On Fri, Jan 9, 2009 at 1:19 AM, ztnews <cronin.vin...@gmail.com> wrote: > > I had a similar failure today, trying to: > > r.install_packages("adapt") > > after some fussing, runing ./sage as root, and using the notebook > interface I could get through the download phase, but same sorts of > failures in just as the gcc kicks in. Seems several of the key R > scripts have "/home/wstein/..." hard wired in to R_HOME_XXX, which > obviously will fail. I tried editing the R startup scripts (among > others) but couldn't get it to work. > > BTW, I installed from the latest Debian tarball into a Debian/VMWARE > machine just today. So installing R packages is still an issue. > > - Cronin
I made this trac #4959: http://trac.sagemath.org/sage_trac/ticket/4959 Michael -- I hope there wasn't already a ticket for this in trac -- it's impossible to search for "r". I couldn't find anything under install_packages. > > > William Stein wrote: >> On Fri, Jan 2, 2009 at 6:57 PM, kcrisman <kcris...@gmail.com> wrote: >> > >> > Dear support, >> > Because I only have OSX and there is this scary warning about it in >> > the documentation for r.install_packages (which incidentally the test >> > for it has no "s", but I don't know if that matters), I was trying to >> > load one on the sagenb site. Probably this is a gross violation of >> > bandwidth or something, >> >> It will surely fail with a permission denied error at some point. What >> package would you like to install? >> >> > but anyway the surprise result under the R >> > interface was >> > >> > install_packages(MASS) >> > Error: could not find function "install_packages" >> >> Try typing >> >> r.install_packages("MASS") >> >> in a normal Sage input cell. You probably forgot the quotes. >> >> Trying this on OS X it definitely fails for me. There is this message: >> >> "sage: r.install_packages("MASS") >> ** You are using OS X. Unfortunately, the R optional package system >> currently doesn't support OS X very well. We are working on this. **" >> >> I wonder who the "We" refers to? :-) >> >> I tried the above on sagenb.org (I'm the admin, so I have permissions). >> It seems to fail as well: >> >> s...@sagenb:~$ sage >> ---------------------------------------------------------------------- >> | Sage Version 3.2.2, Release Date: 2008-12-18 | >> | Type notebook() for the GUI, and license() for information. | >> ---------------------------------------------------------------------- >> sage: r.install_packages("MASS") >> 0.00user 0.02system 0:00.03elapsed 82%CPU (0avgtext+0avgdata 0maxresident)k >> 64inputs+0outputs (1major+209minor)pagefaults 0swaps >> >> R version 2.6.1 (2007-11-26) >> Copyright (C) 2007 The R Foundation for Statistical Computing >> ISBN 3-900051-07-0 >> >> R is free software and comes with ABSOLUTELY NO WARRANTY. >> You are welcome to redistribute it under certain conditions. >> Type 'license()' or 'licence()' for distribution details. >> >> Natural language support but running in an English locale >> >> R is a collaborative project with many contributors. >> Type 'contributors()' for more information and >> 'citation()' on how to cite R or R packages in publications. >> >> Type 'demo()' for some demos, 'help()' for on-line help, or >> 'help.start()' for an HTML browser interface to help. >> Type 'q()' to quit R. >> >> > options(repos="http://cran.r-project.org/"); install.packages("MASS") >> trying URL 'http://cran.r-project.org/src/contrib/VR_7.2-45.tar.gz' >> Content type 'application/x-gzip' length 465054 bytes (454 Kb) >> opened URL >> ================================================== >> downloaded 454 Kb >> >> WARNING: ignoring environment value of R_HOME >> /home/sage/sage/local/lib/R/library >> WARNING: ignoring environment value of R_HOME >> * Installing *source* package 'MASS' ... >> ** libs >> gcc -std=gnu99 -I/home/sage/sage/local/lib/R/include >> -I/home/sage/sage/local/lib/R/include -I/home/sage/sage/local/inlcude >> WARNING: ignoring environment value of R_HOME -fpic >> -I/home/sage/sage/local/include -L/home/sage/sage/local/lib/ -c lqs.c >> -o lqs.o >> gcc: WARNING:: No such file or directory >> gcc: ignoring: No such file or directory >> gcc: environment: No such file or directory >> gcc: value: No such file or directory >> gcc: of: No such file or directory >> gcc: R_HOME: No such file or directory >> make: *** [lqs.o] Error 1 >> ERROR: compilation failed for package 'MASS' >> ** Removing '/home/sage/sage/local/lib/R/library/MASS' >> ** Removing '/home/sage/sage/local/lib/R/library/class' >> ** Removing '/home/sage/sage/local/lib/R/library/nnet' >> ** Removing '/home/sage/sage/local/lib/R/library/spatial' >> >> The downloaded packages are in >> /tmp/RtmpoUnbs5/downloaded_packages >> Updating HTML index of packages in '.Library' >> Warning message: >> In install.packages("MASS") : >> installation of package 'VR' had non-zero exit status >> > >> >> >> >> > >> > which was surprising since tab-completion was how I found this >> > function in the first place. I also got this in the Sage interface >> > with r.install_packages. >> > >> > If anyone knows how I might do this, or if it's not good to do, or >> > whether my Mac will actually allow me to install the optional package >> > after all, OR whether Sage actually includes these by default (which >> > doesn't seem to be the case, but I might have typed something wrong), >> > I would greatly appreciate any information you might have. >> > >> > Thanks! >> > - kcrisman >> > > >> > >> >> >> >> -- >> William Stein >> Associate Professor of Mathematics >> University of Washington >> http://wstein.org > > > -- William Stein Associate Professor of Mathematics University of Washington http://wstein.org --~--~---------~--~----~------------~-------~--~----~ To post to this group, send email to sage-support@googlegroups.com To unsubscribe from this group, send email to sage-support-unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-support URLs: http://www.sagemath.org -~----------~----~----~----~------~----~------~--~---