Brian, Since the problem was fixed by updating packages with checkBuilt=T, wouldn't installing packages fresh using the script have avoided the problem?
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-wind...@r-project.org separately. - Tom On Wed, May 25, 2011 at 07:58, Prof Brian Ripley <rip...@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@r-project.org >> https://stat.ethz.ch/mailman/listinfo/r-sig-mac >> >> > -- > Brian D. Ripley, rip...@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@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
