Merge pull request #142333 from NixOS/r-updates
rPackages: update R, CRAN, and BIOC
This commit is contained in:
Justin Bedő
GitHub
commit
0689e7368d
@ -119,6 +119,6 @@ stdenv.mkDerivation rec {
|
||||
|
||||
platforms = platforms.all;
|
||||
|
||||
maintainers = with maintainers; teams.sage.members;
|
||||
maintainers = with maintainers; [ jbedo ] ++ teams.sage.members;
|
||||
};
|
||||
}
|
||||
|
||||
@ -158,6 +158,38 @@ let
|
||||
in
|
||||
builtins.listToAttrs nameValuePairs;
|
||||
|
||||
# Overrides package definition requiring a home directory to install or to
|
||||
# run tests.
|
||||
# For example,
|
||||
#
|
||||
# overrideRequireHome [
|
||||
# "foo"
|
||||
# ] old
|
||||
#
|
||||
# results in
|
||||
#
|
||||
# {
|
||||
# foo = old.foo.overrideAttrs (oldAttrs: {
|
||||
# preInstall = ''
|
||||
# ${oldAttrs.preInstall or ""}
|
||||
# export HOME=$(mktemp -d)
|
||||
# '';
|
||||
# });
|
||||
# }
|
||||
overrideRequireHome = packageNames: old:
|
||||
let
|
||||
nameValuePairs = map (name: {
|
||||
inherit name;
|
||||
value = (builtins.getAttr name old).overrideAttrs (oldAttrs: {
|
||||
preInstall = ''
|
||||
${oldAttrs.preInstall or ""}
|
||||
export HOME=$(mktemp -d)
|
||||
'';
|
||||
});
|
||||
}) packageNames;
|
||||
in
|
||||
builtins.listToAttrs nameValuePairs;
|
||||
|
||||
# Overrides package definition to skip check.
|
||||
# For example,
|
||||
#
|
||||
@ -211,13 +243,14 @@ let
|
||||
defaultOverrides = old: new:
|
||||
let old0 = old; in
|
||||
let
|
||||
old1 = old0 // (overrideRequireX packagesRequireingX old0);
|
||||
old2 = old1 // (overrideSkipCheck packagesToSkipCheck old1);
|
||||
old3 = old2 // (overrideRDepends packagesWithRDepends old2);
|
||||
old4 = old3 // (overrideNativeBuildInputs packagesWithNativeBuildInputs old3);
|
||||
old5 = old4 // (overrideBuildInputs packagesWithBuildInputs old4);
|
||||
old6 = old5 // (overrideBroken brokenPackages old5);
|
||||
old = old6;
|
||||
old1 = old0 // (overrideRequireX packagesRequiringX old0);
|
||||
old2 = old1 // (overrideRequireHome packagesRequiringHome old1);
|
||||
old3 = old2 // (overrideSkipCheck packagesToSkipCheck old2);
|
||||
old4 = old3 // (overrideRDepends packagesWithRDepends old3);
|
||||
old5 = old4 // (overrideNativeBuildInputs packagesWithNativeBuildInputs old4);
|
||||
old6 = old5 // (overrideBuildInputs packagesWithBuildInputs old5);
|
||||
old7 = old6 // (overrideBroken brokenPackages old6);
|
||||
old = old7;
|
||||
in old // (otherOverrides old new);
|
||||
|
||||
# Recursive override pattern.
|
||||
@ -243,14 +276,14 @@ let
|
||||
adimpro = [ pkgs.imagemagick ];
|
||||
animation = [ pkgs.which ];
|
||||
audio = [ pkgs.portaudio ];
|
||||
BayesSAE = [ pkgs.gsl_1 ];
|
||||
BayesVarSel = [ pkgs.gsl_1 ];
|
||||
BayesSAE = [ pkgs.gsl ];
|
||||
BayesVarSel = [ pkgs.gsl ];
|
||||
BayesXsrc = with pkgs; [ readline.dev ncurses ];
|
||||
bigGP = [ pkgs.mpi ];
|
||||
bio3d = [ pkgs.zlib ];
|
||||
BiocCheck = [ pkgs.which ];
|
||||
Biostrings = [ pkgs.zlib ];
|
||||
bnpmr = [ pkgs.gsl_1 ];
|
||||
bnpmr = [ pkgs.gsl ];
|
||||
cairoDevice = [ pkgs.gtk2.dev ];
|
||||
Cairo = with pkgs; [ libtiff libjpeg cairo.dev x11 fontconfig.lib ];
|
||||
Cardinal = [ pkgs.which ];
|
||||
@ -259,37 +292,39 @@ let
|
||||
curl = [ pkgs.curl.dev ];
|
||||
data_table = [ pkgs.zlib.dev ] ++ lib.optional stdenv.isDarwin pkgs.llvmPackages.openmp;
|
||||
devEMF = with pkgs; [ xorg.libXft.dev x11 ];
|
||||
diversitree = with pkgs; [ gsl_1 fftw ];
|
||||
diversitree = with pkgs; [ gsl fftw ];
|
||||
exactextractr = [ pkgs.geos ];
|
||||
EMCluster = [ pkgs.lapack ];
|
||||
fftw = [ pkgs.fftw.dev ];
|
||||
fftwtools = with pkgs; [ fftw.dev pkg-config ];
|
||||
Formula = [ pkgs.gmp ];
|
||||
gdtools = with pkgs; [ cairo.dev fontconfig.lib freetype.dev ];
|
||||
ggiraph = with pkgs; [ pkgs.libpng.dev ];
|
||||
git2r = with pkgs; [ zlib.dev openssl.dev libssh2.dev libgit2 pkg-config ];
|
||||
GLAD = [ pkgs.gsl_1 ];
|
||||
GLAD = [ pkgs.gsl ];
|
||||
glpkAPI = with pkgs; [ gmp glpk ];
|
||||
gmp = [ pkgs.gmp.dev ];
|
||||
graphscan = [ pkgs.gsl_1 ];
|
||||
gsl = [ pkgs.gsl_1 ];
|
||||
graphscan = [ pkgs.gsl ];
|
||||
gsl = [ pkgs.gsl ];
|
||||
gert = [ pkgs.libgit2 ];
|
||||
haven = with pkgs; [ libiconv zlib.dev ];
|
||||
h5vc = [ pkgs.zlib.dev ];
|
||||
HiCseg = [ pkgs.gsl_1 ];
|
||||
HiCseg = [ pkgs.gsl ];
|
||||
imager = [ pkgs.x11 ];
|
||||
iBMQ = [ pkgs.gsl_1 ];
|
||||
iBMQ = [ pkgs.gsl ];
|
||||
igraph = with pkgs; [ gmp libxml2.dev ];
|
||||
JavaGD = [ pkgs.jdk ];
|
||||
jpeg = [ pkgs.libjpeg.dev ];
|
||||
jqr = [ pkgs.jq.dev ];
|
||||
KFKSDS = [ pkgs.gsl_1 ];
|
||||
KFKSDS = [ pkgs.gsl ];
|
||||
kza = [ pkgs.fftw.dev ];
|
||||
lpsymphony = with pkgs; [ pkg-config gfortran gettext ];
|
||||
lwgeom = with pkgs; [ proj geos gdal ];
|
||||
magick = [ pkgs.imagemagick.dev ];
|
||||
ModelMetrics = lib.optional stdenv.isDarwin pkgs.llvmPackages.openmp;
|
||||
mvabund = [ pkgs.gsl_1 ];
|
||||
mvabund = [ pkgs.gsl ];
|
||||
mwaved = [ pkgs.fftw.dev ];
|
||||
mzR = with pkgs; [ zlib boost159.dev netcdf ];
|
||||
ncdf4 = [ pkgs.netcdf ];
|
||||
nloptr = with pkgs; [ nlopt pkg-config ];
|
||||
n1qn1 = [ pkgs.gfortran ];
|
||||
@ -311,8 +346,8 @@ let
|
||||
readxl = [ pkgs.libiconv ];
|
||||
rcdd = [ pkgs.gmp.dev ];
|
||||
RcppCNPy = [ pkgs.zlib.dev ];
|
||||
RcppGSL = [ pkgs.gsl_1 ];
|
||||
RcppZiggurat = [ pkgs.gsl_1 ];
|
||||
RcppGSL = [ pkgs.gsl ];
|
||||
RcppZiggurat = [ pkgs.gsl ];
|
||||
reprex = [ pkgs.which ];
|
||||
rgdal = with pkgs; [ proj.dev gdal ];
|
||||
rgeos = [ pkgs.geos ];
|
||||
@ -324,7 +359,7 @@ let
|
||||
Rhtslib = with pkgs; [ zlib.dev automake autoconf bzip2.dev xz.dev curl.dev ];
|
||||
rjags = [ pkgs.jags ];
|
||||
rJava = with pkgs; [ zlib bzip2.dev icu xz.dev pcre.dev jdk libzip ];
|
||||
Rlibeemd = [ pkgs.gsl_1 ];
|
||||
Rlibeemd = [ pkgs.gsl ];
|
||||
rmatio = [ pkgs.zlib.dev ];
|
||||
Rmpfr = with pkgs; [ gmp mpfr.dev ];
|
||||
Rmpi = [ pkgs.mpi ];
|
||||
@ -352,12 +387,12 @@ let
|
||||
sf = with pkgs; [ gdal proj geos ];
|
||||
terra = with pkgs; [ gdal proj geos ];
|
||||
showtext = with pkgs; [ zlib libpng icu freetype.dev ];
|
||||
simplexreg = [ pkgs.gsl_1 ];
|
||||
simplexreg = [ pkgs.gsl ];
|
||||
spate = [ pkgs.fftw.dev ];
|
||||
ssanv = [ pkgs.proj ];
|
||||
stsm = [ pkgs.gsl_1 ];
|
||||
stsm = [ pkgs.gsl ];
|
||||
stringi = [ pkgs.icu.dev ];
|
||||
survSNP = [ pkgs.gsl_1 ];
|
||||
survSNP = [ pkgs.gsl ];
|
||||
svglite = [ pkgs.libpng.dev ];
|
||||
sysfonts = with pkgs; [ zlib libpng freetype.dev ];
|
||||
systemfonts = with pkgs; [ fontconfig.dev freetype.dev ];
|
||||
@ -365,7 +400,7 @@ let
|
||||
tesseract = with pkgs; [ tesseract leptonica ];
|
||||
tiff = [ pkgs.libtiff.dev ];
|
||||
tkrplot = with pkgs; [ xorg.libX11 tk.dev ];
|
||||
topicmodels = [ pkgs.gsl_1 ];
|
||||
topicmodels = [ pkgs.gsl ];
|
||||
udunits2 = with pkgs; [ udunits expat ];
|
||||
units = [ pkgs.udunits ];
|
||||
V8 = [ pkgs.v8 ];
|
||||
@ -444,7 +479,6 @@ let
|
||||
tikzDevice = with pkgs; [ which texlive.combined.scheme-medium ];
|
||||
gridGraphics = [ pkgs.which ];
|
||||
adimpro = with pkgs; [ which xorg.xdpyinfo ];
|
||||
mzR = [ pkgs.netcdf ];
|
||||
cluster = [ pkgs.libiconv ];
|
||||
KernSmooth = [ pkgs.libiconv ];
|
||||
nlme = [ pkgs.libiconv ];
|
||||
@ -478,9 +512,12 @@ let
|
||||
Rbowtie = with pkgs; [ zlib.dev ];
|
||||
gaston = with pkgs; [ zlib.dev ];
|
||||
csaw = with pkgs; [ zlib.dev curl ];
|
||||
DirichletMultinomial = with pkgs; [ gsl ];
|
||||
DiffBind = with pkgs; [ zlib.dev ];
|
||||
CNEr = with pkgs; [ zlib ];
|
||||
};
|
||||
|
||||
packagesRequireingX = [
|
||||
packagesRequiringX = [
|
||||
"accrual"
|
||||
"ade4TkGUI"
|
||||
"analogue"
|
||||
@ -670,6 +707,27 @@ let
|
||||
"x12GUI"
|
||||
];
|
||||
|
||||
packagesRequiringHome = [
|
||||
"aroma_affymetrix"
|
||||
"aroma_cn"
|
||||
"aroma_core"
|
||||
"csodata"
|
||||
"DiceView"
|
||||
"MSnID"
|
||||
"OmnipathR"
|
||||
"precommit"
|
||||
"PSCBS"
|
||||
"repmis"
|
||||
"R_cache"
|
||||
"R_filesets"
|
||||
"RKorAPClient"
|
||||
"R_rsp"
|
||||
"scholar"
|
||||
"stepR"
|
||||
"styler"
|
||||
"TreeTools"
|
||||
];
|
||||
|
||||
packagesToSkipCheck = [
|
||||
"Rmpi" # tries to run MPI processes
|
||||
"pbdMPI" # tries to run MPI processes
|
||||
@ -678,6 +736,11 @@ let
|
||||
|
||||
# Packages which cannot be installed due to lack of dependencies or other reasons.
|
||||
brokenPackages = [
|
||||
"av"
|
||||
"rgl"
|
||||
"NetLogoR"
|
||||
"proj4"
|
||||
"x13binary"
|
||||
];
|
||||
|
||||
otherOverrides = old: new: {
|
||||
@ -821,10 +884,6 @@ let
|
||||
PKG_LIBS = "-L${pkgs.blas}/lib -lblas -L${pkgs.lapack}/lib -llapack";
|
||||
});
|
||||
|
||||
EMCluster = old.EMCluster.overrideDerivation (attrs: {
|
||||
patches = [ ./patches/EMCluster.patch ];
|
||||
});
|
||||
|
||||
spMC = old.spMC.overrideDerivation (attrs: {
|
||||
patches = [ ./patches/spMC.patch ];
|
||||
});
|
||||
@ -972,12 +1031,6 @@ let
|
||||
'';
|
||||
});
|
||||
|
||||
R_cache = old.R_cache.overrideDerivation (attrs: {
|
||||
preConfigure = ''
|
||||
export R_CACHE_ROOTPATH=$TMP
|
||||
'';
|
||||
});
|
||||
|
||||
lpsymphony = old.lpsymphony.overrideDerivation (attrs: {
|
||||
preConfigure = ''
|
||||
patchShebangs configure
|
||||
@ -992,12 +1045,37 @@ let
|
||||
buildInputs = [ libsodium.dev ] ++ attrs.buildInputs;
|
||||
});
|
||||
|
||||
keyring = old.keyring.overrideDerivation (attrs: {
|
||||
preConfigure = ''
|
||||
patchShebangs configure
|
||||
'';
|
||||
});
|
||||
|
||||
Rhtslib = old.Rhtslib.overrideDerivation (attrs: {
|
||||
preConfigure = ''
|
||||
substituteInPlace R/zzz.R --replace "-lcurl" "-L${pkgs.curl.out}/lib -lcurl"
|
||||
'';
|
||||
});
|
||||
|
||||
MatchIt = old.MatchIt.overrideDerivation (attrs: {
|
||||
patches = [ (pkgs.fetchpatch {
|
||||
url = "https://github.com/kosukeimai/MatchIt/commit/8c15a1afa16b74eb04a45e7e46f8aca64ed89bcb.patch";
|
||||
sha256 = "sha256-3UI60n49xuX6LniHpTLOUSsHCEAQ7f1FMBVH0jNlW60=";
|
||||
}) ];
|
||||
});
|
||||
|
||||
h2o = old.h2o.overrideDerivation (attrs: {
|
||||
preConfigure = ''
|
||||
# prevent download of jar file during install and postpone to first use
|
||||
sed -i '/downloadJar()/d' R/zzz.R
|
||||
|
||||
# during runtime the package directory is not writable as it's in the
|
||||
# nix store, so store the jar in the user's cache directory instead
|
||||
substituteInPlace R/connection.R --replace \
|
||||
'dest_file <- file.path(dest_folder, "h2o.jar")' \
|
||||
'dest_file <- file.path("~/.cache/", "h2o.jar")'
|
||||
'';
|
||||
});
|
||||
};
|
||||
in
|
||||
self
|
||||
|
||||
@ -1,6 +0,0 @@
|
||||
diff -ru -x '*~' EMCluster_orig/src/Makevars EMCluster/src/Makevars
|
||||
--- EMCluster_orig/src/Makevars 2013-07-05 02:43:25.000000000 +0900
|
||||
+++ EMCluster/src/Makevars 2014-10-25 18:10:19.190992120 +0900
|
||||
@@ -1 +1 @@
|
||||
-PKG_LIBS = $(FLIBS) $(BLAS_LIBS) $(LAPACK_LIBS)
|
||||
+PKG_LIBS = $(FLIBS) $(LAPACK_LIBS) $(BLAS_LIBS)
|
||||
Loading…
Reference in New Issue
Block a user