Why is R holding on to permission to modify excel files? - r

Question

I am reading in some excel data into R in a loop because I have a bunch of files. This is something that I do regularly. I am having some trouble though and I'm not sure even how to make reproducible example. So i have all the files that I want in one directory and I am reading them in using this set of commands:
## Because I want warnings to stop the loop at a certain file so I can diagnose
options(warn=2)
xl_load_in <- c()
for (x in list.files(pattern="*\\.xls")) {
cat(x, "\n ")
u <- read_excel(x,col_types=c("text","text","numeric","numeric","numeric","numeric","numeric","numeric","numeric","numeric","numeric","numeric","text"))
xl_load_in <- tbl_df(rbind(xl_load_in, u))
}
options(warn=0)
So this is both a tool to read in files but also, using the warn toggle, I can diagnose which files aren't reading in correctly.
Now the problem: From a fresh reboot and I can rename and save the excel files in the directory. If, however, I run the above R code, I lose the permission to save or rename the excel file where the loop broke (There are small issues with the excel files that have to rectified manually). For example if I try to rename the file upon which the loop broke I get this windows error:
The action can't be completed because the file is open in RStudio R
Session.
If I reboot, I can again modify the file in question. But before the reboot I can't save or rename the file. Can anyone explain this behaviour where R or Rstudio seems to be taking over my permissions?
Update If I close RStudio, the permissions are returned. If I do the same sequence of commands above using RGUI for Windows, the problem in replicated indicating the issue is not an RStudio problem.
sessionInfo()
R version 3.3.2 (2016-10-31)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)
locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C LC_TIME=English_United States.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] stringr_1.1.0 readxl_0.1.1 lubridate_1.6.0 dplyr_0.5.0 purrr_0.2.2 readr_1.0.0 tidyr_0.6.0 tibble_1.2
[9] ggplot2_2.2.0 tidyverse_1.0.0
loaded via a namespace (and not attached):
[1] Rcpp_0.12.7 assertthat_0.1 R6_2.2.0 grid_3.3.2 plyr_1.8.4 DBI_0.5-1 gtable_0.2.0
[8] magrittr_1.5 scales_0.4.1 stringi_1.1.2 lazyeval_0.2.0 tools_3.3.2 munsell_0.4.3 colorspace_1.3-0