Merge remote-tracking branch 'origin/master' into staging

* origin/master: (693 commits)
  buildGoModule: use go_1_12 instead of go_1_11 (#58103)
  gitAndTools.lab: 0.15.2 -> 0.15.3 (#58091)
  signal-desktop: 1.22.0 -> 1.23.0
  added missing semicolon to documentation
  terminus_font_ttf: 4.46.0 -> 4.47.0
  buildGoModule: remove SSL env vars in favor of cacert in buildInputs (#58071)
  dav1d: init at 0.2.1
  dropbox-cli: 2018.11.28 -> 2019.02.14
  atlassian-confluence: 6.14.1 -> 6.14.2
  maintainers: update email for dywedir
  python.pkgs.hglib: use patch to specify hg path (#57926)
  chkrootkit: 0.52 -> 0.53
  radare2-cutter: 1.7.2 -> 1.8.0
  autorandr: 1.7 -> 1.8
  pythonPackages.pyhepmc: fix build
  llvm-polly/clang-polly: use latest llvm
  apulse: 0.1.11.1 -> 0.1.12, cleanup
  factorio: experimental 0.17.14 → 0.17.16 (#58000)
  sequeler: 0.6.7 -> 0.6.8
  nasc: 0.5.1 -> 0.5.2
  ...

11 files changed, 90 insertions, 61 deletions

diff --git a/pkgs/applications/science/astronomy/gildas/default.nix b/pkgs/applications/science/astronomy/gildas/default.nix
index 186f3f9ca03..8c970440de5 100644
--- a/pkgs/applications/science/astronomy/gildas/default.nix
+++ b/pkgs/applications/science/astronomy/gildas/default.nix
@@ -7,8 +7,8 @@ let
 in
 
 stdenv.mkDerivation rec {
-  srcVersion = "mar19a";
-  version = "20190301_a";
+  srcVersion = "mar19b";
+  version = "20190301_b";
   name = "gildas-${version}";
 
   src = fetchurl {
@@ -16,7 +16,7 @@ stdenv.mkDerivation rec {
     # source code of the previous release to a different directory
     urls = [ "http://www.iram.fr/~gildas/dist/gildas-src-${srcVersion}.tar.gz"
       "http://www.iram.fr/~gildas/dist/archive/gildas/gildas-src-${srcVersion}.tar.gz" ];
-    sha256 = "98085417b0e9785ae1ab1a75c73b7a8b4c1b2ca2873f9474883f7a945488ceff";
+    sha256 = "c3722863e7f3043e2d6e675557421c2eb0978fd21148386440d0139664d19f99";
   };
 
   enableParallelBuilding = true;
diff --git a/pkgs/applications/science/biology/picard-tools/default.nix b/pkgs/applications/science/biology/picard-tools/default.nix
index 2ba5964d610..5a17b547b87 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 = "2.18.25";
+  version = "2.18.27";
 
   src = fetchurl {
     url = "https://github.com/broadinstitute/picard/releases/download/${version}/picard.jar";
-    sha256 = "03d3mnf3gddngn3dhwb00v8k40x6ncgprn22w4vyfr96917p2snx";
+    sha256 = "1pc9mhp35n0dl7j06c1564b797v6iqg6vhmd2xxvysc96hnsbyvc";
   };
 
   nativeBuildInputs = [ makeWrapper ];
diff --git a/pkgs/applications/science/logic/elan/default.nix b/pkgs/applications/science/logic/elan/default.nix
index b5a6a5b963e..693aaa53001 100644
--- a/pkgs/applications/science/logic/elan/default.nix
+++ b/pkgs/applications/science/logic/elan/default.nix
@@ -2,7 +2,7 @@
 
 rustPlatform.buildRustPackage rec {
   name = "elan-${version}";
-  version = "0.7.2";
+  version = "0.7.4";
 
   cargoSha256 = "0vv7kr7rc3lvas7ngp5dp99ajjd5v8k5937ish7zqz1k4970q2f1";
 
@@ -10,7 +10,7 @@ rustPlatform.buildRustPackage rec {
     owner = "kha";
     repo = "elan";
     rev = "v${version}";
-    sha256 = "0844fydfxvacyx02gwxbzpmiamsp22malyy5m4wpvrky4dkpn3qj";
+    sha256 = "0yf8mfgp4l78f5cjq1imh462axaa24jfhn69cgf7prw4jrmw3bch";
   };
 
   nativeBuildInputs = [ pkgconfig ];
diff --git a/pkgs/applications/science/logic/isabelle/default.nix b/pkgs/applications/science/logic/isabelle/default.nix
index ffe50856955..024f2f4e829 100644
--- a/pkgs/applications/science/logic/isabelle/default.nix
+++ b/pkgs/applications/science/logic/isabelle/default.nix
@@ -1,22 +1,20 @@
-{ stdenv, fetchurl, perl, nettools, java, polyml, z3 }:
+{ stdenv, fetchurl, perl, nettools, java, polyml, z3, rlwrap }:
 # nettools needed for hostname
 
-let
-  dirname = "Isabelle2017";
-in
+stdenv.mkDerivation rec {
+  pname = "isabelle";
+  version = "2018";
 
-stdenv.mkDerivation {
-  name = "isabelle-2017";
-  inherit dirname;
+  dirname = "Isabelle${version}";
 
   src = if stdenv.isDarwin
     then fetchurl {
       url = "http://isabelle.in.tum.de/website-${dirname}/dist/${dirname}.dmg";
-      sha256 = "1awgg39i72pivwfijdwffvil3glnpimjz2x04qbl5la2j6la48nb";
+      sha256 = "0jwnvsf5whklq14ihaxs7b9nbic94mm56nvxljrdbvl6y628j9r5";
     }
     else fetchurl {
       url = "https://isabelle.in.tum.de/website-${dirname}/dist/${dirname}_linux.tar.gz";
-      sha256 = "01v1zrajyfamjq5b8v18qr3ffivjckifsvvx2vs13di6wsnmm9gw";
+      sha256 = "1928lwrw1v1p9s23kix30ncpqm8djmrnjixj82f3ni2a8sc3hrsp";
     };
 
   buildInputs = [ perl polyml z3 ]
@@ -25,26 +23,33 @@ stdenv.mkDerivation {
   sourceRoot = dirname;
 
   postPatch = ''
-    ENV=$(type -p env)
-    patchShebangs "."
-    substituteInPlace lib/Tools/env \
-      --replace /usr/bin/env $ENV
-    substituteInPlace lib/Tools/install \
-      --replace /usr/bin/env $ENV
-    sed -i 's|isabelle_java java|${java}/bin/java|g' lib/Tools/java
-    substituteInPlace etc/settings \
-      --subst-var-by ML_HOME "${polyml}/bin"
-    substituteInPlace contrib/jdk/etc/settings \
-      --replace ISABELLE_JDK_HOME= '#ISABELLE_JDK_HOME='
-    substituteInPlace contrib/polyml-*/etc/settings \
-      --replace '$POLYML_HOME/$ML_PLATFORM' ${polyml}/bin \
-      --replace '$POLYML_HOME/$PLATFORM/polyml' ${polyml}/bin/poly
-    substituteInPlace lib/scripts/run-polyml* lib/scripts/polyml-version \
-      --replace '$ML_HOME/poly' ${polyml}/bin/poly
-    substituteInPlace contrib/z3*/etc/settings \
-      --replace '$Z3_HOME/z3' '${z3}/bin/z3'
+    patchShebangs .
 
-    for comp in contrib/jdk contrib/polyml*; do
+    cat >contrib/z3*/etc/settings <<EOF
+      Z3_HOME=${z3}
+      Z3_VERSION=${z3.version}
+      Z3_SOLVER=${z3}/bin/z3
+      Z3_INSTALLED=yes
+    EOF
+
+    cat >contrib/polyml-*/etc/settings <<EOF
+      ML_SYSTEM_64=true
+      ML_SYSTEM=${polyml.name}
+      ML_PLATFORM=${stdenv.system}
+      ML_HOME=${polyml}/bin
+      ML_OPTIONS="--minheap 1000"
+      POLYML_HOME="\$COMPONENT"
+      ML_SOURCES="\$POLYML_HOME/src"
+    EOF
+
+    cat >contrib/jdk/etc/settings <<EOF
+      ISABELLE_JAVA_PLATFORM=${stdenv.system}
+      ISABELLE_JDK_HOME=${java}
+    EOF
+
+    echo ISABELLE_LINE_EDITOR=${rlwrap}/bin/rlwrap >>etc/settings
+
+    for comp in contrib/jdk contrib/polyml-* contrib/z3-*; do
       rm -rf $comp/x86*
     done
     '' + (if ! stdenv.isLinux then "" else ''
diff --git a/pkgs/applications/science/machine-learning/labelimg/default.nix b/pkgs/applications/science/machine-learning/labelimg/default.nix
index 802a03bd4c7..340073b016e 100644
--- a/pkgs/applications/science/machine-learning/labelimg/default.nix
+++ b/pkgs/applications/science/machine-learning/labelimg/default.nix
@@ -6,6 +6,9 @@
       url = "https://github.com/tzutalin/labelImg/archive/v${version}.tar.gz";
       sha256 = "126kc4r7xm9170kh7snqsfkkc868m5bcnswrv7b4cq9ivlrdwbm4";
     };
+    nativeBuildInputs = with python2Packages; [
+      pyqt4
+    ];
     propagatedBuildInputs = with python2Packages; [
       pyqt4
       lxml
diff --git a/pkgs/applications/science/math/R/default.nix b/pkgs/applications/science/math/R/default.nix
index 4283ebd931a..562874ccc13 100644
--- a/pkgs/applications/science/math/R/default.nix
+++ b/pkgs/applications/science/math/R/default.nix
@@ -8,11 +8,11 @@
 }:
 
 stdenv.mkDerivation rec {
-  name = "R-3.5.2";
+  name = "R-3.5.3";
 
   src = fetchurl {
     url = "https://cran.r-project.org/src/base/R-3/${name}.tar.gz";
-    sha256 = "0qjvdic1qd5vndc4f0wjndpm0x18lbvbcc8nkix8saqgy8y8qgg5";
+    sha256 = "1337irx9y0r3jm1rcq1dcwnxsgfhnvgjs5wadcyh17vhpnvkgyib";
   };
 
   dontUseImakeConfigure = true;
diff --git a/pkgs/applications/science/math/nasc/default.nix b/pkgs/applications/science/math/nasc/default.nix
index aef18abaedf..beed2de9759 100644
--- a/pkgs/applications/science/math/nasc/default.nix
+++ b/pkgs/applications/science/math/nasc/default.nix
@@ -2,47 +2,45 @@
 , fetchFromGitHub
 , pkgconfig
 , gtk3
+, glib
 , pantheon
-, gnome3
+, libsoup
 , gtksourceview
 , libgee
 , cmake
 , libqalculate
-, gobject-introspection
-, wrapGAppsHook }:
+, cln
+, wrapGAppsHook
+}:
 
 stdenv.mkDerivation rec {
-  name = "nasc-${version}";
-  version = "0.5.1";
+  pname = "nasc";
+  version = "0.5.2";
 
   src = fetchFromGitHub {
     owner = "parnold-x";
-    repo = "nasc";
+    repo = pname;
     rev = version;
-    sha256 = "13y5fnm7g3xgdxmdydlgly73nigh8maqbf9d6c9bpyzxkxq1csy5";
+    sha256 = "009xmlsgl7r6wp6sczbdp8sjqqd6k2mychx5b4zn7wnrl7435y5y";
   };
 
-  postPatch = ''
-    # libqalculatenasc.so is not installed, and nasc fails to start
-    substituteInPlace libqalculatenasc/CMakeLists.txt --replace SHARED STATIC
-  '';
-
   nativeBuildInputs = [
     cmake
     pantheon.vala
-    gobject-introspection # for setup-hook
     pkgconfig
     wrapGAppsHook
   ];
 
   buildInputs = [
-    pantheon.elementary-icon-theme
+    cln
+    libsoup
+    gtk3
+    glib
     gtksourceview
     libgee
-    gnome3.libsoup
-    pantheon.granite
-    gtk3
     libqalculate
+    pantheon.elementary-icon-theme
+    pantheon.granite
   ];
 
   meta = with stdenv.lib; {
diff --git a/pkgs/applications/science/math/pynac/default.nix b/pkgs/applications/science/math/pynac/default.nix
index 032b2ef0964..f05700b1bd8 100644
--- a/pkgs/applications/science/math/pynac/default.nix
+++ b/pkgs/applications/science/math/pynac/default.nix
@@ -9,14 +9,14 @@
 }:
 
 stdenv.mkDerivation rec {
-  version = "0.7.23";
-  name = "pynac-${version}";
+  version = "0.7.24";
+  pname = "pynac";
 
   src = fetchFromGitHub {
     owner = "pynac";
     repo = "pynac";
     rev = "pynac-${version}";
-    sha256 = "02yhl8v9l6aj3wl6dk9iacz4hdv08i1d750rxpygjp43nlgvvb2h";
+    sha256 = "0i3qxww28576jim0abgkqy9mi2k0lfllgyx8xpfqsqb75ai970ik";
   };
 
   buildInputs = [
diff --git a/pkgs/applications/science/math/sage/sage-src.nix b/pkgs/applications/science/math/sage/sage-src.nix
index 83459021687..dd51059ff01 100644
--- a/pkgs/applications/science/math/sage/sage-src.nix
+++ b/pkgs/applications/science/math/sage/sage-src.nix
@@ -50,6 +50,28 @@ stdenv.mkDerivation rec {
 
     # Fixes a potential race condition which can lead to transient doctest failures.
     ./patches/fix-ecl-race.patch
+
+    # Parallelize docubuild using subprocesses, fixing an isolation issue. See
+    # https://groups.google.com/forum/#!topic/sage-packaging/YGOm8tkADrE
+    (fetchpatch {
+      name = "sphinx-docbuild-subprocesses.patch";
+      url = "https://salsa.debian.org/science-team/sagemath/raw/8a215b17e6f791ddfae6df8ce6d01dfb89acb434/debian/patches/df-subprocess-sphinx.patch";
+      sha256 = "07p9i0fwjgapmfvmi436yn6v60p8pvmxqjc93wsssqgh5kd8qw3n";
+      stripLen = 1;
+    })
+  ];
+
+  # Since sage unfortunately does not release bugfix releases, packagers must
+  # fix those bugs themselves. This is for critical bugfixes, where "critical"
+  # == "causes (transient) doctest failures / somebody complained".
+  bugfixPatches = [
+    # Transient doctest failure in src/sage/modular/abvar/torsion_subgroup.py
+    # https://trac.sagemath.org/ticket/27477
+    (fetchpatch {
+      name = "sig_on_in_matrix_sparce.patch";
+      url = "https://git.sagemath.org/sage.git/patch?id2=10407524b18659e14e184114b61c043fb816f3c2&id=c9b0cc9d0b8748ab85e568f8f57f316c5e8cbe54";
+      sha256 = "0wgp7yvn9sm1ynlhcr4l0hzmvr2n28llg4xc01p6k1zz4im64c17";
+    })
   ];
 
   # Patches needed because of package updates. We could just pin the versions of
@@ -117,7 +139,7 @@ stdenv.mkDerivation rec {
     ./patches/ignore-pip-deprecation.patch
   ];
 
-  patches = nixPatches ++ packageUpgradePatches;
+  patches = nixPatches ++ bugfixPatches ++ packageUpgradePatches;
 
   postPatch = ''
     # make sure shebangs etc are fixed, but sage-python23 still works
diff --git a/pkgs/applications/science/misc/cytoscape/default.nix b/pkgs/applications/science/misc/cytoscape/default.nix
index 36c7884d108..2262e342fc9 100644
--- a/pkgs/applications/science/misc/cytoscape/default.nix
+++ b/pkgs/applications/science/misc/cytoscape/default.nix
@@ -2,11 +2,11 @@
 
 stdenv.mkDerivation rec {
   name = "cytoscape-${version}";
-  version = "3.6.1";
+  version = "3.7.1";
 
   src = fetchurl {
-    url = "http://chianti.ucsd.edu/${name}/${name}.tar.gz";
-    sha256 = "1pkdilv1nw6vvdxk71bwjngr8yafrsqwaqvlakhp8yb342r1jd4s";
+    url = "https://github.com/cytoscape/cytoscape/releases/download/${version}/${name}.tar.gz";
+    sha256 = "1mhsngbwbgdwl70wj7850zg94534lasihwv2ryifardm35mkh48k";
   };
 
   buildInputs = [jre makeWrapper];
diff --git a/pkgs/applications/science/robotics/apmplanner2/default.nix b/pkgs/applications/science/robotics/apmplanner2/default.nix
index 2d579a80369..761766ffdf0 100644
--- a/pkgs/applications/science/robotics/apmplanner2/default.nix
+++ b/pkgs/applications/science/robotics/apmplanner2/default.nix
@@ -5,6 +5,7 @@
 
 stdenv.mkDerivation rec {
   name = "apmplanner2-${version}";
+  # TODO revert Qt59 to Qt5 in pkgs/top-level/all-packages.nix on next release
   version = "2.0.26";
   src = fetchFromGitHub {
     owner = "ArduPilot";