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09/19: gnu: julia: Update to 1.6.1.
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From: |
guix-commits |
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Subject: |
09/19: gnu: julia: Update to 1.6.1. |
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Date: |
Wed, 28 Jul 2021 09:08:21 -0400 (EDT) |
efraim pushed a commit to branch master
in repository guix.
commit 55bb7942486c24524706994336b6068859d599d9
Author: Jean-Baptiste Volatier <jbv@pm.me>
AuthorDate: Sat Jul 3 17:41:58 2021 +0000
gnu: julia: Update to 1.6.1.
* gnu/packages/julia.scm (julia): Update to 1.6.1.
[arguments]: Adjust custom 'prepare-deps phase. Remove custom
'fix-precompile phase. Add new 'shared-objects-path phase to fix paths
to shared objects. Add new 'adjust-test-suite phase to adjust for
differences in bundled vs packaged libraries. Adjust custom
'disable-broken-tests phase for new version. Add symlinks to libs in
'symlink-libraries phase. In make-flags add more finegrained compilation
targets for x86_64-linux. Update make-flags for changes since last
version.
[inputs]: Add nghttp2:lib, gfortran:lib, curl-ssh. Remove arpack-ng,
curl. Sort alphabetically.
[native-inputs]: Add nss-certs. Sort alphabetically.
(libuv-julia): Update to newer revision.
(libunwind-julia)[source]: Add new patch.
(llvm-julia): Inherit from llvm-11.
[source]: Update patch list.
[arguments]: Apply minority of the Julia specific patches in
'julia-patches phase.
[inputs]: Add julia patches.
Co-Authored-By: Nicolò Balzarotti <nicolo@nixo.xyz>.
Co-Authored-By: zimoun <zimon.toutoune@gmail.com>.
Co-Authored-By: Efraim Flashner <efraim@flashner.co.il>.
---
gnu/packages/julia.scm | 414 ++++++++++++++++++++++++++++++++++++-------------
1 file changed, 303 insertions(+), 111 deletions(-)
diff --git a/gnu/packages/julia.scm b/gnu/packages/julia.scm
index abefc38..ca7c1aa 100644
--- a/gnu/packages/julia.scm
+++ b/gnu/packages/julia.scm
@@ -1,9 +1,11 @@
;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2015, 2016, 2017 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2016, 2020, 2021 Efraim Flashner <efraim@flashner.co.il>
-;;; Copyright © 2020 Nicolò Balzarotti <nicolo@nixo.xyz>
+;;; Copyright © 2020, 2021 Nicolò Balzarotti <nicolo@nixo.xyz>
;;; Copyright © 2020 Tim Howes <timhowes@lavabit.com>
;;; Copyright © 2020 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2021 Jean-Baptiste Volatier <jbv@pm.me>
+;;; Copyright © 2021 Simon Tournier <zimon.toutoune@gmail.com>
;;;
;;; This file is part of GNU Guix.
;;;
@@ -30,6 +32,7 @@
#:use-module (gnu packages)
#:use-module (gnu packages algebra)
#:use-module (gnu packages base)
+ #:use-module (gnu packages certs)
#:use-module (gnu packages compression)
#:use-module (gnu packages curl)
#:use-module (gnu packages elf)
@@ -48,14 +51,15 @@
#:use-module (gnu packages ssh)
#:use-module (gnu packages tls)
#:use-module (gnu packages version-control)
+ #:use-module (gnu packages web)
#:use-module (gnu packages wget)
#:use-module (ice-9 match))
(define libuv-julia
- (let ((commit "1fcc6d66f9df74189c74d3d390f02202bb7db953")
- (revision "2"))
+ (let ((commit "fb3e3364c33ae48c827f6b103e05c3f0e78b79a9")
+ (revision "3"))
;; When upgrading Julia, also upgrade this. Get the commit from
- ;; https://github.com/JuliaLang/julia/blob/v1.5.2/deps/libuv.version
+ ;; https://github.com/JuliaLang/julia/blob/v1.6.1/deps/libuv.version
(package
(inherit libuv)
(name "libuv-julia")
@@ -68,7 +72,7 @@
(file-name (string-append name "-" version "-checkout"))
(sha256
(base32
- "040l7f1hk7xyza11sry5cj4fhw05na949865axqqhxnifdvnmfji"))))
+ "1kqpn19d20aka30h6q5h8lnzyp0vw0xzgx0wm4w2r5j6yf76m2hr"))))
(build-system gnu-build-system)
(arguments
(substitute-keyword-arguments (package-arguments libuv)
@@ -97,7 +101,9 @@
(julia-patch "libunwind-prefer-extbl"
"0lr4dafw8qyfh8sw8hhbwkql1dlhqv8px7k81y2l20hhxfgnh2m1")
(julia-patch "libunwind-static-arm"
-
"1jk3bmiw61ypcchqkk1fyg5wh8wpggk574wxyfyaic870zh3lhgq")))))
+ "1jk3bmiw61ypcchqkk1fyg5wh8wpggk574wxyfyaic870zh3lhgq")
+ (julia-patch "libunwind-cfa-rsp"
+
"1aswjhvysahhldbzh1afbf0hsjxrvs6xidsz2i7s1cjkjbdiia1z")))))
(home-page "https://github.com/JuliaLang/tree/master/deps/";)))
(define (julia-patch-url version name)
@@ -105,7 +111,7 @@
"/deps/patches/" name ".patch"))
(define (julia-patch name sha)
- (let ((version "1.5.3"))
+ (let ((version "1.6.1"))
(origin (method url-fetch)
(uri (julia-patch-url version name))
(sha256 (base32 sha))
@@ -113,10 +119,10 @@
(define llvm-julia
(package
- (inherit llvm-9)
+ (inherit llvm-11)
(name "llvm-julia")
(source (origin
- (inherit (package-source llvm-9))
+ (inherit (package-source llvm-11))
;; Those patches are inside the Julia source repo.
;; They are _not_ Julia specific
(https://github.com/julialang/julia#llvm)
;; but they are required to build Julia.
@@ -132,33 +138,69 @@
"19spqc3xsazn1xs9gpcgv9ldadfkv49rmc5khl7sf1dlmhgi4602")
'("llvm-7.0-D44650"
"1h55kkmkiisfj6sk956if2bcj9s0v6n5czn8dxb870vp5nccj3ir")
+ '("llvm-6.0-DISABLE_ABI_CHECKS"
+ "014fawd1ba7yckalypfld22zgic87x9nx3cim42zrwygywd36pyg")
'("llvm9-D50010-VNCoercion-ni"
"1s1d3sjsiq4vxg7ncy5cz56zgy5vcq6ls3iqaiqkvr23wyryqmdx")
- '("llvm-exegesis-mingw"
- "0ph1cj1j7arvf1xq2xcr7qf9g0cpdl14fincgr67vpi520zvd3vp")
- '("llvm-test-plugin-mingw"
- "12z738cnahbf6n381im7i0hxp1m6k9hrnfjlmq9sac46nxly9gnj")
'("llvm7-revert-D44485"
"0f59kq3p3mpwsbmskypbi4zn01l6ig0x7v2rjp08k2r8z8m6fa8n")
- '("llvm-8.0-D66657-codegen-degenerate"
- "1n1ddx19h90bbpimdyd9dh8fsm6gb93xxyqm4ljkxa1k3cx2vm72")
- '("llvm-8.0-D71495-vectorize-freduce"
- "1zff08wvji9lnpskk4b3p5zyjsy5hhy23ynxjqlj9dw7jvvfrf0p")
- '("llvm-D75072-SCEV-add-type"
- "029a3fywsm233vf48mscina24idd50dc75wr70lmimrhwnw27p0z")
- '("llvm-9.0-D65174-limit-merge-stores"
- "04bff1mnblfj9mxfdwr1qdnw3i3szmp60gnhxwas5y68qg33z6j0")
- '("llvm9-D71443-PPC-MC-redef-symbol"
- "1c93nv7rgc9jg5mqrnvv08xib1789qvlql94fwggh18mp3b9hbgy")
- '("llvm-9.0-D78196"
- "08a43hyg7yyqjq2vmfsmppf34xcz60wq6y9zw5fdyhw2h1mcnmns")
+ '("llvm-11-D75072-SCEV-add-type"
+ "176xi1lnbnv2rcs05ywhyb7pd0xgmibayvwzksksg44wg2dh8mbx")
'("llvm-julia-tsan-custom-as"
"0awh40kf6lm4wn1nsjd1bmhfwq7rqj811szanp2xkpspykw9hg9s")
- '("llvm-9.0-D85499"
-
"0vxlr35srvbvihlgrxq15v6dylp90vgi0qahj22j01jgqmdasjkm"))))
+ '("llvm-D80101"
+ "1gsdwmgmpbignvqyxcnlprj899259p3dvdznlncd84ss445qgq3j")
+ '("llvm-D84031"
+ "0nks9sbk7p0r5gyr0idrmm93a5fmdai8kihz9532dx4zhcvvqbjc")
+ '("llvm-10-D85553"
+ "1zjq7j9q2qp56hwkc8yc8f0z7kvam3j7hj8sb7qyd77r255ff78l")
+ '("llvm-10-unique_function_clang-sa"
+ "1jys9w2zqk3dasnxqh0qz5ij7rxi6mkgq9pqjsclmamr5169zyan")
+ ;'("llvm-D88630-clang-cmake"
+ ; "0rs6s71nqnjkny7i69gqazhqj5jqfdr0bkxs2v5a55sfx8fa1k54")
+ '("llvm-11-D85313-debuginfo-empty-arange"
+ "1f672d5385xpgb8yrim8d3b7wg2z1l81agnshm1q61kdvjixqx32")
+ '("llvm-11-D90722-rtdyld-absolute-relocs"
+ "0kmnai229yyxkmpk9lxd180mcnhk2i8d87k2sg89gc8as18w10r6")
+ '("llvm-invalid-addrspacecast-sink"
+ "1n1b7j4s80vj7x5377aj9vyphmxx1q6bm0chhkxp6zsy3mx3g2ry")
+ '("llvm-11-D92906-ppc-setjmp"
+ "0cmd4dsblp7a8m03j16dqxws0ijh55zf4jzzxmj341qxa1gamdp9")
+ '("llvm-11-PR48458-X86ISelDAGToDAG"
+ "0vwzvlhsdazhxg4gj8g2f00a4f8qc5cgac23w575xk3pgba1jh6y")
+ '("llvm-11-D93092-ppc-knownbits"
+ "1748bypsc7c9lbs3fnkv0kwvch6bn85kj98j4jdaz254ig0wa6xj")
+ '("llvm-11-D93154-globalisel-as"
+ "1k5wd4z3pa7zj0gyjkif7viqj906dhqlbb7dc95gig40nbxv6zpj")
+ '("llvm-11-ppc-half-ctr"
+ "0piywisfz6cmw3133kz7vzhiqflq2y7igakqxlym0gi8pqylv7w9")
+ '("llvm-11-ppc-sp-from-bp"
+ "1wmg3485cx5f9pbykyl3jibk1wwv4w1x30hl4jyfndzr2yh8azf9")
+ '("llvm-rGb498303066a6-gcc11-header-fix"
+ "0hkd4rwhvh8g2yh13g29wiwnjpv2yd1hdyiv1ryw8izl25bz9c67")
+ '("llvm-11-D94813-mergeicmps"
+ "0cmy0ywkgyrdcvr9bd6pd912lyd4gcsrib4z0v05dwgcdxhk7y29")
+ '("llvm-11-D94980-CTR-half"
+ "1yf8cxib3z8hz7zi9n6v2g2c6vpfr4slq9hpx8m8yq8f1jbyw3fw")
+ '("llvm-11-D94058-sext-atomic-ops"
+ "1x6p6k6q651z5jcqxx8vj17cxnv196mka7mwn7dpp6c23lwgfdpb")
+ '("llvm-11-D96283-dagcombine-half"
+
"0lv4iq2f8qrcz1xyxfic3bcr5p0aqam3a7c6pp6fnw3riixm096k"))))
(patch-flags '("-p1"))))
(arguments
- (substitute-keyword-arguments (package-arguments llvm-9)
+ (substitute-keyword-arguments (package-arguments llvm-11)
+ ((#:phases phases)
+ `(modify-phases ,phases
+ (add-after 'unpack 'patch-round-two
+ ;; We have to do the patching in two rounds because we can't
+ ;; pass '-p1' and '-p2' in the source field.
+ (lambda* (#:key inputs #:allow-other-keys)
+ (map (lambda (patchname)
+ (invoke "patch" patchname "-p2"))
+ (list "llvm-11-AArch64-FastIsel-bug"
+ "llvm-11-D97435-AArch64-movaddrreg"
+ "llvm-11-D97571-AArch64-loh"
+ "llvm-11-aarch64-addrspace"))))))
((#:configure-flags flags)
`(list ;; Taken from NixOS. Only way I could get libLLVM-6.0.so
"-DCMAKE_BUILD_TYPE=Release"
@@ -177,7 +219,22 @@
;; "-DLLVM_DEFAULT_TARGET_TRIPLE=${stdenv.hostPlatform.config}"
;; "-DLLVM_EXPERIMENTAL_TARGETS_TO_BUILD=WebAssembly"
"-DLLVM_ENABLE_DUMP=ON"
- "-DLLVM_LINK_LLVM_DYLIB=ON"))))))
+ "-DLLVM_LINK_LLVM_DYLIB=ON"))))
+ (inputs
+ (append
+ (package-inputs llvm-11)
+ `(("llvm-11-AArch64-FastIsel-bug"
+ ,(julia-patch "llvm-11-AArch64-FastIsel-bug"
+
"1m2vddj1mw4kbij8hbrx82piyy6bvr2x7wwdnlxfaqcm72ipzyh9"))
+ ("llvm-11-D97435-AArch64-movaddrreg"
+ ,(julia-patch "llvm-11-D97435-AArch64-movaddrreg"
+
"10jnavq9ljkj7j2gqj2zd1pwqpqb5zs3zp9h96pmz0djbmxwa86y"))
+ ("llvm-11-D97571-AArch64-loh"
+ ,(julia-patch "llvm-11-D97571-AArch64-loh"
+
"128zcbg1w1j7hngsf7z1a7alc6lig6l2rqgjp6i8nk3k3f842v6n"))
+ ("llvm-11-aarch64-addrspace"
+ ,(julia-patch "llvm-11-aarch64-addrspace"
+
"0ckbzgfirxrf2d5bpinpngp7gnilbjrk0cbdfyl3h6f5v6i6xj6m")))))))
(define-public libwhich
(package
@@ -223,7 +280,7 @@ libraries. It is also a bit like @code{ldd} and
@code{otool -L}.")
(define-public julia
(package
(name "julia")
- (version "1.5.3")
+ (version "1.6.1")
(source (origin
(method url-fetch)
(uri (string-append
@@ -231,7 +288,7 @@ libraries. It is also a bit like @code{ldd} and
@code{otool -L}.")
version "/julia-" version ".tar.gz"))
(sha256
(base32
- "1zmim82x9kkdcgn0cdi01hmzi59zbszy1sqlygb86xq4hc1n66dy"))
+ "1mfzbjyqcmx7wb1sa7qab5fl78yzd7ap088krqbphbwvpn880srn"))
(patches
(search-patches "julia-SOURCE_DATE_EPOCH-mtime.patch"))))
(build-system gnu-build-system)
@@ -259,14 +316,13 @@ libraries. It is also a bit like @code{ldd} and
@code{otool -L}.")
(string-join (map (lambda (pkg)
(string-append (assoc-ref inputs pkg)
"/lib"))
- '("arpack-ng" "curl" "dsfmt"
+ '("curl" "dsfmt"
"gmp" "lapack"
- "libssh2" "libgit2"
+ "libssh2" "libnghttp2" "libgit2"
"mbedtls" "mpfr"
"openblas" "openlibm" "pcre2"
- "suitesparse"))
- ":"))
- #t))
+ "suitesparse" "gfortran:lib"))
+ ":"))))
;; FIXME: Building the documentation requires Julia packages that
;; would be downloaded from the Internet. We should build them in a
;; separate build phase.
@@ -304,7 +360,7 @@ 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 +376,99 @@ libraries. It is also a bit like @code{ldd} and
@code{otool -L}.")
(substitute* "base/client.jl"
(("/bin/sh") (which "sh")))
#t))
- (add-before 'build 'fix-precompile
- (lambda _
- (substitute* "base/loading.jl"
- (("something(Base.active_project(), \"\")") "\"\""))
- #t))
+ (add-before 'build 'shared-objects-paths
+ (lambda* (#:key inputs #:allow-other-keys)
+ (let ((jlpath
+ (lambda (pkgname)
+ (string-append
+ "stdlib/" pkgname "_jll/src/" pkgname "_jll.jl")))
+ (from
+ (lambda (libname)
+ (string-append "const " libname " = .*\\.so")))
+ (to
+ (lambda* (pkg libname #:optional libname_jl)
+ (string-append
+ "const " (or libname_jl libname) "= \""
+ (assoc-ref inputs pkg) "/lib/" libname ".so"))))
+ (substitute* (jlpath "dSFMT")
+ (((from "libdSFMT")) (to "dsfmt" "libdSFMT")))
+ (substitute* (jlpath "GMP")
+ (((from "libgmp")) (to "gmp" "libgmp"))
+ (((from "libgmpxx")) (to "gmp" "libgmpxx")))
+ (substitute* (jlpath "libLLVM")
+ (((from "libLLVM")) (to "llvm" "libLLVM")))
+ (substitute* (jlpath "LibCURL")
+ (((from "libcurl")) (to "curl" "libcurl")))
+ (substitute* (jlpath "LibGit2")
+ (((from "libgit2")) (to "libgit2" "libgit2")))
+ (substitute* (jlpath "LibSSH2")
+ (((from "libssh2")) (to "libssh2" "libssh2")))
+ (substitute* (jlpath "LibUV")
+ (((from "libuv")) (to "libuv" "libuv")))
+ (substitute* (jlpath "LibUnwind")
+ (((from "libunwind")) (to "libunwind" "libunwind")))
+ (substitute* (jlpath "MPFR")
+ (((from "libmpfr")) (to "mpfr" "libmpfr")))
+ (substitute* (jlpath "MbedTLS")
+ ;; For the newer version of mbedtls-apache:
+ (("libmbedcrypto.so.5") "libmbedcrypto.so.6")
+ (((from "libmbedcrypto")) (to "mbedtls" "libmbedcrypto"))
+ (((from "libmbedtls")) (to "mbedtls" "libmbedtls"))
+ (((from "libmbedx509")) (to "mbedtls" "libmbedx509")))
+ (substitute* (jlpath "nghttp2")
+ (((from "libnghttp2")) (to "libnghttp2" "libnghttp2")))
+ (substitute* (jlpath "OpenBLAS")
+ (((from "libopenblas")) (to "openblas" "libopenblas")))
+ (substitute* (jlpath "OpenLibm")
+ (((from "libopenlibm")) (to "openlibm" "libopenlibm")))
+ (substitute* (jlpath "PCRE2")
+ (((from "libpcre2")) (to "pcre2" "libpcre2" "libpcre2_8")))
+ (substitute* (jlpath "SuiteSparse")
+ (((from "libamd")) (to "suitesparse" "libamd"))
+ (((from "libbtf")) (to "suitesparse" "libbtf"))
+ (((from "libcamd")) (to "suitesparse" "libcamd"))
+ (((from "libccolamd")) (to "suitesparse" "libccolamd"))
+ (((from "libcholmod")) (to "suitesparse" "libcholmod"))
+ (((from "libcolamd")) (to "suitesparse" "libcolamd"))
+ (((from "libklu")) (to "suitesparse" "libklu"))
+ (((from "libldl")) (to "suitesparse" "libldl"))
+ (((from "librbio")) (to "suitesparse" "librbio"))
+ (((from "libspqr")) (to "suitesparse" "libspqr"))
+ (((from "libsuitesparse")) (to "suitesparse"
"libsuitesparse"))
+ (((from "libsuitesparseconfig"))
+ (to "suitesparse" "libsuitesparseconfig"))
+ (((from "libumfpack")) (to "suitesparse" "libumfpack")))
+ (substitute* (jlpath "Zlib")
+ (((from "libz")) (to "zlib" "libz"))))
+ #t))
+ (add-after 'unpack 'adjust-test-suite
+ (lambda* (#:key inputs #:allow-other-keys)
+ (let (;(pcre2 (assoc-ref inputs "pcre2"))
+ (mbedtls-apache (assoc-ref inputs "mbedtls"))
+ (mpfr (assoc-ref inputs "mpfr"))
+ (suitesparse (assoc-ref inputs "suitesparse")))
+ ;; Some tests only check to see if the input is the correct
version.
+ ;(substitute* "stdlib/PCRE2_jll/test/runtests.jl"
+ ; (("10.36.0") ,(package-version pcre2)))
+ (substitute* "stdlib/MbedTLS_jll/test/runtests.jl"
+ (("2.24.0") ,(package-version mbedtls-apache)))
+ (substitute* "stdlib/MPFR_jll/test/runtests.jl"
+ (("4.1.0") ,(package-version mpfr)))
+ (substitute* "stdlib/SuiteSparse_jll/test/runtests.jl"
+ (("5004") ,(string-replace-substring
+ (version-major+minor
+ (package-version suitesparse)) "." "0")))
+ #t)))
(add-before 'check 'disable-broken-tests
(lambda _
+ ;; disabling REPL tests because they require a stdin
+ ;; There are some read-only precompile issues in the 1.6 series.
+ ;; https://github.com/JuliaLang/julia/pull/41614
+ ;; https://github.com/JuliaLang/julia/issues/41156
(substitute* "test/choosetests.jl"
- (("tests = testnames")
- ;; Those failings are not deterministic. They depends on the
- ;; running order. I think it depends on the number of
- ;; runners, disabling it for now
- ;; https://github.com/JuliaLang/julia/issues/34330
- "tests =
filter(e->!in(e,[\"backtrace\",\"exceptions\",\"precompile\",
- \"client\",\"stacktraces\"]),
- testnames)"))
- ;; Marking the test as broken as it's a known bug:
- ;; https://github.com/JuliaLang/julia/issues/32377
- (substitute* "stdlib/REPL/test/replcompletions.jl"
- (("@test count") "@test_broken count"))
- ;; Dates has a similar bug:
+ (("skip_tests = \\[\\]")
+ "skip_tests = [\"REPL\", \"precompile\"]"))
+ ;; Dates/io tests fail on master when networking is unavailable
;; https://github.com/JuliaLang/julia/issues/34655
(substitute* "stdlib/Dates/test/io.jl"
(("\"Dates.Date") "\"Date")
@@ -349,11 +477,67 @@ libraries. It is also a bit like @code{ldd} and
@code{otool -L}.")
;; https://github.com/JuliaLang/julia/issues/35785
(substitute* "test/file.jl"
(("@test dirname\\(t\\) == d") "@test_broken dirname(t) == d"))
- ;; Deprecation test fails with --depwarn=no
- ;; https://github.com/JuliaLang/julia/issues/37673
- (substitute* "test/Makefile"
- (("./runtests.jl") "--depwarn=error ./runtests.jl"))
+ ;; julia embeds a certificate, we are not doing that
+ (substitute* "stdlib/MozillaCACerts_jll/test/runtests.jl"
+ (("@test isfile\\(MozillaCACerts_jll.cacert\\)")
+ "@test_broken isfile(MozillaCACerts_jll.cacert)"))
+ ;; since certificate is not present some tests are failing in
network option
+ (substitute*
"usr/share/julia/stdlib/v1.6/NetworkOptions/test/runtests.jl"
+ (("@test isfile\\(bundled_ca_roots\\(\\)\\)")
+ "@test_broken isfile(bundled_ca_roots())")
+ (("@test ispath\\(ca_roots_path\\(\\)\\)")
+ "@test_broken ispath(ca_roots_path())")
+ (("@test ca_roots_path\\(\\) \\!= bundled_ca_roots\\(\\)")
+ "@test_broken ca_roots_path() != bundled_ca_roots()"))
+ ;; Some digraphs are too wide for some terminals during testing.
+ (substitute* "stdlib/Unicode/test/runtests.jl"
+ (("test collect\\(graphemes") "test_broken collect(grapemes"))
+ ;; WARNING: failed to select UTF-8 encoding, using ASCII
+ ;; Using 'setlocale' doesn't affect the test failures.
+ ;(setlocale LC_ALL "en_US.utf8")
+ ;(setenv "LC_ALL" "en_US.utf8")
+ (substitute* "test/cmdlineargs.jl"
+ (("test v\\[3") "test_broken v[3")
+ (("test isempty\\(v\\[3") "test_broken isempty(v[3"))
#t))
+ (add-before 'install 'symlink-libraries
+ (lambda* (#:key inputs outputs #:allow-other-keys)
+ (let ((link
+ (lambda (pkgname dir pred)
+ (map (lambda (file)
+ (unless (file-exists?
+ (string-append dir (basename file)))
+ (symlink file (string-append dir (basename
file)))))
+ (find-files (string-append (assoc-ref inputs
pkgname)
+ "/lib") pred)))))
+ (link "curl" "usr/lib/" "\\.so") ; missing libpthreads
libLLVM-11jl
+ (link "suitesparse" "usr/lib/julia/" "libbtf\\.so")
+ (link "suitesparse" "usr/lib/julia/" "libklu\\.so")
+ (link "suitesparse" "usr/lib/julia/" "libldl\\.so")
+ (link "suitesparse" "usr/lib/julia/" "librbio\\.so")
+ (link "gmp" "usr/lib/julia/" "libgmpxx\\.so")
+ (link "libuv" "usr/lib/julia/" "libuv\\.so")
+ (link "zlib" "usr/lib/julia/" "libz\\.so")
+ (link "libunwind" "usr/lib/julia/" "libunwind\\.so")
+ (symlink (string-append (assoc-ref inputs "p7zip") "/bin/7z")
+ "usr/libexec/7z")
+ #t)))
+ (add-after 'install 'symlink-llvm-utf8proc
+ (lambda* (#:key inputs outputs #:allow-other-keys)
+ (let* ((out (assoc-ref outputs "out"))
+ (link
+ (lambda (pkgname pred)
+ (map (lambda (file)
+ (unless (file-exists?
+ (string-append out "/lib/julia/"
+ (basename file)))
+ (symlink file (string-append out "/lib/julia/"
+ (basename
file)))))
+ (find-files (string-append (assoc-ref inputs pkgname)
+ "/lib") pred)))))
+ (link "llvm" "libLLVM-11\\.so")
+ (link "utf8proc" "libutf8proc\\.so")
+ #t)))
(add-after 'install 'make-wrapper
(lambda* (#:key inputs outputs #:allow-other-keys)
(let* ((out (assoc-ref outputs "out"))
@@ -362,8 +546,7 @@ libraries. It is also a bit like @code{ldd} and
@code{otool -L}.")
(with-directory-excursion bin
(wrap-program program
`("JULIA_LOAD_PATH" ":" prefix
- ("" "$JULIA_LOAD_PATH")))
- (wrap-program program
+ ("" "$JULIA_LOAD_PATH"))
`("JULIA_DEPOT_PATH" ":" prefix
("" "$JULIA_DEPOT_PATH"))))
#t))))
@@ -371,11 +554,14 @@ libraries. It is also a bit like @code{ldd} and
@code{otool -L}.")
(list
(string-append "prefix=" (assoc-ref %outputs "out"))
- ;; Passing the MARCH flag is necessary to build binary substitutes for
- ;; the supported architectures.
+ ;; Passing the MARCH or JULIA_CPU_TARGET flag is necessary to build
+ ;; binary substitutes for the supported architectures. See also
+ ;;
https://docs.julialang.org/en/v1/devdocs/sysimg/#Specifying-multiple-system-image-targets
,(match (or (%current-target-system)
(%current-system))
- ("x86_64-linux" "MARCH=x86-64")
+ ("x86_64-linux"
+ ;; These are the flags that upstream uses for their binaries.
+
"JULIA_CPU_TARGET=generic;generic,-cx16,clone_all;sandybridge,-xsaveopt,clone_all;haswell,-rdrnd,base(1)")
("i686-linux" "MARCH=pentium4")
("armhf-linux" "JULIA_CPU_TARGET=armv7-a,neon")
("powerpc64le-linux" "JULIA_CPU_TARGET=pwr8")
@@ -384,81 +570,87 @@ libraries. It is also a bit like @code{ldd} and
@code{otool -L}.")
;; and also of targeting the builder's architecture.
(_ "JULIA_CPU_TARGET=generic"))
- "CONFIG_SHELL=bash" ;needed to build bundled libraries
- ;; list of "USE_SYSTEM_*" is here:
- ;; https://github.com/JuliaLang/julia/blob/v1.3.1/Make.inc
+ "CONFIG_SHELL=bash -x" ; needed to build bundled libraries
+ "USE_BINARYBUILDER=0"
+ ;; list (and order!) of "USE_SYSTEM_*" is here:
+ ;; https://github.com/JuliaLang/julia/blob/v1.6.0/Make.inc
+ "USE_SYSTEM_CSL=1"
+ "USE_SYSTEM_LLVM=1"
+ "USE_SYSTEM_LIBUNWIND=1"
+ "USE_SYSTEM_PCRE=1"
+ "USE_SYSTEM_OPENLIBM=1"
"USE_SYSTEM_DSFMT=1"
- "USE_SYSTEM_P7ZIP=1"
- "USE_SYSTEM_LAPACK=1"
"USE_SYSTEM_BLAS=1"
- "USE_BLAS64=0" ;needed when USE_SYSTEM_BLAS=1
+ "USE_SYSTEM_LAPACK=1"
+ "USE_SYSTEM_GMP=1"
+ "USE_SYSTEM_MPFR=1"
+ "USE_SYSTEM_SUITESPARSE=1"
+ "USE_SYSTEM_LIBUV=1"
+ "USE_SYSTEM_UTF8PROC=1"
+ "USE_SYSTEM_MBEDTLS=1"
+ "USE_SYSTEM_LIBSSH2=1"
+ "USE_SYSTEM_NGHTTP2=1"
+ "USE_SYSTEM_CURL=1"
+ "USE_SYSTEM_LIBGIT2=1"
+ "USE_SYSTEM_PATCHELF=1"
+ "USE_SYSTEM_ZLIB=1"
+ "USE_SYSTEM_P7ZIP=1"
+
+ "NO_GIT=1" ; build from release tarball.
+ "USE_BLAS64=0" ; needed when USE_SYSTEM_BLAS=1
"LIBBLAS=-lopenblas"
"LIBBLASNAME=libopenblas"
- "USE_SYSTEM_SUITESPARSE=1"
(string-append "SUITESPARSE_INC=-I "
(assoc-ref %build-inputs "suitesparse")
"/include")
- "USE_GPL_LIBS=1" ;proudly
- "USE_SYSTEM_UTF8PROC=1"
+ "USE_GPL_LIBS=1" ; proudly
(string-append "UTF8PROC_INC="
(assoc-ref %build-inputs "utf8proc")
"/include")
- "USE_SYSTEM_LLVM=1"
- "LLVM_VER=9.0.1"
+ "LLVM_VER=11.0.0"
"USE_LLVM_SHLIB=1"
- "USE_SYSTEM_LIBUNWIND=1"
- "USE_SYSTEM_LIBUV=1"
(string-append "LIBUV="
(assoc-ref %build-inputs "libuv")
"/lib/libuv.so")
(string-append "LIBUV_INC="
(assoc-ref %build-inputs "libuv")
- "/include")
- "USE_SYSTEM_PATCHELF=1"
- "USE_SYSTEM_PCRE=1"
- "USE_SYSTEM_OPENLIBM=1"
- "USE_SYSTEM_MBEDTLS=1"
- "USE_SYSTEM_LIBSSH2=1"
- "USE_SYSTEM_GMP=1"
- "USE_SYSTEM_MPFR=1"
- "USE_SYSTEM_ARPACK=1"
- "USE_SYSTEM_LIBGIT2=1"
- "USE_SYSTEM_ZLIB=1")))
+ "/include"))))
(inputs
- `(("llvm" ,llvm-julia)
- ("p7zip" ,p7zip)
- ;; The bundled version is 3.3.0 so stick to that version. With other
- ;; versions, we get test failures in 'linalg/arnoldi' as described in
- ;; <https://bugs.gnu.org/30282>.
- ("arpack-ng" ,arpack-ng-3.3.0)
-
- ("coreutils" ,coreutils) ;for bindings to "mkdir" and the like
+ `(("coreutils" ,coreutils) ; for bindings to "mkdir" and the like
+ ("curl" ,curl-ssh)
+ ("gfortran" ,gfortran)
+ ;; required for libgcc_s.so
+ ("gfortran:lib" ,gfortran "lib")
+ ("gmp" ,gmp)
("lapack" ,lapack)
- ("openblas" ,openblas) ;Julia does not build with Atlas
- ("libunwind" ,libunwind-julia)
- ("openlibm" ,openlibm)
- ("mbedtls" ,mbedtls-apache)
- ("curl" ,curl)
- ("libgit2" ,libgit2-0.28)
+ ("libgit2" ,libgit2)
+ ("libnghttp2" ,nghttp2 "lib")
("libssh2" ,libssh2)
- ("fortran" ,gfortran)
+ ("libunwind" ,libunwind-julia)
("libuv" ,libuv-julia)
- ("pcre2" ,pcre2)
- ("utf8proc" ,utf8proc)
+ ("llvm" ,llvm-julia)
+ ("mbedtls" ,mbedtls-apache)
("mpfr" ,mpfr)
+ ("openblas" ,openblas)
+ ("openlibm" ,openlibm)
+ ("p7zip" ,p7zip)
+ ;; pcre2-10.35 has a bug with the JIT regex parser:
+ ;;
https://github.com/JuliaLang/julia/issues/40231#issuecomment-812753324
+ ("pcre2" ,pcre2-10.36)
+ ("suitesparse" ,suitesparse)
+ ("utf8proc" ,utf8proc-2.6.1)
("wget" ,wget)
("which" ,which)
("zlib" ,zlib)
- ("gmp" ,gmp)
- ("suitesparse" ,suitesparse)
;; Find dependencies versions here:
- ;;
https://raw.githubusercontent.com/JuliaLang/julia/v1.3.0/deps/Versions.make
- ("libwhich" ,libwhich)
- ("dsfmt" ,dsfmt)))
+ ;;
https://raw.githubusercontent.com/JuliaLang/julia/v1.6.0/deps/Versions.make
+ ("dsfmt" ,dsfmt)
+ ("libwhich" ,libwhich)))
(native-inputs
- `(("openssl" ,openssl)
+ `(("nss-certs" ,nss-certs)
+ ("openssl" ,openssl)
("perl" ,perl)
("patchelf" ,patchelf)
("pkg-config" ,pkg-config)
- branch master updated (b07c7f0 -> c20c9e1), guix-commits, 2021/07/28
- 01/19: gnu: global: Fix lisp install dir., guix-commits, 2021/07/28
- 02/19: gnu: glibc-for-bootstrap: Update patch., guix-commits, 2021/07/28
- 06/19: gnu: openlibm: Fix cross-compiling., guix-commits, 2021/07/28
- 04/19: gnu: Add pcre2-10.36., guix-commits, 2021/07/28
- 05/19: gnu: openlibm: Update to 0.7.4., guix-commits, 2021/07/28
- 09/19: gnu: julia: Update to 1.6.1.,
guix-commits <=
- 10/19: gnu: libuv-julia: Clean up package definition., guix-commits, 2021/07/28
- 03/19: gnu: Add utf8proc-2.6.1., guix-commits, 2021/07/28
- 07/19: gnu: julia-staticarrays: Update to 1.2.5, guix-commits, 2021/07/28
- 08/19: gnu: Add curl-ssh., guix-commits, 2021/07/28
- 11/19: gnu: llvm-julia: Overide build-type., guix-commits, 2021/07/28
- 12/19: gnu: julia: Skip tests on aarch64-linux., guix-commits, 2021/07/28
- 13/19: gnu: Add julia-preferences., guix-commits, 2021/07/28
- 14/19: gnu: julia-jllwrappers: Add julia-preferences., guix-commits, 2021/07/28
- 15/19: gnu: global: Update to 6.6.7., guix-commits, 2021/07/28
- 17/19: gnu: julia-datavalues: Skip tests., guix-commits, 2021/07/28