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Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Thu, 13 May 2021 14:12:03 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 48325 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: To: 48325@debbugs.gnu.org Cc: zimon.toutoune@gmail.com, Jean-Baptiste Volatier , =?utf-8?q?Nicol=C3=B2?= Balzarotti , =?utf-8?q?Nicol=C3=B2?= Balzarotti Received: via spool by 48325-submit@debbugs.gnu.org id=B48325.162091509217120 (code B ref 48325); Thu, 13 May 2021 14:12:03 +0000 Received: (at 48325) by debbugs.gnu.org; 13 May 2021 14:11:32 +0000 Received: from localhost ([127.0.0.1]:44001 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lhC3f-0004Rl-Rz for submit@debbugs.gnu.org; Thu, 13 May 2021 10:11:32 -0400 Received: from mail-wr1-f42.google.com ([209.85.221.42]:44547) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lhC3c-0004Qz-De for 48325@debbugs.gnu.org; Thu, 13 May 2021 10:11:21 -0400 Received: by mail-wr1-f42.google.com with SMTP id e7so8509145wrc.11 for <48325@debbugs.gnu.org>; Thu, 13 May 2021 07:11:20 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=from:to:cc:subject:date:message-id:in-reply-to:references :mime-version:content-transfer-encoding; bh=U8T5RRp63ieaVOe4W9Kuu5N5iwqvgz4MrzdUY0fMa/o=; b=fAF+2l6Ar9K+zllTNgnci+oLAu+aOAvqS4cFgh9wc0ViwuXudknL/s7Y8S3c4yAL4s MiqIt/Z/eIEUjwccG66yS2zZtWd/kff8di8vJEDoyC+9v/5nz0HLmEguxYayEEh5/v4g ZgscgTWutalRmGuxM8a+mUoFWXAxGqr6DkuV1c8sjPL9Qi/t84hQVY8kgD/VTycASIFj 5OTJf+5w4rRieRv7IfCzvwvMEAr6+9Y7wPMix2c9yZQQRjSwDl+aJKhHtYzkMK6Qxr5d TcH2neEPjFxktIA5wKiPRq8eOk5NOt4y/qL4gOCmRlaUTvImo314soZjMDET9JYolQjA 6Dyw== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:from:to:cc:subject:date:message-id:in-reply-to :references:mime-version:content-transfer-encoding; bh=U8T5RRp63ieaVOe4W9Kuu5N5iwqvgz4MrzdUY0fMa/o=; b=f7W5SByZoI6+kDyNNrqWKXZMAQ5GTIPMM5t2KzJjJDlpK4JDo9P57ybjTXAg6prweZ Z5PRVgviykwvijmlsKayxivnQxOObdnJLuom+3v+bwGiiT11NrvUMHN4B/aOmA/aR+Yz abw5lU5//XcO3GTGfT6XmmPxZSnxkk3+sTSacw+o172yqArpvh6oYfJ2nGcfQB006jM7 wMZZeRhLo1ApRVnEij291SvEYrxSCSMJey9O7VvTrASseZb4vqFE7cwt4CKEg09JfEdF B9waT35bm4bMUhEHSRN6BLYSeQtHG0iTbWsQ9/0AlV5F1g5u87AclIkmDaGmlhjlG2FD WHZg== X-Gm-Message-State: AOAM5309RbehLSaqhu0E9wpsOaupDVDocReJNcAwMMYND40kU+jvBJLP ff2MAWhSvJt6jM/iuUw715Yr6MG2ZzM= X-Google-Smtp-Source: ABdhPJyNqovmjqZfA9b8vD87K1HNJ6LenzizZPfJNhzXzl/oHPb6F875F+TmZhkJTcFTFo3j5GnzLA== X-Received: by 2002:adf:ffcc:: with SMTP id x12mr52702126wrs.162.1620915074757; Thu, 13 May 2021 07:11:14 -0700 (PDT) Received: from localhost.localdomain ([193.48.40.110]) by smtp.gmail.com with ESMTPSA id m22sm8930044wml.40.2021.05.13.07.11.14 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Thu, 13 May 2021 07:11:14 -0700 (PDT) From: zimoun Date: Thu, 13 May 2021 16:11:04 +0200 Message-Id: <20210513141105.10274-4-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.30.1 In-Reply-To: <20210513141105.10274-1-zimon.toutoune@gmail.com> References: <20210513140818.10217-1-zimon.toutoune@gmail.com> <20210513141105.10274-1-zimon.toutoune@gmail.com> MIME-Version: 1.0 X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-BeenThere: guix-patches@gnu.org List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org Sender: "Guix-patches" X-getmail-retrieved-from-mailbox: Patches From: Jean-Baptiste Volatier * gnu/packages/julia.scm (julia): Update to 1.6.1. [arguments]: XXXX [inputs]: Add nghttp2:lib, Add gfortran:lib, Remove arpack-ng. [native-inputs]: Add nss-certs. Co-Authored-By: Nicolò Balzarotti . Co-Authored-By: zimoun . --- gnu/packages/julia.scm | 292 +++++++++++++++++++++++++++-------------- 1 file changed, 197 insertions(+), 95 deletions(-) diff --git a/gnu/packages/julia.scm b/gnu/packages/julia.scm index 13c9f7baf1..307ac646b3 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 ;;; Copyright © 2016, 2020 Efraim Flashner -;;; Copyright © 2020 Nicolò Balzarotti +;;; Copyright © 2020, 2021 Nicolò Balzarotti ;;; Copyright © 2020 Tim Howes ;;; Copyright © 2020 Tobias Geerinckx-Rice +;;; Copyright © 2021 Jean-Baptiste Volatier +;;; Copyright © 2021 Simon Tournier ;;; ;;; 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/v1.6.0/deps/libuv.version (package (inherit libuv) (name "libuv-julia") @@ -68,7 +72,7 @@ (file-name (string-append name "-" version "-checkout")) (sha256 (base32 - "040l7f1hk7xyza11sry5cj4fhw05na949865axqqhxnifdvnmfji")))) + "1kqpn19d20aka30h6q5h8lnzyp0vw0xzgx0wm4w2r5j6yf76m2hr")))) (build-system gnu-build-system) (arguments (substitute-keyword-arguments (package-arguments libuv) @@ -97,7 +101,9 @@ (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 +111,7 @@ "/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)) @@ -113,52 +119,10 @@ (define llvm-julia (package - (inherit llvm-9) + (inherit llvm-11) (name "llvm-julia") - (source (origin - (inherit (package-source llvm-9)) - ;; 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. - ;; Discussion: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=919628 - (patches - (map (match-lambda - ((name hash) - (julia-patch name hash))) - (list - '("llvm-D27629-AArch64-large_model_6.0.1" - "1qrshmlqvnasdyc158vfn3hnbigqph3lsq7acb9w8lwkpnnm2j4z") - '("llvm8-D34078-vectorize-fdiv" - "19spqc3xsazn1xs9gpcgv9ldadfkv49rmc5khl7sf1dlmhgi4602") - '("llvm-7.0-D44650" - "1h55kkmkiisfj6sk956if2bcj9s0v6n5czn8dxb870vp5nccj3ir") - '("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-julia-tsan-custom-as" - "0awh40kf6lm4wn1nsjd1bmhfwq7rqj811szanp2xkpspykw9hg9s") - '("llvm-9.0-D85499" - "0vxlr35srvbvihlgrxq15v6dylp90vgi0qahj22j01jgqmdasjkm")))) - (patch-flags '("-p1")))) (arguments - (substitute-keyword-arguments (package-arguments llvm-9) + (substitute-keyword-arguments (package-arguments llvm-11) ((#:configure-flags flags) `(list ;; Taken from NixOS. Only way I could get libLLVM-6.0.so "-DCMAKE_BUILD_TYPE=Release" @@ -177,7 +141,61 @@ ;; "-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")) + ((#:phases phases) + `(modify-phases ,phases + ;; applying patches from julia + ;; list of patches can be found in deps/llvm.mk in julia source + (add-after 'unpack 'julia-patches + (lambda* (#:key inputs outputs #:allow-other-keys) + (let ((patch + (lambda (patchname flag) + (invoke "patch" flag "-i" + (string-append + "julia-src/deps/patches/" + patchname + ".patch"))))) + (mkdir-p "julia-src") + (invoke "tar" "xf" + (assoc-ref inputs "julia-source") + "-C" "julia-src" "--strip-components=1") + (map (lambda (patchname) + (patch patchname "-p1")) + (list "llvm-D27629-AArch64-large_model_6.0.1" + "llvm8-D34078-vectorize-fdiv" + "llvm-7.0-D44650" + "llvm-6.0-DISABLE_ABI_CHECKS" + "llvm9-D50010-VNCoercion-ni" + "llvm7-revert-D44485" + "llvm-11-D75072-SCEV-add-type" + "llvm-julia-tsan-custom-as" + "llvm-D80101" + "llvm-D84031" + "llvm-10-D85553" + "llvm-10-unique_function_clang-sa" + "llvm-11-D85313-debuginfo-empty-arange" + "llvm-11-D90722-rtdyld-absolute-relocs" + "llvm-invalid-addrspacecast-sink" + "llvm-11-D92906-ppc-setjmp" + "llvm-11-PR48458-X86ISelDAGToDAG" + "llvm-11-D93092-ppc-knownbits" + "llvm-11-D93154-globalisel-as" + "llvm-11-ppc-half-ctr" + "llvm-11-ppc-sp-from-bp" + "llvm-rGb498303066a6-gcc11-header-fix" + "llvm-11-D94813-mergeicmps" + "llvm-11-D94980-CTR-half" + "llvm-11-D94058-sext-atomic-ops" + "llvm-11-D96283-dagcombine-half")) + (map (lambda (patchname) + (patch patchname "-p2")) + (list "llvm-11-AArch64-FastIsel-bug" + "llvm-11-D97435-AArch64-movaddrreg" + "llvm-11-D97571-AArch64-loh" + "llvm-11-aarch64-addrspace"))))))))) + (inputs + `(("julia-source" ,(package-source julia)) + ,@(package-inputs llvm-11))))) (define-public libwhich (package @@ -223,7 +241,7 @@ 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 @@ -231,9 +249,7 @@ libraries. It is also a bit like @code{ldd} and @code{otool -L}.") version "/julia-" version ".tar.gz")) (sha256 (base32 - "1zmim82x9kkdcgn0cdi01hmzi59zbszy1sqlygb86xq4hc1n66dy")) - (patches - (search-patches "julia-SOURCE_DATE_EPOCH-mtime.patch")))) + "1mfzbjyqcmx7wb1sa7qab5fl78yzd7ap088krqbphbwvpn880srn")))) (build-system gnu-build-system) (arguments `(#:test-target "test" @@ -259,14 +275,13 @@ 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" "libfortran")) + ":")))) ;; 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 +319,7 @@ 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") @@ -320,27 +335,82 @@ 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(), \"\")") "\"\"")) + (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") + (((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-before 'check 'fix-setenv + (lambda* (#:key inputs #:allow-other-keys) + ;; some tests execute julia in an environment that needs to propagate GUIX_LOCPATH + (substitute* "test/cmdlineargs.jl" + (("\"HOME\"\\s=>\\shomedir\\(\\)") + "\"HOME\" => homedir(), \"GUIX_LOCPATH\" => ENV[\"GUIX_LOCPATH\"]")))) (add-before 'check 'disable-broken-tests (lambda _ (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 = \\[\\]") + ;; disabling REPL tests because they require a stdin + ;; disabling tests for MPFR, MbedTLS and SuiteSparse because they only check for hardcoded versions + "skip_tests = [\"REPL\", \"MPFR_jll\", \"MbedTLS_jll\", \"SuiteSparse_jll\"]")) + ;; 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") @@ -349,11 +419,43 @@ 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()")) #t)) + (add-before 'install 'symlink-libraries + (lambda* (#:key inputs outputs #:allow-other-keys) + (let ((link + (lambda (pkgname dir pred) + (map (lambda (file) + (invoke "ln" "-s" file dir)) + (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") + (invoke "ln" "-s" (string-append (assoc-ref inputs "p7zip") "/bin/7z") "usr/bin/") + #t))) + (add-after 'install 'symlink-llvm-utf8proc + (lambda* (#:key inputs outputs #:allow-other-keys) + (let ((link + (lambda (pkgname pred) + (map (lambda (file) + (invoke "ln" "-s" file (string-append (assoc-ref outputs "out") "/lib/julia/"))) + (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")) @@ -384,7 +486,6 @@ libraries. It is also a bit like @code{ldd} and @code{otool -L}.") "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 "USE_SYSTEM_DSFMT=1" "USE_SYSTEM_P7ZIP=1" "USE_SYSTEM_LAPACK=1" @@ -392,6 +493,8 @@ libraries. It is also a bit like @code{ldd} and @code{otool -L}.") "USE_BLAS64=0" ;needed when USE_SYSTEM_BLAS=1 "LIBBLAS=-lopenblas" "LIBBLASNAME=libopenblas" + ;; https://github.com/JuliaLang/julia/blob/v1.6.0/Make.inc + "USE_SYSTEM_CSL=1" "USE_SYSTEM_SUITESPARSE=1" (string-append "SUITESPARSE_INC=-I " @@ -403,7 +506,7 @@ libraries. It is also a bit like @code{ldd} and @code{otool -L}.") (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" @@ -416,22 +519,17 @@ libraries. It is also a bit like @code{ldd} and @code{otool -L}.") "/include") "USE_SYSTEM_PATCHELF=1" "USE_SYSTEM_PCRE=1" + "USE_SYSTEM_NGHTTP2=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"))) (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 - ;; . - ("arpack-ng" ,arpack-ng-3.3.0) - ("coreutils" ,coreutils) ;for bindings to "mkdir" and the like ("lapack" ,lapack) ("openblas" ,openblas) ;Julia does not build with Atlas @@ -439,12 +537,15 @@ libraries. It is also a bit like @code{ldd} and @code{otool -L}.") ("openlibm" ,openlibm) ("mbedtls" ,mbedtls-apache) ("curl" ,curl) - ("libgit2" ,libgit2-0.28) + ("libnghttp2" ,nghttp2 "lib") + ("libgit2" ,libgit2) ("libssh2" ,libssh2) ("fortran" ,gfortran) + ;; required for libgcc_s.so + ("libfortran" ,gfortran "lib") ("libuv" ,libuv-julia) - ("pcre2" ,pcre2) - ("utf8proc" ,utf8proc) + ("pcre2" ,pcre2-10.36) + ("utf8proc" ,utf8proc-2.6.1) ("mpfr" ,mpfr) ("wget" ,wget) ("which" ,which) @@ -452,7 +553,7 @@ libraries. It is also a bit like @code{ldd} and @code{otool -L}.") ("gmp" ,gmp) ("suitesparse" ,suitesparse) ;; Find dependencies versions here: - ;; https://raw.githubusercontent.com/JuliaLang/julia/v1.3.0/deps/Versions.make + ;; https://raw.githubusercontent.com/JuliaLang/julia/v1.6.0/deps/Versions.make ("libwhich" ,libwhich) ("dsfmt" ,dsfmt))) (native-inputs @@ -460,6 +561,7 @@ libraries. It is also a bit like @code{ldd} and @code{otool -L}.") ("perl" ,perl) ("patchelf" ,patchelf) ("pkg-config" ,pkg-config) + ("nss-certs" ,nss-certs) ("python" ,python-2))) (native-search-paths (list (search-path-specification