RSRuby?

[Michaels]

Hello,
I was hoping someone here can help me with an install of Rsruby. I
have it installed on one box but have been having trouble on my
other. My R libraries are installed in /usr/local/lib64/R/

the mkmf file is as follows. I think it is a linking issue that I
thought would have been solved by export R_HOME=/usr/local/lib64/R/
lib . Is there a way I should link the entire directory?

Thank you for your time,
Michael

"gcc -o conftest -I. -I/usr/lib/ruby/1.8/x86_64-linux -I. -I/usr/
share/
R/include/ -I/usr
/local/lib64/R/lib/include -Wall -g -fno-strict-aliasing -O2 -fPIC
conftest.c -L"/usr
/local/lib64/R/lib/lib" -L"/usr/lib" -rdynamic -Wl,-export-
dynamic -lruby1.8-static
-lR -lpthread -ldl -lcrypt -lm -lc"
/usr/bin/ld: warning: libRblas.so, needed by /usr/lib/libR.so, not
found (try using -rpath or -rpath-link)
/usr/lib/libR.so: undefined reference to `dswap_'
/usr/lib/libR.so: undefined reference to `dgemm_'
/usr/lib/libR.so: undefined reference to `daxpy_'
/usr/lib/libR.so: undefined reference to `drotg_'
/usr/lib/libR.so: undefined reference to `dnrm2_'
/usr/lib/libR.so: undefined reference to `dcopy_'
/usr/lib/libR.so: undefined reference to `zgemm_'
/usr/lib/libR.so: undefined reference to `dscal_'
/usr/lib/libR.so: undefined reference to `ddot_'
/usr/lib/libR.so: undefined reference to `dsyrk_'
/usr/lib/libR.so: undefined reference to `dasum_'
/usr/lib/libR.so: undefined reference to `dtrsm_'
/usr/lib/libR.so: undefined reference to `drot_'
collect2: ld returned 1 exit status

 

[Alex Gutteridge]

Hello,
I was hoping someone here can help me with an install of Rsruby. I
have it installed on one box but have been having trouble on my
other. My R libraries are installed in /usr/local/lib64/R/

the mkmf file is as follows. I think it is a linking issue that I
thought would have been solved by export R_HOME=/usr/local/lib64/R/
lib . Is there a way I should link the entire directory?

Thank you for your time,
Michael

"gcc -o conftest -I. -I/usr/lib/ruby/1.8/x86_64-linux -I. -I/usr/
share/
R/include/ -I/usr
/local/lib64/R/lib/include -Wall -g -fno-strict-aliasing -O2 -fPIC
conftest.c -L"/usr
/local/lib64/R/lib/lib" -L"/usr/lib" -rdynamic -Wl,-export-
dynamic -lruby1.8-static
-lR -lpthread -ldl -lcrypt -lm -lc"
/usr/bin/ld: warning: libRblas.so, needed by /usr/lib/libR.so, not
found (try using -rpath or -rpath-link)
/usr/lib/libR.so: undefined reference to `dswap_'
/usr/lib/libR.so: undefined reference to `dgemm_'
/usr/lib/libR.so: undefined reference to `daxpy_'
/usr/lib/libR.so: undefined reference to `drotg_'
/usr/lib/libR.so: undefined reference to `dnrm2_'
/usr/lib/libR.so: undefined reference to `dcopy_'
/usr/lib/libR.so: undefined reference to `zgemm_'
/usr/lib/libR.so: undefined reference to `dscal_'
/usr/lib/libR.so: undefined reference to `ddot_'
/usr/lib/libR.so: undefined reference to `dsyrk_'
/usr/lib/libR.so: undefined reference to `dasum_'
/usr/lib/libR.so: undefined reference to `dtrsm_'
/usr/lib/libR.so: undefined reference to `drot_'
collect2: ld returned 1 exit status

Hi,

What did you use to install R? From source or packages?

I assume you have libRblas.so in your /usr/local/lib64/R/lib
directory, so did you put /usr/local/lib64/R/lib into LD_LIBRARY_PATH
or ld.so.conf?

Alex Gutteridge

Bioinformatics Center
Kyoto University

 

[Michaels]

I installed R from source. You are right on that file. I ran this
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/lib64/R

I also added /usr/local/lib64/R/lib
to ld.so.conf and ran ldconfig.

Thank you for your help.
Michael

 

[Michaels]

Actually, I think there may be an issue with the environment
variable. after I use export, nothing is added to /etc/environment.
Could this be it?

Thank you again for the help,
Michael