This is the 20170425 update, which includes an updated module set and reports of success with Java and TkTcl-based R packages. In other words, an almost complete victory is achieved. Special thanks to Wes Mason of ITTC.
To use R, here is a set of commands I run to set the environment. This is necessary every time I want to use R with Emacs. Let's call this the magic 5 line stanza, for sake of discussion.
module purge module load legacy module load emacs module use /panfs/pfs.local/work/crmda/tools/modules module load Rstats/3.3
I agree if you say "it is a pain in the rump to have to remember to do that every time I log in." In the old cluster, I was in a position to place those startup commands into all of the CRMDA user environments. That is no longer the case.
I'm checking on ways you can automate this within your own account. Details are posted at the end of this article.
Consider (strongly) obliterating your $HOME/R package folder
When you want to work with R on the CRC cluster, please consider using the R packages we install within the $WORK folder for CRMDA group members. These packages have some special features and if you try to install them in your user folder (under $HOME/R, as R invites you to do if you run "install.packages()" in a session), then they may not compile correctly.
Recently, we have had runtime errors because the R we are recommending, as described below, is not compatible with packages that users build and install with other versions of R (or the same version of R in a different build environment). In particular, if
- You have packages built on the old ACF cluster, or
- You have recently installed packages without loading the modules listed below
then you should delete the packages you have under $HOME/R. I think it is best if you let us try to install what you need, but if you install R packages in your own home folder, please do so only AFTER loading the modules listed below. Please DO NOT load the CRC-provided module "R/3.3". It does not provide the services we need.
The module Rstats/3.3 is built by Wes Mason of ITTC and it is installed into the $WORK folder for CRMDA (hence the module use command above). We work together to make sure the OpenMPI layer is compiled correctly, so it is possible to use Rmpi and the R package parallel. The compiler used is GCC-6.3, which is quite a bit newer than the standard GCC which is provided with the cluster node operating system. This is the principal reason why the CRC-provided "R/3.3" is not acceptable. It does not make sure that the OpenMPI and GCC components are kept in lock-step with R itself. Observe, if we start with an empty session and run
module purge module use /panfs/pfs.local/work/crmda/tools/modules module load Rstats/3.3
we find that we actually load several modules:
$ module list Currently Loaded Modules: 1) compiler/gcc/6.3 2) openmpi/2.0 3) java/1.8.0_131 4) xz/5.2.3 5) icu/59.1 6) tcltk/8.6.6 7) Rstats/3.3
The openmpi version must be kept in lock-step with R and the packages we have installed in the past. gcc-6.3 is the compiler version we use for all of the packages. It is necessary to have that new version because of demands by packages like Rstan and OpenMX. The java and tcltk modules are needed by various R packages, such as rJava and tkrplot. The xz module is a decompression suite, needed to interact with source code itself. The Rstats module itself is, for the most part, a "holding company" that keeps all of this together. It simply loads the requirements of gcc, openmpi, java, xz, icu, and tcltk, and then it accesses the R provided by the CRC system maintainers from /panfs/pfs.local/software/install/MRO/3.3. The R packages provided by the base R install are found in the directory /panfs/pfs.local/work/crmda/tools/mro/3.3/site-library.
The R packages in our collection are, in most cases, going to be updates & replacements of those packages because we are building with the different compiler. Users who load Rstats/3.3 should notice that our directory comes into the user path before the system-wide folder. Inside R, we see:
> .libPaths()  "/panfs/pfs.local/work/crmda/tools/mro/3.3/site-library"  "/panfs/pfs.local/software/install/MRO/3.3/microsoft-r/3.3/lib64/R/library"
In my basic 5 line session starter sequence, I also have modules named legacy and emacs. In my opinion, that is a little dangerous because I'm jumbling together modules from the old and new cluster. That's necessary because I need an IDE with which to interact with R. Emacs was configured with ESS by Wes Mason, and it is in the legacy module set. If you prefer, legacy also provides RStudio version 9.98.978. That is, unfortunately, outdated and unmaintained. I've filed a request with CRC to get a new version of Rstudio.
What do you get if you load our environment?
After the magic 5 line stanza above, within your R session, you have access to these packages (Run "library()" to see all folders your path, and all packages within):
Packages in library '/panfs/pfs.local/work/crmda/tools/mro/3.3/site-library': ADGofTest Anderson-Darling GoF test AER Applied Econometrics with R Amelia A Program for Missing Data BH Boost C++ Header Files BMA Bayesian Model Averaging BradleyTerry2 Bradley-Terry Models Cairo R graphics device using cairo graphics library for creating high-quality bitmap (PNG, JPEG, TIFF), vector (PDF, SVG, PostScript) and display (X11 and Win32) output Cubist Rule- And Instance-Based Regression Modeling DBI R Database Interface DCluster Functions for the Detection of Spatial Clusters of Diseases DEoptimR Differential Evolution Optimization in Pure R Devore7 Data sets from Devore's "Prob and Stat for Eng (7th ed)" DiagrammeR Create Graph Diagrams and Flowcharts Using R ENmisc Neuwirth miscellaneous Ecdat Data Sets for Econometrics Ecfun Functions for Ecdat Formula Extended Model Formulas GPArotation GPA Factor Rotation HistData Data Sets from the History of Statistics and Data Visualization Hmisc Harrell Miscellaneous HyperbolicDist The hyperbolic distribution ISwR Introductory Statistics with R Iso Functions to Perform Isotonic Regression JGR JGR - Java GUI for R JM Joint Modeling of Longitudinal and Survival Data JMdesign Joint Modeling of Longitudinal and Survival Data - Power Calculation JavaGD Java Graphics Device Kendall Kendall rank correlation and Mann-Kendall trend test LearnBayes Functions for Learning Bayesian Inference MCMCglmm MCMC Generalised Linear Mixed Models MCMCpack Markov Chain Monte Carlo (MCMC) Package MCPAN Multiple Comparisons Using Normal Approximation MEMSS Data sets from Mixed-effects Models in S MNP R Package for Fitting the Multinomial Probit Model MPV Data Sets from Montgomery, Peck and Vining's Book MatchIt Nonparametric Preprocessing for Parametric Casual Inference Matching Multivariate and Propensity Score Matching with Balance Optimization MatrixModels Modelling with Sparse And Dense Matrices ModelMetrics Rapid Calculation of Model Metrics MplusAutomation Automating Mplus Model Estimation and Interpretation NMF Algorithms and Framework for Nonnegative Matrix Factorization (NMF) OpenMx Extended Structural Equation Modelling PASWR PROBABILITY and STATISTICS WITH R PBSmapping Mapping Fisheries Data and Spatial Analysis Tools PolynomF Polynomials in R R2HTML HTML Exportation for R Objects R2OpenBUGS Running OpenBUGS from R R6 Classes with Reference Semantics RColorBrewer ColorBrewer Palettes RCurl General Network (HTTP/FTP/...) Client Interface for R RGtk2 R bindings for Gtk 2.8.0 and above RSvgDevice An R SVG graphics device. RandomFields Simulation and Analysis of Random Fields RandomFieldsUtils Utilities for the Simulation and Analysis of Random Fields Rcmdr R Commander RcmdrMisc R Commander Miscellaneous Functions Rcpp Seamless R and C++ Integration RcppArmadillo 'Rcpp' Integration for the 'Armadillo' Templated Linear Algebra Library RcppEigen 'Rcpp' Integration for the 'Eigen' Templated Linear Algebra Library Rd2roxygen Convert Rd to 'Roxygen' Documentation Rmpi Interface (Wrapper) to MPI (Message-Passing Interface) Rook Rook - a web server interface for R SAScii Import ASCII files directly into R using only a SAS input script SASmixed Data sets from "SAS System for Mixed Models" SemiPar Semiparametic Regression SoDA Functions and Examples for "Software for Data Analysis" SparseM Sparse Linear Algebra StanHeaders C++ Header Files for Stan StatDataML Read and Write StatDataML Files SweaveListingUtils Utilities for Sweave Together with TeX 'listings' Package TH.data TH's Data Archive TeachingDemos Demonstrations for Teaching and Learning UsingR Data Sets, Etc. for the Text "Using R for Introductory Statistics", Second Edition VGAM Vector Generalized Linear and Additive Models VIM Visualization and Imputation of Missing Values XML Tools for Parsing and Generating XML Within R and S-Plus Zelig Everyone's Statistical Software abind Combine Multidimensional Arrays acepack ACE and AVAS for Selecting Multiple Regression Transformations actuar Actuarial Functions and Heavy Tailed Distributions ada The R Package Ada for Stochastic Boosting ade4 Analysis of Ecological Data : Exploratory and Euclidean Methods in Environmental Sciences adehabitat Analysis of Habitat Selection by Animals akima Interpolation of Irregularly and Regularly Spaced Data alr3 Data to accompany Applied Linear Regression 3rd edition amap Another Multidimensional Analysis Package aod Analysis of Overdispersed Data ape Analyses of Phylogenetics and Evolution aplpack Another Plot PACKage: stem.leaf, bagplot, faces, spin3R, plotsummary, plothulls, and some slider functions arm Data Analysis Using Regression and Multilevel/Hierarchical Models arules Mining Association Rules and Frequent Itemsets assertthat Easy Pre and Post Assertions backports Reimplementations of Functions Introduced Since R-3.0.0 base64enc Tools for base64 encoding bayesm Bayesian Inference for Marketing/Micro-Econometrics bcp Bayesian Analysis of Change Point Problems bdsmatrix Routines for Block Diagonal Symmetric matrices bestglm Best Subset GLM betareg Beta Regression biglm bounded memory linear and generalized linear models bit A class for vectors of 1-bit booleans bit64 A S3 Class for Vectors of 64bit Integers bitops Bitwise Operations bnlearn Bayesian Network Structure Learning, Parameter Learning and Inference brew Templating Framework for Report Generation brglm Bias reduction in binomial-response generalized linear models. broom Convert Statistical Analysis Objects into Tidy Data Frames caTools Tools: moving window statistics, GIF, Base64, ROC AUC, etc. cairoDevice Embeddable Cairo Graphics Device Driver car Companion to Applied Regression caret Classification and Regression Training cellranger Translate Spreadsheet Cell Ranges to Rows and Columns censReg Censored Regression (Tobit) Models checkmate Fast and Versatile Argument Checks chron Chronological Objects which can Handle Dates and Times clue Cluster Ensembles clv Cluster Validation Techniques cocorresp Co-Correspondence Analysis Methods coda Output Analysis and Diagnostics for MCMC coin Conditional Inference Procedures in a Permutation Test Framework colorspace Color Space Manipulation combinat combinatorics utilities commonmark High Performance CommonMark and Github Markdown Rendering in R copula Multivariate Dependence with Copulas corpcor Efficient Estimation of Covariance and (Partial) Correlation crayon Colored Terminal Output cslogistic Conditionally Specified Logistic Regression cubature Adaptive Multivariate Integration over Hypercubes data.table Extension of `data.frame` deldir Delaunay Triangulation and Dirichlet (Voronoi) Tessellation desc Manipulate DESCRIPTION Files descr Descriptive Statistics dichromat Color Schemes for Dichromats digest Create Compact Hash Digests of R Objects diptest Hartigan's Dip Test Statistic for Unimodality - Corrected distr Object Oriented Implementation of Distributions dlm Bayesian and Likelihood Analysis of Dynamic Linear Models doBy Groupwise Statistics, LSmeans, Linear Contrasts, Utilities doMC Foreach Parallel Adaptor for 'parallel' doMPI Foreach parallel adaptor for the Rmpi package doSNOW Foreach Parallel Adaptor for the 'snow' Package dplyr A Grammar of Data Manipulation dse Dynamic Systems Estimation (Time Series Package) e1071 Misc Functions of the Department of Statistics, Probability Theory Group (Formerly: E1071), TU Wien earth Multivariate Adaptive Regression Splines ecodist Dissimilarity-based functions for ecological analysis effects Effect Displays for Linear, Generalized Linear, and Other Models eha Event History Analysis eiPack eiPack: Ecological Inference and Higher-Dimension Data Management emplik Empirical Likelihood Ratio for Censored/Truncated Data evaluate Parsing and Evaluation Tools that Provide More Details than the Default expint Exponential Integral and Incomplete Gamma Function expm Matrix Exponential, Log, 'etc' faraway Functions and Datasets for Books by Julian Faraway fastICA FastICA Algorithms to perform ICA and Projection Pursuit fastmatch Fast match() function fda Functional Data Analysis ffmanova Fifty-fifty MANOVA fields Tools for Spatial Data flexmix Flexible Mixture Modeling forcats Tools for Working with Categorical Variables (Factors) formatR Format R Code Automatically forward Forward search gam Generalized Additive Models gamlss Generalised Additive Models for Location Scale and Shape gamlss.data GAMLSS Data gamlss.dist Distributions to be Used for GAMLSS Modelling gamm4 Generalized Additive Mixed Models using 'mgcv' and 'lme4' gbm Generalized Boosted Regression Models gclus Clustering Graphics gdata Various R Programming Tools for Data Manipulation gee Generalized Estimation Equation Solver geepack Generalized Estimating Equation Package geoR Analysis of Geostatistical Data geoRglm A Package for Generalised Linear Spatial Models ggm Functions for graphical Markov models ggplot2 Create Elegant Data Visualisations Using the Grammar of Graphics glmc Fitting Generalized Linear Models Subject to Constraints glmmBUGS Generalised Linear Mixed Models with BUGS and JAGS glmmML Generalized Linear Models with Clustering glmnet Lasso and Elastic-Net Regularized Generalized Linear Models glmpath L1 Regularization Path for Generalized Linear Models and Cox Proportional Hazards Model gmodels Various R Programming Tools for Model Fitting gmp Multiple Precision Arithmetic gpclib General Polygon Clipping Library for R gridBase Integration of base and grid graphics gridExtra Miscellaneous Functions for "Grid" Graphics grpreg Regularization Paths for Regression Models with Grouped Covariates gsl Wrapper for the Gnu Scientific Library gsubfn Utilities for strings and function arguments. gtable Arrange 'Grobs' in Tables gtools Various R Programming Tools haven Import and Export 'SPSS', 'Stata' and 'SAS' Files hexbin Hexagonal Binning Routines highr Syntax Highlighting for R Source Code hms Pretty Time of Day htmlTable Advanced Tables for Markdown/HTML htmltools Tools for HTML htmlwidgets HTML Widgets for R httpuv HTTP and WebSocket Server Library httr Tools for Working with URLs and HTTP igraph Network Analysis and Visualization ineq Measuring Inequality, Concentration, and Poverty influence.ME Tools for Detecting Influential Data in Mixed Effects Models influenceR Software Tools to Quantify Structural Importance of Nodes in a Network inline Functions to Inline C, C++, Fortran Function Calls from R iplots iPlots - interactive graphics for R irlba Fast Truncated SVD, PCA and Symmetric Eigendecomposition for Large Dense and Sparse Matrices itertools Iterator Tools jpeg Read and write JPEG images kernlab Kernel-Based Machine Learning Lab knitr A General-Purpose Package for Dynamic Report Generation in R kutils Project Management Tools labeling Axis Labeling laeken Estimation of indicators on social exclusion and poverty languageR Data sets and functions with "Analyzing Linguistic Data: A practical introduction to statistics". lars Least Angle Regression, Lasso and Forward Stagewise latticeExtra Extra Graphical Utilities Based on Lattice lava Latent Variable Models lavaan Latent Variable Analysis lavaan.survey Complex Survey Structural Equation Modeling (SEM) lazyeval Lazy (Non-Standard) Evaluation leaps Regression Subset Selection lme4 Linear Mixed-Effects Models using 'Eigen' and S4 lmeSplines Add smoothing spline modelling capability to nlme. lmec Linear Mixed-Effects Models with Censored Responses lmerTest Tests in Linear Mixed Effects Models lmm Linear Mixed Models lmtest Testing Linear Regression Models locfit Local Regression, Likelihood and Density Estimation. logspline Logspline Density Estimation Routines longitudinal Analysis of Multiple Time Course Data longitudinalData Longitudinal Data lpSolve Interface to 'Lp_solve' v. 5.5 to Solve Linear/Integer Programs ltm Latent Trait Models under IRT lubridate Make Dealing with Dates a Little Easier magic create and investigate magic squares magrittr A Forward-Pipe Operator for R manipulate Interactive Plots for RStudio maps Draw Geographical Maps maptools Tools for Reading and Handling Spatial Objects markdown 'Markdown' Rendering for R matrixcalc Collection of functions for matrix calculations maxLik Maximum Likelihood Estimation and Related Tools mboost Model-Based Boosting mcgibbsit Warnes and Raftery's MCGibbsit MCMC diagnostic mclust Gaussian Mixture Modelling for Model-Based Clustering, Classification, and Density Estimation mcmc Markov Chain Monte Carlo mda Mixture and Flexible Discriminant Analysis mediation Causal Mediation Analysis memisc Tools for Management of Survey Data and the Presentation of Analysis Results memoise Memoisation of Functions mi Missing Data Imputation and Model Checking micEcon Microeconomic Analysis and Modelling mice Multivariate Imputation by Chained Equations microbenchmark Accurate Timing Functions mime Map Filenames to MIME Types minqa Derivative-free optimization algorithms by quadratic approximation misc3d Miscellaneous 3D Plots miscTools Miscellaneous Tools and Utilities mitools Tools for multiple imputation of missing data mix Estimation/Multiple Imputation for Mixed Categorical and Continuous Data mixtools Tools for Analyzing Finite Mixture Models mlbench Machine Learning Benchmark Problems mnormt The Multivariate Normal and t Distributions modelr Modelling Functions that Work with the Pipe modeltools Tools and Classes for Statistical Models msm Multi-State Markov and Hidden Markov Models in Continuous Time multcomp Simultaneous Inference in General Parametric Models munsell Utilities for Using Munsell Colours mvProbit Multivariate Probit Models mvbutils Workspace organization, code and documentation editing, package prep and editing, etc. mvtnorm Multivariate Normal and t Distributions neighbr Classification, Regression, Clustering with K Nearest Neighbors network Classes for Relational Data nloptr R interface to NLopt nnls The Lawson-Hanson algorithm for non-negative least squares (NNLS) nor1mix Normal (1-d) Mixture Models (S3 Classes and Methods) norm Analysis of multivariate normal datasets with missing values nortest Tests for Normality np Nonparametric kernel smoothing methods for mixed data types numDeriv Accurate Numerical Derivatives nws R functions for NetWorkSpaces and Sleigh openssl Toolkit for Encryption, Signatures and Certificates Based on OpenSSL openxlsx Read, Write and Edit XLSX Files ordinal Regression Models for Ordinal Data orthopolynom Collection of functions for orthogonal and orthonormal polynomials pan Multiple Imputation for Multivariate Panel or Clustered Data pander An R Pandoc Writer partDSA Partitioning Using Deletion, Substitution, and Addition Moves party A Laboratory for Recursive Partytioning pbivnorm Vectorized Bivariate Normal CDF pbkrtest Parametric Bootstrap and Kenward Roger Based Methods for Mixed Model Comparison pcaPP Robust PCA by Projection Pursuit permute Functions for Generating Restricted Permutations of Data pixmap Bitmap Images (``Pixel Maps'') pkgKitten Create Simple Packages Which Do not Upset R Package Checks pkgmaker Package development utilities plm Linear Models for Panel Data plotmo Plot a Model's Response and Residuals plotrix Various Plotting Functions pls Partial Least Squares and Principal Component Regression plyr Tools for Splitting, Applying and Combining Data pmml Generate PMML for Various Models pmmlTransformations Transforms Input Data from a PMML Perspective polspline Polynomial Spline Routines polycor Polychoric and Polyserial Correlations polynom A Collection of Functions to Implement a Class for Univariate Polynomial Manipulations portableParallelSeeds Allow Replication of Simulations on Parallel and Serial Computers ppcor Partial and Semi-Partial (Part) Correlation praise Praise Users profileModel Tools for profiling inference functions for various model classes proto Prototype Object-Based Programming proxy Distance and Similarity Measures pscl Political Science Computational Laboratory, Stanford University psidR Build Panel Data Sets from PSID Raw Data pspline Penalized Smoothing Splines psych Procedures for Psychological, Psychometric, and Personality Research purrr Functional Programming Tools quadprog Functions to solve Quadratic Programming Problems. quantreg Quantile Regression rJava Low-Level R to Java Interface randomForest Breiman and Cutler's Random Forests for Classification and Regression randomForestSRC Random Forests for Survival, Regression and Classification (RF-SRC) rattle Graphical User Interface for Data Mining in R rbenchmark Benchmarking routine for R rbugs Fusing R and OpenBugs and Beyond rda Shrunken Centroids Regularized Discriminant Analysis readr Read Rectangular Text Data readxl Read Excel Files registry Infrastructure for R Package Registries relimp Relative Contribution of Effects in a Regression Model rematch Match Regular Expressions with a Nicer 'API' reshape Flexibly Reshape Data reshape2 Flexibly Reshape Data: A Reboot of the Reshape Package rgenoud R Version of GENetic Optimization Using Derivatives rgexf Build, Import and Export GEXF Graph Files rgl 3D Visualization Using OpenGL rlecuyer R Interface to RNG with Multiple Streams rmarkdown Dynamic Documents for R rms Regression Modeling Strategies rngtools Utility functions for working with Random Number Generators robustbase Basic Robust Statistics rockchalk Regression Estimation and Presentation roxygen2 In-Line Documentation for R rpart.plot Plot 'rpart' Models: An Enhanced Version of 'plot.rpart' rpf Response Probability Functions rprojroot Finding Files in Project Subdirectories rrcov Scalable Robust Estimators with High Breakdown Point rstan R Interface to Stan rstudio Tools and Utilities for RStudio rstudioapi Safely Access the RStudio API rvest Easily Harvest (Scrape) Web Pages sandwich Robust Covariance Matrix Estimators scales Scale Functions for Visualization scatterplot3d 3D Scatter Plot segmented Regression Models with Breakpoints/Changepoints Estimation selectr Translate CSS Selectors to XPath Expressions sem Structural Equation Models semTools Useful Tools for Structural Equation Modeling setRNG Set (Normal) Random Number Generator and Seed sets Sets, Generalized Sets, Customizable Sets and Intervals sfsmisc Utilities from "Seminar fuer Statistik" ETH Zurich shapefiles Read and Write ESRI Shapefiles shiny Web Application Framework for R simsem SIMulated Structural Equation Modeling sm Smoothing methods for nonparametric regression and density estimation smoothSurv Survival Regression with Smoothed Error Distribution sna Tools for Social Network Analysis snow Simple Network of Workstations snowFT Fault Tolerant Simple Network of Workstations sourcetools Tools for Reading, Tokenizing and Parsing R Code sp Classes and Methods for Spatial Data spam SPArse Matrix spatialCovariance Computation of Spatial Covariance Matrices for Data on Rectangles spatialkernel Nonparameteric estimation of spatial segregation in a multivariate point process spdep Spatial Dependence: Weighting Schemes, Statistics and Models splancs Spatial and Space-Time Point Pattern Analysis stabledist Stable Distribution Functions stabs Stability Selection with Error Control startupmsg Utilities for Start-Up Messages statmod Statistical Modeling statnet.common Common R Scripts and Utilities Used by the Statnet Project Software stepwise Stepwise detection of recombination breakpoints stringi Character String Processing Facilities stringr Simple, Consistent Wrappers for Common String Operations strucchange Testing, Monitoring, and Dating Structural Changes subselect Selecting Variable Subsets survey Analysis of Complex Survey Samples survival Survival Analysis systemfit Estimating Systems of Simultaneous Equations tables Formula-Driven Table Generation tcltk2 Tcl/Tk Additions tensorA Advanced tensors arithmetic with named indices testthat Unit Testing for R texreg Conversion of R Regression Output to LaTeX or HTML Tables tfplot Time Frame User Utilities tframe Time Frame Coding Kernel tibble Simple Data Frames tidyr Easily Tidy Data with 'spread()' and 'gather()' Functions tidyverse Easily Install and Load 'Tidyverse' Packages timeDate Rmetrics - Chronological and Calendar Objects tis Time Indexes and Time Indexed Series tkrplot TK Rplot tree Classification and Regression Trees triangle Provides the Standard Distribution Functions for the Triangle Distribution trimcluster Cluster analysis with trimming trust Trust Region Optimization ucminf General-Purpose Unconstrained Non-Linear Optimization urca Unit Root and Cointegration Tests for Time Series Data vcd Visualizing Categorical Data vegan Community Ecology Package viridis Default Color Maps from 'matplotlib' viridisLite Default Color Maps from 'matplotlib' (Lite Version) visNetwork Network Visualization using 'vis.js' Library waveslim Basic wavelet routines for one-, two- and three-dimensional signal processing wnominate Roll Call Analysis Software xgboost Extreme Gradient Boosting xml2 Parse XML xtable Export Tables to LaTeX or HTML xts eXtensible Time Series yaml Methods to Convert R Data to YAML and Back zipfR Statistical models for word frequency distributions zoo S3 Infrastructure for Regular and Irregular Time Series (Z's Ordered Observations) Packages in library '/panfs/pfs.local/software/install/MRO/3.3/microsoft-r/3.3/lib64/R/library': KernSmooth Functions for Kernel Smoothing Supporting Wand & Jones (1995) MASS Support Functions and Datasets for Venables and Ripley's MASS Matrix Sparse and Dense Matrix Classes and Methods MicrosoftR Microsoft R umbrella package R6 Classes with Reference Semantics RUnit R Unit test framework RevoIOQ Microsoft R Services Test Suite RevoMods R Functions Modified For Revolution R RevoUtils Microsoft R Utility Package RevoUtilsMath Microsoft R Services Math Utilities Package base The R Base Package boot Bootstrap Functions (Originally by Angelo Canty for S) checkpoint Install Packages from Snapshots on the Checkpoint Server for Reproducibility class Functions for Classification cluster "Finding Groups in Data": Cluster Analysis Extended Rousseeuw et al. codetools Code Analysis Tools for R compiler The R Compiler Package curl A Modern and Flexible Web Client for R datasets The R Datasets Package deployrRserve Binary R server doParallel Foreach Parallel Adaptor for the 'parallel' Package foreach Provides Foreach Looping Construct for R foreign Read Data Stored by Minitab, S, SAS, SPSS, Stata, Systat, Weka, dBase, ... grDevices The R Graphics Devices and Support for Colours and Fonts graphics The R Graphics Package grid The Grid Graphics Package iterators Provides Iterator Construct for R jsonlite A Robust, High Performance JSON Parser and Generator for R lattice Trellis Graphics for R methods Formal Methods and Classes mgcv Mixed GAM Computation Vehicle with GCV/AIC/REML Smoothness Estimation nlme Linear and Nonlinear Mixed Effects Models nnet Feed-Forward Neural Networks and Multinomial Log-Linear Models parallel Support for Parallel computation in R png Read and write PNG images rpart Recursive Partitioning and Regression Trees spatial Functions for Kriging and Point Pattern Analysis splines Regression Spline Functions and Classes stats The R Stats Package stats4 Statistical Functions using S4 Classes survival Survival Analysis tcltk Tcl/Tk Interface tools Tools for Package Development utils The R Utils Package
As usual, if these don't work right, its something I got wrong and will fix. Email me.
As of 2017-04-25, we have solved the problems of compiling Java and tk-based R packages. In other words, we find ourselves roughly back in the place where we were in October, 2016, or perhaps a little bit ahead of that. Now that the gcc issues have been addressed, we are able to stay up to date with changes in the cutting edge packages like Rcpp, Rstan and OpenMx.
If you need other packages, I'll install them if you email me
If you launch R and you don't find packages (in the output of library(), for example), it probably means you forgot the module magic.
If you are having trouble with Rstan, the likely sources of trouble are 1) errors in your ~/.R/Makevars file, or 2) old packages in your home folder ~/R/ that do not cooperate with the new R and the other packages we make available.
Make a module script file
I have another more lesson. Instead of re-typing that stanza whenever it is needed, put those lines in a file. I just tested this. I put module stanza rstats.sh. I saved that in $HOME/bin and made it executable ("chmod +x rstats.sh"). It seems to succeed then to run
Building your own packages?
If we don't build packages for you, you have to build your own. Here is a lesson from the school of hard knocks. In the new CRC cluster, the memory limits of your sessions are strictly enforced. The compiler will often use more than 2GB memory. As a result, when you try to build a package inside R with "install.packages", you may get a vague message of failure. To protect yourself against that, it is wise to ask for an interactive session with more memory. I do this, for example:
$ msub -I -X -l nodes=1:ppn=1,pmem=6144m
That is sufficient to compile Rstan, which is the most intensive package I have tried to build.