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

Wed Feb 17 10:48:15 CET 2010

On 17.02.2010 08:22, Jessica Joganic 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’

Well, R CMD INSTALL expects a source package, you have .

> while in R I get this error:
>
>> download.packages(genetics,destdir=.libPaths())
> Error in unique(pkgs) : object 'genetics' not found

And here you are in the R interpreter which looks for an object called 
"genetics" that does not exist in your workspace. You need to quote the 
name.

Uwe Ligges

> 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
>
> ______________________________________________
> 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.