diff options
author | Marius Bakke <marius@gnu.org> | 2021-07-29 22:34:57 +0200 |
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committer | Marius Bakke <marius@gnu.org> | 2021-07-29 22:34:57 +0200 |
commit | b029be2ee0f81cdcbc14240ff426408085ab0a40 (patch) | |
tree | ed6d0e1bfdadfd28e1eb804e43763b793baa0b42 /gnu/packages/julia.scm | |
parent | bc55f3091bac4677df0cf020381c554921fea179 (diff) | |
parent | ffb381856d0c6cc1a557b789f6b377cfa17002a0 (diff) | |
download | guix-b029be2ee0f81cdcbc14240ff426408085ab0a40.tar.gz guix-b029be2ee0f81cdcbc14240ff426408085ab0a40.zip |
Merge branch 'master' into core-updates-frozen
Conflicts:
gnu/packages/bioinformatics.scm
gnu/packages/cmake.scm
gnu/packages/curl.scm
gnu/packages/emacs-xyz.scm
gnu/packages/gpodder.scm
gnu/packages/music.scm
gnu/packages/patches/glibc-bootstrap-system.patch
gnu/packages/python-xyz.scm
gnu/packages/shells.scm
gnu/packages/statistics.scm
Diffstat (limited to 'gnu/packages/julia.scm')
-rw-r--r-- | gnu/packages/julia.scm | 431 |
1 files changed, 310 insertions, 121 deletions
diff --git a/gnu/packages/julia.scm b/gnu/packages/julia.scm index 97218656cc..df8a74fea5 100644 --- a/gnu/packages/julia.scm +++ b/gnu/packages/julia.scm @@ -1,9 +1,11 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2015, 2016, 2017 Ricardo Wurmus <rekado@elephly.net> ;;; Copyright © 2016, 2020, 2021 Efraim Flashner <efraim@flashner.co.il> -;;; Copyright © 2020 Nicolò Balzarotti <nicolo@nixo.xyz> +;;; Copyright © 2020, 2021 Nicolò Balzarotti <nicolo@nixo.xyz> ;;; Copyright © 2020 Tim Howes <timhowes@lavabit.com> ;;; Copyright © 2020 Tobias Geerinckx-Rice <me@tobias.gr> +;;; Copyright © 2021 Jean-Baptiste Volatier <jbv@pm.me> +;;; Copyright © 2021 Simon Tournier <zimon.toutoune@gmail.com> ;;; ;;; This file is part of GNU Guix. ;;; @@ -30,6 +32,7 @@ #:use-module (gnu packages) #:use-module (gnu packages algebra) #:use-module (gnu packages base) + #:use-module (gnu packages certs) #:use-module (gnu packages compression) #:use-module (gnu packages curl) #:use-module (gnu packages elf) @@ -48,14 +51,15 @@ #:use-module (gnu packages ssh) #:use-module (gnu packages tls) #:use-module (gnu packages version-control) + #:use-module (gnu packages web) #:use-module (gnu packages wget) #:use-module (ice-9 match)) (define libuv-julia - (let ((commit "1fcc6d66f9df74189c74d3d390f02202bb7db953") - (revision "2")) + (let ((commit "fb3e3364c33ae48c827f6b103e05c3f0e78b79a9") + (revision "3")) ;; When upgrading Julia, also upgrade this. Get the commit from - ;; https://github.com/JuliaLang/julia/blob/v1.5.2/deps/libuv.version + ;; https://github.com/JuliaLang/julia/blob/v1.6.1/deps/libuv.version (package (inherit libuv) (name "libuv-julia") @@ -65,16 +69,10 @@ (uri (git-reference (url "https://github.com/JuliaLang/libuv") (commit commit))) - (file-name (string-append name "-" version "-checkout")) + (file-name (git-file-name name version)) (sha256 (base32 - "040l7f1hk7xyza11sry5cj4fhw05na949865axqqhxnifdvnmfji")))) - (build-system gnu-build-system) - (arguments - (substitute-keyword-arguments (package-arguments libuv) - ((#:phases phases) - `(modify-phases ,phases - (delete 'autogen))))) + "1kqpn19d20aka30h6q5h8lnzyp0vw0xzgx0wm4w2r5j6yf76m2hr")))) (home-page "https://github.com/JuliaLang/libuv")))) (define libunwind-julia @@ -97,7 +95,9 @@ (julia-patch "libunwind-prefer-extbl" "0lr4dafw8qyfh8sw8hhbwkql1dlhqv8px7k81y2l20hhxfgnh2m1") (julia-patch "libunwind-static-arm" - "1jk3bmiw61ypcchqkk1fyg5wh8wpggk574wxyfyaic870zh3lhgq"))))) + "1jk3bmiw61ypcchqkk1fyg5wh8wpggk574wxyfyaic870zh3lhgq") + (julia-patch "libunwind-cfa-rsp" + "1aswjhvysahhldbzh1afbf0hsjxrvs6xidsz2i7s1cjkjbdiia1z"))))) (home-page "https://github.com/JuliaLang/tree/master/deps/"))) (define (julia-patch-url version name) @@ -105,7 +105,7 @@ "/deps/patches/" name ".patch")) (define (julia-patch name sha) - (let ((version "1.5.3")) + (let ((version "1.6.1")) (origin (method url-fetch) (uri (julia-patch-url version name)) (sha256 (base32 sha)) @@ -113,10 +113,10 @@ (define llvm-julia (package - (inherit llvm-9) + (inherit llvm-11) (name "llvm-julia") (source (origin - (inherit (package-source llvm-9)) + (inherit (package-source llvm-11)) ;; Those patches are inside the Julia source repo. ;; They are _not_ Julia specific (https://github.com/julialang/julia#llvm) ;; but they are required to build Julia. @@ -132,37 +132,72 @@ "19spqc3xsazn1xs9gpcgv9ldadfkv49rmc5khl7sf1dlmhgi4602") '("llvm-7.0-D44650" "1h55kkmkiisfj6sk956if2bcj9s0v6n5czn8dxb870vp5nccj3ir") + '("llvm-6.0-DISABLE_ABI_CHECKS" + "014fawd1ba7yckalypfld22zgic87x9nx3cim42zrwygywd36pyg") '("llvm9-D50010-VNCoercion-ni" "1s1d3sjsiq4vxg7ncy5cz56zgy5vcq6ls3iqaiqkvr23wyryqmdx") - '("llvm-exegesis-mingw" - "0ph1cj1j7arvf1xq2xcr7qf9g0cpdl14fincgr67vpi520zvd3vp") - '("llvm-test-plugin-mingw" - "12z738cnahbf6n381im7i0hxp1m6k9hrnfjlmq9sac46nxly9gnj") '("llvm7-revert-D44485" "0f59kq3p3mpwsbmskypbi4zn01l6ig0x7v2rjp08k2r8z8m6fa8n") - '("llvm-8.0-D66657-codegen-degenerate" - "1n1ddx19h90bbpimdyd9dh8fsm6gb93xxyqm4ljkxa1k3cx2vm72") - '("llvm-8.0-D71495-vectorize-freduce" - "1zff08wvji9lnpskk4b3p5zyjsy5hhy23ynxjqlj9dw7jvvfrf0p") - '("llvm-D75072-SCEV-add-type" - "029a3fywsm233vf48mscina24idd50dc75wr70lmimrhwnw27p0z") - '("llvm-9.0-D65174-limit-merge-stores" - "04bff1mnblfj9mxfdwr1qdnw3i3szmp60gnhxwas5y68qg33z6j0") - '("llvm9-D71443-PPC-MC-redef-symbol" - "1c93nv7rgc9jg5mqrnvv08xib1789qvlql94fwggh18mp3b9hbgy") - '("llvm-9.0-D78196" - "08a43hyg7yyqjq2vmfsmppf34xcz60wq6y9zw5fdyhw2h1mcnmns") + '("llvm-11-D75072-SCEV-add-type" + "176xi1lnbnv2rcs05ywhyb7pd0xgmibayvwzksksg44wg2dh8mbx") '("llvm-julia-tsan-custom-as" "0awh40kf6lm4wn1nsjd1bmhfwq7rqj811szanp2xkpspykw9hg9s") - '("llvm-9.0-D85499" - "0vxlr35srvbvihlgrxq15v6dylp90vgi0qahj22j01jgqmdasjkm")))) + '("llvm-D80101" + "1gsdwmgmpbignvqyxcnlprj899259p3dvdznlncd84ss445qgq3j") + '("llvm-D84031" + "0nks9sbk7p0r5gyr0idrmm93a5fmdai8kihz9532dx4zhcvvqbjc") + '("llvm-10-D85553" + "1zjq7j9q2qp56hwkc8yc8f0z7kvam3j7hj8sb7qyd77r255ff78l") + '("llvm-10-unique_function_clang-sa" + "1jys9w2zqk3dasnxqh0qz5ij7rxi6mkgq9pqjsclmamr5169zyan") + ;'("llvm-D88630-clang-cmake" + ; "0rs6s71nqnjkny7i69gqazhqj5jqfdr0bkxs2v5a55sfx8fa1k54") + '("llvm-11-D85313-debuginfo-empty-arange" + "1f672d5385xpgb8yrim8d3b7wg2z1l81agnshm1q61kdvjixqx32") + '("llvm-11-D90722-rtdyld-absolute-relocs" + "0kmnai229yyxkmpk9lxd180mcnhk2i8d87k2sg89gc8as18w10r6") + '("llvm-invalid-addrspacecast-sink" + "1n1b7j4s80vj7x5377aj9vyphmxx1q6bm0chhkxp6zsy3mx3g2ry") + '("llvm-11-D92906-ppc-setjmp" + "0cmd4dsblp7a8m03j16dqxws0ijh55zf4jzzxmj341qxa1gamdp9") + '("llvm-11-PR48458-X86ISelDAGToDAG" + "0vwzvlhsdazhxg4gj8g2f00a4f8qc5cgac23w575xk3pgba1jh6y") + '("llvm-11-D93092-ppc-knownbits" + "1748bypsc7c9lbs3fnkv0kwvch6bn85kj98j4jdaz254ig0wa6xj") + '("llvm-11-D93154-globalisel-as" + "1k5wd4z3pa7zj0gyjkif7viqj906dhqlbb7dc95gig40nbxv6zpj") + '("llvm-11-ppc-half-ctr" + "0piywisfz6cmw3133kz7vzhiqflq2y7igakqxlym0gi8pqylv7w9") + '("llvm-11-ppc-sp-from-bp" + "1wmg3485cx5f9pbykyl3jibk1wwv4w1x30hl4jyfndzr2yh8azf9") + '("llvm-rGb498303066a6-gcc11-header-fix" + "0hkd4rwhvh8g2yh13g29wiwnjpv2yd1hdyiv1ryw8izl25bz9c67") + '("llvm-11-D94813-mergeicmps" + "0cmy0ywkgyrdcvr9bd6pd912lyd4gcsrib4z0v05dwgcdxhk7y29") + '("llvm-11-D94980-CTR-half" + "1yf8cxib3z8hz7zi9n6v2g2c6vpfr4slq9hpx8m8yq8f1jbyw3fw") + '("llvm-11-D94058-sext-atomic-ops" + "1x6p6k6q651z5jcqxx8vj17cxnv196mka7mwn7dpp6c23lwgfdpb") + '("llvm-11-D96283-dagcombine-half" + "0lv4iq2f8qrcz1xyxfic3bcr5p0aqam3a7c6pp6fnw3riixm096k")))) (patch-flags '("-p1")))) (arguments - (substitute-keyword-arguments (package-arguments llvm-9) + (substitute-keyword-arguments (package-arguments llvm-11) + ((#:phases phases) + `(modify-phases ,phases + (add-after 'unpack 'patch-round-two + ;; We have to do the patching in two rounds because we can't + ;; pass '-p1' and '-p2' in the source field. + (lambda* (#:key inputs #:allow-other-keys) + (map (lambda (patchname) + (invoke "patch" patchname "-p2")) + (list "llvm-11-AArch64-FastIsel-bug" + "llvm-11-D97435-AArch64-movaddrreg" + "llvm-11-D97571-AArch64-loh" + "llvm-11-aarch64-addrspace")))))) + ((#:build-type _) "Release") ((#:configure-flags flags) - `(list ;; Taken from NixOS. Only way I could get libLLVM-6.0.so - "-DCMAKE_BUILD_TYPE=Release" - + `(list ;; Build a native compiler and the NVPTX backend (NVIDIA) since ;; Julia insists on it, nothing more. This reduces build times and ;; disk usage. @@ -177,7 +212,22 @@ ;; "-DLLVM_DEFAULT_TARGET_TRIPLE=${stdenv.hostPlatform.config}" ;; "-DLLVM_EXPERIMENTAL_TARGETS_TO_BUILD=WebAssembly" "-DLLVM_ENABLE_DUMP=ON" - "-DLLVM_LINK_LLVM_DYLIB=ON")))))) + "-DLLVM_LINK_LLVM_DYLIB=ON")))) + (inputs + (append + (package-inputs llvm-11) + `(("llvm-11-AArch64-FastIsel-bug" + ,(julia-patch "llvm-11-AArch64-FastIsel-bug" + "1m2vddj1mw4kbij8hbrx82piyy6bvr2x7wwdnlxfaqcm72ipzyh9")) + ("llvm-11-D97435-AArch64-movaddrreg" + ,(julia-patch "llvm-11-D97435-AArch64-movaddrreg" + "10jnavq9ljkj7j2gqj2zd1pwqpqb5zs3zp9h96pmz0djbmxwa86y")) + ("llvm-11-D97571-AArch64-loh" + ,(julia-patch "llvm-11-D97571-AArch64-loh" + "128zcbg1w1j7hngsf7z1a7alc6lig6l2rqgjp6i8nk3k3f842v6n")) + ("llvm-11-aarch64-addrspace" + ,(julia-patch "llvm-11-aarch64-addrspace" + "0ckbzgfirxrf2d5bpinpngp7gnilbjrk0cbdfyl3h6f5v6i6xj6m"))))))) (define-public libwhich (package @@ -223,7 +273,7 @@ libraries. It is also a bit like @code{ldd} and @code{otool -L}.") (define-public julia (package (name "julia") - (version "1.5.3") + (version "1.6.1") (source (origin (method url-fetch) (uri (string-append @@ -231,7 +281,7 @@ libraries. It is also a bit like @code{ldd} and @code{otool -L}.") version "/julia-" version ".tar.gz")) (sha256 (base32 - "1zmim82x9kkdcgn0cdi01hmzi59zbszy1sqlygb86xq4hc1n66dy")) + "1mfzbjyqcmx7wb1sa7qab5fl78yzd7ap088krqbphbwvpn880srn")) (patches (search-patches "julia-SOURCE_DATE_EPOCH-mtime.patch")))) (build-system gnu-build-system) @@ -241,6 +291,10 @@ libraries. It is also a bit like @code{ldd} and @code{otool -L}.") (guix build gnu-build-system) (guix build utils)) + ;; The test suite takes many times longer than building and + ;; can easily fail on smaller machines when they run out of memory. + #:tests? ,(not (target-aarch64?)) + ;; Do not strip binaries to keep support for full backtraces. ;; See https://github.com/JuliaLang/julia/issues/17831 #:strip-binaries? #f @@ -259,14 +313,13 @@ libraries. It is also a bit like @code{ldd} and @code{otool -L}.") (string-join (map (lambda (pkg) (string-append (assoc-ref inputs pkg) "/lib")) - '("arpack-ng" "curl" "dsfmt" + '("curl" "dsfmt" "gmp" "lapack" - "libssh2" "libgit2" + "libssh2" "libnghttp2" "libgit2" "mbedtls" "mpfr" "openblas" "openlibm" "pcre2" - "suitesparse")) - ":")) - #t)) + "suitesparse" "gfortran:lib")) + ":")))) ;; FIXME: Building the documentation requires Julia packages that ;; would be downloaded from the Internet. We should build them in a ;; separate build phase. @@ -304,7 +357,7 @@ libraries. It is also a bit like @code{ldd} and @code{otool -L}.") "$(BUILDDIR)/$(EXENAME)-debug\\$\\(EXE\\): $(DOBJS) $(LLT_debug)")) ;; The REPL must be linked with libuv. - (substitute* "ui/Makefile" + (substitute* "cli/Makefile" (("JLDFLAGS \\+= ") (string-append "JLDFLAGS += " (assoc-ref %build-inputs "libuv") @@ -318,27 +371,99 @@ libraries. It is also a bit like @code{ldd} and @code{otool -L}.") (substitute* "base/client.jl" (("/bin/sh") (which "sh"))) #t)) - (add-before 'build 'fix-precompile - (lambda _ - (substitute* "base/loading.jl" - (("something(Base.active_project(), \"\")") "\"\"")) - #t)) + (add-before 'build 'shared-objects-paths + (lambda* (#:key inputs #:allow-other-keys) + (let ((jlpath + (lambda (pkgname) + (string-append + "stdlib/" pkgname "_jll/src/" pkgname "_jll.jl"))) + (from + (lambda (libname) + (string-append "const " libname " = .*\\.so"))) + (to + (lambda* (pkg libname #:optional libname_jl) + (string-append + "const " (or libname_jl libname) "= \"" + (assoc-ref inputs pkg) "/lib/" libname ".so")))) + (substitute* (jlpath "dSFMT") + (((from "libdSFMT")) (to "dsfmt" "libdSFMT"))) + (substitute* (jlpath "GMP") + (((from "libgmp")) (to "gmp" "libgmp")) + (((from "libgmpxx")) (to "gmp" "libgmpxx"))) + (substitute* (jlpath "libLLVM") + (((from "libLLVM")) (to "llvm" "libLLVM"))) + (substitute* (jlpath "LibCURL") + (((from "libcurl")) (to "curl" "libcurl"))) + (substitute* (jlpath "LibGit2") + (((from "libgit2")) (to "libgit2" "libgit2"))) + (substitute* (jlpath "LibSSH2") + (((from "libssh2")) (to "libssh2" "libssh2"))) + (substitute* (jlpath "LibUV") + (((from "libuv")) (to "libuv" "libuv"))) + (substitute* (jlpath "LibUnwind") + (((from "libunwind")) (to "libunwind" "libunwind"))) + (substitute* (jlpath "MPFR") + (((from "libmpfr")) (to "mpfr" "libmpfr"))) + (substitute* (jlpath "MbedTLS") + ;; For the newer version of mbedtls-apache: + (("libmbedcrypto.so.5") "libmbedcrypto.so.6") + (((from "libmbedcrypto")) (to "mbedtls" "libmbedcrypto")) + (((from "libmbedtls")) (to "mbedtls" "libmbedtls")) + (((from "libmbedx509")) (to "mbedtls" "libmbedx509"))) + (substitute* (jlpath "nghttp2") + (((from "libnghttp2")) (to "libnghttp2" "libnghttp2"))) + (substitute* (jlpath "OpenBLAS") + (((from "libopenblas")) (to "openblas" "libopenblas"))) + (substitute* (jlpath "OpenLibm") + (((from "libopenlibm")) (to "openlibm" "libopenlibm"))) + (substitute* (jlpath "PCRE2") + (((from "libpcre2")) (to "pcre2" "libpcre2" "libpcre2_8"))) + (substitute* (jlpath "SuiteSparse") + (((from "libamd")) (to "suitesparse" "libamd")) + (((from "libbtf")) (to "suitesparse" "libbtf")) + (((from "libcamd")) (to "suitesparse" "libcamd")) + (((from "libccolamd")) (to "suitesparse" "libccolamd")) + (((from "libcholmod")) (to "suitesparse" "libcholmod")) + (((from "libcolamd")) (to "suitesparse" "libcolamd")) + (((from "libklu")) (to "suitesparse" "libklu")) + (((from "libldl")) (to "suitesparse" "libldl")) + (((from "librbio")) (to "suitesparse" "librbio")) + (((from "libspqr")) (to "suitesparse" "libspqr")) + (((from "libsuitesparse")) (to "suitesparse" "libsuitesparse")) + (((from "libsuitesparseconfig")) + (to "suitesparse" "libsuitesparseconfig")) + (((from "libumfpack")) (to "suitesparse" "libumfpack"))) + (substitute* (jlpath "Zlib") + (((from "libz")) (to "zlib" "libz")))) + #t)) + (add-after 'unpack 'adjust-test-suite + (lambda* (#:key inputs #:allow-other-keys) + (let (;(pcre2 (assoc-ref inputs "pcre2")) + (mbedtls-apache (assoc-ref inputs "mbedtls")) + (mpfr (assoc-ref inputs "mpfr")) + (suitesparse (assoc-ref inputs "suitesparse"))) + ;; Some tests only check to see if the input is the correct version. + ;(substitute* "stdlib/PCRE2_jll/test/runtests.jl" + ; (("10.36.0") ,(package-version pcre2))) + (substitute* "stdlib/MbedTLS_jll/test/runtests.jl" + (("2.24.0") ,(package-version mbedtls-apache))) + (substitute* "stdlib/MPFR_jll/test/runtests.jl" + (("4.1.0") ,(package-version mpfr))) + (substitute* "stdlib/SuiteSparse_jll/test/runtests.jl" + (("5004") ,(string-replace-substring + (version-major+minor + (package-version suitesparse)) "." "0"))) + #t))) (add-before 'check 'disable-broken-tests (lambda _ + ;; disabling REPL tests because they require a stdin + ;; There are some read-only precompile issues in the 1.6 series. + ;; https://github.com/JuliaLang/julia/pull/41614 + ;; https://github.com/JuliaLang/julia/issues/41156 (substitute* "test/choosetests.jl" - (("tests = testnames") - ;; Those failings are not deterministic. They depends on the - ;; running order. I think it depends on the number of - ;; runners, disabling it for now - ;; https://github.com/JuliaLang/julia/issues/34330 - "tests = filter(e->!in(e,[\"backtrace\",\"exceptions\",\"precompile\", - \"client\",\"stacktraces\"]), - testnames)")) - ;; 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")) - ;; Dates has a similar bug: + (("skip_tests = \\[\\]") + "skip_tests = [\"REPL\", \"precompile\"]")) + ;; Dates/io tests fail on master when networking is unavailable ;; https://github.com/JuliaLang/julia/issues/34655 (substitute* "stdlib/Dates/test/io.jl" (("\"Dates.Date") "\"Date") @@ -347,11 +472,67 @@ libraries. It is also a bit like @code{ldd} and @code{otool -L}.") ;; https://github.com/JuliaLang/julia/issues/35785 (substitute* "test/file.jl" (("@test dirname\\(t\\) == d") "@test_broken dirname(t) == d")) - ;; Deprecation test fails with --depwarn=no - ;; https://github.com/JuliaLang/julia/issues/37673 - (substitute* "test/Makefile" - (("./runtests.jl") "--depwarn=error ./runtests.jl")) + ;; julia embeds a certificate, we are not doing that + (substitute* "stdlib/MozillaCACerts_jll/test/runtests.jl" + (("@test isfile\\(MozillaCACerts_jll.cacert\\)") + "@test_broken isfile(MozillaCACerts_jll.cacert)")) + ;; since certificate is not present some tests are failing in network option + (substitute* "usr/share/julia/stdlib/v1.6/NetworkOptions/test/runtests.jl" + (("@test isfile\\(bundled_ca_roots\\(\\)\\)") + "@test_broken isfile(bundled_ca_roots())") + (("@test ispath\\(ca_roots_path\\(\\)\\)") + "@test_broken ispath(ca_roots_path())") + (("@test ca_roots_path\\(\\) \\!= bundled_ca_roots\\(\\)") + "@test_broken ca_roots_path() != bundled_ca_roots()")) + ;; Some digraphs are too wide for some terminals during testing. + (substitute* "stdlib/Unicode/test/runtests.jl" + (("test collect\\(graphemes") "test_broken collect(grapemes")) + ;; WARNING: failed to select UTF-8 encoding, using ASCII + ;; Using 'setlocale' doesn't affect the test failures. + ;(setlocale LC_ALL "en_US.utf8") + ;(setenv "LC_ALL" "en_US.utf8") + (substitute* "test/cmdlineargs.jl" + (("test v\\[3") "test_broken v[3") + (("test isempty\\(v\\[3") "test_broken isempty(v[3")) #t)) + (add-before 'install 'symlink-libraries + (lambda* (#:key inputs outputs #:allow-other-keys) + (let ((link + (lambda (pkgname dir pred) + (map (lambda (file) + (unless (file-exists? + (string-append dir (basename file))) + (symlink file (string-append dir (basename file))))) + (find-files (string-append (assoc-ref inputs pkgname) + "/lib") pred))))) + (link "curl" "usr/lib/" "\\.so") ; missing libpthreads libLLVM-11jl + (link "suitesparse" "usr/lib/julia/" "libbtf\\.so") + (link "suitesparse" "usr/lib/julia/" "libklu\\.so") + (link "suitesparse" "usr/lib/julia/" "libldl\\.so") + (link "suitesparse" "usr/lib/julia/" "librbio\\.so") + (link "gmp" "usr/lib/julia/" "libgmpxx\\.so") + (link "libuv" "usr/lib/julia/" "libuv\\.so") + (link "zlib" "usr/lib/julia/" "libz\\.so") + (link "libunwind" "usr/lib/julia/" "libunwind\\.so") + (symlink (string-append (assoc-ref inputs "p7zip") "/bin/7z") + "usr/libexec/7z") + #t))) + (add-after 'install 'symlink-llvm-utf8proc + (lambda* (#:key inputs outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (link + (lambda (pkgname pred) + (map (lambda (file) + (unless (file-exists? + (string-append out "/lib/julia/" + (basename file))) + (symlink file (string-append out "/lib/julia/" + (basename file))))) + (find-files (string-append (assoc-ref inputs pkgname) + "/lib") pred))))) + (link "llvm" "libLLVM-11\\.so") + (link "utf8proc" "libutf8proc\\.so") + #t))) (add-after 'install 'make-wrapper (lambda* (#:key inputs outputs #:allow-other-keys) (let* ((out (assoc-ref outputs "out")) @@ -360,8 +541,7 @@ libraries. It is also a bit like @code{ldd} and @code{otool -L}.") (with-directory-excursion bin (wrap-program program `("JULIA_LOAD_PATH" ":" prefix - ("" "$JULIA_LOAD_PATH"))) - (wrap-program program + ("" "$JULIA_LOAD_PATH")) `("JULIA_DEPOT_PATH" ":" prefix ("" "$JULIA_DEPOT_PATH")))) #t)))) @@ -369,11 +549,14 @@ libraries. It is also a bit like @code{ldd} and @code{otool -L}.") (list (string-append "prefix=" (assoc-ref %outputs "out")) - ;; Passing the MARCH flag is necessary to build binary substitutes for - ;; the supported architectures. + ;; Passing the MARCH or JULIA_CPU_TARGET flag is necessary to build + ;; binary substitutes for the supported architectures. See also + ;; https://docs.julialang.org/en/v1/devdocs/sysimg/#Specifying-multiple-system-image-targets ,(match (or (%current-target-system) (%current-system)) - ("x86_64-linux" "MARCH=x86-64") + ("x86_64-linux" + ;; These are the flags that upstream uses for their binaries. + "JULIA_CPU_TARGET=generic;generic,-cx16,clone_all;sandybridge,-xsaveopt,clone_all;haswell,-rdrnd,base(1)") ("i686-linux" "MARCH=pentium4") ("armhf-linux" "JULIA_CPU_TARGET=armv7-a,neon") ("powerpc64le-linux" "JULIA_CPU_TARGET=pwr8") @@ -382,81 +565,87 @@ libraries. It is also a bit like @code{ldd} and @code{otool -L}.") ;; and also of targeting the builder's architecture. (_ "JULIA_CPU_TARGET=generic")) - "CONFIG_SHELL=bash" ;needed to build bundled libraries - ;; list of "USE_SYSTEM_*" is here: - ;; https://github.com/JuliaLang/julia/blob/v1.3.1/Make.inc + "CONFIG_SHELL=bash -x" ; needed to build bundled libraries + "USE_BINARYBUILDER=0" + ;; list (and order!) of "USE_SYSTEM_*" is here: + ;; https://github.com/JuliaLang/julia/blob/v1.6.0/Make.inc + "USE_SYSTEM_CSL=1" + "USE_SYSTEM_LLVM=1" + "USE_SYSTEM_LIBUNWIND=1" + "USE_SYSTEM_PCRE=1" + "USE_SYSTEM_OPENLIBM=1" "USE_SYSTEM_DSFMT=1" - "USE_SYSTEM_P7ZIP=1" - "USE_SYSTEM_LAPACK=1" "USE_SYSTEM_BLAS=1" - "USE_BLAS64=0" ;needed when USE_SYSTEM_BLAS=1 + "USE_SYSTEM_LAPACK=1" + "USE_SYSTEM_GMP=1" + "USE_SYSTEM_MPFR=1" + "USE_SYSTEM_SUITESPARSE=1" + "USE_SYSTEM_LIBUV=1" + "USE_SYSTEM_UTF8PROC=1" + "USE_SYSTEM_MBEDTLS=1" + "USE_SYSTEM_LIBSSH2=1" + "USE_SYSTEM_NGHTTP2=1" + "USE_SYSTEM_CURL=1" + "USE_SYSTEM_LIBGIT2=1" + "USE_SYSTEM_PATCHELF=1" + "USE_SYSTEM_ZLIB=1" + "USE_SYSTEM_P7ZIP=1" + + "NO_GIT=1" ; build from release tarball. + "USE_BLAS64=0" ; needed when USE_SYSTEM_BLAS=1 "LIBBLAS=-lopenblas" "LIBBLASNAME=libopenblas" - "USE_SYSTEM_SUITESPARSE=1" (string-append "SUITESPARSE_INC=-I " (assoc-ref %build-inputs "suitesparse") "/include") - "USE_GPL_LIBS=1" ;proudly - "USE_SYSTEM_UTF8PROC=1" + "USE_GPL_LIBS=1" ; proudly (string-append "UTF8PROC_INC=" (assoc-ref %build-inputs "utf8proc") "/include") - "USE_SYSTEM_LLVM=1" - "LLVM_VER=9.0.1" + "LLVM_VER=11.0.0" "USE_LLVM_SHLIB=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_MBEDTLS=1" - "USE_SYSTEM_LIBSSH2=1" - "USE_SYSTEM_GMP=1" - "USE_SYSTEM_MPFR=1" - "USE_SYSTEM_ARPACK=1" - "USE_SYSTEM_LIBGIT2=1" - "USE_SYSTEM_ZLIB=1"))) + "/include")))) (inputs - `(("llvm" ,llvm-julia) - ("p7zip" ,p7zip) - ;; 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 + `(("coreutils" ,coreutils) ; for bindings to "mkdir" and the like + ("curl" ,curl-ssh) + ("gfortran" ,gfortran) + ;; required for libgcc_s.so + ("gfortran:lib" ,gfortran "lib") + ("gmp" ,gmp) ("lapack" ,lapack) - ("openblas" ,openblas) ;Julia does not build with Atlas - ("libunwind" ,libunwind-julia) - ("openlibm" ,openlibm) - ("mbedtls" ,mbedtls-apache) - ("curl" ,curl) - ("libgit2" ,libgit2-0.28) + ("libgit2" ,libgit2) + ("libnghttp2" ,nghttp2 "lib") ("libssh2" ,libssh2) - ("fortran" ,gfortran) + ("libunwind" ,libunwind-julia) ("libuv" ,libuv-julia) - ("pcre2" ,pcre2) - ("utf8proc" ,utf8proc) + ("llvm" ,llvm-julia) + ("mbedtls" ,mbedtls-apache) ("mpfr" ,mpfr) + ("openblas" ,openblas) + ("openlibm" ,openlibm) + ("p7zip" ,p7zip) + ;; pcre2-10.35 has a bug with the JIT regex parser: + ;; https://github.com/JuliaLang/julia/issues/40231#issuecomment-812753324 + ("pcre2" ,pcre2-10.36) + ("suitesparse" ,suitesparse) + ("utf8proc" ,utf8proc-2.6.1) ("wget" ,wget) ("which" ,which) ("zlib" ,zlib) - ("gmp" ,gmp) - ("suitesparse" ,suitesparse) ;; Find dependencies versions here: - ;; https://raw.githubusercontent.com/JuliaLang/julia/v1.3.0/deps/Versions.make - ("libwhich" ,libwhich) - ("dsfmt" ,dsfmt))) + ;; https://raw.githubusercontent.com/JuliaLang/julia/v1.6.0/deps/Versions.make + ("dsfmt" ,dsfmt) + ("libwhich" ,libwhich))) (native-inputs - `(("openssl" ,openssl) + `(("nss-certs" ,nss-certs) + ("openssl" ,openssl) ("perl" ,perl) ("patchelf" ,patchelf) ("pkg-config" ,pkg-config) |