无法在EC2 Spark群集上安装fOptions R软件包

Question

I have deployed a spark cluster on ec2 using the spark-ec2 script. I am trying to install the 'fOptions' R package in Rstudio on the master but I am getting the following errors while the install.packages() tries to install a depedency called 'gss'

/usr/bin/ld: cannot find -lRlapack /usr/bin/ld: cannot find -lRblas

Warning: Label 23057 at (1) defined but not used
gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG  -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 smolyak.c -o smolyak.o
smolyak.c: In function ‘eval’:
smolyak.c:181:10: warning: variable ‘dummy’ set but not used [-Wunused-but-set-variable]
smolyak.c: In function ‘calccoeff2’:
smolyak.c:381:10: warning: variable ‘dummy’ set but not used [-Wunused-but-set-variable]
smolyak.c: In function ‘fsum’:
smolyak.c:418:10: warning: variable ‘dummy’ set but not used [-Wunused-but-set-variable]
smolyak.c: At top level:
smolyak.c:378:8: warning: ‘calccoeff2’ defined but not used [-Wunused-function]
gcc -m64 -std=gnu99 -shared -L/usr/local/lib64 -o gss.so cdennewton.o cdennewton10.o dcoef.o dcore.o dcrdr.o ddeev.o deval.o dgold.o dmcdc.o dmudr.o dmudr0.o dmudr1.o dnewton.o dnewton10.o dprmut.o dqrslm.o drkl.o dset.o dsidr.o dsidr0.o dsms.o dstup.o dsytr.o dtrev.o gaussq.o hzdaux.o hzdnewton.o hzdnewton10.o llrmnewton.o reg.o smolyak.o -L/usr/lib64/R/lib -lRlapack -L/usr/lib64/R/lib -lRblas -lgfortran -lm -lquadmath -lgfortran -lm -lquadmath -L/usr/lib64/R/lib -lR
/usr/bin/ld: cannot find -lRlapack
/usr/bin/ld: cannot find -lRblas
collect2: ld returned 1 exit status
make: *** [gss.so] Error 1
ERROR: compilation failed for package ‘gss’
* removing ‘/home/rstudio/R/x86_64-redhat-linux-gnu-library/3.2/gss’
Warning in install.packages :
  installation of package ‘gss’ had non-zero exit status

The downloaded source packages are in
    ‘/tmp/RtmpGROBAw/downloaded_packages’

There are many more warnings too. I also tried yum install liblpack3 libperl-dev but I get another error - no package libperl-dev available and same for other packages.

Other packages like ggplot2 were successfully installed and some sample codes are running fine on the spark cluster.

Is there any solution to this error or any work around to install fOptions and its dependencies?

Answer 1

That is a buggy installation of R itself.

It thinks it should have internal LAPACK and BLAS (because of the 'R' in Rlapack and Rblas) which would then automatically be part of the same R installation but they are missing. On a 'normal' Unix system you have

edd@max:~$ R CMD config LAPACK_LIBS
-llapack
edd@max:~$ R CMD config BLAS_LIBS
-lblas
edd@max:~$ 

and that use system versions of LAPACK and BLAS. If and when you configure R to use its own, it shows (as here in my R-devel build)

edd@max:~$ RD CMD config LAPACK_LIBS
-L/usr/local/lib/R-devel/lib/R/lib -lRlapack
edd@max:~$ RD CMD config BLAS_LIBS
-L/usr/local/lib/R-devel/lib/R/lib -lRblas
edd@max:~$ 

but also gives the location. So you need to sort that out with the RedHat version of R you have there.