Packages and version control associated with tinselR

[jennahamlin]

Environment control

One mechanism for providing a unique environment for a package or application is renv. See below for a link to set this up on your machine.

Packages installed on windows machine when installing Tinsel

Below I list all packages that are installed on a windows machine after returning R to only include base R packages.
Following the quick start steps in the README; the list packages below are what is installed using these commands

#install devtools
install.packages("devtools", dep=T)

#install ggtree and treeio
if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("ggtree")

#install from github Tinsel; load library and run application
devtools::install_github("jennahamlin/Tinsel")
Library(Tinsel)
run_app()

[jennahamlin]

renv created by rstudio

renv link
renv vignette

I am attempting to use renv to capture all package dependencies from now on. The main upside to renv compared to packrat is that renv can be initialized any time not necessarily before a new project which is what I could figure out how packrat worked.

[jennahamlin]

Packages installed on windows machine when starting from base R and sessionInfo information

Following this answer, I ran this function to print all packages loaded into the R environment after running the run_dev.R script for Tinsel

print(paste("R", getRversion()))
print("-------------")
for (package_name in sort(loadedNamespaces())) {
    print(paste(package_name, packageVersion(package_name)))
}

[1] "ape 5.4.1"
[1] "assertthat 0.2.1"
[1] "attempt 0.3.1"
[1] "backports 1.1.10"
[1] "base 3.6.0"
[1] "BiocManager 1.30.10"
[1] "callr 3.5.1"
[1] "cli 2.1.0"
[1] "clusterGeneration 1.3.5"
[1] "coda 0.19.4"
[1] "colorspace 1.4.1"
[1] "combinat 0.0.8"
[1] "compiler 3.6.0"
[1] "config 0.3"
[1] "crayon 1.3.4"
[1] "curl 4.3"
[1] "datasets 3.6.0"
[1] "desc 1.2.0"
[1] "devtools 2.3.2"
[1] "digest 0.6.26"
[1] "dockerfiler 0.1.3"
[1] "dplyr 1.0.2"
[1] "ellipsis 0.3.1"
[1] "expm 0.999.5"
[1] "fansi 0.4.1"
[1] "farver 2.0.3"
[1] "fastmap 1.0.1"
[1] "fastmatch 1.1.0"
[1] "fs 1.5.0"
[1] "generics 0.0.2"
[1] "ggplot2 3.3.2"
[1] "ggtree 2.0.4"
[1] "glue 1.4.2"
[1] "golem 0.2.1"
[1] "graphics 3.6.0"
[1] "grDevices 3.6.0"
[1] "grid 3.6.0"
[1] "gtable 0.3.0"
[1] "gtools 3.8.2"
[1] "hms 0.5.3"
[1] "htmltools 0.5.0"
[1] "httpuv 1.5.4"
[1] "igraph 1.2.6"
[1] "jsonlite 1.7.1"
[1] "knitr 1.30"
[1] "labeling 0.4.2"
[1] "later 1.1.0.1"
[1] "lattice 0.20.38"
[1] "lazyeval 0.2.2"
[1] "lifecycle 0.2.0"
[1] "magrittr 1.5"
[1] "maps 3.3.0"
[1] "MASS 7.3.51.4"
[1] "Matrix 1.2.17"
[1] "memoise 1.1.0"
[1] "methods 3.6.0"
[1] "mime 0.9"
[1] "mnormt 2.0.2"
[1] "munsell 0.5.0"
[1] "nlme 3.1.139"
[1] "numDeriv 2016.8.1.1"
[1] "parallel 3.6.0"
[1] "phangorn 2.5.5"
[1] "phylotools 0.2.2"
[1] "phytools 0.7.70"
[1] "pillar 1.4.6"
[1] "pkgbuild 1.1.0"
[1] "pkgconfig 2.0.3"
[1] "pkgload 1.1.0"
[1] "plotrix 3.7.8"
[1] "prettyunits 1.1.1"
[1] "processx 3.4.4"
[1] "promises 1.1.1"
[1] "ps 1.4.0"
[1] "purrr 0.3.4"
[1] "quadprog 1.5.8"
[1] "R6 2.4.1"
[1] "Rcpp 1.0.5"
[1] "readr 1.4.0"
[1] "remotes 2.2.0"
[1] "rlang 0.4.8"
[1] "roxygen2 7.1.1"
[1] "rprojroot 1.3.2"
[1] "rstudioapi 0.11"
[1] "rvcheck 0.1.8"
[1] "scales 1.1.1"
[1] "scatterplot3d 0.3.41"
[1] "sessioninfo 1.1.1"
[1] "shiny 1.5.0"
[1] "shinyjs 2.0.0"
[1] "shinythemes 1.1.2"
[1] "stats 3.6.0"
[1] "stringi 1.5.3"
[1] "stringr 1.4.0"
[1] "testthat 2.3.2"
[1] "tibble 3.0.4"
[1] "tidyr 1.1.2"
[1] "tidyselect 1.1.0"
[1] "tidytree 0.3.3"
[1] "Tinsel 0.0.0.9000"
[1] "tmvnsim 1.0.2"
[1] "tools 3.6.0"
[1] "treeio 1.10.0"
[1] "usethis 1.6.3"
[1] "utils 3.6.0"
[1] "vctrs 0.3.4"
[1] "withr 2.3.0"
[1] "xfun 0.18"
[1] "xml2 1.3.2"
[1] "xtable 1.8.4"
[1] "yaml 2.2.1"

sessionInfo()
R version 3.6.0 (2019-04-26)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18363)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C LC_TIME=English_United States.1252

attached base packages:
[1] stats graphics grDevices utils datasets methods base

other attached packages:
[1] shiny_1.5.0 Tinsel_0.0.0.9000 testthat_2.3.2