R: 3.6.3 --> 4.0.0 & update packages

pkgs/applications/editors/rstudio/default.nix

@@ -1,4 +1,4 @@
-{ lib, mkDerivation, fetchurl, fetchFromGitHub, makeDesktopItem, cmake, boost, zlib
+{ lib, mkDerivation, fetchurl, fetchpatch, fetchFromGitHub, makeDesktopItem, cmake, boost, zlib
 , openssl, R, qtbase, qtxmlpatterns, qtsensors, qtwebengine, qtwebchannel
 , libuuid, hunspellDicts, unzip, ant, jdk, gnumake, makeWrapper, pandoc
 , llvmPackages
@@ -8,7 +8,7 @@ with lib;
 let
   verMajor = "1";
   verMinor = "2";
-  verPatch = "5033";
+  verPatch = "5042";
   version = "${verMajor}.${verMinor}.${verPatch}";
   ginVer = "2.1.2";
   gwtVer = "2.8.1";
@@ -26,11 +26,19 @@ mkDerivation rec {
     owner = "rstudio";
     repo = "rstudio";
     rev = "v${version}";
-    sha256 = "0f3p2anz9xay2859bxj3bvyj582igsp628qxsccpkgn0jifvi4np";
+    sha256 = "1n67fa357v51j3z1ma8v2ydfsx3y8n10k2svmfcf4mdzsi8w0kc5";
   };
 
   # Hack RStudio to only use the input R and provided libclang.
-  patches = [ ./r-location.patch ./clang-location.patch ];
+  patches = [ ./r-location.patch ./clang-location.patch
+              (fetchpatch {
+                # Fetch a patch to ensure Rstudio compiles against R
+                # 4.0.0, should be removed next 1.2.X Rstudio update
+                # or possibly 1.3.X
+                url = "https://github.com/rstudio/rstudio/commit/3fb2397c2f208bb8ace0bbaf269481ccb96b5b20.patch";
+                sha256 = "0qpgjy6aash0fc0xbns42cwpj3nsw49nkbzwyq8az01xwg81g0f3";
+              })
+            ];
   postPatch = ''
     substituteInPlace src/cpp/core/r_util/REnvironmentPosix.cpp --replace '@R@' ${R}
     substituteInPlace src/cpp/core/libclang/LibClang.cpp \

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
@@ -12,27 +12,24 @@
 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 ''

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
+
+