r-modules: Fix a number of popular R packages

The R V8 package still depends on V8 3.14 so this is also included.

pkgs/development/libraries/v8/3.14.nix

···
+# This old version of V8 is still needed for the R V8 module
+{ stdenv, callPackage, fetchFromGitHub, gyp, readline, python, which, icu, ... }:
+
+assert readline != null;
+
+with stdenv.lib;
+let
+  version = "3.14.5.10";
+  sha256 = "08vhl84166x13b3cbx8y0g99yqx772zd33gawsa1nxqkyrykql6k";
+
+  arch = if stdenv.is64bit then "x64" else "ia32";
+
+in
+stdenv.mkDerivation rec {
+  name = "v8-${version}";
+  inherit version;
+
+  src = fetchFromGitHub {
+    owner = "v8";
+    repo = "v8";
+    rev = "${version}";
+    inherit sha256;
+  };
+  patchPhase = ''
+    sed -i 's,#!/usr/bin/env python,#!${python}/bin/python,' build/gyp_v8
+    sed -i 's,#!/usr/bin/python,#!${python}/bin/python,' build/gyp_v8
+  '';
+
+  configurePhase = ''
+    PYTHONPATH="tools/generate_shim_headers:$PYTHONPATH" \
+    PYTHONPATH="$(toPythonPath ${gyp}):$PYTHONPATH" \
+      build/gyp_v8 \
+        -f make \
+        --generator-output="out" \
+        -Dflock_index=0 \
+        -Dv8_enable_i18n_support=1 \
+        -Duse_system_icu=1 \
+        -Dconsole=readline \
+        -Dcomponent=shared_library \
+        -Dv8_target_arch=${arch}
+  '';
+
+  nativeBuildInputs = [ which ];
+  buildInputs = [ readline python icu ];
+
+  # http://code.google.com/p/v8/issues/detail?id=2149
+  NIX_CFLAGS_COMPILE = concatStringsSep " " [
+    "-Wno-error=strict-overflow"
+    "-Wno-unused-local-typedefs"
+    "-Wno-aggressive-loop-optimizations"
+  ];
+
+  buildFlags = [
+    "LINK=g++"
+    "-C out"
+    "builddir=$(CURDIR)/Release"
+    "BUILDTYPE=Release"
+  ];
+
+  postPatch = stdenv.lib.optionalString (!stdenv.cc.isClang) ''
+    sed -i build/standalone.gyp -e 's,-Wno-format-pedantic,,g'
+  '';
+
+  enableParallelBuilding = true;
+
+  installPhase = ''
+    install -vD out/Release/d8 "$out/bin/d8"
+    ${if stdenv.system == "x86_64-darwin" then ''
+    install -vD out/Release/lib.target/libv8.dylib "$out/lib/libv8.dylib"
+    '' else ''
+    install -vD out/Release/lib.target/libv8.so "$out/lib/libv8.so"
+    ''}
+    cp -vr include "$out/"
+  '';
+
+  postFixup = if stdenv.isDarwin then ''
+    install_name_tool -change /usr/local/lib/libv8.dylib $out/lib/libv8.dylib -change /usr/lib/libgcc_s.1.dylib ${stdenv.cc.cc.lib}/lib/libgcc_s.1.dylib $out/bin/d8
+    install_name_tool -id $out/lib/libv8.dylib -change /usr/lib/libgcc_s.1.dylib ${stdenv.cc.cc.lib}/lib/libgcc_s.1.dylib $out/lib/libv8.dylib
+  '' else null;
+
+  meta = with stdenv.lib; {
+    description = "Google's open source JavaScript engine";
+    platforms = platforms.linux;
+    license = licenses.bsd3;
+  };
+}

pkgs/development/r-modules/default.nix

···
     fftwtools = [ pkgs.fftw.dev ];
     Formula = [ pkgs.gmp ];
     geoCount = [ pkgs.gsl_1 ];
+    gdtools = [ pkgs.cairo.dev pkgs.fontconfig.lib pkgs.freetype.dev ];
     git2r = [ pkgs.zlib.dev pkgs.openssl.dev ];
     GLAD = [ pkgs.gsl_1 ];
     glpkAPI = [ pkgs.gmp pkgs.glpk ];
···
     graphscan = [ pkgs.gsl_1 ];
     gsl = [ pkgs.gsl_1 ];
     h5 = [ pkgs.hdf5-cpp pkgs.which ];
+    haven = [ pkgs.libiconv ];
     h5vc = [ pkgs.zlib.dev ];
     HiCseg = [ pkgs.gsl_1 ];
     imager = [ pkgs.x11 ];
     iBMQ = [ pkgs.gsl_1 ];
-    igraph = [ pkgs.gmp ];
+    igraph = [ pkgs.gmp pkgs.libxml2.dev ];
     JavaGD = [ pkgs.jdk ];
     jpeg = [ pkgs.libjpeg.dev ];
     KFKSDS = [ pkgs.gsl_1 ];
     kza = [ pkgs.fftw.dev ];
     libamtrack = [ pkgs.gsl_1 ];
+    magick = [ pkgs.imagemagick.dev ];
     mixcat = [ pkgs.gsl_1 ];
     mvabund = [ pkgs.gsl_1 ];
     mwaved = [ pkgs.fftw.dev ];
     ncdf4 = [ pkgs.netcdf ];
     nloptr = [ pkgs.nlopt ];
-    openssl = [ pkgs.openssl.dev ];
+    odbc = [ pkgs.unixODBC ];
+    openssl = [ pkgs.openssl pkgs.openssl.dev ];
     outbreaker = [ pkgs.gsl_1 ];
     pander = [ pkgs.pandoc pkgs.which ];
     pbdMPI = [ pkgs.openmpi ];
     pbdNCDF4 = [ pkgs.netcdf ];
     pbdPROF = [ pkgs.openmpi ];
     pbdZMQ = [ pkgs.which ];
+    pdftools = [ pkgs.poppler.dev ];
     PKI = [ pkgs.openssl.dev ];
     png = [ pkgs.libpng.dev ];
     PopGenome = [ pkgs.zlib.dev ];
     proj4 = [ pkgs.proj ];
+    protolite = [ pkgs.protobuf ];
     qtbase = [ pkgs.qt4 ];
     qtpaint = [ pkgs.qt4 ];
     R2GUESS = [ pkgs.gsl_1 ];
···
     RAppArmor = [ pkgs.libapparmor ];
     rapportools = [ pkgs.which ];
     rapport = [ pkgs.which ];
+    readxl = [ pkgs.libiconv ];
     rbamtools = [ pkgs.zlib.dev ];
     rcdd = [ pkgs.gmp.dev ];
     RcppCNPy = [ pkgs.zlib.dev ];
···
     rmatio = [ pkgs.zlib.dev ];
     Rmpfr = [ pkgs.gmp pkgs.mpfr.dev ];
     Rmpi = [ pkgs.openmpi ];
-    RMySQL = [ pkgs.zlib pkgs.mysql.lib ];
+    RMySQL = [ pkgs.zlib pkgs.mysql.lib pkgs.mariadb pkgs.openssl.dev ];
     RNetCDF = [ pkgs.netcdf pkgs.udunits ];
     RODBCext = [ pkgs.libiodbc ];
     RODBC = [ pkgs.libiodbc ];
+    rpanel = [ pkgs.bwidget ];
     rpg = [ pkgs.postgresql ];
     rphast = [ pkgs.pcre.dev pkgs.zlib pkgs.bzip2 pkgs.gzip pkgs.readline ];
     Rpoppler = [ pkgs.poppler ];
-    RPostgreSQL = [ pkgs.postgresql ];
+    RPostgreSQL = [ pkgs.postgresql pkgs.postgresql ];
     RProtoBuf = [ pkgs.protobuf ];
     rPython = [ pkgs.python ];
     RSclient = [ pkgs.openssl.dev ];
···
     rtfbs = [ pkgs.zlib pkgs.pcre.dev pkgs.bzip2 pkgs.gzip pkgs.readline ];
     rtiff = [ pkgs.libtiff.dev ];
     runjags = [ pkgs.jags ];
+    RSymphony = [ pkgs.symphony ];
     RVowpalWabbit = [ pkgs.zlib.dev pkgs.boost ];
     rzmq = [ pkgs.zeromq3 ];
     SAVE = [ pkgs.zlib pkgs.bzip2 pkgs.icu pkgs.lzma pkgs.pcre ];
···
     seewave = [ pkgs.fftw.dev pkgs.libsndfile.dev ];
     seqinr = [ pkgs.zlib.dev ];
     seqminer = [ pkgs.zlib.dev pkgs.bzip2 ];
+    sf = [ pkgs.gdal pkgs.proj pkgs.geos ];
     showtext = [ pkgs.zlib pkgs.libpng pkgs.icu pkgs.freetype.dev ];
     simplexreg = [ pkgs.gsl_1 ];
     SOD = [ pkgs.opencl-headers ];
···
     survSNP = [ pkgs.gsl_1 ];
     sysfonts = [ pkgs.zlib pkgs.libpng pkgs.freetype.dev ];
     TAQMNGR = [ pkgs.zlib.dev ];
+    tesseract = [ pkgs.tesseract pkgs.leptonica ];
     tiff = [ pkgs.libtiff.dev ];
     TKF = [ pkgs.gsl_1 ];
     tkrplot = [ pkgs.xorg.libX11 pkgs.tk.dev ];
     topicmodels = [ pkgs.gsl_1 ];
     udunits2 = [ pkgs.udunits pkgs.expat ];
-    V8 = [ pkgs.v8 ];
+    V8 = [ pkgs.v8_3_14 ];
     VBLPCM = [ pkgs.gsl_1 ];
     VBmix = [ pkgs.gsl_1 pkgs.fftw pkgs.qt4 ];
     WhopGenome = [ pkgs.zlib.dev ];
···
     chebpol = [ pkgs.pkgconfig ];
     fftw = [ pkgs.pkgconfig ];
     geoCount = [ pkgs.pkgconfig ];
+    gdtools = [ pkgs.pkgconfig ];
     kza = [ pkgs.pkgconfig ];
+    magick = [ pkgs.pkgconfig ];
     mwaved = [ pkgs.pkgconfig ];
+    odbc = [ pkgs.pkgconfig ];
+    openssl = [ pkgs.pkgconfig ];
+    pdftools = [ pkgs.pkgconfig ];
+    sf = [ pkgs.pkgconfig ];
     showtext = [ pkgs.pkgconfig ];
     spate = [ pkgs.pkgconfig ];
     stringi = [ pkgs.pkgconfig ];
+    sys = [ pkgs.libapparmor ];
     sysfonts = [ pkgs.pkgconfig ];
+    tesseract = [ pkgs.pkgconfig ];
     Cairo = [ pkgs.pkgconfig ];
     Rsymphony = [ pkgs.pkgconfig pkgs.doxygen pkgs.graphviz pkgs.subversion ];
     qtutils = [ pkgs.qt4 ];
···
     });
 
     RMySQL = old.RMySQL.overrideDerivation (attrs: {
-      patches = [ ./patches/RMySQL.patch ];
       MYSQL_DIR="${pkgs.mysql.lib}";
+      preConfigure = ''
+        patchShebangs configure
+        '';
     });
 
     devEMF = old.devEMF.overrideDerivation (attrs: {
···
 
     openssl = old.openssl.overrideDerivation (attrs: {
       OPENSSL_INCLUDES = "${pkgs.openssl.dev}/include";
+      preConfigure = ''
+        sed -i.bak 's|^\( *PKG_LIBS_VERSIONED=\).*$|\1$PKG_LIBS|' configure
+        '';
     });
 
     Rserve = old.Rserve.overrideDerivation (attrs: {
···
     });
 
     V8 = old.V8.overrideDerivation (attrs: {
-      preConfigure = "export V8_INCLUDES=${pkgs.v8}/include";
+      preConfigure = ''
+        export INCLUDE_DIR=${pkgs.v8_3_14}/include
+        export LIB_DIR=${pkgs.v8_3_14}/lib
+        patchShebangs configure
+        '';
+    });
+
+    acs = old.acs.overrideDerivation (attrs: {
+      preConfigure = ''
+        patchShebangs configure
+        '';
+    });
+
+    gdtools = old.gdtools.overrideDerivation (attrs: {
+      preConfigure = ''
+        patchShebangs configure
+        '';
+      NIX_LDFLAGS = "-lfontconfig -lfreetype";
+    });
+
+    magick = old.magick.overrideDerivation (attrs: {
+      preConfigure = ''
+        patchShebangs configure
+        '';
+    });
+
+    protolite = old.protolite.overrideDerivation (attrs: {
+      preConfigure = ''
+        patchShebangs configure
+        '';
+    });
+
+    rpanel = old.rpanel.overrideDerivation (attrs: {
+      preConfigure = ''
+        export TCLLIBPATH="${pkgs.bwidget}/lib/bwidget${pkgs.bwidget.version}"
+      '';
+      TCLLIBPATH = "${pkgs.bwidget}/lib/bwidget${pkgs.bwidget.version}";
+    });
+
+    OpenMx = old.OpenMx.overrideDerivation (attrs: {
+      preConfigure = ''
+        patchShebangs configure
+        '';
+    });
+
+    odbc = old.odbc.overrideDerivation (attrs: {
+      preConfigure = ''
+        patchShebangs configure
+        '';
+    });
+
+    x13binary = old.x13binary.overrideDerivation (attrs: {
+      preConfigure = ''
+        patchShebangs configure
+        '';
+    });
+
+    geojsonio = old.geojsonio.overrideDerivation (attrs: {
+      preConfigure = ''
+        export SSL_CERT_FILE=${pkgs.cacert}/etc/ssl/certs/ca-bundle.crt
+        '';
+    });
+
+    rstan = old.rstan.overrideDerivation (attrs: {
+      NIX_CFLAGS_COMPILE = "${attrs.NIX_CFLAGS_COMPILE} -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION";
     });
 
   };

pkgs/top-level/all-packages.nix

···
     gnutls = gnutls;
   });
 
+  # 3.14 is needed for R V8 module in ../development/r-modules/default.nix
+  v8_3_14 = callPackage ../development/libraries/v8/3.14.nix {
+    inherit (python2Packages) python gyp;
+    cctools = darwin.cctools;
+    stdenv = overrideCC stdenv gcc5;
+  };
+
   v8_3_16_14 = callPackage ../development/libraries/v8/3.16.14.nix {
     inherit (python2Packages) python gyp;
     cctools = darwin.cctools;