Cannot install an R package from Github

It’s not uncommon for utilities (in R or other languages/tools) to be able to deal with simple file paths and schema-based URLs (e.g., https://... or file:///...), I think the number of tools that equally deal with Windows’ UNC paths (i.e., \\server\share\path) is much less. While I believe that R is doing it just fine for finding the files (otherwise you’d have other problems by having your only two .libPaths() be UNC shares), the underlying tools (including gcc) might not.

I think the way-forward is to install the new package(s) into a directory that is not a network share. I also think this can be a temporary location, where the packages, once installed, can be moved/migrated over to the network share.

Below is a function that simplifies creation of a temporary directory, install to that directory, then move to the network share. (It doesn’t actually check if the tgt directory is a network share, the assumption is that you would not need to use this is your first library path is local.)

#' Install a package(s) using a temp-local directory
#'
#' On Windows, if '.libPaths()' starts with a UNC network share,
#' package compilation might not work correctly. This function creates
#' a temporary local directory, executes the desired code in 'expr',
#' and moves any new packages into the normal first library path.
#' 
#' @param expr expression such as 'install.packages("car")' or
#'   'devtools::install_github(...)'; the expression must natively
#'   install into the first of '.libPaths()', but if you try something
#'   like 'install.packages(.., lib="some/other/path"), then the
#'   temporary libpath will not be used (and may fail)
#' @param tgt character, the directory to move the isntalled
#'   package(s)
#' @param cleanup logical, whether to remove the temporary libpath
#' @return nothing
with_local_libpath <- function(expr, tgt = .libPaths()[1], cleanup = TRUE) {
  if (length(tgt) > 1) {
    warning("'tgt' must be length 1")
    tgt <- tgt[[1]]
  }
  if (length(tgt) < 1 || !dir.exists(tgt)) {
    stop("'tgt' must be length 1 and an existing directory")
  }

  dir.create(tmplib <- tempfile(pattern = "local_libpath_"))
  message("Local (temp) libpath: ", sQuote(tmplib))
  oldlib <- .libPaths()
  .libPaths(c(tmplib, oldlib))
  on.exit(.libPaths(oldlib), add = TRUE)

  force(expr)

  newstuff <- list.files(tmplib, full.names = TRUE)
  if (length(newstuff)) {
    newdirs <- file.path(oldlib[1], basename(newstuff))
    message("New packages found: ", paste(sQuote(basename(newstuff)), collapse = ", "))
    message("Moving to: ", sQuote(tgt))
    file.copy(newstuff, tgt, recursive = TRUE)
    if (cleanup) {
      message("Cleaning up")
      unlink(tmplib, recursive = TRUE)
    }
  } else {
    message("No new packages found (?)")
  }
  invisible()
}

I tested this with some simple examples, but not extensively, so caveat emptor. I don’t have a network-mounted lib-path, so I’ll force one (to a server I maintain):

.libPaths(c("\\\\myserver/r2evans/R/win.library/3.5", .libPaths()))

Failing installation:

remotes::install_github("gaborcsardi/notifier@d92b1b6")
# Downloading GitHub repo gaborcsardi/notifier@d92b1b6
# v  checking for file 'C:\Users\r2\AppData\Local\Temp\RtmpWgKbkW\remotes43cc57193c83\gaborcsardi-notifier-d92b1b6/DESCRIPTION' (377ms)
# -  preparing 'notifier':
# v  checking DESCRIPTION meta-information
# -  checking for LF line-endings in source and make files and shell scripts
# -  checking for empty or unneeded directories
# -  building 'notifier_1.0.0.tar.gz'
#    
# Installing package into '\\myserver/r2evans/R/win.library/3.5'
# (as 'lib' is unspecified)
# * installing *source* package 'notifier' ...
# ** R
# ** inst
# Error in file.create(to[okay]) : 
#   (converted from warning) cannot create file '\myserver/r2evans/R/win.library/3.5/notifier/R.ico', reason 'No such file or directory'
# * removing '\\myserver/r2evans/R/win.library/3.5/notifier'
# In R CMD INSTALL
# Error: Failed to install 'notifier' from GitHub:
#   (converted from warning) installation of package 'C:/Users/r2/AppData/Local/Temp/RtmpWgKbkW/file43cc60c05cc/notifier_1.0.0.tar.gz' had non-zero exit status

(I chose a specific version because of https://github.com/gaborcsardi/notifier/issues/22. While the error is different than your error, I suspect that the failure is for a similar/related reason.)

Successful installation:

with_local_libpath(remotes::install_github("gaborcsardi/notifier@d92b1b6"))
# Local (temp) libpath: 'C:\Users\r2\AppData\Local\Temp\RtmpWgKbkW\local_libpath_43ccbf98e2'
# Downloading GitHub repo gaborcsardi/notifier@d92b1b6
# v  checking for file 'C:\Users\r2\AppData\Local\Temp\RtmpWgKbkW\remotes43cc7cb66d1f\gaborcsardi-notifier-d92b1b6/DESCRIPTION' (396ms)
# -  preparing 'notifier':
# v  checking DESCRIPTION meta-information
# -  checking for LF line-endings in source and make files and shell scripts
# -  checking for empty or unneeded directories
# -  building 'notifier_1.0.0.tar.gz'
#    
# Installing package into 'C:/Users/r2/AppData/Local/Temp/RtmpWgKbkW/local_libpath_43ccbf98e2'
# (as 'lib' is unspecified)
# * installing *source* package 'notifier' ...
# ** R
# ** inst
# ** byte-compile and prepare package for lazy loading
# ** help
# *** installing help indices
#   converting help for package 'notifier'
#     finding HTML links ... done
#     notify                                  html  
# ** building package indices
# ** testing if installed package can be loaded
# *** arch - i386
# *** arch - x64
# * DONE (notifier)
# In R CMD INSTALL
# New packages found: 'notifier'
# Moving to: '\\myserver/r2evans/R/win.library/3.5'
# Cleaning up

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