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Miklos Kiss

2008-Jul-12 03:32 UTC

[R] Another failed attempt to install an R package in Ubuntu

I am running Ubuntu 8.04 through Wubi on a HP Pavilion dv4000 (my home
computer) and I recently installed R 2.7.1.  I attempted to install the
randomForest package from within the R environment and from the Linux
terminal.  Both attempts failed.  I've tried several mirrors but with no
luck.  Below is an example of the series of error messages I got when R told
me that the installation wasn't going well.

It tells me that several header files are missing.  For some reason it is
also trying to install them in
'/home/mik/R/i486-pc-linux-gnu-library/2.7'
but my R library packages are located in '/usr/lib/R/library'.  I tried
downloading various x11dev packages and such, as suggested in similar
threads in this forum, but that didn't seem to help.

I'm really new (installed Ubuntu less than 4 months ago) to Linux but
I've
been using R for about a year.  If anyone can point me in the right
direction on how to correctly install this package, I'd very much appreciate
it.

Thank you,
Miklos Kiss

 install.packages()
--- Please select a CRAN mirror for use in this session ---
Loading Tcl/Tk interface ... done
Warning in install.packages() :
  argument 'lib' is missing: using
'/home/mik/R/i486-pc-linux-gnu-library/2.7'
trying URL 'http://cran.mtu.edu/src/contrib/randomForest_4.5-25.tar.gz'
Content type 'application/x-gzip' length 70212 bytes (68 Kb)
opened URL
=================================================downloaded 68 Kb

* Installing *source* package 'randomForest' ...
** libs
gcc -std=gnu99 -I/usr/share/R/include      -fpic  -g -O2 -c classTree.c -o
classTree.o
In file included from classTree.c:15:
/usr/share/R/include/R.h:28:20: error: stdlib.h: No such file or directory
/usr/share/R/include/R.h:29:19: error: stdio.h: No such file or directory
In file included from
/usr/lib/gcc/i486-linux-gnu/4.2.3/include/syslimits.h:7,
                 from /usr/lib/gcc/i486-linux-gnu/4.2.3/include/limits.h:11,
                 from /usr/share/R/include/R.h:30,
                 from classTree.c:15:
/usr/lib/gcc/i486-linux-gnu/4.2.3/include/limits.h:122:61: error: limits.h:
No such file or directory
In file included from classTree.c:15:
/usr/share/R/include/R.h:32:18: error: math.h: No such file or directory
/usr/share/R/include/R.h:33:19: error: errno.h: No such file or directory
In file included from /usr/share/R/include/R.h:50,
                 from classTree.c:15:
/usr/share/R/include/R_ext/RS.h:24:39: error: string.h: No such file or
directory
classTree.c: In function ?catmax_?:
classTree.c:305: warning: implicit declaration of function ?pow?
classTree.c:305: warning: incompatible implicit declaration of built-in
function ?pow?
make: *** [classTree.o] Error 1
ERROR: compilation failed for package 'randomForest'
** Removing '/home/mik/R/i486-pc-linux-gnu-library/2.7/randomForest'

The downloaded packages are in
	/tmp/RtmpT83A76/downloaded_packages
Warning message:
In install.packages() :
  installation of package 'randomForest' had non-zero exit status

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IAIN GALLAGHER

2008-Jul-12 11:00 UTC

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[R] Another failed attempt to install an R package in Ubuntu

Hi Miklos.

If you want to install R packages to the /usr/lib/R/library directory you need
to start R with 'root' user privileges. Ordinary users do not have the
appropriate permissions to write to this directory. At the command line type:

sudo R

type your password when prompted. 

You won't need to do this for using R or the packages though; you can start
R with you normal user permissions ie in the usual way. There are many online
tutorials for the linux permission system... have a google ;-)

Your error messages suggest you missing some header files (eg stdlib.h is the
header file for the general purpose C library) used to build code. At the
command line try this:

sudo apt-get install build-essentials

That will install many of the files you need. There are many apt-get primers on
the web as well; it's worth having a look.

Hope this helps somewhat.

Cheers

Iain

Miklos Kiss <mzkiss@gmail.com> wrote: 
I am running Ubuntu 8.04 through Wubi on a HP Pavilion dv4000 (my home
computer) and I recently installed R 2.7.1.  I attempted to install the
randomForest package from within the R environment and from the Linux
terminal.  Both attempts failed.  I've tried several mirrors but with no
luck.  Below is an example of the series of error messages I got when R told
me that the installation wasn't going well.

It tells me that several header files are missing.  For some reason it is
also trying to install them in
'/home/mik/R/i486-pc-linux-gnu-library/2.7'
but my R library packages are located in '/usr/lib/R/library'.  I tried
downloading various x11dev packages and such, as suggested in similar
threads in this forum, but that didn't seem to help.

I'm really new (installed Ubuntu less than 4 months ago) to Linux but
I've
been using R for about a year.  If anyone can point me in the right
direction on how to correctly install this package, I'd very much appreciate
it.

Thank you,
Miklos Kiss

 install.packages()
--- Please select a CRAN mirror for use in this session ---
Loading Tcl/Tk interface ... done
Warning in install.packages() :
  argument 'lib' is missing: using
'/home/mik/R/i486-pc-linux-gnu-library/2.7'
trying URL 'http://cran.mtu.edu/src/contrib/randomForest_4.5-25.tar.gz'
Content type 'application/x-gzip' length 70212 bytes (68 Kb)
opened URL
=================================================downloaded 68 Kb

* Installing *source* package 'randomForest' ...
** libs
gcc -std=gnu99 -I/usr/share/R/include      -fpic  -g -O2 -c classTree.c -o
classTree.o
In file included from classTree.c:15:
/usr/share/R/include/R.h:28:20: error: stdlib.h: No such file or directory
/usr/share/R/include/R.h:29:19: error: stdio.h: No such file or directory
In file included from
/usr/lib/gcc/i486-linux-gnu/4.2.3/include/syslimits.h:7,
                 from /usr/lib/gcc/i486-linux-gnu/4.2.3/include/limits.h:11,
                 from /usr/share/R/include/R.h:30,
                 from classTree.c:15:
/usr/lib/gcc/i486-linux-gnu/4.2.3/include/limits.h:122:61: error: limits.h:
No such file or directory
In file included from classTree.c:15:
/usr/share/R/include/R.h:32:18: error: math.h: No such file or directory
/usr/share/R/include/R.h:33:19: error: errno.h: No such file or directory
In file included from /usr/share/R/include/R.h:50,
                 from classTree.c:15:
/usr/share/R/include/R_ext/RS.h:24:39: error: string.h: No such file or
directory
classTree.c: In function ‘catmax_’:
classTree.c:305: warning: implicit declaration of function ‘pow’
classTree.c:305: warning: incompatible implicit declaration of built-in
function ‘pow’
make: *** [classTree.o] Error 1
ERROR: compilation failed for package 'randomForest'
** Removing '/home/mik/R/i486-pc-linux-gnu-library/2.7/randomForest'

The downloaded packages are in
 /tmp/RtmpT83A76/downloaded_packages
Warning message:
In install.packages() :
  installation of package 'randomForest' had non-zero exit status

-- 
View this message in context:
http://www.nabble.com/Another-failed-attempt-to-install-an-R-package-in-Ubuntu-tp18415721p18415721.html
Sent from the R help mailing list archive at Nabble.com.

______________________________________________
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.


	[[alternative HTML version deleted]]

Matti Pastell

2008-Jul-12 15:26 UTC

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[R] Another failed attempt to install an R package in Ubuntu

Hello Miklos,
Do you have the "build-essential" package installed in Ubuntu? If not
try
installing it, as it will install the basic tools needed for compiling
things from source. Also as Iain pointed out run R with "sudo R" from
the
terminal if you want to install packages for all users i.e to
usr/lib/R/library.

BR,
Matti



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Vincent Goulet

2008-Jul-13 04:25 UTC

head link

[R] Another failed attempt to install an R package in Ubuntu

MIklos,

You may have missed this part of the Ubuntu README on CRAN:

	Users who need to compile packages should also install the r-base-dev  
package:

	sudo apt-get install r-base-dev
This will fetch all the standard tools you need to compile packages.

If you have more Ubuntu specific questions, please post them to R-SIG- 
Debian.

Best,

Vincent

Le ven. 11 juil. ? 23:32, Miklos Kiss a ?crit :
>
> I am running Ubuntu 8.04 through Wubi on a HP Pavilion dv4000 (my home
> computer) and I recently installed R 2.7.1.  I attempted to install  
> the
> randomForest package from within the R environment and from the Linux
> terminal.  Both attempts failed.  I've tried several mirrors but  
> with no
> luck.  Below is an example of the series of error messages I got  
> when R told
> me that the installation wasn't going well.
>
> It tells me that several header files are missing.  For some reason  
> it is
> also trying to install them in '/home/mik/R/i486-pc-linux-gnu- 
> library/2.7'
> but my R library packages are located in '/usr/lib/R/library'.  I  
> tried
> downloading various x11dev packages and such, as suggested in similar
> threads in this forum, but that didn't seem to help.
>
> I'm really new (installed Ubuntu less than 4 months ago) to Linux  
> but I've
> been using R for about a year.  If anyone can point me in the right
> direction on how to correctly install this package, I'd very much  
> appreciate
> it.
>
> Thank you,
> Miklos Kiss
>
> install.packages()
> --- Please select a CRAN mirror for use in this session ---
> Loading Tcl/Tk interface ... done
> Warning in install.packages() :
>  argument 'lib' is missing: using
> '/home/mik/R/i486-pc-linux-gnu-library/2.7'
> trying URL 'http://cran.mtu.edu/src/contrib/ 
> randomForest_4.5-25.tar.gz'
> Content type 'application/x-gzip' length 70212 bytes (68 Kb)
> opened URL
> =================================================> downloaded 68 Kb
>
> * Installing *source* package 'randomForest' ...
> ** libs
> gcc -std=gnu99 -I/usr/share/R/include      -fpic  -g -O2 -c  
> classTree.c -o
> classTree.o
> In file included from classTree.c:15:
> /usr/share/R/include/R.h:28:20: error: stdlib.h: No such file or  
> directory
> /usr/share/R/include/R.h:29:19: error: stdio.h: No such file or  
> directory
> In file included from
> /usr/lib/gcc/i486-linux-gnu/4.2.3/include/syslimits.h:7,
>                 from /usr/lib/gcc/i486-linux-gnu/4.2.3/include/ 
> limits.h:11,
>                 from /usr/share/R/include/R.h:30,
>                 from classTree.c:15:
> /usr/lib/gcc/i486-linux-gnu/4.2.3/include/limits.h:122:61: error:  
> limits.h:
> No such file or directory
> In file included from classTree.c:15:
> /usr/share/R/include/R.h:32:18: error: math.h: No such file or  
> directory
> /usr/share/R/include/R.h:33:19: error: errno.h: No such file or  
> directory
> In file included from /usr/share/R/include/R.h:50,
>                 from classTree.c:15:
> /usr/share/R/include/R_ext/RS.h:24:39: error: string.h: No such file  
> or
> directory
> classTree.c: In function ?catmax_?:
> classTree.c:305: warning: implicit declaration of function ?pow?
> classTree.c:305: warning: incompatible implicit declaration of built- 
> in
> function ?pow?
> make: *** [classTree.o] Error 1
> ERROR: compilation failed for package 'randomForest'
> ** Removing
'/home/mik/R/i486-pc-linux-gnu-library/2.7/randomForest'
>
> The downloaded packages are in
> 	/tmp/RtmpT83A76/downloaded_packages
> Warning message:
> In install.packages() :
>  installation of package 'randomForest' had non-zero exit status
>
> -- 
> View this message in context:
http://www.nabble.com/Another-failed-attempt-to-install-an-R-package-in-Ubuntu-tp18415721p18415721.html
> Sent from the R help mailing list archive at Nabble.com.
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.

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