[R] error message when downloading packages using the OS X shell

Wed Feb 17 08:22:08 CET 2010

Thank you all for your help thus far. I have taken care of the destdir
issue (you do need to specify a destdir, something I never had to do
with OS X 10.4). However, a delightful new message has popped up. Has
anyone seen this one before? I've tried both an R CMD INSTALL command
from the shell and the download.packages() command within the R
environment but neither works. In the terminal I get this error:

$ R CMD INSTALL genetics_1.3.4.tgz
Warning: invalid package ‘genetics_1.3.4.tgz’

while in R I get this error:

> download.packages(genetics,destdir=.libPaths())
Error in unique(pkgs) : object 'genetics' not found

The errors are not worded the same but they appear to be suggesting
the same issue. I've tried the names of 6 or so different packages
just to see what would happen but it's always the same message. And,
in answer to Ista, I am using download.packages() instead of
install.packages() because they are both giving me the same error
message but at least download.packages() gives me some response by
loading a Tcl/Tk interface to select my CRAN mirror so I at least know
it's working.

Thank you all!
Jessica

On Mon, Feb 15, 2010 at 11:11 PM, Ista Zahn <istazahn at gmail.com> wrote:
>
> Hi Jessica,
> As far as I know that's the expected behavior (at least it's not OS
> X-specific: I get the same on OpenSuse 11.2). What happens if you do
>
> download.packages("ape", destdir = "~/Desktop/")
>
> ?
>
> Also, out of curiosity, why are you using download.packages() instead
> of install.packages()?
>
> Best,
> Ista
>
> On Mon, Feb 15, 2010 at 10:51 PM, Jessica Joganic <jjoganic at gmail.com> wrote:
> > I apologize for not including my entire script. What I typed into the shell
> > was:
> >
> > *download.packages(ape)*
> >
> > to which R responded with a Tcl/Tk interface allowing me to set my CRAN.
> > After I did so it proceeded to spit out the following error:
> >
> > *Loading Tcl/Tk interface ... done*
> > Error in **file.info* <http://file.info>*(x) : argument "destdir" is
> > missing, with no default*
> >
> > Let me know if that doesn't clarify my query. If this ends up being a
> > product of my preferring the terminal over the R.app then I'll post to the
> > Mac people and see what they have to say.
> >
> > Jessica
> > **
> >
> > On Mon, Feb 15, 2010 at 9:06 PM, David Winsemius <dwinsemius at comcast.net>wrote:
> >
> >>
> >> On Feb 15, 2010, at 8:58 PM, Jessica Joganic wrote:
> >>
> >>  Hi Fellow R Users,
> >>> I recently upgraded to Mac OS X 10.5 (Snow Leopard) and had some issues
> >>> downloading and running R 2.10.1. I fixed the tcl/tk problem I was
> >>> originally having but it was replaced with another. I run R out of the
> >>> shell
> >>> (terminal) and when I ask it to download.packages() it gives me the
> >>> following message:
> >>>
> >>> *Loading Tcl/Tk interface ... done*
> >>> *Error in file.info(x) : argument "destdir" is missing, with no default*
> >>> *
> >>> *
> >>>
> >>
> >> I am a bit puzzled by that function call. I would have expected there to be
> >> some arguments in the call. What were you expecting to be the results?
> >>  After I run that function, I get a window of CRAN sites to choose and after
> >> choosing the CMU site I get:
> >>
> >> > download.packages()
> >> --- Please select a CRAN mirror for use in this session ---
> >>
> >> Loading Tcl/Tk interface ... done
> >> Error in file.info(x) : argument "destdir" is missing, with no default
> >>
> >>  I searched around on the help archives and various online message boards
> >>> and
> >>> the most I could discern was that the directory where the library is
> >>> located
> >>> isn't being recognized by R (it should recognize it by default). I tried
> >>> setting the "destdir" argument manually to no avail. I am able to
> >>> successfully download and install packages with no problem if I run the
> >>> actual R program out of the Applications folder,
> >>>
> >>
> >> Heh, the thing you are calling the "actual R program" is probably the
> >> R-GUI, typically named R.app or R64.app, and it is a front-end to the R
> >> executable.
> >>
> >>
> >>  however I prefer to use the
> >>> shell. I did find one mention of a recognized issue with OS X 10.5 and R
> >>> 2.10.1 conflicting when trying to download packages, which results in the
> >>> library pathway being broken. The only problem is the fix for this problem
> >>>
> >>
> >>  given in the R manual doesn't work. Has anyone had a similar problem or
> >>> have
> >>> any ideas as to how to solve this?
> >>>
> >>
> >> It happens for me as well, but I guess I don't see it as a problem, since I
> >> did not offer a sensible set of arguments to the function. (Plus, I always
> >> use the GUI despite Rolf Turner's efforts to shame me into being a terminal
> >> dude.) You may want to post follow-ups to the Mac-SIG mailing list where
> >> this would be amore appropriate question:
> >>
> >> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
> >>
> >>>
> >>>  --
> >>
> >> David Winsemius, MD
> >> Heritage Laboratories
> >> West Hartford, CT
> >>
> >>
> >
> >
> > --
> > Jessica L Joganic
> > Graduate Student
> > Department of Anthropology
> > Campus Box 1114
> > Washington University
> > St. Louis, MO 63130-4899
> > email: jljogani at artsci.wustl.edu
> >
> >        [[alternative HTML version deleted]]
> >
> > ______________________________________________
> > R-help at r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> > and provide commented, minimal, self-contained, reproducible code.
> >
>
>
>
> --
> Ista Zahn
> Graduate student
> University of Rochester
> Department of Clinical and Social Psychology
> http://yourpsyche.org

--
Jessica L Joganic
Graduate Student
Department of Anthropology
Campus Box 1114
Washington University
St. Louis, MO 63130-4899
email: jljogani at artsci.wustl.edu