Installing and Updating Problematic R packages

.R

# A gist describing common problems (and solutions) when R packages won't update.
# This gist is divided into sections with each section representing a common or known problem. 
# At the beginning of each section is a short description of the problem and the R output that likely prompted you to look for this gist.
# Following the problem is code for one or more potential solutions to try.
# These problems and solutions are aimed at National Park Service users and may be specific to government systems 
# (i.e. user likely does not have admin rights so those solutions are not included).

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#### cannot download packages from github ####
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# download from github fails:
  devtools::install_github("nationalparkservice/NPSdataverse")
  # Error in utils::download.file(url, path, method = method, quiet = quiet,  : 
  # download from 'https://api.github.com/repos/nationalparkservice/NPSdataverse/tarball/HEAD' failed

#1. reset .Renviron file download options:
 options(download.file.method = "wininet")

#2. ignore warnings abuot deprecated methods
#3. retry package installation:
  devtools::install_github("nationalparkservice/NPSdataverse")
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#### github times out/requires token ########
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#1. See this much more informative gist on using github with R/Rstudio:
 # https://gist.github.com/Z3tt/3dab3535007acf108391649766409421
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##### Loaded Package won't update ############
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#If the package is already loaded:
  install.packages("cli")
  # Error in install.packages : Updating loaded packages

  #1. unload and detach the package
  detach("package:cli", unload = TRUE)
  
  #2. then try again:
  install.packages("cli")
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##### Permissions Denied! ####################
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# R cannot remove a previous version of a package and gives you "permissions denied".
# You likely DO have permissions to write to this location
# The problem is the '00LOCK' directory, which has locked you out of the folder.

install.package("cli")
 #... some time later these messages crop up:
 #package ‘cli’ successfully unpacked and MD5 sums checked
 #Warning: cannot remove prior installation of package ‘cli’
 #Warning: restored ‘cli’

 #In file.copy(savedcopy, lib, recursive = TRUE) :
 #  problem copying C:\Users\rlbaker\AppData\Local\R\win-library\4.2\00LOCK\cli\libs\x64\cli.dll to C:\Users\rlbaker\AppData\Local\R\win-library\4.2\cli\libs\x64\cli.dll: Permission denied

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# Solution 1: attempt to remove the 00LOCK folder in R:
  #1. install a package management package...very meta. 
  install.packages("pacman")
  
  #2. remove the 00LOCK folder (or attempt to)
  pacman::p_unlock(lib.loc = pacman::p_path())

  #if successful:
   #The following 00LOCK has been deleted:
   #/Users/rlbaker/AppData/Local/R/win-library/4.2/00LOCK-cli following 00LOCK has been deleted:

  #if unsuccessful:
   #No 00LOCK detected in:
   #C:/Users/rlbaker/AppData/Local/R/win-library/4.2
   
  #. retry package installation:
  install.packages("cli")

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# Solution 2: manually remove the offending package using windows file explorer:
 #1. Locate packages:
  .libPaths()
  #[1] "C:/Users/rlbaker/AppData/Local/R/win-library/4.2"
  #[2] "C:/Program Files/R/R-4.2.0/library" 

 #2. Navigate to the package in windows explorer and delete it. 
 #3. Restart R/Rstudio, and try the install again.
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##### Manage Package Locations ###############
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# Where are my packages being saved?
  .libPaths()
  #[1] "C:/Users/rlbaker/AppData/Local/R/win-library/4.2"
  #[2] "C:/Program Files/R/R-4.2.0/library" 

# Swap the existing default library locations:
  .libPaths( c(.libPaths()[2], .libPaths()[1]) )

## add a new or different library location:
 #1. In windows explorer, make a new folder (or find an existing one).
 #2. Add the folder as the default location for packages:
 .libPaths( c("C:/Users/rlbaker/documents/my_new_packages", .libPaths() )
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