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
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
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