We have R 2.2.1 installed on a Linux cluster that seems to have problems loading
either of our shared object libraries for packages. This seems to be happening
on both local and global versions of packages that we install. However, we have
only noticed this problem in the past 3 months on this R installation, whereas
some users had success before then. It could be that something on our system
changed, but I am not an admin so I wouldn't know where to look. Can anyone
help with this problem?
## A LOCAL INSTALLATION OF HAPLO.STATS APPEARS SUCCESSFUL
[sinnwell at dnode0 rpack]$ R CMD INSTALL -l /home/sinnwell/rdir/tmplib
haplo.stats
* Installing *source* package 'haplo.stats' ...
** libs
make: `haplo.stats.so' is up to date.
** R
** data
** demo
** inst
** preparing package for lazy loading
** help
>>> Building/Updating help pages for package 'haplo.stats'
Formats: text html latex example
** building package indices ...
* DONE (haplo.stats)
## TRY AND LOAD THE LOCALLY INSTALLED LIBRARY, YET THE SYSTEM COMMAND SHOWS THE
.so FILE IS THERE
R> library(haplo.stats, lib.loc="/home/sinnwell/rdir/tmplib/")
Error in dyn.load(x, as.logical(local), as.logical(now)) :
unable to load shared library
'/home/sinnwell/rdir/tmplib/haplo.stats/libs/haplo.stats.so':
/home/sinnwell/rdir/tmplib/haplo.stats/libs/haplo.stats.so: cannot open shared
object file: No such file or directory
Error in library(haplo.stats, lib.loc = "/home/sinnwell/rdir/tmplib/")
:
.First.lib failed for 'haplo.stats'
R> system('ls -al /home/sinnwell/rdir/tmplib/haplo.stats/libs')
total 88
drwxr-xr-x 2 sinnwell sinnwell 4096 Aug 24 15:14 .
drwxr-xr-x 13 sinnwell sinnwell 4096 Aug 24 15:14 ..
-rwxr-xr-x 1 sinnwell sinnwell 61566 Aug 24 15:14 haplo.stats.so
R> version
_
platform i686-pc-linux-gnu
arch i686
os linux-gnu
system i686, linux-gnu
status
major 2
minor 2.1
year 2005
month 12
day 20
svn rev 36812
language R
Also, the .First.lib for haplo.stats looks like this:
.First.lib <- function(lib, pkg) {
library.dynam("haplo.stats", pkg, lib)
}
Thanks for you suggestions,
Jason Sinnwell
=========================== Jason Sinnwell
Mayo Clinic, Rochester
Division of Biostatistics
ph: 507.284.3270
fax: 507.284.9542
"Sinnwell, Jason P." <Sinnwell.Jason at mayo.edu> writes:> We have R 2.2.1 installed on a Linux cluster that seems to have problems loading either of our shared object libraries for packages. This seems to be happening on both local and global versions of packages that we install. However, we have only noticed this problem in the past 3 months on this R installation, whereas some users had success before then. It could be that something on our system changed, but I am not an admin so I wouldn't know where to look. Can anyone help with this problem? > > ## A LOCAL INSTALLATION OF HAPLO.STATS APPEARS SUCCESSFUL > [sinnwell at dnode0 rpack]$ R CMD INSTALL -l /home/sinnwell/rdir/tmplib haplo.stats > * Installing *source* package 'haplo.stats' ... > ** libs > make: `haplo.stats.so' is up to date. > ** R > ** data > ** demo > ** inst > ** preparing package for lazy loading > > ** help > >>> Building/Updating help pages for package 'haplo.stats' > Formats: text html latex example > ** building package indices ... > * DONE (haplo.stats) > > ## TRY AND LOAD THE LOCALLY INSTALLED LIBRARY, YET THE SYSTEM COMMAND SHOWS THE .so FILE IS THERE > > R> library(haplo.stats, lib.loc="/home/sinnwell/rdir/tmplib/") > Error in dyn.load(x, as.logical(local), as.logical(now)) : > unable to load shared library '/home/sinnwell/rdir/tmplib/haplo.stats/libs/haplo.stats.so': > /home/sinnwell/rdir/tmplib/haplo.stats/libs/haplo.stats.so: cannot open shared object file: No such file or directory > Error in library(haplo.stats, lib.loc = "/home/sinnwell/rdir/tmplib/") : > .First.lib failed for 'haplo.stats' > R> system('ls -al /home/sinnwell/rdir/tmplib/haplo.stats/libs') > total 88 > drwxr-xr-x 2 sinnwell sinnwell 4096 Aug 24 15:14 . > drwxr-xr-x 13 sinnwell sinnwell 4096 Aug 24 15:14 .. > -rwxr-xr-x 1 sinnwell sinnwell 61566 Aug 24 15:14 haplo.stats.soHmmmm.. Does "mount -l" show something interesting on the filesystem containing the .so file? (e.g., option noexec). -- O__ ---- Peter Dalgaard ?ster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk) FAX: (+45) 35327907
I don't know if mount -l shows "something interesting" below. We're wondering if there is an issue with the gcc compiler, which has been updated since we last updated R. Do you see anything that could be wrong with the info below? We plan on updating to R 2.3.1, hoping that will clear things up. Thanks for your help, Jason [sinnwell at dnode0 haplo.stats]$ which gcc /usr/bin/gcc [sinnwell at dnode0 haplo.stats]$ ls -al /usr/bin/gcc -rwxr-xr-x 2 root root 103336 Mar 8 15:18 /usr/bin/gcc [sinnwell at dnode0 haplo.stats]$ ls -al /usr/local/biotools/r total 36 drwxr-xr-x 4 magee rcf 4096 May 1 13:17 . drwxr-xr-x 23 magee rcf 4096 Jun 21 15:25 .. lrwxrwxrwx 1 root root 7 May 1 13:17 current -> R-2.2.1 drwxr-xr-x 5 magee rcf 4096 Jan 3 2005 R-2.0.1 drwxr-xr-x 5 magee rcf 4096 Feb 22 2006 R-2.2.1 [sinnwell at dnode0 rpack]$ gcc -dumpversion 3.4.5 [sinnwell at dnode0 rpack]$ mount -l /dev/sda5 on / type ext3 (rw) [/] none on /proc type proc (rw) none on /sys type sysfs (rw) none on /dev/pts type devpts (rw,gid=5,mode=620) usbfs on /proc/bus/usb type usbfs (rw) /dev/sda1 on /boot type ext3 (rw) [/boot] none on /dev/shm type tmpfs (rw) /dev/sda10 on /local1 type ext3 (rw) [/local1] /dev/sda9 on /tmp type ext3 (rw) [/tmp] /dev/sda7 on /usr type ext3 (rw) [/usr] /dev/sda8 on /var type ext3 (rw) [/var] none on /proc/sys/fs/binfmt_misc type binfmt_misc (rw) sunrpc on /var/lib/nfs/rpc_pipefs type rpc_pipefs (rw) rcfcluster-nfs2:/home on /home type nfs (rw,rsize=8192,wsize=8192,intr,timeo=15,addr=172.23.70.7) rcfcluster-nfs2:/data on /data type nfs (rw,rsize=8192,wsize=8192,intr,timeo=15,addr=172.23.70.7) rcfcluster-nfs2:/scratch on /scratch type nfs (rw,rsize=8192,wsize=8192,intr,timeo=15,addr=172.23.70.7)> -----Original Message----- > From: pd at pubhealth.ku.dk [mailto:pd at pubhealth.ku.dk] On > Behalf Of Peter Dalgaard > Sent: Thursday, August 24, 2006 6:02 PM > To: Sinnwell, Jason P. > Cc: 'r-help at stat.math.ethz.ch' > Subject: Re: [R] Problem in library.dynam problems on Linux > > "Sinnwell, Jason P." <Sinnwell.Jason at mayo.edu> writes: > > > We have R 2.2.1 installed on a Linux cluster that seems to > have problems loading either of our shared object libraries > for packages. This seems to be happening on both local and > global versions of packages that we install. However, we > have only noticed this problem in the past 3 months on this R > installation, whereas some users had success before then. It > could be that something on our system changed, but I am not > an admin so I wouldn't know where to look. Can anyone help > with this problem? > > > > ## A LOCAL INSTALLATION OF HAPLO.STATS APPEARS SUCCESSFUL > > [sinnwell at dnode0 rpack]$ R CMD INSTALL -l > /home/sinnwell/rdir/tmplib > > haplo.stats > > * Installing *source* package 'haplo.stats' ... > > ** libs > > make: `haplo.stats.so' is up to date. > > ** R > > ** data > > ** demo > > ** inst > > ** preparing package for lazy loading > > > > ** help > > >>> Building/Updating help pages for package 'haplo.stats' > > Formats: text html latex example > > ** building package indices ... > > * DONE (haplo.stats) > > > > ## TRY AND LOAD THE LOCALLY INSTALLED LIBRARY, YET THE > SYSTEM COMMAND > > SHOWS THE .so FILE IS THERE > > > > R> library(haplo.stats, lib.loc="/home/sinnwell/rdir/tmplib/") > > Error in dyn.load(x, as.logical(local), as.logical(now)) : > > unable to load shared library > '/home/sinnwell/rdir/tmplib/haplo.stats/libs/haplo.stats.so': > > > /home/sinnwell/rdir/tmplib/haplo.stats/libs/haplo.stats.so: cannot > > open shared object file: No such file or directory Error in > library(haplo.stats, lib.loc = "/home/sinnwell/rdir/tmplib/") : > > .First.lib failed for 'haplo.stats' > > R> system('ls -al /home/sinnwell/rdir/tmplib/haplo.stats/libs') > > total 88 > > drwxr-xr-x 2 sinnwell sinnwell 4096 Aug 24 15:14 . > > drwxr-xr-x 13 sinnwell sinnwell 4096 Aug 24 15:14 .. > > -rwxr-xr-x 1 sinnwell sinnwell 61566 Aug 24 15:14 haplo.stats.so > > Hmmmm.. Does "mount -l" show something interesting on the > filesystem containing the .so file? (e.g., option noexec). > > -- > O__ ---- Peter Dalgaard ?ster Farimagsgade 5, Entr.B > c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K > (*) \(*) -- University of Copenhagen Denmark Ph: > (+45) 35327918 > ~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk) FAX: > (+45) 35327907 >