push sheeet

pkgs/development/r-modules/README.md

@@ -0,0 +1 @@
+Moved to [/doc/languages-frameworks/r.section.md](/doc/languages-frameworks/r.section.md)

pkgs/development/r-modules/generate-r-packages.R

@@ -0,0 +1,117 @@
+#!/usr/bin/env Rscript
+
+# This script can be used to generate the .json file for a given R package set
+# that is part of the `rPackages` tree
+#
+# See R section of the nixpkgs manual for an example of how to use this script
+
+library(data.table)
+library(parallel)
+library(BiocManager)
+library(jsonlite)
+
+# always order strings according to POSIX ordering
+locale <- Sys.setlocale(locale = "C")
+
+biocVersion <- BiocManager:::.version_map()
+biocVersion <- biocVersion[biocVersion$R == getRversion()[, 1:2],c("Bioc", "BiocStatus")]
+if ("release" %in% biocVersion$BiocStatus) {
+  biocVersion <-  as.character(biocVersion[biocVersion$BiocStatus == "release", "Bioc"])
+} else {
+  biocVersion <-  max(as.character(biocVersion$Bioc))
+}
+
+mirrorUrls <- list( bioc=paste0("http://bioconductor.org/packages/", biocVersion, "/bioc/src/contrib/")
+                  , "bioc-annotation"=paste0("http://bioconductor.org/packages/", biocVersion, "/data/annotation/src/contrib/")
+                  , "bioc-experiment"=paste0("http://bioconductor.org/packages/", biocVersion, "/data/experiment/src/contrib/")
+                  , cran="https://cran.r-project.org/src/contrib/"
+                  )
+
+mirrorType <- commandArgs(trailingOnly=TRUE)[1]
+stopifnot(mirrorType %in% names(mirrorUrls))
+
+packagesFile <- paste(mirrorType, 'packages.json', sep='-')
+prevPkgs <- fromJSON(packagesFile)$packages
+
+write(paste("downloading package lists"), stderr())
+pkgTables <- lapply(mirrorUrls, function(url) as.data.table(available.packages(url, filters=c("R_version", "OS_type", "duplicates")), method="libcurl"))
+knownPackageNames <- c(unique(do.call("rbind", pkgTables)$Package))
+
+pkgTable <- pkgTables[mirrorType][[1]]
+mirrorUrl <- mirrorUrls[mirrorType][[1]]
+
+escapeName <- function(name) {
+    gsub(".", "_", switch(name, "import" = "r_import", "assert" = "r_assert", name), fixed=TRUE)
+}
+
+nixPrefetch <- function(name, version) {
+  prevPkg <- prevPkgs[[escapeName(name)]]
+  if (!is.null(prevPkg) && prevPkg$version == version)
+    prevPkg$sha256
+
+  else {
+    # avoid nix-prefetch-url because it often fails to fetch/hash large files
+    url <- paste0(mirrorUrl, name, "_", version, ".tar.gz")
+    tmp <- tempfile(pattern=paste0(name, "_", version), fileext=".tar.gz")
+    cmd <- paste0("wget -q -O '", tmp, "' '", url, "'")
+    if(mirrorType == "cran"){
+      archiveUrl <- paste0(mirrorUrl, "Archive/", name, "/", name, "_", version, ".tar.gz")
+      cmd <- paste0(cmd, " || wget -q -O '", tmp, "' '", archiveUrl, "'")
+    }
+    cmd <- paste0(cmd, " && nix-hash --type sha256 --base32 --flat '", tmp, "'")
+    cmd <- paste0(cmd, " && echo >&2 '  added ", name, " v", version, "'")
+    cmd <- paste0(cmd, " ; rm -rf '", tmp, "'")
+    system(cmd, intern=TRUE)
+  }
+
+}
+
+formatPackage <- function(name, version, sha256, depends, imports, linkingTo) {
+    options(warn=5)
+    depends <- paste( if (is.na(depends)) "" else gsub("[ \t\n]+", "", depends)
+                    , if (is.na(imports)) "" else gsub("[ \t\n]+", "", imports)
+                    , if (is.na(linkingTo)) "" else gsub("[ \t\n]+", "", linkingTo)
+                    , sep=","
+                    )
+    depends <- unlist(strsplit(depends, split=",", fixed=TRUE))
+    depends <- lapply(depends, gsub, pattern="([^ \t\n(]+).*", replacement="\\1")
+    depends <- depends[depends %in% knownPackageNames]
+    depends <- lapply(depends, escapeName)
+    depends <- paste(depends)
+    depends <- sort(unique(depends))
+    list(name=unbox(name), version=unbox(version), sha256=unbox(sha256), depends=depends)
+}
+
+cl <- makeCluster(10)
+clusterExport(cl, c("escapeName", "nixPrefetch", "prevPkgs", "mirrorUrl", "mirrorType", "knownPackageNames"))
+
+write(paste("updating", mirrorType, "packages"), stderr())
+pkgTable$sha256 <- parApply(cl, pkgTable, 1, function(p) nixPrefetch(p[1], p[2]))
+
+stopCluster(cl)
+
+pkgs <- lapply(1:nrow(pkgTable), function(i) with(pkgTable[i,], formatPackage(Package, Version, sha256, Depends, Imports, LinkingTo)))
+names(pkgs) <- lapply(pkgs, function(p) escapeName(p$name))
+
+# Mark deleted packages as broken
+brokenPkgs <- lapply(prevPkgs[setdiff(names(prevPkgs), names(pkgs))], function(p)
+  list(name=unbox(p$name),
+       version=unbox(p$version),
+       sha256=unbox(p$sha256),
+       depends=p$depends,
+       broken=unbox(T)))
+
+# sort packages by their non-escaped names
+pkgs <- pkgs[order(sapply(pkgs, function(p) p$name))]
+brokenPkgs<- brokenPkgs[order(sapply(brokenPkgs, function(p) p$name))]
+
+# empty named list
+extraArgs = setNames(list(), character(0))
+
+if (mirrorType != "cran") {
+  extraArgs=list(biocVersion=unbox(paste(biocVersion)))
+}
+
+cat(toJSON(list(extraArgs=extraArgs, packages=c(pkgs, brokenPkgs)), pretty=TRUE))
+cat("\n")
+write("done", stderr())

pkgs/development/r-modules/generate-shell.nix

@@ -0,0 +1,24 @@
+with import ../../.. { };
+
+stdenv.mkDerivation {
+  name = "generate-r-packages-shell";
+
+  buildCommand = "exit 1";
+
+  buildInputs = [
+    wget
+    cacert
+    nix
+  ];
+
+  nativeBuildInputs = [
+    (rWrapper.override {
+      packages = with rPackages; [
+        data_table
+        parallel
+        BiocManager
+        jsonlite
+      ];
+    })
+  ];
+}

pkgs/development/r-modules/generic-builder.nix

@@ -0,0 +1,83 @@
+{
+  stdenv,
+  lib,
+  R,
+  xvfb-run,
+  util-linux,
+  gettext,
+  gfortran,
+  libiconv,
+}:
+
+{
+  name,
+  buildInputs ? [ ],
+  requireX ? false,
+  ...
+}@attrs:
+
+stdenv.mkDerivation (
+  {
+    buildInputs =
+      buildInputs
+      ++ [
+        R
+        gettext
+      ]
+      ++ lib.optionals requireX [
+        util-linux
+        xvfb-run
+      ]
+      ++ lib.optionals stdenv.hostPlatform.isDarwin [
+        gfortran
+        libiconv
+      ];
+
+    env.NIX_CFLAGS_COMPILE = lib.optionalString stdenv.hostPlatform.isDarwin "-I${lib.getInclude stdenv.cc.libcxx}/include/c++/v1";
+
+    enableParallelBuilding = true;
+
+    configurePhase = ''
+      runHook preConfigure
+      export MAKEFLAGS+="''${enableParallelBuilding:+-j$NIX_BUILD_CORES}"
+      export R_LIBS_SITE="$R_LIBS_SITE''${R_LIBS_SITE:+:}$out/library"
+      runHook postConfigure
+    '';
+
+    buildPhase = ''
+      runHook preBuild
+      runHook postBuild
+    '';
+
+    installFlags = if attrs.doCheck or true then [ ] else [ "--no-test-load" ];
+
+    rCommand =
+      if requireX then
+        # Unfortunately, xvfb-run has a race condition even with -a option, so that
+        # we acquire a lock explicitly.
+        "flock ${xvfb-run} xvfb-run -a -e xvfb-error R"
+      else
+        "R";
+
+    installPhase = ''
+      runHook preInstall
+      mkdir -p $out/library
+      $rCommand CMD INSTALL --built-timestamp='1970-01-01 00:00:00 UTC' $installFlags --configure-args="$configureFlags" -l $out/library .
+      runHook postInstall
+    '';
+
+    postFixup = ''
+      if test -e $out/nix-support/propagated-build-inputs; then
+          ln -s $out/nix-support/propagated-build-inputs $out/nix-support/propagated-user-env-packages
+      fi
+    '';
+
+    checkPhase = ''
+      # noop since R CMD INSTALL tests packages
+    '';
+  }
+  // attrs
+  // {
+    name = "r-" + name;
+  }
+)

pkgs/development/r-modules/patches/CNEr.patch

@@ -0,0 +1,48 @@
+diff --git a/src/ucsc/common.c b/src/ucsc/common.c
+index a3fc893..e4198d3 100644
+--- a/src/ucsc/common.c
++++ b/src/ucsc/common.c
+@@ -341,7 +341,7 @@ if (count > 1)
+     }
+ }
+ 
+-void slUniqify(void *pList, int (*compare )(const void *elem1,  const void *elem2), void (*free)())
++void slUniqify(void *pList, int (*compare )(const void *elem1,  const void *elem2), void (*freeFunc)())
+ /* Return sorted list with duplicates removed.
+  * Compare should be same type of function as slSort's compare (taking
+  * pointers to pointers to elements.  Free should take a simple
+@@ -356,7 +356,7 @@ while ((el = slPopHead(&oldList)) != NULL)
+     {
+     if ((newList == NULL) || (compare(&newList, &el) != 0))
+         slAddHead(&newList, el);
+-    else if (free != NULL)
++    else if (freeFunc != NULL)
+         free(el);
+     }
+ slReverse(&newList);
+diff --git a/src/ucsc/hash.c b/src/ucsc/hash.c
+index 320b360..6ed9c70 100644
+--- a/src/ucsc/hash.c
++++ b/src/ucsc/hash.c
+@@ -611,7 +611,7 @@ if ((hash = *pHash) != NULL)
+     }
+ }
+ 
+-void hashFreeWithVals(struct hash **pHash, void (freeFunc)())
++void hashFreeWithVals(struct hash **pHash, void (*freeFunc)(void **))
+ /* Free up hash table and all values associated with it. freeFunc is a
+  * function to free an entry, should take a pointer to a pointer to an
+  * entry. */
+diff --git a/src/ucsc/hash.h b/src/ucsc/hash.h
+index a7fc017..0d06bb9 100644
+--- a/src/ucsc/hash.h
++++ b/src/ucsc/hash.h
+@@ -244,7 +244,7 @@ void freeHashAndVals(struct hash **pHash);
+ /* Free up hash table and all values associated with it.
+  * (Just calls freeMem on each hel->val) */
+ 
+-void hashFreeWithVals(struct hash **pHash, void (freeFunc)());
++void hashFreeWithVals(struct hash **pHash, void (*freeFunc)(void **));
+ /* Free up hash table and all values associated with it. freeFunc is a
+  * function to free an entry, should take a pointer to a pointer to an
+  * entry. */

pkgs/development/r-modules/patches/FLAMES.patch

@@ -0,0 +1,17 @@
+diff --git a/src/Makevars b/src/Makevars
+index 4f3fa42ce752..e48e45561292 100755
+--- a/src/Makevars
++++ b/src/Makevars
+@@ -24,12 +24,6 @@ FILES = $(CFILES) $(CPPFILES)
+ SOURCES = $(FILES)
+ OBJECTS = $(CPPFILES:.cpp=.o) $(CFILES:.c=.o)
+ 
+-strippedLib: $(SHLIB)
+-	if test -e "/usr/bin/strip" & test -e "/bin/uname" & [[ `uname` == "Linux" ]] ; then /usr/bin/strip --strip-debug $(SHLIB); fi
+-clean:
+-	rm $(OBJECTS)
+-.phony: strippedLib clean
+-
+ RHTSLIB_LIBS=$(shell "${R_HOME}/bin${R_ARCH_BIN}/Rscript" -e \
+     'Rhtslib::pkgconfig("PKG_LIBS")')
+ RHTSLIB_CPPFLAGS=$(shell "${R_HOME}/bin${R_ARCH_BIN}/Rscript" -e \

pkgs/development/r-modules/patches/RAppArmor.patch

@@ -0,0 +1,20 @@
+diff -ru -x '*~' RAppArmor_orig/configure RAppArmor/configure
+--- RAppArmor_orig/configure	2013-12-17 11:23:00.000000000 +0900
++++ RAppArmor/configure	2014-10-18 22:22:39.641341244 +0900
+@@ -1,15 +1,2 @@
+-if [ ! -e /usr/include/sys/apparmor.h ]
+-then
+-  echo "sys/apparmor.h not found. Make sure libapparmor-dev is installed."
+-  exit 1
+-fi
+-
+-LIBFILE=$(/sbin/ldconfig -p | egrep -oh " [-_a-zA-Z0-9/]*/libapparmor.so(.1)?$")
+-
+-if [ -z "$LIBFILE" ]
+-then
+-  echo "libapparmor.so not found. Make sure libapparmor-dev is installed."
+-  exit 1
+-fi 
+-
++LIBFILE="$LIBAPPARMOR_HOME/lib/libapparmor.so.1"
+ echo "PKG_LIBS="$LIBFILE > src/Makevars

pkgs/development/r-modules/patches/Rhdf5lib.patch

@@ -0,0 +1,79 @@
+diff --git a/R/zzz.R b/R/zzz.R
+index 97becd7..803ca39 100644
+--- a/R/zzz.R
++++ b/R/zzz.R
+@@ -20,7 +20,7 @@ pkgconfig <- function(opt = c("PKG_CXX_LIBS", "PKG_C_LIBS", "PKG_CXX_HL_LIBS", "
+ 
+   path <- Sys.getenv(
+     x = "RHDF5LIB_RPATH",
+-    unset = system.file("lib", package="Rhdf5lib", mustWork=TRUE)
++    unset = ""
+   )
+ 
+   if (nzchar(.Platform$r_arch)) {
+@@ -59,7 +59,7 @@ pkgconfig <- function(opt = c("PKG_CXX_LIBS", "PKG_C_LIBS", "PKG_CXX_HL_LIBS", "
+                               sprintf('-L%s -lhdf5 %s',
+                                       patharch, winlibs)
+                             }, {
+-                              sprintf('"%s/libhdf5.a"%s%s', 
++                              sprintf('-lhdf5',
+                                       patharch, .getSzipLoc(patharch), .getDynamicLinks())
+                             }
+                      )
+@@ -70,7 +70,7 @@ pkgconfig <- function(opt = c("PKG_CXX_LIBS", "PKG_C_LIBS", "PKG_CXX_HL_LIBS", "
+                               sprintf('-L%s -lhdf5_cpp -lhdf5 %s',
+                                       patharch, winlibs)
+                             }, {
+-                              sprintf('"%s/libhdf5_cpp.a" "%s/libhdf5.a"%s%s',
++                              sprintf('-lhdf5_cpp -lhdf5',
+                                       patharch, patharch, .getSzipLoc(patharch), .getDynamicLinks())
+                             }
+                      )
+@@ -81,7 +81,7 @@ pkgconfig <- function(opt = c("PKG_CXX_LIBS", "PKG_C_LIBS", "PKG_CXX_HL_LIBS", "
+                               sprintf('-L%s -lhdf5_hl -lhdf5 %s',
+                                       patharch, winlibs)
+                             }, {
+-                              sprintf('"%s/libhdf5_hl.a" "%s/libhdf5.a"%s%s', 
++                              sprintf('-lhdf5_hl -lhdf5',
+                                       patharch, patharch, .getSzipLoc(patharch), .getDynamicLinks())
+                             }
+                      )
+@@ -92,7 +92,7 @@ pkgconfig <- function(opt = c("PKG_CXX_LIBS", "PKG_C_LIBS", "PKG_CXX_HL_LIBS", "
+                               sprintf('-L%s -lhdf5_hl_cpp -lhdf5_hl -lhdf5_cpp -lhdf5 %s',
+                                       patharch, winlibs)
+                             }, {
+-                              sprintf('"%s/libhdf5_hl_cpp.a" "%s/libhdf5_hl.a" "%s/libhdf5_cpp.a" "%s/libhdf5.a"%s%s',
++                              sprintf('-lhdf5_hl_cpp -lhdf5_hl -lhdf5_cpp -lhdf5',
+                                       patharch, patharch, patharch, patharch, .getSzipLoc(patharch), .getDynamicLinks())
+                             }
+                      )
+@@ -124,6 +124,7 @@ getHdf5Version <- function() {
+ #'
+ #' @keywords internal
+ .getDynamicLinks <- function() {
++  return("")
+   sysname <- Sys.info()['sysname']
+   if(sysname == "Windows") {
+     links <- "-lz"
+diff --git a/src/Makevars.in b/src/Makevars.in
+index addb6a0..590784a 100644
+--- a/src/Makevars.in
++++ b/src/Makevars.in
+@@ -18,7 +18,7 @@ USER_LIB_DIR = ${R_PACKAGE_DIR}/lib${R_ARCH}/
+ 
+ PKG_CPPFLAGS = -I${USER_INCLUDE_DIR} ${ZLIB_INCLUDE}
+ PKG_CFLAGS = ${ZLIB_LIB}
+-PKG_LIBS = "${USER_LIB_DIR}libhdf5.a" @SZIP_LIB@ -lz
++PKG_LIBS = -lhdf5 -lsz
+ 
+ 
+ 
+@@ -26,7 +26,7 @@ all: $(SHLIB)
+ 
+ $(SHLIB): Rhdf5lib.o
+ 
+-Rhdf5lib.o: copy-hdf5 @COPY_SZIP@
++Rhdf5lib.o:
+ 
+ copy-szip: copy-hdf5
+ 	cp hdf5/libaec-1.0.4/build/szip/lib/libsz.a "${USER_LIB_DIR}"

pkgs/development/r-modules/patches/Rserve.patch

@@ -0,0 +1,15 @@
+diff -ru -x '*~' Rserve_orig/src/Makevars.in Rserve/src/Makevars.in
+--- Rserve_orig/src/Makevars.in	2013-08-22 06:09:33.000000000 +0900
++++ Rserve/src/Makevars.in	2014-11-09 21:36:31.184590320 +0900
+@@ -12,8 +12,9 @@
+ 	$(CC) -DSTANDALONE_RSERVE -DRSERV_DEBUG -DNODAEMON -I. -Iinclude $(ALL_CPPFLAGS) $(ALL_CFLAGS) $(PKG_CPPFLAGS) $(PKG_CFLAGS) -o Rserve.dbg $(SERVER_SRC) $(ALL_LIBS) $(PKG_LIBS)
+ 
+ # merging to bin/Rserve works only if installed from sources, won't work for binary
+-	-./mergefat Rserve "$(R_HOME)/bin/Rserve"
+-	-./mergefat Rserve.dbg "$(R_HOME)/bin/Rserve.dbg"
++	mkdir $(out)/bin
++	-./mergefat Rserve "$(out)/bin/Rserve"
++	-./mergefat Rserve.dbg "$(out)/bin/Rserve.dbg"
+ 
+ client: config.h
+ 	cp config.h client/cxx/

pkgs/development/r-modules/patches/immunotation.patch

@@ -0,0 +1,47 @@
+diff --git a/R/AFND_interface.R b/R/AFND_interface.R
+index b62e8e0..0f22d85 100644
+--- a/R/AFND_interface.R
++++ b/R/AFND_interface.R
+@@ -244,9 +244,9 @@ check_population <- function(hla_population) {
+ #' @return list of valid countries, regions and ethnic origin
+ #' @keywords internal
+ get_valid_geographics <- function() {
+-    url <- "http://www.allelefrequencies.net/hla6006a.asp?"
+-    html_input <- getURL(url, read_method = "html")
+-    
++    # http://www.allelefrequencies.net/hla6006a.asp?
++    html_input <- xml2::read_html("nix-valid-geographics")
++      
+     rvest_tables <- rvest::html_table(html_input, fill = TRUE)
+     
+     # country
+diff --git a/R/external_resources_input.R b/R/external_resources_input.R
+index c4b1dc1..8fc5881 100644
+--- a/R/external_resources_input.R
++++ b/R/external_resources_input.R
+@@ -74,16 +74,17 @@ getURL <- function(URL, N.TRIES=2L,
+ # MHC I
+ # netmhcI_input_template is an internal variable containing list of valid 
+ # NetMHCpan input alleles
+-netmhcI_input_template <- getURL(
+-    URL="https://services.healthtech.dtu.dk/services/NetMHCpan-4.1/allele.list",
+-    read_method = "delim", delim = "\t",
+-    col_names = c("netmhc_input", "hla_chain_name", "HLA_gene"))
++netmhcI_input_template <- readr::read_delim(
++        # https://services.healthtech.dtu.dk/services/NetMHCpan-4.1/allele.list
++	"nix-NetMHCpan-4.1-allele-list",
++	delim = "\t",
++	skip = 0,
++        col_names = c("netmhc_input", "hla_chain_name", "HLA_gene")
++    )
+ 
+ # MHC II
+-lines <- getURL(
+-    URL = paste0("https://services.healthtech.dtu.dk/services/",
+-    "NetMHCIIpan-4.0/alleles_name.list"),
+-    read_method = "lines")
++# https://services.healthtech.dtu.dk/services/NetMHCIIpan-4.0/alleles_name.list
++lines <- readr::read_lines("nix-NETMHCIIpan-4.0-alleles-name-list")
+ lines_rep <- stringr::str_replace_all(lines, "\t+|\\s\\s+", "\t")
+ netmhcII_input_template <- suppressWarnings(
+     suppressMessages(read.delim(textConnection(lines_rep), sep = "\t")))

pkgs/development/r-modules/patches/rhdf5.patch

@@ -0,0 +1,47 @@
+diff --git a/src/Makevars b/src/Makevars
+index 713b44c..704ac17 100644
+--- a/src/Makevars
++++ b/src/Makevars
+@@ -1,5 +1,5 @@
+ RHDF5_LIBS = $(shell "$(R_HOME)/bin${R_ARCH_BIN}/Rscript" -e 'Rhdf5lib::pkgconfig("PKG_C_LIBS")')
+-PKG_LIBS = $(RHDF5_LIBS)
++PKG_LIBS = $(RHDF5_LIBS) -lhdf5
+ 
+ #PKG_CFLAGS = -Wall
+ 
+diff --git a/src/h5testLock.c b/src/h5testLock.c
+index b326444..5d58b4a 100644
+--- a/src/h5testLock.c
++++ b/src/h5testLock.c
+@@ -8,16 +8,16 @@ SEXP _h5fileLock(SEXP _file_name) {
+   int lk = -1;
+ 
+   /* create the temporary file */
+-  fd = HDopen(file_name, O_RDWR | O_CREAT | O_TRUNC, 0666);
++  fd = open(file_name, O_RDWR | O_CREAT | O_TRUNC, 0666);
+ 
+   /* try to lock file */
+-  lk = HDflock(fd, LOCK_EX | LOCK_NB);
++  lk = flock(fd, LOCK_EX | LOCK_NB);
+   
+   /* unlock so we can remove */
+-  HDflock(fd, LOCK_UN);
++  flock(fd, LOCK_UN);
+   
+   /* close */
+-  HDclose(fd);
++  close(fd);
+   
+   /* return value of lock attempt */
+   PROTECT(Rval = allocVector(INTSXP, 1));
+diff --git a/src/h5testLock.h b/src/h5testLock.h
+index 2c1c5e4..25914ff 100644
+--- a/src/h5testLock.h
++++ b/src/h5testLock.h
+@@ -1,5 +1,5 @@
+ #include <fcntl.h>
++#include <unistd.h>
+ #include "myhdf5.h"
+-#include <H5private.h>
+ 
+ SEXP _h5fileLock();

pkgs/development/r-modules/patches/rhdf5filters.patch

@@ -0,0 +1,12 @@
+diff --git a/src/Makevars.in b/src/Makevars.in
+--- a/src/Makevars.in
++++ b/src/Makevars.in
+@@ -15,7 +15,7 @@ RANLIB := @RANLIB@
+ MAKE := @MAKE@
+ AR := @AR@
+-PKG_CPPFLAGS := @CPPFLAGS@ -I"@RHDF5_INCLUDE@"
++PKG_CPPFLAGS := @CPPFLAGS@
+ PKG_LDFLAGS := @LDFLAGS@
+ export
+
+ all: copying $(SHLIB)

pkgs/development/r-modules/patches/universalmotif.patch

@@ -0,0 +1,10 @@
+diff --git a/src/Makevars b/src/Makevars
+index 6e08950..e66fbbd 100644
+--- a/src/Makevars
++++ b/src/Makevars
+@@ -1,5 +1 @@
+ CXX_STD=CXX11
+-PKG_LIBS=`"$(R_HOME)/bin/Rscript" -e "RcppThread::LdFlags()"`
+-strippedLib: $(SHLIB)
+-		if test -e "/usr/bin/strip" & test -e "/bin/uname" & [[ `uname` == "Linux" ]] ; then /usr/bin/strip --strip-debug $(SHLIB); fi
+-.phony: strippedLib

pkgs/development/r-modules/test-evaluation.nix

@@ -0,0 +1,21 @@
+# Run
+#
+#   nix-build test-evaluation.nix --dry-run
+#
+# to test whether the R package set evaluates properly.
+
+let
+
+  config = {
+    allowBroken = true;
+    allowUnfree = true;
+  };
+
+  inherit (import ../../.. { inherit config; }) pkgs;
+
+  rWrapper = pkgs.rWrapper.override {
+    packages = pkgs.lib.filter pkgs.lib.isDerivation (pkgs.lib.attrValues pkgs.rPackages);
+  };
+
+in
+rWrapper

pkgs/development/r-modules/wrapper-radian.nix

@@ -0,0 +1,47 @@
+{
+  lib,
+  runCommand,
+  R,
+  radian,
+  makeWrapper,
+  recommendedPackages,
+  packages,
+  wrapR ? false,
+}:
+
+runCommand (radian.name + "-wrapper")
+  {
+    preferLocalBuild = true;
+    allowSubstitutes = false;
+
+    buildInputs = [
+      R
+      radian
+    ]
+    ++ recommendedPackages
+    ++ packages;
+
+    nativeBuildInputs = [ makeWrapper ];
+
+    passthru = { inherit recommendedPackages; };
+
+    meta = radian.meta // {
+      # To prevent builds on hydra
+      hydraPlatforms = [ ];
+      # prefer wrapper over the package
+      priority = (radian.meta.priority or lib.meta.defaultPriority) - 1;
+    };
+  }
+  (
+    ''
+      makeWrapper "${radian}/bin/radian" "$out/bin/radian" \
+        --prefix "R_LIBS_SITE" ":" "$R_LIBS_SITE"
+    ''
+    + lib.optionalString wrapR ''
+      cd ${R}/bin
+      for exe in *; do
+        makeWrapper "${R}/bin/$exe" "$out/bin/$exe" \
+          --prefix "R_LIBS_SITE" ":" "$R_LIBS_SITE"
+      done
+    ''
+  )

pkgs/development/r-modules/wrapper-rstudio.nix

@@ -0,0 +1,69 @@
+{
+  lib,
+  stdenv,
+  runCommand,
+  R,
+  rstudio,
+  makeWrapper,
+  recommendedPackages,
+  packages,
+  fontconfig,
+}:
+
+runCommand (rstudio.name + "-wrapper")
+  {
+    preferLocalBuild = true;
+    allowSubstitutes = false;
+
+    nativeBuildInputs = [ makeWrapper ];
+    dontWrapQtApps = true;
+
+    buildInputs = [
+      R
+      rstudio
+    ]
+    ++ recommendedPackages
+    ++ packages;
+
+    # rWrapper points R to a specific set of packages by using a wrapper
+    # (as in https://nixos.org/nixpkgs/manual/#r-packages) which sets
+    # R_LIBS_SITE.  Ordinarily, it would be possible to make RStudio use
+    # this same set of packages by simply overriding its version of R
+    # with the wrapped one, however, RStudio internally overrides
+    # R_LIBS_SITE.  The below works around this by turning R_LIBS_SITE
+    # into an R file (fixLibsR) which achieves the same effect, then
+    # uses R_PROFILE_USER to load this code at startup in RStudio.
+    fixLibsR = "fix_libs.R";
+  }
+  (
+    ''
+      mkdir -p $out
+      echo "# Autogenerated by wrapper-rstudio.nix from R_LIBS_SITE" > $out/$fixLibsR
+      echo -n ".libPaths(c(.libPaths(), \"" >> $out/$fixLibsR
+      echo -n $R_LIBS_SITE | sed -e 's/:/", "/g' >> $out/$fixLibsR
+      echo -n "\"))" >> $out/$fixLibsR
+      echo >> $out/$fixLibsR
+    ''
+    + (
+      if rstudio.server then
+        ''
+          makeWrapper ${rstudio}/bin/rsession $out/bin/rsession \
+            --set R_PROFILE_USER $out/$fixLibsR --set FONTCONFIG_FILE ${fontconfig.out}/etc/fonts/fonts.conf
+
+          makeWrapper ${rstudio}/bin/rserver $out/bin/rserver \
+            --add-flags --rsession-path=$out/bin/rsession
+        ''
+      else
+        ''
+          ${lib.optionalString stdenv.hostPlatform.isLinux ''
+            # symlink files from unwrapped rstudio so that the desktop file and the icons
+            # are also installed when using the wrapped version
+            # TODO: figure out how to handle darwin .app structures
+            ln -s ${rstudio}/share $out
+          ''}
+
+          makeWrapper ${rstudio}/bin/rstudio $out/bin/rstudio \
+            --set R_PROFILE_USER $out/$fixLibsR
+        ''
+    )
+  )

pkgs/development/r-modules/wrapper.nix

@@ -0,0 +1,38 @@
+{
+  lib,
+  symlinkJoin,
+  R,
+  makeWrapper,
+  recommendedPackages,
+  packages,
+}:
+symlinkJoin {
+  name = R.name + "-wrapper";
+  preferLocalBuild = true;
+  allowSubstitutes = false;
+
+  buildInputs = [ R ] ++ recommendedPackages ++ packages;
+  paths = [ R ];
+
+  nativeBuildInputs = [ makeWrapper ];
+
+  postBuild = ''
+    cd ${R}/bin
+    for exe in *; do
+      rm "$out/bin/$exe"
+
+      makeWrapper "${R}/bin/$exe" "$out/bin/$exe" \
+        --prefix "R_LIBS_SITE" ":" "$R_LIBS_SITE"
+    done
+  '';
+
+  # Make the list of recommended R packages accessible to other packages such as rpy2
+  passthru = { inherit recommendedPackages; };
+
+  meta = R.meta // {
+    # To prevent builds on hydra
+    hydraPlatforms = [ ];
+    # prefer wrapper over the package
+    priority = (R.meta.priority or lib.meta.defaultPriority) - 1;
+  };
+}