packages failed to load - Now fixed

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.

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)
}

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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

      [[alternative HTML version deleted]]

--
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]]