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
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
···
On 8 Aug 2007, at 09:47, Michaels wrote:
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
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
···
On Aug 7, 10:09 pm, Alex Gutteridge <al...@kuicr.kyoto-u.ac.jp> wrote:
On 8 Aug 2007, at 09:47, Michaels wrote:
> 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?
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
···
On Aug 7, 11:19 pm, Michaels <fixedincome...@gmail.com> wrote:
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
On Aug 7, 10:09 pm, Alex Gutteridge <al...@kuicr.kyoto-u.ac.jp> wrote:
> On 8 Aug 2007, at 09:47, Michaels wrote:
> > 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?