Error in installation of R package

[MPagel]

Problem:

After installation of the github repo I was unable to immediately run listSupportedDialects, getting a "no package" error. In my case, the package "cli" needed to be updated, which is "impossible" within the R environment alone.

Solution:

> unloadNamespace('cli')

Then with R session still running, navigate to your user's library directory, which you can find by reading the output of

> library()
or in R Studio
> .rs.defaultUserLibraryPath()

rename the "cli" folder to e.g. "cli_backup" or delete it

reinstall cli (to the latest version)
> install.packages("cli")

then re-run
> devtools::install_github("OHDSI/CommonDataModel")

details below the bump

After installing the github repo via the suggested devtools mechanism, I ran

> CommonDataModel::listSupportedDialects()
Error in loadNamespace(x) : there is no package called ‘CommonDataModel’
> library(CommonDataModel) # same error using single or double quotes
Error in library(CommonDataModel) : 
  there is no package called ‘CommonDataModel’
> devtools::install_github("OHDSI/CommonDataModel") # trying again
Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : 
  namespace ‘cli’ 3.2.0 is already loaded, but >= 3.3.0 is required
> install.packages("cli")
Installing package into ‘C:/Users/mpagel/OneDrive - Emory University/Documents/R/win-library/4.1’
(as ‘lib’ is unspecified)
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.1/cli_3.6.1.zip'
Content type 'application/zip' length 1388241 bytes (1.3 MB)
downloaded 1.3 MB

package ‘cli’ successfully unpacked and MD5 sums checked
Warning in install.packages :
  cannot remove prior installation of package ‘cli’
Warning in install.packages :
  problem copying C:\Users\mpagel\OneDrive - Emory University\Documents\R\win-library\4.1\00LOCK\cli\libs\x64\cli.dll to C:\Users\mpagel\OneDrive - Emory University\Documents\R\win-library\4.1\cli\libs\x64\cli.dll: Permission denied
Warning in install.packages :
  restored ‘cli’

The downloaded binary packages are in
	C:\Users\mpagel\AppData\Local\Temp\RtmpcZjM6W\downloaded_packages
> detach("package:cli", unload = TRUE, character.only = TRUE)
Error in detach("package:cli", unload = TRUE, character.only = TRUE) : 
  invalid 'name' argument
> sessionInfo()
R version 4.1.3 (2022-03-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 22000)

Matrix products: default

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

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

loaded via a namespace (and not attached):
[1] compiler_4.1.3    cli_3.2.0         tools_4.1.3       data.table_1.14.2
> unloadNamespace('cli')

> install.packages("cli")
Installing package into ‘C:/Users/mpagel/OneDrive - Emory University/Documents/R/win-library/4.1’
(as ‘lib’ is unspecified)
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.1/cli_3.6.1.zip'
Content type 'application/zip' length 1388241 bytes (1.3 MB)
downloaded 1.3 MB

package ‘cli’ successfully unpacked and MD5 sums checked
Warning in install.packages :
  cannot remove prior installation of package ‘cli’
Warning in install.packages :
  problem copying C:\Users\mpagel\OneDrive - Emory University\Documents\R\win-library\4.1\00LOCK\cli\libs\x64\cli.dll to C:\Users\mpagel\OneDrive - Emory University\Documents\R\win-library\4.1\cli\libs\x64\cli.dll: Permission denied
Warning in install.packages :
  restored ‘cli’

The downloaded binary packages are in
	C:\Users\mpagel\AppData\Local\Temp\RtmpcZjM6W\downloaded_packages

Manually re-naming cli.dll to cli.dll.bak did NOT allow me to update -- it simply tried to write from the LOCK location to the bak file. So, you either have to delete the .dll as per https://community.rstudio.com/t/how-to-update-cli-package/141134/2 or rename the package directory R\win-library\4.1\cli

then you can run

> install.packages("cli")
Installing package into ‘C:/Users/mpagel/OneDrive - Emory University/Documents/R/win-library/4.1’
(as ‘lib’ is unspecified)
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.1/cli_3.6.1.zip'
Content type 'application/zip' length 1388241 bytes (1.3 MB)
downloaded 1.3 MB

package ‘cli’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
	C:\Users\mpagel\AppData\Local\Temp\Rtmpie0j8R\downloaded_packages
> devtools::install_github("OHDSI/CommonDataModel")