Andrew Harley
2013-Feb-05 03:07 UTC
[R] ncdf4 installation problem: undefined symbol [SEC=UNCLASSIFIED]
Hello,
I'm trying to install ncdf4 on RHEL 5.8, R version 2.15.1.
Previously installed is netcdf 3.6.2 from Red Hat, so I've compiled and
installed netcdf 4.2.1.1 (with hdf5 and zlib as per install instructions, and
also set --enable-netcdf4 option) into /usr/local.
When attempting to install ncdf4 it is failing with:
** testing if installed package can be loaded
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared object
'/usr/lib64/R/library/ncdf4/libs/ncdf4.so':
/usr/lib64/R/library/ncdf4/libs/ncdf4.so: undefined symbol: nc_inq_var_deflate
Error: loading failed
Execution halted
I'm guessing I'm missing somewhere that I need to specify the path, but
the configure script picks up version netcdf 4.2.1.1 and explicitly setting
LD_LIBRARY_PATH to /usr/local/lib doesn't help either. Can anyone please
help with where I should be looking? Full command output below:
$ R CMD INSTALL ncdf4_1.6.1.tar.gz
* installing to library '/usr/lib64/R/library'
* installing *source* package 'ncdf4' ...
** package 'ncdf4' successfully unpacked and MD5 sums checked
checking for nc-config... yes
Using nc-config: nc-config
Output of nc-config --all:
This netCDF 4.2.1.1 has been built with the following features:
--cc -> gcc
--cflags -> -I/usr/local/include -I/usr/local/include
--libs -> -L/usr/local/lib -lnetcdf
--has-c++ -> no
--cxx ->
--has-c++4 -> no
--cxx4 ->
--fc ->
--fflags ->
--flibs ->
--has-f90 -> no
--has-dap -> no
--has-nc2 -> yes
--has-nc4 -> yes
--has-hdf5 -> yes
--has-hdf4 -> no
--has-pnetcdf-> no
--has-szlib ->
--prefix -> /usr/local
--includedir-> /usr/local/include
--version -> netCDF 4.2.1.1
---
netcdf.m4: about to set rpath, here is source string: >-L/usr/local/lib
-lnetcdf<
netcdf.m4: final rpath: -Wl,-rpath,/usr/local/lib
Netcdf library version: netCDF 4.2.1.1
Netcdf library has version 4 interface present: yes
Netcdf library was compiled with C compiler: gcc
configure: creating ./config.status
config.status: creating R/load.R
config.status: creating src/Makevars
********************** Results of ncdf4 package configure *******************
netCDF v4 CPP flags = -I/usr/local/include -I/usr/local/include
netCDF v4 LD flags = -Wl,-rpath,/usr/local/lib -L/usr/local/lib -lnetcdf
netCDF v4 runtime path = -Wl,-rpath,/usr/local/lib
******************************************************************************
** libs
gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG -I/usr/local/include
-I/usr/local/include -I/usr/local/include -fpic -O2 -g -pipe -Wall
-Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4
-m64 -mtune=generic -c ncdf.c -o ncdf.o
gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG -I/usr/local/include
-I/usr/local/include -I/usr/local/include -fpic -O2 -g -pipe -Wall
-Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4
-m64 -mtune=generic -c ncdf2.c -o ncdf2.o
gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG -I/usr/local/include
-I/usr/local/include -I/usr/local/include -fpic -O2 -g -pipe -Wall
-Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4
-m64 -mtune=generic -c ncdf3.c -o ncdf3.o
gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG -I/usr/local/include
-I/usr/local/include -I/usr/local/include -fpic -O2 -g -pipe -Wall
-Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4
-m64 -mtune=generic -c src_ncdf4.c -o src_ncdf4.o
gcc -m64 -std=gnu99 -shared -L/usr/local/lib64 -o ncdf4.so ncdf.o ncdf2.o
ncdf3.o src_ncdf4.o -Wl,-rpath,/usr/local/lib -L/usr/local/lib -lnetcdf
-L/usr/lib64/R/lib -lR
installing to /usr/lib64/R/library/ncdf4/libs
** R
** preparing package for lazy loading
** help
*** installing help indices
converting help for package 'ncdf4'
finding HTML links ... done
ancdf4 html
Rd warning: /tmp/RtmpSxjZ1u/R.INSTALL3e7b250a942e/ncdf4/man/ancdf4.Rd:58:
missing file link 'ncvar_put'
Rd warning: /tmp/RtmpSxjZ1u/R.INSTALL3e7b250a942e/ncdf4/man/ancdf4.Rd:76:
missing file link 'ncvar_put'
ancvar_put html
nc_close html
nc_create html
nc_enddef html
nc_open html
nc_redef html
nc_sync html
nc_version html
ncatt_get html
ncatt_put html
ncdf4-internal html
ncdim_def html
ncvar_add html
ncvar_change_missval html
ncvar_def html
Rd warning: /tmp/RtmpSxjZ1u/R.INSTALL3e7b250a942e/ncdf4/man/ncvar_def.Rd:67:
missing file link 'ncvar_put'
Rd warning: /tmp/RtmpSxjZ1u/R.INSTALL3e7b250a942e/ncdf4/man/ncvar_def.Rd:100:
missing file link 'ncvar_put'
ncvar_get html
Rd warning: /tmp/RtmpSxjZ1u/R.INSTALL3e7b250a942e/ncdf4/man/ncvar_get.Rd:77:
missing file link 'ncvar_put'
ncvar_rename html
print.ncdf4 html
** building package indices
** testing if installed package can be loaded
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared object
'/usr/lib64/R/library/ncdf4/libs/ncdf4.so':
/usr/lib64/R/library/ncdf4/libs/ncdf4.so: undefined symbol: nc_inq_var_deflate
Error: loading failed
Execution halted
ERROR: loading failed
* removing '/usr/lib64/R/library/ncdf4'
Thanks,
Andrew Harley
Linux Systems Administrator
Climate and Water Division (ICT Operations)
Bureau of Meteorology, Australia
03 9616 8441
http://www.bom.gov.au/water/
David W. Pierce
2013-Feb-05 16:59 UTC
[R] ncdf4 installation problem: undefined symbol [SEC=UNCLASSIFIED]
On Mon, Feb 4, 2013 at 7:07 PM, Andrew Harley <A.Harley at bom.gov.au> wrote:> Hello, > > I'm trying to install ncdf4 on RHEL 5.8, R version 2.15.1. > > Previously installed is netcdf 3.6.2 from Red Hat, so I've compiled and installed netcdf 4.2.1.1 (with hdf5 and zlib as per install instructions, and also set --enable-netcdf4 option) into /usr/local. > > When attempting to install ncdf4 it is failing with: > > ** testing if installed package can be loaded > Error in dyn.load(file, DLLpath = DLLpath, ...) : > unable to load shared object '/usr/lib64/R/library/ncdf4/libs/ncdf4.so': > /usr/lib64/R/library/ncdf4/libs/ncdf4.so: undefined symbol: nc_inq_var_deflate > Error: loading failed > Execution haltedHi Andrew, I think it's reasonably likely that some components of the old netcdf library installation are being found by mistake. The compiler system makes it easy to include library locations, but hard to exclude library locations, so this kind of error is not uncommon. I suggest first removing all instances of the old libnetcdf and netcdf.h from your machine, and then try again. Regards, --Dave <rest of previous message is below>> > I'm guessing I'm missing somewhere that I need to specify the path, but the configure script picks up version netcdf 4.2.1.1 and explicitly setting LD_LIBRARY_PATH to /usr/local/lib doesn't help either. Can anyone please help with where I should be looking? Full command output below: > > $ R CMD INSTALL ncdf4_1.6.1.tar.gz > * installing to library '/usr/lib64/R/library' > * installing *source* package 'ncdf4' ... > ** package 'ncdf4' successfully unpacked and MD5 sums checked > checking for nc-config... yes > Using nc-config: nc-config > Output of nc-config --all: > > This netCDF 4.2.1.1 has been built with the following features: > > --cc -> gcc > --cflags -> -I/usr/local/include -I/usr/local/include > --libs -> -L/usr/local/lib -lnetcdf > > --has-c++ -> no > --cxx -> > --has-c++4 -> no > --cxx4 -> > > --fc -> > --fflags -> > --flibs -> > --has-f90 -> no > > --has-dap -> no > --has-nc2 -> yes > --has-nc4 -> yes > --has-hdf5 -> yes > --has-hdf4 -> no > --has-pnetcdf-> no > --has-szlib -> > > --prefix -> /usr/local > --includedir-> /usr/local/include > --version -> netCDF 4.2.1.1 > > --- > netcdf.m4: about to set rpath, here is source string: >-L/usr/local/lib -lnetcdf< > netcdf.m4: final rpath: -Wl,-rpath,/usr/local/lib > Netcdf library version: netCDF 4.2.1.1 > Netcdf library has version 4 interface present: yes > Netcdf library was compiled with C compiler: gcc > configure: creating ./config.status > config.status: creating R/load.R > config.status: creating src/Makevars > > ********************** Results of ncdf4 package configure ******************* > > netCDF v4 CPP flags = -I/usr/local/include -I/usr/local/include > netCDF v4 LD flags = -Wl,-rpath,/usr/local/lib -L/usr/local/lib -lnetcdf > netCDF v4 runtime path = -Wl,-rpath,/usr/local/lib > > ****************************************************************************** > > ** libs > gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG -I/usr/local/include -I/usr/local/include -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c ncdf.c -o ncdf.o > gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG -I/usr/local/include -I/usr/local/include -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c ncdf2.c -o ncdf2.o > gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG -I/usr/local/include -I/usr/local/include -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c ncdf3.c -o ncdf3.o > gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG -I/usr/local/include -I/usr/local/include -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c src_ncdf4.c -o src_ncdf4.o > gcc -m64 -std=gnu99 -shared -L/usr/local/lib64 -o ncdf4.so ncdf.o ncdf2.o ncdf3.o src_ncdf4.o -Wl,-rpath,/usr/local/lib -L/usr/local/lib -lnetcdf -L/usr/lib64/R/lib -lR > installing to /usr/lib64/R/library/ncdf4/libs > ** R > ** preparing package for lazy loading > ** help > *** installing help indices > converting help for package 'ncdf4' > finding HTML links ... done > ancdf4 html > Rd warning: /tmp/RtmpSxjZ1u/R.INSTALL3e7b250a942e/ncdf4/man/ancdf4.Rd:58: missing file link 'ncvar_put' > Rd warning: /tmp/RtmpSxjZ1u/R.INSTALL3e7b250a942e/ncdf4/man/ancdf4.Rd:76: missing file link 'ncvar_put' > ancvar_put html > nc_close html > nc_create html > nc_enddef html > nc_open html > nc_redef html > nc_sync html > nc_version html > ncatt_get html > ncatt_put html > ncdf4-internal html > ncdim_def html > ncvar_add html > ncvar_change_missval html > ncvar_def html > Rd warning: /tmp/RtmpSxjZ1u/R.INSTALL3e7b250a942e/ncdf4/man/ncvar_def.Rd:67: missing file link 'ncvar_put' > Rd warning: /tmp/RtmpSxjZ1u/R.INSTALL3e7b250a942e/ncdf4/man/ncvar_def.Rd:100: missing file link 'ncvar_put' > ncvar_get html > Rd warning: /tmp/RtmpSxjZ1u/R.INSTALL3e7b250a942e/ncdf4/man/ncvar_get.Rd:77: missing file link 'ncvar_put' > ncvar_rename html > print.ncdf4 html > ** building package indices > ** testing if installed package can be loaded > Error in dyn.load(file, DLLpath = DLLpath, ...) : > unable to load shared object '/usr/lib64/R/library/ncdf4/libs/ncdf4.so': > /usr/lib64/R/library/ncdf4/libs/ncdf4.so: undefined symbol: nc_inq_var_deflate > Error: loading failed > Execution halted > ERROR: loading failed > * removing '/usr/lib64/R/library/ncdf4' > > Thanks, > > Andrew Harley > Linux Systems Administrator > Climate and Water Division (ICT Operations) > Bureau of Meteorology, Australia > 03 9616 8441 > http://www.bom.gov.au/water/ > > ______________________________________________ > R-help at r-project.org 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.-- David W. Pierce Division of Climate, Atmospheric Science, and Physical Oceanography Scripps Institution of Oceanography, La Jolla, California, USA (858) 534-8276 (voice) / (858) 534-8561 (fax) dpierce at ucsd.edu