Merge pull request #86081 from jabranham/update-r

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/0001-Disable-test-pending-upstream-fix.patch

@@ -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
-

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
+ 
+ 

pkgs/development/r-modules/bioc-packages.nix

@@ -197,7 +197,7 @@ in with self; {
   CrispRVariants = derive2 { name="CrispRVariants"; version="1.10.1"; sha256="0n1mw3ybbdaybbcms12cj4vy21wahq5srny0qnbxjlzyl1zjbpr0"; depends=[AnnotationDbi BiocParallel Biostrings GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 gridExtra IRanges reshape2 Rsamtools S4Vectors]; };
   CytoDx = derive2 { name="CytoDx"; version="1.2.1"; sha256="05apvaf4dmkdfsp2aary14i7znjyzk0k6rqcbsk6m98fkp3d9r8b"; depends=[doParallel dplyr flowCore glmnet rpart rpart_plot]; };
   CytoML = derive2 { name="CytoML"; version="1.8.1"; sha256="18isg4kjdn975q8vpziisnyxj1jxm4lkq7hi9jy4imf7bffc234i"; depends=[base64enc Biobase data_table flowCore flowUtils flowWorkspace ggcyto graph jsonlite ncdfFlow openCyto plyr RBGL Rgraphviz XML]; };
-  DAPAR = derive2 { name="DAPAR"; version="1.14.5"; sha256="0s09y5kpivaichzmfchksaayxchdmqgldcba0waxfxzsapwfb9p1"; depends=[AnnotationDbi Cairo clusterProfiler cp4p DAPARdata doParallel dplyr factoextra FactoMineR foreach ggplot2 gplots graph highcharter impute knitr lattice limma lme4 Matrix MSnbase norm openxlsx pcaMethods png preprocessCore RColorBrewer readxl reshape2 scales siggenes stringr tidyr tidyverse tmvtnorm vioplot vsn]; };
+  DAPAR = derive2 { name="DAPAR"; version="1.14.5"; sha256="0s09y5kpivaichzmfchksaayxchdmqgldcba0waxfxzsapwfb9p1"; depends=[AnnotationDbi Cairo clusterProfiler cp4p DAPARdata doParallel dplyr factoextra FactoMineR foreach ggplot2 gplots graph highcharter imp4p impute knitr lattice limma lme4 Matrix MSnbase norm openxlsx pcaMethods png preprocessCore RColorBrewer readxl reshape2 scales siggenes stringr tidyr tidyverse tmvtnorm vioplot vsn]; };
   DART = derive2 { name="DART"; version="1.30.0"; sha256="0dxwy95p43c0shx30y95sj1pl64kqkh2bsnj680q196zgyg937s6"; depends=[igraph]; };
   DBChIP = derive2 { name="DBChIP"; version="1.26.0"; sha256="1wk8nvfcfhsymhbi6id0kd1jzcykh6hhikl2040g0v6gi252gv2v"; depends=[DESeq edgeR]; };
   DChIPRep = derive2 { name="DChIPRep"; version="1.12.0"; sha256="1avcjr7r54grh3yn5pjbzji3syc8vvah9as7asv3cwmyqzaya4r0"; depends=[assertthat ChIPpeakAnno DESeq2 fdrtool GenomicRanges ggplot2 plyr purrr reshape2 S4Vectors smoothmest soGGi SummarizedExperiment tidyr]; };
@@ -491,8 +491,8 @@ in with self; {
   MSnID = derive2 { name="MSnID"; version="1.16.1"; sha256="077n6ljcnnl7q4w0qj8v46vm4sjk9vzzfqf7wsc6lz0wmyzqdng3"; depends=[Biobase data_table doParallel dplyr foreach iterators MSnbase mzID mzR ProtGenerics R_cache Rcpp reshape2]; };
   MSnbase = derive2 { name="MSnbase"; version="2.8.3"; sha256="1kl1d7byphnfpmbl5fzbgs68dxskhpsdyx7ka51bpfn0nv3pp492"; depends=[affy Biobase BiocGenerics BiocParallel digest ggplot2 impute IRanges lattice MALDIquant MASS mzID mzR pcaMethods plyr preprocessCore ProtGenerics Rcpp S4Vectors scales vsn XML]; };
   MSstats = derive2 { name="MSstats"; version="3.14.1"; sha256="1bgvdq1mfq6rxjf5ag2slrhy4056906wghsirrymf53nw3qz5g6s"; depends=[data_table doSNOW dplyr foreach ggplot2 ggrepel gplots limma lme4 marray MASS minpack_lm preprocessCore randomForest reshape2 snow stringr survival tidyr]; };
-  MSstatsQC = derive2 { name="MSstatsQC"; version="2.0.1"; sha256="1f6gv1fqm5h6xs91wc1bamyri47qggb872qzriwzvff7ydn0q1ag"; depends=[dplyr ggExtra ggplot2 MSnbase plotly qcmetrics]; };
-  MSstatsQCgui = derive2 { name="MSstatsQCgui"; version="1.2.1"; sha256="1k7dhiayf885ax1mg03yg1w4mamk3j1gsm7phszxl3i0j3c2gks7"; depends=[dplyr ggExtra gridExtra MSstatsQC plotly shiny]; };
+  MSstatsQC = derive2 { name="MSstatsQC"; version="2.0.1"; sha256="1f6gv1fqm5h6xs91wc1bamyri47qggb872qzriwzvff7ydn0q1ag"; depends=[dplyr ggExtra ggplot2 MSnbase plotly qcmetrics RecordLinkage]; };
+  MSstatsQCgui = derive2 { name="MSstatsQCgui"; version="1.2.1"; sha256="1k7dhiayf885ax1mg03yg1w4mamk3j1gsm7phszxl3i0j3c2gks7"; depends=[dplyr ggExtra gridExtra MSstatsQC plotly RecordLinkage shiny]; };
   MSstatsTMT = derive2 { name="MSstatsTMT"; version="1.1.2"; sha256="0aaw3qillcfrjczdmd7s21v551hclnq8fn2zvn91wyr4i82q43rr"; depends=[data_table dplyr ggplot2 limma lme4 matrixStats MSstats nlme reshape2 tidyr]; };
   MTseeker = derive2 { name="MTseeker"; version="1.0.6"; sha256="0fsb7k6pkl15q8csygpsjrz4jvy20mfd5rfmhl7q7ffj4d7sprxh"; depends=[Biobase BiocGenerics Biostrings circlize GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges gmapR Homo_sapiens IRanges jsonlite Rsamtools rtracklayer S4Vectors SummarizedExperiment VariantAnnotation VariantTools viridis xml2]; };
   MVCClass = derive2 { name="MVCClass"; version="1.56.0"; sha256="1hw36gd1z19dir6fl7j3dzqzi5p1668zbwpcz7l21hbyycv27l0j"; depends=[]; };
@@ -670,7 +670,7 @@ in with self; {
   RUVSeq = derive2 { name="RUVSeq"; version="1.16.1"; sha256="0qk7q3ab7k133divfkp54zsmvsmb9p8r09pkh2caswrzrn8achzv"; depends=[Biobase EDASeq edgeR MASS]; };
   RUVcorr = derive2 { name="RUVcorr"; version="1.14.0"; sha256="05lg37rmf9skqcpnd08v6wnh7sfs449hwwq6nw2hkgy9faip14lz"; depends=[BiocParallel bladderbatch corrplot gridExtra lattice MASS psych reshape2 snowfall]; };
   RUVnormalize = derive2 { name="RUVnormalize"; version="1.16.0"; sha256="1habqdv35v9ypvfmfaxjqpka67bs6hzf4ph9b0gqd67mbfnb49dv"; depends=[Biobase RUVnormalizeData]; };
-  RVS = derive2 { name="RVS"; version="1.4.4"; sha256="1zvbin60p81qyk2c0m88dl94ivzyf4cpjdf2hnw8igmvlxszmb8k"; depends=[gRain kinship2 snpStats]; };
+  RVS = derive2 { name="RVS"; version="1.4.4"; sha256="1zvbin60p81qyk2c0m88dl94ivzyf4cpjdf2hnw8igmvlxszmb8k"; depends=[GENLIB gRain kinship2 snpStats]; };
   RaggedExperiment = derive2 { name="RaggedExperiment"; version="1.6.0"; sha256="1w02nnxpmx05gn6d9kjnahdn9kynbg1szm96c03gh4961zknn3r3"; depends=[BiocGenerics GenomeInfoDb GenomicRanges IRanges S4Vectors SummarizedExperiment]; };
   RandomWalkRestartMH = derive2 { name="RandomWalkRestartMH"; version="1.2.0"; sha256="022vckcc46bkhfhi2fzgawhf54hi6y2p5ia4v3x3lj221d7hcaax"; depends=[dnet igraph Matrix]; };
   RankProd = derive2 { name="RankProd"; version="3.8.0"; sha256="0jmpwpmj3y13ylk7riyicywpring14dhq4862jgalsjjwa22zzd0"; depends=[gmp Rmpfr]; };

pkgs/development/r-modules/default.nix

@@ -328,7 +328,6 @@ let
     Rpoppler = [ pkgs.poppler ];
     RPostgreSQL = [ pkgs.postgresql pkgs.postgresql ];
     RProtoBuf = [ pkgs.protobuf ];
-    rPython = [ pkgs.python ];
     RSclient = [ pkgs.openssl.dev ];
     Rserve = [ pkgs.openssl ];
     Rssa = [ pkgs.fftw.dev ];
@@ -425,7 +424,6 @@ let
     Rsymphony = [ pkgs.pkgconfig pkgs.doxygen pkgs.graphviz pkgs.subversion ];
     tcltk2 = [ pkgs.tcl pkgs.tk ];
     tikzDevice = [ pkgs.which pkgs.texlive.combined.scheme-medium ];
-    rPython = [ pkgs.which ];
     gridGraphics = [ pkgs.which ];
     adimpro = [ pkgs.which pkgs.xorg.xdpyinfo ];
     mzR = [ pkgs.netcdf ];