On May 25, 2011, at 7:17 AM, Tom Hopper wrote: > 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. >
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-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 > > _______________________________________________ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
