;; collection of build targets and a list of libraries to link ;; collection of build targets and a list of libraries to link
;; against. ;; against.
(substitute* "src/flisp/Makefile" (substitute* "src/flisp/Makefile"
(("\\$\\(BUILDDIR\\)/\\$\\(EXENAME\\): \\$\\(OBJS\\) \\$\\(LIBFILES_release\\)") (("\\$\\(BUILDDIR\\)/\\$\\(EXENAME\\)\\$\\(EXE\\): \\$\\(OBJS\\) \\$\\(LIBFILES_release\\)")
"$(BUILDDIR)/$(EXENAME): $(OBJS) $(LLT_release)") "$(BUILDDIR)/$(EXENAME)$(EXE): $(OBJS) $(LLT_release)")
(("\\$\\(BUILDDIR\\)/\\$\\(EXENAME\\)-debug: \\$\\(DOBJS\\) \\$\\(LIBFILES_debug\\)") (("\\$\\(BUILDDIR\\)/\\$\\(EXENAME\\)-debug$(EXE): \\$\\(DOBJS\\) \\$\\(LIBFILES_debug\\)")
"$(BUILDDIR)/$(EXENAME)-debug: $(DOBJS) $(LLT_debug)")) "$(BUILDDIR)/$(EXENAME)-debug\\$\\(EXE\\): $(DOBJS) $(LLT_debug)"))
;; The REPL must be linked with libuv. ;; The REPL must be linked with libuv.
(substitute* "ui/Makefile" (substitute* "ui/Makefile"
@ -300,35 +291,46 @@
(substitute* "base/client.jl" (substitute* "base/client.jl"
(("/bin/sh") (which "sh"))) (("/bin/sh") (which "sh")))
#t)) #t))
(add-after 'unpack 'hardcode-paths (add-before 'build 'fix-precompile
(lambda _ (lambda _
(substitute* "stdlib/InteractiveUtils/src/InteractiveUtils.jl" (substitute* "base/loading.jl"
(("`which") (string-append "`" (which "which"))) (("something(Base.active_project(), \"\")") "\"\""))
(("`wget") (string-append "`" (which "wget"))))
#t)) #t))
(add-before 'check 'disable-broken-tests (add-before 'check 'disable-broken-tests
(lambda _ (lambda _
(define (touch file-name)
(call-with-output-file file-name (const #t)))
;; FIXME: All git tests works except this one. But *THIS* "fix"
;; is not working, so right now I'm disabling all libgit2.jl tests
;; (substitute* "stdlib/LibGit2/test/libgit2.jl"
;; (("!LibGit2.use_http_path(cfg, github_cred)") "true")
;; (("LibGit2.use_http_path(cfg, mygit_cred)") "true"))
(map (lambda (test)
(delete-file test)
(touch test))
'("stdlib/Sockets/test/runtests.jl"
"stdlib/Distributed/test/runtests.jl"
;; FIXME: see above
"stdlib/LibGit2/test/libgit2.jl"))
(substitute* "test/choosetests.jl" (substitute* "test/choosetests.jl"
;; These tests fail, probably because some of the input (("tests = testnames")
;; binaries have been stripped and thus backtraces don't look ;; Those failings are not deterministic. They depends on the
;; as expected. ;; running order. I think it depends on the number of
(("\"backtrace\",") "") ;; runners, disabling it for now
(("\"cmdlineargs\",") "")) ;; https://github.com/JuliaLang/julia/issues/34330
#t))) "tests = filter(e->!in(e,[\"backtrace\",\"exceptions\",
\"stress\",\"precompile\",
\"client\",\"stacktraces\"]),
testnames)"))
;; When HOME is not set, julia calls uv_os_homedir, which in
;; turns call getpwuid_r. Add the HOME env variable to the
;; external julia call to fix this
(substitute* "test/cmdlineargs.jl"
(("\"JULIA_PROJECT\"") "\"HOME\"=>\"/tmp\", \"JULIA_PROJECT\""))
;; Marking the test as broken as it's a known bug:
;; https://github.com/JuliaLang/julia/issues/32377
(substitute* "stdlib/REPL/test/replcompletions.jl"
(("@test count") "@test_broken count"))
#t))
(add-after 'install 'make-wrapper
(lambda* (#:key inputs outputs #:allow-other-keys)
(let* ((out (assoc-ref outputs "out"))
(bin (string-append out "/bin"))
(program "julia"))
(with-directory-excursion bin
(wrap-program program
`("JULIA_LOAD_PATH" ":" prefix
("" "$JULIA_LOAD_PATH")))
(wrap-program program
`("JULIA_DEPOT_PATH" ":" prefix
("" "$JULIA_DEPOT_PATH"))))
#t))))
#:make-flags #:make-flags
(list (list
(string-append "prefix=" (assoc-ref %outputs "out")) (string-append "prefix=" (assoc-ref %outputs "out"))
@ -346,25 +348,20 @@
(_ "MARCH=UNSUPPORTED")) (_ "MARCH=UNSUPPORTED"))
"CONFIG_SHELL=bash" ;needed to build bundled libraries "CONFIG_SHELL=bash" ;needed to build bundled libraries
"USE_SYSTEM_DSFMT=0" ;not packaged for Guix and upstream has no ;; list of "USE_SYSTEM_*" is here:
;build system for a shared library. ;; https://github.com/JuliaLang/julia/blob/v1.3.1/Make.inc
"USE_SYSTEM_DSFMT=1"
"USE_SYSTEM_P7ZIP=1"
"USE_SYSTEM_LAPACK=1" "USE_SYSTEM_LAPACK=1"
"USE_SYSTEM_BLAS=1" "USE_SYSTEM_BLAS=1"
"USE_BLAS64=0" ;needed when USE_SYSTEM_BLAS=1 "USE_BLAS64=0" ;needed when USE_SYSTEM_BLAS=1
"LIBBLAS=-lopenblas" "LIBBLAS=-lopenblas"
"LIBBLASNAME=libopenblas" "LIBBLASNAME=libopenblas"
"USE_SYSTEM_FFTW=1" "USE_SYSTEM_SUITESPARSE=1"
"LIBFFTWNAME=libfftw3" (string-append "SUITESPARSE_INC=-I "
"LIBFFTWFNAME=libfftw3f" (assoc-ref %build-inputs "suitesparse")
"/include")
;; 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_GPL_LIBS=1" ;proudly
"USE_SYSTEM_UTF8PROC=1" "USE_SYSTEM_UTF8PROC=1"
(string-append "UTF8PROC_INC=" (string-append "UTF8PROC_INC="
@ -390,11 +387,16 @@
"USE_SYSTEM_MPFR=1" "USE_SYSTEM_MPFR=1"
"USE_SYSTEM_ARPACK=1" "USE_SYSTEM_ARPACK=1"
"USE_SYSTEM_LIBGIT2=1" "USE_SYSTEM_LIBGIT2=1"
"USE_SYSTEM_ZLIB=1" (string-append "LIBUV="
"USE_SYSTEM_OPENSPECFUN=1"))) (assoc-ref %build-inputs "libuv")
"/lib/libuv.so")
(string-append "LIBUV_INC="
(assoc-ref %build-inputs "libuv")
"/include")
"USE_SYSTEM_ZLIB=1")))
(inputs (inputs
`(("llvm" ,llvm-julia) `(("llvm" ,llvm-julia)
("p7zip" ,p7zip)
;; The bundled version is 3.3.0 so stick to that version. With other ;; 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 ;; versions, we get test failures in 'linalg/arnoldi' as described in
;; <https://bugs.gnu.org/30282>. ;; <https://bugs.gnu.org/30282>.
@ -403,12 +405,12 @@
("coreutils" ,coreutils) ;for bindings to "mkdir" and the like ("coreutils" ,coreutils) ;for bindings to "mkdir" and the like
("lapack" ,lapack) ("lapack" ,lapack)
("openblas" ,openblas) ;Julia does not build with Atlas ("openblas" ,openblas) ;Julia does not build with Atlas
("libunwind" ,libunwind) ("libunwind" ,libunwind-julia)
("openlibm" ,openlibm) ("openlibm" ,openlibm)
("openspecfun" ,openspecfun) ("mbedtls" ,mbedtls-apache)
("curl" ,curl)
("libgit2" ,libgit2) ("libgit2" ,libgit2)
("fftw" ,fftw) ("libssh2" ,libssh2)
("fftwf" ,fftwf)
("fortran" ,gfortran) ("fortran" ,gfortran)
("libuv" ,libuv-julia) ("libuv" ,libuv-julia)
("pcre2" ,pcre2) ("pcre2" ,pcre2)
@ -418,31 +420,9 @@
("which" ,which) ("which" ,which)
("zlib" ,zlib) ("zlib" ,zlib)
("gmp" ,gmp) ("gmp" ,gmp)
("virtualenv" ,python2-virtualenv) ("suitesparse" ,suitesparse)
;; FIXME: The following inputs are downloaded from upstream to allow us ;; Find dependencies versions here:
;; to use the lightweight Julia release tarball. Ideally, these inputs ;; https://raw.githubusercontent.com/JuliaLang/julia/v1.3.0/deps/Versions.make
;; would eventually be replaced with proper Guix packages.
;; TODO: run "make -f contrib/repackage_system_suitesparse4.make" to copy static lib
;; Find dependency versions here:
;; https://raw.githubusercontent.com/JuliaLang/julia/77a2c1e245c85812dc1c7687540beedecc52758f/deps/Versions.make
("rmath"
,(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/JuliaLang/Rmath-julia")
(commit "v0.1")))
(file-name "rmath-julia-0.1-checkout")
(sha256
(base32
"1zkpy0cg5zivq40zbhbdgj9128fqzs2j94wkwih8nc6xaj3gp9p6"))))
("suitesparse"
,(origin
(method url-fetch)
(uri "http://faculty.cse.tamu.edu/davis/SuiteSparse/SuiteSparse-4.4.5.tar.gz")
(sha256
(base32
"1jcbxb8jx5wlcixzf6n5dca2rcfx6mlcms1k2rl5gp67ay3bix43"))))
("objconv" ("objconv"
,(origin ,(origin
(method url-fetch) (method url-fetch)
@ -467,15 +447,7 @@
(sha256 (sha256
(base32 (base32
"1p7zg31kpmpbmh1znrk1xrbd074agx13b9q4dcw8n2zrwwdlbz3b"))))) "1p7zg31kpmpbmh1znrk1xrbd074agx13b9q4dcw8n2zrwwdlbz3b")))))
("dsfmt" ("dsfmt" ,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 (native-inputs
`(("openssl" ,openssl) `(("openssl" ,openssl)
("perl" ,perl) ("perl" ,perl)
@ -485,7 +457,10 @@
(native-search-paths (native-search-paths
(list (search-path-specification (list (search-path-specification
(variable "JULIA_LOAD_PATH") (variable "JULIA_LOAD_PATH")
(files (list "share/julia/packages/"))))) (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. ;; Julia is not officially released for ARM and MIPS.
;; See https://github.com/JuliaLang/julia/issues/10639 ;; See https://github.com/JuliaLang/julia/issues/10639
(supported-systems '("i686-linux" "x86_64-linux" "aarch64-linux")) (supported-systems '("i686-linux" "x86_64-linux" "aarch64-linux"))

28
gnu/packages/patches/julia-SOURCE_DATE_EPOCH-mtime.patch 100644
View File

@ -0,0 +1,28 @@
--- /dev/null
+++ b/gnu/packages/patches/julia-SOURCE_DATE_EPOCH-mtime.patch
@@ -0,0 +1,22 @@
+Fix one of upstream non-determinism, tracked here:
+
+https://github.com/JuliaLang/julia/issues/34115
+https://github.com/JuliaLang/julia/issues/25900
+
+
+Patch by Nicoló Balzarotti <nicolo@nixo.xyz>.
+
+--- a/base/loading.jl
++++ b/base/loading.jl
+@@ -807,7 +807,10 @@
+ path = normpath(joinpath(dirname(prev), _path))
+ end
+ if _track_dependencies[]
+- push!(_require_dependencies, (mod, path, mtime(path)))
++ push!(_require_dependencies,
++ (mod, path,
++ haskey(ENV, "SOURCE_DATE_EPOCH") ?
++ parse(Float64, ENV["SOURCE_DATE_EPOCH"]) : mtime(path)))
+ end
+ return path, prev
+ end
--
2.26.0