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help

Aurelien Chateigner

2018-11-05

Introduction

This vignette exists as help is limited by CRAN to 5 seconds runs, and it depends a lot on user’s connection. It will also explain the advance use of the package.

Using anyLib

Loading the package

To load anyLib, simply :

library(anyLib)

For the purpose of the demonstration, installations in this vignette are done in a dummy library:

lib <- normalizePath(tempdir(), "/")
f1 <- paste(lib, "folder1", sep = "/")
dir.create(f1)
.libPaths(f1)

Install and load 1 package

CRAN package

So, if one wants to install a simple CRAN package and load it, simply:

anyLib("apercu", lib = f1)
#> also installing the dependencies 'assertthat', 'cli', 'crayon', 'digest', 'magrittr', 'praise', 'R6', 'rlang', 'withr', 'pls', 'testthat'
#> package 'assertthat' correctement décompressé et sommes MD5 vérifiées
#> package 'cli' correctement décompressé et sommes MD5 vérifiées
#> package 'crayon' correctement décompressé et sommes MD5 vérifiées
#> package 'digest' correctement décompressé et sommes MD5 vérifiées
#> package 'magrittr' correctement décompressé et sommes MD5 vérifiées
#> package 'praise' correctement décompressé et sommes MD5 vérifiées
#> package 'R6' correctement décompressé et sommes MD5 vérifiées
#> package 'rlang' correctement décompressé et sommes MD5 vérifiées
#> package 'withr' correctement décompressé et sommes MD5 vérifiées
#> package 'pls' correctement décompressé et sommes MD5 vérifiées
#> package 'testthat' correctement décompressé et sommes MD5 vérifiées
#> package 'apercu' correctement décompressé et sommes MD5 vérifiées
#> 
#> The downloaded binary packages are in
#>  C:\Users\achateigner\AppData\Local\Temp\RtmpshD88Y\downloaded_packages
#> Loading required package: apercu
#> apercu 
#>   TRUE

Source package

For a source package:

anyLib(system.file("dummyPackage_0.1.0.tar.gz", package = "anyLib"),
       source = TRUE, lib = f1, loadLib = f1)
#> Loading required package: dummyPackage
#> dummyPackage 
#>         TRUE

Bioconductor package

For a Bioconductor package:

anyLib("limma", lib = f1, loadLib = f1)
#> Loading required package: limma
#> Warning in library(package, lib.loc = lib.loc, character.only = TRUE,
#> logical.return = TRUE, : there is no package called 'limma'
#> limma 
#> FALSE

github package

And for github, to install, one needs the name in the format “maintainerName/packageName”:

anyLib("achateigner/dummyPackage", force = TRUE, lib = f1, loadLib = f1)
#> dummyPackage 
#>         TRUE

But to load it once installed, one only needs its name:

anyLib("dummyPackage", lib = f1, loadLib = f1)
#> dummyPackage 
#>         TRUE

Install and load a list of packages

To install and load a list of packages, from various places, with the names. I install them in a different folder:

f2 <- paste(lib, "folder2", sep = "/")
dir.create(f2)
anyLib(list("apercu", "limma", "achateigner/dummyPackage"), lib = f2,
       loadLib = f2)
#> package 'apercu' correctement décompressé et sommes MD5 vérifiées
#> 
#> The downloaded binary packages are in
#>  C:\Users\achateigner\AppData\Local\Temp\RtmpshD88Y\downloaded_packages
#> Loading required package: apercu
#> Loading required package: limma
#> Warning in library(package, lib.loc = lib.loc, character.only = TRUE,
#> logical.return = TRUE, : there is no package called 'limma'
#> Loading required package: dummyPackage
#> Warning in library(package, lib.loc = lib.loc, character.only = TRUE,
#> logical.return = TRUE, : there is no package called 'dummyPackage'
#>       apercu        limma dummyPackage 
#>         TRUE        FALSE        FALSE

To install and load from a list of packages in an object:

f3 <- paste(lib, "folder3", sep = "/")
dir.create(f3)
packagesNeeded <- list("apercu", "limma", "achateigner/dummyPackage")
anyLib(packagesNeeded, lib = f3, loadLib = f3)
#> package 'apercu' correctement décompressé et sommes MD5 vérifiées
#> 
#> The downloaded binary packages are in
#>  C:\Users\achateigner\AppData\Local\Temp\RtmpshD88Y\downloaded_packages
#> Loading required package: apercu
#> Loading required package: limma
#> Warning in library(package, lib.loc = lib.loc, character.only = TRUE,
#> logical.return = TRUE, : there is no package called 'limma'
#> Loading required package: dummyPackage
#> Warning in library(package, lib.loc = lib.loc, character.only = TRUE,
#> logical.return = TRUE, : there is no package called 'dummyPackage'
#>       apercu        limma dummyPackage 
#>         TRUE        FALSE        FALSE

Advanced options

If one wants to reinstall a package or force the update (force = TRUE), not update the Bioconductor packages (autoUpdate = FALSE), install in a different lib and load from a set of libs:

f4 <- paste(lib, "folder4", sep = "/")
dir.create(f4)
anyLib(packagesNeeded,
       force = TRUE,
       autoUpdate = FALSE,
       lib = f4,
       loadLib = c(f1, f4))
#> package 'apercu' correctement décompressé et sommes MD5 vérifiées
#> 
#> The downloaded binary packages are in
#>  C:\Users\achateigner\AppData\Local\Temp\RtmpshD88Y\downloaded_packages
#> Loading required package: apercu
#> Loading required package: limma
#> Warning in library(package, lib.loc = lib.loc, character.only = TRUE,
#> logical.return = TRUE, : there is no package called 'limma'
#> Loading required package: dummyPackage
#>       apercu        limma dummyPackage 
#>         TRUE        FALSE         TRUE

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
Health stats visible at Monitor.