R: 4.0.4 -> 4.1.0

Co-authored-by: Mauricio Collares <244239+collares@users.noreply.github.com>

pkgs/applications/science/math/R/default.nix

@@ -13,11 +13,11 @@ assert (!blas.isILP64) && (!lapack.isILP64);
 
 stdenv.mkDerivation rec {
   pname = "R";
-  version = "4.0.4";
+  version = "4.1.0";
 
   src = fetchurl {
     url = "https://cran.r-project.org/src/base/R-${lib.versions.major version}/${pname}-${version}.tar.gz";
-    sha256 = "0bl098xcv8v316kqnf43v6gb4kcsv31ydqfm1f7qr824jzb2fgsj";
+    sha256 = "109732arm6dq6d6v3fl1nyx63lcvv9569j8g6r3s2b18sxcqkrp8";
   };
 
   dontUseImakeConfigure = true;
@@ -30,7 +30,19 @@ stdenv.mkDerivation rec {
 
   patches = [
     ./no-usr-local-search-paths.patch
-    ./fix-failing-test.patch
+  ] ++ lib.optionals (!withRecommendedPackages) [
+    (fetchpatch {
+       name = "fix-tests-without-recommended-packages.patch";
+       url = "https://github.com/wch/r-source/commit/7715c67cabe13bb15350cba1a78591bbb76c7bac.patch";
+       # this part of the patch reverts something that was committed after R 4.1.0, so ignore it.
+       excludes = [ "tests/Pkgs/xDir/pkg/DESCRIPTION" ];
+       sha256 = "sha256-iguLndCIuKuCxVCi/4NSu+9RzBx5JyeHx3K6IhpYshQ=";
+    })
+    (fetchpatch {
+      name = "use-codetools-conditionally.patch";
+      url = "https://github.com/wch/r-source/commit/7543c28b931db386bb254e58995973493f88e30d.patch";
+      sha256 = "sha256-+yHXB5AItFyQjSxfogxk72DrSDGiBh7OiLYFxou6Xlk=";
+    })
   ];
 
   prePatch = lib.optionalString stdenv.isDarwin ''

pkgs/applications/science/math/R/fix-failing-test.patch

@@ -1,25 +0,0 @@
-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
- 
-