Commit 3c3ab170 authored by Philippe Grosjean's avatar Philippe Grosjean
Browse files

Update install.R

parent f91f5cb3
Pipeline #248036 passed with stage
in 34 minutes and 56 seconds
# From SDD bookdowns, BioDataScienceX & r.snippets (except ggvis & directlabels)
# (search for 'library(', 'require(', 'package =' and ::)
install.packages(c("ade4", "anytime", "ape", "assertthat", "automap",
"available", "backports", "base64enc", "bit", "bit64", "blob", "bookdown",
"broom", "ca", "car", "cartography", "circular", "cli", "corrplot", "crayon",
"curl", "data.table", "DBI", "dbplyr", "devtools", "DiagrammeR", "digest",
"DT", "evaluate", "factoextra", "FactoMineR", "fansi", "faraway",
"fastcluster", "fastmap", "flashClust", "fortunes", "flipdownr", "GGally",
"gganimate", "ggdendro", "ggfortify", "ggpubr", "ggrepel", "ggridges", "ggsn",
"ggsom", "glue", "gridExtra", "gstat", "here", "htmltools", "htmlwidgets",
"httpuv", "httr", "ipred", "iterators", "janitor", "jsonlite", "knitr",
"kohonen", "later", "lattice", "lintr", "lobstr", "lme4", "lmerTest",
"lubridate", "magrittr", "mapedit", "mapview", "markdown", "memoise",
"microbenchmark", "mime", "miniUI", "mlbench", "modelr", "mongolite",
"mosaic", "multcomp", "naniar", "nanotime", "nparcomp", "odbc",
"palmerpenguins", "pander", "PKI", "plotly", "pROC", "promises", "pryr",
"purrr", "pwr", "R6", "raster", "RColorBrewer", "Rcpp", "RcppCCTZ", "readxl",
"rgl", "remotes", "rlang", "rmarkdown", "ROCR", "rprojroot", "RSQLite", "sf",
"sessioninfo", "shiny", "shinyjs", "shinytest", "skimr", "spData", "stars",
"stringi", "stringr", "SuppDists", "tidyr", "tmap", "tmaptools", "TSA",
"UsingR", "vctrs", "vegan", "vembedr", "viridis", "visdat", "withr", "xfun",
"xtable", "yaml", "zoo"))
options(timeout = 600)
Ncpus <- parallel::detectCores(logical = FALSE)
install.packages(c("ade4", "anytime", "ape", "assertthat", "attachment",
"automap", "available", "backports", "base64enc", "BiocManager", "bit",
"bit64", "blob", "bookdown", "boot", "broom", "broom.mixed", "ca", "car",
"circular", "cli", "corrplot", "crayon", "curl", "data.table", "DBI",
"dbplyr", "devtools", "DiagrammeR", "digest", "DT", "evaluate", "factoextra",
"FactoMineR", "fansi", "faraway", "fastcluster", "fastmap", "flashClust",
"fortunes", "flipdownr", "gdtools", "GGally", "gganimate", "ggdendro",
"ggfortify", "ggpubr", "ggrepel", "ggridges", "ggsn", "ggsom", "glue",
"gridExtra", "gstat", "here", "htmltools", "htmlwidgets", "httpuv", "httr",
"ipred", "iterators", "janitor", "jsonlite", "knitr", "kohonen", "later",
"lattice", "lintr", "lobstr", "lme4", "lmerTest", "lubridate", "magrittr",
"mapedit","maps", "mapsf", "mapview", "markdown", "memoise", "microbenchmark",
"mime", "miniUI", "mlbench", "modelr", "mongolite", "mosaic", "multcomp",
"naniar", "nanotime", "nparcomp", "odbc", "palmerpenguins", "pander", "PKI",
"plotly", "pROC", "promises", "pryr", "purrr", "pwr", "R6", "randomForest",
"raster", "RColorBrewer", "Rcpp", "RcppCCTZ", "readxl", "rgl", "remotes",
"rlang", "rmarkdown", "ROCR", "rpart", "rpart.plot", "rprojroot", "RSQLite",
"sf", "sessioninfo", "shiny", "shinyjs", "shinytest", "skimr", "spData",
"stars", "stringi", "stringr", "SuppDists", "svglite", "tidyr", "tmap",
"tmaptools", "TSA", "UsingR", "vctrs", "vegan", "vembedr", "viridis",
"visdat", "withr", "xfun", "xtable", "yaml", "zoo"), Ncpus = Ncpus)
BiocManager::install(c("graph", "ComplexHeatmap", "Rgraphviz",
"RDRToolbox"), update = FALSE, ask = FALSE)
# Dependencies for packages installed with install_from_url()
install.packages(c("getPass", "ggplotify", "magick", "proto", "randomForest",
"renv", "shinylogs", "shinytoastr", "tsibble"))
"renv", "shinylogs", "shinytoastr", "tsibble"), Ncpus = Ncpus)
# For packages not on CRAN, I install from URL (note: remotes::install_github()
# or remotes::install_url() are problematic because they call GitHub API with
......@@ -65,11 +73,12 @@ install_from_url("
# More R Markdown formats
install.packages(c("distill", "flexdashboard", "pagedown", "posterdown",
"rticles", "xaringan"))
"rticles", "xaringan"), Ncpus = Ncpus)
# More RStudio Addins
install.packages(c("blogdown", "convertr", "covr", "esquisse", "ggExtra",
"golem", "pins", "pkgdown", "questionr", "reprex", "styler", "todor"))
"golem", "pins", "pkgdown", "questionr", "reprex", "styler", "todor"),
Ncpus = Ncpus)
# More useful package not used in the courses
install.packages(c("abind", "agricolae", "akima", "archivist",
......@@ -88,12 +97,12 @@ install.packages(c("abind", "agricolae", "akima", "archivist",
"officedown", "officer", "opencpu", "pagedown", "patchwork", "piggyback",
"plumber", "png", "prettyunits", "printr", "quantreg", "R62S3", "ranger",
"RANN", "RcppExamples", "Rd2roxygen", "recipes", "renv", "reticulate",
"rpart.plot", "rvest", "rvg", "seasonal", "shinybusy", "shinydashboard",
"shinylogs", "shinytoastr", "smotefamily", "spelling", "stargazer",
"stlplus", "survminer", "svDialogs", "svGUI", "svSweave", "sys", "tab",
"tables", "tableschema.r", "tactile", "targets", "tester", "texreg", "tiff",
"titanic", "varSelRF", "vip", "vroom", "writexl", "xgboost", "xts",
"zeallot", "zip", "ztable"))
"rvest", "rvg", "seasonal", "shinybusy", "shinydashboard", "shinylogs",
"shinytoastr", "smotefamily", "spelling", "stargazer", "stlplus", "survminer",
"svDialogs", "svGUI", "svSweave", "sys", "tab", "tables", "tableschema.r",
"tactile", "targets", "tester", "texreg", "tiff", "titanic", "varSelRF",
"vip", "vroom", "writexl", "xgboost", "xts", "zeallot", "zip", "ztable"),
Ncpus = Ncpus)
# BioDataScience|1|2|3
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