We had a couple of new package requests. I'm taking the occasion, as we approach the holiday celebrating American independence, to update the other R packages. There are still complications building newer rstan, I log in every month or so and try for a few hours. Otherwise I think we are working:
Remember, that packages you have in your HOME folder, such as R/x86/3.3 or R/x86/3.4 will PRECEDE the ones I provide systemwide. So if you have an old one, then that's what R will use for you. Because your packages are in version-specific folder (note 3.3 and 3.4 on end of path), it WILL be necessary for you to install packages for R 3.4 if you update the environment file (described next).
It is important to set your R selection in the environment (fully described here: R Modules: Super Exciting New Updates) because, if you don't, then you might launch a parallel job that will use different/inconsistent packages and versions of R on different nodes. This was a very hard-to-understand problem in the new cluster. So configure one of the environment scripts "crmda_env.sh" (for R 3.3) and "crmda_env-test.sh" (for R 3.4). I am thinking hard on what new pleasant names we could use for those scripts.
For R-3.4, the package set that comes along with the R environment we provide (via crmda_env-test.sh) are in the second block here, while the ones provided by central sysadmin are in the first block (with indicated directory). The ones in the first set, which I do not administer, are out of date. There's a philosophical problem here. Some people think the packages should never be updated for replication purposes, but generally I tend to want the newest. If users want older packages, they can install in $HOME/R, of course. The out-of-date-packages problem is more serious in R-3.3 that 3.4, and maybe users ought to adopt that anyway.
Right now, here is the situation:
/panfs/pfs.local/software/install/MRO/3.4.0/microsoft-r/3.4/lib64/R/library
KernSmooth 2.23-15
MASS 7.3-47
Matrix 1.2-9
MicrosoftR 3.4.0.0068
R6 2.2.0
RUnit 0.4.26
RevoIOQ 8.0.7
RevoMods 11.0.0
RevoUtils 10.0.4
RevoUtilsMath 10.0.0
base 3.4.0
boot 1.3-19
checkpoint 0.4.0
class 7.3-14
cluster 2.0.6
codetools 0.2-15
compiler 3.4.0
curl 2.6
datasets 3.4.0
deployrRserve 9.0.0
doParallel 1.0.10
foreach 1.4.4
foreign 0.8-67
grDevices 3.4.0
graphics 3.4.0
grid 3.4.0
iterators 1.0.8
jsonlite 1.4
lattice 0.20-35
methods 3.4.0
mgcv 1.8-17
nlme 3.1-131
nnet 7.3-12
parallel 3.4.0
png 0.1-7
rpart 4.1-11
spatial 7.3-11
splines 3.4.0
stats 3.4.0
stats4 3.4.0
survival 2.41-3
tcltk 3.4.0
tools 3.4.0
utils 3.4.0
/panfs/pfs.local/work/crmda/tools/mro/3.4/site-library
ADGofTest 0.3
AER 1.2-5
Amelia 1.7.5
BH 1.66.0-1
BMA 3.18.8
BradleyTerry2 1.0-8
CVST 0.2-2
Cairo 1.5-9
Cubist 0.2.2
DBI 1.0.0
DCluster 0.2-7
DEoptimR 1.0-8
DRR 0.0.3
Devore7 0.7.6
DiagrammeR 1.0.0
DiceKriging 1.5.5
ENmisc 1.2-7
Ecdat 0.3-1
Ecfun 0.1-7
Formula 1.2-3
GPArotation 2014.11-1
HistData 0.8-4
Hmisc 4.1-1
HyperbolicDist 0.6-2
ISOcodes 2018.06.29
ISwR 2.0-7
Iso 0.0-17
JM 1.4-8
JMdesign 1.1
JavaGD 0.6-1
Kendall 2.2
Lahman 6.0-0
LearnBayes 2.15.1
MCMCpack 1.4-3
MCPAN 1.1-21
MEMSS 0.9-2
MNP 3.1-0
MPV 1.53
MatchIt 3.0.2
Matching 4.9-3
MatrixModels 0.4-1
ModelMetrics 1.1.0
MplusAutomation 0.7-2
NLP 0.1-11
NMF 0.21.0
PASWR 1.1
PolynomF 1.0-2
R2HTML 2.3.2
R2OpenBUGS 3.2-3.2
R6 2.2.2
RColorBrewer 1.1-2
RCurl 1.95-4.10
RGtk2 2.20.35
RMySQL 0.10.15
RPostgreSQL 0.6-2
RSQLite 2.1.1
RSvgDevice 0.6.4.4
RUnit 0.4.32
RandomFields 3.1.50
RandomFieldsUtils 0.3.25
Rcmdr 2.4-4
RcmdrMisc 1.0-10
Rcpp 0.12.17
RcppArmadillo 0.8.600.0.0
RcppEigen 0.3.3.4.0
RcppRoll 0.3.0
Rd2roxygen 1.6.2
Rmpi 0.6-7
Rook 1.1-1
SAScii 1.0
SASmixed 1.0-4
SQUAREM 2017.10-1
SemiPar 1.0-4.2
SnowballC 0.5.1
SoDA 1.0-6
SparseM 1.77
StanHeaders 2.17.2
StatDataML 1.0-26
SweaveListingUtils 0.7.7
TH.data 1.0-8
TTR 0.23-3
TeachingDemos 2.10
UsingR 2.0-6
VGAM 1.0-5
VIM 4.7.0
XML 3.98-1.11
Zelig 5.1.6
abind 1.4-5
acepack 1.4.1
actuar 2.3-1
ada 2.0-5
ade4 1.7-11
akima 0.6-2
alr3 2.0.8
amap 0.8-16
aod 1.3
ape 5.1
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 4.0.2
bdsmatrix 1.3-3
bestglm 0.37
betareg 3.1-0
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
blob 1.1.1
bnlearn 4.3
brew 1.0-6
brglm 0.6.1
broom 0.4.4
caTools 1.17.1
cairoDevice 2.25
callr 2.0.4
car 3.0-0
carData 3.0-1
caret 6.0-80
cellranger 1.1.0
censReg 0.5-26
checkmate 1.8.5
chron 2.3-52
cli 1.0.0
clipr 0.4.1
clue 0.3-55
clv 0.3-2.1
cocorresp 0.3-0
coda 0.19-1
coin 1.2-2
colorspace 1.3-2
combinat 0.0-8
copula 0.999-18
corpcor 1.6.9
covr 3.1.0
crayon 1.3.4
crosstalk 1.0.0
cubature 1.4
data.table 1.11.4
dbplyr 1.2.1
ddalpha 1.3.4
debugme 1.1.0
deldir 0.1-15
descr 1.1.4
dichromat 2.0-0
digest 0.6.15
dimRed 0.1.0
diptest 0.75-7
distr 2.6.2
dlm 1.1-5
doBy 4.6-1
doMC 1.3.5
doMPI 0.2.2
doParallel 1.0.11
doSNOW 1.0.16
dotCall64 0.9-5.2
downloader 0.4
dplyr 0.7.6
dse 2015.12-1
e1071 1.6-8
earth 4.6.3
ecodist 2.0.1
effects 4.0-2
egcm 1.0.12
eha 2.5.1
eiPack 0.1-7
emplik 1.0-3
estimability 1.3
evaluate 0.10.1
expint 0.1-5
expm 0.999-2
fBasics 3042.89
fUnitRoots 3042.79
faraway 1.0.7
fastICA 1.2-1
fastmatch 1.1-0
fda 2.4.7
ffmanova 0.2-2
fields 9.6
flexmix 2.3-14
forcats 0.3.0
foreach 1.4.4
formatR 1.5
forward 1.0.3
gam 1.15
gamlss 5.1-0
gamlss.data 5.0-1
gamlss.dist 5.0-6
gamm4 0.2-5
gbm 2.1.3
gclus 1.3.1
gdata 2.18.0
gee 4.13-19
geepack 1.2-1
geoR 1.7-5.2
geoRglm 0.9-11
geometry 0.3-6
ggm 2.3
ggplot2 2.2.1
glmc 0.2-4
glmmBUGS 2.4.2
glmmML 1.0.3
glmnet 2.0-16
glmpath 0.98
glue 1.2.0
gmodels 2.18.1
gmp 0.5-13.1
gower 0.1.2
gpclib 1.5-5
grf 0.10.0
gridBase 0.4-7
gridExtra 2.3
grpreg 3.1-4
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
hms 0.4.2
htmlTable 1.12
htmltools 0.3.6
htmlwidgets 1.2
httpuv 1.4.4.2
httr 1.3.1
hunspell 2.9
igraph 1.2.1
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 0.9-6
irlba 2.3.2
iterators 1.0.9
itertools 0.1-3
janeaustenr 0.1.5
jomo 2.6-2
jpeg 0.1-8
jsonlite 1.5
kernlab 0.9-26
knitr 1.20
kutils 1.46
labeling 0.3
laeken 0.4.6
languageR 1.4.1
lars 1.2
later 0.7.3
latticeExtra 0.6-28
lava 1.6.2
lavaan 0.6-1
lavaan.survey 1.1.3.1
lazyeval 0.2.1
leaps 3.0
libcoin 1.0-1
lme4 1.1-17
lmeSplines 1.1-10
lmec 1.0
lmm 1.2
lmtest 0.9-36
locfit 1.5-9.1
logspline 2.1.11
longitudinal 1.1.12
longitudinalData 2.4.1
lpSolve 5.6.13
ltm 1.1-1
lubridate 1.7.4
magic 1.5-8
magrittr 1.5
manipulate 1.0.1
manipulateWidget 0.10.0
maps 3.3.0
maptools 0.9-2
markdown 0.8
matrixcalc 1.0-3
maxLik 1.3-4
mboost 2.9-0
mcgibbsit 1.1.0
mclust 5.4.1
mcmc 0.9-5
mda 0.4-10
memisc 0.99.14.9
memoise 1.1.0
mi 1.0
micEcon 0.6-14
mice 3.1.0
microbenchmark 1.4-4
mime 0.5
miniUI 0.1.1.1
minqa 1.2.4
misc3d 0.8-4
miscTools 0.6-22
mitml 0.3-5
mitools 2.3
mix 1.0-10
mixtools 1.1.0
mlbench 2.1-1
mnormt 1.5-5
modelr 0.1.2
modeltools 0.2-21
msm 1.6.6
multcomp 1.4-8
munsell 0.5.0
mvProbit 0.1-8
mvbutils 2.7.4.1
mvtnorm 1.0-8
network 1.13.0.1
nloptr 1.0.4
nnls 1.4
nor1mix 1.2-3
norm 1.0-9.5
nortest 1.0-4
np 0.60-8
numDeriv 2016.8-1
nws 1.7.0.1
nycflights13 1.0.0
openssl 1.0.1
openxlsx 4.1.0
ordinal 2018.4-19
orthopolynom 1.0-5
pan 1.6
pander 0.6.1
partDSA 0.9.14
party 1.3-0
partykit 1.2-2
pbivnorm 0.6.0
pbkrtest 0.4-7
pcaPP 1.9-73
permute 0.9-4
pillar 1.2.3
pixmap 0.4-11
pkgKitten 0.1.4
pkgconfig 2.0.1
pkgmaker 0.27
plm 1.6-6
plogr 0.2.0
plotmo 3.4.1
plotrix 3.7-2
pls 2.6-0
plyr 1.8.4
pmml 1.5.4
pmmlTransformations 1.3.1
png 0.1-7
polspline 1.1.13
polycor 0.7-9
polynom 1.3-9
portableParallelSeeds 0.97
ppcor 1.1
pracma 2.1.4
praise 1.0.0
prettyunits 1.0.2
processx 3.1.0
prodlim 2018.04.18
profileModel 0.5-9
promises 1.0.1
proto 1.0.0
proxy 0.4-22
pscl 1.5.2
psidR 1.5
pspline 1.0-18
psych 1.8.4
purrr 0.2.5
quadprog 1.5-5
quantmod 0.4-13
quantreg 5.36
qvcalc 0.9-1
rJava 0.9-10
randomForest 4.6-14
randomForestSRC 2.6.1
rattle 5.1.0
rbenchmark 1.0.0
rbugs 0.5-9
rda 1.0.2-2
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 0.2.0
reshape 0.8.7
reshape2 1.4.3
rex 1.1.2
rgenoud 5.8-2.0
rgexf 0.15.3
rgl 0.99.16
rio 0.5.10
rlang 0.2.1
rlecuyer 0.3-4
rmarkdown 1.10
rms 5.1-2
rngtools 1.3.1
robustbase 0.93-1
rockchalk 1.8.111
roxygen2 6.0.1
rpart.plot 2.2.0
rpf 0.59
rprojroot 1.3-2
rrcov 1.4-4
rstan 2.17.3
rstudioapi 0.7
rvest 0.3.2
sandwich 2.4-0
scales 0.5.0
scatterplot3d 0.3-41
segmented 0.5-3.0
selectr 0.4-1
sem 3.1-9
semTools 0.5-0
setRNG 2013.9-1
sets 1.0-18
sfsmisc 1.1-2
shapefiles 0.7
shiny 1.1.0
simsem 0.5-14
slam 0.1-43
sm 2.2-5.5
smoothSurv 2.0
sna 2.4
snow 0.4-2
snowFT 1.6-0
sourcetools 0.1.7
sp 1.3-1
spData 0.2.9.0
spam 2.2-0
spatialCovariance 0.6-9
spdep 0.7-7
splancs 2.01-40
stabledist 0.7-1
stabs 0.6-3
startupmsg 0.9.4
statmod 1.4.30
statnet.common 4.1.4
stepwise 0.3
stopwords 0.9.0
stringi 1.2.3
stringr 1.3.1
strucchange 1.5-1
subselect 0.14
survey 3.33-2
systemfit 1.1-22
tables 0.8.4
tcltk2 1.2-11
tensorA 0.36
testthat 2.0.0
texreg 1.36.23
tfplot 2015.12-1
tframe 2015.12-1
tibble 1.4.2
tidyr 0.8.1
tidyselect 0.2.4
tidytext 0.1.9
tidyverse 1.2.1
timeDate 3043.102
timeSeries 3042.102
tinytex 0.5
tis 1.34
tm 0.7-4
tokenizers 0.2.1
topicmodels 0.2-7
tree 1.0-39
triangle 0.11
trimcluster 0.1-2
trust 0.1-7
tseries 0.10-45
ucminf 1.1-4
urca 1.3-0
utf8 1.1.4
vcd 1.4-4
vegan 2.5-2
viridis 0.5.1
viridisLite 0.3.0
visNetwork 2.0.4
waveslim 1.7.5
webshot 0.5.0
whisker 0.3-2
withr 2.1.2
wnominate 1.2.5
xml2 1.2.0
xtable 1.8-2
xts 0.10-2
yaml 2.1.19
zip 1.0.0
zipfR 0.6-10
zoo 1.8-2
And the session info was:
> sessionInfo()
R version 3.4.0 (2017-04-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux Server release 6.4 (Santiago)
Matrix products: default
BLAS: /panfs/pfs.local/software/install/MRO/3.4.0/microsoft-r/3.4/lib64/R/lib/libRblas.so
LAPACK: /panfs/pfs.local/software/install/MRO/3.4.0/microsoft-r/3.4/lib64/R/lib/libRlapack.so
locale:
[1] C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] RevoUtilsMath_10.0.0
loaded via a namespace (and not attached):
[1] compiler_3.4.0 RevoUtils_10.0.4 tools_3.4.0
For R-3.3, the packages are provided via an environment file (crmda_env.sh). The package list will be mostly the same, however the effort to compile the latest versions of these packages fails: c("inum", "Rmpi", "partykit", "OpenMx", "mboost"). Rmpi is a foundational piece an I'll try to figure out what is wrong. Anyway, here is the firecracker 3.3 package list.
/panfs/pfs.local/software/install/MRO/3.3/microsoft-r/3.3/lib64/R/library
KernSmooth 2.23-15
MASS 7.3-45
Matrix 1.2-7.1
MicrosoftR 3.3.2.0000
R6 2.2.0
RUnit 0.4.26
RevoIOQ 8.0.6
RevoMods 10.0.0
RevoUtils 10.0.2
RevoUtilsMath 10.0.0
base 3.3.2
boot 1.3-18
checkpoint 0.3.18
class 7.3-14
cluster 2.0.5
codetools 0.2-15
compiler 3.3.2
curl 2.2
datasets 3.3.2
deployrRserve 9.0.0
doParallel 1.0.10
foreach 1.4.3
foreign 0.8-67
grDevices 3.3.2
graphics 3.3.2
grid 3.3.2
iterators 1.0.8
jsonlite 1.1
lattice 0.20-34
methods 3.3.2
mgcv 1.8-15
nlme 3.1-128
nnet 7.3-12
parallel 3.3.2
png 0.1-7
rpart 4.1-10
spatial 7.3-11
splines 3.3.2
stats 3.3.2
stats4 3.3.2
survival 2.39-5
tcltk 3.3.2
tools 3.3.2
utils 3.3.2
/panfs/pfs.local/work/crmda/tools/mro/3.3/site-library
ADGofTest 0.3
AER 1.2-5
Amelia 1.7.5
BH 1.66.0-1
BMA 3.18.8
BradleyTerry2 1.0-8
CVST 0.2-2
Cairo 1.5-9
Cubist 0.2.2
DBI 1.0.0
DCluster 0.2-7
DEoptimR 1.0-8
DRR 0.0.3
Devore7 0.7.6
DiagrammeR 1.0.0
DiceKriging 1.5.5
ENmisc 1.2-7
Ecdat 0.3-1
Ecfun 0.1-7
Formula 1.2-3
GPArotation 2014.11-1
HistData 0.8-4
Hmisc 4.1-1
HyperbolicDist 0.6-2
ISOcodes 2018.06.29
ISwR 2.0-7
Iso 0.0-17
JGR 1.8-4
JM 1.4-8
JMdesign 1.1
JavaGD 0.6-1
Kendall 2.2
Lahman 6.0-0
LearnBayes 2.15.1
MCMCglmm 2.25
MCMCpack 1.4-3
MCPAN 1.1-21
MEMSS 0.9-2
MNP 3.1-0
MPV 1.53
MatchIt 3.0.2
Matching 4.9-3
MatrixModels 0.4-1
ModelMetrics 1.1.0
MplusAutomation 0.7-2
NLP 0.1-11
NMF 0.21.0
OpenMx 2.8.3
PASWR 1.1
PBSmapping 2.70.5
PolynomF 1.0-2
R2HTML 2.3.2
R2OpenBUGS 3.2-3.2
R6 2.2.2
RColorBrewer 1.1-2
RCurl 1.95-4.10
RGtk2 2.20.31
RMySQL 0.10.15
RPostgreSQL 0.6-2
RSQLite 2.1.1
RSvgDevice 0.6.4.4
RUnit 0.4.32
RandomFields 3.1.50
RandomFieldsUtils 0.3.25
Rcmdr 2.4-1
RcmdrMisc 1.0-7
Rcpp 0.12.17
RcppArmadillo 0.8.600.0.0
RcppEigen 0.3.3.4.0
RcppRoll 0.3.0
Rd2roxygen 1.6.2
Rmpi 0.6-6
Rook 1.1-1
SAScii 1.0
SASmixed 1.0-4
SQUAREM 2017.10-1
SemiPar 1.0-4.2
SnowballC 0.5.1
SoDA 1.0-6
SparseM 1.77
StanHeaders 2.17.2
StatDataML 1.0-26
SweaveListingUtils 0.7.7
TH.data 1.0-8
TTR 0.23-3
TeachingDemos 2.10
UsingR 2.0-6
VGAM 1.0-3
VIM 4.7.0
XML 3.98-1.11
Zelig 5.1.6
abind 1.4-5
acepack 1.4.1
actuar 2.3-1
ada 2.0-5
ade4 1.7-11
adehabitat 1.8.20
akima 0.6-2
alr3 2.0.8
amap 0.8-16
aod 1.3
ape 5.1
aplpack 1.3.2
arm 1.10-1
arules 1.5-4
assertthat 0.2.0
backports 1.1.2
base64enc 0.1-3
bayesm 3.1-0.1
bcp 4.0.2
bdsmatrix 1.3-3
bestglm 0.37
betareg 3.1-0
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
blob 1.1.1
bnlearn 4.3
brew 1.0-6
brglm 0.6.1
broom 0.4.4
caTools 1.17.1
cairoDevice 2.25
callr 2.0.4
car 3.0-0
carData 3.0-1
caret 6.0-80
cellranger 1.1.0
censReg 0.5-26
checkmate 1.8.5
chron 2.3-52
cli 1.0.0
clipr 0.4.1
clue 0.3-55
clv 0.3-2.1
cocorresp 0.3-0
coda 0.19-1
coin 1.2-2
colorspace 1.3-2
combinat 0.0-8
commonmark 1.5
copula 0.999-18
corpcor 1.6.9
covr 3.1.0
crayon 1.3.4
crosstalk 1.0.0
cslogistic 0.1-3
cubature 1.4
data.table 1.11.4
dbplyr 1.2.1
ddalpha 1.3.4
debugme 1.1.0
deldir 0.1-15
desc 1.2.0
descr 1.1.4
dichromat 2.0-0
digest 0.6.15
dimRed 0.1.0
diptest 0.75-7
distr 2.6.2
dlm 1.1-5
doBy 4.6-1
doMC 1.3.5
doMPI 0.2.2
doParallel 1.0.11
doSNOW 1.0.16
dotCall64 0.9-5.2
downloader 0.4
dplyr 0.7.6
dse 2015.12-1
e1071 1.6-8
earth 4.6.3
ecodist 2.0.1
effects 4.0-2
egcm 1.0.12
eha 2.5.1
eiPack 0.1-7
emplik 1.0-3
estimability 1.3
evaluate 0.10.1
expint 0.1-5
expm 0.999-2
fBasics 3042.89
fUnitRoots 3042.79
faraway 1.0.7
fastICA 1.2-1
fastmatch 1.1-0
fda 2.4.7
ffmanova 0.2-2
fields 9.6
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