Installing optional R package on sagenb.org

[kcrisman]

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, but anyway the surprise result under the R
interface was

install_packages(MASS)
Error: could not find function "install_packages"

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]

On Fri, Jan 2, 2009 at 6:57 PM, kcrisman <kcri...@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:

sage@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

[mabshoff]

On Jan 2, 7:32 pm, "William Stein" <wst...@gmail.com> 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"

Mmh, we are not installing some recommended packages, but I don't
think it matters here.

> 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?  :-)

Well, we might want to upgrade R to 2.8, too.

> I tried the above on sagenb.org (I'm the admin, so I have permissions).
> It seems to fail as well:
>
> sage@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

<SNIP>

> 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

^^^^ this is obviously a bad idea on the part of R's developers.

<SNIP>

> --
> William Stein

Cheers,

Michael

[ztnews]

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]

On Fri, Jan 9, 2009 at 1:19 AM, ztnews <cronin...@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.