R help - Feb 2010 - error message when downloading packages using the OS X shell

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 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, 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?

Greatest appreciation,
Jessica

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

	[[alternative HTML version deleted]]

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

Hi everyone,
I've tried your various suggestions and through a combination of them
I think I've managed to make it work. This latest version appears to
be much more finicky than earlier ones. Thank you so much for all your
help!

Best to all,
Jessica
> On Wed, Feb 17, 2010 at 6:32 AM, Ista Zahn <istazahn at gmail.com>
wrote:
>> 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



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