Merge branch 'master' into core-updates

 Conflicts:
	etc/news.scm
	gnu/local.mk
	gnu/packages/check.scm
	gnu/packages/cross-base.scm
	gnu/packages/gimp.scm
	gnu/packages/java.scm
	gnu/packages/mail.scm
	gnu/packages/sdl.scm
	gnu/packages/texinfo.scm
	gnu/packages/tls.scm
	gnu/packages/version-control.scm

1 files changed, 262 insertions, 287 deletions

diff --git a/gnu/packages/julia.scm b/gnu/packages/julia.scm
index 65a5e42beb..6dd53b9283 100644
--- a/gnu/packages/julia.scm
+++ b/gnu/packages/julia.scm
@@ -1,6 +1,7 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2015, 2016, 2017 Ricardo Wurmus <rekado@elephly.net>
-;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2016, 2020 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2020 Nicolò Balzarotti <nicolo@nixo.xyz>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -28,6 +29,7 @@
   #:use-module (gnu packages algebra)
   #:use-module (gnu packages base)
   #:use-module (gnu packages compression)
+  #:use-module (gnu packages curl)
   #:use-module (gnu packages elf)
   #:use-module (gnu packages gcc)
   #:use-module (gnu packages llvm)
@@ -41,29 +43,30 @@
   #:use-module (gnu packages python)
   #:use-module (gnu packages python-xyz)
   #:use-module (gnu packages textutils)
+  #:use-module (gnu packages ssh)
   #:use-module (gnu packages tls)
   #:use-module (gnu packages version-control)
   #:use-module (gnu packages wget)
   #:use-module (ice-9 match))
 
 (define libuv-julia
-  (let ((commit "26dbe5672c33fc885462c509fe2a9b36f35866fd")
-        (revision "6"))
-    ;; When upgrading Julia, also upgrade this.
-    ;; Get the commit from https://github.com/JuliaLang/julia/blob/v1.1.1/deps/libuv.version
+  (let ((commit "35b1504507a7a4168caae3d78db54d1121b121e1")
+        (revision "1"))
+    ;; When upgrading Julia, also upgrade this.  Get the commit from
+    ;; https://github.com/JuliaLang/julia/blob/v1.3.1/deps/libuv.version
     (package
       (inherit libuv)
       (name "libuv-julia")
-      (version (string-append "1.9.0-" revision "." (string-take commit 8)))
+      (version (git-version "2.0.0" revision commit))
       (source (origin
                 (method git-fetch)
                 (uri (git-reference
-                      (url "https://github.com/JuliaLang/libuv.git")
-                      (commit commit)))
+                       (url "https://github.com/JuliaLang/libuv.git")
+                       (commit commit)))
                 (file-name (string-append name "-" version "-checkout"))
                 (sha256
                  (base32
-                  "17pn2xmqaramilx897s9grs966i5246gi6sric5alch4g9j4685n"))))
+                  "0dn3v6fdp1z382pqg3nhjzk60l61ky9b65mfgaj29fv2da95rwjs"))))
       (build-system gnu-build-system)
       (arguments
        (substitute-keyword-arguments (package-arguments libuv)
@@ -72,93 +75,115 @@
              (delete 'autogen)))))
       (home-page "https://github.com/JuliaLang/libuv"))))
 
-(define (llvm-patch-url version name)
+(define libunwind-julia
+  ;; The Julia projects requires their patched version.
+  ;; Get from https://github.com/JuliaLang/julia/tree/master/deps/patches
+  (package
+    (inherit libunwind)
+    (name "libunwind-julia")
+    (version "1.3.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "mirror://savannah/libunwind/libunwind-"
+                           version ".tar.gz"))
+       (sha256
+        (base32
+         "1y0l08k6ak1mqbfj6accf9s5686kljwgsl4vcqpxzk5n74wpm6a3"))
+       (patches
+        (list
+         (julia-patch "libunwind-prefer-extbl"
+                      "0lr4dafw8qyfh8sw8hhbwkql1dlhqv8px7k81y2l20hhxfgnh2m1")
+         (julia-patch "libunwind-static-arm"
+                      "1jk3bmiw61ypcchqkk1fyg5wh8wpggk574wxyfyaic870zh3lhgq")))))
+    (home-page "https://github.com/JuliaLang/tree/master/deps/")))
+
+(define (julia-patch-url version name)
   (string-append "https://raw.githubusercontent.com/JuliaLang/julia/v" version
-		 "/deps/patches/" name))
+                 "/deps/patches/" name))
 
-(define (llvm-patch name sha)
-  (let ((version "1.1.1"))
+(define (julia-patch name sha)
+  (let ((version "1.3.1"))
     (origin (method url-fetch)
-	    (uri (llvm-patch-url version name))
-	    (sha256 (base32 sha))
-	    (file-name name))))
+            (uri (julia-patch-url version name))
+            (sha256 (base32 sha))
+            (file-name name))))
 
 (define llvm-julia
   (package
     (inherit llvm-6)
     (name "llvm-julia")
     (source (origin
-              (method url-fetch)
-              (uri "http://releases.llvm.org/6.0.1/llvm-6.0.1.src.tar.xz")
-              (sha256
-               (base32
-                "1qpls3vk85lydi5b4axl0809fv932qgsqgdgrk098567z4jc7mmn"))
+              (inherit (package-source llvm-6))
               ;; 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
-               (list
-	        (llvm-patch "llvm-6.0-D44650.patch"
-			    "1336q4vqayr94wdcnlmcxh90mjdh34dzw9x2cbiqjnx9b1j8fxyb")
-	        (llvm-patch "llvm-6.0-DISABLE_ABI_CHECKS.patch"
-			    "014fawd1ba7yckalypfld22zgic87x9nx3cim42zrwygywd36pyg")
-	        (llvm-patch "llvm-6.0-NVPTX-addrspaces.patch"
-			    "1qdi2zmrjsrj0h84zv2vyly2hjcn4f67mfy0s1q353g4v4jkscqc")
-	        (llvm-patch "llvm-6.0.0_D27296-libssp.patch"
-			    "0s5hi2r1j63i8m6ig1346crx2aiv9f7rgb3mg80kw1wx5y7pdpfh")
-	        (llvm-patch "llvm-D27629-AArch64-large_model_6.0.1.patch"
-			    "1qrshmlqvnasdyc158vfn3hnbigqph3lsq7acb9w8lwkpnnm2j4z")
-	        (llvm-patch "llvm-D34078-vectorize-fdiv.patch"
-			    "1696hg84a0jxcnggvqsc2cdp271hf9a44p4qsd078qm1mfawkaay")
-	        (llvm-patch "llvm-D42262-jumpthreading-not-i1.patch"
-			    "1c8w210gwidbnkkw8anp17dk5pnxws2fl3mb2qxh7y9wzfpixgaq")
-	        (llvm-patch "llvm-D44892-Perf-integration.patch"
-			    "0r37jd0ssh2k1pndkfd5blgpg9z90im4vlzprhb0n0wwz45g4b05")
-	        (llvm-patch "llvm-D46460.patch"
-			    "1miqgswdc0qvbaf4571c2xkxyp9ais06b1bcpa83sq22vr4hbsfb")
-	        (llvm-patch "llvm-D49832-SCEVPred.patch"
-			    "0v5c88hgqj6dymv3j86ca5mhpqab5fbnrvjiw1nvnrnya9l4dlbn")
-	        (llvm-patch "llvm-D50010-VNCoercion-ni.patch"
-			    "0iblb3q1xixwrb12jpb89h3ywmqmzdp6aqp416j4ncwakyjhhfkp")
-	        (llvm-patch "llvm-D50167-scev-umin.patch"
-			    "1f2rakcnnyhr7w10k7gqg0k0491pyvx5ijplivw557f714ys3q6v")
-	        (llvm-patch "llvm-OProfile-line-num.patch"
-			    "1jvbbmwyags0xfwamb13qrf3rgcz9i1r03m9lava7swag8xb78c7")
-	        (llvm-patch "llvm-PPC-addrspaces.patch"
-			    "1f23nhsxh2s3jskbgs7da9nwg3s1hrkbk5aahl08x41wi3mny01p")
-	        (llvm-patch "llvm-rL323946-LSRTy.patch"
-			    "10cz3vy1yw0w643z7xx021wa4kymx9fcm3bjg61s6vzdqd6d9fns")
-	        (llvm-patch "llvm-rL326967-aligned-load.patch"
-			    "04jxnv32yj5x17hqhi8g2p8rhgp38gmjzr871w7z8s44pq10v9v4")
-	        (llvm-patch "llvm-rL327898.patch"
-			    "15ah49gbsll23z28kpyahi5vl0fh3fkxcgd1zmxxdcl96s3x8bnq")))))
+                (map (match-lambda
+                       ((name hash)
+                        (julia-patch name hash)))
+                     (list
+                       '("llvm-6.0-D44650"
+                         "1336q4vqayr94wdcnlmcxh90mjdh34dzw9x2cbiqjnx9b1j8fxyb")
+                       '("llvm-6.0-DISABLE_ABI_CHECKS"
+                         "014fawd1ba7yckalypfld22zgic87x9nx3cim42zrwygywd36pyg")
+                       '("llvm-6.0-NVPTX-addrspaces"
+                         "1qdi2zmrjsrj0h84zv2vyly2hjcn4f67mfy0s1q353g4v4jkscqc")
+                       '("llvm-6.0.0_D27296-libssp"
+                         "0s5hi2r1j63i8m6ig1346crx2aiv9f7rgb3mg80kw1wx5y7pdpfh")
+                       '("llvm-D27629-AArch64-large_model_6.0.1"
+                         "1qrshmlqvnasdyc158vfn3hnbigqph3lsq7acb9w8lwkpnnm2j4z")
+                       '("llvm-D34078-vectorize-fdiv"
+                         "1696hg84a0jxcnggvqsc2cdp271hf9a44p4qsd078qm1mfawkaay")
+                       '("llvm-D42262-jumpthreading-not-i1"
+                         "1c8w210gwidbnkkw8anp17dk5pnxws2fl3mb2qxh7y9wzfpixgaq")
+                       '("llvm-D44892-Perf-integration"
+                         "0r37jd0ssh2k1pndkfd5blgpg9z90im4vlzprhb0n0wwz45g4b05")
+                       '("llvm-D46460"
+                         "1miqgswdc0qvbaf4571c2xkxyp9ais06b1bcpa83sq22vr4hbsfb")
+                       '("llvm-D49832-SCEVPred"
+                         "0v5c88hgqj6dymv3j86ca5mhpqab5fbnrvjiw1nvnrnya9l4dlbn")
+                       '("llvm-D50010-VNCoercion-ni"
+                         "0iblb3q1xixwrb12jpb89h3ywmqmzdp6aqp416j4ncwakyjhhfkp")
+                       '("llvm-D50167-scev-umin"
+                         "1f2rakcnnyhr7w10k7gqg0k0491pyvx5ijplivw557f714ys3q6v")
+                       '("llvm-OProfile-line-num"
+                         "1jvbbmwyags0xfwamb13qrf3rgcz9i1r03m9lava7swag8xb78c7")
+                       '("llvm-PPC-addrspaces"
+                         "1f23nhsxh2s3jskbgs7da9nwg3s1hrkbk5aahl08x41wi3mny01p")
+                       '("llvm-rL323946-LSRTy"
+                         "10cz3vy1yw0w643z7xx021wa4kymx9fcm3bjg61s6vzdqd6d9fns")
+                       '("llvm-rL326967-aligned-load"
+                         "04jxnv32yj5x17hqhi8g2p8rhgp38gmjzr871w7z8s44pq10v9v4")
+                       '("llvm-rL327898"
+                         "15ah49gbsll23z28kpyahi5vl0fh3fkxcgd1zmxxdcl96s3x8bnq"))))))
     (arguments
      (substitute-keyword-arguments (package-arguments llvm-6)
        ((#:configure-flags flags)
         `(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"
 
-	  "-DLLVM_INSTALL_UTILS=ON"
-	  "-DLLVM_BUILD_TESTS=ON"
-	  "-DLLVM_ENABLE_FFI=ON"
-	  "-DLLVM_ENABLE_RTTI=ON"
-          ;; "-DLLVM_HOST_TRIPLE=${stdenv.hostPlatform.config}"
-          ;; "-DLLVM_DEFAULT_TARGET_TRIPLE=${stdenv.hostPlatform.config}"
-	  ;; "-DLLVM_EXPERIMENTAL_TARGETS_TO_BUILD=WebAssembly"
-	  "-DLLVM_ENABLE_DUMP=ON"
-	  "-DLLVM_LINK_LLVM_DYLIB=ON"))))))
+           "-DLLVM_INSTALL_UTILS=ON"
+           "-DLLVM_BUILD_TESTS=ON"
+           "-DLLVM_ENABLE_FFI=ON"
+           "-DLLVM_ENABLE_RTTI=ON"
+           ;; "-DLLVM_HOST_TRIPLE=${stdenv.hostPlatform.config}"
+           ;; "-DLLVM_DEFAULT_TARGET_TRIPLE=${stdenv.hostPlatform.config}"
+           ;; "-DLLVM_EXPERIMENTAL_TARGETS_TO_BUILD=WebAssembly"
+           "-DLLVM_ENABLE_DUMP=ON"
+           "-DLLVM_LINK_LLVM_DYLIB=ON"))))))
 
 (define-public julia
   (package
     (name "julia")
-    (version "1.1.1")
+    (version "1.3.1")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -166,7 +191,9 @@
                     version "/julia-" version ".tar.gz"))
               (sha256
                (base32
-                "0hk983mywimclgnjc41zmlppm5kfdz2aj85ky07p49ilcqxi998f"))))
+                "1nwkmr9j55g1zkxdchnid1h022s0is52vx23niksshgvh793g41x"))
+              (patches
+               (search-patches "julia-SOURCE_DATE_EPOCH-mtime.patch"))))
     (build-system gnu-build-system)
     (arguments
      `(#:test-target "test"
@@ -188,32 +215,27 @@
          (add-after 'unpack 'prepare-deps
            (lambda* (#:key inputs #:allow-other-keys)
              (mkdir "deps/srccache")
-             (copy-file (assoc-ref inputs "dsfmt")
-                        "deps/srccache/dsfmt-2.2.3.tar.gz")
+             ;; no USE_SYSTEM_{OBJCONV/LIBWHICH} option
              (copy-file (assoc-ref inputs "objconv")
                         "deps/srccache/objconv.zip")
-             (copy-file (assoc-ref inputs "suitesparse")
-                        "deps/srccache/SuiteSparse-4.4.5.tar.gz")
-             (copy-file (string-append (assoc-ref inputs "virtualenv")
-                                       "/bin/virtualenv")
-                        "julia-env")
              (copy-file (assoc-ref inputs "libwhich")
                         (string-append "deps/srccache/libwhich-"
                                        "81e9723c0273d78493dc8c8ed570f68d9ce7e89e"
                                        ".tar.gz"))
-             (copy-file (assoc-ref inputs "rmath")
-                        "deps/srccache/Rmath-julia-0.1.tar.gz")
 
-	     ;; needed by libwhich
-	     (setenv "LD_LIBRARY_PATH"
-		     (string-join (map (lambda (pkg)
+             ;; needed by libwhich
+             (setenv "LD_LIBRARY_PATH"
+                     (string-join (map (lambda (pkg)
                                          (string-append (assoc-ref inputs pkg)
                                                         "/lib"))
-                                       '("arpack-ng" "fftw" "gmp" "lapack"
-			                 "libgit2" "mpfr" "openblas" "openlibm"
-			                 "openspecfun" "pcre2"))
+                                       '("arpack-ng" "curl" "dsfmt"
+                                         "gmp" "lapack"
+                                         "libssh2" "libgit2"
+                                         "mbedtls" "mpfr"
+                                         "openblas" "openlibm" "pcre2"
+                                         "suitesparse"))
                                   ":"))
-	     #t))
+             #t))
          ;; FIXME: Building the documentation requires Julia packages that
          ;; would be downloaded from the Internet.  We should build them in a
          ;; separate build phase.
@@ -229,172 +251,152 @@
            ;; Some tests require a home directory to be set.
            (lambda _ (setenv "HOME" "/tmp") #t))
          (add-after 'unpack 'hardcode-soname-map
-          ;; ./src/runtime_ccall.cpp creates a map from library names to paths
-          ;; using the output of "/sbin/ldconfig -p".  Since ldconfig is not
-          ;; used in Guix, we patch runtime_ccall.cpp to contain a static map.
-          (lambda* (#:key inputs #:allow-other-keys)
-            (use-modules (ice-9 match))
-            (substitute* "src/runtime_ccall.cpp"
-              ;; Patch out invocations of '/sbin/ldconfig' to avoid getting
-              ;; error messages about missing '/sbin/ldconfig' on Guix System.
-              (("popen\\(.*ldconfig.*\\);")
-               "NULL;\n")
-
-              ;; Populate 'sonameMap'.
-              (("jl_read_sonames.*;")
-               (string-join
-                (map (match-lambda
-                       ((input libname soname)
-                        (string-append
-                         "sonameMap[\"" libname "\"] = "
-                         "\"" (assoc-ref inputs input) "/lib/" soname "\";")))
-                     '(("libc"        "libc"           "libc.so.6")
-                       ("pcre2"       "libpcre2-8"     "libpcre2-8.so")
-                       ("mpfr"        "libmpfr"        "libmpfr.so")
-                       ("openblas"    "libblas"        "libopenblas.so")
-                       ("arpack-ng"   "libarpack"      "libarpack.so")
-                       ("lapack"      "liblapack"      "liblapack.so")
-                       ("libgit2"     "libgit2"        "libgit2.so")
-                       ("gmp"         "libgmp"         "libgmp.so")
-                       ("openspecfun" "libopenspecfun" "libopenspecfun.so")
-                       ("fftw"        "libfftw3"       "libfftw3_threads.so")
-                       ("fftwf"       "libfftw3f"      "libfftw3f_threads.so"))))))
-            (substitute* "base/math.jl"
-              (("const libm = Base.libm_name")
-               (string-append "const libm = \""
-                              (assoc-ref inputs "openlibm")
-                              "/lib/libopenlibm.so"
-                              "\""))
-              (("const openspecfun = \"libopenspecfun\"")
-               (string-append "const openspecfun = \""
-                              (assoc-ref inputs "openspecfun")
-                              "/lib/libopenspecfun.so"
-                              "\"")))
-            #t))
+           ;; ./src/runtime_ccall.cpp creates a map from library names to paths
+           ;; using the output of "/sbin/ldconfig -p".  Since ldconfig is not
+           ;; used in Guix, we patch runtime_ccall.cpp to contain a static map.
+           (lambda* (#:key inputs #:allow-other-keys)
+             (substitute* "base/math.jl"
+               (("const libm = Base.libm_name")
+                (string-append "const libm = \""
+                               (assoc-ref inputs "openlibm")
+                               "/lib/libopenlibm.so"
+                               "\"")))
+             #t))
          (add-before 'build 'fix-include-and-link-paths
-          (lambda* (#:key inputs #:allow-other-keys)
-            ;; LIBUTF8PROC is a linker flag, not a build target.  It is
-            ;; included in the LIBFILES_* variable which is used as a
-            ;; collection of build targets and a list of libraries to link
-            ;; against.
-            (substitute* "src/flisp/Makefile"
-              (("\\$\\(BUILDDIR\\)/\\$\\(EXENAME\\): \\$\\(OBJS\\) \\$\\(LIBFILES_release\\)")
-               "$(BUILDDIR)/$(EXENAME): $(OBJS) $(LLT_release)")
-              (("\\$\\(BUILDDIR\\)/\\$\\(EXENAME\\)-debug: \\$\\(DOBJS\\) \\$\\(LIBFILES_debug\\)")
-               "$(BUILDDIR)/$(EXENAME)-debug: $(DOBJS) $(LLT_debug)"))
+           (lambda* (#:key inputs #:allow-other-keys)
+             ;; LIBUTF8PROC is a linker flag, not a build target.  It is
+             ;; included in the LIBFILES_* variable which is used as a
+             ;; collection of build targets and a list of libraries to link
+             ;; against.
+             (substitute* "src/flisp/Makefile"
+               (("\\$\\(BUILDDIR\\)/\\$\\(EXENAME\\)\\$\\(EXE\\): \\$\\(OBJS\\) \\$\\(LIBFILES_release\\)")
+                "$(BUILDDIR)/$(EXENAME)$(EXE): $(OBJS) $(LLT_release)")
+               (("\\$\\(BUILDDIR\\)/\\$\\(EXENAME\\)-debug$(EXE): \\$\\(DOBJS\\) \\$\\(LIBFILES_debug\\)")
+                "$(BUILDDIR)/$(EXENAME)-debug\\$\\(EXE\\): $(DOBJS) $(LLT_debug)"))
 
-            ;; The REPL must be linked with libuv.
-            (substitute* "ui/Makefile"
-              (("JLDFLAGS \\+= ")
-               (string-append "JLDFLAGS += "
-                              (assoc-ref %build-inputs "libuv")
-                              "/lib/libuv.so ")))
+             ;; The REPL must be linked with libuv.
+             (substitute* "ui/Makefile"
+               (("JLDFLAGS \\+= ")
+                (string-append "JLDFLAGS += "
+                               (assoc-ref %build-inputs "libuv")
+                               "/lib/libuv.so ")))
 
-            (substitute* "base/Makefile"
-              (("\\$\\(build_includedir\\)/uv/errno.h")
-               (string-append (assoc-ref inputs "libuv")
-                              "/include/uv/errno.h")))
-            #t))
+             (substitute* "base/Makefile"
+               (("\\$\\(build_includedir\\)/uv/errno.h")
+                (string-append (assoc-ref inputs "libuv")
+                               "/include/uv/errno.h")))
+             #t))
          (add-before 'build 'replace-default-shell
-          (lambda _
-            (substitute* "base/client.jl"
-              (("/bin/sh") (which "sh")))
-            #t))
-         (add-after 'unpack 'hardcode-paths
            (lambda _
-             (substitute* "stdlib/InteractiveUtils/src/InteractiveUtils.jl"
-               (("`which") (string-append "`" (which "which")))
-               (("`wget")  (string-append "`" (which "wget"))))
+             (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 'check 'disable-broken-tests
            (lambda _
-             (define (touch file-name)
-               (call-with-output-file file-name (const #t)))
-	     ;; FIXME: All git tests works except this one. But *THIS* "fix"
-             ;; is not working, so right now I'm disabling all libgit2.jl tests
-	     ;; (substitute* "stdlib/LibGit2/test/libgit2.jl"
-	     ;; (("!LibGit2.use_http_path(cfg, github_cred)") "true")
-	     ;; (("LibGit2.use_http_path(cfg, mygit_cred)") "true"))
-             (map (lambda (test)
-                    (delete-file test)
-                    (touch test))
-	          '("stdlib/Sockets/test/runtests.jl"
-		    "stdlib/Distributed/test/runtests.jl"
-                    ;; FIXME: see above
-		    "stdlib/LibGit2/test/libgit2.jl"))
-	     (substitute* "test/choosetests.jl"
-	       ;; These tests fail, probably because some of the input
-	       ;; binaries have been stripped and thus backtraces don't look
-	       ;; as expected.
-	       (("\"backtrace\",") "")
-	       (("\"cmdlineargs\",") ""))
-	     #t)))
+             (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\",
+                                          \"stress\",\"precompile\",
+                                          \"client\",\"stacktraces\"]),
+                                       testnames)"))
+             ;; When HOME is not set, julia calls uv_os_homedir, which in
+             ;; turns call getpwuid_r. Add the HOME env variable to the
+             ;; external julia call to fix this
+             (substitute* "test/cmdlineargs.jl"
+               (("\"JULIA_PROJECT\"") "\"HOME\"=>\"/tmp\", \"JULIA_PROJECT\""))
+             ;; 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"))
+             #t))
+       (add-after 'install 'make-wrapper
+         (lambda* (#:key inputs outputs #:allow-other-keys)
+           (let* ((out (assoc-ref outputs "out"))
+                  (bin (string-append out "/bin"))
+                  (program "julia"))
+             (with-directory-excursion bin
+               (wrap-program program
+                             `("JULIA_LOAD_PATH" ":" prefix
+                               ("" "$JULIA_LOAD_PATH")))
+               (wrap-program program
+                             `("JULIA_DEPOT_PATH" ":" prefix
+                               ("" "$JULIA_DEPOT_PATH"))))
+             #t))))
        #:make-flags
        (list
-        (string-append "prefix=" (assoc-ref %outputs "out"))
-        (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"))
-
-        "CONFIG_SHELL=bash"     ;needed to build bundled libraries
-        "USE_SYSTEM_DSFMT=0"    ;not packaged for Guix and upstream has no
-                                ;build system for a shared library.
-        "USE_SYSTEM_LAPACK=1"
-        "USE_SYSTEM_BLAS=1"
-        "USE_BLAS64=0"          ;needed when USE_SYSTEM_BLAS=1
-        "LIBBLAS=-lopenblas"
-        "LIBBLASNAME=libopenblas"
+         (string-append "prefix=" (assoc-ref %outputs "out"))
+         (string-append "PREFIX=" (assoc-ref %outputs "out"))
 
-        "USE_SYSTEM_FFTW=1"
-        "LIBFFTWNAME=libfftw3"
-        "LIBFFTWFNAME=libfftw3f"
+         ;; 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"))
 
-        ;; TODO: Suitesparse does not install shared libraries, so we cannot
-        ;; use the suitesparse package.
-        ;; "USE_SYSTEM_SUITESPARSE=1"
-        ;; (string-append "SUITESPARSE_INC=-I "
-        ;;                (assoc-ref %build-inputs "suitesparse")
-        ;;                "/include")
+         "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"
+         "USE_SYSTEM_BLAS=1"
+         "USE_BLAS64=0"          ;needed when USE_SYSTEM_BLAS=1
+         "LIBBLAS=-lopenblas"
+         "LIBBLASNAME=libopenblas"
 
-        "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=6.0.1"
+         "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=6.0.1"
 
-	"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_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_GMP=1"
-	"USE_SYSTEM_MPFR=1"
-	"USE_SYSTEM_ARPACK=1"
-	"USE_SYSTEM_LIBGIT2=1"
-	"USE_SYSTEM_ZLIB=1"
-	"USE_SYSTEM_OPENSPECFUN=1")))
+         "USE_SYSTEM_GMP=1"
+         "USE_SYSTEM_MPFR=1"
+         "USE_SYSTEM_ARPACK=1"
+         "USE_SYSTEM_LIBGIT2=1"
+         (string-append "LIBUV="
+                        (assoc-ref %build-inputs "libuv")
+                        "/lib/libuv.so")
+         (string-append "LIBUV_INC="
+                        (assoc-ref %build-inputs "libuv")
+                        "/include")
+         "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>.
@@ -403,12 +405,12 @@
        ("coreutils" ,coreutils) ;for bindings to "mkdir" and the like
        ("lapack" ,lapack)
        ("openblas" ,openblas) ;Julia does not build with Atlas
-       ("libunwind" ,libunwind)
+       ("libunwind" ,libunwind-julia)
        ("openlibm" ,openlibm)
-       ("openspecfun" ,openspecfun)
+       ("mbedtls" ,mbedtls-apache)
+       ("curl" ,curl)
        ("libgit2" ,libgit2)
-       ("fftw" ,fftw)
-       ("fftwf" ,fftwf)
+       ("libssh2" ,libssh2)
        ("fortran" ,gfortran)
        ("libuv" ,libuv-julia)
        ("pcre2" ,pcre2)
@@ -418,31 +420,9 @@
        ("which" ,which)
        ("zlib" ,zlib)
        ("gmp" ,gmp)
-       ("virtualenv" ,python2-virtualenv)
-       ;; FIXME: The following inputs are downloaded from upstream to allow us
-       ;; to use the lightweight Julia release tarball.  Ideally, these inputs
-       ;; would eventually be replaced with proper Guix packages.
-
-       ;; TODO: run "make -f contrib/repackage_system_suitesparse4.make" to copy static lib
-       ;; Find dependency versions here:
-       ;; https://raw.githubusercontent.com/JuliaLang/julia/77a2c1e245c85812dc1c7687540beedecc52758f/deps/Versions.make
-       ("rmath"
-	,(origin
-	   (method git-fetch)
-	   (uri (git-reference
-                 (url "https://github.com/JuliaLang/Rmath-julia")
-                 (commit "v0.1")))
-           (file-name "rmath-julia-0.1-checkout")
-	   (sha256
-	    (base32
-	     "1zkpy0cg5zivq40zbhbdgj9128fqzs2j94wkwih8nc6xaj3gp9p6"))))
-       ("suitesparse"
-        ,(origin
-           (method url-fetch)
-           (uri "http://faculty.cse.tamu.edu/davis/SuiteSparse/SuiteSparse-4.4.5.tar.gz")
-           (sha256
-            (base32
-             "1jcbxb8jx5wlcixzf6n5dca2rcfx6mlcms1k2rl5gp67ay3bix43"))))
+       ("suitesparse" ,suitesparse)
+       ;; Find dependencies versions here:
+       ;; https://raw.githubusercontent.com/JuliaLang/julia/v1.3.0/deps/Versions.make
        ("objconv"
         ,(origin
            (method url-fetch)
@@ -453,29 +433,21 @@
             (base32
              "0wp6ld9vk11f4nnkn56627zmlv9k5vafi99qa3yyn1pgcd61zcfs"))))
        ("libwhich"
-	,(let ((commit "81e9723c0273d78493dc8c8ed570f68d9ce7e89e"))
+        ,(let ((commit "81e9723c0273d78493dc8c8ed570f68d9ce7e89e"))
            (origin
              ;; Note: We use a /tarball URL, but that's because Julia's build
              ;; system checks the hash of that tarball; thus we can't use
              ;; 'git-fetch'.
-	     (method url-fetch)
-	     (uri (string-append
-                   "https://api.github.com/repos/vtjnash/libwhich/tarball/"
-                   commit))
+             (method url-fetch)
+             (uri (string-append
+                    "https://api.github.com/repos/vtjnash/libwhich/tarball/"
+                    commit))
              (file-name (string-append "libwhich-" (string-take commit 7)
                                        ".tar.gz"))
-	     (sha256
-	      (base32
-	       "1p7zg31kpmpbmh1znrk1xrbd074agx13b9q4dcw8n2zrwwdlbz3b")))))
-       ("dsfmt"
-        ,(origin
-           (method url-fetch)
-           (uri (string-append
-                 "http://www.math.sci.hiroshima-u.ac.jp/~m-mat/MT/"
-                 "SFMT/dSFMT-src-2.2.3.tar.gz"))
-           (sha256
-            (base32
-             "03kaqbjbi6viz0n33dk5jlf6ayxqlsq4804n7kwkndiga9s4hd42"))))))
+             (sha256
+              (base32
+               "1p7zg31kpmpbmh1znrk1xrbd074agx13b9q4dcw8n2zrwwdlbz3b")))))
+       ("dsfmt" ,dsfmt)))
     (native-inputs
      `(("openssl" ,openssl)
        ("perl" ,perl)
@@ -483,9 +455,12 @@
        ("pkg-config" ,pkg-config)
        ("python" ,python-2)))
     (native-search-paths
-     (list (search-path-specification
-            (variable "JULIA_LOAD_PATH")
-            (files (list "share/julia/packages/")))))
+      (list (search-path-specification
+              (variable "JULIA_LOAD_PATH")
+              (files (list "share/julia/packages/")))
+            (search-path-specification
+              (variable "JULIA_DEPOT_PATH")
+              (files (list "share/julia/")))))
     ;; Julia is not officially released for ARM and MIPS.
     ;; See https://github.com/JuliaLang/julia/issues/10639
     (supported-systems '("i686-linux" "x86_64-linux" "aarch64-linux"))