Merge pull request #80759 from Thra11/fix-r

Fix R

pkgs/applications/science/math/R/0001-Disable-test-pending-upstream-fix.patch

@@ -0,0 +1,26 @@
+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
+

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

@@ -7,7 +7,6 @@
 # R as of writing does not support outputting both .so and .a files; it outputs:
 #     --enable-R-static-lib conflicts with --enable-R-shlib and will be ignored
 , static ? false
-, javaSupport ? (!stdenv.hostPlatform.isAarch32 && !stdenv.hostPlatform.isAarch64)
 }:
 
 stdenv.mkDerivation rec {
@@ -23,12 +22,15 @@ stdenv.mkDerivation rec {
   buildInputs = [
     bzip2 gfortran libX11 libXmu libXt libXt libjpeg libpng libtiff ncurses
     pango pcre perl readline texLive xz zlib less texinfo graphviz icu
-    pkgconfig bison imake which openblas curl tcl tk
+    pkgconfig bison imake which openblas curl tcl tk jdk
-  ] ++ stdenv.lib.optionals stdenv.isDarwin [ Cocoa Foundation libobjc libcxx ]
+  ] ++ stdenv.lib.optionals stdenv.isDarwin [ Cocoa Foundation libobjc libcxx ];
-    ++ stdenv.lib.optional javaSupport jdk;
 
   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
   ];
 
   prePatch = stdenv.lib.optionalString stdenv.isDarwin ''
@@ -57,7 +59,7 @@ stdenv.mkDerivation rec {
       CC=$(type -p cc)
       CXX=$(type -p c++)
       FC="${gfortran}/bin/gfortran" F77="${gfortran}/bin/gfortran"
-      ${stdenv.lib.optionalString javaSupport "JAVA_HOME=\"${jdk}\""}
+      JAVA_HOME="${jdk}"
       RANLIB=$(type -p ranlib)
       R_SHELL="${stdenv.shell}"
   '' + stdenv.lib.optionalString stdenv.isDarwin ''