Skip to content

problem on upgrading to RH6.2 (was problem with ts pack

5 messages · Jari Oksanen, Christian Posse, Peter Dalgaard

Jari Oksanen
# 
plummer at iarc.fr said:
I have similar problems with R 1.0.1 on RH6.2 (pre-compiled rpm binaries). 
Some of the old packages ceased to work and when I tried to re-install them 
through `R INSTALL package.tar.gz', some just fail and give similar error 
messages. My `ts' works, but it is of the old original version, and I don't 
dare to check if it stops working after re-installation. However, re-installed 
`tripack' gives the following error message:

 > library(tripack)
Error in dyn.load(x, as.logical(local), as.logical(now)) : 
	unable to load shared library "/usr/lib/R/library/tripack/libs/tripack.so":
  /usr/lib/R/library/tripack/libs/tripack.so: undefined symbol: ?

If I first gunzip the package, I get another undefined symbol, but the net 
effect is the unchanged: a failure to load a library. Otherwise the message is 
the same as for `ts' above.

Downgrading to the old binaries of the package does not help, since they fail 
for other reasons, in this case because they can't find e_wsfe. This, I think, 
is caused by libf2g growing independent of libf2c which had this function 
(originally in libI77.a).

cheers, jari oksanen
Peter Dalgaard
# 
Jari Oksanen <jhoksane at ecology.helsinki.fi> writes:
You're doing better than me, I just get a segfault... It seems that
something is seriously wrong with dyn.loading Fortran on RH6.2.
Upgrading the C/Fortran compilers to gcc 2.95.1 or newer seems to cure
it.

I'll be d**ned if I can figure out what is going wrong, but .so files
created with  2.95.1 work with R compiled with egcs-1.1.2 and .so
files created with egcs-1.1.2 cause segfaults when used with R
compiled with 2.95.1, so the problem is likely in the shared libraries
themselves.
Christian Posse
# 
Prof. Ripley was correct suggesting a title with an RH6.2
problem and not a problem concerning the ts package.
In fact, it is far worse than I thought and is similar to
what Jair Oksanen and Peter Dalgaard wrote.

The situation is the following:

- The RPM  R-base-1.0.1-2.i386.rpm  from statlib works fine
under RH 6.2. Loading the libraries in the base works fine too.
Most contrib packages installed with this version of R with
R INSTALL  work except for  tripack, acepack, akima,
mclust (segfault!), leaps,   and so on. (I stopped trying all of them.....)
Strange messages of undefined symbols :
Error in dyn.load(x, as.logical(local), as.logical(now)) :
        unable to load shared library
"/usr/lib/R/library/tripack/libs/tripack.s
o":
  /usr/lib/R/library/tripack/libs/tripack.so: undefined symbol: ?


The situation is far worse  with the version of R built by myself
after having downloaded the *.tgz file from statlib. With this
version, R base works fine, but impossible to load successfully
any library, even the one in the base packages
(Just in case, the R-base*src.rpm provides the same source code
and therefore I got the same problems).

Note, my PC is pure vanilla. I just got it brand new and  I installed
RH6.2. Then I tried to build R and got all these problems.
RH6.2 comes with

<18>root at cuky/R: gcc --version
egcs-2.91.66

How can I compare that with what Peter Dalgaard wrote
( I have been confused for a long time between the different
brands of gcc, true gcc or egcs flavor).
Peter Dalgaard wrote:
You're doing better than me, I just get a segfault... It seems that
  something is seriously wrong with dyn.loading Fortran on RH6.2.
  Upgrading the C/Fortran compilers to gcc 2.95.1 or newer seems to cure
  it.

  I'll be d**ned if I can figure out what is going wrong, but .so files
  created with  2.95.1 work with R compiled with egcs-1.1.2 and .so
  files created with egcs-1.1.2 cause segfaults when used with R
  compiled with 2.95.1, so the problem is likely in the shared libraries
  themselves.

Thanks for all answers so far.
Christian


----- Original Message -----
From: "Jari Oksanen" <jhoksane at ecology.helsinki.fi>
To: "r-help" <r-help at stat.math.ethz.ch>
Sent: Thursday, May 25, 2000 2:39 AM
Subject: Re: [R] problem on upgrading to RH6.2 (was problem with ts pack


plummer at iarc.fr said:
I have similar problems with R 1.0.1 on RH6.2 (pre-compiled rpm binaries).
Some of the old packages ceased to work and when I tried to re-install them
through `R INSTALL package.tar.gz', some just fail and give similar error
messages. My `ts' works, but it is of the old original version, and I don't
dare to check if it stops working after re-installation. However,
re-installed
`tripack' gives the following error message:

 > library(tripack)
Error in dyn.load(x, as.logical(local), as.logical(now)) :
unable to load shared library "/usr/lib/R/library/tripack/libs/tripack.so":
  /usr/lib/R/library/tripack/libs/tripack.so: undefined symbol: ?

If I first gunzip the package, I get another undefined symbol, but the net
effect is the unchanged: a failure to load a library. Otherwise the message
is
the same as for `ts' above.

Downgrading to the old binaries of the package does not help, since they
fail
for other reasons, in this case because they can't find e_wsfe. This, I
think,
is caused by libf2g growing independent of libf2c which had this function
(originally in libI77.a).

cheers, jari oksanen
--
Jari Oksanen - Dept Ecol Env Sci, Univ Helsinki, 15140 Lahti
Ph. +358 3 89220312, Fax -- 89220289, Mobile +358 40 5136529
jari.oksanen at helsinki.fi    http://www.helsinki.fi/~jhoksane



-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.
-.-
r-help mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html
Send "info", "help", or "[un]subscribe"
(in the "body", not the subject !)  To: r-help-request at stat.math.ethz.ch
_._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._.
_._

-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-
r-help mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html
Send "info", "help", or "[un]subscribe"
(in the "body", not the subject !)  To: r-help-request at stat.math.ethz.ch
_._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._
Peter Dalgaard
# 
"Christian Posse" <posse at talariainc.com> writes:
[pd at blueberry pd]$ rpm -q egcs    
egcs-1.1.2-30
[pd at blueberry pd]$ gcc --version
egcs-2.91.66

It's the same one. So it's pretty odd that you cannot build the
packaces supplied with R (I assume "make check" fails?). That has
worked for me all the time. I don't think I have anything out of the
ordinary in my setup, except

$ more .Rconf 
CFLAGS="-Wall -g -O2"
FFLAGS="-Wall -g -O2"
Christian Posse
# 
I finally found a way around though the underlying problem
persists. It seems that the problem is with g77. Only
the packages using FORTRAN failed to be loaded correctly
in either way (R from rpm or built from scratch).

The solution was to build R from the source using the flag

--with-f2c

with ./configure.

All contrib packages installed with this version of R are loaded 
correctly and, as far as I can superficially see, work.
make check gives positive feedback.

Has anyone encountered the same problem?
Christian

----- Original Message ----- 
From: "Peter Dalgaard BSA" <p.dalgaard at biostat.ku.dk>
To: "Christian Posse" <posse at talariainc.com>
Cc: "r-help" <r-help at stat.math.ethz.ch>
Sent: Thursday, May 25, 2000 11:20 AM
Subject: Re: [R] problem on upgrading to RH6.2 (Update)
-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-
r-help mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html
Send "info", "help", or "[un]subscribe"
(in the "body", not the subject !)  To: r-help-request at stat.math.ethz.ch
_._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._