Would it be possible to get some assistance with this matter. I have recently started analysing shotgun proteomics data using R and have gotten a bit stuck at this point where i would like to use MSGFgui package to quickly evaluate the preliminary data. However, MSGFgui while it does load (using MSGFgui()), the app itself will not allow be to upload data and returns a cannot open file access denied message an example of which is (warning in file.info(files): cannot open file "C:/System volume information": Access is denied) on the console screen. I have tried updating packages, Rstudio and R itself, deleting the package and reinstalling etc to no avail. 

The session info is attached below. Any help would be very much appreciated!

R version 3.4.3 (2017-11-30)

Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

Matrix products: default

locale:
[1] LC_COLLATE=English_United Kingdom.1252  LC_CTYPE=English_United Kingdom.1252    LC_MONETARY=English_United Kingdom.1252
[4] LC_NUMERIC=C                            LC_TIME=English_United Kingdom.1252    

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

other attached packages:
 [1] MSGFgui_1.12.0   xlsx_0.5.7       xlsxjars_0.6.1   rJava_0.9-9      mzR_2.12.0       Rcpp_0.12.15     shinyjs_1.0     
 [8] shinyFiles_0.6.2 shinyAce_0.2.1   shiny_1.0.5     

loaded via a namespace (and not attached):
 [1] BiocGenerics_0.24.0 doParallel_1.0.11   xtable_1.8-2        R6_2.2.2            foreach_1.4.4       plyr_1.8.4         
 [7] MSGFplus_1.12.0     tools_3.4.3         parallel_3.4.3      mzID_1.16.0         Biobase_2.38.0      iterators_1.0.9    
[13] htmltools_0.3.6     ProtGenerics_1.10.0 yaml_2.1.16         digest_0.6.14       RJSONIO_1.3-0       codetools_0.2-15   
[19] mime_0.5            compiler_3.4.3      XML_3.98-1.9        jsonlite_1.5        httpuv_1.3.5