Merge master into staging-next

5 files changed, 216 insertions, 16 deletions

diff --git a/pkgs/development/compilers/julia/1.3.nix b/pkgs/development/compilers/julia/1.3.nix
new file mode 100644
index 000000000000..5b1300ba240b
--- /dev/null
+++ b/pkgs/development/compilers/julia/1.3.nix
@@ -0,0 +1,170 @@
+{ stdenv, fetchurl, fetchzip, fetchFromGitHub
+# build tools
+, gfortran, m4, makeWrapper, patchelf, perl, which, python2
+, cmake
+# libjulia dependencies
+, libunwind, readline, utf8proc, zlib
+# standard library dependencies
+, curl, fftwSinglePrec, fftw, gmp, libgit2, mpfr, openlibm, openspecfun, pcre2
+# linear algebra
+, openblas, arpack
+# Darwin frameworks
+, CoreServices, ApplicationServices
+}:
+
+with stdenv.lib;
+
+# All dependencies must use the same OpenBLAS.
+let
+  arpack_ = arpack;
+in
+let
+  arpack = arpack_.override { inherit openblas; };
+in
+
+let 
+  majorVersion = "1";
+  minorVersion = "3";
+  maintenanceVersion = "1";
+  src_sha256 = "0q9a7yc3b235psrwl5ghyxgwly25lf8n818l8h6bkf2ymdbsv5p6";
+  version = "${majorVersion}.${minorVersion}.${maintenanceVersion}";
+in 
+
+stdenv.mkDerivation rec {
+  pname = "julia";
+  inherit version;
+
+   src = fetchzip {
+     url = "https://github.com/JuliaLang/julia/releases/download/v${majorVersion}.${minorVersion}.${maintenanceVersion}/julia-${majorVersion}.${minorVersion}.${maintenanceVersion}-full.tar.gz";
+     sha256 = src_sha256;
+   };
+
+  prePatch = ''
+    export PATH=$PATH:${cmake}/bin
+    '';
+
+  patches = [
+    ./use-system-utf8proc-julia-1.3.patch
+
+    # Julia recompiles a precompiled file if the mtime stored *in* the
+    # .ji file differs from the mtime of the .ji file.  This
+    # doesn't work in Nix because Nix changes the mtime of files in
+    # the Nix store to 1. So patch Julia to accept mtimes of 1.
+    ./allow_nix_mtime.patch
+  ];
+
+  postPatch = ''
+    patchShebangs . contrib
+    for i in backtrace cmdlineargs; do
+      mv test/$i.jl{,.off}
+      touch test/$i.jl
+    done
+    rm stdlib/Sockets/test/runtests.jl && touch stdlib/Sockets/test/runtests.jl
+    rm stdlib/Distributed/test/runtests.jl && touch stdlib/Distributed/test/runtests.jl
+    sed -e 's/Invalid Content-Type:/invalid Content-Type:/g' -i ./stdlib/LibGit2/test/libgit2.jl
+    sed -e 's/Failed to resolve /failed to resolve /g' -i ./stdlib/LibGit2/test/libgit2.jl
+  '';
+
+  buildInputs = [
+    arpack fftw fftwSinglePrec gmp libgit2 libunwind mpfr
+    pcre2.dev openblas openlibm openspecfun readline utf8proc
+    zlib
+  ]
+  ++ stdenv.lib.optionals stdenv.isDarwin [CoreServices ApplicationServices]
+  ;
+
+  nativeBuildInputs = [ curl gfortran m4 makeWrapper patchelf perl python2 which ];
+
+  makeFlags =
+    let
+      arch = head (splitString "-" stdenv.system);
+      march = { x86_64 = stdenv.hostPlatform.platform.gcc.arch or "x86-64"; i686 = "pentium4"; }.${arch}
+              or (throw "unsupported architecture: ${arch}");
+      # Julia requires Pentium 4 (SSE2) or better
+      cpuTarget = { x86_64 = "x86-64"; i686 = "pentium4"; }.${arch}
+                  or (throw "unsupported architecture: ${arch}");
+      # Julia applies a lot of patches to its dependencies, so for now do not use the system LLVM
+      # https://github.com/JuliaLang/julia/tree/master/deps/patches
+    in [
+      "ARCH=${arch}"
+      "MARCH=${march}"
+      "JULIA_CPU_TARGET=${cpuTarget}"
+      "PREFIX=$(out)"
+      "prefix=$(out)"
+      "SHELL=${stdenv.shell}"
+
+      "USE_SYSTEM_BLAS=1"
+      "USE_BLAS64=${if openblas.blas64 then "1" else "0"}"
+      "LIBBLAS=-lopenblas"
+      "LIBBLASNAME=libopenblas"
+
+      "USE_SYSTEM_LAPACK=1"
+      "LIBLAPACK=-lopenblas"
+      "LIBLAPACKNAME=libopenblas"
+
+      "USE_SYSTEM_ARPACK=1"
+      "USE_SYSTEM_FFTW=1"
+      "USE_SYSTEM_GMP=1"
+      "USE_SYSTEM_LIBGIT2=1"
+      "USE_SYSTEM_LIBUNWIND=1"
+
+      "USE_SYSTEM_MPFR=1"
+      "USE_SYSTEM_OPENLIBM=1"
+      "USE_SYSTEM_OPENSPECFUN=1"
+      "USE_SYSTEM_PATCHELF=1"
+      "USE_SYSTEM_PCRE=1"
+      "PCRE_CONFIG=${pcre2.dev}/bin/pcre2-config"
+      "PCRE_INCL_PATH=${pcre2.dev}/include/pcre2.h"
+      "USE_SYSTEM_READLINE=1"
+      "USE_SYSTEM_UTF8PROC=1"
+      "USE_SYSTEM_ZLIB=1"
+
+      "USE_BINARYBUILDER=0"
+    ];
+
+  LD_LIBRARY_PATH = makeLibraryPath [
+    arpack fftw fftwSinglePrec gmp libgit2 mpfr openblas openlibm
+    openspecfun pcre2
+  ];
+
+  enableParallelBuilding = true;
+
+  doCheck = !stdenv.isDarwin;
+  checkTarget = "testall";
+  # Julia's tests require read/write access to $HOME
+  preCheck = ''
+    export HOME="$NIX_BUILD_TOP"
+  '';
+
+  preBuild = ''
+    sed -e '/^install:/s@[^ ]*/doc/[^ ]*@@' -i Makefile
+    sed -e '/[$](DESTDIR)[$](docdir)/d' -i Makefile
+    export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}
+  '';
+
+  postInstall = ''
+    # Symlink shared libraries from LD_LIBRARY_PATH into lib/julia,
+    # as using a wrapper with LD_LIBRARY_PATH causes segmentation
+    # faults when program returns an error:
+    #   $ julia -e 'throw(Error())'
+    find $(echo $LD_LIBRARY_PATH | sed 's|:| |g') -maxdepth 1 -name '*.${if stdenv.isDarwin then "dylib" else "so"}*' | while read lib; do
+      if [[ ! -e $out/lib/julia/$(basename $lib) ]]; then
+        ln -sv $lib $out/lib/julia/$(basename $lib)
+      fi
+    done
+  '';
+
+  passthru = {
+    inherit majorVersion minorVersion maintenanceVersion;
+    site = "share/julia/site/v${majorVersion}.${minorVersion}";
+  };
+
+  meta = {
+    description = "High-level performance-oriented dynamical language for technical computing";
+    homepage = https://julialang.org/;
+    license = stdenv.lib.licenses.mit;
+    maintainers = with stdenv.lib.maintainers; [ raskin rob garrison ];
+    platforms = [ "i686-linux" "x86_64-linux" "x86_64-darwin" ];
+    broken = stdenv.isi686;
+  };
+}
diff --git a/pkgs/development/compilers/julia/use-system-utf8proc-julia-1.3.patch b/pkgs/development/compilers/julia/use-system-utf8proc-julia-1.3.patch
new file mode 100644
index 000000000000..63e0ba9ab057
--- /dev/null
+++ b/pkgs/development/compilers/julia/use-system-utf8proc-julia-1.3.patch
@@ -0,0 +1,24 @@
+---
+ src/flisp/Makefile | 6 +++---
+ 1 file changed, 3 insertions(+), 3 deletions(-)
+
+
+diff --git a/src/flisp/Makefile b/src/flisp/Makefile
+index d97075e..6bebca7 100644
+--- a/src/flisp/Makefile
++++ b/src/flisp/Makefile
+@@ -32,9 +32,9 @@ OBJS := $(SRCS:%.c=$(BUILDDIR)/%.o)
+ DOBJS := $(SRCS:%.c=$(BUILDDIR)/%.dbg.obj)
+ LLT_release := $(LLT_BUILDDIR)/libsupport.a
+ LLT_debug := $(LLT_BUILDDIR)/libsupport-debug.a
+-LIBFILES_release := $(LLT_release) $(LIBUV) $(LIBUTF8PROC)
+-LIBFILES_debug := $(LLT_debug) $(LIBUV) $(LIBUTF8PROC)
+-LIBS :=
++LIBFILES_release := $(LLT_release) $(LIBUV)
++LIBFILES_debug := $(LLT_debug) $(LIBUV)
++LIBS := $(LIBUTF8PROC)
+ ifneq ($(OS),WINNT)
+ LIBS += -lpthread
+ endif
+
+-- 
diff --git a/pkgs/development/compilers/mint/default.nix b/pkgs/development/compilers/mint/default.nix
index 5f72bd3649b1..78cce113e9b4 100644
--- a/pkgs/development/compilers/mint/default.nix
+++ b/pkgs/development/compilers/mint/default.nix
@@ -1,15 +1,15 @@
-{ lib, fetchFromGitHub, crystal, zlib, openssl_1_0_2, duktape, which, libyaml }:
+{ lib, fetchFromGitHub, crystal, zlib, openssl, duktape, which, libyaml }:
 crystal.buildCrystalPackage rec {
-  version = "0.5.0";
+  version = "0.7.1";
   pname = "mint";
   src = fetchFromGitHub {
     owner = "mint-lang";
     repo = "mint";
     rev = version;
-    sha256 = "0vxbx38c390rd2ysvbwgh89v2232sh5rbsp3nk9wzb70jybpslvl";
+    sha256 = "18cg96kl4dn89bj6fm3080zzyd1r7rsfi17agdjjayd2v9fgs95l";
   };
 
-  buildInputs = [ openssl_1_0_2 ];
+  buildInputs = [ openssl ];
 
   # Update with
   #   nix-shell -p crystal2nix --run crystal2nix
diff --git a/pkgs/development/compilers/mint/shards.nix b/pkgs/development/compilers/mint/shards.nix
index dc6866e3af3d..b3583ac2cbaa 100644
--- a/pkgs/development/compilers/mint/shards.nix
+++ b/pkgs/development/compilers/mint/shards.nix
@@ -8,8 +8,8 @@
   ameba = {
     owner = "veelenga";
     repo = "ameba";
-    rev = "v0.9.1";
-    sha256 = "05q2ki9dpg23pllalv5p27f1m287kiicp97ziz0z7vv0vg1r8smj";
+    rev = "v0.10.1";
+    sha256 = "0dcw7px7g0c5pxpdlirhirqzhcc7gdwdfiwb9kgm4x1k74ghjgxq";
   };
   baked_file_system = {
     owner = "schovi";
@@ -26,8 +26,8 @@
   dotenv = {
     owner = "gdotdesign";
     repo = "cr-dotenv";
-    rev = "v0.2.0";
-    sha256 = "0zi2y1j2546xjhdzn7icmry0cjv82cx2cqmpgx5ml37c2pnb7kp7";
+    rev = "v0.3.1";
+    sha256 = "1xp7c3g8dj1hqk2b885qr4y0s8661gpp9q28lv6rhr0ckllc6zgz";
   };
   exception_page = {
     owner = "crystal-loot";
@@ -47,6 +47,12 @@
     rev = "v0.4.0";
     sha256 = "1w9ib6j4xhwxdxx58nzc06gw7ci7vga03vgj1z1bnklamb0b0l0k";
   };
+  markd = {
+    owner = "icyleaf";
+    repo = "markd";
+    rev = "v0.2.0";
+    sha256 = "0n27fndd77mlkgw1r4pf0sa8fz4gwsh7dpnjck95c0ml91cr8j1a";
+  };
   radix = {
     owner = "luislavena";
     repo = "radix";
diff --git a/pkgs/development/compilers/openjdk/8.nix b/pkgs/development/compilers/openjdk/8.nix
index 4231845792a9..f47d7939e48c 100644
--- a/pkgs/development/compilers/openjdk/8.nix
+++ b/pkgs/development/compilers/openjdk/8.nix
@@ -29,49 +29,49 @@ let
   jdk8 = fetchurl {
              name = "jdk8-${repover}.tar.gz";
              url = "${baseurl}/archive/${repover}.tar.gz";
-             sha256 = if stdenv.isAarch64 then "ca978112ca1bbdcafac231b39a23dc4da786eff8147c4e72b9807785afee48bb"
+             sha256 = if stdenv.isAarch64 then "0qpmr267qcxhmw398zbl1axd161yxn4k4hfz1jlxlmdvg70p7h90"
                       else "1crs4hmzmgm6fkwfq0d3xz9lph0nd33fngrqv2rz1mkkqcrjx18z";
           };
   langtools = fetchurl {
              name = "langtools-${repover}.tar.gz";
              url = "${baseurl}/langtools/archive/${repover}.tar.gz";
-             sha256 = if stdenv.isAarch64 then "ca978112ca1bbdcafac231b39a23dc4da786eff8147c4e72b9807785afee48bb"
+             sha256 = if stdenv.isAarch64 then "1rhhi4kgmxvnyl3ic5p008p1n7zyji5nw99blm1lr5fw7ry7df24"
                       else "1aaxd1rl7dlk4kxdivvqvripsbn0d5vny0jvjksycsm97vrfiry4";
           };
   hotspot = fetchurl {
              name = "hotspot-${repover}.tar.gz";
              url = "${baseurl}/hotspot/archive/${repover}.tar.gz";
-             sha256 = if stdenv.isAarch64 then "ca978112ca1bbdcafac231b39a23dc4da786eff8147c4e72b9807785afee48bb"
+             sha256 = if stdenv.isAarch64 then "0lphrhjqlavd6qlkh7h4sd2bqf5gd0cchkcnvy87703fbd7gy5ii"
                       else "18i4if16zikgda9k5bgqyx0p2104db23zlnclq512178z0p9yycb";
           };
   corba = fetchurl {
              name = "corba-${repover}.tar.gz";
              url = "${baseurl}/corba/archive/${repover}.tar.gz";
-             sha256 = if stdenv.isAarch64 then "ca978112ca1bbdcafac231b39a23dc4da786eff8147c4e72b9807785afee48bb"
+             sha256 = if stdenv.isAarch64 then "18h0v566v420d00na6x4jrs41v4aa39byk15fi8k6dcn0dmirhvg"
                       else "1298k8p2dsj7xc4h2ayk5nl4ssrcgncn06ysyqrmnwrb8gj8s1w4";
           };
   jdk = fetchurl {
              name = "jdk-${repover}.tar.gz";
              url = "${baseurl}/jdk/archive/${repover}.tar.gz";
-             sha256 = if stdenv.isAarch64 then "ca978112ca1bbdcafac231b39a23dc4da786eff8147c4e72b9807785afee48bb"
+             sha256 = if stdenv.isAarch64 then "0xxy7rkj8ah263nnzkd4mg9dai5qix3l9cyilm47dig5hv7g8aq0"
                       else "0vqlbks3cy3cnmnrnhbjkqinvp8bcy2h96xvx81cvlza4s2hszvz";
           };
   jaxws = fetchurl {
              name = "jaxws-${repover}.tar.gz";
              url = "${baseurl}/jaxws/archive/${repover}.tar.gz";
-             sha256 = if stdenv.isAarch64 then "ca978112ca1bbdcafac231b39a23dc4da786eff8147c4e72b9807785afee48bb"
+             sha256 = if stdenv.isAarch64 then "0ajqm2l9g5w5ag5s4vl4ldpbm99pqa6d342hrzvv7psqn3zf6ar5"
                       else "1wg9fbiz09arj0llavnzrmbhw8nx0dw8dcjkrzxw78rj1cadflzc";
           };
   jaxp = fetchurl {
              name = "jaxp-${repover}.tar.gz";
              url = "${baseurl}/jaxp/archive/${repover}.tar.gz";
-             sha256 = if stdenv.isAarch64 then "ca978112ca1bbdcafac231b39a23dc4da786eff8147c4e72b9807785afee48bb"
+             sha256 = if stdenv.isAarch64 then "03zjh6xvza05abxz9d9j2w9xndw9n07f8lrn6dymj7f4imals831"
                       else "1i5xrk8r8pcgnc68zrgp3hd1a1nzcm99swpmdnlb424qlg5nnrcf";
           };
   nashorn = fetchurl {
              name = "nashorn-${repover}.tar.gz";
              url = "${baseurl}/nashorn/archive/${repover}.tar.gz";
-             sha256 = if stdenv.isAarch64 then "ca978112ca1bbdcafac231b39a23dc4da786eff8147c4e72b9807785afee48bb"
+             sha256 = if stdenv.isAarch64 then "0n809w264ndxksva9c81x0m1fsyg8c627w571f72xxxl9c1bnrmp"
                       else "0qlxaz7sriy709vcyzz48s2v4p5h4d31my33whip018c4j5gkfqq";
           };
   openjdk8 = stdenv.mkDerivation {