On Wed, May 25, 2011 at 9:52 AM, Tom Hopper <[email protected]> wrote: > On Wed, May 25, 2011 at 15:23, Simon Urbanek > <[email protected]>wrote: > >> >> On May 25, 2011, at 7:17 AM, Tom Hopper wrote: >> >> > On Wed, May 25, 2011 at 11:50, Prof Brian Ripley <[email protected] >> >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. >> > > Ignoring the personal attack, I'd like to get back to the thread, and my > question. > > Having read through the thread a couple of times, my understanding is that > Ian Reeve updated R for Mac using the installer, then installed all of the > packages he wanted from CRAN. As I understand the thread, after this update, > an old package compiled under 2.12 was, inexplicably, located in his 2.13 > library. That it was a package problem and not something else was confirmed > by resolving the problem with update.packages(checkBuilt=T), rather than the > other methods suggested. It seems to me that either the R installer did not > update correctly, perhaps by retaining a link to the 2.12 directory, or Ian > accidentally copied a package over rather than reinstalling everything fresh > from CRAN. I believe that you, Simon, suggested the latter as a possibility. > I refer to the former possibility as a "bug," because, to the best of my > knowledge, it should happen and shouldn't be possible. Use other > terminology, if you like. Ian then asked if he should delete the old > directory before performing an upgrade, to which you responded that doing so > shouldn't be necessary, and we should just "install new R and then use > Package Manager to install packages." > > As I understood this, it means a file was accidentally copied over when it > shouldn't have been, so the fix is to install packages directly from CRAN > using the Package Manager, a script or some other method, just so long as > there's no copying. Alternatively, copying must be followed by > update.packages(checkBuilt=T). > > Now, I'm sure that I have this wrong, someplace, and since I update multiple > computers on multiple platforms, without your expertise in R, I'm trying to > understand this well enough so that I can avoid similar problems. If I > install a new version of R and then, without doing anything else, either use > the Package Manager or a script to install the packages I want, would I > encounter the same problem?
You should not. Sean >> 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 [email protected] separately. >> >>> >> >>> - Tom >> >>> >> >>> On Wed, May 25, 2011 at 07:58, Prof Brian Ripley < >> [email protected] >> >>>> 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 >> >>>>> [email protected] >> >>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac >> >>>>> >> >>>>> >> >>>>> -- >> >>>> Brian D. Ripley, [email protected] >> >>>> 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 >> >>> [email protected] >> >>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac >> >>> >> >>> >> >> -- >> >> Brian D. Ripley, [email protected] >> >> 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 >> > [email protected] >> > https://stat.ethz.ch/mailman/listinfo/r-sig-mac >> > >> > >> >> > > [[alternative HTML version deleted]] > > _______________________________________________ > R-SIG-Mac mailing list > [email protected] > https://stat.ethz.ch/mailman/listinfo/r-sig-mac > _______________________________________________ R-SIG-Mac mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/r-sig-mac
