nixpkgs/pkgs/development/r-modules/default.nix

955 lines
27 KiB
Nix
Raw Normal View History

/* This file defines the composition for CRAN (R) packages. */
{ R, pkgs, overrides }:
let
inherit (pkgs) cacert fetchurl stdenv lib;
buildRPackage = pkgs.callPackage ./generic-builder.nix {
inherit R;
inherit (pkgs.darwin.apple_sdk.frameworks) Cocoa Foundation;
inherit (pkgs) gettext gfortran;
};
# Generates package templates given per-repository settings
#
# some packages, e.g. cncaGUI, require X running while installation,
# so that we use xvfb-run if requireX is true.
mkDerive = {mkHomepage, mkUrls}: args:
lib.makeOverridable ({
name, version, sha256,
depends ? [],
doCheck ? true,
requireX ? false,
broken ? false,
hydraPlatforms ? R.meta.hydraPlatforms
}: buildRPackage {
name = "${name}-${version}";
src = fetchurl {
inherit sha256;
urls = mkUrls (args // { inherit name version; });
};
inherit doCheck requireX;
propagatedBuildInputs = depends;
nativeBuildInputs = depends;
meta.homepage = mkHomepage (args // { inherit name; });
meta.platforms = R.meta.platforms;
meta.hydraPlatforms = hydraPlatforms;
meta.broken = broken;
});
# Templates for generating Bioconductor and CRAN packages
# from the name, version, sha256, and optional per-package arguments above
#
deriveBioc = mkDerive {
2018-08-04 06:19:08 +00:00
mkHomepage = {name, biocVersion, ...}: "https://bioconductor.org/packages/${biocVersion}/bioc/html/${name}.html";
mkUrls = {name, version, biocVersion}: [ "mirror://bioc/${biocVersion}/bioc/src/contrib/${name}_${version}.tar.gz"
"mirror://bioc/${biocVersion}/bioc/src/contrib/Archive/${name}/${name}_${version}.tar.gz"
"mirror://bioc/${biocVersion}/bioc/src/contrib/Archive/${name}_${version}.tar.gz" ];
};
deriveBiocAnn = mkDerive {
2018-08-04 06:19:08 +00:00
mkHomepage = {name, ...}: "http://www.bioconductor.org/packages/${name}.html";
2018-02-15 05:22:52 +00:00
mkUrls = {name, version, biocVersion}: [ "mirror://bioc/${biocVersion}/data/annotation/src/contrib/${name}_${version}.tar.gz" ];
};
deriveBiocExp = mkDerive {
2018-08-04 06:19:08 +00:00
mkHomepage = {name, ...}: "http://www.bioconductor.org/packages/${name}.html";
2018-02-15 05:22:52 +00:00
mkUrls = {name, version, biocVersion}: [ "mirror://bioc/${biocVersion}/data/experiment/src/contrib/${name}_${version}.tar.gz" ];
};
deriveCran = mkDerive {
2018-08-04 06:19:08 +00:00
mkHomepage = {name, snapshot, ...}: "http://mran.revolutionanalytics.com/snapshot/${snapshot}/web/packages/${name}/";
mkUrls = {name, version, snapshot}: [ "http://mran.revolutionanalytics.com/snapshot/${snapshot}/src/contrib/${name}_${version}.tar.gz" ];
};
# Overrides package definitions with nativeBuildInputs.
# For example,
#
# overrideNativeBuildInputs {
# foo = [ pkgs.bar ]
# } old
#
# results in
#
# {
# foo = old.foo.overrideDerivation (attrs: {
# nativeBuildInputs = attrs.nativeBuildInputs ++ [ pkgs.bar ];
# });
# }
overrideNativeBuildInputs = overrides: old:
2015-02-19 20:50:42 +00:00
lib.mapAttrs (name: value:
(builtins.getAttr name old).overrideDerivation (attrs: {
nativeBuildInputs = attrs.nativeBuildInputs ++ value;
})
) overrides;
# Overrides package definitions with buildInputs.
# For example,
#
# overrideBuildInputs {
# foo = [ pkgs.bar ]
# } old
#
# results in
#
# {
# foo = old.foo.overrideDerivation (attrs: {
# buildInputs = attrs.buildInputs ++ [ pkgs.bar ];
# });
# }
overrideBuildInputs = overrides: old:
2015-02-19 20:50:42 +00:00
lib.mapAttrs (name: value:
(builtins.getAttr name old).overrideDerivation (attrs: {
buildInputs = attrs.buildInputs ++ value;
})
) overrides;
2015-02-19 20:51:24 +00:00
# Overrides package definitions with new R dependencies.
# For example,
#
# overrideRDepends {
# foo = [ self.bar ]
# } old
#
# results in
#
# {
# foo = old.foo.overrideDerivation (attrs: {
# nativeBuildInputs = attrs.nativeBuildInputs ++ [ self.bar ];
# propagatedNativeBuildInputs = attrs.propagatedNativeBuildInputs ++ [ self.bar ];
# });
# }
overrideRDepends = overrides: old:
lib.mapAttrs (name: value:
(builtins.getAttr name old).overrideDerivation (attrs: {
nativeBuildInputs = attrs.nativeBuildInputs ++ value;
propagatedNativeBuildInputs = attrs.propagatedNativeBuildInputs ++ value;
})
) overrides;
# Overrides package definition requiring X running to install.
# For example,
#
# overrideRequireX [
# "foo"
# ] old
#
# results in
#
# {
# foo = old.foo.override {
# requireX = true;
# };
# }
overrideRequireX = packageNames: old:
let
nameValuePairs = map (name: {
inherit name;
value = (builtins.getAttr name old).override {
requireX = true;
};
}) packageNames;
in
builtins.listToAttrs nameValuePairs;
# Overrides package definition to skip check.
# For example,
#
# overrideSkipCheck [
# "foo"
# ] old
#
# results in
#
# {
# foo = old.foo.override {
# doCheck = false;
# };
# }
overrideSkipCheck = packageNames: old:
let
nameValuePairs = map (name: {
inherit name;
value = (builtins.getAttr name old).override {
doCheck = false;
};
}) packageNames;
in
builtins.listToAttrs nameValuePairs;
# Overrides package definition to mark it broken.
# For example,
#
# overrideBroken [
# "foo"
# ] old
#
# results in
#
# {
# foo = old.foo.override {
# broken = true;
# };
# }
overrideBroken = packageNames: old:
let
nameValuePairs = map (name: {
inherit name;
value = (builtins.getAttr name old).override {
broken = true;
};
}) packageNames;
in
builtins.listToAttrs nameValuePairs;
defaultOverrides = old: new:
let old0 = old; in
let
old1 = old0 // (overrideRequireX packagesRequireingX old0);
old2 = old1 // (overrideSkipCheck packagesToSkipCheck old1);
2015-02-19 20:51:24 +00:00
old3 = old2 // (overrideRDepends packagesWithRDepends old2);
old4 = old3 // (overrideNativeBuildInputs packagesWithNativeBuildInputs old3);
old5 = old4 // (overrideBuildInputs packagesWithBuildInputs old4);
old6 = old5 // (overrideBroken brokenPackages old5);
old = old6;
in old // (otherOverrides old new);
# Recursive override pattern.
# `_self` is a collection of packages;
# `self` is `_self` with overridden packages;
# packages in `_self` may depends on overridden packages.
self = (defaultOverrides _self self) // overrides;
2018-08-02 15:50:58 +00:00
_self = { inherit buildRPackage; } //
import ./bioc-packages.nix { inherit self; derive = deriveBioc; } //
import ./bioc-annotation-packages.nix { inherit self; derive = deriveBiocAnn; } //
import ./bioc-experiment-packages.nix { inherit self; derive = deriveBiocExp; } //
import ./cran-packages.nix { inherit self; derive = deriveCran; };
# tweaks for the individual packages and "in self" follow
2015-02-19 20:51:24 +00:00
packagesWithRDepends = {
2015-02-19 20:53:36 +00:00
FactoMineR = [ self.car ];
2015-06-16 10:06:07 +00:00
pander = [ self.codetools ];
2015-02-19 20:51:24 +00:00
};
packagesWithNativeBuildInputs = {
arrow = [ pkgs.pkg-config pkgs.arrow-cpp ];
adimpro = [ pkgs.imagemagick ];
2018-02-15 05:22:52 +00:00
animation = [ pkgs.which ];
audio = [ pkgs.portaudio ];
BayesSAE = [ pkgs.gsl_1 ];
BayesVarSel = [ pkgs.gsl_1 ];
2017-01-06 16:30:04 +00:00
BayesXsrc = [ pkgs.readline.dev pkgs.ncurses ];
bigGP = [ pkgs.mpi ];
2017-02-27 12:51:55 +00:00
bio3d = [ pkgs.zlib ];
BiocCheck = [ pkgs.which ];
Biostrings = [ pkgs.zlib ];
bnpmr = [ pkgs.gsl_1 ];
2017-01-06 16:41:42 +00:00
cairoDevice = [ pkgs.gtk2.dev ];
2017-01-06 16:11:23 +00:00
Cairo = [ pkgs.libtiff pkgs.libjpeg pkgs.cairo.dev pkgs.x11 pkgs.fontconfig.lib ];
Cardinal = [ pkgs.which ];
chebpol = [ pkgs.fftw ];
ChemmineOB = [ pkgs.openbabel pkgs.pkg-config ];
2016-09-09 13:12:54 +00:00
curl = [ pkgs.curl.dev ];
data_table = [pkgs.zlib.dev] ++ lib.optional stdenv.isDarwin pkgs.llvmPackages.openmp;
2017-01-06 16:58:58 +00:00
devEMF = [ pkgs.xorg.libXft.dev pkgs.x11 ];
diversitree = [ pkgs.gsl_1 pkgs.fftw ];
EMCluster = [ pkgs.lapack ];
2017-01-06 17:15:14 +00:00
fftw = [ pkgs.fftw.dev ];
2017-01-06 17:16:44 +00:00
fftwtools = [ pkgs.fftw.dev ];
2015-02-19 20:53:36 +00:00
Formula = [ pkgs.gmp ];
gdtools = [ pkgs.cairo.dev pkgs.fontconfig.lib pkgs.freetype.dev ];
git2r = [ pkgs.zlib.dev pkgs.openssl.dev pkgs.libssh2.dev pkgs.libgit2 pkgs.pkg-config ];
GLAD = [ pkgs.gsl_1 ];
glpkAPI = [ pkgs.gmp pkgs.glpk ];
2017-01-06 17:20:41 +00:00
gmp = [ pkgs.gmp.dev ];
graphscan = [ pkgs.gsl_1 ];
gsl = [ pkgs.gsl_1 ];
gert = [ pkgs.libgit2 ];
2018-07-12 09:07:27 +00:00
haven = [ pkgs.libiconv pkgs.zlib.dev ];
h5vc = [ pkgs.zlib.dev ];
HiCseg = [ pkgs.gsl_1 ];
imager = [ pkgs.x11 ];
iBMQ = [ pkgs.gsl_1 ];
igraph = [ pkgs.gmp pkgs.libxml2.dev ];
JavaGD = [ pkgs.jdk ];
2017-01-06 18:17:19 +00:00
jpeg = [ pkgs.libjpeg.dev ];
2018-08-19 22:08:28 +00:00
jqr = [ pkgs.jq.dev ];
KFKSDS = [ pkgs.gsl_1 ];
2017-01-06 18:18:27 +00:00
kza = [ pkgs.fftw.dev ];
2021-05-24 17:09:06 +00:00
lwgeom = [ pkgs.gdal pkgs.geos pkgs.proj ];
magick = [ pkgs.imagemagick.dev ];
ModelMetrics = lib.optional stdenv.isDarwin pkgs.llvmPackages.openmp;
mvabund = [ pkgs.gsl_1 ];
2017-01-06 18:19:27 +00:00
mwaved = [ pkgs.fftw.dev ];
ncdf4 = [ pkgs.netcdf ];
nloptr = [ pkgs.nlopt pkgs.pkg-config ];
n1qn1 = [ pkgs.gfortran ];
odbc = [ pkgs.unixODBC ];
2015-06-16 10:06:07 +00:00
pander = [ pkgs.pandoc pkgs.which ];
pbdMPI = [ pkgs.mpi ];
pbdPROF = [ pkgs.mpi ];
pbdZMQ = lib.optionals stdenv.isDarwin [ pkgs.which ];
pdftools = [ pkgs.poppler.dev ];
2019-03-06 10:39:48 +00:00
phytools = [ pkgs.which ];
2017-01-06 18:23:42 +00:00
PKI = [ pkgs.openssl.dev ];
png = [ pkgs.libpng.dev ];
proj4 = [ pkgs.proj ];
protolite = [ pkgs.protobuf ];
2017-01-06 18:30:56 +00:00
R2SWF = [ pkgs.zlib pkgs.libpng pkgs.freetype.dev ];
2015-03-19 13:14:28 +00:00
RAppArmor = [ pkgs.libapparmor ];
2015-06-16 10:29:02 +00:00
rapportools = [ pkgs.which ];
rapport = [ pkgs.which ];
readxl = [ pkgs.libiconv ];
2017-01-06 18:34:30 +00:00
rcdd = [ pkgs.gmp.dev ];
2017-01-06 18:35:20 +00:00
RcppCNPy = [ pkgs.zlib.dev ];
RcppGSL = [ pkgs.gsl_1 ];
RcppZiggurat = [ pkgs.gsl_1 ];
2018-07-11 14:05:56 +00:00
reprex = [ pkgs.which ];
rgdal = [ pkgs.proj.dev pkgs.gdal ];
rgeos = [ pkgs.geos ];
Rglpk = [ pkgs.glpk ];
2017-01-06 18:51:28 +00:00
RGtk2 = [ pkgs.gtk2.dev ];
rhdf5 = [ pkgs.zlib ];
2021-06-03 19:29:59 +00:00
Rhdf5lib = [ pkgs.zlib.dev ];
2021-03-14 18:12:53 +00:00
Rhpc = [ pkgs.zlib pkgs.bzip2.dev pkgs.icu pkgs.xz.dev pkgs.mpi pkgs.pcre.dev ];
Rhtslib = [ pkgs.zlib.dev pkgs.automake pkgs.autoconf pkgs.bzip2.dev pkgs.xz.dev pkgs.curl.dev ];
rjags = [ pkgs.jags ];
2021-03-14 18:12:53 +00:00
rJava = [ pkgs.zlib pkgs.bzip2.dev pkgs.icu pkgs.xz.dev pkgs.pcre.dev pkgs.jdk pkgs.libzip ];
Rlibeemd = [ pkgs.gsl_1 ];
2017-01-06 19:01:17 +00:00
rmatio = [ pkgs.zlib.dev ];
2017-01-06 19:02:17 +00:00
Rmpfr = [ pkgs.gmp pkgs.mpfr.dev ];
Rmpi = [ pkgs.mpi ];
RMySQL = [ pkgs.zlib pkgs.libmysqlclient pkgs.openssl.dev ];
RNetCDF = [ pkgs.netcdf pkgs.udunits ];
RODBC = [ pkgs.libiodbc ];
rpanel = [ pkgs.bwidget ];
Rpoppler = [ pkgs.poppler ];
RPostgreSQL = [ pkgs.postgresql pkgs.postgresql ];
RProtoBuf = [ pkgs.protobuf ];
2017-01-06 19:09:43 +00:00
RSclient = [ pkgs.openssl.dev ];
Rserve = [ pkgs.openssl ];
2017-01-06 19:13:30 +00:00
Rssa = [ pkgs.fftw.dev ];
runjags = [ pkgs.jags ];
2017-01-06 19:22:07 +00:00
RVowpalWabbit = [ pkgs.zlib.dev pkgs.boost ];
rzmq = [ pkgs.zeromq pkgs.pkg-config ];
clustermq = [ pkgs.zeromq ];
2021-03-14 18:12:53 +00:00
SAVE = [ pkgs.zlib pkgs.bzip2 pkgs.icu pkgs.xz pkgs.pcre ];
sdcTable = [ pkgs.gmp pkgs.glpk ];
2017-01-06 15:31:30 +00:00
seewave = [ pkgs.fftw.dev pkgs.libsndfile.dev ];
2017-01-06 19:26:40 +00:00
seqinr = [ pkgs.zlib.dev ];
2017-01-06 19:28:22 +00:00
seqminer = [ pkgs.zlib.dev pkgs.bzip2 ];
sf = [ pkgs.gdal pkgs.proj pkgs.geos ];
2017-01-06 19:29:12 +00:00
showtext = [ pkgs.zlib pkgs.libpng pkgs.icu pkgs.freetype.dev ];
simplexreg = [ pkgs.gsl_1 ];
2017-01-06 19:30:01 +00:00
spate = [ pkgs.fftw.dev ];
ssanv = [ pkgs.proj ];
stsm = [ pkgs.gsl_1 ];
stringi = [ pkgs.icu.dev ];
survSNP = [ pkgs.gsl_1 ];
svglite = [ pkgs.libpng.dev ];
2017-01-06 18:27:45 +00:00
sysfonts = [ pkgs.zlib pkgs.libpng pkgs.freetype.dev ];
systemfonts = [ pkgs.fontconfig.dev pkgs.freetype.dev ];
2017-01-06 19:31:16 +00:00
TAQMNGR = [ pkgs.zlib.dev ];
tesseract = [ pkgs.tesseract pkgs.leptonica ];
2017-01-06 19:32:48 +00:00
tiff = [ pkgs.libtiff.dev ];
2017-01-06 19:37:33 +00:00
tkrplot = [ pkgs.xorg.libX11 pkgs.tk.dev ];
topicmodels = [ pkgs.gsl_1 ];
udunits2 = [ pkgs.udunits pkgs.expat ];
units = [ pkgs.udunits ];
V8 = [ pkgs.v8 ];
2017-01-06 19:39:44 +00:00
XBRL = [ pkgs.zlib pkgs.libxml2.dev ];
2018-02-26 01:47:57 +00:00
xml2 = [ pkgs.libxml2.dev ] ++ lib.optionals stdenv.isDarwin [ pkgs.perl ];
2016-09-09 12:36:49 +00:00
XML = [ pkgs.libtool pkgs.libxml2.dev pkgs.xmlsec pkgs.libxslt ];
2017-01-06 19:42:00 +00:00
affyPLM = [ pkgs.zlib.dev ];
2017-01-06 19:43:55 +00:00
bamsignals = [ pkgs.zlib.dev ];
2017-01-06 19:45:14 +00:00
BitSeq = [ pkgs.zlib.dev ];
DiffBind = [ pkgs.zlib ];
ShortRead = [ pkgs.zlib.dev ];
2017-01-06 19:49:49 +00:00
oligo = [ pkgs.zlib.dev ];
2017-01-06 19:51:14 +00:00
gmapR = [ pkgs.zlib.dev ];
2017-01-06 19:52:16 +00:00
Rsubread = [ pkgs.zlib.dev ];
XVector = [ pkgs.zlib.dev ];
2020-08-20 06:42:21 +00:00
Rsamtools = [ pkgs.zlib.dev pkgs.curl.dev ];
2017-01-06 19:53:12 +00:00
rtracklayer = [ pkgs.zlib.dev ];
2017-01-06 19:47:08 +00:00
affyio = [ pkgs.zlib.dev ];
2020-08-20 06:42:21 +00:00
VariantAnnotation = [ pkgs.zlib.dev pkgs.curl.dev ];
2017-01-06 19:54:40 +00:00
snpStats = [ pkgs.zlib.dev ];
hdf5r = [ pkgs.hdf5.dev ];
};
packagesWithBuildInputs = {
# sort -t '=' -k 2
gam = lib.optionals stdenv.isDarwin [ pkgs.libiconv ];
RcppArmadillo = lib.optionals stdenv.isDarwin [ pkgs.libiconv ];
quantreg = lib.optionals stdenv.isDarwin [ pkgs.libiconv ];
rmutil = lib.optionals stdenv.isDarwin [ pkgs.libiconv ];
robustbase = lib.optionals stdenv.isDarwin [ pkgs.libiconv ];
SparseM = lib.optionals stdenv.isDarwin [ pkgs.libiconv ];
hexbin = lib.optionals stdenv.isDarwin [ pkgs.libiconv ];
2015-02-19 20:53:36 +00:00
svKomodo = [ pkgs.which ];
nat = [ pkgs.which ];
nat_templatebrains = [ pkgs.which ];
2018-05-11 14:53:10 +00:00
pbdZMQ = lib.optionals stdenv.isDarwin [ pkgs.darwin.binutils ];
clustermq = [ pkgs.pkg-config ];
2015-02-19 20:53:36 +00:00
RMark = [ pkgs.which ];
RPushbullet = [ pkgs.which ];
2018-06-20 01:37:00 +00:00
RcppEigen = [ pkgs.libiconv ];
RCurl = [ pkgs.curl.dev ];
R2SWF = [ pkgs.pkg-config ];
rgl = [ pkgs.libGLU pkgs.libGLU.dev pkgs.libGL pkgs.xlibsWrapper ];
RGtk2 = [ pkgs.pkg-config ];
RProtoBuf = [ pkgs.pkg-config ];
Rpoppler = [ pkgs.pkg-config ];
XML = [ pkgs.pkg-config ];
cairoDevice = [ pkgs.pkg-config ];
chebpol = [ pkgs.pkg-config ];
fftw = [ pkgs.pkg-config ];
gdtools = [ pkgs.pkg-config ];
2018-08-19 22:08:28 +00:00
jqr = [ pkgs.jq.lib ];
kza = [ pkgs.pkg-config ];
2021-05-24 17:09:06 +00:00
lwgeom = [ pkgs.pkg-config pkgs.proj.dev pkgs.sqlite.dev ];
magick = [ pkgs.pkg-config ];
mwaved = [ pkgs.pkg-config ];
odbc = [ pkgs.pkg-config ];
openssl = [ pkgs.pkg-config ];
pdftools = [ pkgs.pkg-config ];
sf = [ pkgs.pkg-config pkgs.sqlite.dev pkgs.proj.dev ];
showtext = [ pkgs.pkg-config ];
spate = [ pkgs.pkg-config ];
stringi = [ pkgs.pkg-config ];
sysfonts = [ pkgs.pkg-config ];
systemfonts = [ pkgs.pkg-config ];
tesseract = [ pkgs.pkg-config ];
Cairo = [ pkgs.pkg-config ];
CLVTools = [ pkgs.gsl ];
JMcmprsk = [ pkgs.gsl ];
mashr = [ pkgs.gsl ];
hadron = [ pkgs.gsl ];
AMOUNTAIN = [ pkgs.gsl ];
Rsymphony = [ pkgs.pkg-config pkgs.doxygen pkgs.graphviz pkgs.subversion ];
tcltk2 = [ pkgs.tcl pkgs.tk ];
2015-11-24 16:17:54 +00:00
tikzDevice = [ pkgs.which pkgs.texlive.combined.scheme-medium ];
2015-02-19 20:53:36 +00:00
gridGraphics = [ pkgs.which ];
adimpro = [ pkgs.which pkgs.xorg.xdpyinfo ];
2016-03-25 07:30:20 +00:00
mzR = [ pkgs.netcdf ];
cluster = [ pkgs.libiconv ];
KernSmooth = [ pkgs.libiconv ];
nlme = [ pkgs.libiconv ];
Matrix = [ pkgs.libiconv ];
mgcv = [ pkgs.libiconv ];
2019-09-23 23:06:26 +00:00
minqa = [ pkgs.libiconv ];
2018-06-20 02:08:29 +00:00
igraph = [ pkgs.libiconv ];
ape = [ pkgs.libiconv ];
expm = [ pkgs.libiconv ];
mnormt = [ pkgs.libiconv ];
2019-09-23 22:59:04 +00:00
pan = [ pkgs.libiconv ];
phangorn = [ pkgs.libiconv ];
quadprog = [ pkgs.libiconv ];
2019-09-23 22:23:25 +00:00
randomForest = [ pkgs.libiconv ];
2019-08-06 12:41:47 +00:00
sundialr = [ pkgs.libiconv ];
2019-09-24 00:36:22 +00:00
ucminf = [ pkgs.libiconv ];
glmnet = [ pkgs.libiconv ];
mvtnorm = [ pkgs.libiconv ];
2020-05-15 03:00:58 +00:00
statmod = [ pkgs.libiconv ];
};
packagesRequireingX = [
"accrual"
"ade4TkGUI"
"analogue"
"analogueExtra"
"AnalyzeFMRI"
"AnnotLists"
"AnthropMMD"
"aplpack"
"asbio"
"BAT"
"BCA"
"betapart"
"BiodiversityR"
"bio_infer"
"bipartite"
"biplotbootGUI"
"blender"
"cairoDevice"
"CCTpack"
"cncaGUI"
"cocorresp"
"CommunityCorrelogram"
"confidence"
"constrainedKriging"
"ConvergenceConcepts"
"cpa"
"DALY"
"dave"
"Deducer"
"DeducerPlugInExample"
"DeducerPlugInScaling"
"DeducerSpatial"
"DeducerSurvival"
"DeducerText"
"Demerelate"
"detrendeR"
"dpa"
"dynamicGraph"
"dynBiplotGUI"
"EasyqpcR"
"EcoVirtual"
"exactLoglinTest"
"fat2Lpoly"
"fbati"
"FD"
"feature"
"FeedbackTS"
"FFD"
"fgui"
"fisheyeR"
"forams"
"forensim"
"FreeSortR"
"fscaret"
"gcmr"
"geomorph"
"geoR"
"georob"
"GGEBiplotGUI"
"gnm"
"GrapheR"
"GroupSeq"
"gsubfn"
"GUniFrac"
"gWidgets2RGtk2"
"gWidgets2tcltk"
"HH"
"HiveR"
"ic50"
"iDynoR"
"in2extRemes"
"iplots"
"isopam"
"IsotopeR"
"JGR"
"KappaGUI"
"likeLTD"
"logmult"
"LS2Wstat"
"MareyMap"
"memgene"
"metacom"
"Meth27QC"
"migui"
"miniGUI"
"mixsep"
"MplusAutomation"
"mpmcorrelogram"
"mritc"
"multgee"
"multibiplotGUI"
"OligoSpecificitySystem"
"onemap"
"OpenRepGrid"
"paleoMAS"
"pbatR"
"PBSadmb"
"PBSmodelling"
"PCPS"
"pez"
"phylotools"
"picante"
"plotSEMM"
"plsRbeta"
"plsRglm"
"PopGenReport"
"poppr"
"powerpkg"
"PredictABEL"
"prefmod"
"PrevMap"
"r4ss"
"RandomFields"
"rareNMtests"
"rAverage"
"Rcmdr"
"RcmdrPlugin_coin"
"RcmdrPlugin_depthTools"
"RcmdrPlugin_DoE"
"RcmdrPlugin_EACSPIR"
"RcmdrPlugin_EBM"
"RcmdrPlugin_EcoVirtual"
"RcmdrPlugin_EZR"
"RcmdrPlugin_FactoMineR"
"RcmdrPlugin_HH"
"RcmdrPlugin_IPSUR"
"RcmdrPlugin_KMggplot2"
"RcmdrPlugin_lfstat"
"RcmdrPlugin_MA"
"RcmdrPlugin_MPAStats"
"RcmdrPlugin_orloca"
"RcmdrPlugin_plotByGroup"
"RcmdrPlugin_pointG"
"RcmdrPlugin_ROC"
"RcmdrPlugin_sampling"
"RcmdrPlugin_SCDA"
"RcmdrPlugin_SLC"
"RcmdrPlugin_sos"
"RcmdrPlugin_steepness"
"RcmdrPlugin_survival"
"RcmdrPlugin_TeachingDemos"
"RcmdrPlugin_temis"
"RcmdrPlugin_UCA"
"recluster"
"relimp"
"rgl"
"RHRV"
"rich"
"RNCEP"
"RSDA"
"RSurvey"
"simba"
"Simile"
"SimpleTable"
"SOLOMON"
"soundecology"
"spatsurv"
"sqldf"
"SSDforR"
"statcheck"
"StatDA"
"STEPCAM"
"stosim"
"strvalidator"
"stylo"
"svDialogstcltk"
"svIDE"
"svSocket"
"svWidgets"
"SYNCSA"
"SyNet"
"tcltk2"
"TestScorer"
"TIMP"
"tkrplot"
"tmap"
"tspmeta"
"TTAinterfaceTrendAnalysis"
"twiddler"
"vcdExtra"
"VecStatGraphs3D"
"vegan"
"vegan3d"
"vegclust"
"x12GUI"
];
packagesToSkipCheck = [
2017-07-01 08:12:30 +00:00
"Rmpi" # tries to run MPI processes
"pbdMPI" # tries to run MPI processes
2020-08-20 06:42:21 +00:00
"data_table" # fails to rename shared library before check
];
# Packages which cannot be installed due to lack of dependencies or other reasons.
2015-02-22 16:45:12 +00:00
brokenPackages = [
];
otherOverrides = old: new: {
2015-07-22 11:42:23 +00:00
stringi = old.stringi.overrideDerivation (attrs: {
postInstall = let
icuName = "icudt52l";
icuSrc = pkgs.fetchzip {
url = "http://static.rexamine.com/packages/${icuName}.zip";
sha256 = "0hvazpizziq5ibc9017i1bb45yryfl26wzfsv05vk9mc1575r6xj";
stripRoot = false;
};
in ''
${attrs.postInstall or ""}
cp ${icuSrc}/${icuName}.dat $out/library/stringi/libs
'';
});
2015-05-15 11:47:27 +00:00
xml2 = old.xml2.overrideDerivation (attrs: {
preConfigure = ''
export LIBXML_INCDIR=${pkgs.libxml2.dev}/include/libxml2
patchShebangs configure
'';
2015-05-15 11:47:27 +00:00
});
rzmq = old.rzmq.overrideDerivation (attrs: {
preConfigure = "patchShebangs configure";
});
clustermq = old.clustermq.overrideDerivation (attrs: {
preConfigure = "patchShebangs configure";
});
2017-01-06 16:11:23 +00:00
Cairo = old.Cairo.overrideDerivation (attrs: {
NIX_LDFLAGS = "-lfontconfig";
});
curl = old.curl.overrideDerivation (attrs: {
2015-09-09 18:29:20 +00:00
preConfigure = "patchShebangs configure";
});
RcppParallel = old.RcppParallel.overrideDerivation (attrs: {
preConfigure = "patchShebangs configure";
});
ggbio = old.ggbio.overrideDerivation (attrs: {
patches = [
(pkgs.fetchpatch {
url = "https://github.com/tengfei/ggbio/commit/b04a9840cf5c0bd0514db2536f2e610bbd364727.patch";
sha256 = "blwtObyIYo1UBWz4nlmcJ8Nyw/n0qwmJrtwFWuoUyMg=";
})
];
});
RcppArmadillo = old.RcppArmadillo.overrideDerivation (attrs: {
patchPhase = "patchShebangs configure";
});
data_table = old.data_table.overrideDerivation (attrs: {
2020-08-20 06:42:21 +00:00
NIX_CFLAGS_COMPILE = attrs.NIX_CFLAGS_COMPILE + " -fopenmp";
patchPhase = "patchShebangs configure";
});
ModelMetrics = old.ModelMetrics.overrideDerivation (attrs: {
NIX_CFLAGS_COMPILE = attrs.NIX_CFLAGS_COMPILE
+ lib.optionalString stdenv.isDarwin " -fopenmp";
});
rpf = old.rpf.overrideDerivation (attrs: {
patchPhase = "patchShebangs configure";
});
BayesXsrc = old.BayesXsrc.overrideDerivation (attrs: {
patches = [ ./patches/BayesXsrc.patch ];
});
Rhdf5lib = old.Rhdf5lib.overrideDerivation (attrs: {
patches = [ ./patches/Rhdf5lib.patch ];
});
rJava = old.rJava.overrideDerivation (attrs: {
preConfigure = ''
export JAVA_CPPFLAGS=-I${pkgs.jdk}/include/
export JAVA_HOME=${pkgs.jdk}
'';
});
JavaGD = old.JavaGD.overrideDerivation (attrs: {
preConfigure = ''
export JAVA_CPPFLAGS=-I${pkgs.jdk}/include/
export JAVA_HOME=${pkgs.jdk}
'';
});
2018-08-19 22:08:28 +00:00
jqr = old.jqr.overrideDerivation (attrs: {
preConfigure = ''
patchShebangs configure
'';
});
pbdZMQ = old.pbdZMQ.overrideDerivation (attrs: {
postPatch = lib.optionalString stdenv.isDarwin ''
for file in R/*.{r,r.in}; do
2018-05-11 14:53:10 +00:00
sed -i 's#system("which \(\w\+\)"[^)]*)#"${pkgs.darwin.cctools}/bin/\1"#g' $file
done
'';
});
Rmpi = old.Rmpi.overrideDerivation (attrs: {
configureFlags = [
"--with-Rmpi-type=OPENMPI"
];
});
Rmpfr = old.Rmpfr.overrideDerivation (attrs: {
configureFlags = [
"--with-mpfr-include=${pkgs.mpfr.dev}/include"
];
});
RVowpalWabbit = old.RVowpalWabbit.overrideDerivation (attrs: {
configureFlags = [
"--with-boost=${pkgs.boost.dev}" "--with-boost-libdir=${pkgs.boost.out}/lib"
];
});
RAppArmor = old.RAppArmor.overrideDerivation (attrs: {
patches = [ ./patches/RAppArmor.patch ];
2019-09-08 23:38:31 +00:00
LIBAPPARMOR_HOME = pkgs.libapparmor;
});
RMySQL = old.RMySQL.overrideDerivation (attrs: {
MYSQL_DIR="${pkgs.libmysqlclient}";
preConfigure = ''
patchShebangs configure
2017-07-09 15:43:03 +00:00
'';
2015-02-19 20:53:36 +00:00
});
devEMF = old.devEMF.overrideDerivation (attrs: {
NIX_CFLAGS_LINK = "-L${pkgs.xorg.libXft.out}/lib -lXft";
2017-01-06 16:58:58 +00:00
NIX_LDFLAGS = "-lX11";
});
slfm = old.slfm.overrideDerivation (attrs: {
PKG_LIBS = "-L${pkgs.blas}/lib -lblas -L${pkgs.lapack}/lib -llapack";
});
SamplerCompare = old.SamplerCompare.overrideDerivation (attrs: {
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 ];
});
openssl = old.openssl.overrideDerivation (attrs: {
2020-10-23 12:40:18 +00:00
preConfigure = ''
patchShebangs configure
'';
2017-10-06 12:01:40 +00:00
PKGCONFIG_CFLAGS = "-I${pkgs.openssl.dev}/include";
PKGCONFIG_LIBS = "-Wl,-rpath,${pkgs.openssl.out}/lib -L${pkgs.openssl.out}/lib -lssl -lcrypto";
});
2019-12-05 04:00:19 +00:00
websocket = old.websocket.overrideDerivation (attrs: {
PKGCONFIG_CFLAGS = "-I${pkgs.openssl.dev}/include";
PKGCONFIG_LIBS = "-Wl,-rpath,${pkgs.openssl.out}/lib -L${pkgs.openssl.out}/lib -lssl -lcrypto";
});
Rserve = old.Rserve.overrideDerivation (attrs: {
patches = [ ./patches/Rserve.patch ];
configureFlags = [
"--with-server" "--with-client"
];
});
nloptr = old.nloptr.overrideDerivation (attrs: {
# Drop bundled nlopt source code. Probably unnecessary, but I want to be
# sure we're using the system library, not this one.
preConfigure = "rm -r src/nlopt_src";
});
V8 = old.V8.overrideDerivation (attrs: {
postPatch = ''
substituteInPlace configure \
--replace " -lv8_libplatform" ""
'';
preConfigure = ''
export INCLUDE_DIR=${pkgs.v8}/include
export LIB_DIR=${pkgs.v8}/lib
patchShebangs configure
'';
});
acs = old.acs.overrideDerivation (attrs: {
preConfigure = ''
patchShebangs configure
'';
});
gdtools = old.gdtools.overrideDerivation (attrs: {
preConfigure = ''
patchShebangs configure
'';
NIX_LDFLAGS = "-lfontconfig -lfreetype";
});
magick = old.magick.overrideDerivation (attrs: {
preConfigure = ''
patchShebangs configure
'';
});
libgeos = old.libgeos.overrideDerivation (attrs: {
preConfigure = ''
patchShebangs configure
'';
});
protolite = old.protolite.overrideDerivation (attrs: {
preConfigure = ''
patchShebangs configure
'';
});
rpanel = old.rpanel.overrideDerivation (attrs: {
preConfigure = ''
export TCLLIBPATH="${pkgs.bwidget}/lib/bwidget${pkgs.bwidget.version}"
'';
TCLLIBPATH = "${pkgs.bwidget}/lib/bwidget${pkgs.bwidget.version}";
});
RPostgres = old.RPostgres.overrideDerivation (attrs: {
preConfigure = ''
export INCLUDE_DIR=${pkgs.postgresql}/include
export LIB_DIR=${pkgs.postgresql.lib}/lib
patchShebangs configure
'';
});
OpenMx = old.OpenMx.overrideDerivation (attrs: {
preConfigure = ''
patchShebangs configure
'';
});
odbc = old.odbc.overrideDerivation (attrs: {
preConfigure = ''
patchShebangs configure
'';
});
x13binary = old.x13binary.overrideDerivation (attrs: {
preConfigure = ''
patchShebangs configure
'';
});
geojsonio = old.geojsonio.overrideDerivation (attrs: {
buildInputs = [ cacert ] ++ attrs.buildInputs;
});
rstan = old.rstan.overrideDerivation (attrs: {
NIX_CFLAGS_COMPILE = "${attrs.NIX_CFLAGS_COMPILE} -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION";
});
2018-03-10 03:01:49 +00:00
mongolite = old.mongolite.overrideDerivation (attrs: {
preConfigure = ''
patchShebangs configure
'';
PKGCONFIG_CFLAGS = "-I${pkgs.openssl.dev}/include -I${pkgs.cyrus_sasl.dev}/include -I${pkgs.zlib.dev}/include";
PKGCONFIG_LIBS = "-Wl,-rpath,${pkgs.openssl.out}/lib -L${pkgs.openssl.out}/lib -L${pkgs.cyrus_sasl.out}/lib -L${pkgs.zlib.out}/lib -lssl -lcrypto -lsasl2 -lz";
});
ps = old.ps.overrideDerivation (attrs: {
preConfigure = "patchShebangs configure";
});
rlang = old.rlang.overrideDerivation (attrs: {
preConfigure = "patchShebangs configure";
});
systemfonts = old.systemfonts.overrideDerivation (attrs: {
preConfigure = "patchShebangs configure";
});
littler = old.littler.overrideAttrs (attrs: with pkgs; {
2021-03-14 18:12:53 +00:00
buildInputs = [ pcre xz zlib bzip2 icu which ] ++ attrs.buildInputs;
postInstall = ''
install -d $out/bin $out/share/man/man1
ln -s ../library/littler/bin/r $out/bin/r
ln -s ../library/littler/bin/r $out/bin/lr
ln -s ../../../library/littler/man-page/r.1 $out/share/man/man1
# these won't run without special provisions, so better remove them
rm -r $out/library/littler/script-tests
'';
});
};
in
self