On Wed, May 25, 2011 at 11:50, Prof Brian Ripley <rip...@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. Thank you, Tom > >> 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 >> >> > -- > 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
