Hello, Recently updated Ubuntu to 10.04, I have installed the r-base and r-base-dev packages from CRAN with sudo apt-get install r-base But now when I want to start R I get the following error: gpetris at definetti:~$ R /usr/lib/R/bin/exec/R: symbol lookup error: /usr/local/lib/libreadline.so.6: undefined symbol: PC Any clue??? Has anybody seen that before? I have tried to reinstall the readline libraries, both as a ubuntu package and from sources, but the error did not go away.... Thanks in advance, Giovanni -- Giovanni Petris <GPetris at uark.edu> Associate Professor Department of Mathematical Sciences University of Arkansas - Fayetteville, AR 72701 Ph: (479) 575-6324, 575-8630 (fax) http://definetti.uark.edu/~gpetris/
On Wed, Aug 18, 2010 at 11:36 AM, Giovanni Petris <gpetris at uark.edu> wrote:> > Hello, > > Recently updated Ubuntu to 10.04, I have installed the r-base and > r-base-dev packages from CRAN with > > sudo apt-get install r-base > > But now when I want to start R I get the following error: > > gpetris at definetti:~$ R > /usr/lib/R/bin/exec/R: symbol lookup > error: /usr/local/lib/libreadline.so.6: undefined symbol: PCThat .so file is in /usr/local/lib and did not come from an Ubuntu package.> > Any clue??? Has anybody seen that before? I have tried to reinstall the > readline libraries, both as a ubuntu package and from sources, but the > error did not go away.... > > Thanks in advance, > Giovanni > > > > > -- > > Giovanni Petris ?<GPetris at uark.edu> > Associate Professor > Department of Mathematical Sciences > University of Arkansas - Fayetteville, AR 72701 > Ph: (479) 575-6324, 575-8630 (fax) > http://definetti.uark.edu/~gpetris/ > > _______________________________________________ > R-SIG-Debian mailing list > R-SIG-Debian at r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-debian >
On 18 August 2010 at 11:36, Giovanni Petris wrote:
| Hello,
|
| Recently updated Ubuntu to 10.04, I have installed the r-base and
| r-base-dev packages from CRAN with
|
| sudo apt-get install r-base
|
| But now when I want to start R I get the following error:
|
| gpetris at definetti:~$ R
| /usr/lib/R/bin/exec/R: symbol lookup
| error: /usr/local/lib/libreadline.so.6: undefined symbol: PC
|
| Any clue??? Has anybody seen that before? I have tried to reinstall the
| readline libraries, both as a ubuntu package and from sources, but the
| error did not go away....
There must be some local issue on your system that makes it non-standard.
There are literally hundreds of us running this R version and built every day
from the same binaries.
The best clue is
error: /usr/local/lib/libreadline.so.6: undefined symbol: PC
which clearly indicates that you have a version of readline masquerading as
version 6 ... which is then used to run R but fails for incompatibility.
That is, sorry to be blunt, your fault and issue. Remove that library (with
some care, you could first rename or move to a hidden directory) and then run
'sudo ldconfig' to update the shared library cache used by the system.
Then
try R. Or, as an alternative to running R:
edd at max:~$ ldd /usr/lib/R/bin/exec/R
linux-vdso.so.1 => (0x00007fff24c72000)
libR.so => /usr/lib/libR.so (0x00007f828a3fe000)
libc.so.6 => /lib/libc.so.6 (0x00007f828a07b000)
libblas.so.3gf => /usr/lib/libblas.so.3gf (0x00007f8289ddf000)
libgfortran.so.3 => /usr/lib/libgfortran.so.3 (0x00007f8289af2000)
libm.so.6 => /lib/libm.so.6 (0x00007f828986f000)
libreadline.so.6 => /lib/libreadline.so.6 (0x00007f828962d000)
libpcre.so.3 => /lib/libpcre.so.3 (0x00007f82893ff000)
libbz2.so.1.0 => /lib/libbz2.so.1.0 (0x00007f82891ee000)
libz.so.1 => /lib/libz.so.1 (0x00007f8288fd6000)
libdl.so.2 => /lib/libdl.so.2 (0x00007f8288dd2000)
/lib64/ld-linux-x86-64.so.2 (0x00007f828a994000)
libgcc_s.so.1 => /lib/libgcc_s.so.1 (0x00007f8288bbb000)
libncurses.so.5 => /lib/libncurses.so.5 (0x00007f8288977000)
edd at max:~$
As you can, nothing is pulled in from /usr/local and I run R against the
libraries provided by the package management system as it was meant to be
used.
You should get there too.
Hth, Dirk
--
Dirk Eddelbuettel | edd at debian.org | http://dirk.eddelbuettel.com
On 08/18/2010 12:52 PM, Douglas Bates wrote:> On Wed, Aug 18, 2010 at 11:36 AM, Giovanni Petris<gpetris at uark.edu> wrote: >> >> Hello, >> >> Recently updated Ubuntu to 10.04, I have installed the r-base and >> r-base-dev packages from CRAN with >> >> sudo apt-get install r-base >> >> But now when I want to start R I get the following error: >> >> gpetris at definetti:~$ R >> /usr/lib/R/bin/exec/R: symbol lookup >> error: /usr/local/lib/libreadline.so.6: undefined symbol: PC > > That .so file is in /usr/local/lib and did not come from an Ubuntu package.Yes. Not sure where this came from, but make sure that libreadline 6.1-1 is installed via apt or synaptic. You may also have other versions of libreadline.so or libreadline.so.6 linked to this somewhere else on the system, so make sure nothing links to this file. Michael>> >> Any clue??? Has anybody seen that before? I have tried to reinstall the >> readline libraries, both as a ubuntu package and from sources, but the >> error did not go away.... >> >> Thanks in advance, >> Giovanni >> >> >> >> >> -- >> >> Giovanni Petris<GPetris at uark.edu> >> Associate Professor >> Department of Mathematical Sciences >> University of Arkansas - Fayetteville, AR 72701 >> Ph: (479) 575-6324, 575-8630 (fax) >> http://definetti.uark.edu/~gpetris/ >> >> _______________________________________________ >> R-SIG-Debian mailing list >> R-SIG-Debian at r-project.org >> https://stat.ethz.ch/mailman/listinfo/r-sig-debian >> > > _______________________________________________ > R-SIG-Debian mailing list > R-SIG-Debian at r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-debian-- Dr. Michael A. Rutter School of Science Penn State Erie, The Behrend College Station Road Erie, PA 16563 http://math.bd.psu.edu/faculty/rutter