R and packages

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R and packages

Erin Hodgess
Dear R People:

Here is yet another strange problem.  

I'm using R in one of my classes.  However, the computer lab has something
called "Deep Freeze" and the students cannot save anything to the hard drive.

I had R installed and things were working well.  They would save their
.Rdata files to disks.

Now, we need to add more packages.  We can't download and we can't
bring them in via zip files (already tried both!)  When the zip files
are expanded, of course they build new directories......

I'm completely annoyed because learning to download packages
and installing them from local zips are actually important tasks!
We're also losing good teaching/learning time!

Anyhow, what I would like to do is produce a sort of combination R
installation exe with our extra libraries as part of the package.

Does anyone have any suggestions on how this could be done, please?

This is R for Windows, Version 2.2.1

Thanks for any help!  Sorry about the totally weird problem!

Sincerely,
Erin Hodgess
Associate Professor
Department of Computer and Mathematical Sciences
University of Houston - Downtown
mailto: [hidden email]

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Re: R and packages

Duncan Murdoch
On 2/20/2006 8:07 PM, Erin Hodgess wrote:

> Dear R People:
>
> Here is yet another strange problem.  
>
> I'm using R in one of my classes.  However, the computer lab has something
> called "Deep Freeze" and the students cannot save anything to the hard drive.
>
> I had R installed and things were working well.  They would save their
> .Rdata files to disks.
>
> Now, we need to add more packages.  We can't download and we can't
> bring them in via zip files (already tried both!)  When the zip files
> are expanded, of course they build new directories......

You can probably use .libPaths() to add a new install location that is
writeable.  You'll likely get a few error messages because R can't
update the help indices, but the packages should be available.
>
> I'm completely annoyed because learning to download packages
> and installing them from local zips are actually important tasks!
> We're also losing good teaching/learning time!
>
> Anyhow, what I would like to do is produce a sort of combination R
> installation exe with our extra libraries as part of the package.

You could also do this, if you have the tools installed to do a build.
See the R Installation and Administration manual, Installing R Under
Windows, Building from Source, Building the Installer (section 3.1.9 in
the PDF version).  You can either build with extra packages from source,
or make an image from an installed copy.  In either case you'll need to
install a lot of build tools, but fewer for the second option.

Duncan Murdoch

>
> Does anyone have any suggestions on how this could be done, please?
>
> This is R for Windows, Version 2.2.1
>
> Thanks for any help!  Sorry about the totally weird problem!
>
> Sincerely,
> Erin Hodgess
> Associate Professor
> Department of Computer and Mathematical Sciences
> University of Houston - Downtown
> mailto: [hidden email]
>
> ______________________________________________
> [hidden email] mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html

______________________________________________
[hidden email] mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
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Re: R and packages

Duncan Murdoch
In reply to this post by Erin Hodgess
On 2/20/2006 8:07 PM, Erin Hodgess wrote:
 > Dear R People:
 >
 > Here is yet another strange problem.
 >
 > I'm using R in one of my classes.  However, the computer lab has
something
 > called "Deep Freeze" and the students cannot save anything to the
hard drive.
 >
 > I had R installed and things were working well.  They would save their
 > .Rdata files to disks.
 >
 > Now, we need to add more packages.  We can't download and we can't
 > bring them in via zip files (already tried both!)  When the zip files
 > are expanded, of course they build new directories......

You can probably use .libPaths() to add a new install location that is
writeable.  You'll likely get a few error messages because R can't
update the help indices, but the packages should be available.
 >
 > I'm completely annoyed because learning to download packages
 > and installing them from local zips are actually important tasks!
 > We're also losing good teaching/learning time!
 >
 > Anyhow, what I would like to do is produce a sort of combination R
 > installation exe with our extra libraries as part of the package.

You could also do this, if you have the tools installed to do a build.
See the R Installation and Administration manual, Installing R Under
Windows, Building from Source, Building the Installer (section 3.1.9 in
the PDF version).  You can either build with extra packages from source,
or make an image from an installed copy.  In either case you'll need to
install a lot of build tools, but fewer for the second option.

Duncan Murdoch

 >
 > Does anyone have any suggestions on how this could be done, please?
 >
 > This is R for Windows, Version 2.2.1
 >
 > Thanks for any help!  Sorry about the totally weird problem!
 >
 > Sincerely,
 > Erin Hodgess
 > Associate Professor
 > Department of Computer and Mathematical Sciences
 > University of Houston - Downtown
 > mailto: [hidden email]
 >
 > ______________________________________________
 > [hidden email] mailing list
 > https://stat.ethz.ch/mailman/listinfo/r-help

______________________________________________
[hidden email] mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
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Re: R and packages

JohnDee
In reply to this post by Erin Hodgess
You want to take the sysad by the hairy of his chinny-chin-chin and explain
the issue in short sentences.  He or she ought to be able produce a solution
without difficulty, and should not have any problems about doing so.  It IS
their job.  

JD  

On Monday 20 February 2006 17:07, Erin Hodgess wrote:

> Dear R People:
>
> Here is yet another strange problem.
>
> I'm using R in one of my classes.  However, the computer lab has something
> called "Deep Freeze" and the students cannot save anything to the hard
> drive.
>
> I had R installed and things were working well.  They would save their
> .Rdata files to disks.
>
> Now, we need to add more packages.  We can't download and we can't
> bring them in via zip files (already tried both!)  When the zip files
> are expanded, of course they build new directories......
>
> I'm completely annoyed because learning to download packages
> and installing them from local zips are actually important tasks!
> We're also losing good teaching/learning time!
>
> Anyhow, what I would like to do is produce a sort of combination R
> installation exe with our extra libraries as part of the package.
>
> Does anyone have any suggestions on how this could be done, please?
>
> This is R for Windows, Version 2.2.1
>
> Thanks for any help!  Sorry about the totally weird problem!
>
> Sincerely,
> Erin Hodgess
> Associate Professor
> Department of Computer and Mathematical Sciences
> University of Houston - Downtown
> mailto: [hidden email]
>
> ______________________________________________
> [hidden email] mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide!
> http://www.R-project.org/posting-guide.html

______________________________________________
[hidden email] mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
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Re: R and packages

stevenmh
Agreed.
Hank
On Feb 21, 2006, at 2:40 AM, J Dougherty wrote:

> You want to take the sysad by the hairy of his chinny-chin-chin and  
> explain
> the issue in short sentences.  He or she ought to be able produce a  
> solution
> without difficulty, and should not have any problems about doing  
> so.  It IS
> their job.
>
> JD
>
> On Monday 20 February 2006 17:07, Erin Hodgess wrote:
>> Dear R People:
>>
>> Here is yet another strange problem.
>>
>> I'm using R in one of my classes.  However, the computer lab has  
>> something
>> called "Deep Freeze" and the students cannot save anything to the  
>> hard
>> drive.
>>
>> I had R installed and things were working well.  They would save  
>> their
>> .Rdata files to disks.
>>
>> Now, we need to add more packages.  We can't download and we can't
>> bring them in via zip files (already tried both!)  When the zip files
>> are expanded, of course they build new directories......
>>
>> I'm completely annoyed because learning to download packages
>> and installing them from local zips are actually important tasks!
>> We're also losing good teaching/learning time!
>>
>> Anyhow, what I would like to do is produce a sort of combination R
>> installation exe with our extra libraries as part of the package.
>>
>> Does anyone have any suggestions on how this could be done, please?
>>
>> This is R for Windows, Version 2.2.1
>>
>> Thanks for any help!  Sorry about the totally weird problem!
>>
>> Sincerely,
>> Erin Hodgess
>> Associate Professor
>> Department of Computer and Mathematical Sciences
>> University of Houston - Downtown
>> mailto: [hidden email]
>>
>> ______________________________________________
>> [hidden email] mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide!
>> http://www.R-project.org/posting-guide.html
>
> ______________________________________________
> [hidden email] mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide! http://www.R-project.org/posting- 
> guide.html

______________________________________________
[hidden email] mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
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Re: R and packages

Thomas Lumley
In reply to this post by Erin Hodgess
On Mon, 20 Feb 2006, Erin Hodgess wrote:

> Dear R People:
>
> Here is yet another strange problem.
>
> I'm using R in one of my classes.  However, the computer lab has something
> called "Deep Freeze" and the students cannot save anything to the hard drive.
>
> I had R installed and things were working well.  They would save their
> .Rdata files to disks.
>
> Now, we need to add more packages.  We can't download and we can't
> bring them in via zip files (already tried both!)  When the zip files
> are expanded, of course they build new directories......

I would suggest making this the system administrator's problem.  Either
your site really has a policy that would prohibit R packages (in which
case trying to subvert it may not be a good idea) or it is exactly the
sort of problem that system administrators are supposed to solve.

Distrust for R binary (and even source) packages is not a completely
unreasonable attitude. They can execute arbitrary code on your computer
and, in contrast to R itself, you usually have no real knowledge of who
wrote them.

  -thomas



> I'm completely annoyed because learning to download packages
> and installing them from local zips are actually important tasks!
> We're also losing good teaching/learning time!
>
> Anyhow, what I would like to do is produce a sort of combination R
> installation exe with our extra libraries as part of the package.
>
> Does anyone have any suggestions on how this could be done, please?
>
> This is R for Windows, Version 2.2.1
>
> Thanks for any help!  Sorry about the totally weird problem!
>
> Sincerely,
> Erin Hodgess
> Associate Professor
> Department of Computer and Mathematical Sciences
> University of Houston - Downtown
> mailto: [hidden email]
>
> ______________________________________________
> [hidden email] mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
>

Thomas Lumley Assoc. Professor, Biostatistics
[hidden email] University of Washington, Seattle

______________________________________________
[hidden email] mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
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Re: R and packages

Liaw, Andy
In reply to this post by Erin Hodgess
From: Thomas Lumley

>
> On Mon, 20 Feb 2006, Erin Hodgess wrote:
>
> > Dear R People:
> >
> > Here is yet another strange problem.
> >
> > I'm using R in one of my classes.  However, the computer
> lab has something
> > called "Deep Freeze" and the students cannot save anything
> to the hard drive.
> >
> > I had R installed and things were working well.  They would
> save their
> > .Rdata files to disks.
> >
> > Now, we need to add more packages.  We can't download and we can't
> > bring them in via zip files (already tried both!)  When the
> zip files
> > are expanded, of course they build new directories......
>
> I would suggest making this the system administrator's
> problem.  Either
> your site really has a policy that would prohibit R packages
> (in which
> case trying to subvert it may not be a good idea) or it is
> exactly the
> sort of problem that system administrators are supposed to solve.
>
> Distrust for R binary (and even source) packages is not a completely
> unreasonable attitude. They can execute arbitrary code on
> your computer
> and, in contrast to R itself, you usually have no real
> knowledge of who
> wrote them.
>
>   -thomas
>
>
>
> > I'm completely annoyed because learning to download packages
> > and installing them from local zips are actually important tasks!
> > We're also losing good teaching/learning time!
> >
> > Anyhow, what I would like to do is produce a sort of combination R
> > installation exe with our extra libraries as part of the package.
> >
> > Does anyone have any suggestions on how this could be done, please?
> >
> > This is R for Windows, Version 2.2.1

In case the sysadmin refuses to make it his/her problem, this would be a
good alternative.  It's not hard to build a custom R installer that includes
packages of your choice.  It's all documented.  Look in the R-admin manual
(e.g., http://cran.r-project.org/doc/manuals/R-admin.html) and search for
EXTRA_PKGS.

Andy



> > Thanks for any help!  Sorry about the totally weird problem!
> >
> > Sincerely,
> > Erin Hodgess
> > Associate Professor
> > Department of Computer and Mathematical Sciences
> > University of Houston - Downtown
> > mailto: [hidden email]
> >
> > ______________________________________________
> > [hidden email] mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guide!
> http://www.R-project.org/posting-guide.html
> >
>
> Thomas Lumley Assoc. Professor, Biostatistics
> [hidden email] University of Washington, Seattle
>
> ______________________________________________
> [hidden email] mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide!
> http://www.R-project.org/posting-guide.html
>
>

______________________________________________
[hidden email] mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html