diff --git a/pkgs/applications/science/math/R/default.nix b/pkgs/applications/science/math/R/default.nix index 827c817fd1a6..0c9f700bd423 100644 --- a/pkgs/applications/science/math/R/default.nix +++ b/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 '' diff --git a/pkgs/applications/science/math/R/fix-failing-test.patch b/pkgs/applications/science/math/R/fix-failing-test.patch deleted file mode 100644 index 5fb3b3b9c317..000000000000 --- a/pkgs/applications/science/math/R/fix-failing-test.patch +++ /dev/null @@ -1,25 +0,0 @@ -From e8f54bc562eb301d204b5f880614be58a2b39a2b Mon Sep 17 00:00:00 2001 -From: maechler -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(, "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 - -