If R package is already install - load it; if not installed, install it

Question

[melissachua90]

I want to create a function to install only missing packages. If the package is already install, just load it. My R function below failed to install any of the packages (KEGGREST, EnrichmentBrowser, org.Hs.eg.db). Why?

# Install missing packages or load the package if already installed
if(!requireNamespace('BiocManager', quietly=TRUE)){
  install_version('BiocManager', version='3.14', repos="http://cran.us.r-project.org")
}
require('BiocManager')

  packages=c("KEGGREST", "EnrichmentBrowser", "org.Hs.eg.db")
  package.check <- sapply(
    packages,
    FUN = function(x) {
      if (!requireNamespace(x, quietly=TRUE)){
        BiocManager::install(x, dependencies=TRUE)
      }
      library(x, character.only=TRUE)
    }
  )

Traceback:

Error in library(x, character.only = TRUE) :
  there is no package called ‘KEGGREST’
Calls: sapply -> lapply -> FUN -> library
In addition: There were 50 or more warnings (use warnings() to see the first 50)
Execution halted

Answer 1

[Kevin Blighe]

Hi, I would do it like this, first ensuring that BiocManager is installed, and then using that as the installer. Also note the use of sapply() (not a big difference maybe) and requireNamespace():

if (!requireNamespace('BiocManager', quietly = TRUE)) {
    install.packages('BiocManager')
}
require('BiocManager')

# Install missing packages or load the package if already installed    
  packages <- c('KEGGREST', 'EnrichmentBrowser', 'org.Hs.eg.db')
  package.check <- sapply(
    packages,
    FUN = function(x) {
      if (!requireNamespace(x, quietly = TRUE)) {
        BiocManager::install(x, dependencies = TRUE)
      }
      library(x, character.only = TRUE)
    }
  )

Kind regards,

Kevin

[melissachua90]

It returns a new error:

Error in contrib.url(repos, type) : trying to use CRAN without setting a mirror Calls: install.packages -> startsWith -> contrib.url Execution halted

[Kevin Blighe]

From where are you running R - RStudio on Windows? You basically need to first configure your mirror for CRAN. This is a problem that is unrelated [directly] to the code that I have posted.

[melissachua90]

I'm using a remote server without sudo permissions.

[Kevin Blighe]

Then that may be a problem. Perhaps, for now, can you try:

install.packages('BiocManager', repos = 'http://cran.us.r-project.org')

[melissachua90]

I specified a Bioconductor version which is compatible to the packages that I want to install. However, the code is unable to install any of the packages.

Error in library(x, character.only = TRUE) :
  there is no package called ‘KEGGREST’
Calls: sapply -> lapply -> FUN -> library
In addition: There were 50 or more warnings (use warnings() to see the first 50)
Execution halted

[Kevin Blighe]

...and if you try to install KEGGREST manually? You probably run into access issues, in which case the code that you wrote -- and that I further developed -- will neither be able to install the package.