R help - Sep 2007 - Problem in installing packages on linux machine...

Hi,

I am trying to install RSQLite package on my Fedora workstation. I 
tried to install other packages as well, but each time I got the same 
error messages saying "compilation error" and "non zero exit
status".
Do I have to specify "lib="? I never specified the library path before
when I was using Fedora Core 6.


Warning in install.packages("RSQLite") : argument 'lib' is
missing:
using '/usr/lib/R/library'
--- Please select a CRAN mirror for use in this session ---
Loading Tcl/Tk interface ... done
trying URL
'http://cran.cnr.Berkeley.edu/src/contrib/RSQLite_0.5-6.tar.gz'
Content type 'application/x-gzip' length 710241 bytes
opened URL
=================================================downloaded 693Kb

gcc -std=gnu99 -shared -L/usr/local/lib -o RSQLite.so RS-DBI.o 
RS-SQLite.o sqlite-all.o   -L/usr/lib/R/lib -lR
/usr/bin/ld: skipping incompatible /usr/lib/R/lib/libR.so when 
searching for -lR
/usr/bin/ld: cannot find -lR
collect2: ld returned 1 exit status
make: *** [RSQLite.so] Error 1
chmod: cannot access `/usr/lib/R/library/RSQLite/libs/*': No such file 
or directory
ERROR: compilation failed for package 'RSQLite'
** Removing '/usr/lib/R/library/RSQLite'

The downloaded packages are in
        /tmp/RtmpHQ5Y7C/downloaded_packages
Warning message:
installation of package 'RSQLite' had non-zero exit status in: 
install.packages("RSQLite")

I appreciate your help.....

Thank you very much

Taka

Hi, try install packages whit 'sudo'.

$sudo R

-- 
Henrique Dallazuanna
Curitiba-Paraná-Brasil
25° 25' 40" S 49° 16' 22" O

On 08/09/2007, tkobayas@indiana.edu <tkobayas@indiana.edu>
wrote:
>
> Hi,
>
> I am trying to install RSQLite package on my Fedora workstation. I
> tried to install other packages as well, but each time I got the same
> error messages saying "compilation error" and "non zero exit
status".
> Do I have to specify "lib="? I never specified the library path
before
> when I was using Fedora Core 6.
>
>
> Warning in install.packages("RSQLite") : argument 'lib'
is missing:
> using '/usr/lib/R/library'
> --- Please select a CRAN mirror for use in this session ---
> Loading Tcl/Tk interface ... done
> trying URL
'http://cran.cnr.Berkeley.edu/src/contrib/RSQLite_0.5-6.tar.gz'
> Content type 'application/x-gzip' length 710241 bytes
> opened URL
> =================================================> downloaded 693Kb
>
> gcc -std=gnu99 -shared -L/usr/local/lib -o RSQLite.so RS-DBI.o
> RS-SQLite.o sqlite-all.o   -L/usr/lib/R/lib -lR
> /usr/bin/ld: skipping incompatible /usr/lib/R/lib/libR.so when
> searching for -lR
> /usr/bin/ld: cannot find -lR
> collect2: ld returned 1 exit status
> make: *** [RSQLite.so] Error 1
> chmod: cannot access `/usr/lib/R/library/RSQLite/libs/*': No such file
> or directory
> ERROR: compilation failed for package 'RSQLite'
> ** Removing '/usr/lib/R/library/RSQLite'
>
> The downloaded packages are in
>         /tmp/RtmpHQ5Y7C/downloaded_packages
> Warning message:
> installation of package 'RSQLite' had non-zero exit status in:
> install.packages("RSQLite")
>
> I appreciate your help.....
>
> Thank you very much
>
> Taka
>
> ______________________________________________
> R-help@stat.math.ethz.ch 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]]

Your problem is not related to missing file permissions but to a problem
with the linker (ld). As you can see from the error message, ld cannot
find a compatible libR.so so compilation fails. You did not specify
which architecture you're on but in case it is a 64-bit platform, the
following thread might be helpful: 

http://tolstoy.newcastle.edu.au/R/e2/help/07/07/22071.html

BTW, the correct command for running R as root is "su -c R" or
"sudo R".
Furthermore, lib is optional and defaults to .libPaths()[1],
see ?install.packages

 <tkobayas <at> indiana.edu> writes:
> 
> Hi,
> 
> Still got the same error message. I did "su R" when I got the
error
> message for the first time. I have never seen this error message.....
I 
> will be googling for solutions as well...
> 
> Thank you.
> 
> Quoting Henrique Dallazuanna <wwwhsd <at> gmail.com>:
> 
> > Hi, try install packages whit 'sudo'.
> >
> > $sudo R
> >
> > --
> > Henrique Dallazuanna
> > Curitiba-Paran?-Brasil
> > 25? 25' 40" S 49? 16' 22" O
> >
> > On 08/09/2007, tkobayas <at> indiana.edu <tkobayas <at>
indiana.edu>
wrote:
> >>
> >> Hi,
> >>
> >> I am trying to install RSQLite package on my Fedora workstation. I
> >> tried to install other packages as well, but each time I got the
same
> >> error messages saying "compilation error" and "non
zero exit
status".
> >> Do I have to specify "lib="? I never specified the
library path
before
> >> when I was using Fedora Core 6.
> >>
> >>
> >> Warning in install.packages("RSQLite") : argument
'lib' is missing:
> >> using '/usr/lib/R/library'
> >> --- Please select a CRAN mirror for use in this session ---
> >> Loading Tcl/Tk interface ... done
> >> trying URL
'http://cran.cnr.Berkeley.edu/src/contrib/RSQLite_0.5-6.tar.gz'
> >> Content type 'application/x-gzip' length 710241 bytes
> >> opened URL
> >> =================================================> >>
downloaded 693Kb
> >>
> >> gcc -std=gnu99 -shared -L/usr/local/lib -o RSQLite.so RS-DBI.o
> >> RS-SQLite.o sqlite-all.o   -L/usr/lib/R/lib -lR
> >> /usr/bin/ld: skipping incompatible /usr/lib/R/lib/libR.so when
> >> searching for -lR
> >> /usr/bin/ld: cannot find -lR
> >> collect2: ld returned 1 exit status
> >> make: *** [RSQLite.so] Error 1
> >> chmod: cannot access `/usr/lib/R/library/RSQLite/libs/*': No
such
file
> >> or directory
> >> ERROR: compilation failed for package 'RSQLite'
> >> ** Removing '/usr/lib/R/library/RSQLite'
> >>
> >> The downloaded packages are in
> >>         /tmp/RtmpHQ5Y7C/downloaded_packages
> >> Warning message:
> >> installation of package 'RSQLite' had non-zero exit status
in:
> >> install.packages("RSQLite")
> >>
> >> I appreciate your help.....
> >>
> >> Thank you very much
> >>
> >> Taka
> >>
> >> ______________________________________________
> >> R-help <at> stat.math.ethz.ch 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.
> >>
> >
> 
> ------------------------------------
> Takatsugu Kobayashi
> PhD Student
> Indiana University, Dept. Geography
> 
> ______________________________________________
> R-help <at> stat.math.ethz.ch 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.
> 
>