From patchwork Sun May 9 21:53:57 2021 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Patchwork-Submitter: Jean-Baptiste Volatier X-Patchwork-Id: 29188 Return-Path: X-Original-To: patchwork@mira.cbaines.net Delivered-To: patchwork@mira.cbaines.net Received: by mira.cbaines.net (Postfix, from userid 113) id 7331727BC81; Mon, 10 May 2021 02:07:23 +0100 (BST) X-Spam-Checker-Version: SpamAssassin 3.4.2 (2018-09-13) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-2.8 required=5.0 tests=BAYES_00,DKIM_SIGNED, MAILING_LIST_MULTI,RCVD_IN_MSPIKE_H4,RCVD_IN_MSPIKE_WL,SPF_HELO_PASS, T_DKIM_INVALID,URIBL_BLOCKED autolearn=unavailable autolearn_force=no version=3.4.2 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id E939527BC82 for ; Mon, 10 May 2021 02:07:17 +0100 (BST) Received: from localhost ([::1]:55630 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1lfuOD-0005fh-48 for patchwork@mira.cbaines.net; Sun, 09 May 2021 21:07:17 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:40484) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1lfu0m-0003CF-Hh for guix-patches@gnu.org; Sun, 09 May 2021 20:43:04 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:45272) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1lfu0k-00070X-IO for guix-patches@gnu.org; Sun, 09 May 2021 20:43:03 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1lfu0k-00025Y-Ek for guix-patches@gnu.org; Sun, 09 May 2021 20:43:02 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#48325] update of julia to 1.6.1 Resent-From: Jean-Baptiste Volatier Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Mon, 10 May 2021 00:43:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: report 48325 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: To: 48325@debbugs.gnu.org X-Debbugs-Original-To: "guix-patches@gnu.org" Received: via spool by submit@debbugs.gnu.org id=B.16206073437982 (code B ref -1); Mon, 10 May 2021 00:43:02 +0000 Received: (at submit) by debbugs.gnu.org; 10 May 2021 00:42:23 +0000 Received: from localhost ([127.0.0.1]:56818 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lfu04-00024d-Od for submit@debbugs.gnu.org; Sun, 09 May 2021 20:42:23 -0400 Received: from lists.gnu.org ([209.51.188.17]:50610) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lfrNd-0004BS-Ef for submit@debbugs.gnu.org; Sun, 09 May 2021 17:54:31 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:46682) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1lfrNc-0005Ms-Si for guix-patches@gnu.org; Sun, 09 May 2021 17:54:29 -0400 Received: from mail-40131.protonmail.ch ([185.70.40.131]:29110) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1lfrNW-000252-FI for guix-patches@gnu.org; Sun, 09 May 2021 17:54:27 -0400 Date: Sun, 09 May 2021 21:53:57 +0000 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=pm.me; s=protonmail; t=1620597253; bh=ai6+QyDRcPJbaiMLdiz3oCn+KuX3rJFOXsf1OoBbOq4=; h=Date:To:From:Reply-To:Subject:From; b=dmydWR0nmDALBrZVq+H1t8iB+45/9pqJi/YVZouOopgdbsksWDE9Aq4MU4YdSJCCv /TM6mEcj9PzllAhtNhy1WNEXAO4Fe33U6uPxrSV1fUekDlzImwRXJBpz3B1OYodlcs UL59TN3I8+IysH4OCXbxiJJ6FozwDFBa95dldMENipHPJZcj4sL8dm0Q2Su67GhDaY 02P6mBxNZa2bkNyLjjWpw/Ed6oNIfaWS8D/AjloHYmOi6Xx8nLud9iChIewJtkuhxu UCYvSZibeEbK5UOmaKclBu2+982DA1URYexbdLAVDnNLkoNjy82HnPTxAP8FixNgIM F0SAUd8/ptmUA== Message-ID: MIME-Version: 1.0 Received-SPF: pass client-ip=185.70.40.131; envelope-from=jbv@pm.me; helo=mail-40131.protonmail.ch X-Spam_score_int: -7 X-Spam_score: -0.8 X-Spam_bar: / X-Spam_report: (-0.8 / 5.0 requ) BAYES_00=-1.9, DKIM_SIGNED=0.1, DKIM_VALID=-0.1, DKIM_VALID_AU=-0.1, DKIM_VALID_EF=-0.1, PDS_OTHER_BAD_TLD=1.997, RCVD_IN_DNSWL_LOW=-0.7, RCVD_IN_MSPIKE_H4=-0.01, RCVD_IN_MSPIKE_WL=-0.01, SPF_HELO_PASS=-0.001, SPF_PASS=-0.001 autolearn=no autolearn_force=no X-Spam_action: no action X-Mailman-Approved-At: Sun, 09 May 2021 20:42:19 -0400 X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-Mailman-Approved-At: Sun, 09 May 2021 21:07:09 -0400 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" Reply-to: Jean-Baptiste Volatier X-ACL-Warn: , Jean-Baptiste Volatier via Guix-patches X-Patchwork-Original-From: Jean-Baptiste Volatier via Guix-patches via From: Jean-Baptiste Volatier X-getmail-retrieved-from-mailbox: Patches Hi ! I would like to submit this patch to update julia to 1.6.1. Best regards, JB. From d0fad0eab1f41420c00cb4d4c233ce7079b58ec3 Mon Sep 17 00:00:00 2001 From: Jean-Baptiste Volatier Date: Sun, 9 May 2021 23:36:03 +0200 Subject: [PATCH] gnu: julia: update to 1.6.1 gnu: openlibm: update to 0.7.4 gnu: pcre2: update to 10.56 gnu: utf8proc: update to 2.6.1 --- gnu/packages/julia.scm | 349 ++++++++++++++++++++++++------------- gnu/packages/maths.scm | 6 +- gnu/packages/pcre.scm | 4 +- gnu/packages/textutils.scm | 21 ++- 4 files changed, 242 insertions(+), 138 deletions(-) diff --git a/gnu/packages/julia.scm b/gnu/packages/julia.scm index 13c9f7baf1..73ccdc80ee 100644 --- a/gnu/packages/julia.scm +++ b/gnu/packages/julia.scm @@ -1,9 +1,10 @@ ;;; 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 ;;; ;;; This file is part of GNU Guix. ;;; @@ -30,6 +31,7 @@ #: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 +50,15 @@ #: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 +71,7 @@ (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 +100,9 @@ (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 +110,7 @@ "/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)) @@ -113,71 +118,77 @@ (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" + "-DCMAKE_BUILD_TYPE=Release" + + ;; Build a native compiler and the NVPTX backend (NVIDIA) since + ;; Julia insists on it, nothing more. This reduces build times and + ;; disk usage. + ,(string-append "-DLLVM_TARGETS_TO_BUILD=" (system->llvm-target)) + "-DLLVM_EXPERIMENTAL_TARGETS_TO_BUILD=NVPTX" - ;; Build a native compiler and the NVPTX backend (NVIDIA) since - ;; Julia insists on it, nothing more. This reduces build times and - ;; disk usage. - ,(string-append "-DLLVM_TARGETS_TO_BUILD=" (system->llvm-target)) - "-DLLVM_EXPERIMENTAL_TARGETS_TO_BUILD=NVPTX" + "-DLLVM_INSTALL_UTILS=ON" + "-DLLVM_BUILD_TESTS=ON" + "-DLLVM_ENABLE_FFI=ON" + "-DLLVM_ENABLE_RTTI=ON" + ;; "-DLLVM_HOST_TRIPLE=${stdenv.hostPlatform.config}" + ;; "-DLLVM_DEFAULT_TARGET_TRIPLE=${stdenv.hostPlatform.config}" + ;; "-DLLVM_EXPERIMENTAL_TARGETS_TO_BUILD=WebAssembly" + "-DLLVM_ENABLE_DUMP=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")) - "-DLLVM_INSTALL_UTILS=ON" - "-DLLVM_BUILD_TESTS=ON" - "-DLLVM_ENABLE_FFI=ON" - "-DLLVM_ENABLE_RTTI=ON" - ;; "-DLLVM_HOST_TRIPLE=${stdenv.hostPlatform.config}" - ;; "-DLLVM_DEFAULT_TARGET_TRIPLE=${stdenv.hostPlatform.config}" - ;; "-DLLVM_EXPERIMENTAL_TARGETS_TO_BUILD=WebAssembly" - "-DLLVM_ENABLE_DUMP=ON" - "-DLLVM_LINK_LLVM_DYLIB=ON")))))) + #t))))))) + (inputs + `(("julia-source" ,(package-source julia)) + ,@(package-inputs llvm-11))))) (define-public libwhich (package @@ -223,7 +234,7 @@ 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 +242,7 @@ 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" @@ -259,12 +268,12 @@ 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")) + "suitesparse" "libfortran")) ":")) #t)) ;; FIXME: Building the documentation requires Julia packages that @@ -304,7 +313,7 @@ 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 +329,82 @@ 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"))) + ;; FAILING: OpenBLAS + (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\"]")) #t)) (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 +413,43 @@ 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 ;; FIXME change build to install + (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")) @@ -371,27 +467,28 @@ 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. - ,(match (or (%current-target-system) - (%current-system)) - ("x86_64-linux" "MARCH=x86-64") - ("i686-linux" "MARCH=pentium4") - ("aarch64-linux" "MARCH=armv8-a") - ;; Prevent errors when querying this package on unsupported - ;; platforms, e.g. when running "guix package --search=" - (_ "MARCH=UNSUPPORTED")) + ;; Passing the MARCH flag is necessary to build binary substitutes for + ;; the supported architectures. + ,(match (or (%current-target-system) + (%current-system)) + ("x86_64-linux" "MARCH=x86-64") + ("i686-linux" "MARCH=pentium4") + ("aarch64-linux" "MARCH=armv8-a") + ;; Prevent errors when querying this package on unsupported + ;; platforms, e.g. when running "guix package --search=" + (_ "MARCH=UNSUPPORTED")) - "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" - "USE_SYSTEM_BLAS=1" - "USE_BLAS64=0" ;needed when USE_SYSTEM_BLAS=1 - "LIBBLAS=-lopenblas" - "LIBBLASNAME=libopenblas" + "CONFIG_SHELL=bash" ;needed to build bundled libraries + ;; list of "USE_SYSTEM_*" is here: + ;; https://github.com/JuliaLang/julia/blob/v1.6.0/Make.inc + "USE_SYSTEM_CSL=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 + "LIBBLAS=-lopenblas" + "LIBBLASNAME=libopenblas" "USE_SYSTEM_SUITESPARSE=1" (string-append "SUITESPARSE_INC=-I " @@ -403,7 +500,7 @@ 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" @@ -416,43 +513,43 @@ 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 + ("coreutils" ,coreutils) ;for bindings to "mkdir" and the like ("lapack" ,lapack) - ("openblas" ,openblas) ;Julia does not build with Atlas + ("openblas" ,openblas) ;Julia does not build with Atlas ("libunwind" ,libunwind-julia) ("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) ("mpfr" ,mpfr) + ("nss-certs" ,nss-certs) ; required to precompile + ("glibc-locales" ,glibc-locales) ("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 + ;; https://raw.githubusercontent.com/JuliaLang/julia/v1.6.0/deps/Versions.make ("libwhich" ,libwhich) ("dsfmt" ,dsfmt))) (native-inputs diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 9f7bdb9bb1..7be5d418e7 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -3959,7 +3959,7 @@ access to BLIS implementations via traditional BLAS routine calls.") (define-public openlibm (package (name "openlibm") - (version "0.6.0") + (version "0.7.4") (source (origin (method git-fetch) @@ -3968,11 +3968,11 @@ access to BLIS implementations via traditional BLAS routine calls.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "08wfchmmr5200fvmn1kwq9byc1fhsq46hn0y5k8scdl74771c7gh")))) + (base32 "1azms0lpxb7vxb3bln5lyz0wpwx6jnzbffkclclpq2v5aiw8d14i")))) (build-system gnu-build-system) (arguments `(#:make-flags - (list (string-append "prefix=" (assoc-ref %outputs "out"))) + (list (string-append "prefix=" (assoc-ref %outputs "out")) "CC=gcc") #:phases ;; no configure script (modify-phases %standard-phases (delete 'configure)) diff --git a/gnu/packages/pcre.scm b/gnu/packages/pcre.scm index ab48168567..42b2052598 100644 --- a/gnu/packages/pcre.scm +++ b/gnu/packages/pcre.scm @@ -89,14 +89,14 @@ POSIX regular expression API.") (define-public pcre2 (package (name "pcre2") - (version "10.35") + (version "10.36") (source (origin (method url-fetch) (uri (string-append "mirror://sourceforge/pcre/pcre2/" version "/pcre2-" version ".tar.bz2")) (sha256 (base32 - "04s6kmk9qdd4rjz477h547j4bx7hfz0yalpvrm381rqc5ghaijww")))) + "0p3699msps07p40g9426lvxa3b41rg7k2fn7qxl2jm0kh4kkkvx9")))) (build-system gnu-build-system) (inputs `(("bzip2" ,bzip2) ("readline" ,readline) diff --git a/gnu/packages/textutils.scm b/gnu/packages/textutils.scm index ab34373705..d82675bf79 100644 --- a/gnu/packages/textutils.scm +++ b/gnu/packages/textutils.scm @@ -63,6 +63,7 @@ #:use-module (gnu packages python-build) #:use-module (gnu packages python-xyz) #:use-module (gnu packages readline) + #:use-module (gnu packages ruby) #:use-module (gnu packages slang) #:use-module (gnu packages web)) @@ -146,7 +147,7 @@ libenca and several charset conversion libraries and tools.") (define-public utf8proc (package (name "utf8proc") - (version "2.5.0") + (version "2.6.1") (source (origin (method git-fetch) @@ -155,7 +156,7 @@ libenca and several charset conversion libraries and tools.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "1xlkazhdnja4lksn5c9nf4bln5gjqa35a8gwlam5r0728w0h83qq")))) + (base32 "1zqc6airkzkssbjxanx5v8blfk90180gc9id0dx8ncs54f1ib8w7")))) (build-system gnu-build-system) (native-inputs (let ((UNICODE_VERSION "13.0.0")) ; defined in data/Makefile @@ -167,6 +168,13 @@ libenca and several charset conversion libraries and tools.") UNICODE_VERSION "/ucd/NormalizationTest.txt")) (sha256 (base32 "07g0ya4f6zfzvpp24ccxkb2yq568kh83gls85rjl950nv5fya3nn")))) + ("DerivedCoreProperties.txt" + ,(origin + (method url-fetch) + (uri (string-append "https://www.unicode.org/Public/" + UNICODE_VERSION "/ucd/DerivedCoreProperties.txt")) + (sha256 + (base32 "0j12x112cd8fpgazkc8izxnhhpia44p1m36ff8yapslxndcmzm55")))) ("GraphemeBreakTest.txt" ,(origin (method url-fetch) @@ -177,10 +185,12 @@ libenca and several charset conversion libraries and tools.") (base32 "07f8rrvcsq4pibdz6zxggxy8w7zjjqyw2ggclqlhalyv45yv7prj")))) ;; For tests. - ("perl" ,perl)))) + ("perl" ,perl) + ("ruby" ,ruby)))) (arguments '(#:make-flags (list "CC=gcc" (string-append "prefix=" (assoc-ref %outputs "out"))) + #:tests? #t #:phases (modify-phases %standard-phases (delete 'configure) @@ -189,10 +199,7 @@ libenca and several charset conversion libraries and tools.") (for-each (lambda (i) (copy-file (assoc-ref inputs i) (string-append "data/" i))) - '("NormalizationTest.txt" "GraphemeBreakTest.txt")) - (substitute* "data/GraphemeBreakTest.txt" - (("÷") "/") - (("×") "+")) + '("NormalizationTest.txt" "DerivedCoreProperties.txt" "GraphemeBreakTest.txt")) #t))))) (home-page "https://juliastrings.github.io/utf8proc/") (synopsis "C library for processing UTF-8 Unicode data") -- 2.31.1