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Resent-From: Jean-Baptiste Volatier Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Sat, 03 Jul 2021 17:43:01 +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: Maxime Devos , Jean-Baptiste Volatier , zimoun , 48325@debbugs.gnu.org, Ludovic =?UTF-8?Q?Court=C3=A8s?= Received: via spool by 48325-submit@debbugs.gnu.org id=B48325.162533414330421 (code B ref 48325); Sat, 03 Jul 2021 17:43:01 +0000 Received: (at 48325) by debbugs.gnu.org; 3 Jul 2021 17:42:23 +0000 Received: from localhost ([127.0.0.1]:39818 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lzjef-0007uM-5a for submit@debbugs.gnu.org; Sat, 03 Jul 2021 13:42:22 -0400 Received: from mail-4316.protonmail.ch ([185.70.43.16]:59985) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lzjeb-0007ts-72 for 48325@debbugs.gnu.org; Sat, 03 Jul 2021 13:42:11 -0400 Date: Sat, 03 Jul 2021 17:41:58 +0000 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=pm.me; s=protonmail; t=1625334122; bh=002+DEioll+luE9jtifkjzy9XGnF7yqbM5L9oJHpVZQ=; h=Date:To:From:Reply-To:Subject:In-Reply-To:References:From; b=LjVUuEaYKPHeApZKlEpy4b0KIYqxGdms/JpV63YiRS8BXUwZ7iN8l6EkEuwp0+H8N /3XbMLFPd7x/QasLUvvYmT5F7y5Zkn+Dg2gjp2nP7DXh4I7D9hD8VUb2ayEriHi1yG r7sB9FokvsP0F+KzVIcuY7SgUnlWpKAKDlJ8P3U0KhQ2jTM99lO9JgRHeh78jjj/aw XMggcZf9uCEFYaTkySuut5RdNssrlKcDslSV6H0hF7pNTjnf2LrOz/lFuES2aN4hWw 2WubXxht7ajsTbJO9C5l55tyjypCTSeeu+vMMl42kPQL0flOcVQ9qXDKZJEY+L3adO ZgMwHmDXv15Kg== Message-ID: <20210703174116.21259-6-jbv@pm.me> In-Reply-To: <20210703174116.21259-1-jbv@pm.me> References: <87pmx0kn5p.fsf_-_@gnu.org> <87zgw2znuf.fsf@guix.i-did-not-set--mail-host-address--so-tickle-me> <86v96ejt4s.fsf@gmail.com> <20210629132128.22249-1-jbv@pm.me> <20210629132128.22249-4-jbv@pm.me> <20210703174116.21259-1-jbv@pm.me> MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable 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+larch=yhetil.org@gnu.org Sender: "Guix-patches" Reply-to: Jean-Baptiste Volatier X-ACL-Warn: , Jean-Baptiste Volatier via Guix-patches From: Jean-Baptiste Volatier via Guix-patches via X-Migadu-Flow: FLOW_IN ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=yhetil.org; s=key1; t=1625334196; h=from:from:sender:sender:reply-to:reply-to:subject:subject:date:date: message-id:message-id:to:to:cc:mime-version:mime-version: content-type:content-type: content-transfer-encoding:content-transfer-encoding:resent-cc: resent-from:resent-sender:resent-message-id:in-reply-to:in-reply-to: references:references:list-id:list-help:list-unsubscribe: list-subscribe:list-post:dkim-signature; bh=002+DEioll+luE9jtifkjzy9XGnF7yqbM5L9oJHpVZQ=; b=ED4Rj96XCSk3r+PGG4p8Hw/Bp+8uLbSqS0LiQ1Diicu0TNylFYZNiDxyXQY2uphR9Victk rRnpzENssLDUfqT5DWFsVJJeqq9tUCaBE5jxP2tTYHF7xChQf2zSBZe1msI0IpwedFWe31 nYIVlrJaN8PQy402DlQI/HdiRlgvBWwcjHt+GBgqQCASNhI86zsflBOegXOlrxz953qnNA 3Hf0kNsh9HLZZyUJjpdhx9940ksNUBK1O2fqcNnvOmJzWl9gNWLcbHhThu1PV2F1G4WPQO xZGxpUgcYJr6VXGUScY52ggUjbgDdDvJzJguxcxAlKb3v+Jyesp679w25noWKQ== ARC-Seal: i=1; s=key1; d=yhetil.org; t=1625334196; a=rsa-sha256; cv=none; b=b++GB4hm+NrkM2pDpVpMmZc7WYzx/j/DEx4amjzzEl89IIXSVllBma8SEFJ+aik+aFSc9B NuEFTCzxUgli68hCBxAC1m4ucBLor9jZJJluOoVhVwL7sIJ0mxrpY6O4Z/uypKk8T3t1q4 w7yW8ZE5I5RwmvuOo1Q19f+cZPITdcKYuJ4KygFDfwqmnN8OgJ1zVd3Cuc5rdh042PEjEo iEN5OALcn8+Qu8v87XA6JXMXpxb80FUad+VVMN6h6/60ZiutvO7Y+VfncCliTsx5vr74k5 41L2SPd4eQ0ZtRyjXpL9jIgd0TTdWKP2fAIq10PRd+0EhN0Ye1aJAg6EjHqtyQ== ARC-Authentication-Results: i=1; aspmx1.migadu.com; dkim=fail ("headers rsa verify failed") header.d=pm.me header.s=protonmail header.b=LjVUuEaY; dmarc=pass (policy=none) header.from=gnu.org; spf=pass (aspmx1.migadu.com: domain of guix-patches-bounces@gnu.org designates 209.51.188.17 as permitted sender) smtp.mailfrom=guix-patches-bounces@gnu.org X-Migadu-Spam-Score: -1.41 Authentication-Results: aspmx1.migadu.com; dkim=fail ("headers rsa verify failed") header.d=pm.me header.s=protonmail header.b=LjVUuEaY; dmarc=pass (policy=none) header.from=gnu.org; spf=pass (aspmx1.migadu.com: domain of guix-patches-bounces@gnu.org designates 209.51.188.17 as permitted sender) smtp.mailfrom=guix-patches-bounces@gnu.org X-Migadu-Queue-Id: B5E3116CDB X-Spam-Score: -1.41 X-Migadu-Scanner: scn1.migadu.com X-TUID: WSLjcU+oXf10 * gnu/packages/julia.scm (julia): Update to 1.6.1. [arguments]<#:phases>: Fixed paths to shared objects in 'shared-objects-paths phase, Fix tests that did not propagate GUIX_LOCPATH in 'fix-setenv, Add symlinks to libs in 'symlink-libraries [arguments]<:make-flags>: Added generic,-cx16 target for better compatibili= ty [inputs]: Add nghttp2:lib, Add gfortran:lib, Add curl-ssh, Remove arpack-ng= . [native-inputs]: Add nss-certs. * gnu/packages/julia.scm (curl-ssh): New variable. * gnu/packages/julia.scm (llvm-julia): Update to 11.0.0 [source]: Move julia specific patches to a julia-patches phase. [arguments]<#:phases>: Apply julia specific patches in 'julia-patches phase Co-Authored-By: Nicol=C3=B2 Balzarotti . Co-Authored-By: zimoun . --- gnu/packages/julia.scm | 353 ++++++++++++++++++++++++++++------------- 1 file changed, 239 insertions(+), 114 deletions(-) diff --git a/gnu/packages/julia.scm b/gnu/packages/julia.scm index 13c9f7baf1..9903bb009b 100644 --- a/gnu/packages/julia.scm +++ b/gnu/packages/julia.scm @@ -1,9 +1,11 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright =C2=A9 2015, 2016, 2017 Ricardo Wurmus ;;; Copyright =C2=A9 2016, 2020 Efraim Flashner -;;; Copyright =C2=A9 2020 Nicol=C3=B2 Balzarotti +;;; Copyright =C2=A9 2020, 2021 Nicol=C3=B2 Balzarotti ;;; Copyright =C2=A9 2020 Tim Howes ;;; Copyright =C2=A9 2020 Tobias Geerinckx-Rice +;;; Copyright =C2=A9 2021 Jean-Baptiste Volatier +;;; Copyright =C2=A9 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" "0lr4dafw8qyfh8sw8hhbwkql1dlhqv8px7k81y2l20hhxfgnh2m= 1") (julia-patch "libunwind-static-arm" - "1jk3bmiw61ypcchqkk1fyg5wh8wpggk574wxyfyaic870zh3lhg= q"))))) + "1jk3bmiw61ypcchqkk1fyg5wh8wpggk574wxyfyaic870zh3lhg= q") + (julia-patch "libunwind-cfa-rsp" + "1aswjhvysahhldbzh1afbf0hsjxrvs6xidsz2i7s1cjkjbdiia1= z"))))) (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/juliala= ng/julia#llvm) - ;; but they are required to build Julia. - ;; Discussion: https://bugs.debian.org/cgi-bin/bugreport.cgi= ?bug=3D919628 - (patches - (map (match-lambda - ((name hash) - (julia-patch name hash))) - (list - '("llvm-D27629-AArch64-large_model_6.0.1" - "1qrshmlqvnasdyc158vfn3hnbigqph3lsq7acb9w8lwkpnnm2j= 4z") - '("llvm8-D34078-vectorize-fdiv" - "19spqc3xsazn1xs9gpcgv9ldadfkv49rmc5khl7sf1dlmhgi46= 02") - '("llvm-7.0-D44650" - "1h55kkmkiisfj6sk956if2bcj9s0v6n5czn8dxb870vp5nccj3= ir") - '("llvm9-D50010-VNCoercion-ni" - "1s1d3sjsiq4vxg7ncy5cz56zgy5vcq6ls3iqaiqkvr23wyryqm= dx") - '("llvm-exegesis-mingw" - "0ph1cj1j7arvf1xq2xcr7qf9g0cpdl14fincgr67vpi520zvd3= vp") - '("llvm-test-plugin-mingw" - "12z738cnahbf6n381im7i0hxp1m6k9hrnfjlmq9sac46nxly9g= nj") - '("llvm7-revert-D44485" - "0f59kq3p3mpwsbmskypbi4zn01l6ig0x7v2rjp08k2r8z8m6fa= 8n") - '("llvm-8.0-D66657-codegen-degenerate" - "1n1ddx19h90bbpimdyd9dh8fsm6gb93xxyqm4ljkxa1k3cx2vm= 72") - '("llvm-8.0-D71495-vectorize-freduce" - "1zff08wvji9lnpskk4b3p5zyjsy5hhy23ynxjqlj9dw7jvvfrf= 0p") - '("llvm-D75072-SCEV-add-type" - "029a3fywsm233vf48mscina24idd50dc75wr70lmimrhwnw27p= 0z") - '("llvm-9.0-D65174-limit-merge-stores" - "04bff1mnblfj9mxfdwr1qdnw3i3szmp60gnhxwas5y68qg33z6= j0") - '("llvm9-D71443-PPC-MC-redef-symbol" - "1c93nv7rgc9jg5mqrnvv08xib1789qvlql94fwggh18mp3b9hb= gy") - '("llvm-9.0-D78196" - "08a43hyg7yyqjq2vmfsmppf34xcz60wq6y9zw5fdyhw2h1mcnm= ns") - '("llvm-julia-tsan-custom-as" - "0awh40kf6lm4wn1nsjd1bmhfwq7rqj811szanp2xkpspykw9hg= 9s") - '("llvm-9.0-D85499" - "0vxlr35srvbvihlgrxq15v6dylp90vgi0qahj22j01jgqmdasj= km")))) - (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=3DRelease" @@ -177,7 +141,61 @@ ;; "-DLLVM_DEFAULT_TARGET_TRIPLE=3D${stdenv.hostPlatform.config= }" ;; "-DLLVM_EXPERIMENTAL_TARGETS_TO_BUILD=3DWebAssembly" "-DLLVM_ENABLE_DUMP=3DON" - "-DLLVM_LINK_LLVM_DYLIB=3DON")))))) + "-DLLVM_LINK_LLVM_DYLIB=3DON")) + ((#: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=3D1") + (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 @@ -220,10 +238,22 @@ libraries. It is also a bit like @code{ldd} and @code{otool -L}.") (license license:expat))) +(define curl-ssh + (package + (inherit curl) + (arguments + (substitute-keyword-arguments (package-arguments curl) + ((#:configure-flags flags) + `(cons "--with-libssh2" ,flags)))) + (inputs + `(("libssh2" ,libssh2) + ,@(package-inputs curl))) + )) + (define-public julia (package (name "julia") - (version "1.5.3") + (version "1.6.1") (source (origin (method url-fetch) (uri (string-append @@ -231,9 +261,7 @@ 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 +287,13 @@ libraries. It is also a bit like @code{ldd} and @cod= e{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 i= n a ;; separate build phase. @@ -304,7 +331,7 @@ 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 \\+=3D ") (string-append "JLDFLAGS +=3D " (assoc-ref %build-inputs "libuv") @@ -320,27 +347,82 @@ libraries. It is also a bit like @code{ldd} and @cod= e{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 " =3D .*\\.so"))) + (to + (lambda* (pkg libname #:optional libname_jl) + (string-append + "const " (or libname_jl libname) "=3D \"" + (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" "libsuitespa= rse")) + (((from "libsuitesparseconfig")) (to "suitesparse" "libsu= itesparseconfig")) + (((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 p= ropagate GUIX_LOCPATH + (substitute* "test/cmdlineargs.jl" + (("\"HOME\"\\s=3D>\\shomedir\\(\\)") + "\"HOME\" =3D> homedir(), \"GUIX_LOCPATH\" =3D> ENV[\"GUIX= _LOCPATH\"]")))) (add-before 'check 'disable-broken-tests (lambda _ (substitute* "test/choosetests.jl" - (("tests =3D 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 =3D 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 =3D \\[\\]") + ;; disabling REPL tests because they require a stdin + ;; disabling tests for MPFR, MbedTLS and SuiteSparse becau= se they only check for hardcoded versions + "skip_tests =3D [\"REPL\", \"MPFR_jll\", \"MbedTLS_jll\", = \"SuiteSparse_jll\"]")) + ;; Dates/io tests fail on master when networking is unavailab= le ;; https://github.com/JuliaLang/julia/issues/34655 (substitute* "stdlib/Dates/test/io.jl" (("\"Dates.Date") "\"Date") @@ -349,11 +431,43 @@ libraries. It is also a bit like @code{ldd} and @cod= e{otool -L}.") ;; https://github.com/JuliaLang/julia/issues/35785 (substitute* "test/file.jl" (("@test dirname\\(t\\) =3D=3D d") "@test_broken dirname(t)= =3D=3D d")) - ;; Deprecation test fails with --depwarn=3Dno - ;; https://github.com/JuliaLang/julia/issues/37673 - (substitute* "test/Makefile" - (("./runtests.jl") "--depwarn=3Derror ./runtests.jl")) + ;; julia embeds a certificate, we are not doing that + (substitute* "stdlib/MozillaCACerts_jll/test/runtests.jl" + (("@test isfile\\(MozillaCACerts_jll.cacert\\)") "@test_bro= ken 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 is= path(ca_roots_path())") + (("@test ca_roots_path\\(\\) \\!=3D bundled_ca_roots\\(\\)"= ) "@test_broken ca_roots_path() !=3D 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 pk= gname) "/lib") pred))))) + (link "curl" "usr/lib/" "\\.so") ;; missing libpthreads lib= LLVM-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 pk= gname) "/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")) @@ -370,7 +484,10 @@ libraries. It is also a bit like @code{ldd} and @code= {otool -L}.") #:make-flags (list (string-append "prefix=3D" (assoc-ref %outputs "out")) - + ;; Adding generic,-cx16 target to the list of defaults target for= better compatibility + ;; clone_all is required otherwise julia complains during compila= tion + ;; see https://docs.julialang.org/en/v1/devdocs/sysimg/#Specifyin= g-multiple-system-image-targets + "JULIA_CPU_TARGET=3Dgeneric;generic,-cx16,clone_all;sandybridge,-= xsaveopt,clone_all;haswell,-rdrnd,base(1)" ;; Passing the MARCH flag is necessary to build binary substitute= s for ;; the supported architectures. ,(match (or (%current-target-system) @@ -382,69 +499,76 @@ libraries. It is also a bit like @code{ldd} and @cod= e{otool -L}.") ;; platforms, e.g. when running "guix package --search=3D= " (_ "MARCH=3DUNSUPPORTED")) - "CONFIG_SHELL=3Dbash" ;needed to build bundled libraries + "CONFIG_SHELL=3Dbash -x" ;needed to build bundled libraries + "USE_BINARYBUILDER=3D0" ;; list of "USE_SYSTEM_*" is here: - ;; https://github.com/JuliaLang/julia/blob/v1.3.1/Make.inc + ;; https://github.com/JuliaLang/julia/blob/v1.6.0/Make.inc + ;; + "USE_SYSTEM_CSL=3D1" + "USE_SYSTEM_LLVM=3D1" + "USE_SYSTEM_LIBUNWIND=3D1" + "USE_SYSTEM_PCRE=3D1" + "USE_SYSTEM_OPENLIBM=3D1" + "USE_SYSTEM_DSFMT=3D1" + "USE_SYSTEM_BLAS=3D1" + "USE_SYSTEM_LAPACK=3D1" + "USE_SYSTEM_GMP=3D1" + "USE_SYSTEM_MPFR=3D1" + "USE_SYSTEM_SUITESPARSE=3D1" + "USE_SYSTEM_LIBUV=3D1" + "USE_SYSTEM_UTF8PROC=3D1" + "USE_SYSTEM_MBEDTLS=3D1" + "USE_SYSTEM_LIBSSH2=3D1" + "USE_SYSTEM_NGHTTP2=3D1" + "USE_SYSTEM_CURL=3D1" + "USE_SYSTEM_LIBGIT2=3D1" + "USE_SYSTEM_PATCHELF=3D1" + "USE_SYSTEM_ZLIB=3D1" + "USE_SYSTEM_P7ZIP=3D1" "USE_SYSTEM_DSFMT=3D1" "USE_SYSTEM_P7ZIP=3D1" "USE_SYSTEM_LAPACK=3D1" - "USE_SYSTEM_BLAS=3D1" + "USE_SYSTEM_CURL=3D1" "USE_BLAS64=3D0" ;needed when USE_SYSTEM_BLAS=3D1 "LIBBLAS=3D-lopenblas" "LIBBLASNAME=3Dlibopenblas" - "USE_SYSTEM_SUITESPARSE=3D1" (string-append "SUITESPARSE_INC=3D-I " (assoc-ref %build-inputs "suitesparse") "/include") + "USE_GPL_LIBS=3D1" ;proudly - "USE_SYSTEM_UTF8PROC=3D1" (string-append "UTF8PROC_INC=3D" (assoc-ref %build-inputs "utf8proc") "/include") - "USE_SYSTEM_LLVM=3D1" - "LLVM_VER=3D9.0.1" + "LLVM_VER=3D11.0.0" "USE_LLVM_SHLIB=3D1" - "USE_SYSTEM_LIBUNWIND=3D1" - "USE_SYSTEM_LIBUV=3D1" (string-append "LIBUV=3D" (assoc-ref %build-inputs "libuv") "/lib/libuv.so") (string-append "LIBUV_INC=3D" (assoc-ref %build-inputs "libuv") - "/include") - "USE_SYSTEM_PATCHELF=3D1" - "USE_SYSTEM_PCRE=3D1" - "USE_SYSTEM_OPENLIBM=3D1" - "USE_SYSTEM_MBEDTLS=3D1" - "USE_SYSTEM_LIBSSH2=3D1" - "USE_SYSTEM_GMP=3D1" - "USE_SYSTEM_MPFR=3D1" - "USE_SYSTEM_ARPACK=3D1" - "USE_SYSTEM_LIBGIT2=3D1" - "USE_SYSTEM_ZLIB=3D1"))) + "/include")))) (inputs `(("llvm" ,llvm-julia) ("p7zip" ,p7zip) - ;; The bundled version is 3.3.0 so stick to that version. With oth= er - ;; 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 ("libunwind" ,libunwind-julia) ("openlibm" ,openlibm) ("mbedtls" ,mbedtls-apache) - ("curl" ,curl) - ("libgit2" ,libgit2-0.28) + ("curl" ,curl-ssh) + ("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 +576,7 @@ 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/Ve= rsions.make + ;; https://raw.githubusercontent.com/JuliaLang/julia/v1.6.0/deps/Ve= rsions.make ("libwhich" ,libwhich) ("dsfmt" ,dsfmt))) (native-inputs @@ -460,6 +584,7 @@ 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 -- 2.32.0