[bug#48325] [PATCH v5 5/5] DRAFT gnu: julia: Update to 1.6.1.

[Efraim Flashner <efraim@flashner.co.il>]

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On Sat, Jul 03, 2021 at 05:41:58PM +0000, Jean-Baptiste Volatier via Guix-patches via wrote:
> * gnu/packages/julia.scm (julia): Update to 1.6.1.
> [arguments]<#:phases>: Fixed paths to shared objects in
> 'shared-objects-paths phase, Fix tests that did not propagate
> GUIX_LOCPATH in 'fix-setenv, Add symlinks to libs in 'symlink-libraries
> [arguments]<:make-flags>: Added generic,-cx16 target for better compatibility
> [inputs]: Add nghttp2:lib, Add gfortran:lib, Add curl-ssh, Remove arpack-ng.
> [native-inputs]: Add nss-certs.
> 
> * gnu/packages/julia.scm (curl-ssh): New variable.
> 
> * gnu/packages/julia.scm (llvm-julia): Update to 11.0.0
> [source]: Move julia specific patches to a julia-patches phase.
> [arguments]<#:phases>: Apply julia specific patches in 'julia-patches phase
> 
> Co-Authored-By: Nicolò Balzarotti <nicolo@nixo.xyz>.
> Co-Authored-By: zimoun <zimon.toutoune@gmail.com>.
> ---
>  gnu/packages/julia.scm | 353 ++++++++++++++++++++++++++++-------------
>  1 file changed, 239 insertions(+), 114 deletions(-)
> 
> diff --git a/gnu/packages/julia.scm b/gnu/packages/julia.scm
> index 13c9f7baf1..9903bb009b 100644
> --- a/gnu/packages/julia.scm
> +++ b/gnu/packages/julia.scm
> @@ -1,9 +1,11 @@
>  ;;; GNU Guix --- Functional package management for GNU
>  ;;; Copyright © 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>
> +;;; 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/v1.6.0/deps/libuv.version
>      (package
>        (inherit libuv)
>        (name "libuv-julia")
> @@ -68,7 +72,7 @@
>                  (file-name (string-append name "-" version "-checkout"))
>                  (sha256
>                   (base32
> -                  "040l7f1hk7xyza11sry5cj4fhw05na949865axqqhxnifdvnmfji"))))
> +                  "1kqpn19d20aka30h6q5h8lnzyp0vw0xzgx0wm4w2r5j6yf76m2hr"))))
>        (build-system gnu-build-system)
>        (arguments
>         (substitute-keyword-arguments (package-arguments libuv)
> @@ -97,7 +101,9 @@
>           (julia-patch "libunwind-prefer-extbl"
>                        "0lr4dafw8qyfh8sw8hhbwkql1dlhqv8px7k81y2l20hhxfgnh2m1")
>           (julia-patch "libunwind-static-arm"
> -                      "1jk3bmiw61ypcchqkk1fyg5wh8wpggk574wxyfyaic870zh3lhgq")))))
> +                      "1jk3bmiw61ypcchqkk1fyg5wh8wpggk574wxyfyaic870zh3lhgq")
> +         (julia-patch "libunwind-cfa-rsp"
> +                      "1aswjhvysahhldbzh1afbf0hsjxrvs6xidsz2i7s1cjkjbdiia1z")))))
>      (home-page "https://github.com/JuliaLang/tree/master/deps/")))
> 
>  (define (julia-patch-url version name)
> @@ -105,7 +111,7 @@
>                   "/deps/patches/" name ".patch"))
> 
>  (define (julia-patch name sha)
> -  (let ((version "1.5.3"))
> +  (let ((version "1.6.1"))
>      (origin (method url-fetch)
>              (uri (julia-patch-url version name))
>              (sha256 (base32 sha))
> @@ -113,52 +119,10 @@
> 
>  (define llvm-julia
>    (package
> -    (inherit llvm-9)
> +    (inherit llvm-11)
>      (name "llvm-julia")
> -    (source (origin
> -              (inherit (package-source llvm-9))
> -              ;; Those patches are inside the Julia source repo.
> -              ;; They are _not_ Julia specific (https://github.com/julialang/julia#llvm)
> -              ;; but they are required to build Julia.
> -              ;; Discussion: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=919628
> -              (patches
> -               (map (match-lambda
> -                      ((name hash)
> -                       (julia-patch name hash)))
> -                    (list
> -                     '("llvm-D27629-AArch64-large_model_6.0.1"
> -                       "1qrshmlqvnasdyc158vfn3hnbigqph3lsq7acb9w8lwkpnnm2j4z")
> -                     '("llvm8-D34078-vectorize-fdiv"
> -                       "19spqc3xsazn1xs9gpcgv9ldadfkv49rmc5khl7sf1dlmhgi4602")
> -                     '("llvm-7.0-D44650"
> -                       "1h55kkmkiisfj6sk956if2bcj9s0v6n5czn8dxb870vp5nccj3ir")
> -                     '("llvm9-D50010-VNCoercion-ni"
> -                       "1s1d3sjsiq4vxg7ncy5cz56zgy5vcq6ls3iqaiqkvr23wyryqmdx")
> -                     '("llvm-exegesis-mingw"
> -                       "0ph1cj1j7arvf1xq2xcr7qf9g0cpdl14fincgr67vpi520zvd3vp")
> -                     '("llvm-test-plugin-mingw"
> -                       "12z738cnahbf6n381im7i0hxp1m6k9hrnfjlmq9sac46nxly9gnj")
> -                     '("llvm7-revert-D44485"
> -                       "0f59kq3p3mpwsbmskypbi4zn01l6ig0x7v2rjp08k2r8z8m6fa8n")
> -                     '("llvm-8.0-D66657-codegen-degenerate"
> -                       "1n1ddx19h90bbpimdyd9dh8fsm6gb93xxyqm4ljkxa1k3cx2vm72")
> -                     '("llvm-8.0-D71495-vectorize-freduce"
> -                       "1zff08wvji9lnpskk4b3p5zyjsy5hhy23ynxjqlj9dw7jvvfrf0p")
> -                     '("llvm-D75072-SCEV-add-type"
> -                       "029a3fywsm233vf48mscina24idd50dc75wr70lmimrhwnw27p0z")
> -                     '("llvm-9.0-D65174-limit-merge-stores"
> -                       "04bff1mnblfj9mxfdwr1qdnw3i3szmp60gnhxwas5y68qg33z6j0")
> -                     '("llvm9-D71443-PPC-MC-redef-symbol"
> -                       "1c93nv7rgc9jg5mqrnvv08xib1789qvlql94fwggh18mp3b9hbgy")
> -                     '("llvm-9.0-D78196"
> -                       "08a43hyg7yyqjq2vmfsmppf34xcz60wq6y9zw5fdyhw2h1mcnmns")
> -                     '("llvm-julia-tsan-custom-as"
> -                       "0awh40kf6lm4wn1nsjd1bmhfwq7rqj811szanp2xkpspykw9hg9s")
> -                     '("llvm-9.0-D85499"
> -                       "0vxlr35srvbvihlgrxq15v6dylp90vgi0qahj22j01jgqmdasjkm"))))
> -              (patch-flags '("-p1"))))
>      (arguments
> -     (substitute-keyword-arguments (package-arguments llvm-9)
> +     (substitute-keyword-arguments (package-arguments llvm-11)
>         ((#:configure-flags flags)
>          `(list ;; Taken from NixOS. Only way I could get libLLVM-6.0.so
>             "-DCMAKE_BUILD_TYPE=Release"
> @@ -177,7 +141,61 @@
>             ;; "-DLLVM_DEFAULT_TARGET_TRIPLE=${stdenv.hostPlatform.config}"
>             ;; "-DLLVM_EXPERIMENTAL_TARGETS_TO_BUILD=WebAssembly"
>             "-DLLVM_ENABLE_DUMP=ON"
> -           "-DLLVM_LINK_LLVM_DYLIB=ON"))))))
> +           "-DLLVM_LINK_LLVM_DYLIB=ON"))
> +       ((#:phases phases)
> +        `(modify-phases ,phases
> +           ;; applying patches from julia
> +           ;; list of patches can be found in deps/llvm.mk in julia source
> +           (add-after 'unpack 'julia-patches
> +             (lambda* (#:key inputs outputs #:allow-other-keys)
> +               (let ((patch
> +                      (lambda (patchname flag)
> +                        (invoke "patch" flag "-i"
> +                                (string-append
> +                                 "julia-src/deps/patches/"
> +                                 patchname
> +                                 ".patch")))))
> +                 (mkdir-p "julia-src")
> +                 (invoke "tar" "xf"
> +                         (assoc-ref inputs "julia-source")
> +                         "-C" "julia-src" "--strip-components=1")
> +                 (map (lambda (patchname)
> +                        (patch patchname "-p1"))
> +                      (list "llvm-D27629-AArch64-large_model_6.0.1"
> +                            "llvm8-D34078-vectorize-fdiv"
> +                            "llvm-7.0-D44650"
> +                            "llvm-6.0-DISABLE_ABI_CHECKS"
> +                            "llvm9-D50010-VNCoercion-ni"
> +                            "llvm7-revert-D44485"
> +                            "llvm-11-D75072-SCEV-add-type"
> +                            "llvm-julia-tsan-custom-as"
> +                            "llvm-D80101"
> +                            "llvm-D84031"
> +                            "llvm-10-D85553"
> +                            "llvm-10-unique_function_clang-sa"
> +                            "llvm-11-D85313-debuginfo-empty-arange"
> +                            "llvm-11-D90722-rtdyld-absolute-relocs"
> +                            "llvm-invalid-addrspacecast-sink"
> +                            "llvm-11-D92906-ppc-setjmp"
> +                            "llvm-11-PR48458-X86ISelDAGToDAG"
> +                            "llvm-11-D93092-ppc-knownbits"
> +                            "llvm-11-D93154-globalisel-as"
> +                            "llvm-11-ppc-half-ctr"
> +                            "llvm-11-ppc-sp-from-bp"
> +                            "llvm-rGb498303066a6-gcc11-header-fix"
> +                            "llvm-11-D94813-mergeicmps"
> +                            "llvm-11-D94980-CTR-half"
> +                            "llvm-11-D94058-sext-atomic-ops"
> +                            "llvm-11-D96283-dagcombine-half"))
> +                 (map (lambda (patchname)
> +                        (patch patchname "-p2"))
> +                      (list "llvm-11-AArch64-FastIsel-bug"
> +                            "llvm-11-D97435-AArch64-movaddrreg"
> +                            "llvm-11-D97571-AArch64-loh"
> +                            "llvm-11-aarch64-addrspace")))))))))
> +    (inputs
> +     `(("julia-source" ,(package-source julia))
> +       ,@(package-inputs llvm-11)))))
> 
>  (define-public libwhich
>    (package
> @@ -220,10 +238,22 @@
>  libraries.  It is also a bit like @code{ldd} and @code{otool -L}.")
>      (license license:expat)))
> 

IMO since this package inherits from curl it should go next to curl, but
be a hidden package.

> +(define curl-ssh
> +  (package
> +    (inherit curl)
> +    (arguments
> +     (substitute-keyword-arguments (package-arguments curl)
> +       ((#:configure-flags flags)
> +        `(cons "--with-libssh2" ,flags))))
> +    (inputs
> +     `(("libssh2" ,libssh2)
> +       ,@(package-inputs curl)))
> +    ))
> +
>  (define-public julia
>    (package
>      (name "julia")
> -    (version "1.5.3")
> +    (version "1.6.1")
>      (source (origin
>                (method url-fetch)
>                (uri (string-append
> @@ -231,9 +261,7 @@ libraries.  It is also a bit like @code{ldd} and @code{otool -L}.")
>                      version "/julia-" version ".tar.gz"))
>                (sha256
>                 (base32
> -                "1zmim82x9kkdcgn0cdi01hmzi59zbszy1sqlygb86xq4hc1n66dy"))
> -              (patches
> -               (search-patches "julia-SOURCE_DATE_EPOCH-mtime.patch"))))
> +                "1mfzbjyqcmx7wb1sa7qab5fl78yzd7ap088krqbphbwvpn880srn"))))
>      (build-system gnu-build-system)
>      (arguments
>       `(#:test-target "test"
> @@ -259,14 +287,13 @@ libraries.  It is also a bit like @code{ldd} and @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 +331,7 @@ libraries.  It is also a bit like @code{ldd} and @code{otool -L}.")
>                  "$(BUILDDIR)/$(EXENAME)-debug\\$\\(EXE\\): $(DOBJS) $(LLT_debug)"))
> 
>               ;; The REPL must be linked with libuv.
> -             (substitute* "ui/Makefile"
> +             (substitute* "cli/Makefile"
>                 (("JLDFLAGS \\+= ")
>                  (string-append "JLDFLAGS += "
>                                 (assoc-ref %build-inputs "libuv")
> @@ -320,27 +347,82 @@ 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")

After updating mbedtls-apache I added the following two lines here:
;; 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-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 +431,43 @@ 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)

can we use the 'symlink' function here rather than shelling out to 'ln'?
Also for the other instances of it in this patch.

> +                             (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"))
> @@ -370,7 +484,10 @@ libraries.  It is also a bit like @code{ldd} and @code{otool -L}.")
>         #:make-flags
>         (list
>          (string-append "prefix=" (assoc-ref %outputs "out"))
> -
> +         ;; Adding generic,-cx16 target to the list of defaults target for better compatibility
> +         ;; clone_all is required otherwise julia complains during compilation
> +         ;; see https://docs.julialang.org/en/v1/devdocs/sysimg/#Specifying-multiple-system-image-targets
> +         "JULIA_CPU_TARGET=generic;generic,-cx16,clone_all;sandybridge,-xsaveopt,clone_all;haswell,-rdrnd,base(1)"

Passing JULIA_CPU_TARGET unconditionally here will likely break julia on
i686. On the other architectures it will be overridden. It would be best
to put it with the x86_64 MARCH architecture and adapt the comment there
to mention setting the MARCH and optionally the JULIA_CPU_TARGET on a
per-architecture basis.

>           ;; Passing the MARCH flag is necessary to build binary substitutes for
>           ;; the supported architectures.
>           ,(match (or (%current-target-system)
> @@ -382,69 +499,76 @@ libraries.  It is also a bit like @code{ldd} and @code{otool -L}.")
>                   ;; platforms, e.g. when running "guix package --search="
>                   (_ "MARCH=UNSUPPORTED"))
> 
> -         "CONFIG_SHELL=bash"     ;needed to build bundled libraries
> +         "CONFIG_SHELL=bash -x"     ;needed to build bundled libraries
> +         "USE_BINARYBUILDER=0"
>           ;; list of "USE_SYSTEM_*" is here:
> -         ;; https://github.com/JuliaLang/julia/blob/v1.3.1/Make.inc
> +         ;; https://github.com/JuliaLang/julia/blob/v1.6.0/Make.inc
> +         ;;

As long as these all got moved around I'd keep them sorted either
quasi-alphabetically or in the order they appear in the Make.inc file. I
didn't check the file to see if that was the case.

> +         "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_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"
>           "USE_SYSTEM_DSFMT=1"
>           "USE_SYSTEM_P7ZIP=1"
>           "USE_SYSTEM_LAPACK=1"
> -         "USE_SYSTEM_BLAS=1"
> +         "USE_SYSTEM_CURL=1"
>           "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"
>           (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
>         ("lapack" ,lapack)
>         ("openblas" ,openblas) ;Julia does not build with Atlas
>         ("libunwind" ,libunwind-julia)
>         ("openlibm" ,openlibm)
>         ("mbedtls" ,mbedtls-apache)
> -       ("curl" ,curl)
> -       ("libgit2" ,libgit2-0.28)
> +       ("curl" ,curl-ssh)
> +       ("libnghttp2" ,nghttp2 "lib")
> +       ("libgit2" ,libgit2)
>         ("libssh2" ,libssh2)
>         ("fortran" ,gfortran)
> +       ;; required for libgcc_s.so
> +       ("libfortran" ,gfortran "lib")
>         ("libuv" ,libuv-julia)
> -       ("pcre2" ,pcre2)
> -       ("utf8proc" ,utf8proc)
> +       ("pcre2" ,pcre2-10.36)
> +       ("utf8proc" ,utf8proc-2.6.1)
>         ("mpfr" ,mpfr)
>         ("wget" ,wget)
>         ("which" ,which)
> @@ -452,7 +576,7 @@ libraries.  It is also a bit like @code{ldd} and @code{otool -L}.")
>         ("gmp" ,gmp)
>         ("suitesparse" ,suitesparse)
>         ;; Find dependencies versions here:
> -       ;; https://raw.githubusercontent.com/JuliaLang/julia/v1.3.0/deps/Versions.make
> +       ;; https://raw.githubusercontent.com/JuliaLang/julia/v1.6.0/deps/Versions.make
>         ("libwhich" ,libwhich)
>         ("dsfmt" ,dsfmt)))
>      (native-inputs
> @@ -460,6 +584,7 @@ libraries.  It is also a bit like @code{ldd} and @code{otool -L}.")
>         ("perl" ,perl)
>         ("patchelf" ,patchelf)
>         ("pkg-config" ,pkg-config)
> +       ("nss-certs" ,nss-certs)

try to keep the libraries sorted alphabetically, it reduces the chance
of duplication.

>         ("python" ,python-2)))
>      (native-search-paths
>        (list (search-path-specification
> --
> 2.32.0
> 
> 
> 
> 
> 

-- 
Efraim Flashner   <efraim@flashner.co.il>   אפרים פלשנר
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