* [bug#48325] julia-1.6 guix [not found] ` <87pmxzfth8.fsf@guixSD.i-did-not-set--mail-host-address--so-tickle-me> @ 2021-05-10 7:07 ` Nicolò Balzarotti 2021-05-10 11:29 ` Jean-Baptiste Volatier via Guix-patches via 0 siblings, 1 reply; 11+ messages in thread From: Nicolò Balzarotti @ 2021-05-10 7:07 UTC (permalink / raw) To: Jean-Baptiste Volatier; +Cc: 48325 [-- Attachment #1: Type: text/plain, Size: 703 bytes --] I'll forward here the review I sent you privately. I want to add that it built ok. I tried building but julia-benchmarktools and julia-staticarrays are failing. Version 0.7.0 works fine and should work both on 1.6 (tested) and 1.5 (untested) [fn:1] so we should apply it before the julia update. I tried updating StaticArrays, but the build still fails. I opened a bug report here [fn:2]. I attached here the patch, if you can please apply it before yours, apply my suggestions and send the updated patch [fn:1] https://github.com/JuliaCI/BenchmarkTools.jl/blob/e058ff249215671c196f2c24a0a3f401de27b718/test/TrialsTests.jl#L217 [fn:2] https://github.com/JuliaArrays/StaticArrays.jl/issues/912 [-- Warning: decoded text below may be mangled, UTF-8 assumed --] [-- Attachment #2: 0001-gnu-julia-benchmarktools-Update-to-0.7.0.patch --] [-- Type: text/x-patch, Size: 1302 bytes --] From 1376c9103b315492b123eeea1ffc93f81163a809 Mon Sep 17 00:00:00 2001 From: nixo <nicolo@nixo.xyz> Date: Mon, 10 May 2021 08:55:16 +0200 Subject: [PATCH] gnu: julia-benchmarktools: Update to 0.7.0. * gnu/packages/julia-xyz.scm (julia-benchmarktools): Update to 0.7.0. --- gnu/packages/julia-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm index 9812162ce1..04eddbd8b2 100644 --- a/gnu/packages/julia-xyz.scm +++ b/gnu/packages/julia-xyz.scm @@ -76,7 +76,7 @@ be GPU compatible without throwing away the wrapper.") (define-public julia-benchmarktools (package (name "julia-benchmarktools") - (version "0.5.0") + (version "0.7.0") (source (origin (method git-fetch) @@ -85,7 +85,7 @@ be GPU compatible without throwing away the wrapper.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "0nsx21m3i5h22lkgyrmfj6r085va6ag40khwssqs8y7l0wz98lvp")))) + (base32 "000izw9pj7cbh9r35nnwg2ijkb9dpfd5nkl2889b8b2dpsh4fi63")))) (build-system julia-build-system) (propagated-inputs `(("julia-json" ,julia-json))) (home-page "https://github.com/JuliaCI/BenchmarkTools.jl") -- 2.31.1 [-- Attachment #3: Type: text/plain, Size: 4424 bytes --] Nicolò Balzarotti <anothersms@gmail.com> writes: > seems to be ok (applied fine). A few notes about the patch > > [...] >> `(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" > Here it's difficult to see if there are changes, you should undo the > indent edit. If indentation is wrong, it should be fixed in a separate commit. > >> + ;; "-DLLVM_HOST_TRIPLE=${stdenv.hostPlatform.config}" >> + ;; "-DLLVM_DEFAULT_TARGET_TRIPLE=${stdenv.hostPlatform.config}" >> + ;; "-DLLVM_EXPERIMENTAL_TARGETS_TO_BUILD=WebAssembly" > Those seems to be taken from nixos, but is there a reason why are those > commented? > >> + (invoke "patch" flag "-i" (string-append >> "julia-src/deps/patches/" patchname ".patch"))))) > Line too long > >> + (mkdir-p "julia-src") >> + (invoke "tar" "xf" (assoc-ref inputs "julia-source") >> "-C" "julia-src" "--strip-components=1") > DITTO > >> + (map (lambda (patchname) >> + (patch patchname "-p1")) (list >> "llvm-D27629-AArch64-large_model_6.0.1" > Here we can slpit the line before (list > >> >> - "-DLLVM_LINK_LLVM_DYLIB=ON")))))) >> + #t))))))) > Returning #t should not be needed anymore > >> + (inputs >> + `(("julia-source" ,(package-source julia)) >> + ,@(package-inputs llvm-11))))) >> >> - "suitesparse")) >> + "suitesparse" "libfortran")) >> ":")) >> #t)) > We can remove this #t now > >> + (string-append "stdlib/" pkgname "_jll/src/" >> pkgname "_jll.jl"))) > Long line >> + (lambda* (#:key inputs #:allow-other-keys) >> + ;; some tests execute julia in an environment that needs >> to propagate GUIX_LOCPATH > Good catch, I was wondering which ENV variable was needed > >> + (substitute* "test/cmdlineargs.jl" >> + (("\"HOME\"\\s=>\\shomedir\\(\\)") "\"HOME\" => >> homedir(), \"GUIX_LOCPATH\" => ENV[\"GUIX_LOCPATH\"]")) >> #t)) > again, long line and #t >> + (add-before 'install 'symlink-libraries ;; FIXME change >> build to install > What does this comment refer to? >> (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")) >> > Again the indentation stuff > > ^ permalink raw reply related [flat|nested] 11+ messages in thread
* [bug#48325] julia-1.6 guix 2021-05-10 7:07 ` [bug#48325] julia-1.6 guix Nicolò Balzarotti @ 2021-05-10 11:29 ` Jean-Baptiste Volatier via Guix-patches via 2021-05-11 0:07 ` zimoun 0 siblings, 1 reply; 11+ messages in thread From: Jean-Baptiste Volatier via Guix-patches via @ 2021-05-10 11:29 UTC (permalink / raw) To: Nicolò Balzarotti; +Cc: 48325 [-- Attachment #1: Type: text/plain, Size: 566 bytes --] Hi, Find attached the updated patch. I applied your suggestions. Nicolò Balzarotti wrote: >>> - ;; "-DLLVM_HOST_TRIPLE=${stdenv.hostPlatform.config}" >>> - ;; "-DLLVM_DEFAULT_TARGET_TRIPLE=${stdenv.hostPlatform.config}" >>> - ;; "-DLLVM_EXPERIMENTAL_TARGETS_TO_BUILD=WebAssembly" >> Those seems to be taken from nixos, but is there a reason why are those >> commented? No clue, this was already there. >>> build to install >>> >>> What does this comment refer to? Some leftover I forgot to remove. Cheers, jB [-- Warning: decoded text below may be mangled, UTF-8 assumed --] [-- Attachment #2: 0001-gnu-julia-update-to-1.6.1.patch --] [-- Type: text/x-patch; name=0001-gnu-julia-update-to-1.6.1.patch, Size: 30369 bytes --] From e610dacab669ce84fe8f263a01aefff1fe49b6aa Mon Sep 17 00:00:00 2001 From: Jean-Baptiste Volatier <jbv@pm.me> Date: Mon, 10 May 2021 09:57:23 +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: julia-benchmarktools: update to 0.7.0 --- gnu/packages/julia-xyz.scm | 4 +- gnu/packages/julia.scm | 293 +++++++++++++++++++++++++------------ gnu/packages/maths.scm | 6 +- gnu/packages/pcre.scm | 4 +- gnu/packages/textutils.scm | 21 ++- 5 files changed, 219 insertions(+), 109 deletions(-) diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm index db3e3b846d..b6272c0b4d 100644 --- a/gnu/packages/julia-xyz.scm +++ b/gnu/packages/julia-xyz.scm @@ -100,7 +100,7 @@ be GPU compatible without throwing away the wrapper.") (define-public julia-benchmarktools (package (name "julia-benchmarktools") - (version "0.5.0") + (version "0.7.0") (source (origin (method git-fetch) @@ -109,7 +109,7 @@ be GPU compatible without throwing away the wrapper.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "0nsx21m3i5h22lkgyrmfj6r085va6ag40khwssqs8y7l0wz98lvp")))) + (base32 "000izw9pj7cbh9r35nnwg2ijkb9dpfd5nkl2889b8b2dpsh4fi63")))) (build-system julia-build-system) (propagated-inputs `(("julia-json" ,julia-json))) (home-page "https://github.com/JuliaCI/BenchmarkTools.jl") diff --git a/gnu/packages/julia.scm b/gnu/packages/julia.scm index 13c9f7baf1..39627eeed0 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 <rekado@elephly.net> ;;; Copyright © 2016, 2020 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> ;;; ;;; 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)) @@ -113,52 +118,10 @@ (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 +140,61 @@ ;; "-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 +240,7 @@ 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 +248,7 @@ 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 +274,13 @@ 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 +318,7 @@ 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 +334,83 @@ 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\"]")))) (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" @@ -416,43 +519,43 @@ 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 - ;; <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 ("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 ^ permalink raw reply related [flat|nested] 11+ messages in thread
* [bug#48325] julia-1.6 guix 2021-05-10 11:29 ` Jean-Baptiste Volatier via Guix-patches via @ 2021-05-11 0:07 ` zimoun 2021-05-11 9:18 ` Nicolò Balzarotti 0 siblings, 1 reply; 11+ messages in thread From: zimoun @ 2021-05-11 0:07 UTC (permalink / raw) To: Jean-Baptiste Volatier; +Cc: 48325, Nicolò Balzarotti Hi Jean-Baptiste, Thanks for the patch. Here some minor comments. On Mon, 10 May 2021 at 11:29, Jean-Baptiste Volatier <jbv@pm.me> wrote: > From e610dacab669ce84fe8f263a01aefff1fe49b6aa Mon Sep 17 00:00:00 2001 > From: Jean-Baptiste Volatier <jbv@pm.me> > Date: Mon, 10 May 2021 09:57:23 +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: julia-benchmarktools: update to 0.7.0 Please, split this patch. One per update, i.e., 5 patches I guess. > diff --git a/gnu/packages/julia.scm b/gnu/packages/julia.scm > index 13c9f7baf1..39627eeed0 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 <rekado@elephly.net> > ;;; Copyright © 2016, 2020 Efraim Flashner <efraim@flashner.co.il> > -;;; Copyright © 2020 Nicolò Balzarotti <nicolo@nixo.xyz> > +;;; Copyright © 2020, 2021 Nicolò Balzarotti <nicolo@nixo.xyz> Just to be sure, if Nicoló is co-author, it should be worth to add them in the commit message, something like: Co-Authored-By: Nicolò Balzarotti <nicolo@nixo.xyz>. > - (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 +140,61 @@ > ;; "-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"))))))))) I am not convinced by this move of patches from ’source’ to ’phases’. My understanding about the usual way is to let the patch in the source field. Is this move motivated by something special? > - '("arpack-ng" "curl" "dsfmt" I have not read the Julia ChangeLog. Do they remove Arpack? This should be mentioned in the commit message. > + '("curl" "dsfmt" > "gmp" "lapack" > - "libssh2" "libgit2" > + "libssh2" "libnghttp2" "libgit2" Idem for libnghttp2. > "mbedtls" "mpfr" > "openblas" "openlibm" "pcre2" > - "suitesparse")) > - ":")) > - #t)) > + "suitesparse" "libfortran")) Idem for libfortran. > - (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) [...] > + ;; FAILING: OpenBLAS What does it mean? > + (add-before 'install 'symlink-libraries [...] > + (link "zlib" "usr/lib/julia/" "libz\\.so") Does this fix <http://issues.guix.gnu.org/48238> ? If yes, cool and thank you! :-) So it should be mentioned in the commit message, something like: --8<---------------cut here---------------start------------->8--- * gnu: julia: Update to 1.6.1. Fixes <https://bug.gnu.org/48238>. * gnu/packages/julia.scm (julia): Update to 1.6.1. [arguments]: …stuff that changed… [inputs]: Add foo, Remove bar. Co-Authored-By: Nicolò Balzarotti <nicolo@nixo.xyz>. --8<---------------cut here---------------end--------------->8--- Does it make sense? > - "USE_SYSTEM_ARPACK=1" What is the motivation for removing Arpack? Sorry if my question is naive. > "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 > - ;; <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 This is not a change. Even if the new indentation is correct, please let avoid cosmetic change in the same commit updating a complex package. Because then digging in the history becomes more complex. :-) > ("lapack" ,lapack) > - ("openblas" ,openblas) ;Julia does not build with Atlas > + ("openblas" ,openblas) ;Julia does not build with Atlas Idem. > ("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 Hum? Is it really necessary? > + ("glibc-locales" ,glibc-locales) Idem. Is it really necessary? Because it is a “big“ packages which drastically increases the closure size of the Julia package. Thanks again for the patch. Cheers, simon ^ permalink raw reply [flat|nested] 11+ messages in thread
* [bug#48325] julia-1.6 guix 2021-05-11 0:07 ` zimoun @ 2021-05-11 9:18 ` Nicolò Balzarotti 2021-05-11 9:53 ` Nicolò Balzarotti 2021-05-11 9:55 ` zimoun 0 siblings, 2 replies; 11+ messages in thread From: Nicolò Balzarotti @ 2021-05-11 9:18 UTC (permalink / raw) To: zimoun, Jean-Baptiste Volatier; +Cc: 48325 zimoun <zimon.toutoune@gmail.com> writes: > Hi Jean-Baptiste, > > Thanks for the patch. Here some minor comments. > > Please, split this patch. One per update, i.e., 5 patches I guess. > Some changes should probably be committed together since current julia will fail to build with newer deps versions, but at least for utf8proc I'm sure this can be splitted. > Just to be sure, if Nicoló is co-author, it should be worth to add them > in the commit message, something like: > > Co-Authored-By: Nicolò Balzarotti <nicolo@nixo.xyz>. > Yep I helped a bit >> - '("arpack-ng" "curl" "dsfmt" > > I have not read the Julia ChangeLog. Do they remove Arpack? This > should be mentioned in the commit message. Yep, see for example: https://github.com/JuliaLang/julia/commit/0196cf1ff549ac120d8c556d610927d76d679722 > >> + '("curl" "dsfmt" >> "gmp" "lapack" >> - "libssh2" "libgit2" >> + "libssh2" "libnghttp2" "libgit2" > > Idem for libnghttp2. > Yep they added libnghttp2 https://github.com/JuliaLang/julia/blob/bb5b98e72a151c41471d8cc14cacb495d647fb7f/stdlib/nghttp2_jll/src/nghttp2_jll.jl >> "mbedtls" "mpfr" >> "openblas" "openlibm" "pcre2" >> - "suitesparse")) >> - ":")) >> - #t)) >> + "suitesparse" "libfortran")) > > Idem for libfortran. I just realized this is not sorted, would you mind fixing it? Also, there are still a few #t which can be removed (like this one in 'prepare-deps) > >> - (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) > > [...] > >> + ;; FAILING: OpenBLAS > > What does it mean? > I think it's a leftover which can be removed > >> + (add-before 'install 'symlink-libraries > > [...] > >> + (link "zlib" "usr/lib/julia/" "libz\\.so") > > Does this fix > > <http://issues.guix.gnu.org/48238> > > ? > Does it make sense? > I just tried running > cd /gnu/store/fp5by15552ihyppxppigmbxs981rd08h-julia-1.6.1 > find -type f -exec grep '/tmp/guix-build-julia-1.5.3.drv-0' {} \; and it returns nothing. Also, your Pkg.add("GZip"); using GZip worked (but it printed ┌ Error: curl_easy_setopt: 48 └ @ Downloads.Curl ~/guix-build-julia-1.6.1.drv-0/julia-1.6.1/usr/share/julia/stdlib/v1.6/Downloads/src/Curl/utils.jl:36 which might be worth investigating) >> - "USE_SYSTEM_ARPACK=1" > > What is the motivation for removing Arpack? Sorry if my question is > naive. As before, it's no longer used by Julia > >> "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 >> - ;; <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 > > This is not a change. Even if the new indentation is correct, please > let avoid cosmetic change in the same commit updating a complex package. > Because then digging in the history becomes more complex. :-) > Agreed >> + ("nss-certs" ,nss-certs) ; required to precompile > > Hum? Is it really necessary? > I think that the alternative is to disable a few tests. I opened a bug report a few months ago here: https://github.com/JuliaLang/julia/issues/40185 >> + ("glibc-locales" ,glibc-locales) > > Idem. Is it really necessary? Because it is a “big“ packages which > drastically increases the closure size of the Julia package. > I think it's the same as before (fixes a few tests) but I cannot verify this, Jean-Baptiste do you know what breaks when this is removed? > > Thanks again for the patch. > Yep, thanks Jean-Baptiste and Simon for your review Nicolò ^ permalink raw reply [flat|nested] 11+ messages in thread
* [bug#48325] julia-1.6 guix 2021-05-11 9:18 ` Nicolò Balzarotti @ 2021-05-11 9:53 ` Nicolò Balzarotti 2021-05-11 9:55 ` zimoun 1 sibling, 0 replies; 11+ messages in thread From: Nicolò Balzarotti @ 2021-05-11 9:53 UTC (permalink / raw) To: zimoun, Jean-Baptiste Volatier; +Cc: 48325 >> cd /gnu/store/fp5by15552ihyppxppigmbxs981rd08h-julia-1.6.1 >> find -type f -exec grep '/tmp/guix-build-julia-1.5.3.drv-0' {} \; > I just realized I should have run > find -type f -exec grep '/tmp/guix-build-julia-1.6.1.drv-0' {} \; Binary file ./bin/.julia-real matches Binary file ./lib/julia/sys.so matches Binary file ./lib/julia/libccalltest.so.debug matches Binary file ./lib/julia/libjulia-internal.so.1.6 matches Binary file ./lib/julia/libllvmcalltest.so matches Binary file ./lib/libjulia.so.1.6 matches Binary file ./share/julia/base.cache matches ^ permalink raw reply [flat|nested] 11+ messages in thread
* [bug#48325] julia-1.6 guix 2021-05-11 9:18 ` Nicolò Balzarotti 2021-05-11 9:53 ` Nicolò Balzarotti @ 2021-05-11 9:55 ` zimoun 2021-05-11 10:18 ` Nicolò Balzarotti 1 sibling, 1 reply; 11+ messages in thread From: zimoun @ 2021-05-11 9:55 UTC (permalink / raw) To: Nicolò Balzarotti, Jean-Baptiste Volatier; +Cc: 48325 Hi, On Tue, 11 May 2021 at 11:18, Nicolò Balzarotti <anothersms@gmail.com> wrote: > zimoun <zimon.toutoune@gmail.com> writes: >> Please, split this patch. One per update, i.e., 5 patches I guess. > > Some changes should probably be committed together since current julia > will fail to build with newer deps versions, but at least for utf8proc > I'm sure this can be splitted. The issue is that the update of pcre2 is a ’core-updates’ change, IIUC: guix refresh -l pcre2 so the package cannot be simply updated. This one also should be splitted, IMHO. Is the current julia@1.5.3 ’will fail’ for sure or probably ’would fail’ with openlibm@0.7.4 and julia-benchmarktools@0.7.0? I have not tried yet. :-) >>> + (add-before 'install 'symlink-libraries >> >> [...] >> >>> + (link "zlib" "usr/lib/julia/" "libz\\.so") >> >> Does this fix >> >> <http://issues.guix.gnu.org/48238> >> >> ? >> Does it make sense? >> > I just tried running >> cd /gnu/store/fp5by15552ihyppxppigmbxs981rd08h-julia-1.6.1 >> find -type f -exec grep '/tmp/guix-build-julia-1.5.3.drv-0' {} \; > > and it returns nothing. Also, your Pkg.add("GZip"); using GZip worked Cool! > (but it printed > > ┌ Error: curl_easy_setopt: 48 > └ @ Downloads.Curl > ~/guix-build-julia-1.6.1.drv-0/julia-1.6.1/usr/share/julia/stdlib/v1.6/Downloads/src/Curl/utils.jl:36 > > which might be worth investigating) Thanks for trying and reporting. Did you use a --pure or --container environment? >>> + ("nss-certs" ,nss-certs) ; required to precompile >> >> Hum? Is it really necessary? >> > I think that the alternative is to disable a few tests. I opened a bug > report a few months ago here: > https://github.com/JuliaLang/julia/issues/40185 > >>> + ("glibc-locales" ,glibc-locales) >> >> Idem. Is it really necessary? Because it is a “big“ packages which >> drastically increases the closure size of the Julia package. >> > > I think it's the same as before (fixes a few tests) but I cannot verify > this, Jean-Baptiste do you know what breaks when this is removed? Well, ‘guix size glibc-locales’ reports ~922MiB. Although this package is probably already on the store, I would prefer to avoid to add it as an input. Currently, ’guix size julia’ says ~1080MiB. How much with the glibc-locales as inputs? Thanks for the patch and the explanations. Cheers, simon ^ permalink raw reply [flat|nested] 11+ messages in thread
* [bug#48325] julia-1.6 guix 2021-05-11 9:55 ` zimoun @ 2021-05-11 10:18 ` Nicolò Balzarotti 2021-05-11 11:38 ` Jean-Baptiste Volatier via Guix-patches via 2021-05-11 13:13 ` [bug#48325] update of julia to 1.6.1 zimoun 0 siblings, 2 replies; 11+ messages in thread From: Nicolò Balzarotti @ 2021-05-11 10:18 UTC (permalink / raw) To: zimoun, Jean-Baptiste Volatier; +Cc: 48325 [-- Attachment #1: Type: text/plain, Size: 2803 bytes --] zimoun <zimon.toutoune@gmail.com> writes: > Hi, > > On Tue, 11 May 2021 at 11:18, Nicolò Balzarotti <anothersms@gmail.com> wrote: >> zimoun <zimon.toutoune@gmail.com> writes: > >>> Please, split this patch. One per update, i.e., 5 patches I guess. >> >> Some changes should probably be committed together since current julia >> will fail to build with newer deps versions, but at least for utf8proc >> I'm sure this can be splitted. > > The issue is that the update of pcre2 is a ’core-updates’ change, IIUC: > > guix refresh -l pcre2 > > so the package cannot be simply updated. This one also should be > splitted, IMHO. > > Is the current julia@1.5.3 ’will fail’ for sure or probably ’would fail’ > with openlibm@0.7.4 and julia-benchmarktools@0.7.0? I have not tried > yet. :-) > > >>>> + (add-before 'install 'symlink-libraries >>> >>> [...] >>> >>>> + (link "zlib" "usr/lib/julia/" "libz\\.so") >>> >>> Does this fix >>> >>> <http://issues.guix.gnu.org/48238> >>> >>> ? >>> Does it make sense? >>> >> I just tried running >>> cd /gnu/store/fp5by15552ihyppxppigmbxs981rd08h-julia-1.6.1 >>> find -type f -exec grep '/tmp/guix-build-julia-1.5.3.drv-0' {} \; >> >> and it returns nothing. Also, your Pkg.add("GZip"); using GZip worked > > Cool! > >> (but it printed >> >> ┌ Error: curl_easy_setopt: 48 >> └ @ Downloads.Curl >> ~/guix-build-julia-1.6.1.drv-0/julia-1.6.1/usr/share/julia/stdlib/v1.6/Downloads/src/Curl/utils.jl:36 >> >> which might be worth investigating) > > Thanks for trying and reporting. Did you use a --pure or --container > environment? Nope, I just changed home with > HOME=/tmp julia > I tried with a container now: ./pre-inst-env guix environment --ad-hoc julia nss-certs --container export SSL_CERT_DIR=$GUIX_ENVIRONMENT/etc/ssl/certs/ export SSL_CERT_FILE=$GUIX_ENVIRONMENT/etc/ssl/certs/ca-certificates.crt export GIT_SSL_CAINFO="$SSL_CERT_FILE" julia -e 'using Pkg; Pkg.add("GZip"); using GZip' Same error ┌ Error: curl_easy_setopt: 48 └ @ Downloads.Curl /tmp/guix-build-julia-1.6.1.drv-0/julia-1.6.1/usr/share/julia/stdlib/v1.6/Downloads/src/Curl/utils.jl:36 But GZip works (I tried the example on the homepage: import GZip fh = GZip.open("infile.gz") s = readline(fh) close(fh)) > Well, ‘guix size glibc-locales’ reports ~922MiB. Although this package > is probably already on the store, I would prefer to avoid to add it as > an input. Currently, ’guix size julia’ says ~1080MiB. How much with > the glibc-locales as inputs? ./pre-inst-env guix size julia 1205.6 MiB glibc-locales does not appear in the closure size (I attached the output). The biggest change seams to lie in Julia itself (~+130Mb) [-- Attachment #2: size.log --] [-- Type: application/octet-stream, Size: 5129 bytes --] store item total self /gnu/store/xvl59r030h7qc4fdz713x5qj83g6b0px-llvm-julia-11.0.0 332.5 261.1 21.7% /gnu/store/njx8q2cb7hwl289xavhhsrk9in2798js-julia-1.6.1 1205.6 215.1 17.8% /gnu/store/03nf5zlk8lf6xafwn3a0p9s28c9lid27-suitesparse-5.9.0 299.2 171.3 14.2% /gnu/store/rfm558jgb7334zlgywc82fs1jqslql52-gfortran-7.5.0 241.1 122.4 10.2% /gnu/store/rn75fm7adgx3pw5j8pg3bczfqq1y17lk-gcc-7.5.0 178.5 107.3 8.9% /gnu/store/bs9pl1f805ins80xaf4s3n35a0x2lyq3-openblas-0.3.9 187.2 78.0 6.5% /gnu/store/18hp7flyb3yid3yp49i6qcdq0sbi5l1n-guile-3.0.2 132.8 53.2 4.4% /gnu/store/741057r2x06zwg6zcmqmdyv51spm6n9i-gfortran-7.5.0-lib 76.6 38.2 3.2% /gnu/store/fa6wj5bxkj5ll1d7292a70knmyl7a0cr-glibc-2.31 38.4 36.7 3.0% /gnu/store/01b4w3m6mp55y531kyi1g8shh722kwqm-gcc-7.5.0-lib 71.0 32.6 2.7% /gnu/store/jpx83q2s7dhpzjnj93w8zywxb3g7x35i-lapack-3.9.0 120.2 11.0 0.9% /gnu/store/9h9153akbd6g2520mcl2d0vgbvyfi5qm-openssl-1.1.1i 77.4 6.4 0.5% /gnu/store/zzkly5rbfvahwqgcs7crz0ilpi7x5g5p-ncurses-6.2 76.9 5.9 0.5% /gnu/store/198dw01d3mp26ghdxym5hsi60lfynm9m-gnutls-3.6.15 140.8 5.4 0.4% /gnu/store/l3bq4jyvkqwaqsmxb4dsfn4i1q2vdb10-p7zip-16.02 77.4 5.4 0.4% /gnu/store/av65fmjs2iahr25vljpajs2vxhfl7glp-bdb-5.3.28 75.4 4.4 0.4% /gnu/store/q5s876bc5yghh6na3ibvfxlvj6fcj17l-mit-krb5-1.18 76.3 4.3 0.4% /gnu/store/bg69nwbnd8d3nnpgy24ihk2ijq05wnkz-pcre2-10.36 84.0 4.0 0.3% /gnu/store/vdipv3c6f3g429rbbv8aa5m640isilxk-openldap-2.4.50 161.3 3.9 0.3% /gnu/store/vsd9pwimckwsafmf804jrdq020bzwkm8-mbedtls-apache-2.23.0 75.8 3.8 0.3% /gnu/store/61pv34q6kad3cii1pngyairvxbxgdm1n-isl-0.22.1 77.0 3.2 0.3% /gnu/store/35afkywncrr5xsb4cxcljf6rpjcb7f61-gmp-6.2.0 73.8 2.7 0.2% /gnu/store/qc926v75q54k94mwgz6gn4s02sjgrr03-tbb-2020.3 73.4 2.4 0.2% /gnu/store/4i9lvjz9z9j4kj412jpqv4zxjcik9qcb-libunistring-0.9.10 73.4 2.4 0.2% /gnu/store/aqi8ammnbwipg9a1aayrff3yz2ffpgxm-libgit2-1.1.0 95.6 1.9 0.2% /gnu/store/5jf395qa3v4amdi60850rz2a15zlsrza-mpfr-4.0.2 75.6 1.8 0.2% /gnu/store/mmhimfwmmidf09jw1plw3aw1g1zn2nkh-bash-static-5.0.16 1.6 1.6 0.1% /gnu/store/qc3k3kd458pgrqsc7ih641160q81npwq-libgcrypt-1.8.5 74.5 1.5 0.1% /gnu/store/knp4rkdm39ph4brkbzsp07q248nfffi1-readline-8.0.4 78.3 1.4 0.1% /gnu/store/krpyb0zi700dcrg9cc8932w4v0qivdg9-pkg-config-0.29.2 72.3 1.3 0.1% /gnu/store/8w6s8bfy3i6dfka46k4wmgygq310cm6s-curl-7.74.0 162.9 1.1 0.1% /gnu/store/pwcp239kjf7lnj5i4lkdzcfcxwcfyk72-bash-minimal-5.0.16 39.4 1.0 0.1% /gnu/store/fvhj74pghapbjvsvj27skvkra1by1965-bash-minimal-5.0.16 72.0 1.0 0.1% /gnu/store/1dq8cl4i0jhpiysw98gcmw1b5kyv8fwp-openlibm-0.7.4 72.0 1.0 0.1% /gnu/store/9rk1sdzb9lqsi38knfi2pq5gqxfxi8d0-libgpg-error-1.37 73.0 1.0 0.1% /gnu/store/9860f1abqj8wjjnwl8a9v54pdcc3bhgf-xz-5.2.4 73.0 0.9 0.1% /gnu/store/mz5fvdfks10rmwxf29n95bp9bim6wq7g-nettle-3.5.1 74.7 0.9 0.1% /gnu/store/20bgydwiszx3wrdqg7py2lby20dz09bg-cyrus-sasl-2.1.27 84.2 0.9 0.1% /gnu/store/zg126cjicrpm2p6zc08ra5vh4ddag7ww-libgc-8.0.4 71.8 0.8 0.1% /gnu/store/53nfwpng3scv1c7w7smscvq1r4ciax7s-libssh2-1.9.0 75.5 0.7 0.1% /gnu/store/1nfwkl6qbfrac4s6qm0rfaaz2ckgrvmj-metis-5.1.0 71.7 0.7 0.1% /gnu/store/gh15s3j1chndm1lwibf3l9m6x4s26gbp-utf8proc-2.6.1 71.7 0.7 0.1% /gnu/store/g5a71hqhx1i86zvgnwxj6wdpizpz1lxz-libunwind-julia-1.3.1 73.6 0.6 0.1% /gnu/store/5yjp2rlvhjbxn02w5vby35ymrs0fmcjb-gdbm-1.18.1 71.6 0.6 0.0% /gnu/store/pzm72ywfyqv1g0h4571p6zlhg566cwwd-libidn2-2.3.0 73.8 0.5 0.0% /gnu/store/a9f7wmc75hbpg520phw9z4l9asm3qvsw-bzip2-1.0.8 72.5 0.4 0.0% /gnu/store/lgrnkwh7w5yawgqaglwj1pls5vwz1nz7-mpc-1.1.0 76.0 0.4 0.0% /gnu/store/0zawnjiv9aan8spa8vfwl1fwfmkzv5g5-nghttp2-1.41.0-lib 71.4 0.4 0.0% /gnu/store/rnc7x74sdbgaz5nlbnjwabmwkcypknw0-libuv-julia-2.0.0-3.fb3e336 71.4 0.3 0.0% /gnu/store/g2s5jfkfd4k973wb58476b1bbv9zpm6m-zlib-1.2.11 38.6 0.2 0.0% /gnu/store/rykm237xkmq7rl1p0nwass01p090p88x-zlib-1.2.11 71.2 0.2 0.0% /gnu/store/vb12knxd3cdrgnk548l4f6m628ikg8pf-libtasn1-4.16.0 71.2 0.2 0.0% /gnu/store/bw15z9kh9c65ycc2vbhl2izwfwfva7p1-libffi-3.3 71.2 0.2 0.0% /gnu/store/i5a9qb07y9xjh9ry8hp6km43kji16nmd-libltdl-2.4.6 71.2 0.2 0.0% /gnu/store/bbpvh28a0srim3hsrmx0a366i23awyyk-http-parser-2.9.4-1.ec8b5ee 71.1 0.1 0.0% /gnu/store/12y2nvkaqsm5qp04afcva5439zxz9r6z-dsfmt-2.2.3 71.0 0.0 0.0% /gnu/store/z9f5wz66dzgxad673w49c2v06s531i6a-libwhich-1.1.0 71.0 0.0 0.0% total: 1205.6 MiB ^ permalink raw reply [flat|nested] 11+ messages in thread
* [bug#48325] julia-1.6 guix 2021-05-11 10:18 ` Nicolò Balzarotti @ 2021-05-11 11:38 ` Jean-Baptiste Volatier via Guix-patches via 2021-05-12 8:43 ` zimoun 2021-05-11 13:13 ` [bug#48325] update of julia to 1.6.1 zimoun 1 sibling, 1 reply; 11+ messages in thread From: Jean-Baptiste Volatier via Guix-patches via @ 2021-05-11 11:38 UTC (permalink / raw) To: Nicolò Balzarotti; +Cc: 48325, zimoun [-- Attachment #1: Type: text/plain, Size: 2897 bytes --] I splitted the patch in 5. If it is not possible to update pcre2, we only need to disable a couple of tests. zimoun <zimon.toutoune@gmail.com> writes: > I am not convinced by this move of patches from ’source’ to ’phases’. > My understanding about the usual way is to let the patch in the source > field. Is this move motivated by something special? Yes. Some of the patches need to be applied with the "-p1" flag some with "-p2". In the source field it is not possible to do so. So I would need to modify beforehand the "p2" patches for example, and I could not think of a nice way to do that without including the patches directly in gnu/packages/patches which does not seem like a nice option. And since all these patches are in julia source, I thought it was nicer this way. > I have not read the Julia ChangeLog. Do they remove Arpack? This > should be mentioned in the commit message. Yes they did, I updated the commit message. Same with the other new dependencies. >> + (link "zlib" "usr/lib/julia/" "libz\\.so") > Does this fix > > <http://issues.guix.gnu.org/48238> > ? If yes, cool and thank you! :-) So it should be mentioned in the > commit message, something like: No it does not. Reason for this is that the install target of the makefile copies a bunch of libraries from the build directory to the install directory. I guess "normally" you rely on the makefile to also build these libraries for you. In our case many libraries are missing in this folder at the end of the build target so I create the symlinks so the install target works and also julia can later on find the libraries. For some reason utf8proc and libLLVM-11 need to be symlinked directly in the install directory, this is done in the next phase. >> + ("nss-certs" ,nss-certs) ; required to precompile > Hum? Is it really necessary? I think it is necessary for some of the tests. So I moved it to native-inputs is that correct ? >> + ("glibc-locales" ,glibc-locales) > Idem. Is it really necessary? Because it is a “big“ packages which > drastically increases the closure size of the Julia package. It's not! Good find, this was committed inadvertently when I was looking for the reason why some tests were complaining of not finding locales. Turns out that these tests were happening in a julia process started without the GUIX_LOCPATH environment variable. Nicolò Balzarotti <anothersms@gmail.com> wrote: > julia -e 'using Pkg; Pkg.add("GZip"); using GZip' > Same error > ┌ Error: curl_easy_setopt: 48 > └ @ Downloads.Curl /tmp/guix-build-julia-1.6.1.drv-0/julia-1.6.1/usr/share/julia/stdlib/v1.6/Downloads/src/Curl/utils.jl:36 I have the same "bug" here though everything works correctly. I suspect it is due to a mismatch in the libcurl version. Cheers, JB. [-- Warning: decoded text below may be mangled, UTF-8 assumed --] [-- Attachment #2: 0005-gnu-julia-benchmarktools-update-to-0.7.0.patch --] [-- Type: text/x-patch; name=0005-gnu-julia-benchmarktools-update-to-0.7.0.patch, Size: 1251 bytes --] From 57643ede25c2bf860c847f3355295b0e351842a5 Mon Sep 17 00:00:00 2001 From: Jean-Baptiste Volatier <jbv@pm.me> Date: Tue, 11 May 2021 10:52:17 +0200 Subject: [PATCH 5/5] gnu: julia-benchmarktools: update to 0.7.0 --- gnu/packages/julia-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm index db3e3b846d..b6272c0b4d 100644 --- a/gnu/packages/julia-xyz.scm +++ b/gnu/packages/julia-xyz.scm @@ -100,7 +100,7 @@ be GPU compatible without throwing away the wrapper.") (define-public julia-benchmarktools (package (name "julia-benchmarktools") - (version "0.5.0") + (version "0.7.0") (source (origin (method git-fetch) @@ -109,7 +109,7 @@ be GPU compatible without throwing away the wrapper.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "0nsx21m3i5h22lkgyrmfj6r085va6ag40khwssqs8y7l0wz98lvp")))) + (base32 "000izw9pj7cbh9r35nnwg2ijkb9dpfd5nkl2889b8b2dpsh4fi63")))) (build-system julia-build-system) (propagated-inputs `(("julia-json" ,julia-json))) (home-page "https://github.com/JuliaCI/BenchmarkTools.jl") -- 2.31.1 [-- Warning: decoded text below may be mangled, UTF-8 assumed --] [-- Attachment #3: 0001-gnu-utf8proc-update-to-2.6.1.patch --] [-- Type: text/x-patch; name=0001-gnu-utf8proc-update-to-2.6.1.patch, Size: 3369 bytes --] From a49942cd937f049f5ea8479a135ba50894fdeef5 Mon Sep 17 00:00:00 2001 From: Jean-Baptiste Volatier <jbv@pm.me> Date: Tue, 11 May 2021 10:49:56 +0200 Subject: [PATCH 1/5] gnu: utf8proc: update to 2.6.1 --- gnu/packages/textutils.scm | 21 ++++++++++++++------- 1 file changed, 14 insertions(+), 7 deletions(-) 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 [-- Warning: decoded text below may be mangled, UTF-8 assumed --] [-- Attachment #4: 0002-gnu-pcre2-update-to-10.56.patch --] [-- Type: text/x-patch; name=0002-gnu-pcre2-update-to-10.56.patch, Size: 1103 bytes --] From 96ef77bba818f2260646aa78cc4abbd1d69fe063 Mon Sep 17 00:00:00 2001 From: Jean-Baptiste Volatier <jbv@pm.me> Date: Tue, 11 May 2021 10:50:51 +0200 Subject: [PATCH 2/5] gnu: pcre2: update to 10.56 --- gnu/packages/pcre.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) 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) -- 2.31.1 [-- Warning: decoded text below may be mangled, UTF-8 assumed --] [-- Attachment #5: 0003-gnu-openlibm-update-to-0.7.4.patch --] [-- Type: text/x-patch; name=0003-gnu-openlibm-update-to-0.7.4.patch, Size: 1401 bytes --] From 75a196730ef507ec75bcf673005154b6c7e0c2a4 Mon Sep 17 00:00:00 2001 From: Jean-Baptiste Volatier <jbv@pm.me> Date: Tue, 11 May 2021 10:51:11 +0200 Subject: [PATCH 3/5] gnu: openlibm: update to 0.7.4 --- gnu/packages/maths.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) 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)) -- 2.31.1 [-- Warning: decoded text below may be mangled, UTF-8 assumed --] [-- Attachment #6: 0004-gnu-julia-update-to-1.6.1.patch --] [-- Type: text/x-patch; name=0004-gnu-julia-update-to-1.6.1.patch, Size: 24553 bytes --] From 7f380bbc3aac04f274d85b9a79041c6bd8b3c681 Mon Sep 17 00:00:00 2001 From: Jean-Baptiste Volatier <jbv@pm.me> Date: Tue, 11 May 2021 11:04:46 +0200 Subject: [PATCH 4/5] gnu: julia: update to 1.6.1 MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/julia.scm (julia): Update to 1.6.1. [inputs]: Add nghttp2:lib, Add gfortran:lib, Remove arpack-ng [native-inputs]: Add nss-certs Co-Authored-By: Nicolò Balzarotti <nicolo@nixo.xyz>. --- gnu/packages/julia.scm | 287 ++++++++++++++++++++++++++++------------- 1 file changed, 194 insertions(+), 93 deletions(-) diff --git a/gnu/packages/julia.scm b/gnu/packages/julia.scm index 13c9f7baf1..cc178cb935 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 <rekado@elephly.net> ;;; Copyright © 2016, 2020 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> ;;; ;;; 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)) @@ -113,52 +118,10 @@ (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 +140,61 @@ ;; "-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 +240,7 @@ 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 +248,7 @@ 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 +274,13 @@ 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 +318,7 @@ 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 +334,82 @@ 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 +418,43 @@ 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 +485,6 @@ 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 +492,8 @@ 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 +505,7 @@ 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 +518,17 @@ 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 - ;; <https://bugs.gnu.org/30282>. - ("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 @@ -439,9 +536,12 @@ 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) @@ -452,7 +552,7 @@ 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 +560,7 @@ 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 -- 2.31.1 ^ permalink raw reply related [flat|nested] 11+ messages in thread
* [bug#48325] julia-1.6 guix 2021-05-11 11:38 ` Jean-Baptiste Volatier via Guix-patches via @ 2021-05-12 8:43 ` zimoun 0 siblings, 0 replies; 11+ messages in thread From: zimoun @ 2021-05-12 8:43 UTC (permalink / raw) To: Jean-Baptiste Volatier, Nicolò Balzarotti; +Cc: 48325 Hi, On Tue, 11 May 2021 at 11:38, Jean-Baptiste Volatier <jbv@pm.me> wrote: > I splitted the patch in 5. If it is not possible to update pcre2, we only > need to disable a couple of tests. Well, 1 tests are failing, if I am correct. However, I am not sure it is an option to remove this dependency. The package utf8proc leads also to a big rebuild, for instance ’subversion’ which implies a lot. :-) I have not finished yet to test and I should send a patch set today or tomorrow… > zimoun <zimon.toutoune@gmail.com> writes: >> I am not convinced by this move of patches from ’source’ to ’phases’. >> My understanding about the usual way is to let the patch in the source >> field. Is this move motivated by something special? > > Yes. Some of the patches need to be applied with the "-p1" flag some with > "-p2". In the source field it is not possible to do so. So I would > need to modify beforehand the "p2" patches for example, and I could not > think of a nice way to do that without including the patches directly > in gnu/packages/patches which does not seem like a nice option. > And since all these patches are in julia source, I thought it was > nicer this way. …because I am not clear with this, yet. >>> + (link "zlib" "usr/lib/julia/" "libz\\.so") > >> Does this fix >> >> <http://issues.guix.gnu.org/48238> > >> ? If yes, cool and thank you! :-) So it should be mentioned in the >> commit message, something like: > > No it does not. Reason for this is that the install target of the > makefile copies a bunch of libraries from the build directory > to the install directory. I guess "normally" you rely on the makefile > to also build these libraries for you. In our case many libraries are > missing in this folder at the end of the build target > so I create the symlinks so the install target works > and also julia can later on find the libraries. > For some reason utf8proc and libLLVM-11 need to be symlinked directly > in the install directory, this is done in the next phase. Thanks for the explanations. Let discuss that in the aforementioned bug#48238. :-) >>> + ("nss-certs" ,nss-certs) ; required to precompile > >> Hum? Is it really necessary? > > I think it is necessary for some of the tests. So I moved it to > native-inputs is that correct ? Yes, that’s my understanding. Cheers, simon ^ permalink raw reply [flat|nested] 11+ messages in thread
* [bug#48325] update of julia to 1.6.1 2021-05-11 10:18 ` Nicolò Balzarotti 2021-05-11 11:38 ` Jean-Baptiste Volatier via Guix-patches via @ 2021-05-11 13:13 ` zimoun 2021-05-11 13:46 ` Jean-Baptiste Volatier via Guix-patches via 1 sibling, 1 reply; 11+ messages in thread From: zimoun @ 2021-05-11 13:13 UTC (permalink / raw) To: Nicolò Balzarotti; +Cc: Jean-Baptiste Volatier, 48325 Hi Nicolò, On mar., 11 mai 2021 at 12:18, Nicolò Balzarotti <anothersms@gmail.com> wrote: >>>> <http://issues.guix.gnu.org/48238> [...] >>> (but it printed >>> >>> ┌ Error: curl_easy_setopt: 48 >>> └ @ Downloads.Curl >>> ~/guix-build-julia-1.6.1.drv-0/julia-1.6.1/usr/share/julia/stdlib/v1.6/Downloads/src/Curl/utils.jl:36 >>> >>> which might be worth investigating) [...] > Same error > ┌ Error: curl_easy_setopt: 48 > └ @ Downloads.Curl /tmp/guix-build-julia-1.6.1.drv-0/julia-1.6.1/usr/share/julia/stdlib/v1.6/Downloads/src/Curl/utils.jl:36 Soemthing appears to me wrong somewhere. Why does the build directory appear in the output directory? This reference should not appear, IMHO. Applying the last 5 patches, I get (without-tests, just to speedup the feedback :-)): ./pre-inst-env guix build --no-grafts julia --without-tests=julia /gnu/store/xbg7kwpylal63gqqb84185j54ib52aji-julia-1.6.1 find $(./pre-inst-env guix build --no-grafts julia --without-tests=julia) \ -type f -exec grep '/tmp/guix-build-julia-1.6.1' {} \; Fichier binaire /gnu/store/xbg7kwpylal63gqqb84185j54ib52aji-julia-1.6.1/bin/.julia-real correspondant Fichier binaire /gnu/store/xbg7kwpylal63gqqb84185j54ib52aji-julia-1.6.1/lib/julia/libllvmcalltest.so correspondant Fichier binaire /gnu/store/xbg7kwpylal63gqqb84185j54ib52aji-julia-1.6.1/lib/julia/libjulia-internal.so.1.6 correspondant Fichier binaire /gnu/store/xbg7kwpylal63gqqb84185j54ib52aji-julia-1.6.1/lib/julia/libccalltest.so.debug correspondant Fichier binaire /gnu/store/xbg7kwpylal63gqqb84185j54ib52aji-julia-1.6.1/lib/julia/sys.so correspondant Fichier binaire /gnu/store/xbg7kwpylal63gqqb84185j54ib52aji-julia-1.6.1/lib/libjulia.so.1.6 correspondant Fichier binaire /gnu/store/xbg7kwpylal63gqqb84185j54ib52aji-julia-1.6.1/share/julia/base.cache correspondant Well, let first converge to a patch set updating Julia then let discuss if this very same patch set fixes the bug or if the fix will be done in another patch. WDYT? Cheers, simon ^ permalink raw reply [flat|nested] 11+ messages in thread
* [bug#48325] update of julia to 1.6.1 2021-05-11 13:13 ` [bug#48325] update of julia to 1.6.1 zimoun @ 2021-05-11 13:46 ` Jean-Baptiste Volatier via Guix-patches via 0 siblings, 0 replies; 11+ messages in thread From: Jean-Baptiste Volatier via Guix-patches via @ 2021-05-11 13:46 UTC (permalink / raw) To: zimoun; +Cc: 48325, Nicolò Balzarotti zimoun <zimon.toutoune@gmail.com> wrote: >> ┌ Error: curl_easy_setopt: 48 >> └ @ Downloads.Curl /tmp/guix-build-julia-1.6.1.drv-0/julia-1.6.1/usr/share/julia/stdlib/v1.6/Downloads/src/Curl/utils.jl:36 > > Soemthing appears to me wrong somewhere. Why does the build directory > appear in the output directory? This reference should not appear, IMHO. I think this is Julia related, during the build process the code from the stdlib is precompiled in the sysimage and the paths are stored then. I sometimes create custom sysimage to package some julia based apps and I have the same behavior on a non-Guix system. Some info about sysimages [1] from the doc of PackageCompiler, a project that makes it easy to create custom sysimages. That could also be a potential future improvement, make it easy for users to create variants of the julia guix package with different sysimages. That way we can make it much faster to load julia packages that are not part of stdlib, Plots.jl for example. [1] https://julialang.github.io/PackageCompiler.jl/dev/sysimages/#What-is-a-sysimage-1 > Well, let first converge to a patch set updating Julia then let discuss > if this very same patch set fixes the bug or if the fix will be done in > another patch. WDYT? Agreed. Cheers, JB ^ permalink raw reply [flat|nested] 11+ messages in thread
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2021-05-10 7:07 ` [bug#48325] julia-1.6 guix Nicolò Balzarotti
2021-05-10 11:29 ` Jean-Baptiste Volatier via Guix-patches via
2021-05-11 0:07 ` zimoun
2021-05-11 9:18 ` Nicolò Balzarotti
2021-05-11 9:53 ` Nicolò Balzarotti
2021-05-11 9:55 ` zimoun
2021-05-11 10:18 ` Nicolò Balzarotti
2021-05-11 11:38 ` Jean-Baptiste Volatier via Guix-patches via
2021-05-12 8:43 ` zimoun
2021-05-11 13:13 ` [bug#48325] update of julia to 1.6.1 zimoun
2021-05-11 13:46 ` Jean-Baptiste Volatier via Guix-patches via
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