Hi Everyone,

I have a few fairly basic questions about upgrading and installing R
packages. First off, I am using Ubuntu Hardy Heron and have R 2.7.1
installed and working perfectly. I usually access R via Emacs ESS interface
which I am still trying to get the hang of. My questions and issues are as
follows:

Question 1:  I started R and wanted to upgrade the installed R packages. So,
I issue the command >upgrade.packages()
 and after selecting the CRAN mirror sites, I get the following message:

lattice :
 Version 0.17-8 installed in /usr/lib/R/library
 Version 0.17-10 available at http://www.ibiblio.org/pub/languages/R/CRAN
Update (y/N/c)?

(To this, I respond with  "y", but then I get the following:)


Warning in install.packages(update[instlib == l, "Package"], l, contriburl =
contriburl,  :
  'lib = "/usr/lib/R/library"' is not writable


(Off course, it is NOT writable because it did not ask for the
administrative password.

Would you like to create a personal library
'~/R/i486-pc-linux-gnu-library/2.7'
to install packages into?  (y/n)


I do not want to create new directories; I just want to upgrade where the
older version already exists. So I respond with "n" and get this:)


Error in install.packages(update[instlib == l, "Package"], l, contriburl =
contriburl,  :
  unable to install packages


My question is how do I go about upgrading AND installing packages from
within R by using administrative account? I must say that at least for now,
I was able to get around this issue by staring R as:

sudo R

and then using upgrade.packages(). But I would like a better solution when I
am already in an R session.


Question 2: When I started R via

sudo R

and issued >upgrade.packages()

I had problem upgrading lattice package. I got the following error message:

* Installing *source* package 'lattice' ...
** libs
gcc -std=gnu99 -I/usr/share/R/include      -fpic  -g -O2 -c init.c -o init.o
In file included from init.c:2:
/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 init.c:2:
/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 init.c:2:
/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 init.c:2:
/usr/share/R/include/R_ext/RS.h:24:39: error: string.h: No such file or
directory
In file included from init.c:3:
/usr/share/R/include/Rinternals.h:770: error: expected declaration
specifiers or '...' before 'FILE'
/usr/share/R/include/Rinternals.h:773: error: expected declaration
specifiers or '...' before 'FILE'
make: *** [init.o] Error 1
ERROR: compilation failed for package 'lattice'
** Removing '/usr/lib/R/library/lattice'
** Restoring previous '/usr/lib/R/library/lattice'

The downloaded packages are in
    /tmp/Rtmpj37zYN/downloaded_packages
Updating HTML index of packages in '.Library'
Warning message:
In install.packages(update[instlib == l, "Package"], l, contriburl =
contriburl,  :
  installation of package 'lattice' had non-zero exit status



Even >upgrade.packages(dependencies = TRUE) resulted in the same error. Does
anyone know if this is just a problem on my system or perhaps someone else
has run into the same issue. What does this all mean? What I do not
understand is why are there .h missing files? How the heck did lattice get
installed in the first place if these header files were missing?

Question 3: This is more of a general question that has been on my mind for
sometime. If I just want to install some packages/data base etc that I would
like to be "local", perhaps in my home directory, which library path would
be recommended? Sometimes I feel that I would like to download some database
or other packaged code that I want to play around with but would later like
to get rid of, a library in the home directory that is still in R's path
might be better. I would appreciate suggestions. What are others doing in
this situation? Currently I have the following outcome of .libPaths()
command:

> .libPaths()
[1] "/usr/local/lib/R/site-library" "/usr/lib/R/site-library"
[3] "/usr/lib/R/library"

Which library path should I choose?

Best regards,

Tariq

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