[R-SIG-Mac] packages failed to load - Now fixed

[Prof Brian Ripley]

On Wed, 25 May 2011, Tom Hopper wrote:

> Brian,
>
> Since the problem was fixed by updating packages with checkBuilt=T, wouldn't
> installing packages fresh using the script have avoided the problem?

No, because it checks if they are already installed *as I said*.

>
> Perhaps section 2.8 of the Windows FAQ should be incorporated into the Mac
> FAQ? The checkBuilt trick is otherwise not brought to our attention.
>
> The FAQ could also be clearer on whether recommended packages can be
> replaced with older versions using this method; it's much easier to
> copy-and-paste everything in the directory than to hunt-and-peck for only
> the packages that aren't installed by default. I'll submit that suggestion
> to R-windows at r-project.org separately.
>
> - Tom
>
> On Wed, May 25, 2011 at 07:58, Prof Brian Ripley <ripley at stats.ox.ac.uk>wrote:
>
>> It's really odd that people blog about their own inefficient scripts rather
>> than read the R documentation.
>>
>> Because this scripts checks (very inefficiently) if a package is already
>> installed, it would not solve the problem discussed in this thread.  And
>> install.packages() takes a vector of packages, and 'survival' is a
>> recommended package and should always be installed.
>>
>> Because people have differing needs there are different ways to do this.
>>  But the ideas of
>>
>>
>> http://cran.r-project.org/bin/windows/base/rw-FAQ.html#What_0027s-the-best-way-to-upgrade_003f
>>
>> suit many.
>>
>>
>>
>> On Wed, 25 May 2011, Tom Hopper wrote:
>>
>>  There's a handy script to automate the update process that I came across
>>> some time ago at
>>>
>>> https://bridgewater.wordpress.com/2010/12/21/my-favorite-r-packages-installed-with-one-command/
>>>
>>> When you run the script, it will automatically install the libraries that
>>> you set up in the script. When you run it, it will install into the first
>>> location in .libPaths(). If you want packages installed in ~/Library/R...,
>>> then you need to check the "Default Library Paths" option in
>>> R-->Preferences-->Startup. Alternatively, you could supply the lib=
>>> argument
>>> to the install.packages() call. With a little extra code, you could even
>>> define the install location for each package individually.
>>>
>>> Here's a shortened version:
>>> # Essential R packages: 2011-01-02
>>> # Originally from: R packages I use commonly: 12/21/2010 twitter:
>>> drbridgewater
>>> #     Jeff S. A. Bridgewater
>>> #
>>>
>>> https://bridgewater.wordpress.com/2010/12/21/my-favorite-r-packages-installed-with-one-command/
>>> #
>>>
>>> #list all packages currently installed
>>> p<-c()
>>>
>>> #add essential packages:
>>> p<-c(p,"survival")
>>> p<-c(p,"Hmisc")
>>> # add more packages here
>>>
>>> # UPDATE the repository list to point to your local repositories
>>> repositories<-c("http://mirrors.softliste.de/cran/","
>>> http://mirrors.softliste.de/cran/")
>>> install_package<-function(pack,repositories)
>>> {
>>> if(!(pack %in% row.names(installed.packages())))
>>> {
>>> update.packages(repos=repositories, ask=F)
>>> install.packages(pack, repos=repositories, dependencies=T)
>>> }
>>> require(pack,character.only=TRUE)
>>> }
>>>
>>> for( pack in p)
>>> {
>>> install_package(pack,repositories)
>>> }
>>>
>>>        [[alternative HTML version deleted]]
>>>
>>> _______________________________________________
>>> R-SIG-Mac mailing list
>>> R-SIG-Mac at r-project.org
>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>>
>>>
>> --
>> Brian D. Ripley,                  ripley at stats.ox.ac.uk
>> Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
>> University of Oxford,             Tel:  +44 1865 272861 (self)
>> 1 South Parks Road,                     +44 1865 272866 (PA)
>> Oxford OX1 3TG, UK                Fax:  +44 1865 272595
>>
>
> 	[[alternative HTML version deleted]]
>
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-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595