Post-mortem debugging: Clarify and document what happens to loaded packages when the dump is written and loaded again

[aryoda]

What happens to the search path search(), are the loaded environments contained in the dump file or are the packages only referenced?

Does load load the packages again that were loaded when the dump was written?

...

[aryoda]

Result:

save.image does NEITHER store the objects of the loaded packages ("namespaces") NOR the search path!

This means

1. you cannot step through your source code in a reproducible way after loading the image
   if your source code calls functions of non-default packages
2. the program state is not exactly reproducible if objects are stored within a package namespace

TODO

Document this in the function header of tryCatchLog and other (planned) documentations.

Proove:

# Test code to evaluate the "save.image" behaviour for loaded packages and the search path

initial.search <- search()
initial.loadedNamespaces <- loadedNamespaces()

library(data.table)
library(ggplot2)

current.search <- search()
current.loadedNamespaces <- loadedNamespaces()

save.image("test.Rdata")



stop("Restart the R session now")
# Now restart the R session to have a clean environment and check whether the loaded image
# contains the search path and loaded packages ("namespaces"):



load("test.Rdata")


search()
# [1] ".GlobalEnv" "tools:rstudio" "package:stats" "package:graphics" "package:grDevices" "package:utils" "package:datasets" "package:methods" "Autoloads" "package:base"

initial.search
# [1] ".GlobalEnv" "tools:rstudio" "package:stats" "package:graphics" "package:grDevices" "package:utils" "package:datasets" "package:methods" "Autoloads" "package:base"


setdiff(initial.search, search() )
# character(0)

loadedNamespaces()
# [1] "rsconnect" "graphics"  "tools"     "utils"     "grDevices" "stats"     "datasets"  "methods"   "base"     

initial.loadedNamespaces
# [1] "rsconnect" "graphics"  "tools"     "utils"     "grDevices" "stats"     "datasets"  "methods"   "base"     

# RESULT:
# "save.image" does NEITHER store the objects of the loaded packages ("namespaces") NOR the search path!
# This means you cannot step through your source code in a reproducible way after loading the image
# if your source code calls functions of non-default packages!

setdiff(initial.loadedNamespaces, loadedNamespaces())
# character(0)

current.search
# [1] ".GlobalEnv" "package:ggplot2" "package:data.table" "tools:rstudio" "package:stats" "package:graphics" "package:grDevices" "package:utils" "package:datasets" "package:methods" "Autoloads" "package:base"

current.loadedNamespaces
# [1] "colorspace" "scales" "plyr" "rsconnect" "graphics" "tools" "gtable" "utils" "grDevices" "Rcpp" "stats" "ggplot2" "datasets" "grid" "data.table" "methods" "chron" "munsell" "base"

[aryoda]

This behaviour is documented now in the help for the tryCatchLog function and in the training slides for error handling (see https://github.com/aryoda/R_trainings).