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

Wed Feb 17 13:32:09 CET 2010

Hi Jessica,
I still think you're making it more difficult by trying to download
and install packages in a two-step process instead of using
install.package(). What exactly happens when you try

install.packages("ape")

?

-Ista

On Wed, Feb 17, 2010 at 2:22 AM, Jessica Joganic
<jljogani at artsci.wustl.edu> wrote:
> 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
>

-- 
Ista Zahn
Graduate student
University of Rochester
Department of Clinical and Social Psychology
http://yourpsyche.org