Merge remote-tracking branch 'origin/master' into wip-texlive

1 files changed, 180 insertions, 82 deletions

diff --git a/gnu/packages/julia.scm b/gnu/packages/julia.scm
index fa9709c40c..43254f25fd 100644
--- a/gnu/packages/julia.scm
+++ b/gnu/packages/julia.scm
@@ -47,9 +47,12 @@
   #:use-module (ice-9 match))
 
 (define libuv-julia
-  (let ((commit "52d72a52cc7ccd570929990f010ed16e2ec604c8")
-        (revision "5"))
-    (package (inherit libuv)
+  (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
+    (package
+      (inherit libuv)
       (name "libuv-julia")
       (version (string-append "1.9.0-" revision "." (string-take commit 8)))
       (source (origin
@@ -60,7 +63,7 @@
                 (file-name (string-append name "-" version "-checkout"))
                 (sha256
                  (base32
-                  "1daxh6ci6q7znxxajr3bm16dd53ragm0d681wf4kzg542qnjq3lh"))))
+                  "17pn2xmqaramilx897s9grs966i5246gi6sric5alch4g9j4685n"))))
       (build-system gnu-build-system)
       (arguments
        (substitute-keyword-arguments (package-arguments libuv)
@@ -69,22 +72,93 @@
              (delete 'autogen)))))
       (home-page "https://github.com/JuliaLang/libuv"))))
 
-(define libunwind-for-julia
+(define (llvm-patch-url version name)
+  (string-append "https://raw.githubusercontent.com/JuliaLang/julia/v" version
+		 "/deps/patches/" name))
+
+(define (llvm-patch name sha)
+  (let ((version "1.1.1"))
+    (origin (method url-fetch)
+	    (uri (llvm-patch-url version name))
+	    (sha256 (base32 sha))
+	    (file-name name))))
+
+(define llvm-julia
   (package
-    (inherit libunwind)
-    (version "1.1-julia2")
+    (inherit llvm-6)
+    (name "llvm-julia")
     (source (origin
               (method url-fetch)
-              (uri (string-append "https://s3.amazonaws.com/julialang/src/"
-                                  "libunwind-" version ".tar.gz"))
+              (uri "http://releases.llvm.org/6.0.1/llvm-6.0.1.src.tar.xz")
               (sha256
                (base32
-                "0499x7sg2v18a6cry6l8y713cgmic0adnjph8i0xr1db9p7n8qyv"))))))
+                "1qpls3vk85lydi5b4axl0809fv932qgsqgdgrk098567z4jc7mmn"))
+              ;; 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")))))
+    (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"
+
+          ;; 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"))))))
 
 (define-public julia
   (package
     (name "julia")
-    (version "0.6.0")
+    (version "1.1.1")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -92,7 +166,7 @@
                     version "/julia-" version ".tar.gz"))
               (sha256
                (base32
-                "0rd6lcc9sic10q1j3c6f9qr901i1c4554m93n2sz5b3mh37byqhw"))))
+                "0hk983mywimclgnjc41zmlppm5kfdz2aj85ky07p49ilcqxi998f"))))
     (build-system gnu-build-system)
     (arguments
      `(#:test-target "test"
@@ -123,9 +197,23 @@
              (copy-file (string-append (assoc-ref inputs "virtualenv")
                                        "/bin/virtualenv")
                         "julia-env")
-             (copy-file (assoc-ref inputs "unicode-data")
-                        "doc/UnicodeData.txt")
-             #t))
+             (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)
+                                         (string-append (assoc-ref inputs pkg)
+                                                        "/lib"))
+                                       '("arpack-ng" "fftw" "gmp" "lapack"
+			                 "libgit2" "mpfr" "openblas" "openlibm"
+			                 "openspecfun" "pcre2"))
+                                  ":"))
+	     #t))
          ;; FIXME: Building the documentation requires Julia packages that
          ;; would be downloaded from the Internet.  We should build them in a
          ;; separate build phase.
@@ -168,19 +256,9 @@
                        ("lapack"      "liblapack"      "liblapack.so")
                        ("libgit2"     "libgit2"        "libgit2.so")
                        ("gmp"         "libgmp"         "libgmp.so")
-                       ("openlibm"    "libopenlibm"    "libopenlibm.so")
                        ("openspecfun" "libopenspecfun" "libopenspecfun.so")
                        ("fftw"        "libfftw3"       "libfftw3_threads.so")
                        ("fftwf"       "libfftw3f"      "libfftw3f_threads.so"))))))
-            (substitute* "base/fft/FFTW.jl"
-              (("const libfftw = Base.libfftw_name")
-               (string-append "const libfftw = \""
-                              (assoc-ref inputs "fftw") "/lib/libfftw3_threads.so"
-                              "\""))
-              (("const libfftwf = Base.libfftwf_name")
-               (string-append "const libfftwf = \""
-                              (assoc-ref inputs "fftwf") "/lib/libfftw3f_threads.so"
-                              "\"")))
             (substitute* "base/math.jl"
               (("const libm = Base.libm_name")
                (string-append "const libm = \""
@@ -192,11 +270,6 @@
                               (assoc-ref inputs "openspecfun")
                               "/lib/libopenspecfun.so"
                               "\"")))
-            (substitute* "base/pcre.jl"
-              (("const PCRE_LIB = \"libpcre2-8\"")
-               (string-append "const PCRE_LIB = \""
-                              (assoc-ref inputs "pcre2")
-                              "/lib/libpcre2-8.so" "\"")))
             #t))
          (add-before 'build 'fix-include-and-link-paths
           (lambda* (#:key inputs #:allow-other-keys)
@@ -218,9 +291,9 @@
                               "/lib/libuv.so ")))
 
             (substitute* "base/Makefile"
-              (("\\$\\(build_includedir\\)/uv-errno.h")
+              (("\\$\\(build_includedir\\)/uv/errno.h")
                (string-append (assoc-ref inputs "libuv")
-                              "/include/uv-errno.h")))
+                              "/include/uv/errno.h")))
             #t))
          (add-before 'build 'replace-default-shell
           (lambda _
@@ -229,37 +302,37 @@
             #t))
          (add-after 'unpack 'hardcode-paths
            (lambda _
-             (substitute* "base/interactiveutil.jl"
+             (substitute* "stdlib/InteractiveUtils/src/InteractiveUtils.jl"
                (("`which") (string-append "`" (which "which")))
                (("`wget")  (string-append "`" (which "wget"))))
              #t))
          (add-before 'check 'disable-broken-tests
            (lambda _
-             ;; Adjust expected error messages to match what current libgit2
-             ;; provides.
-             (substitute* "test/libgit2.jl"
-               (("Invalid Content-Type") "invalid Content-Type")
-               (("Failed to resolve path") "failed to resolve path"))
-
-             (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\",") "")
-               (("\"compile\",") "")
-               (("\"replutil\",") "")
-               (("\"cmdlineargs\",") "")
-               ;; FIXME: This test fails with the following error:
-               ;; Error in testset file:
-               ;; Test Failed
-               ;;   Expression: download("ba\0d", "good")
-               ;;     Expected: ArgumentError
-               ;;       Thrown: Base.UVError
-               (("\"file\",") ""))
-             #t)))
+             (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)))
        #: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.
@@ -278,6 +351,8 @@
         "USE_SYSTEM_LAPACK=1"
         "USE_SYSTEM_BLAS=1"
         "USE_BLAS64=0"          ;needed when USE_SYSTEM_BLAS=1
+        "LIBBLAS=-lopenblas"
+        "LIBBLASNAME=libopenblas"
 
         "USE_SYSTEM_FFTW=1"
         "LIBFFTWNAME=libfftw3"
@@ -296,26 +371,29 @@
                        (assoc-ref %build-inputs "utf8proc")
                        "/include")
         "USE_SYSTEM_LLVM=1"
-        "USE_LLVM_SHLIB=0" ; FIXME: fails when set to 1
+	"LLVM_VER=6.0.1"
 
-        "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_OPENSPECFUN=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")))
     (inputs
-     `(("llvm" ,llvm-3.9.1)
+     `(("llvm" ,llvm-julia)
 
        ;; 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
@@ -325,7 +403,7 @@
        ("coreutils" ,coreutils) ;for bindings to "mkdir" and the like
        ("lapack" ,lapack)
        ("openblas" ,openblas) ;Julia does not build with Atlas
-       ("libunwind" ,libunwind-for-julia)
+       ("libunwind" ,libunwind)
        ("openlibm" ,openlibm)
        ("openspecfun" ,openspecfun)
        ("libgit2" ,libgit2)
@@ -346,6 +424,18 @@
        ;; 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)
@@ -362,6 +452,21 @@
            (sha256
             (base32
              "0wp6ld9vk11f4nnkn56627zmlv9k5vafi99qa3yyn1pgcd61zcfs"))))
+       ("libwhich"
+	,(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))
+             (file-name (string-append "libwhich-" (string-take commit 7)
+                                       ".tar.gz"))
+	     (sha256
+	      (base32
+	       "1p7zg31kpmpbmh1znrk1xrbd074agx13b9q4dcw8n2zrwwdlbz3b")))))
        ("dsfmt"
         ,(origin
            (method url-fetch)
@@ -376,14 +481,7 @@
        ("perl" ,perl)
        ("patchelf" ,patchelf)
        ("pkg-config" ,pkg-config)
-       ("python" ,python-2)
-       ("unicode-data"
-        ,(origin
-           (method url-fetch)
-           (uri "http://www.unicode.org/Public/9.0.0/ucd/UnicodeData.txt")
-           (sha256
-            (base32
-             "13zfannnr6sa6s27ggvcvzmh133ndi38pfyxsssvjmw2s8ac9pv8"))))))
+       ("python" ,python-2)))
     ;; 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"))