Merge branch 'master' into staging

Hydra: ?compare=1415329

pkgs/development/compilers/ccl/default.nix

@@ -1,11 +1,11 @@
-{ stdenv, fetchsvn, fetchpatch, gcc, glibc, m4, coreutils }:
+{ stdenv, fetchurl, gcc, glibc, m4, coreutils }:
 
 let
   options = rec {
     /* TODO: there are also MacOS, FreeBSD and Windows versions */
     x86_64-linux = {
       arch = "linuxx86";
-      sha256 = "0g6mkl207ri3ib9w85i9w0sv7srz784pbxidz0d95p6qkvg6shba";
+      sha256 = "0hs1f3z7crgzvinpj990kv9gvbsipxvcvwbmk54n51nasvc5025q";
       runtime = "lx86cl64";
       kernel = "linuxx8664";
     };
@@ -17,7 +17,7 @@ let
     };
     armv7l-linux = {
       arch = "linuxarm";
-      sha256 = "0k6wxwyg3pmbb5xdkwma0i3rvbjmy3p604g4minjjc1drzsn1i0q";
+      sha256 = "0p0l1dzsygb6i1xxgbipjpxkn46xhq3jm41a34ga1qqp4x8lkr62";
       runtime = "armcl";
       kernel = "linuxarm";
     };
@@ -30,21 +30,13 @@ assert builtins.hasAttr stdenv.system options;
 
 stdenv.mkDerivation rec {
   name     = "ccl-${version}";
-  version  = "1.11";
-  revision = "16313";
+  version  = "1.11.5";
 
-  src = fetchsvn {
-    url = "http://svn.clozure.com/publicsvn/openmcl/release/${version}/${cfg.arch}/ccl";
-    rev = revision;
+  src = fetchurl {
+    url = "https://github.com/Clozure/ccl/releases/download/v${version}/ccl-${version}-${cfg.arch}.tar.gz";
     sha256 = cfg.sha256;
   };
 
-  patches = fetchpatch {
-    name = "ccl-1.11-glibc-2.26.patch";
-    url = https://patch-diff.githubusercontent.com/raw/Clozure/ccl/pull/80.patch;
-    sha256 = "02v6287w0nppfpvkn9dyd5rvq2zkgd47ia9gs17hrww2hgzr6agd";
-  };
-
   buildInputs = [ gcc glibc m4 ];
 
   CCL_RUNTIME = cfg.runtime;
@@ -52,7 +44,6 @@ stdenv.mkDerivation rec {
 
   postPatch = ''
     substituteInPlace lisp-kernel/${CCL_KERNEL}/Makefile \
-      --replace "svnversion" "echo ${revision}" \
       --replace "/bin/rm"    "${coreutils}/bin/rm" \
       --replace "/bin/echo"  "${coreutils}/bin/echo"
 

pkgs/development/compilers/sbcl/default.nix

@@ -1,4 +1,4 @@
-{ stdenv, fetchurl, fetchgit, writeText, sbclBootstrap
+{ stdenv, fetchurl, writeText, sbclBootstrap
 , sbclBootstrapHost ? "${sbclBootstrap}/bin/sbcl --disable-debugger --no-userinit --no-sysinit"
 , threadSupport ? (stdenv.isi686 || stdenv.isx86_64 || "aarch64-linux" == stdenv.system)
   # Meant for sbcl used for creating binaries portable to non-NixOS via save-lisp-and-die.
@@ -9,16 +9,11 @@
 
 stdenv.mkDerivation rec {
   name    = "sbcl-${version}";
-  version = "1.4.1.0.20171104";
+  version = "1.4.2";
 
-  #src = fetchurl {
-  #  url    = "mirror://sourceforge/project/sbcl/sbcl/${version}/${name}-source.tar.bz2";
-  #  sha256 = "1qdaf847g5p2zgq00ax5hdy4r82bl3ss382psd0kkca1h83cdiz8";
-  #};
-  src = fetchgit {
-    url    = "https://git.code.sf.net/p/sbcl/sbcl";
-    sha256 = "1fq34h8h8pax5q17w84kwv5amiaag3ikkq3cdmb31r64736mxi6r";
-    rev    = "11aa57d23bc464d6a6867a80e946907404ceadd1";
+  src = fetchurl {
+    url    = "mirror://sourceforge/project/sbcl/sbcl/${version}/${name}-source.tar.bz2";
+    sha256 = "05s7wsx6bsnx4h6w3d8yim9apbvi8ih0glmvkmgjz7nrad4abjwd";
   };
 
   patchPhase = ''

pkgs/development/haskell-modules/configuration-common.nix

@@ -453,8 +453,10 @@ self: super: {
   # https://github.com/basvandijk/threads/issues/10
   threads = dontCheck super.threads;
 
-  # https://github.com/purescript/purescript/pull/3041
-  purescript = doJailbreak super.purescript;
+  # https://github.com/NixOS/nixpkgs/issues/32138
+  purescript = super.purescript.override {
+    optparse-applicative = self.optparse-applicative_0_14_0_0;
+  };
 
   # Missing module.
   rematch = dontCheck super.rematch;            # https://github.com/tcrayford/rematch/issues/5

pkgs/development/interpreters/j/default.nix

@@ -1,57 +1,79 @@
-{ stdenv, fetchurl, readline }:
+{ stdenv, fetchFromGitHub, readline, libedit }:
 
 stdenv.mkDerivation rec {
   name = "j-${version}";
-  version = "701_b";
-  src = fetchurl {
-    url = "http://www.jsoftware.com/download/j${version}_source.tar.gz";
-    sha256 = "1gmjlpxcd647x690c4dxnf8h6ays8ndir6cib70h3zfnkrc34cys";
+  version = "806";
+  jtype = "release";
+  src = fetchFromGitHub {
+    owner = "jsoftware";
+    repo = "jsource";
+    rev = "j${version}-${jtype}";
+    sha256 = "0b9sbd5hbyr5454k0p53f03lpf03sz8mqwszaqi0vcs73bsprdjs";
   };
-  buildInputs = [ readline ];
+
+  buildInputs = [ readline libedit ];
   bits = if stdenv.is64bit then "64" else "32";
+  platform =
+    /*if stdenv.isRaspberryPi then "raspberry" else*/
+    if stdenv.isLinux then "linux" else
+    if stdenv.isDarwin then "darwin" else
+    "unknown";
 
   doCheck = true;
 
   buildPhase = ''
-    sed -i bin/jconfig -e '
-        s@bits=32@bits=${bits}@g;
-        s@readline=0@readline=1@;
-        s@LIBREADLINE=""@LIBREADLINE=" -lreadline "@;
-        s@-W1,soname,libj.so@-Wl,-soname,libj.so@
-        '
-    sed -i bin/build_libj -e 's@>& make.txt@ 2>\&1 | tee make.txt@'
+    export SOURCE_DIR=$(pwd)
+    export HOME=$TMPDIR
+    export JBIN=$HOME/j${bits}/bin
+    export JLIB=$SOURCE_DIR/jlibrary
+    mkdir -p $JBIN
 
-    sed -i f2.c -e 's/_isnan(\*wv)/_isnan(y)/'
+    cd make
 
-    touch *.c *.h
-    sh -o errexit bin/build_jconsole
-    [ -e j/bin/jconsole ]
-    sh -o errexit bin/build_libj
-    [ -e j/bin/libj.so ]
-    sh -o errexit bin/build_defs
-    [ -e defs/hostdefs.ijs ] && [ -e defs/netdefs.ijs ]
-    sh -o errexit bin/build_tsdll
-    [ -x libtsdll.so ]
+    patchShebangs .
+    sed -i jvars.sh -e '
+      s@~/gitdev/jsource@$SOURCE_DIR@;
+      s@~/jbld@$HOME@;
+      s@linux@${platform}@;
+      '
 
-    sed -i j/bin/profile.ijs -e "
-        s@userx=[.] *'.j'@userx=. '/.j'@;
-        s@bin,'/profilex.ijs'@user,'/profilex.ijs'@ ;
-        /install=./ainstall=. install,'/share/j'
-        "
+    sed -i $JLIB/bin/profile.ijs -e "s@'/usr/share/j/.*'@'$out/share/j'@;"
+
+    # For future versions, watch
+    # https://github.com/jsoftware/jsource/pull/4
+    cp ./jvars.sh $HOME
+
+    echo '
+      #define jversion   "${version}"
+      #define jplatform  "${platform}"
+      #define jtype      "${jtype}"         // release,beta,...
+      #define jlicense   "GPL3"
+      #define jbuilder   "unknown"  // website or email
+      ' > ../jsrc/jversion.h
+
+    ./build_jconsole.sh j${bits}
+    ./build_libj.sh j${bits}
   '';
 
   checkPhase = ''
-    echo 'i. 5' | j/bin/jconsole | fgrep "0 1 2 3 4"
+    echo 'i. 5' | $JBIN/jconsole | fgrep "0 1 2 3 4"
+
+    # Now run the real tests
+    cd $SOURCE_DIR/test
+    # for f in *.ijs
+    # do
+    #   echo $f
+    #   $JBIN/jconsole < $f
+    # done
   '';
 
   installPhase = ''
     mkdir -p "$out"
-    cp -r j/bin "$out/bin"
-    rm "$out/bin/profilex_template.ijs"
+    cp -r $JBIN "$out/bin"
 
     mkdir -p "$out/share/j"
-
-    cp -r docs j/addons j/system "$out/share/j"
+    cp -r $JLIB/{addons,system} "$out/share/j"
+    cp -r $JLIB/bin "$out"
   '';
 
   meta = with stdenv.lib; {

pkgs/development/libraries/armadillo/default.nix

@@ -1,12 +1,12 @@
 { stdenv, fetchurl, cmake, openblasCompat, superlu, hdf5 }:
 
 stdenv.mkDerivation rec {
-  version = "7.800.1";
+  version = "8.300.0";
   name = "armadillo-${version}";
 
   src = fetchurl {
     url = "mirror://sourceforge/arma/armadillo-${version}.tar.xz";
-    sha256 = "1nxq2jp4jlvinynv0l04rpdzpnkzdsng0d5vi3hilc0hlsjnbnjs";
+    sha256 = "0g6wcfrmb2hndz995wrlc80v6d39mhxf26lmycaqv5bjfq050ic5";
   };
 
   nativeBuildInputs = [ cmake ];

pkgs/development/libraries/armadillo/use-unix-config-on-OS-X.patch

@@ -1,10 +1,9 @@
 --- a/CMakeLists.txt
 +++ b/CMakeLists.txt
-@@ -84,7 +84,7 @@ message(STATUS "DETECT_HDF5                = ${DETECT_HDF5}"               )
- ##
- ## Find LAPACK and BLAS libraries, or their optimised versions
- ##
--
+@@ -152,6 +152,7 @@ message(STATUS "DETECT_HDF5                = ${DETECT_HDF5}"               )
+
+ set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} "${CMAKE_CURRENT_SOURCE_DIR}/cmake_aux/Modules/")
+
 +set(APPLE false)
  if(APPLE)
    

pkgs/development/libraries/science/math/fenics/default.nix

@@ -158,7 +158,7 @@ stdenv.mkDerivation {
   meta = {
     description = "The FEniCS Problem Solving Environment in Python and C++";
     homepage = http://fenicsproject.org/;
-    platforms = stdenv.lib.platforms.all;
+    platforms = stdenv.lib.platforms.darwin;
     license = stdenv.lib.licenses.lgpl3;
   };
 }

pkgs/development/libraries/udunits/default.nix

@@ -13,7 +13,7 @@ stdenv.mkDerivation rec {
     buildInputs = [ expat ];
 
     meta = with stdenv.lib; {
-      homepage = http://www.unidata.ucar.edu/software/udunits/;
+      homepage = https://www.unidata.ucar.edu/software/udunits/;
       description = "A C-based package for the programatic handling of units of physical quantities";
       license = licenses.bsdOriginal;
       platforms = platforms.linux;

pkgs/development/ocaml-modules/ipaddr/default.nix

@@ -1,24 +1,24 @@
 { stdenv, buildOcaml, fetchurl, ocamlbuild, findlib
-, topkg, sexplib, ppx_sexp_conv, opam }:
+, jbuilder, sexplib, ppx_sexp_conv, ppx_deriving }:
 
 buildOcaml rec {
   name = "ipaddr";
-  version = "2.7.2";
+  version = "2.8.0";
 
   src = fetchurl {
     url = "https://github.com/mirage/ocaml-ipaddr/archive/${version}.tar.gz";
-    sha256 = "0mnjw1xjr8vyn5x1nnbbxfxhs77znwrkz8c144w47zk2pc3xrh9d";
+    sha256 = "1amb1pbm9ybpxy6190qygpj6nmbzzs2r6vx4xh5r6v89szx9rfxw";
   };
 
-  buildInputs = [ findlib ocamlbuild topkg ppx_sexp_conv opam ];
-  propagatedBuildInputs = [ sexplib ];
+  buildInputs = [ findlib ocamlbuild jbuilder ppx_sexp_conv ];
+  propagatedBuildInputs = [ ppx_deriving sexplib ];
 
-  inherit (topkg) buildPhase installPhase;
+  inherit (jbuilder) installPhase;
 
   meta = with stdenv.lib; {
     homepage = https://github.com/mirage/ocaml-ipaddr;
     description = "A library for manipulation of IP (and MAC) address representations ";
-    license = licenses.mit;
+    license = licenses.isc;
     maintainers = [ maintainers.ericbmerritt ];
   };
 }

pkgs/development/python-modules/git-annex-adapter/default.nix

@@ -0,0 +1,49 @@
+{ stdenv, buildPythonPackage, isPy3k, fetchFromGitHub, fetchurl
+, eject, pygit2, gitMinimal, git-annex }:
+
+buildPythonPackage rec {
+  pname = "git-annex-adapter";
+  version = "0.2.0";
+  name = "${pname}-${version}";
+
+  disabled = (!isPy3k);
+
+  # There is only a wheel on PyPI - build from source instead
+  src = fetchFromGitHub {
+    owner = "alpernebbi";
+    repo = pname;
+    rev = "v${version}";
+    sha256 = "1sbgp4ivgw4m8nngrlb1f78xdnssh639c1khv4z98753w3sdsxdz";
+  };
+
+  prePatch = ''
+    substituteInPlace git_annex_adapter/process.py \
+      --replace "'git', 'annex'" "'${git-annex}/bin/git-annex'" \
+      --replace "'git-annex'" "'${git-annex}/bin/git-annex'"
+  '';
+
+  # TODO: Remove for next version
+  patches = fetchurl {
+    url = "https://github.com/alpernebbi/git-annex-adapter/commit/9f64c4b99cae7b681820c6c7382e1e40489f4d1e.patch";
+    sha256 = "1hbw8651amjskakvs1wv2msd1wryrq0vpryvbispg5267rs8q7hp";
+  };
+
+  nativeBuildInputs = [
+    eject # `rev` is needed in tests/test_process.py
+  ];
+
+  propagatedBuildInputs = [ pygit2 gitMinimal ];
+
+  buildInputs = [ git-annex ];
+
+  checkPhase = ''
+    python -m unittest
+  '';
+
+  meta = with stdenv.lib; {
+    homepage = https://github.com/alpernebbi/git-annex-adapter;
+    description = "Call git-annex commands from Python";
+    license = licenses.gpl3Plus;
+    maintainers = with maintainers; [ dotlambda ];
+  };
+}

pkgs/development/r-modules/default.nix

@@ -303,7 +303,6 @@ let
     rcdd = [ pkgs.gmp.dev ];
     RcppCNPy = [ pkgs.zlib.dev ];
     RcppGSL = [ pkgs.gsl_1 ];
-    RcppOctave = [ pkgs.zlib pkgs.bzip2.dev pkgs.icu pkgs.lzma.dev pkgs.pcre.dev pkgs.octave ];
     RcppZiggurat = [ pkgs.gsl_1 ];
     rgdal = [ pkgs.proj pkgs.gdal ];
     rgeos = [ pkgs.geos ];

pkgs/development/tools/build-managers/gup/default.nix

@@ -1,8 +1,8 @@
 { stdenv, fetchFromGitHub, lib, python, which }:
 let
-  version = "0.6.0";
+  version = "0.7.0";
   src = fetchFromGitHub {
-    sha256 = "053xnx39jh9kn9l572z4k0q7bbxjpisf1fm9aq27ybj2ha1rh6wr";
+    sha256 = "1pwnmlq2pgkkln9sgz4wlb9dqlqw83bkf105qljnlvggc21zm3pv";
     rev = "version-${version}";
     repo = "gup";
     owner = "timbertson";

pkgs/development/tools/drip/default.nix

@@ -0,0 +1,40 @@
+{ stdenv, fetchFromGitHub, jdk, which, makeWrapper }:
+
+stdenv.mkDerivation rec {
+  name = "${pname}-${version}";
+  pname = "drip";
+  version = "0.2.4";
+
+  src = fetchFromGitHub {
+    repo = pname;
+    owner = "ninjudd";
+    rev = version;
+    sha256 = "1zl62wdwfak6z725asq5lcqb506la1aavj7ag78lvp155wyh8aq1";
+  };
+
+  nativeBuildInputs = [ makeWrapper ];
+
+  buildInputs = [ jdk ];
+
+  postPatch = ''
+    patchShebangs .
+  '';
+
+  installPhase = ''
+    runHook preInstall
+    mkdir $out
+    cp ./* $out -r
+    wrapProgram $out/bin/drip \
+      --prefix PATH : "${which}/bin"
+    $out/bin/drip version
+    runHook postInstall
+  '';
+
+  meta = with stdenv.lib; {
+    description = "A launcher for the Java Virtual Machine intended to be a drop-in replacement for the java command, only faster";
+    license = licenses.epl10;
+    homepage = https://github.com/ninjudd/drip;
+    platforms = platforms.linux;
+    maintainers = [ maintainers.rybern ];
+  };
+}

pkgs/development/tools/jo/default.nix

@@ -2,14 +2,14 @@
 
 stdenv.mkDerivation rec {
   name = "jo-${version}";
-  version = "1.0";
+  version = "1.1";
 
   src = fetchFromGitHub {
     owner = "jpmens";
     repo = "jo";
 
     rev = "v${version}";
-    sha256="0vyi0aaxsp6x3cvym7mlcfdsxjhj5h0b00mqc42mg8kc95cyp2c1";
+    sha256="1gn9fa37mfb85dfjznyfgciibf142kp0gisc2l2pnz0zrakbvvy3";
   };
 
   enableParallelBuilding = true;

pkgs/development/tools/misc/gdbgui/default.nix

@@ -5,16 +5,20 @@ in
 python27Packages.buildPythonApplication rec {
     name = "${pname}-${version}";
     pname = "gdbgui";
-    version = "0.9.0.1";
+    version = "0.9.1.0";
 
     buildInputs = [ gdb ];
     propagatedBuildInputs = builtins.attrValues deps.packages;
 
     src = python27Packages.fetchPypi {
       inherit pname version;
-      sha256 = "1gjc7dycrc4zafhrd9yib7qnh4agh7cpa6rlw4p5405rlmwmsbj3";
+      sha256 = "0ybgkk4h9zwhbx5d0j0fmfzxxgg8f6apm8v7djavm0ldpr6f5z26";
     };
 
+    postPatch = ''
+      echo ${version} > gdbgui/VERSION.txt
+    '';
+
     postInstall = ''
       wrapProgram $out/bin/gdbgui \
                   --prefix PATH : ${stdenv.lib.makeBinPath [ gdb ]}