Merge branch 'master'

21 files changed, 134 insertions, 71 deletions

diff --git a/pkgs/applications/science/astronomy/gpredict/default.nix b/pkgs/applications/science/astronomy/gpredict/default.nix
index 148963d64c08..9bacf6d90417 100644
--- a/pkgs/applications/science/astronomy/gpredict/default.nix
+++ b/pkgs/applications/science/astronomy/gpredict/default.nix
@@ -1,20 +1,20 @@
-{ stdenv, fetchurl, pkgconfig
-, gtk2-x11, glib, curl, goocanvas, intltool
+{ stdenv, fetchurl, pkgconfig, intltool
+, gtk3, glib, curl, goocanvas2, gpsd
+, hamlib, wrapGAppsHook
 }:
 
 let
-  version = "1.3";
-in
-stdenv.mkDerivation {
+  version = "2.2.1";
+in stdenv.mkDerivation {
   name = "gpredict-${version}";
 
   src = fetchurl {
-    url = "https://sourceforge.net/projects/gpredict/files/Gpredict/${version}/gpredict-${version}.tar.gz";
-    sha256 = "18ym71r2f5mwpnjcnrpwrk3py2f6jlqmj8hzp89wbcm1ipnvxxmh";
+    url = "https://github.com/csete/gpredict/releases/download/v${version}/gpredict-${version}.tar.bz2";
+    sha256 = "0hwf97kng1zy8rxyglw04x89p0bg07zq30hgghm20yxiw2xc8ng7";
   };
 
-  buildInputs = [ curl glib gtk2-x11 goocanvas ];
-  nativeBuildInputs = [ pkgconfig intltool ];
+  nativeBuildInputs = [ pkgconfig intltool wrapGAppsHook ];
+  buildInputs = [ curl glib gtk3 goocanvas2 gpsd hamlib ];
 
   meta = with stdenv.lib; {
     description = "Real time satellite tracking and orbit prediction";
@@ -27,7 +27,7 @@ stdenv.mkDerivation {
     '';
     license = licenses.gpl2;
     platforms = platforms.linux;
-    homepage = "https://sourceforge.net/projects/gpredict/";
-    maintainers = [ maintainers.markuskowa ];
+    homepage = http://gpredict.oz9aec.net/;
+    maintainers = [ maintainers.markuskowa maintainers.cmcdragonkai ];
   };
 }
diff --git a/pkgs/applications/science/biology/bcftools/default.nix b/pkgs/applications/science/biology/bcftools/default.nix
index db12fc00c87c..5e899568a7df 100644
--- a/pkgs/applications/science/biology/bcftools/default.nix
+++ b/pkgs/applications/science/biology/bcftools/default.nix
@@ -3,11 +3,11 @@
 stdenv.mkDerivation rec {
   name = "${pname}-${version}";
   pname = "bcftools";
-  version = "1.6";
+  version = "1.7";
 
   src = fetchurl {
     url = "https://github.com/samtools/bcftools/releases/download/${version}/${name}.tar.bz2";
-    sha256 = "10prgmf09a13mk18840938ijqgfc9y92hfc7sa2gcv07ddri0c19";
+    sha256 = "1l82sgw86l1626b7kxv3h0696lbj7317bb48rvqb1zqd3gcn6kyx";
   };
 
   nativeBuildInputs = [ perl ];
diff --git a/pkgs/applications/science/biology/bowtie2/default.nix b/pkgs/applications/science/biology/bowtie2/default.nix
index f04b81ea9795..829672d64cc2 100644
--- a/pkgs/applications/science/biology/bowtie2/default.nix
+++ b/pkgs/applications/science/biology/bowtie2/default.nix
@@ -2,14 +2,14 @@
 
 stdenv.mkDerivation rec {
   pname = "bowtie2";
-  version = "2.3.4";
+  version = "2.3.4.1";
   name = "${pname}-${version}";
 
   src = fetchFromGitHub {
     owner = "BenLangmead";
     repo = pname;
     rev = "v${version}";
-    sha256 = "15k86ln1xgqkyk8ms09cgdhagz49jpvr6ij6mha1f9ga5fxnnp1m";
+    sha256 = "07cvcy6483araayj41arjzpxjmf4fmn4iqyl6gp6zmrbzw72wwzj";
   };
 
   buildInputs = [ zlib tbb ];
diff --git a/pkgs/applications/science/biology/igv/default.nix b/pkgs/applications/science/biology/igv/default.nix
index 13cb407391c0..7825da0100ad 100644
--- a/pkgs/applications/science/biology/igv/default.nix
+++ b/pkgs/applications/science/biology/igv/default.nix
@@ -2,11 +2,11 @@
 
 stdenv.mkDerivation rec {
   name = "igv-${version}";
-  version = "2.4.6";
+  version = "2.4.8";
 
   src = fetchurl {
     url = "http://data.broadinstitute.org/igv/projects/downloads/2.4/IGV_${version}.zip";
-    sha256 = "00p9xhfn6snzm31q9l3dxccsj7rhlci8n3pgpy3k67q91mi2hkna";
+    sha256 = "1ca4lsb5j00066sd1gy8jr8jhzpd9142fhj4khb8nc45010wib0q";
   };
 
   buildInputs = [ unzip jre ];
diff --git a/pkgs/applications/science/biology/picard-tools/default.nix b/pkgs/applications/science/biology/picard-tools/default.nix
index 5578a41f4441..a065fdf4489a 100644
--- a/pkgs/applications/science/biology/picard-tools/default.nix
+++ b/pkgs/applications/science/biology/picard-tools/default.nix
@@ -2,11 +2,11 @@
 
 stdenv.mkDerivation rec {
   name = "picard-tools-${version}";
-  version = "2.17.4";
+  version = "2.17.10";
 
   src = fetchurl {
     url = "https://github.com/broadinstitute/picard/releases/download/${version}/picard.jar";
-    sha256 = "00ffi8kkrlh72vjjkjpgi8zys3r9hkdk4xi82kcahch8pix4qzf2";
+    sha256 = "0lf9appcs66mxmirzbys09xhq38kpa4ldxwwzrr9y2cklnxjn4hg";
   };
 
   buildInputs = [ jre makeWrapper ];
diff --git a/pkgs/applications/science/electronics/pcb/default.nix b/pkgs/applications/science/electronics/pcb/default.nix
index 34bdd3d47c86..b9bbcd695f17 100644
--- a/pkgs/applications/science/electronics/pcb/default.nix
+++ b/pkgs/applications/science/electronics/pcb/default.nix
@@ -1,4 +1,7 @@
-{ stdenv, fetchurl, pkgconfig, gtk2, bison, intltool, flex, netpbm, imagemagick, dbus, xlibsWrapper, libGLU_combined, shared_mime_info, tcl, tk, gnome2, pangox_compat, gd, xorg }:
+{ stdenv, fetchurl, pkgconfig, gtk2, bison, intltool, flex
+, netpbm, imagemagick, dbus, xlibsWrapper, libGLU_combined
+, shared-mime-info, tcl, tk, gnome2, pangox_compat, gd, xorg
+}:
 
 stdenv.mkDerivation rec {
   name = "pcb-${version}";
@@ -10,7 +13,11 @@ stdenv.mkDerivation rec {
   };
 
   nativeBuildInputs = [ pkgconfig ];
-  buildInputs = [ gtk2 bison intltool flex netpbm imagemagick dbus xlibsWrapper libGLU_combined tcl shared_mime_info tk gnome2.gtkglext pangox_compat gd xorg.libXmu ];
+  buildInputs = [
+    gtk2 bison intltool flex netpbm imagemagick dbus xlibsWrapper
+    libGLU_combined tcl shared-mime-info tk
+    gnome2.gtkglext pangox_compat gd xorg.libXmu
+  ];
 
   configureFlags = ["--disable-update-desktop-database"];
 
diff --git a/pkgs/applications/science/electronics/verilator/default.nix b/pkgs/applications/science/electronics/verilator/default.nix
index e34383865576..dade8296e996 100644
--- a/pkgs/applications/science/electronics/verilator/default.nix
+++ b/pkgs/applications/science/electronics/verilator/default.nix
@@ -2,11 +2,11 @@
 
 stdenv.mkDerivation rec {
   name    = "verilator-${version}";
-  version = "3.900";
+  version = "3.920";
 
   src = fetchurl {
     url    = "http://www.veripool.org/ftp/${name}.tgz";
-    sha256 = "0yvbibcysdiw6mphda0lfs56wz6v450px2420x0hbd3rc7k53s2b";
+    sha256 = "1zs3d6h5sbz455fwpgg89h81hkfn92ary8bmhjinc1rd8fm3hp1b";
   };
 
   enableParallelBuilding = true;
diff --git a/pkgs/applications/science/logic/cryptoverif/default.nix b/pkgs/applications/science/logic/cryptoverif/default.nix
index 47077c2e255b..3257977f5b5a 100644
--- a/pkgs/applications/science/logic/cryptoverif/default.nix
+++ b/pkgs/applications/science/logic/cryptoverif/default.nix
@@ -2,11 +2,11 @@
 
 stdenv.mkDerivation rec {
   name = "cryptoverif-${version}";
-  version = "1.22";
+  version = "1.28";
 
   src = fetchurl {
     url    = "http://prosecco.gforge.inria.fr/personal/bblanche/cryptoverif/cryptoverif${version}.tar.gz";
-    sha256 = "17fbmv0askgfnhs5a0ilhizvrr93jkmq82ybm3cgyxhh2zrk0rq1";
+    sha256 = "0vssz751g1nn8wclkiwgghpm475jl00xkivc164vgbr9acxsr7n7";
   };
 
   buildInputs = [ ocaml ];
diff --git a/pkgs/applications/science/logic/tlaplus/default.nix b/pkgs/applications/science/logic/tlaplus/default.nix
new file mode 100644
index 000000000000..b1eb171b20b1
--- /dev/null
+++ b/pkgs/applications/science/logic/tlaplus/default.nix
@@ -0,0 +1,40 @@
+{ stdenv, fetchFromGitHub, makeWrapper
+, jdk, jre, ant
+}:
+
+stdenv.mkDerivation rec {
+  name = "tlaplus-${version}";
+  version = "1.5.6";
+
+  src = fetchFromGitHub {
+    owner  = "tlaplus";
+    repo   = "tlaplus";
+    rev    = "refs/tags/v${version}";
+    sha256 = "0966mvgxamknj4hsp980qbxwda886w1dv309kn7isxn0420lfv4f";
+  };
+
+  buildInputs = [ makeWrapper jdk ant ];
+
+  buildPhase = "ant -f tlatools/customBuild.xml compile dist";
+  installPhase = ''
+    mkdir -p $out/share/java $out/bin
+    cp tlatools/dist/*.jar $out/share/java
+
+    makeWrapper ${jre}/bin/java $out/bin/tlc2 \
+      --add-flags "-cp $out/share/java/tla2tools.jar tlc2.TLC"
+    makeWrapper ${jre}/bin/java $out/bin/tla2sany \
+      --add-flags "-cp $out/share/java/tla2tools.jar tla2sany.SANY"
+    makeWrapper ${jre}/bin/java $out/bin/pcal \
+      --add-flags "-cp $out/share/java/tla2tools.jar pcal.trans"
+    makeWrapper ${jre}/bin/java $out/bin/tla2tex \
+      --add-flags "-cp $out/share/java/tla2tools.jar tla2tex.TLA"
+  '';
+
+  meta = {
+    description = "An algorithm specification language with model checking tools";
+    homepage    = http://lamport.azurewebsites.net/tla/tla.html;
+    license     = stdenv.lib.licenses.mit;
+    platforms   = stdenv.lib.platforms.unix;
+    maintainers = [ stdenv.lib.maintainers.thoughtpolice ];
+  };
+}
diff --git a/pkgs/applications/science/math/caffe/default.nix b/pkgs/applications/science/math/caffe/default.nix
index 8dc3e3ce43dc..d7357c5048d5 100644
--- a/pkgs/applications/science/math/caffe/default.nix
+++ b/pkgs/applications/science/math/caffe/default.nix
@@ -7,17 +7,19 @@
 , hdf5-cpp
 , leveldb
 , lmdb
-, opencv
+, opencv3
 , protobuf
 , snappy
-, atlas
 , doxygen
+, openblas
 , cudaSupport ? true, cudatoolkit
 , cudnnSupport ? false, cudnn ? null
+, ncclSupport ? false, nccl ? null
 , pythonSupport ? false, python ? null, numpy ? null
 }:
 
 assert cudnnSupport -> cudaSupport;
+assert ncclSupport -> cudaSupport;
 assert pythonSupport -> (python != null && numpy != null);
 
 stdenv.mkDerivation rec {
@@ -35,14 +37,19 @@ stdenv.mkDerivation rec {
 
   nativeBuildInputs = [ cmake doxygen ];
 
-  cmakeFlags = [
-    "-DCUDA_ARCH_NAME=All"
-    (if pythonSupport then "-Dpython_version=${python.version}" else "-DBUILD_python=OFF")
-  ] ++ lib.optional (!cudaSupport) "-DCPU_ONLY=ON";
+  cmakeFlags =
+    [ (if pythonSupport then "-Dpython_version=${python.version}" else "-DBUILD_python=OFF")
+      "-DBLAS=open"
+    ] ++ (if cudaSupport then [
+           "-DCUDA_ARCH_NAME=All"
+           "-DCUDA_HOST_COMPILER=${cudatoolkit.cc}/bin/cc"
+         ] else [ "-DCPU_ONLY=ON" ])
+      ++ lib.optional ncclSupport "-DUSE_NCCL=ON";
 
-  buildInputs = [ boost google-gflags glog protobuf hdf5-cpp lmdb leveldb snappy opencv atlas ]
+  buildInputs = [ boost google-gflags glog protobuf hdf5-cpp lmdb leveldb snappy opencv3 openblas ]
                 ++ lib.optional cudaSupport cudatoolkit
                 ++ lib.optional cudnnSupport cudnn
+                ++ lib.optional ncclSupport nccl
                 ++ lib.optionals pythonSupport [ python numpy ];
 
   propagatedBuildInputs = lib.optional pythonSupport python.pkgs.protobuf;
diff --git a/pkgs/applications/science/math/cbc/default.nix b/pkgs/applications/science/math/cbc/default.nix
index 7643c912db4b..6de77d81be6f 100644
--- a/pkgs/applications/science/math/cbc/default.nix
+++ b/pkgs/applications/science/math/cbc/default.nix
@@ -1,11 +1,11 @@
 { lib, stdenv, fetchurl, zlib, bzip2 }:
 
 stdenv.mkDerivation {
-  name = "cbc-2.9.5";
+  name = "cbc-2.9.9";
 
   src = fetchurl {
-    url = "http://www.coin-or.org/download/source/Cbc/Cbc-2.9.5.tgz";
-    sha256 = "0kmsg9qpajh5jhnql04m6akpdjzlppxfz99q320vw5bkzgl3i18w";
+    url = "http://www.coin-or.org/download/source/Cbc/Cbc-2.9.9.tgz";
+    sha256 = "1w8axdzm05xf5y13c31w7rc5z6ywxqxiwafnxcq3p195kgj0915a";
   };
 
   configureFlags = "-C";
diff --git a/pkgs/applications/science/math/cntk/default.nix b/pkgs/applications/science/math/cntk/default.nix
index bef695fc650a..07740f4c8aea 100644
--- a/pkgs/applications/science/math/cntk/default.nix
+++ b/pkgs/applications/science/math/cntk/default.nix
@@ -12,28 +12,22 @@ let
   cub = fetchFromGitHub {
     owner = "NVlabs";
     repo = "cub";
-    rev = "1.4.1";
-    sha256 = "1lcdwblz03c0yq1lxndg566kg14b5qm14x5qixjbmz6wq85kgmqc";
+    rev = "1.7.4";
+    sha256 = "0ksd5n1lxqhm5l5cd2lps4cszhjkf6gmzahaycs7nxb06qci8c66";
   };
 
 in stdenv.mkDerivation rec {
   name = "CNTK-${version}";
-  version = "2.2";
+  version = "2.4";
 
   # Submodules
   src = fetchgit {
     url = "https://github.com/Microsoft/CNTK";
     rev = "v${version}";
-    sha256 = "0q4knrwiyphb2fbqf9jzqvkz2jzj6jmbmang3lavdvsh7z0n8zz9";
+    sha256 = "0m28wb0ljixcpi14g3gcfiraimh487yxqhd9yrglgyvjb69x597y";
   };
 
-  patches = [
-    # Fix "'exp' was not declared"
-    (fetchpatch {
-      url = "https://github.com/imriss/CNTK/commit/ef1cca6df95cc507deb8471df2c0dd8cbfeef23b.patch";
-      sha256 = "0z7xyrxwric0c4h7rfs05f544mcq6d10wgs0vvfcyd2pcf410hy7";
-    })
-  ];
+  patches = [ ./fix_std_bind.patch ];
 
   nativeBuildInputs = [ cmake ];
 
@@ -48,8 +42,10 @@ in stdenv.mkDerivation rec {
     "--with-boost=${boost.dev}"
     "--with-protobuf=${protobuf}"
     "--with-mpi=${openmpi}"
+    "--cuda=${if cudaSupport then "yes" else "no"}"
+    # FIXME
+    "--asgd=no"
   ] ++ lib.optionals cudaSupport [
-    "--cuda=yes"
     "--with-cuda=${cudatoolkit}"
     "--with-gdk-include=${cudatoolkit}/include"
     "--with-gdk-nvml-lib=${nvidia_x11}/lib"
@@ -85,16 +81,12 @@ in stdenv.mkDerivation rec {
     cp bin/cntk $out/bin
   '';
 
-  hardeningDisable = [ "format" ];
-
-  # on 2.2: fatal error: tensorboard/tensorboard.pb.h: No such file or directory
-  enableParallelBuilding = false;
+  enableParallelBuilding = true;
 
   meta = with lib; {
-    homepage = "https://github.com/Microsoft/CNTK";
+    homepage = https://github.com/Microsoft/CNTK;
     description = "An open source deep-learning toolkit";
     license = if onebitSGDSupport then licenses.unfreeRedistributable else licenses.mit;
     maintainers = with maintainers; [ abbradar ];
-    broken = true; # Never succeeded to build.
   };
 }
diff --git a/pkgs/applications/science/math/cntk/fix_std_bind.patch b/pkgs/applications/science/math/cntk/fix_std_bind.patch
new file mode 100644
index 000000000000..df97a0c66669
--- /dev/null
+++ b/pkgs/applications/science/math/cntk/fix_std_bind.patch
@@ -0,0 +1,11 @@
+diff -ru3 CNTK-old/Source/CNTKv2LibraryDll/EvaluatorWrapper.h CNTK-new/Source/CNTKv2LibraryDll/EvaluatorWrapper.h
+--- CNTK-old/Source/CNTKv2LibraryDll/EvaluatorWrapper.h	1970-01-01 03:00:01.000000000 +0300
++++ CNTK-new/Source/CNTKv2LibraryDll/EvaluatorWrapper.h	2018-02-25 18:16:16.330269647 +0300
+@@ -9,6 +9,7 @@
+ #include <boost/noncopyable.hpp>
+ #include <memory>
+ #include <vector>
++#include <functional>
+ 
+ #include "CNTKLibrary.h"
+ #include "CNTKLibraryC.h"
diff --git a/pkgs/applications/science/math/fricas/default.nix b/pkgs/applications/science/math/fricas/default.nix
index ccdd666e90bd..7e5233180cc6 100644
--- a/pkgs/applications/science/math/fricas/default.nix
+++ b/pkgs/applications/science/math/fricas/default.nix
@@ -1,7 +1,7 @@
 { stdenv, fetchurl, sbcl, libX11, libXpm, libICE, libSM, libXt, libXau, libXdmcp }:
 
 let
-  version = "1.3.1";
+  version = "1.3.2";
   name = "fricas-" + version;
 in
 stdenv.mkDerivation {
@@ -9,7 +9,7 @@ stdenv.mkDerivation {
 
   src = fetchurl {
     url    = "http://sourceforge.net/projects/fricas/files/fricas/${version}/${name}-full.tar.bz2";
-    sha256 = "0c2wgj1c3mh5f8msx1ckxpnhm0dyq7dqf1wk6aiyysh8xn57cjkx";
+    sha256 = "17a3vfvsn2idydqslf5r6z3sk6a5bdgj6z1n3dmnwmpkc4z152vr";
   };
 
   buildInputs = [ sbcl libX11 libXpm libICE libSM libXt libXau libXdmcp ];
diff --git a/pkgs/applications/science/math/lp_solve/default.nix b/pkgs/applications/science/math/lp_solve/default.nix
index efa0c1751d4c..0cf834c8cdea 100644
--- a/pkgs/applications/science/math/lp_solve/default.nix
+++ b/pkgs/applications/science/math/lp_solve/default.nix
@@ -3,11 +3,11 @@
 stdenv.mkDerivation rec {
 
   name = "lp_solve-${version}";
-  version = "5.5.2.0";
+  version = "5.5.2.5";
 
   src = fetchurl {
     url = "mirror://sourceforge/project/lpsolve/lpsolve/${version}/lp_solve_${version}_source.tar.gz";
-    sha256 = "176c7f023mb6b8bfmv4rfqnrlw88lsg422ca74zjh19i2h5s69sq";
+    sha256 = "12pj1idjz31r7c2mb5w03vy1cmvycvbkx9z29s40qdmkp1i7q6i0";
   };
 
   patches = [ ./isnan.patch ];
diff --git a/pkgs/applications/science/math/mxnet/default.nix b/pkgs/applications/science/math/mxnet/default.nix
index d2f3d0c5f337..ce9c214b3f0c 100644
--- a/pkgs/applications/science/math/mxnet/default.nix
+++ b/pkgs/applications/science/math/mxnet/default.nix
@@ -8,7 +8,7 @@ assert cudnnSupport -> cudaSupport;
 
 stdenv.mkDerivation rec {
   name = "mxnet-${version}";
-  version = "0.11.0";
+  version = "1.1.0";
 
   # Submodules needed
   src = fetchgit {
@@ -23,9 +23,12 @@ stdenv.mkDerivation rec {
               ++ lib.optionals cudaSupport [ cudatoolkit nvidia_x11 ]
               ++ lib.optional cudnnSupport cudnn;
 
-  cmakeFlags = [
-    (if cudaSupport then "-DCUDA_ARCH_NAME=All" else "-DUSE_CUDA=OFF")
-  ] ++ lib.optional (!cudnnSupport) "-DUSE_CUDNN=OFF";
+  cmakeFlags =
+    (if cudaSupport then [
+      "-DCUDA_ARCH_NAME=All"
+      "-DCUDA_HOST_COMPILER=${cudatoolkit.cc}/bin/cc"
+    ] else [ "-DUSE_CUDA=OFF" ])
+    ++ lib.optional (!cudnnSupport) "-DUSE_CUDNN=OFF";
 
   installPhase = ''
     install -Dm755 libmxnet.so $out/lib/libmxnet.so
@@ -36,7 +39,7 @@ stdenv.mkDerivation rec {
 
   meta = with stdenv.lib; {
     description = "Lightweight, Portable, Flexible Distributed/Mobile Deep Learning with Dynamic, Mutation-aware Dataflow Dep Scheduler";
-    homepage = "https://mxnet.incubator.apache.org/";
+    homepage = https://mxnet.incubator.apache.org/;
     maintainers = with maintainers; [ abbradar ];
     license = licenses.asl20;
     platforms = platforms.linux;
diff --git a/pkgs/applications/science/math/pari/default.nix b/pkgs/applications/science/math/pari/default.nix
index 0bae80782059..a1ddbd9ab17d 100644
--- a/pkgs/applications/science/math/pari/default.nix
+++ b/pkgs/applications/science/math/pari/default.nix
@@ -4,11 +4,11 @@
 stdenv.mkDerivation rec {
 
   name = "pari-${version}";
-  version = "2.9.3";
+  version = "2.9.4";
 
   src = fetchurl {
     url = "http://pari.math.u-bordeaux.fr/pub/pari/unix/${name}.tar.gz";
-    sha256 = "0qqal1lpggd6dvs19svnz0dil86xk0xkcj5s3b7104ibkmvjfsp7";
+    sha256 = "0ir6m3a8r46md5x6zk4xf159qra7aqparby9zk03k81hjrrxr72g";
   };
 
   buildInputs = [ gmp readline libX11 libpthreadstubs tex perl ];
diff --git a/pkgs/applications/science/math/sage/default.nix b/pkgs/applications/science/math/sage/default.nix
index 007cb68177e5..eed964e3fa57 100644
--- a/pkgs/applications/science/math/sage/default.nix
+++ b/pkgs/applications/science/math/sage/default.nix
@@ -30,6 +30,7 @@
 , texinfo
 , hevea
 , buildDocs ? false
+, optimize ? false # optimize sage to the current system (obviously impure)
 }:
 
 stdenv.mkDerivation rec {
@@ -139,7 +140,6 @@ stdenv.mkDerivation rec {
   configureFlags = stdenv.lib.optionals(buildDocs) [ "--docdir=$(doc)" ];
   preConfigure = ''
     export SAGE_NUM_THREADS="$NIX_BUILD_CORES"
-    export SAGE_ATLAS_ARCH=fast
 
     export HOME=/tmp/sage-home
     export SAGE_ROOT="$PWD"
@@ -160,6 +160,9 @@ stdenv.mkDerivation rec {
     mkdir -p "$doc"
     export SAGE_DOC="$doc"
     export SAGE_DOCBUILD_OPTS="--no-pdf-links -k"
+  ''
+  + stdenv.lib.optionalString (!optimize) ''
+    export SAGE_FAT_BINARY=yes
   '';
 
   buildFlags = if (buildDocs) then "doc" else "build";
diff --git a/pkgs/applications/science/math/wxmaxima/default.nix b/pkgs/applications/science/math/wxmaxima/default.nix
index c7f74071c24f..67cdaa4055ac 100644
--- a/pkgs/applications/science/math/wxmaxima/default.nix
+++ b/pkgs/applications/science/math/wxmaxima/default.nix
@@ -4,13 +4,13 @@
 
 stdenv.mkDerivation rec {
   name = "wxmaxima-${version}";
-  version = "17.10.1";
+  version = "18.02.0";
 
   src = fetchFromGitHub {
     owner = "andrejv";
     repo = "wxmaxima";
     rev = "Version-${version}";
-    sha256 = "088h8dlc9chkppwl4ck9i0fgf2d1dcpi5kq8qbpr5w75vhwsb6qm";
+    sha256 = "0s7bdykc77slqix28cyaa6x8wvxrn8461mkdgxflvi2apwsl56aa";
   };
 
   buildInputs = [ wxGTK maxima gnome3.defaultIconTheme ];
diff --git a/pkgs/applications/science/misc/root/default.nix b/pkgs/applications/science/misc/root/default.nix
index a7b3d2292be0..00ca1d2c7abe 100644
--- a/pkgs/applications/science/misc/root/default.nix
+++ b/pkgs/applications/science/misc/root/default.nix
@@ -4,11 +4,11 @@
 
 stdenv.mkDerivation rec {
   name = "root-${version}";
-  version = "6.10.08";
+  version = "6.12.06";
 
   src = fetchurl {
     url = "https://root.cern.ch/download/root_v${version}.source.tar.gz";
-    sha256 = "12mddl6pqwwc9nr4jqzp6h1jm4zycazd3v88dz306m1nmk97dlic";
+    sha256 = "1557b9sdragsx9i15qh6lq7fn056bgi87d31kxdl4vl0awigvp5f";
   };
 
   nativeBuildInputs = [ pkgconfig ];
diff --git a/pkgs/applications/science/misc/tulip/default.nix b/pkgs/applications/science/misc/tulip/default.nix
index d2590bc0b8d4..8560d900a4fa 100644
--- a/pkgs/applications/science/misc/tulip/default.nix
+++ b/pkgs/applications/science/misc/tulip/default.nix
@@ -1,13 +1,13 @@
 { fetchurl, stdenv, libxml2, freetype, libGLU_combined, glew, qt4
 , cmake, makeWrapper, libjpeg, python }:
 
-let version = "4.9.0"; in
+let version = "5.1.0"; in
 stdenv.mkDerivation rec {
   name = "tulip-${version}";
 
   src = fetchurl {
     url = "mirror://sourceforge/auber/${name}_src.tar.gz";
-    sha256 = "0phc7972brvm0v6lfk4ghq9b2b4jsj6c15xlbgnvhhcxhc99wba3";
+    sha256 = "1i70y8b39gkpxfalr9844pa3l4bnnyw5y7ngxdqibil96k2b9q9h";
   };
 
   buildInputs = [ libxml2 freetype glew libGLU_combined qt4 libjpeg python ];