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R: Update CRAN and bioconductor packages

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This commit is contained in:
Alex Branham
2020-01-23 21:22:55 -05:00
parent 385b9aee08
commit e206c37550
3 changed files with 1760 additions and 1745 deletions
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23
pkgs/development/r-modules/default.nix
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@@ -264,7 +264,6 @@ let
gmp = [ pkgs.gmp.dev ];
graphscan = [ pkgs.gsl_1 ];
gsl = [ pkgs.gsl_1 ];
h5 = [ pkgs.hdf5-cpp pkgs.which ];
haven = [ pkgs.libiconv pkgs.zlib.dev ];
h5vc = [ pkgs.zlib.dev ];
HiCseg = [ pkgs.gsl_1 ];
@@ -293,7 +292,6 @@ let
phytools = [ pkgs.which ];
PKI = [ pkgs.openssl.dev ];
png = [ pkgs.libpng.dev ];
PopGenome = [ pkgs.zlib.dev ];
proj4 = [ pkgs.proj ];
protolite = [ pkgs.protobuf ];
qtbase = [ pkgs.qt4 ];
@@ -317,7 +315,6 @@ let
Rhdf5lib = [ pkgs.zlib ];
Rhpc = [ pkgs.zlib pkgs.bzip2.dev pkgs.icu pkgs.lzma.dev pkgs.openmpi pkgs.pcre.dev ];
Rhtslib = [ pkgs.zlib.dev pkgs.automake pkgs.autoconf ];
RJaCGH = [ pkgs.zlib.dev ];
rjags = [ pkgs.jags ];
rJava = [ pkgs.zlib pkgs.bzip2.dev pkgs.icu pkgs.lzma.dev pkgs.pcre.dev pkgs.jdk pkgs.libzip ];
Rlibeemd = [ pkgs.gsl_1 ];
@@ -367,7 +364,6 @@ let
udunits2 = [ pkgs.udunits pkgs.expat ];
units = [ pkgs.udunits ];
V8 = [ pkgs.v8_3_14 ];
VBLPCM = [ pkgs.gsl_1 ];
WhopGenome = [ pkgs.zlib.dev ];
XBRL = [ pkgs.zlib pkgs.libxml2.dev ];
xml2 = [ pkgs.libxml2.dev ] ++ lib.optionals stdenv.isDarwin [ pkgs.perl ];
@@ -392,7 +388,6 @@ let
# sort -t '=' -k 2
svKomodo = [ pkgs.which ];
nat = [ pkgs.which ];
nat_nblast = [ pkgs.which ];
nat_templatebrains = [ pkgs.which ];
pbdZMQ = lib.optionals stdenv.isDarwin [ pkgs.darwin.binutils ];
RMark = [ pkgs.which ];
@@ -413,7 +408,6 @@ let
fftw = [ pkgs.pkgconfig ];
geoCount = [ pkgs.pkgconfig ];
gdtools = [ pkgs.pkgconfig ];
JuniperKernel = lib.optionals stdenv.isDarwin [ pkgs.darwin.binutils ];
jqr = [ pkgs.jq.lib ];
kza = [ pkgs.pkgconfig ];
magick = [ pkgs.pkgconfig ];
@@ -435,8 +429,6 @@ let
rPython = [ pkgs.which ];
gridGraphics = [ pkgs.which ];
adimpro = [ pkgs.which pkgs.xorg.xdpyinfo ];
PET = [ pkgs.which pkgs.xorg.xdpyinfo pkgs.imagemagick ];
dti = [ pkgs.which pkgs.xorg.xdpyinfo pkgs.imagemagick ];
mzR = [ pkgs.netcdf ];
cluster = [ pkgs.libiconv ];
KernSmooth = [ pkgs.libiconv ];
@@ -524,7 +516,6 @@ let
"fscaret"
"fSRM"
"gcmr"
"GeoGenetix"
"geomorph"
"geoR"
"geoRglm"
@@ -571,7 +562,6 @@ let
"mritc"
"multgee"
"multibiplotGUI"
"nodiv"
"OligoSpecificitySystem"
"onemap"
"OpenRepGrid"
@@ -644,7 +634,6 @@ let
"rsgcc"
"RSurvey"
"RunuranGUI"
"sharpshootR"
"simba"
"Simile"
"SimpleTable"
@@ -668,7 +657,6 @@ let
"SYNCSA"
"SyNet"
"tcltk2"
"TED"
"TestScorer"
"TIMP"
"titan"
@@ -768,17 +756,6 @@ let
'';
});
JuniperKernel = old.JuniperKernel.overrideDerivation (attrs: {
postPatch = lib.optionalString stdenv.isDarwin ''
for file in {R,src}/*.R; do
sed -i 's#system("which \(otool\|install_name_tool\)"[^)]*)#"${pkgs.darwin.cctools}/bin/\1"#g' $file
done
'';
preConfigure = ''
patchShebangs configure
'';
});
jqr = old.jqr.overrideDerivation (attrs: {
preConfigure = ''
patchShebangs configure