My R start up script seems to be producing errors

Question

I noticed a week ago that my R start up script starting running the below following the line Type 'q()' to quit R

The only thing I did different was to set my Cran mirror in the Rprofile.site file.

I tried online and also in other Stackoverflow posts put couldn't find a solution. I was told online though that the Cran mirror setting I performed should have nothing to do with this.

Can you please help?

Attempting to load the environment ‘package:R.utils’
R.methodsS3 v1.2.2 (2010-11-17) successfully loaded. See ?R.methodsS3 for help.
R.oo v1.9.3 (2012-03-18) successfully loaded. See ?R.oo for help.

Attaching package: ‘R.oo’

The following object(s) are masked from ‘package:R.methodsS3’:

    throw.default

The following object(s) are masked from ‘package:methods’:

    getClass, getClasses, getMethods

The following object(s) are masked from ‘package:base’:

    attach, detach, gc, load, save

R.utils v1.12.1 (2012-03-20) successfully loaded. See ?R.utils for help.

Attaching package: ‘R.utils’

The following object(s) are masked from ‘package:utils’:

    timestamp

The following object(s) are masked from ‘package:base’:

    cat, commandArgs, getOption, inherits, isOpen, lapply, parse,
    warnings

And here is my Rprofile.site file specs:

# Things you might want to change
# options(papersize="a4")
# options(editor="notepad")
# options(pager="internal")

# set the default help type
# options(help_type="text")
options(help_type="html")

# set a site library
# .Library.site <- file.path(chartr("\\", "/", R.home()), "site-library")

# set a CRAN mirror
 local({r <- getOption("repos")
   r["CRAN"] <- "http://cran.cnr.Berkeley.edu"
   options(repos=r)})

# Give a fortune cookie, but only to interactive sessions
# (This would need the fortunes package to be installed.)
#  if (interactive()) 
#    fortunes::fortune()

I suggest you also post the contents of `Rprofile.site` here. It seems fairly clear that you have an instruction to load `R.Utils` http://cran.r-project.org/web/packages/R.utils/index.html somewhere in your initialization script. I presume you don't want this? — Andrie, Jun 11 '12 at 21:11
Dan, @Andrie meant to edit that into your question. It's difficult to read as a comment. — Joshua Ulrich, Jun 11 '12 at 21:38
My guess is that you are (implicitly) loading a workspace that requires those packages. Do you have an `.RData` file in the starting directory? If you move/remove it, do you still see this behavior? — Brian Diggs, Jun 11 '12 at 22:12
@Brain Is the starting directory for R the same as where the Rprofile.site file is? For me that's C:\R\R-2.15.0\etc I don't see any .RData file there or at the level above or the root C:\R — daniellopez46, Jun 11 '12 at 22:41
In the R header that is printed does it mention anything about a previously saved workspace? Perhaps you could add the bit **before** the Roo-related text you already showed. — Gavin Simpson, Jun 12 '12 at 07:44
Also, start R using the `--vanilla` flag and see if the problem persists. If it does, rename your `.Rprofile.site` file temporarily and start R again (without the `--vanilla` flag). If problem still persists, check for hidden files `.Rhistory` and `.RData` in the place where R starts or where you are starting R. See the [Invoking R](http://cran.r-project.org/doc/manuals/R-intro.html#Invoking-R) section of the R Installation & Administration Manual. — Gavin Simpson, Jun 12 '12 at 07:56

My R start up script seems to be producing errors

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