diff mbox series

[bug#48325,v3,4/5] DRAFT gnu: julia: Update to 1.6.1.

Message ID 20210513141105.10274-4-zimon.toutoune@gmail.com
State New
Headers show
Series DRAFT: Update julia to 1.6.1. | expand

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Commit Message

zimoun May 13, 2021, 2:11 p.m. UTC
From: Jean-Baptiste Volatier <jbv@pm.me>

* gnu/packages/julia.scm (julia): Update to 1.6.1.
[arguments]: XXXX
[inputs]: Add nghttp2:lib, Add gfortran:lib, Remove arpack-ng.
[native-inputs]: Add nss-certs.

Co-Authored-By: Nicolò Balzarotti <nicolo@nixo.xyz>.
Co-Authored-By: zimoun <zimon.toutoune@gmail.com>.
---
 gnu/packages/julia.scm | 292 +++++++++++++++++++++++++++--------------
 1 file changed, 197 insertions(+), 95 deletions(-)
diff mbox series

Patch

diff --git a/gnu/packages/julia.scm b/gnu/packages/julia.scm
index 13c9f7baf1..307ac646b3 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
@@ -223,7 +241,7 @@  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 +249,7 @@  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 +275,13 @@  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 +319,7 @@  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 +335,82 @@  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 +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"
@@ -416,22 +519,17 @@  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
@@ -439,12 +537,15 @@  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)
+       ("pcre2" ,pcre2-10.36)
+       ("utf8proc" ,utf8proc-2.6.1)
        ("mpfr" ,mpfr)
        ("wget" ,wget)
        ("which" ,which)
@@ -452,7 +553,7 @@  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 +561,7 @@  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