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
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