From gregory_r_warnes@groton.pfizer.com  Tue Oct 22 14:46:40 2002
From: gregory_r_warnes@groton.pfizer.com (Warnes, Gregory R)
Date: Tue, 22 Oct 2002 09:46:40 -0400
Subject: Loading packages at startup
Message-ID: <D7A3CFD7825BD6119B880002A58F06C20149D0EF@groexmb02.pfizer.com>



> 4) One problem with saving an R session and then restoring it is that
>    the packages in use are not reloaded.  Quitting an R session and
>    saving could write .Rpackages in the current directory (with the
>    library recorded if it were not the default).  Then restarting a
>    session in that directory would restore the loaded packages
>    automatically.


I've been using another approach for this.   For the R + Zope tools that
I've developed here (Yes, they will be released once I finally get through
all the red tape!) I needed a way to store all of the information about a
session, including loaded packages and the search path.

At the end of this message, I list two functions, save.session() and
load.session() which I wrote to accomplish this.  In addition, I have an .Rd
documentation file for them, and can provide that if anyone is interested.

The functions save.session() records the list of loaded packages into a
variable named ".save.session.packages" which is then saved as part of
save.image().   The load.session() function then uses load() to reload the
saved image and uses the ".save.session.packages" function to reload the
packages.  A similar thing happens for the search path.   This works well
and seems less hazard-prone than overwriting the users '.Rpackages' file for
two reasons:  1) the loaded package list and search path are preserved with
the data, and 2) we aren't messing with the user's files...

One enhancement that would be desirable is to allow the user to request that
the search path or the packages not be restored.  Of course, both can be
avoided by just using load() instead of load.session() on the data file.

-Greg

save.session <- function(file=".RSession",...)
  {
    if(!is.null(dev.list()))
       warning("Open graphics devices will not be saved or restored.")

    cat("Saving search path..\n")
    .save.session.search <<- search()
    
    cat("Saving list of loaded packages..\n")
    .save.session.packages <<- .packages()
   
    cat("Saving all data...\n")
    save(list=ls(envir = .GlobalEnv, all.names = TRUE), file=file, ...)
    cat("Done.\n")
  }

restore.session <- function(file=".RSession",...)
  {
    cat("Loading all data...\n")
    load(file,envir = .GlobalEnv,...)

    cat("Loading packages...\n")
    sapply( rev(.save.session.packages), library, character.only=T )

    cat("Restoring search path...\n")

    pad <- function(x,n) c( rep(NA,n-length(x)), x )
    
    current.search <- search()[-1]
    saved.search <- .save.session.search[-1]

    identical <- pad(current.search, length(saved.search)) == saved.search 
    
    for( i in saved.search[!identical] )
      {
        if( charmatch( "file:", i, nomatch=FALSE) )
          attach(sub( "file:", "", "file:test" ) )
        else if (charmatch( "package:", i, nomatch=FALSE)  )
          stop(paste("Somehow we missed loading package",i))
        else
          {
            do.call("attach",list(as.name(i)))
          }
               
      }

    rm(list=c(".save.session.packages",
              ".save.session.search"),
       envir = .GlobalEnv )
         
    
    cat("Done.\n")
  }    



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Loading packages at startup
Warnes, Gregory R