[R-SIG-Mac] Problem with packages after update to R 2.6

[Simon Urbanek]

On Oct 5, 2007, at 7:52 AM, Michael Kubovy wrote:

> On Oct 5, 2007, at 7:16 AM, Sean Davis wrote:
>
>> Michael Kubovy wrote:
>>> Dear R-Mac people,
>>>
>>> After successfully updating R and JGR on
>>> Hardware Overview:
>>>
>>>    Model Name:	Mac Pro
>>>    Model Identifier:	MacPro1,1
>>>    Processor Name:	Dual-Core Intel Xeon
>>>
>>> System Software Overview:
>>>
>>>    System Version:	Mac OS X 10.4.10 (8R2232)
>>>    Kernel Version:	Darwin 8.10.1
>>>
>>> I followed Ripley's advice to
>>>> update.packages(checkBuilt=TRUE, ask=FALSE)
>>>
>>> I then realized that I did not have any of the packages beyond
>>> the  default. So I ran
>>>> install.packages
>>> ('car','Hmisc','doBy','lme4','gmodels','gplots','gdata')
>>> Warning in install.packages("car", "Hmisc", "doBy", "lme4",
>>> "gmodels", "gplots",  :
>>>    'lib = "Hmisc"' is not writable
>>> Would you like to create a personal library
>>> '~/R/i386-apple-darwin8.10.1-library/2.6'
>>> to install packages into?  (y/n) y
>>> Error in available[, "Bundle"] : incorrect number of dimensions
>>>> install.packages
>>> ('car','Hmisc','doBy','lme4','gmodels','gplots','gdata')
>>> Warning in install.packages("car", "Hmisc", "doBy", "lme4",
>>> "gmodels", "gplots",  :
>>>    'lib = "Hmisc"' is not writable
>>> Error in install.packages("car", "Hmisc", "doBy", "lme4",
>>> "gmodels",  "gplots",  :
>>>    unable to install packages
>>>
>>
>> Try making the list of packages into a character vector:
>>
>> install.packages(c
>> ('car','Hmisc','doBy','lme4','gmodels','gplots','gdata'))
>>
>> Does that work for you?
>
> Good point. My error.
>
> But there are packages that won't install even if I install them one
> by one. Hmisc is an example.
>

Can you be more specific, please? (i.e. what error message do you get?)


> More importantly:
>
> 1. what caused R's amnesia about all of my non-default packages  
> upon upgrade?
>

The 'amnesia' depends on where you installed them. The system-wide  
location is always version-dependent, the custom locations may or may  
not be version-dependent - check your .libPaths(). Packages are  
dependent on the R version used, so when upgrading from 2.5.x to  
2.6.x you have to re-install them anyway. The GUI provides an easy  
way to upgrade package from previous R versions even if R cannot see  
them (Package Installer: Get List, then click on the magnifying glass  
in the search field and "Select Packages from R 2.5", then Install  
Selected).


> 2. why didn't
> update.packages(checkBuilt=TRUE, ask=FALSE)
> work?

Can you be more specific? As I understand it you had no old packages,  
so it was working ...

Cheers,
Simon