R 3.5.1 and packages on cluster

In the KU HPC cluster, we now have a module for R-3.5.1 and there is a CRMDA
module, Rstats, that will link together R with the collection of packages I maintain.

The list of packages that were installed today is below. We have a few that won't compile
with the available resources (tkrplot), but the big happy news is we have success with
Rstan for the first time in quite a while. Special thanks to help from rstan-dev forums.

How to use this:

In your ~/.bashrc, add these lines. Or log in on a compute node and run these lines
interactively:

$ export PATH=/panfs/pfs.local/work/crmda/tools/bin:$PATH
$ source crmda_env-3.5.sh

After that, you should see:

$ module list

Currently Loaded Modules:
  1) legacy       3) compiler/gcc/6.3   5) java/1.8.0_131   7) icu/59.1      9) Rstats/3.5.1
  2) emacs/24.5   4) openmpi/1.10       6) xz/5.2.3         8) tcltk/8.6.6  10) mplus/7.3

Packages installed today

/panfs/pfs.local/software/install/MRO/3.5.1/ropen/3.5.1/lib64/R/library
base    3.5.1
boot    1.3-20
checkpoint  0.4.4
class   7.3-14
cluster 2.0.7-1
codetools   0.2-15
compiler    3.5.1
curl    3.2
datasets    3.5.1
deployrRserve   9.0.0
doParallel  1.0.13
foreach 1.5.0
foreign 0.8-71
graphics    3.5.1
grDevices   3.5.1
grid    3.5.1
iterators   1.0.10
jsonlite    1.5
KernSmooth  2.23-15
lattice 0.20-35
MASS    7.3-50
Matrix  1.2-14
methods 3.5.1
mgcv    1.8-24
MicrosoftR  3.5.1.3
nlme    3.1-137
nnet    7.3-12
parallel    3.5.1
png 0.1-7
R6  2.2.2
RevoIOQ 10.0.0
RevoMods    11.0.1
RevoUtils   11.0.1
RevoUtilsMath   11.0.0
rpart   4.1-13
RUnit   0.4.32
sp  1.3-1
spatial 7.3-11
splines 3.5.1
stats   3.5.1
stats4  3.5.1
survival    2.42-6
tcltk   3.5.1
tools   3.5.1
utils   3.5.1
/panfs/pfs.local/work/crmda/tools/mro/3.5/site-library
abind   1.4-5
acepack 1.4.1
actuar  2.3-1
ada 2.0-5
ade4    1.7-13
ADGofTest   0.3
AER 1.2-5
akima   0.6-2
alr3    2.0.8
amap    0.8-16
Amelia  1.7.5
aod 1.3
ape 5.2
aplpack 1.3.2
arm 1.10-1
arules  1.6-1
assertthat  0.2.0
backports   1.1.2
base64enc   0.1-3
bayesm  3.1-0.1
bcp 4.0.3
bdsmatrix   1.3-3
bestglm 0.37
betareg 3.1-1
BH  1.66.0-1
bibtex  0.4.2
biglm   0.9-1
bindr   0.1.1
bindrcpp    0.2.2
bit 1.1-14
bit64   0.9-7
bitops  1.0-6
BMA 3.18.9
bnlearn 4.4
BradleyTerry2   1.0-8
brew    1.0-6
brglm   0.6.1
broom   0.5.0
Cairo   1.5-9
cairoDevice 2.25
callr   3.0.0
car 3.0-2
carData 3.0-2
caret   6.0-80
caTools 1.17.1.1
cellranger  1.1.0
censReg 0.5-26
checkmate   1.8.5
chron   2.3-53
cli 1.0.1
clipr   0.4.1
clue    0.3-56
clv 0.3-2.1
cocorresp   0.3-0
coda    0.19-2
coin    1.2-2
colorspace  1.3-2
combinat    0.0-8
commonmark  1.6
copula  0.999-18
corpcor 1.6.9
crayon  1.3.4
crosstalk   1.0.0
cubature    1.4-1
Cubist  0.2.2
CVST    0.2-2
data.table  1.11.8
DBI 1.0.0
dbplyr  1.2.2
DCluster    0.2-7
ddalpha 1.3.4
deldir  0.1-15
DEoptimR    1.0-8
desc    1.2.0
descr   1.1.4
Devore7 0.7.6
DiagrammeR  1.0.0
DiceKriging 1.5.6
dichromat   2.0-0
digest  0.6.18
dimRed  0.1.0
diptest 0.75-7
distr   2.7.0
dlm 1.1-5
doBy    4.6-2
doMC    1.3.5
doMPI   0.2.2
doSNOW  1.0.16
dotCall64   1.0-0
downloader  0.4
dplyr   0.7.7
DRR 0.0.3
dse 2015.12-1
e1071   1.7-0
earth   4.6.3
Ecdat   0.3-1
Ecfun   0.1-7
ecodist 2.0.1
effects 4.0-3
egcm    1.0.12
eha 2.6.0
eiPack  0.1-7
emplik  1.0-4.3
ENmisc  1.2-7
estimability    1.3
evaluate    0.12
expint  0.1-5
expm    0.999-3
fansi   0.4.0
faraway 1.0.7
fastICA 1.2-1
fastmatch   1.1-0
fBasics 3042.89
fda 2.4.8
ffmanova    0.2-2
fields  9.6
flexmix 2.3-14
forcats 0.3.0
formatR 1.5
Formula 1.2-3
forward 1.0.4
fs  1.2.6
fUnitRoots  3042.79
futile.logger   1.4.3
futile.options  1.0.1
gam 1.16
gamlss  5.1-2
gamlss.data 5.1-0
gamlss.dist 5.1-0
gamm4   0.2-5
gbm 2.1.4
gclus   1.3.1
gdata   2.18.0
gee 4.13-19
geepack 1.2-1
geometry    0.3-6
geoR    1.7-5.2.1
geoRglm 0.9-11
ggm 2.3
ggplot2 3.1.0
glmc    0.2-4
glmmBUGS    2.4.2
glmmML  1.0.3
glmnet  2.0-16
glmpath 0.98
glue    1.3.0
gmodels 2.18.1
gmp 0.5-13.2
goftest 1.1-1
gower   0.1.2
GPArotation 2014.11-1
gpclib  1.5-5
grf 0.10.1
gridBase    0.4-7
gridExtra   2.3
grpreg  3.2-0
gsl 1.9-10.3
gss 2.1-9
gsubfn  0.7
gtable  0.2.0
gtools  3.8.1
haven   1.1.2
hexbin  1.27.2
highr   0.7
HistData    0.8-4
Hmisc   4.1-1
hms 0.4.2
htmlTable   1.12
htmltools   0.3.6
htmlwidgets 1.3
httpuv  1.4.5
httr    1.3.1
hunspell    2.9
HyperbolicDist  0.6-2
igraph  1.2.2
ineq    0.2-13
influence.ME    0.9-9
influenceR  0.1.0
inline  0.3.15
inum    1.0-0
iplots  1.1-7.1
ipred   0.9-8
irlba   2.3.2
Iso 0.0-17
ISOcodes    2018.06.29
ISwR    2.0-7
itertools   0.1-3
janeaustenr 0.1.5
JavaGD  0.6-1
JGR 1.8-6
JM  1.4-8
JMdesign    1.1
jomo    2.6-4
jpeg    0.1-8
Kendall 2.2
kernlab 0.9-27
knitr   1.20
kutils  1.51
labeling    0.3
laeken  0.4.6
lambda.r    1.2.3
languageR   1.4.1
lars    1.2
later   0.7.5
latticeExtra    0.6-28
lava    1.6.3
lavaan  0.6-3
lavaan.survey   1.1.3.1
lazyeval    0.2.1
leaps   3.0
LearnBayes  2.15.1
libcoin 1.0-1
lme4    1.1-18-1
lmec    1.0
lmerTest    3.0-1
lmeSplines  1.1-10
lmm 1.2
lmtest  0.9-36
locfit  1.5-9.1
logspline   2.1.11
longitudinal    1.1.12
longitudinalData    2.4.1
loo 2.0.0
lpSolve 5.6.13
ltm 1.1-1
lubridate   1.7.4
magic   1.5-9
magrittr    1.5
manipulate  1.0.1
manipulateWidget    0.10.0
maps    3.3.0
maptools    0.9-4
markdown    0.8
Matching    4.9-3
MatchIt 3.0.2
matrixcalc  1.0-3
MatrixModels    0.4-1
matrixStats 0.54.0
maxLik  1.3-4
mboost  2.9-1
mcgibbsit   1.1.0
mclust  5.4.1
mcmc    0.9-5
MCMCglmm    2.26
MCMCpack    1.4-4
MCPAN   1.1-21
mda 0.4-10
mediation   4.4.6
memisc  0.99.14.12
memoise 1.1.0
MEMSS   0.9-2
mi  1.0
mice    3.3.0
micEcon 0.6-14
microbenchmark  1.4-6
mime    0.6
miniUI  0.1.1.1
minqa   1.2.4
misc3d  0.8-4
miscTools   0.6-22
mitml   0.3-6
mitools 2.3
mix 1.0-10
mixtools    1.1.0
mlbench 2.1-1
mnormt  1.5-5
MNP 3.1-0
ModelMetrics    1.2.2
modelr  0.1.2
modeltools  0.2-22
MplusAutomation 0.7-2
MPV 1.53
msm 1.6.6
multcomp    1.4-8
munsell 0.5.0
mvbutils    2.7.4.1
mvProbit    0.1-8
mvtnorm 1.0-8
network 1.13.0.1
nloptr  1.2.1
NLP 0.2-0
NMF 0.21.0
nnls    1.4
nor1mix 1.2-3
norm    1.0-9.5
nortest 1.0-4
np  0.60-9
numDeriv    2016.8-1
nws 1.7.0.1
openssl 1.0.2
openxlsx    4.1.0
ordinal 2018.8-25
orthopolynom    1.0-5
pan 1.6
pander  0.6.3
partDSA 0.9.14
party   1.3-1
partykit    1.2-2
PASWR   1.1
pbivnorm    0.6.0
pbkrtest    0.4-7
PBSmapping  2.70.5
pcaPP   1.9-73
permute 0.9-4
pillar  1.3.0
pixmap  0.4-11
pkgbuild    1.0.2
pkgconfig   2.0.2
pkgKitten   0.1.4
pkgload 1.0.2
pkgmaker    0.27
plm 1.6-6
plogr   0.2.0
plotmo  3.5.0
plotrix 3.7-4
pls 2.7-0
plyr    1.8.4
pmml    1.5.6
pmmlTransformations 1.3.2
polspline   1.1.13
polyclip    1.9-1
polycor 0.7-9
polynom 1.3-9
PolynomF    1.0-2
portableParallelSeeds   0.97
ppcor   1.1
pracma  2.1.8
praise  1.0.0
prettyunits 1.0.2
processx    3.2.0
prodlim 2018.04.18
profileModel    0.5-9
promises    1.0.1
proto   1.0.0
proxy   0.4-22
ps  1.2.1
pscl    1.5.2
psidR   1.9
pspline 1.0-18
psych   1.8.10
purrr   0.2.5
quadprog    1.5-5
quantmod    0.4-13
quantreg    5.36
qvcalc  0.9-1
R2HTML  2.3.2
R2OpenBUGS  3.2-3.2
R6  2.3.0
RandomFields    3.1.50
RandomFieldsUtils   0.3.25
randomForest    4.6-14
randomForestSRC 2.7.0
rattle  5.2.0
rbenchmark  1.0.0
rbugs   0.5-9
Rcmdr   2.5-1
RcmdrMisc   2.5-1
RColorBrewer    1.1-2
Rcpp    0.12.19
RcppArmadillo   0.9.100.5.0
RcppEigen   0.3.3.4.0
RcppRoll    0.3.0
RCurl   1.95-4.11
Rd2roxygen  1.7
rda 1.0.2-2.1
readr   1.1.1
readstata13 0.9.2
readxl  1.1.0
recipes 0.1.3
registry    0.5
relimp  1.0-5
rematch 1.0.1
repr    0.15.0
reprex  0.2.1
reshape 0.8.8
reshape2    1.4.3
rgexf   0.15.3
rgl 0.99.16
RGtk2   2.20.35
rio 0.5.10
rJava   0.9-10
rlang   0.3.0.1
rlecuyer    0.3-4
rmarkdown   1.10
Rmpi    0.6-7
rms 5.1-2
rngtools    1.3.1
robustbase  0.93-3
rockchalk   1.8.126
Rook    1.1-1
roxygen2    6.1.1
rpart.plot  3.0.5
rpf 0.59
rprojroot   1.3-2
rrcov   1.4-4
rstan   2.18.1
rstudioapi  0.8
RSvgDevice  0.6.4.4
rvest   0.3.2
sandwich    2.5-0
SAScii  1.0
SASmixed    1.0-4
scales  1.0.0
scatterplot3d   0.3-41
segmented   0.5-3.0
selectr 0.4-1
sem 3.1-9
SemiPar 1.0-4.2
semTools    0.5-1
setRNG  2013.9-1
sets    1.0-18
sfsmisc 1.1-2
shapefiles  0.7
shiny   1.2.0
simsem  0.5-14
slam    0.1-43
sm  2.2-5.6
smoothSurv  2.0.1
sna 2.4
snow    0.4-3
SnowballC   0.5.1
snowFT  1.6-0
SoDA    1.0-6
sourcetools 0.1.7
spam    2.2-0
SparseM 1.77
spatialCovariance   0.6-9
spatialkernel   0.4-23
spatstat    1.57-1
spatstat.data   1.4-0
spatstat.utils  1.13-0
spData  0.2.9.4
spdep   0.7-9
splancs 2.01-40
SQUAREM 2017.10-1
stabledist  0.7-1
stabs   0.6-3
StanHeaders 2.18.0
startupmsg  0.9.5
StatDataML  1.0-26
statmod 1.4.30
statnet.common  4.1.4
stepwise    0.3
stopwords   0.9.0
stringi 1.2.4
stringr 1.3.1
strucchange 1.5-1
subselect   0.14
survey  3.34
systemfit   1.1-22
tables  0.8.4
tcltk2  1.2-11
TeachingDemos   2.10
tensor  1.5
tensorA 0.36.1
testthat    2.0.1
texreg  1.36.23
tfplot  2015.12-1
tframe  2015.12-1
TH.data 1.0-9
tibble  1.4.2
tidyr   0.8.2
tidyselect  0.2.5
tidytext    0.2.0
tidyverse   1.2.1
timeDate    3043.102
timeSeries  3042.102
tinytex 0.9
tis 1.34
tm  0.7-5
tokenizers  0.2.1
topicmodels 0.2-7
tree    1.0-39
triangle    0.11
trimcluster 0.1-2.1
trust   0.1-7
tseries 0.10-45
TTR 0.23-4
ucminf  1.1-4
urca    1.3-0
UsingR  2.0-6
utf8    1.1.4
vcd 1.4-4
vegan   2.5-3
VGAM    1.0-6
VIM 4.7.0
viridis 0.5.1
viridisLite 0.3.0
visNetwork  2.0.4
waveslim    1.7.5
webshot 0.5.1
whisker 0.3-2
withr   2.1.2
wnominate   1.2.5
xfun    0.4
xgboost 0.71.2
XML 3.98-1.16
xml2    1.2.0
xtable  1.8-3
xts 0.11-2
yaml    2.2.0
Zelig   5.1.6
zip 1.0.0
zipfR   0.6-10
zoo 1.8-4
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