Packages on OpenCPU

To get an up-to-date list of packages on OpenCPU, look at http://opencpu2.psych.bio.uni-goettingen.de/ocpu/library/

Dependencies

Some of the following packages have apt-dependencies. At least the following packages are needed minimum one of the following R packages:

apt-get install build-essential gfortran libapparmor-dev libapparmor-dev libboost-all-dev libcairo2-dev libcurl4-gnutls-dev libfontconfig1-dev libgfortran-7-dev libgsl-dev libjpeg-dev liblapack-dev libmariadbclient-dev libpng-config libproj-dev libsodium-dev libsodium-dev libssl-dev libudunits2-dev libxml2-dev mesa-common-dev

List of Packages

Currently, a way to set up packages might be to run:

install.packages(Ncpus = 4, pkgs = c("abind", "acepack", "AER", "AICcmodavg", "akima", "alr4", "Amelia", 
"ape", "aplpack", "arm", "ash", "backports", "BatchExperiments", 
"BatchJobs", "BayesFactor", "bayesplot", "BB", "BBmisc", "bbmle", 
"bdsmatrix", "BH", "BiasedUrn", "bindr", "bindrcpp", "bit", "bit64", 
"bitops", "blme", "blob", "bridgesampling", "brms", "Brobdingnag", 
"broom", "Cairo", "callr", "car", "carData", "caTools", "cellranger", 
"checkmate", "chron", "CircStats", "cmprsk", "coda", "codebook", 
"coin", "colorspace", "colourpicker", "combinat", "commonmark", 
"CompQuadForm", "corpcor", "coxme", "crosstalk", "cubature", 
"d3Network", "data.table", "DBI", "dbplyr", "deldir", "desc", 
"descr", "dfoptim", "DiagrammeR", "dichromat", "doParallel", 
"dotCall64", "downloader", "dplyr", "DT", "dtplyr", "dygraphs", 
"eaf", "effects", "ellipse", "emdbook", "emmeans", "emoa", "Epi", 
"estimability", "etm", "expm", "extrafont", "extrafontdb", "fail", 
"fdrtool", "fields", "fmsb", "FNN", "foreach", "formatR", "Formula", 
"futile.logger", "futile.options", "future", "gamm4", "gdata", 
"gdtools", "gee", "geepack", "genetics", "geosphere", "GGally", 
"ggalt", "ggeffects", "ggforce", "ggfortify", "ggiraph", "ggmap", 
"ggplot2", "ggraph", "ggrepel", "ggthemes", "ggvis", "gistr", 
"glasso", "glmmTMB", "globals", "gmailr", "googlesheets", "googleVis", 
"gplots", "gridBase", "gridExtra", "gridSVG", "gstat", "gtable", 
"gtools", "hexbin", "hflights", "highcharter", "Hmisc", "HSAUR3", 
"htmlTable", "htmltools", "htmlwidgets", "hunspell", "igraph", 
"igraphdata", "influenceR", "inline", "intervals", "irace", "irlba", 
"irr", "iterators", "jpeg", "kinship2", "knitrBootstrap", "koRpus", 
"labeling", "Lahman", "lambda.r", "latticeExtra", "lava", "lavaan", 
"lavaan.survey", "lazyeval", "leaflet", "leaps", "lhs", "likert", 
"lintr", "lisrelToR", "listenv", "lme4", "lmerTest", "lmtest", 
"logspline", "loo", "lpSolve", "lsmeans", "lubridate", "mapproj", 
"maps", "maptools", "MasterBayes", "Matching", "MatchIt", "matrixcalc", 
"MatrixModels", "matrixStats", "maxLik", "mcmc", "MCMCglmm", 
"MCMCpack", "memisc", "merTools", "meta", "MetABEL", "metacom", 
"metafor", "metagen", "metaLik", "metap", "MetaPCA", "MetaSKAT", 
"metatest", "Metatron", "metricsgraphics", "mets", "mgcv", "mi", 
"mice", "miniUI", "minqa", "miscTools", "mnormt", "modelr", "modeltools", 
"mpt", "multcomp", "MuMIn", "munsell", "mvtnorm", "network", 
"nleqslv", "nloptr", "NMF", "nor1mix", "numDeriv", "officer", 
"optextras", "optimx", "orthopolynom", "packrat", "ParamHelpers", 
"pbapply", "pbivnorm", "pbkrtest", "pedigreemm", "permute", "pkgKitten", 
"pkgmaker", "PKI", "plogr", "plotly", "plotROC", "plyr", "png", 
"polspline", "polynom", "praise", "prediction", "prettyunits", 
"prodlim", "progress", "proj4", "proto", "pryr", "psych", "purrr", 
"pwr", "qrencoder", "quadprog", "quantmod", "QuantPsyc", "quantreg", 
"randomForest", "RAppArmor", "raster", "rasterVis", "rbokeh", 
"R.cache", "Rcgmin", "RColorBrewer", "RcppArmadillo", "RcppEigen", 
"RCurl", "readxl", "registry", "rematch", "repr", "reprex", "reshape", 
"reshape2", "rex", "rgexf", "rgl", "rglwidget", "RgoogleMaps", 
"rjson", "RJSONIO", "rlist", "rmarkdown", "rmeta", "R.methodsS3", 
"rms", "rngtools", "rockchalk", "R.oo", "Rook", "roxygen2", "rprojroot", 
"R.rsp", "rsconnect", "RSQLite", "rstan", "rstanarm", "rstantools", 
"Rttf2pt1", "RUnit", "R.utils", "rversions", "rvest", "rvg", 
"Rvmmin", "RWiener", "sandwich", "scales", "scatterplot3d", "selectr", 
"sem", "semTools", "setRNG", "shiny", "shinyAce", "shinyBS", 
"shinyFiles", "shinyjs", "shinystan", "shinythemes", "simsem", 
"sjlabelled", "sjmisc", "sjPlot", "sjstats", "SKAT", "skimr", 
"SMVar", "sna", "snakecase", "sodium", "sourcetools", "sp", "spacetime", 
"spam", "SparseM", "SQUAREM", "StanHeaders", "statmod", "statnet.common", 
"stringdist", "strucchange", "survey", "survival", "svglite", 
"svUnit", "tables", "tensorA", "testthat", "TH.data", "threejs", 
"tidyselect", "tidyverse", "timereg", "TMB", "tripack", "tseries", 
"TTR", "tufte", "tutorial", "tweenr", "twitteR", "ucminf", "udunits2", 
"units", "unmarked", "urlshorteneR", "uuid", "vcd", "vegan", 
"VGAM", "viridis", "viridisLite", "visNetwork", "waffle", "wesanderson", 
"xfun", "XML", "xml2", "xtable", "xts", "Zelig", "zipcode", "zoo", 
"RMySQL", "assertthat", "base64enc", "boot", "brew", "class", 
"cli", "cluster", "codetools", "crayon", "curl", "devtools", 
"digest", "evaluate", "feather", "forcats", "foreign", "git2r", 
"glue", "haven", "highr", "hms", "httpuv", "httr", "jsonlite", 
"KernSmooth", "knitr", "lattice", "magrittr", "markdown", "MASS", 
"Matrix", "memoise", "mime", "nlme", "nnet", "opencpu", "openssl", 
"pander", "pillar", "pkgconfig", "protolite", "R6", "rappdirs", 
"Rcpp", "readr", "rlang", "rpart", "rstudioapi", "sendmailR", 
"spatial", "stringi", "stringr", "sys", "tibble", "unix", "utf8", 
"webutils", "whisker", "withr", "yaml", "zip"))
devtools::install_github("rubenarslan/formr")

There is a bug in OpenCPU where we can get an "unloading error" when updating packages that are part of the core OpenCPU set. Therefore, we should always run the following to remove dupes.

An old package could hide in any library

.libPaths(c( "/usr/local/lib/opencpu/site-library", 
						 "/usr/local/lib/R/site-library",
						 "/usr/lib/R/site-library",
						 "/usr/lib/R/library",   
						"/usr/lib/opencpu/library"  ))

Get a list of duplicated packages

library(tidyverse)
pkgs <- installed.packages()
pkgs <- as.data.frame(pkgs)

dupes <- pkgs %>% select(Package, Version, LibPath) %>% 
	group_by(Package) %>% 
	filter(n_distinct(Version, na.rm = TRUE) > 1) 

Check which version is installed in which library

dupes %>% 
	spread(LibPath, Version) %>% 
	knitr::kable()

Remove any duplicates which older versions

dupes %>% 
	group_by(Package) %>% 
	arrange(desc(Version)) %>% 
	filter(Version != first(Version)) %>% 
	purrr::pmap(~ remove.packages(..1, ..3))