Merge commit '683c68232e91f76386db979c461d8fbe2a018782'

16 files changed, 59 insertions, 55 deletions

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