Merge commit '683c68232e91f76386db979c461d8fbe2a018782'

53 files changed, 416 insertions, 160 deletions

diff --git a/nixpkgs/pkgs/applications/science/astronomy/kstars/default.nix b/nixpkgs/pkgs/applications/science/astronomy/kstars/default.nix
new file mode 100644
index 000000000000..0b53e3e85ac3
--- /dev/null
+++ b/nixpkgs/pkgs/applications/science/astronomy/kstars/default.nix
@@ -0,0 +1,48 @@
+{
+  mkDerivation, lib, fetchgit,
+  extra-cmake-modules,
+
+  kconfig, kdoctools, kguiaddons, ki18n, kinit, kiconthemes, kio,
+  knewstuff, kplotting, kwidgetsaddons, kxmlgui,
+
+  qtx11extras, qtwebsockets,
+
+  eigen, zlib,
+
+  cfitsio, indilib, xplanet
+}:
+
+mkDerivation {
+  name = "kstars";
+  
+  src = fetchgit {
+    url = "https://anongit.kde.org/kstars.git";
+    rev = "7acc527939280edd22823371dc4e22494c6c626a";
+    sha256 = "1n1lgi7p3dj893fdnzjbnrha40p4apl0dy8zppcabxwrb1khb84v";
+  };
+  
+  nativeBuildInputs = [ extra-cmake-modules kdoctools ];
+  buildInputs = [
+    kconfig kdoctools kguiaddons ki18n kinit kiconthemes kio
+    knewstuff kplotting kwidgetsaddons kxmlgui
+
+    qtx11extras qtwebsockets
+
+    eigen zlib
+
+    cfitsio indilib xplanet
+  ];
+
+  meta = with lib; {
+    description = "Virtual planetarium astronomy software";
+    homepage = "https://kde.org/applications/education/org.kde.kstars";
+    longDescription = ''
+      It provides an accurate graphical simulation of the night sky, from any location on Earth, at any date and time.
+      The display includes up to 100 million stars, 13.000 deep-sky objects, all 8 planets, the Sun and Moon, and thousands of comets, asteroids, supernovae, and satellites.
+      For students and teachers, it supports adjustable simulation speeds in order to view phenomena that happen over long timescales, the KStars Astrocalculator to predict conjunctions, and many common astronomical calculations.
+    '';
+    license = licenses.gpl2;
+    platforms = platforms.linux;
+    maintainers = with maintainers; [ timput ];
+  };
+}
diff --git a/nixpkgs/pkgs/applications/science/astronomy/stellarium/default.nix b/nixpkgs/pkgs/applications/science/astronomy/stellarium/default.nix
index a0cd535f362c..7ef7776c0fe8 100644
--- a/nixpkgs/pkgs/applications/science/astronomy/stellarium/default.nix
+++ b/nixpkgs/pkgs/applications/science/astronomy/stellarium/default.nix
@@ -6,13 +6,13 @@
 
 mkDerivation rec {
   pname = "stellarium";
-  version = "0.20.0";
+  version = "0.20.1";
 
   src = fetchFromGitHub {
     owner = "Stellarium";
     repo = "stellarium";
     rev = "v${version}";
-    sha256 = "1732dxkgyqd4xf0ry7v930vcbv60l8iry596869z1d47j2piibs4";
+    sha256 = "1x8svan03k1x9jwqflimbpj7jpg6mjrbz26bg1sbhsqdlc8rbhky";
   };
 
   nativeBuildInputs = [ cmake perl wrapQtAppsHook ];
diff --git a/nixpkgs/pkgs/applications/science/biology/EZminc/default.nix b/nixpkgs/pkgs/applications/science/biology/EZminc/default.nix
index 978615fa4592..7502a4ffd2ab 100644
--- a/nixpkgs/pkgs/applications/science/biology/EZminc/default.nix
+++ b/nixpkgs/pkgs/applications/science/biology/EZminc/default.nix
@@ -1,18 +1,18 @@
-{ stdenv, fetchFromGitHub, cmake, pkgconfig, libminc, bicpl, itk, fftwFloat, gsl }:
+{ stdenv, fetchFromGitHub, cmake, pkgconfig, libminc, bicpl, itk4, fftwFloat, gsl }:
 
 stdenv.mkDerivation rec {
   pname = "EZminc";
-  name  = "${pname}-unstable-2019-07-25";
+  name  = "${pname}-unstable-2019-03-12";
 
   src = fetchFromGitHub {
     owner  = "BIC-MNI";
     repo   = pname;
-    rev    = "9591edd5389a5bda2c1f606816c7cdb35c065adf";
-    sha256 = "02k87qbpx0f48l2lbcjmlqx82py684z3sfi29va5icfg3hjd6j7b";
+    rev    = "5e3333ee356f914d34d66d33ea8df809c7f7fa51";
+    sha256 = "0wy8cppf5xpgfqvgb3mqs1cjh81n6qzkk6zxv29wvng8nar9wsy4";
   };
 
   nativeBuildInputs = [ cmake pkgconfig ];
-  buildInputs = [ itk libminc bicpl fftwFloat gsl ];
+  buildInputs = [ itk4 libminc bicpl fftwFloat gsl ];
 
   cmakeFlags = [ "-DLIBMINC_DIR=${libminc}/lib/"
                  "-DEZMINC_BUILD_TOOLS=TRUE"
diff --git a/nixpkgs/pkgs/applications/science/biology/dcm2niix/default.nix b/nixpkgs/pkgs/applications/science/biology/dcm2niix/default.nix
index 8ea3588fa8ca..59b173ac98cd 100644
--- a/nixpkgs/pkgs/applications/science/biology/dcm2niix/default.nix
+++ b/nixpkgs/pkgs/applications/science/biology/dcm2niix/default.nix
@@ -6,14 +6,14 @@
 }:
 
 stdenv.mkDerivation rec {
-  version = "1.0.20190902";
+  version = "1.0.20200331";
   pname = "dcm2niix";
 
   src = fetchFromGitHub {
     owner = "rordenlab";
     repo = "dcm2niix";
     rev = "v${version}";
-    sha256 = "0h8jsadgv831lqb0jhnaxm7lldirmnp5agrhgg5bcxvn860fl15b";
+    sha256 = "1cncfwhyhmg18n970lkn6yvp0i74ajznsl8dqz00asqfzmg681n1";
   };
 
   enableParallelBuilding = true;
diff --git a/nixpkgs/pkgs/applications/science/biology/mosdepth/default.nix b/nixpkgs/pkgs/applications/science/biology/mosdepth/default.nix
index 569c63afa7a1..21af5b82207b 100644
--- a/nixpkgs/pkgs/applications/science/biology/mosdepth/default.nix
+++ b/nixpkgs/pkgs/applications/science/biology/mosdepth/default.nix
@@ -4,8 +4,8 @@ let
   hts-nim = fetchFromGitHub {
     owner = "brentp";
     repo = "hts-nim";
-    rev = "v0.2.14";
-    sha256 = "0d1z4b6mrppmz3hgkxd4wcy79w68icvhi7q7n3m2k17n8f3xbdx3";
+    rev = "v0.3.4";
+    sha256 = "0670phk1bq3l9j2zaa8i5wcpc5dyfrc0l2a6c21g0l2mmdczffa7";
   };
 
   docopt = fetchFromGitHub {
@@ -17,13 +17,13 @@ let
 
 in stdenv.mkDerivation rec {
   pname = "mosdepth";
-  version = "0.2.6";
+  version = "0.2.9";
 
   src = fetchFromGitHub {
     owner = "brentp";
     repo = "mosdepth";
     rev = "v${version}";
-    sha256 = "0i9pl9lsli3y84ygxanrr525gfg8fs9h481944cbzsmqmbldwvgk";
+    sha256 = "01gm9gj2x2zs4yx6wk761fi1papi7qr3gp4ln1kkn8n2f9y9h849";
   };
 
   buildInputs = [ nim ];
diff --git a/nixpkgs/pkgs/applications/science/biology/mrtrix/default.nix b/nixpkgs/pkgs/applications/science/biology/mrtrix/default.nix
index 6959b2caab8a..528277e05e38 100644
--- a/nixpkgs/pkgs/applications/science/biology/mrtrix/default.nix
+++ b/nixpkgs/pkgs/applications/science/biology/mrtrix/default.nix
@@ -1,17 +1,17 @@
 { stdenv, lib, fetchFromGitHub, python, makeWrapper
-, eigen, fftw, libtiff, zlib, ants, bc
+, eigen, fftw, libtiff, libpng, zlib, ants, bc
 , qt5, libGL, libGLU, libX11, libXext
 , withGui ? true }:
 
 stdenv.mkDerivation rec {
   pname = "mrtrix";
-  version = "3.0_RC3_latest";
+  version = "3.0.0";
 
   src = fetchFromGitHub {
     owner  = "MRtrix3";
     repo   = "mrtrix3";
     rev    = version;
-    sha256 = "184nv524p8j94qicjy9l288bqcgl2yxqqs55a7042i0gfsnwp51c";
+    sha256 = "1vvmmbw3m0bdfwp4szr62ygzsvkj0ss91cx5zlkspsr1rff05f9b";
     fetchSubmodules = true;
   };
 
@@ -22,7 +22,9 @@ stdenv.mkDerivation rec {
     python
     fftw
     libtiff
-    zlib ] ++ lib.optionals withGui [
+    libpng
+    zlib
+  ] ++ lib.optionals withGui [
     libGL
     libGLU
     libX11
@@ -34,9 +36,14 @@ stdenv.mkDerivation rec {
   installCheckInputs = [ bc ];
 
   postPatch = ''
-    patchShebangs ./build ./configure ./run_tests ./bin/population_template
+    patchShebangs ./build ./configure ./run_tests ./bin/*
+
+    # patching interpreters before fixup is needed for tests:
+    patchShebangs ./bin/*
+    patchShebangs testing/binaries/data/vectorstats/*py
+
     substituteInPlace ./run_tests  \
-      --replace 'git submodule update --init >> $LOGFILE 2>&1' ""
+      --replace 'git submodule update --init $datadir >> $LOGFILE 2>&1' ""
   '';
 
   configurePhase = ''
@@ -50,7 +57,13 @@ stdenv.mkDerivation rec {
     (cd testing && ../build)
   '';
 
-  installCheckPhase = "./run_tests";
+  installCheckPhase = ''
+    ./run_tests units
+    ./run_tests binaries
+
+    # can also `./run_tests scripts`, but this fails due to lack of FSL package
+    # (and there's no convenient way to disable individual tests)
+  '';
   doInstallCheck = true;
 
   installPhase = ''
@@ -63,7 +76,9 @@ stdenv.mkDerivation rec {
 
   postInstall = ''
     for prog in $out/bin/*; do
-      wrapProgram $prog --prefix PATH : ${lib.makeBinPath [ ants ]}
+      if [[ -x "$prog" ]]; then
+        wrapProgram $prog --prefix PATH : ${lib.makeBinPath [ ants ]}
+      fi
     done
   '';
 
diff --git a/nixpkgs/pkgs/applications/science/biology/picard-tools/default.nix b/nixpkgs/pkgs/applications/science/biology/picard-tools/default.nix
index 246c98768101..5073d0f0f324 100644
--- a/nixpkgs/pkgs/applications/science/biology/picard-tools/default.nix
+++ b/nixpkgs/pkgs/applications/science/biology/picard-tools/default.nix
@@ -2,11 +2,11 @@
 
 stdenv.mkDerivation rec {
   pname = "picard-tools";
-  version = "2.22.2";
+  version = "2.22.4";
 
   src = fetchurl {
     url = "https://github.com/broadinstitute/picard/releases/download/${version}/picard.jar";
-    sha256 = "11mzz483f89pb2s8jmwhl12d0m6k41kmi4xh0i6hq69rxrqi8l4s";
+    sha256 = "0gzna5df8nk42l7mc0qbp9h73gwr1030jnw10fawjp6ql6213kdd";
   };
 
   nativeBuildInputs = [ makeWrapper ];
diff --git a/nixpkgs/pkgs/applications/science/biology/quast/default.nix b/nixpkgs/pkgs/applications/science/biology/quast/default.nix
new file mode 100644
index 000000000000..e3c3ea23c2c0
--- /dev/null
+++ b/nixpkgs/pkgs/applications/science/biology/quast/default.nix
@@ -0,0 +1,58 @@
+{ stdenv, fetchurl, python3Packages, zlib, bash, coreutils }:
+
+let
+  pythonPackages = python3Packages;
+  inherit (pythonPackages) python;
+in
+
+pythonPackages.buildPythonApplication rec {
+  pname = "quast";
+  version = "5.0.2";
+
+  src = fetchurl {
+    url = "https://github.com/ablab/quast/releases/download/${pname}_${version}/${pname}-${version}.tar.gz";
+    sha256 = "13ml8qywbb4cc7wf2x7z5mz1rjqg51ab8wkizwcg4f6c40zgif6d";
+  };
+
+  pythonPath = with pythonPackages; [ simplejson joblib setuptools matplotlib ];
+
+  nativeBuildInputs = [ coreutils ];
+
+  buildInputs = [ zlib ] ++ pythonPath;
+
+  dontConfigure = true;
+
+  dontBuild = true;
+
+  installPhase = ''
+    substituteInPlace quast_libs/bedtools/Makefile \
+      --replace "/bin/bash" "${bash}/bin/bash"
+    mkdir -p "$out/${python.sitePackages}"
+    export PYTHONPATH="$out/${python.sitePackages}:$PYTHONPATH"
+    ${python.interpreter} setup.py install \
+      --install-lib=$out/${python.sitePackages} \
+      --prefix="$out"
+  '';
+
+   postFixup = ''
+   for file in $(find $out -type f -type f -perm /0111); do
+       old_rpath=$(patchelf --print-rpath $file) && \
+       patchelf --set-rpath $old_rpath:${stdenv.cc.cc.lib}/lib $file || true
+   done
+   # Link to the master program
+   ln -s $out/bin/quast.py $out/bin/quast
+  '';
+
+  dontPatchELF = true;
+
+  # Tests need to download data files, so manual run after packaging is needed
+  doCheck = false;
+
+  meta = with stdenv.lib ; {
+    description = "Evaluates genome assemblies by computing various metrics";
+    homepage = "https://github.com/ablab/quast";
+    license = licenses.gpl2;
+    maintainers = [ maintainers.bzizou ];
+    platforms = platforms.all;
+  };
+}
diff --git a/nixpkgs/pkgs/applications/science/biology/stacks/default.nix b/nixpkgs/pkgs/applications/science/biology/stacks/default.nix
index 93a02a46bd88..12c865162425 100644
--- a/nixpkgs/pkgs/applications/science/biology/stacks/default.nix
+++ b/nixpkgs/pkgs/applications/science/biology/stacks/default.nix
@@ -2,10 +2,10 @@
     
 stdenv.mkDerivation rec {
   pname = "stacks";
-  version = "2.52";
+  version = "2.53";
   src = fetchurl {
     url = "http://catchenlab.life.illinois.edu/stacks/source/${pname}-${version}.tar.gz";
-    sha256 = "0gq3kbj910jsq591wylzjmd23srjlsssmrckmf46m4ysjqdqd8vm";
+    sha256 = "1zchds205nwdqch1246953dr8c0019yas178qbq3jypbxvmgq7pf";
   };
 
   buildInputs = [ zlib ];
diff --git a/nixpkgs/pkgs/applications/science/chemistry/marvin/default.nix b/nixpkgs/pkgs/applications/science/chemistry/marvin/default.nix
index c54fb3444bb0..9512a288d80c 100644
--- a/nixpkgs/pkgs/applications/science/chemistry/marvin/default.nix
+++ b/nixpkgs/pkgs/applications/science/chemistry/marvin/default.nix
@@ -4,12 +4,12 @@ with stdenv.lib;
 
 stdenv.mkDerivation rec {
   pname = "marvin";
-  version = "20.9.0";
+  version = "20.10.0";
 
   src = fetchurl {
     name = "marvin-${version}.deb";
     url = "http://dl.chemaxon.com/marvin/${version}/marvin_linux_${versions.majorMinor version}.deb";
-    sha256 = "1c6q1vb96jsb37g5qbhzcnasd5pdqjyc190yg3caw3gwrd97889q";
+    sha256 = "042ndlns48pa6mn6wyrp4q9c1v0a2vzcnhw5l766zdnxdjyv0acx";
   };
 
   nativeBuildInputs = [ dpkg makeWrapper ];
diff --git a/nixpkgs/pkgs/applications/science/chemistry/octopus/default.nix b/nixpkgs/pkgs/applications/science/chemistry/octopus/default.nix
index f30954367cf7..adb31d326509 100644
--- a/nixpkgs/pkgs/applications/science/chemistry/octopus/default.nix
+++ b/nixpkgs/pkgs/applications/science/chemistry/octopus/default.nix
@@ -2,7 +2,7 @@
 , libyaml, libxc, fftw, blas, lapack, gsl, netcdf, arpack, autoreconfHook
 }:
 
-assert (!blas.is64bit) && (!lapack.is64bit);
+assert (!blas.isILP64) && (!lapack.isILP64);
 
 stdenv.mkDerivation rec {
   pname = "octopus";
diff --git a/nixpkgs/pkgs/applications/science/electronics/caneda/default.nix b/nixpkgs/pkgs/applications/science/electronics/caneda/default.nix
index 6f832013e8ca..c90ceac6788f 100644
--- a/nixpkgs/pkgs/applications/science/electronics/caneda/default.nix
+++ b/nixpkgs/pkgs/applications/science/electronics/caneda/default.nix
@@ -1,6 +1,6 @@
-{stdenv, fetchFromGitHub, cmake, qtbase, qttools, qtsvg, qwt }:
+{ mkDerivation, stdenv, fetchFromGitHub, cmake, qtbase, qttools, qtsvg, qwt }:
 
-stdenv.mkDerivation rec {
+mkDerivation rec {
   pname = "caneda";
   version = "0.3.1";
 
diff --git a/nixpkgs/pkgs/applications/science/electronics/eagle/eagle.nix b/nixpkgs/pkgs/applications/science/electronics/eagle/eagle.nix
index 7c5942d825a9..58bdd5c722da 100644
--- a/nixpkgs/pkgs/applications/science/electronics/eagle/eagle.nix
+++ b/nixpkgs/pkgs/applications/science/electronics/eagle/eagle.nix
@@ -13,11 +13,11 @@ let
   in
   mkDerivation rec {
     pname = "eagle";
-    version = "9.6.0";
+    version = "9.6.1";
 
     src = fetchurl {
       url = "https://eagle-updates.circuits.io/downloads/${builtins.replaceStrings ["."] ["_"] version}/Autodesk_EAGLE_${version}_English_Linux_64bit.tar.gz";
-      sha256 = "1crkyc7ws2zz5dfs00h6rj4z2hyqb97kp6r4hxhmcgg5647ij4z8";
+      sha256 = "1iq4aahrh4g3549vbr7gka5y2h7f17n3yafzl21njc2mkqb12jdw";
     };
 
     desktopItem = makeDesktopItem {
diff --git a/nixpkgs/pkgs/applications/science/electronics/kicad/update.sh b/nixpkgs/pkgs/applications/science/electronics/kicad/update.sh
index 7dc0b008b6c2..f048ccde4ec8 100755
--- a/nixpkgs/pkgs/applications/science/electronics/kicad/update.sh
+++ b/nixpkgs/pkgs/applications/science/electronics/kicad/update.sh
@@ -1,6 +1,8 @@
 #!/usr/bin/env nix-shell
 #!nix-shell -i bash -p coreutils git nix curl
 
+set -e
+
 # this script will generate versions.nix in the right location
 # this should contain the versions' revs and hashes
 # the stable revs are stored only for ease of skipping
@@ -50,12 +52,11 @@ for arg in "$@"; do
 done
 
 here="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )"
-now=$(date --iso-8601)
+now=$(date --iso-8601 --utc)
 
 file="${here}/versions.nix"
 # just in case this runs in parallel
-rand="$(head -c 3 /dev/urandom | base64)"
-tmp="${here}/,versions.nix.${rand}"
+tmp="${here}/,versions.nix.${RANDOM}"
 
 # libraries currently on github, move to $gitlab/libraries planned
 libs=( symbols templates footprints packages3d )
@@ -112,16 +113,16 @@ for version in "${all_versions[@]}"; do
 
     echo "Checking src" >&2
     src_rev="$(${get_rev} "${gitlab}"/code/kicad.git "${version}" | cut -f1)"
-    ret="$(grep -sm 1 "\"${pname}\"" -A 4 "${file}" | grep -sm 1 "${src_rev}")"
+    has_rev="$(grep -sm 1 "\"${pname}\"" -A 4 "${file}" | grep -sm 1 "${src_rev}" || true)"
     has_hash="$(grep -sm 1 "\"${pname}\"" -A 5 "${file}" | grep -sm 1 "sha256")"
-    if [[ -n ${ret} && -n ${has_hash} && -z ${clean} ]]; then
+    if [[ -n ${has_rev} && -n ${has_hash} && -z ${clean} ]]; then
       echo "Reusing old ${pname}.src.sha256, already latest .rev" >&2
       grep -sm 1 "\"${pname}\"" -A 5 "${file}" | grep -sm 1 "rev" -A 1
     else
           printf "%8srev =\t\t\t\"%s\";\n" "" "${src_rev}"
           printf "%8ssha256 =\t\t\"%s\";\n" \
             "" "$(${prefetch} "${gitlab_pre}${src_rev}")"
-          (( count++ ))
+          count=$((count+1))
     fi
         printf "%6s};\n" ""
       printf "%4s};\n" ""
@@ -132,25 +133,25 @@ for version in "${all_versions[@]}"; do
 
         echo "Checking i18n" >&2
         i18n_rev="$(${get_rev} "${i18n}" "${version}" | cut -f1)"
-        ret="$(grep -sm 1 "\"${pname}\"" -A 11 "${file}" | grep -sm 1 "${i18n_rev}")"
+        has_rev="$(grep -sm 1 "\"${pname}\"" -A 11 "${file}" | grep -sm 1 "${i18n_rev}" || true)"
         has_hash="$(grep -sm 1 "\"${pname}\"" -A 12 "${file}" | grep -sm 1 "i18n.sha256")"
-        if [[ -n ${ret} && -n ${has_hash} && -z ${clean} ]]; then
+        if [[ -n ${has_rev} && -n ${has_hash} && -z ${clean} ]]; then
           echo "Reusing old kicad-i18n-${today}.src.sha256, already latest .rev" >&2
           grep -sm 1 "\"${pname}\"" -A 12 "${file}" | grep -sm 1 "i18n" -A 1
         else
           printf "%8si18n.rev =\t\t\"%s\";\n" "" "${i18n_rev}"
           printf "%8si18n.sha256 =\t\t\"%s\";\n" "" \
             "$(${prefetch} "${i18n_pre}${i18n_rev}")"
-          (( count++ ))
+          count=$((count+1))
         fi
 
           for lib in "${libs[@]}"; do
             echo "Checking ${lib}" >&2
             url="${github}-${lib}.git"
             lib_rev="$(${get_rev} "${url}" "${version}" | cut -f1)"
-            ret="$(grep -sm 1 "\"${pname}\"" -A 19 "${file}" | grep -sm 1 "${lib_rev}" -A 1)"
+            has_rev="$(grep -sm 1 "\"${pname}\"" -A 19 "${file}" | grep -sm 1 "${lib_rev}" || true)"
             has_hash="$(grep -sm 1 "\"${pname}\"" -A 20 "${file}" | grep -sm 1 "${lib}.sha256")"
-            if [[ -n ${ret} && -n ${has_hash} && -z ${clean} ]]; then
+            if [[ -n ${has_rev} && -n ${has_hash} && -z ${clean} ]]; then
               echo "Reusing old kicad-${lib}-${today}.src.sha256, already latest .rev" >&2
               grep -sm 1 "\"${pname}\"" -A 20 "${file}" | grep -sm 1 "${lib}" -A 1
             else
@@ -161,7 +162,7 @@ for version in "${all_versions[@]}"; do
               printf "\"%s\";\n" "${lib_rev}"
               printf "%8s%s.sha256 =\t\"%s\";\n" "" \
               "${lib}" "$(${prefetch} "${github}-${lib}/archive/${lib_rev}.tar.gz")"
-              (( count++ ))
+              count=$((count+1))
             fi
           done
         printf "%6s};\n" ""
@@ -175,6 +176,11 @@ done
 printf "}\n"
 } > "${tmp}"
 
+if grep '""' "${tmp}"; then
+	echo "empty value detected, out of space?" >&2
+	exit "1"
+fi
+
 mv "${tmp}" "${file}"
 
 printf "\nFinished\nMoved output to %s\n\n" "${file}" >&2
diff --git a/nixpkgs/pkgs/applications/science/electronics/kicad/versions.nix b/nixpkgs/pkgs/applications/science/electronics/kicad/versions.nix
index 6b9a981a87c4..174532d69625 100644
--- a/nixpkgs/pkgs/applications/science/electronics/kicad/versions.nix
+++ b/nixpkgs/pkgs/applications/science/electronics/kicad/versions.nix
@@ -27,25 +27,25 @@
   };
   "kicad-unstable" = {
     kicadVersion = {
-      version =			"2020-02-10";
+      version =			"2020-04-25";
       src = {
-        rev =			"1190e60dd426d246661e478db3287f266ec6cda2";
-        sha256 =		"0cgfad07j69cks97llj4hf3kga0d5qf728s89xwxrzcwm06k62bi";
+        rev =			"3759799d1e03b2da6a0dcd72273e4978880fc8f1";
+        sha256 =		"0ba14fla8m5zli68wfjkfc4ymvj4j8z92y3jigxs8hys0450bybi";
       };
     };
     libVersion = {
-      version =			"2020-02-10";
+      version =			"2020-04-25";
       libSources = {
-        i18n.rev =		"26786c4ca804bad7eb072f1ef381f00b5a2ff3ee";
-        i18n.sha256 =		"0iqr1xfw4s677afjy9bn5y41z4isp327f9y90wypkxiwwq3dfkfl";
-        symbols.rev =		"35b7da2d211d7cc036b37ad7f5e40ef03faa1bc7";
-        symbols.sha256 =	"0wbfw1swbfvfp47cn48pxpqlygjs3xh568ydrrs51v3w102x8y64";
-        templates.rev =		"0c0490897f803ab8b7c3dad438b7eb1f80e0417c";
-        templates.sha256 =	"0cs3bm3zb5ngw5ldn0lzw5bvqm4kvcidyrn76438alffwiz2b15g";
-        footprints.rev =	"9357b6f09312966c57fec9f66a516941d79c3038";
-        footprints.sha256 =	"0cgah1q0h012ffwfl220k7qb6hgbs0i91spq2j4v3lgpfr4g638d";
-        packages3d.rev =	"de368eb739abe41dfc3163e0e370477e857f9cc1";
-        packages3d.sha256 =	"0b3p5v8g24h6l7q3sbqz7ns0gnrf9l89glj86m5ybhizvls9vrrs";
+        i18n.rev =		"fc14baa52ca56a58b0048ab860bf31887d3cf8eb";
+        i18n.sha256 =		"05nayab7dkjyq7g3i9q7k55hcckpc0cmq4bbklmxx16rx4rbhzc6";
+        symbols.rev =		"0f9ff2d17237f90bb649bf0a52b6d454f68197e8";
+        symbols.sha256 =	"1a54428syn2xksc00n2bvh1alrx2vrqmp7cg7d2rn8nlq8yk4qd5";
+        templates.rev =		"7db8d4d0ea0711f1961d117853547fb3edbc3857";
+        templates.sha256 =	"1hppcsrkn4dk6ggby6ckh0q65qxkywrbyxa4lwpaf7pxjyv498xg";
+        footprints.rev =	"61df6d8853b4c68cca0ac87784c0a33cff9394d3";
+        footprints.sha256 =	"0blmhk8pwd4mi6rlsr4lf4lq7j01h6xbpbvr3pm8pmw8zylhi54v";
+        packages3d.rev =	"88bcf2e817fe000bb2c05e14489afc3b1a4e10ed";
+        packages3d.sha256 =	"0z9p1fn5xbz940kr5jz2ibzf09hpdi1c9izmabkffvrnfy6408x6";
       };
     };
   };
diff --git a/nixpkgs/pkgs/applications/science/electronics/librepcb/default.nix b/nixpkgs/pkgs/applications/science/electronics/librepcb/default.nix
index 7e0894fb337d..de01b095e381 100644
--- a/nixpkgs/pkgs/applications/science/electronics/librepcb/default.nix
+++ b/nixpkgs/pkgs/applications/science/electronics/librepcb/default.nix
@@ -2,14 +2,14 @@
 
 mkDerivation {
   pname = "librepcb";
-  version = "0.1.3";
+  version = "0.1.4";
 
   src = fetchFromGitHub {
     owner = "LibrePCB";
     repo = "LibrePCB";
     fetchSubmodules = true;
-    rev = "56bc60d347ff67df0fe1d57807d03f0606de557f";
-    sha256 = "0z6jn5zawp0x5i9zda7l787jnsv3yl8aqwnpii3g4hsnf2q3hhrh";
+    rev = "ae04eef5a71b5ba66ae2cee6b631c1c933ace535";
+    sha256 = "0wk5qny1jb6n4mwyyrs7syir3hmwxlwazcd80bpxharmsj7p0rzc";
   };
 
   enableParallelBuilding = true;
diff --git a/nixpkgs/pkgs/applications/science/electronics/magic-vlsi/0001-strip-bin-prefix.patch b/nixpkgs/pkgs/applications/science/electronics/magic-vlsi/0001-strip-bin-prefix.patch
new file mode 100644
index 000000000000..1cef96ea1408
--- /dev/null
+++ b/nixpkgs/pkgs/applications/science/electronics/magic-vlsi/0001-strip-bin-prefix.patch
@@ -0,0 +1,10 @@
+diff --git a/scripts/makedbh b/scripts/makedbh
+index 01e4fa5..d6299c6 100755
+--- a/scripts/makedbh
++++ b/scripts/makedbh
+@@ -1,4 +1,4 @@
+-#!/bin/csh -f
++#!/usr/bin/env tcsh
+ #
+ # makes the "database.h" (1st argument, $1) file from "database.h.in"
+ # (2nd argument, $2), setting various mask operation definitions
diff --git a/nixpkgs/pkgs/applications/science/electronics/magic-vlsi/0002-fix-format-security.patch b/nixpkgs/pkgs/applications/science/electronics/magic-vlsi/0002-fix-format-security.patch
new file mode 100644
index 000000000000..37ae35195503
--- /dev/null
+++ b/nixpkgs/pkgs/applications/science/electronics/magic-vlsi/0002-fix-format-security.patch
@@ -0,0 +1,19 @@
+diff --git a/database/DBio.c b/database/DBio.c
+index 93c4b0b..292ea5f 100644
+--- a/database/DBio.c
++++ b/database/DBio.c
+@@ -2378,12 +2378,12 @@ DBCellWriteFile(cellDef, f)
+ 
+ #define FPRINTF(f,s)\
+ {\
+-     if (fprintf(f,s) == EOF) goto ioerror;\
++     if (fprintf(f,"%s",s) == EOF) goto ioerror;\
+      DBFileOffset += strlen(s);\
+ }
+ #define FPRINTR(f,s)\
+ {\
+-     if (fprintf(f,s) == EOF) return 1;\
++     if (fprintf(f,"%s",s) == EOF) return 1;\
+      DBFileOffset += strlen(s);\
+ }
+ 
diff --git a/nixpkgs/pkgs/applications/science/electronics/magic-vlsi/default.nix b/nixpkgs/pkgs/applications/science/electronics/magic-vlsi/default.nix
new file mode 100644
index 000000000000..62b830547e53
--- /dev/null
+++ b/nixpkgs/pkgs/applications/science/electronics/magic-vlsi/default.nix
@@ -0,0 +1,36 @@
+{ stdenv, fetchurl, m4, tcsh, libX11, tcl, tk, cairo, ncurses, mesa_glu, python3 }:
+
+stdenv.mkDerivation {
+  pname = "magic-vlsi";
+  version = "8.3.5";
+
+  src = fetchurl {
+    url = "http://opencircuitdesign.com/magic/archive/magic-8.3.5.tgz";
+    sha256 = "0wv4zmxlqjfaakgp802icn0cd9f8ylkz2sppix83axq8p5cg90yq";
+  };
+
+  buildInputs = [ m4 tcsh libX11 tcl tk cairo ncurses mesa_glu ];
+  nativeBuildInputs = [ python3 ];
+
+  configureFlags = [
+    "--with-tcl=${tcl}"
+    "--with-tk=${tk}"
+    "--disable-werror"
+  ];
+
+  postPatch = ''
+    patchShebangs scripts/*
+  '';
+
+  patches = [
+    ./0001-strip-bin-prefix.patch
+    ./0002-fix-format-security.patch
+  ];
+
+  meta = with stdenv.lib; {
+    description = "VLSI layout tool written in Tcl";
+    homepage = "http://opencircuitdesign.com/magic/";
+    license = licenses.mit;
+    maintainers = [ maintainers.dkudriavtsev ];
+  };
+}
diff --git a/nixpkgs/pkgs/applications/science/logic/cryptominisat/default.nix b/nixpkgs/pkgs/applications/science/logic/cryptominisat/default.nix
index 113c6307c40b..8c1b3bd03694 100644
--- a/nixpkgs/pkgs/applications/science/logic/cryptominisat/default.nix
+++ b/nixpkgs/pkgs/applications/science/logic/cryptominisat/default.nix
@@ -2,13 +2,13 @@
 
 stdenv.mkDerivation rec {
   pname = "cryptominisat";
-  version = "5.6.8";
+  version = "5.7.0";
 
   src = fetchFromGitHub {
     owner  = "msoos";
     repo   = "cryptominisat";
     rev    = version;
-    sha256 = "0csimmy1nvkfcsxjra9bm4mlcyxa3ac8zarm88zfb7640ca0d0wv";
+    sha256 = "0ny5ln8fc0irprs04qw01c9mppps8q27lkx01a549zazwhj4b5rm";
   };
 
   buildInputs = [ python3 boost ];
diff --git a/nixpkgs/pkgs/applications/science/logic/elan/default.nix b/nixpkgs/pkgs/applications/science/logic/elan/default.nix
index ea3b05850990..743bbf163c2f 100644
--- a/nixpkgs/pkgs/applications/science/logic/elan/default.nix
+++ b/nixpkgs/pkgs/applications/science/logic/elan/default.nix
@@ -2,16 +2,16 @@
 
 rustPlatform.buildRustPackage rec {
   pname = "elan";
-  version = "0.8.0";
+  version = "0.10.0";
 
   src = fetchFromGitHub {
     owner = "kha";
     repo = "elan";
     rev = "v${version}";
-    sha256 = "0n2ncssjcmp3x5kbnci7xbq5fgcihlr3vaglyhhwzrxkjy2vpmpd";
+    sha256 = "0aw538shvpfbk481y0gw3z97nsazdnk8qh8fwsb6ji62p2r51v6f";
   };
 
-  cargoSha256 = "1pkg0n7kxckr0zhr8dr12b9fxg5q185kj3r9k2rmnkj2dpa2mxh3";
+  cargoSha256 = "0zg3q31z516049v9fhli4yxldx9fg31k2qfx4ag8rmyvpgy9xh6c";
 
   nativeBuildInputs = [ pkgconfig ];
 
@@ -22,7 +22,7 @@ rustPlatform.buildRustPackage rec {
   postInstall = ''
     pushd $out/bin
     mv elan-init elan
-    for link in lean leanpkg leanchecker leanc; do
+    for link in lean leanpkg leanchecker leanc leanmake; do
       ln -s elan $link
     done
     popd
diff --git a/nixpkgs/pkgs/applications/science/logic/lean/default.nix b/nixpkgs/pkgs/applications/science/logic/lean/default.nix
index 36df6ae0658f..c80c163562be 100644
--- a/nixpkgs/pkgs/applications/science/logic/lean/default.nix
+++ b/nixpkgs/pkgs/applications/science/logic/lean/default.nix
@@ -2,13 +2,13 @@
 
 stdenv.mkDerivation rec {
   pname = "lean";
-  version = "3.9.0";
+  version = "3.10.0";
 
   src = fetchFromGitHub {
     owner  = "leanprover-community";
     repo   = "lean";
     rev    = "v${version}";
-    sha256 = "0sklw211cmqp4y0c6nycfavpdxdpfwhq9a4sbwdlqd5agyf85h1j";
+    sha256 = "0nmh09x3scfqg0bg1qf8b7z67s11hbfd7kr1h6k1zw94fyn2mg8q";
   };
 
   nativeBuildInputs = [ cmake ];
diff --git a/nixpkgs/pkgs/applications/science/logic/tlaplus/default.nix b/nixpkgs/pkgs/applications/science/logic/tlaplus/default.nix
index 3476b5ea9d90..14944f5e19b0 100644
--- a/nixpkgs/pkgs/applications/science/logic/tlaplus/default.nix
+++ b/nixpkgs/pkgs/applications/science/logic/tlaplus/default.nix
@@ -1,24 +1,24 @@
 { stdenv, fetchFromGitHub, makeWrapper
-, jdk, jre, ant
+, adoptopenjdk-bin, jre, ant
 }:
 
 stdenv.mkDerivation rec {
   pname = "tlaplus";
-  version = "1.5.6";
+  version = "1.7.0";
 
   src = fetchFromGitHub {
     owner  = "tlaplus";
     repo   = "tlaplus";
     rev    = "refs/tags/v${version}";
-    sha256 = "0966mvgxamknj4hsp980qbxwda886w1dv309kn7isxn0420lfv4f";
+    sha256 = "1mm6r9bq79zks50yk0agcpdkw9yy994m38ibmgpb3bi3wkpq9891";
   };
 
-  buildInputs = [ makeWrapper jdk ant ];
+  buildInputs = [ makeWrapper adoptopenjdk-bin ant ];
 
-  buildPhase = "ant -f tlatools/customBuild.xml compile dist";
+  buildPhase = "ant -f tlatools/org.lamport.tlatools/customBuild.xml compile dist";
   installPhase = ''
     mkdir -p $out/share/java $out/bin
-    cp tlatools/dist/*.jar $out/share/java
+    cp tlatools/org.lamport.tlatools/dist/*.jar $out/share/java
 
     makeWrapper ${jre}/bin/java $out/bin/tlc2 \
       --add-flags "-cp $out/share/java/tla2tools.jar tlc2.TLC"
diff --git a/nixpkgs/pkgs/applications/science/logic/verifast/default.nix b/nixpkgs/pkgs/applications/science/logic/verifast/default.nix
index c5e8078eff2a..49618d2586b1 100644
--- a/nixpkgs/pkgs/applications/science/logic/verifast/default.nix
+++ b/nixpkgs/pkgs/applications/science/logic/verifast/default.nix
@@ -43,7 +43,7 @@ stdenv.mkDerivation rec {
   meta = {
     description = "Verification for C and Java programs via separation logic";
     homepage    = "http://people.cs.kuleuven.be/~bart.jacobs/verifast/";
-    license     = stdenv.lib.licenses.msrla;
+    license     = stdenv.lib.licenses.mit;
     platforms   = [ "x86_64-linux" ];
     maintainers = [ stdenv.lib.maintainers.thoughtpolice ];
   };
diff --git a/nixpkgs/pkgs/applications/science/machine-learning/fasttext/default.nix b/nixpkgs/pkgs/applications/science/machine-learning/fasttext/default.nix
index 2ae5e0eeddcd..64124594e1e2 100644
--- a/nixpkgs/pkgs/applications/science/machine-learning/fasttext/default.nix
+++ b/nixpkgs/pkgs/applications/science/machine-learning/fasttext/default.nix
@@ -2,13 +2,13 @@
 
 stdenv.mkDerivation rec {
   pname = "fasttext";
-  version = "0.9.1";
+  version = "0.9.2";
 
   src = fetchFromGitHub {
     owner = "facebookresearch";
     repo = "fastText";
     rev = "v${version}";
-    sha256 = "1cbzz98qn8aypp4r5kwwwc9wiq5bwzv51kcsb15xjfs9lz8h3rii";
+    sha256 = "07cz2ghfq6amcljaxpdr5chbd64ph513y8zqmibfx2xwfp74xkhn";
   };
 
   nativeBuildInputs = [ cmake ];
diff --git a/nixpkgs/pkgs/applications/science/machine-learning/shogun/default.nix b/nixpkgs/pkgs/applications/science/machine-learning/shogun/default.nix
index 33871df87f33..031ca55a0480 100644
--- a/nixpkgs/pkgs/applications/science/machine-learning/shogun/default.nix
+++ b/nixpkgs/pkgs/applications/science/machine-learning/shogun/default.nix
@@ -13,7 +13,7 @@
 assert pythonSupport -> pythonPackages != null;
 assert opencvSupport -> opencv != null;
 
-assert (!blas.is64bit) && (!lapack.is64bit);
+assert (!blas.isILP64) && (!lapack.isILP64);
 
 let
   pname = "shogun";
diff --git a/nixpkgs/pkgs/applications/science/math/R/0001-Disable-test-pending-upstream-fix.patch b/nixpkgs/pkgs/applications/science/math/R/0001-Disable-test-pending-upstream-fix.patch
deleted file mode 100644
index 7bf32df0b7a3..000000000000
--- a/nixpkgs/pkgs/applications/science/math/R/0001-Disable-test-pending-upstream-fix.patch
+++ /dev/null
@@ -1,26 +0,0 @@
-From 85ede2cf452800710de136f4f864921d3bb9773c Mon Sep 17 00:00:00 2001
-From: Tom Hall <tahall256@protonmail.ch>
-Date: Fri, 21 Feb 2020 22:56:06 +0000
-Subject: [PATCH] Disable test pending upstream fix
-
-See https://bugs.r-project.org/bugzilla/show_bug.cgi?id=17718
----
- tests/reg-tests-1d.R | 2 +-
- 1 file changed, 1 insertion(+), 1 deletion(-)
-
-diff --git a/tests/reg-tests-1d.R b/tests/reg-tests-1d.R
-index 9b551a1fc8..18ce6027ed 100644
---- a/tests/reg-tests-1d.R
-+++ b/tests/reg-tests-1d.R
-@@ -3079,7 +3079,7 @@ stopifnot(exprs = {
-     x[1:52] %% 3 == 2:1
-    -x[1:52] %% 3 == 1:2
- }) # larger x suffer from cancellation (well, warning too early now):
--tools::assertWarning(x[60:68] %% 3)
-+#tools::assertWarning(x[60:68] %% 3)
- 
- 
- ## Hilmar Berger's on R-devel list: 'data.frame() == NULL' etc
--- 
-2.24.1
-
diff --git a/nixpkgs/pkgs/applications/science/math/R/default.nix b/nixpkgs/pkgs/applications/science/math/R/default.nix
index 836ce004fff2..52da3b4a1ac9 100644
--- a/nixpkgs/pkgs/applications/science/math/R/default.nix
+++ b/nixpkgs/pkgs/applications/science/math/R/default.nix
@@ -1,5 +1,5 @@
 { stdenv, fetchurl, bzip2, gfortran, libX11, libXmu, libXt, libjpeg, libpng
-, libtiff, ncurses, pango, pcre, perl, readline, tcl, texLive, tk, xz, zlib
+, libtiff, ncurses, pango, pcre2, perl, readline, tcl, texLive, tk, xz, zlib
 , less, texinfo, graphviz, icu, pkgconfig, bison, imake, which, jdk, blas, lapack
 , curl, Cocoa, Foundation, libobjc, libcxx, tzdata, fetchpatch
 , withRecommendedPackages ? true
@@ -9,30 +9,27 @@
 , static ? false
 }:
 
-assert (!blas.is64bit) && (!lapack.is64bit);
+assert (!blas.isILP64) && (!lapack.isILP64);
 
 stdenv.mkDerivation rec {
-  name = "R-3.6.3";
+  name = "R-4.0.0";
 
   src = fetchurl {
-    url = "https://cran.r-project.org/src/base/R-3/${name}.tar.gz";
-    sha256 = "13xaxwfbzj0bd6rn2n27z0n04lb93mcyq991w4vdbbg8v282jc49";
+    url = "https://cran.r-project.org/src/base/R-4/${name}.tar.gz";
+    sha256 = "0h1995smlyiyhx7gpg9paxsfqrcn6g9bbp5h9r47i6an3clv1gh6";
   };
 
   dontUseImakeConfigure = true;
 
   buildInputs = [
     bzip2 gfortran libX11 libXmu libXt libXt libjpeg libpng libtiff ncurses
-    pango pcre perl readline texLive xz zlib less texinfo graphviz icu
+    pango pcre2 perl readline texLive xz zlib less texinfo graphviz icu
     pkgconfig bison imake which blas lapack curl tcl tk jdk
   ] ++ stdenv.lib.optionals stdenv.isDarwin [ Cocoa Foundation libobjc libcxx ];
 
   patches = [
     ./no-usr-local-search-paths.patch
-  ] ++ stdenv.lib.optionals stdenv.hostPlatform.isAarch64 [
-    # Remove a test which fails on aarch64.
-    # See https://bugs.r-project.org/bugzilla/show_bug.cgi?id=17718
-    ./0001-Disable-test-pending-upstream-fix.patch
+    ./fix-failing-test.patch
   ];
 
   prePatch = stdenv.lib.optionalString stdenv.isDarwin ''
diff --git a/nixpkgs/pkgs/applications/science/math/R/fix-failing-test.patch b/nixpkgs/pkgs/applications/science/math/R/fix-failing-test.patch
new file mode 100644
index 000000000000..5fb3b3b9c317
--- /dev/null
+++ b/nixpkgs/pkgs/applications/science/math/R/fix-failing-test.patch
@@ -0,0 +1,25 @@
+From e8f54bc562eb301d204b5f880614be58a2b39a2b Mon Sep 17 00:00:00 2001
+From: maechler <maechler@00db46b3-68df-0310-9c12-caf00c1e9a41>
+Date: Mon, 30 Mar 2020 19:15:59 +0000
+Subject: [PATCH] no longer fail in norm() check for broken OpenBLAS Lapack
+ 3.9.0
+
+git-svn-id: https://svn.r-project.org/R/trunk@78112 00db46b3-68df-0310-9c12-caf00c1e9a41
+---
+ tests/reg-tests-1d.R | 3 ++-
+ 1 file changed, 2 insertions(+), 1 deletion(-)
+
+diff --git a/tests/reg-tests-1d.R b/tests/reg-tests-1d.R
+index 6b7de765a95..fafd6911e7a 100644
+--- a/tests/reg-tests-1d.R
++++ b/tests/reg-tests-1d.R
+@@ -3836,7 +3836,8 @@ stopifnot(is.na( norm(diag(c(1, NA)), "2") ))
+ ## norm(<matrix-w-NA>, "F")
+ (m <- cbind(0, c(NA, 0), 0:-1))
+ nTypes <- eval(formals(base::norm)$type) # "O" "I" "F" "M" "2"
+-stopifnot(is.na( print(vapply(nTypes, norm, 0., x = m)) )) # print(): show NA *or* NaN
++print( # stopifnot( -- for now, as Lapack is still broken in some OpenBLAS -- FIXME
++    is.na( print(vapply(nTypes, norm, 0., x = m)) )) # print(): show NA *or* NaN
+ ## "F" gave non-NA with LAPACK 3.9.0, before our patch in R-devel and R-patched
+ 
+ 
diff --git a/nixpkgs/pkgs/applications/science/math/cemu/default.nix b/nixpkgs/pkgs/applications/science/math/cemu/default.nix
index f91e5be51700..b41135229dd7 100644
--- a/nixpkgs/pkgs/applications/science/math/cemu/default.nix
+++ b/nixpkgs/pkgs/applications/science/math/cemu/default.nix
@@ -4,7 +4,7 @@
 , SDL2
 , libGL
 , libarchive
-, libusb
+, libusb-compat-0_1
 , qtbase
 , qmake
 , git
@@ -33,7 +33,7 @@ mkDerivation rec {
     SDL2
     libGL
     libarchive
-    libusb
+    libusb-compat-0_1
     qtbase
     libpng_apng
   ];
diff --git a/nixpkgs/pkgs/applications/science/math/giac/default.nix b/nixpkgs/pkgs/applications/science/math/giac/default.nix
index be3c1e6dcc88..ea9c921f19e1 100644
--- a/nixpkgs/pkgs/applications/science/math/giac/default.nix
+++ b/nixpkgs/pkgs/applications/science/math/giac/default.nix
@@ -5,7 +5,7 @@
 }:
 
 assert enableGUI -> libGLU != null && libGL != null && xorg != null && fltk != null;
-assert (!blas.is64bit) && (!lapack.is64bit);
+assert (!blas.isILP64) && (!lapack.isILP64);
 
 stdenv.mkDerivation rec {
   pname = "giac${lib.optionalString enableGUI "-with-xcas"}";
diff --git a/nixpkgs/pkgs/applications/science/math/gmsh/default.nix b/nixpkgs/pkgs/applications/science/math/gmsh/default.nix
index 8ece2e7819cf..946beff8003f 100644
--- a/nixpkgs/pkgs/applications/science/math/gmsh/default.nix
+++ b/nixpkgs/pkgs/applications/science/math/gmsh/default.nix
@@ -1,7 +1,7 @@
 { stdenv, fetchurl, cmake, blas, lapack, gfortran, gmm, fltk, libjpeg
 , zlib, libGL, libGLU, xorg, opencascade-occt }:
 
-assert (!blas.is64bit) && (!lapack.is64bit);
+assert (!blas.isILP64) && (!lapack.isILP64);
 
 stdenv.mkDerivation rec {
   pname = "gmsh";
diff --git a/nixpkgs/pkgs/applications/science/math/mathematica/10.nix b/nixpkgs/pkgs/applications/science/math/mathematica/10.nix
index c7da7b16da8f..277fb1984c44 100644
--- a/nixpkgs/pkgs/applications/science/math/mathematica/10.nix
+++ b/nixpkgs/pkgs/applications/science/math/mathematica/10.nix
@@ -8,7 +8,7 @@
 , gcc
 , glib
 , ncurses
-, opencv
+, opencv2
 , openssl
 , unixODBC
 , xorg
@@ -49,7 +49,7 @@ stdenv.mkDerivation rec {
     gcc.libc
     glib
     ncurses
-    opencv
+    opencv2
     openssl
     unixODBC
     libxml2
diff --git a/nixpkgs/pkgs/applications/science/math/mathematica/11.nix b/nixpkgs/pkgs/applications/science/math/mathematica/11.nix
index 898d6a486351..1c698a5e5428 100644
--- a/nixpkgs/pkgs/applications/science/math/mathematica/11.nix
+++ b/nixpkgs/pkgs/applications/science/math/mathematica/11.nix
@@ -10,7 +10,7 @@
 , gcc
 , glib
 , ncurses
-, opencv
+, opencv2
 , openssl
 , unixODBC
 , xkeyboard_config
@@ -46,7 +46,7 @@ stdenv.mkDerivation rec {
     gcc.libc
     glib
     ncurses
-    opencv
+    opencv2
     openssl
     unixODBC
     xkeyboard_config
diff --git a/nixpkgs/pkgs/applications/science/math/mathematica/9.nix b/nixpkgs/pkgs/applications/science/math/mathematica/9.nix
index 617ac8657132..d0967485c01f 100644
--- a/nixpkgs/pkgs/applications/science/math/mathematica/9.nix
+++ b/nixpkgs/pkgs/applications/science/math/mathematica/9.nix
@@ -8,7 +8,7 @@
 , gcc
 , glib
 , ncurses
-, opencv
+, opencv2
 , openssl
 , unixODBC
 , xorg
@@ -46,7 +46,7 @@ stdenv.mkDerivation rec {
     gcc.libc
     glib
     ncurses
-    opencv
+    opencv2
     openssl
     unixODBC
   ] ++ (with xorg; [
diff --git a/nixpkgs/pkgs/applications/science/math/mathematica/default.nix b/nixpkgs/pkgs/applications/science/math/mathematica/default.nix
index 7831640b1244..94d72eec6ae4 100644
--- a/nixpkgs/pkgs/applications/science/math/mathematica/default.nix
+++ b/nixpkgs/pkgs/applications/science/math/mathematica/default.nix
@@ -11,7 +11,7 @@
 , glib
 , libssh2
 , ncurses
-, opencv
+, opencv2
 , openssl
 , unixODBC
 , xkeyboard_config
@@ -47,7 +47,7 @@ stdenv.mkDerivation rec {
     glib
     libssh2
     ncurses
-    opencv
+    opencv2
     openssl
     stdenv.cc.cc.lib
     unixODBC
diff --git a/nixpkgs/pkgs/applications/science/math/mxnet/default.nix b/nixpkgs/pkgs/applications/science/math/mxnet/default.nix
index 87d46850f140..b006a9dd18d1 100644
--- a/nixpkgs/pkgs/applications/science/math/mxnet/default.nix
+++ b/nixpkgs/pkgs/applications/science/math/mxnet/default.nix
@@ -8,11 +8,11 @@ assert cudnnSupport -> cudaSupport;
 
 stdenv.mkDerivation rec {
   pname = "mxnet";
-  version = "1.4.1";
+  version = "1.6.0";
 
   src = fetchurl {
     url = "https://github.com/apache/incubator-mxnet/releases/download/${version}/apache-mxnet-src-${version}-incubating.tar.gz";
-    sha256 = "1d0lhlpdaxycjzpwwrpgjd3v2q2ka89v5rr13ddxayy7ld2hxiaj";
+    sha256 = "1vvdb7pfh63kb9fzs6gqp95q550a3ck4cj9mqxlk9wwhkh30dsq1";
   };
 
   nativeBuildInputs = [ cmake perl ];
diff --git a/nixpkgs/pkgs/applications/science/math/rofi-calc/default.nix b/nixpkgs/pkgs/applications/science/math/rofi-calc/default.nix
index 842265cf3d5f..84adb2358d24 100644
--- a/nixpkgs/pkgs/applications/science/math/rofi-calc/default.nix
+++ b/nixpkgs/pkgs/applications/science/math/rofi-calc/default.nix
@@ -12,13 +12,13 @@
 
 stdenv.mkDerivation rec {
   pname = "rofi-calc";
-  version = "1.6";
+  version = "1.7";
 
   src = fetchFromGitHub {
     owner = "svenstaro";
     repo = pname;
     rev = "v${version}";
-    sha256 = "00pz0s99pihjdjy8pl4ckg2qciyp32k439lmjb5iazwck512ar92";
+    sha256 = "046x2zpvza7n0m81s75qkvmnpkvsvvyqqqjxcqzj7by0llpqs7wa";
   };
 
   nativeBuildInputs = [
diff --git a/nixpkgs/pkgs/applications/science/math/sage/sage-env.nix b/nixpkgs/pkgs/applications/science/math/sage/sage-env.nix
index c0dfeef1119b..626e1bf1ea92 100644
--- a/nixpkgs/pkgs/applications/science/math/sage/sage-env.nix
+++ b/nixpkgs/pkgs/applications/science/math/sage/sage-env.nix
@@ -54,7 +54,7 @@
 , less
 }:
 
-assert (!blas.is64bit) && (!lapack.is64bit);
+assert (!blas.isILP64) && (!lapack.isILP64);
 
 # This generates a `sage-env` shell file that will be sourced by sage on startup.
 # It sets up various environment variables, telling sage where to find its
diff --git a/nixpkgs/pkgs/applications/science/math/sage/sage-src.nix b/nixpkgs/pkgs/applications/science/math/sage/sage-src.nix
index cd465a8c413a..4791d12450a9 100644
--- a/nixpkgs/pkgs/applications/science/math/sage/sage-src.nix
+++ b/nixpkgs/pkgs/applications/science/math/sage/sage-src.nix
@@ -29,6 +29,14 @@ stdenv.mkDerivation rec {
       url = "https://git.sagemath.org/sage.git/patch?id2=8bdc326ba57d1bb9664f63cf165a9e9920cc1afc&id=dc673c17555efca611f68398d5013b66e9825463";
       sha256 = "1hhannz7xzprijakn2w2d0rhd5zv2zikik9p51i87bas3nc658f7";
     })
+    
+    # `is_unitary` test in `matrix_double_dense.pyx` fails with some BLAS implementations
+    # https://trac.sagemath.org/ticket/29297 should be included in 9.1
+    (fetchpatch {
+      name = "is_unitary-special-case.patch";
+      url = "https://git.sagemath.org/sage.git/patch?id=cc3eb9ffa991e328b09028d32aab7e7cc2ddbb6a";
+      sha256 = "0jq4w8hnp5c9q99011ldr4n3knvm1rx2g85z0hidv3i9x868p0ay";
+    })
 
     # Unfortunately inclusion in upstream sage was rejected. Instead the bug was
     # fixed in python, but of course not backported to 2.7. So we'll probably
diff --git a/nixpkgs/pkgs/applications/science/math/sage/sage-with-env.nix b/nixpkgs/pkgs/applications/science/math/sage/sage-with-env.nix
index 77bc65c2be12..87c1e07f5307 100644
--- a/nixpkgs/pkgs/applications/science/math/sage/sage-with-env.nix
+++ b/nixpkgs/pkgs/applications/science/math/sage/sage-with-env.nix
@@ -23,7 +23,7 @@
 }:
 
 # lots of segfaults with (64 bit) blas
-assert (!blas.is64bit) && (!lapack.is64bit);
+assert (!blas.isILP64) && (!lapack.isILP64);
 
 # Wrapper that combined `sagelib` with `sage-env` to produce an actually
 # executable sage. No tests are run yet and no documentation is built.
diff --git a/nixpkgs/pkgs/applications/science/math/sage/sagelib.nix b/nixpkgs/pkgs/applications/science/math/sage/sagelib.nix
index 92b4e8efa2ec..830d806a8bcd 100644
--- a/nixpkgs/pkgs/applications/science/math/sage/sagelib.nix
+++ b/nixpkgs/pkgs/applications/science/math/sage/sagelib.nix
@@ -53,7 +53,7 @@
 , pplpy
 }:
 
-assert (!blas.is64bit) && (!lapack.is64bit);
+assert (!blas.isILP64) && (!lapack.isILP64);
 
 # This is the core sage python package. Everything else is just wrappers gluing
 # stuff together. It is not very useful on its own though, since it will not
diff --git a/nixpkgs/pkgs/applications/science/misc/foldingathome/client.nix b/nixpkgs/pkgs/applications/science/misc/foldingathome/client.nix
index 9a29fde0a438..74a53902ee09 100644
--- a/nixpkgs/pkgs/applications/science/misc/foldingathome/client.nix
+++ b/nixpkgs/pkgs/applications/science/misc/foldingathome/client.nix
@@ -10,7 +10,7 @@
 }:
 let
   majMin = stdenv.lib.versions.majorMinor version;
-  version = "7.5.1";
+  version = "7.6.9";
 
   fahclient = stdenv.mkDerivation rec {
     inherit version;
@@ -18,7 +18,7 @@ let
 
     src = fetchurl {
       url = "https://download.foldingathome.org/releases/public/release/fahclient/debian-stable-64bit/v${majMin}/fahclient_${version}_amd64.deb";
-      hash = "sha256-7+RwYdMoZnJZwYFbmLxsN9ozk2P7jpOGZz9qlvTTfSY=";
+      sha256 = "1v4yijjjdq9qx1fp60flp9ya6ywl9qdsgkzwmzjzp8sd5gfvhyr6";
     };
 
     nativeBuildInputs = [
diff --git a/nixpkgs/pkgs/applications/science/misc/foldingathome/control.nix b/nixpkgs/pkgs/applications/science/misc/foldingathome/control.nix
index e8eba4c2ab2f..72217689ff18 100644
--- a/nixpkgs/pkgs/applications/science/misc/foldingathome/control.nix
+++ b/nixpkgs/pkgs/applications/science/misc/foldingathome/control.nix
@@ -8,7 +8,7 @@
 }:
 let
   majMin = stdenv.lib.versions.majorMinor version;
-  version = "7.5.1";
+  version = "7.6.9";
 
   python = python2.withPackages
     (
@@ -25,7 +25,7 @@ stdenv.mkDerivation rec {
 
   src = fetchurl {
     url = "https://download.foldingathome.org/releases/public/release/fahcontrol/debian-stable-64bit/v${majMin}/fahcontrol_${version}-1_all.deb";
-    hash = "sha256-ydN4I6vmZpI9kD+/TXxgWc+AQqIIlUvABEycWmY1tNg=";
+    sha256 = "1fh7ybbp3qlqzh18c4gva3aaymv7d31mqchrv235a1axldha1s9s";
   };
 
   nativeBuildInputs = [
diff --git a/nixpkgs/pkgs/applications/science/misc/foldingathome/viewer.nix b/nixpkgs/pkgs/applications/science/misc/foldingathome/viewer.nix
index 03fa54cd7338..a35df650300b 100644
--- a/nixpkgs/pkgs/applications/science/misc/foldingathome/viewer.nix
+++ b/nixpkgs/pkgs/applications/science/misc/foldingathome/viewer.nix
@@ -11,7 +11,7 @@
 }:
 let
   majMin = stdenv.lib.versions.majorMinor version;
-  version = "7.5.1";
+  version = "7.6.9";
 in
 stdenv.mkDerivation rec {
   inherit version;
@@ -19,7 +19,7 @@ stdenv.mkDerivation rec {
 
   src = fetchurl {
     url = "https://download.foldingathome.org/releases/public/release/fahviewer/debian-stable-64bit/v${majMin}/fahviewer_${version}_amd64.deb";
-    hash = "sha256-yH0zGjX8aNBEJ5lq7wWydcpp2rO+9Ah++q9eJ+ldeyk=";
+    sha256 = "04wr86g11wpmsczzwzak4gvalcihb47rn3zp6qriawhxyac9nf93";
   };
 
   nativeBuildInputs = [
diff --git a/nixpkgs/pkgs/applications/science/misc/rink/default.nix b/nixpkgs/pkgs/applications/science/misc/rink/default.nix
index 839fc8f95463..5d592c233b62 100644
--- a/nixpkgs/pkgs/applications/science/misc/rink/default.nix
+++ b/nixpkgs/pkgs/applications/science/misc/rink/default.nix
@@ -24,7 +24,7 @@ rustPlatform.buildRustPackage rec {
 
   meta = with stdenv.lib; {
     description = "Unit-aware calculator";
-    homepage = "http://rink.tiffnix.com";
+    homepage = "https://rink.tiffnix.com";
     license = with licenses; [ mpl20 gpl3 ];
     maintainers = with maintainers; [ sb0 filalex77 ];
   };
diff --git a/nixpkgs/pkgs/applications/science/misc/snakemake/default.nix b/nixpkgs/pkgs/applications/science/misc/snakemake/default.nix
index 34bdaf6bacf8..741330e4ad29 100644
--- a/nixpkgs/pkgs/applications/science/misc/snakemake/default.nix
+++ b/nixpkgs/pkgs/applications/science/misc/snakemake/default.nix
@@ -2,7 +2,7 @@
 
 python3Packages.buildPythonApplication rec {
   pname = "snakemake";
-  version = "5.13.0";
+  version = "5.16.0";
 
   propagatedBuildInputs = with python3Packages; [
     appdirs
@@ -22,13 +22,13 @@ python3Packages.buildPythonApplication rec {
 
   src = python3Packages.fetchPypi {
     inherit pname version;
-    sha256 = "11snr7sgv70d3y63s5svijfx8f4xpggh96g8chr6lccl4mi1s9x9";
+    sha256 = "0jlf3y8b1gdv5xz37yk9b5g2b65zkk45p15x0ypvd2blpzy80537";
   };
 
   doCheck = false; # Tests depend on Google Cloud credentials at ${HOME}/gcloud-service-key.json
 
   meta = with stdenv.lib; {
-    homepage = "http://snakemake.bitbucket.io";
+    homepage = "https://snakemake.readthedocs.io";
     license = licenses.mit;
     description = "Python-based execution environment for make-like workflows";
     longDescription = ''
diff --git a/nixpkgs/pkgs/applications/science/molecular-dynamics/gromacs/default.nix b/nixpkgs/pkgs/applications/science/molecular-dynamics/gromacs/default.nix
index fadd60d9ebbf..d345827ed4eb 100644
--- a/nixpkgs/pkgs/applications/science/molecular-dynamics/gromacs/default.nix
+++ b/nixpkgs/pkgs/applications/science/molecular-dynamics/gromacs/default.nix
@@ -9,11 +9,11 @@
 }:
 
 stdenv.mkDerivation {
-  name = "gromacs-2020.1";
+  name = "gromacs-2020.2";
 
   src = fetchurl {
-    url = "ftp://ftp.gromacs.org/pub/gromacs/gromacs-2020.1.tar.gz";
-    sha256 = "1kwrk3i1dxp8abhqqsl049lh361n4910h0415g052f8shdc6arp1";
+    url = "ftp://ftp.gromacs.org/pub/gromacs/gromacs-2020.2.tar.gz";
+    sha256 = "1wyjgcdl30wy4hy6jvi9lkq53bqs9fgfq6fri52dhnb3c76y8rbl";
   };
 
   nativeBuildInputs = [ cmake ];
diff --git a/nixpkgs/pkgs/applications/science/physics/elmerfem/default.nix b/nixpkgs/pkgs/applications/science/physics/elmerfem/default.nix
new file mode 100644
index 000000000000..46cc32fa168e
--- /dev/null
+++ b/nixpkgs/pkgs/applications/science/physics/elmerfem/default.nix
@@ -0,0 +1,49 @@
+{ stdenv, fetchFromGitHub, cmake, git, gfortran, openmpi, blas, liblapack, qt4, qwt6_qt4, pkg-config }:
+
+stdenv.mkDerivation rec {
+  pname = "elmerfem";
+  version = "8.4";
+
+  src = fetchFromGitHub {
+    owner = "elmercsc";
+    repo = "elmerfem";
+    rev = "release-${version}";
+    sha256 = "0vk31lplxlng173q8jjcpbyj1gaf98jvkqjvi9077d1nslya7vpm";
+  };
+
+  hardeningDisable = [ "format" ];
+
+  nativeBuildInputs = [ cmake pkg-config git ];
+  buildInputs = [ gfortran openmpi blas liblapack qt4 qwt6_qt4 ];
+
+  preConfigure = ''
+    patchShebangs ./
+  '';
+
+  storepath = placeholder "out";
+
+  cmakeFlags = [
+  "-DELMER_INSTALL_LIB_DIR=${storepath}/lib"
+  "-DWITH_OpenMP:BOOLEAN=TRUE"
+  "-DWITH_MPI:BOOLEAN=TRUE"
+  "-DWITH_ELMERGUI:BOOLEAN=TRUE"
+  "-DCMAKE_INSTALL_LIBDIR=lib"
+  "-DCMAKE_INSTALL_INCLUDEDIR=include"
+  "-DCMAKE_OpenGL_GL_PREFERENCE=GLVND"
+  ];
+
+  patches = [
+    ./fix-cmake.patch
+  ];
+
+  enableParallelBuilding = true;
+
+  meta = with stdenv.lib; {
+    homepage = "https://elmerfem.org/";
+    description = "A finite element software for multiphysical problems.";
+    platforms = platforms.unix;
+    maintainers = [ maintainers.wulfsta ];
+    license = licenses.lgpl21;
+  };
+
+}
diff --git a/nixpkgs/pkgs/applications/science/physics/elmerfem/fix-cmake.patch b/nixpkgs/pkgs/applications/science/physics/elmerfem/fix-cmake.patch
new file mode 100644
index 000000000000..098f65207330
--- /dev/null
+++ b/nixpkgs/pkgs/applications/science/physics/elmerfem/fix-cmake.patch
@@ -0,0 +1,13 @@
+diff --exclude '*~' -ruN A/torch/CMakeLists.txt B/torch/CMakeLists.txt
+--- A/fem/tests/CMakeLists.txt	2020-04-23 02:35:03.243388917 -0400
++++ B/fem/tests/CMakeLists.txt	2018-12-19 20:18:40.671857320 -0400
+@@ -14,7 +14,7 @@ 
+ SET(MESH2D_BIN "${CMAKE_BINARY_DIR}/meshgen2d/src/Mesh2D")
+
+ MACRO(SUBDIRLIST result curdir depth)
+   set(glob_pattern "*")
+-  FOREACH(D RANGE 1 depth)
++  FOREACH(D RANGE 1 ${depth})
+     FILE(GLOB children RELATIVE ${curdir} ${glob_pattern}) 
+     FOREACH(child ${children})
+       IF(IS_DIRECTORY ${curdir}/${child})
diff --git a/nixpkgs/pkgs/applications/science/physics/sherpa/default.nix b/nixpkgs/pkgs/applications/science/physics/sherpa/default.nix
index 85b2ddd4d07a..314fc5225004 100644
--- a/nixpkgs/pkgs/applications/science/physics/sherpa/default.nix
+++ b/nixpkgs/pkgs/applications/science/physics/sherpa/default.nix
@@ -2,11 +2,11 @@
 
 stdenv.mkDerivation rec {
   pname = "sherpa";
-  version = "2.2.8";
+  version = "2.2.9";
 
   src = fetchurl {
     url = "https://www.hepforge.org/archive/sherpa/SHERPA-MC-${version}.tar.gz";
-    sha256 = "1al1imdrknvbcy8k113xysc14lln4msbv281bf0kx7p73wz59mv3";
+    sha256 = "1z7vws97k6zfzyqx0dkv2kq8d83dibi73i5jiqk5a22yplp6bnjh";
   };
 
   buildInputs = [ gfortran sqlite lhapdf rivet ];
@@ -21,13 +21,11 @@ stdenv.mkDerivation rec {
     "--enable-rivet=${rivet}"
   ];
 
-  CXXFLAGS = "-std=c++11"; # needed for rivet on OSX
-
-  meta = {
+  meta = with stdenv.lib; {
     description = "Simulation of High-Energy Reactions of PArticles in lepton-lepton, lepton-photon, photon-photon, lepton-hadron and hadron-hadron collisions";
-    license     = stdenv.lib.licenses.gpl2;
-    homepage    = "https://gitlab.com/sherpa-team/sherpa";
-    platforms   = stdenv.lib.platforms.unix;
-    maintainers = with stdenv.lib.maintainers; [ veprbl ];
+    license = licenses.gpl2;
+    homepage = "https://gitlab.com/sherpa-team/sherpa";
+    platforms = platforms.unix;
+    maintainers = with maintainers; [ veprbl ];
   };
 }
diff --git a/nixpkgs/pkgs/applications/science/robotics/gazebo/default.nix b/nixpkgs/pkgs/applications/science/robotics/gazebo/default.nix
index aea298b65485..86572e73c756 100644
--- a/nixpkgs/pkgs/applications/science/robotics/gazebo/default.nix
+++ b/nixpkgs/pkgs/applications/science/robotics/gazebo/default.nix
@@ -1,7 +1,7 @@
 { stdenv, fetchurl, cmake, pkgconfig, boost, protobuf, freeimage
   , boost-build, boost_process
   , xorg_sys_opengl, tbb, ogre, tinyxml-2
-  , libtar, glxinfo,  libusb, libxslt, ignition
+  , libtar, glxinfo,  libusb-compat-0_1, libxslt, ignition
   , pythonPackages, utillinux
 
   # these deps are hidden; cmake doesn't catch them
@@ -52,7 +52,7 @@ stdenv.mkDerivation rec {
     tinyxml-2
     libtar
     glxinfo
-    libusb
+    libusb-compat-0_1
     libxslt
     ignition.math2
     sdformat
diff --git a/nixpkgs/pkgs/applications/science/robotics/mavproxy/default.nix b/nixpkgs/pkgs/applications/science/robotics/mavproxy/default.nix
index 0348d0153099..c354dad80428 100644
--- a/nixpkgs/pkgs/applications/science/robotics/mavproxy/default.nix
+++ b/nixpkgs/pkgs/applications/science/robotics/mavproxy/default.nix
@@ -3,11 +3,11 @@
 
 buildPythonApplication rec {
   pname = "MAVProxy";
-  version = "1.8.18";
+  version = "1.8.19";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "1fi4m3591wws5cq43q8aljf91mzs6i9yhn9rimhpfrskbyf9knvm";
+    sha256 = "1rbq2nm01212rp5xbl8p8kjl2mpgfppkwjsq3lnfw1v6g0m4359h";
   };
 
   propagatedBuildInputs = [