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

[Simon Urbanek]

On May 25, 2011, at 7:17 AM, Tom Hopper wrote:

> On Wed, May 25, 2011 at 11:50, Prof Brian Ripley <ripley at stats.ox.ac.uk>wrote:
> 
>> 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*.
> 
> 
> Sorry, my question was poorly structured. I understood your original
> statement, and was following up with regards to the update process of R for
> Mac and some of its inner workings. Since I don't have your knowledge of the
> software, and am unlikely to develop such knowledge in the foreseeable
> future, I (perhaps incorrectly) addressed my question to you.
> 
> I take it from your response that the problem that Ian Reeve encountered is
> due to an unresolved bug in R and that there was nothing that could have
> been done to get the packages to correctly install when moving from 2.12 to
> 2.13.0, short of including checkBuilt=T.
> 

No, you got it completely backwards! The script you referred to is useless in that case (and I told you that you are entirely off topic with that!), it has nothing to do with R. There is no "bug" in R mentioned anywhere in the thread, so you are really inventing things here. Please *do* read the e-mails you are receiving.

Thanks,
Simon


> 
> 
>> 
>>> 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]]
>>> 
>>> _______________________________________________
>>> 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
>> 
> 
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