none
Loading SVD library on Microsoft R Open 3.2.4 RRS feed

  • Question

  • Hi everyone,

    Has anyone had success loading or installing the SVD package in Microsoft R Open 3.2.4 build?  When I try to load or install it, I get an error regarding an undefined symbol "lsame_".  Complete dump below.

    Thanks in advance!

     sudo R CMD INSTALL svd_0.4.tar.gz

    * installing to library ‘/usr/lib64/MRO-3.2.4/R-3.2.4/lib/R/library’

    * installing *source* package ‘svd’ ...

    ** package ‘svd’ successfully unpacked and MD5 sums checked

    ** libs

    gcc -std=gnu99 -I/usr/lib64/MRO-3.2.4/R-3.2.4/lib/R/include -DNDEBUG  -I/usr/local/include   -I../inst/include -fpic  -g -O2  -c extmat.c -o extmat.o

    gfortran   -fpic  -g -O2  -c propack/dlansvd_irl.f -o propack/dlansvd_irl.o

    gfortran   -fpic  -g -O2  -c propack/printstat.f -o propack/printstat.o

    gfortran   -fpic  -g -O2  -c propack/second.f -o propack/second.o

    gcc -std=gnu99 -I/usr/lib64/MRO-3.2.4/R-3.2.4/lib/R/include -DNDEBUG  -I/usr/local/include   -I../inst/include -fpic  -g -O2  -c propack/propack_svd.c -o propack/propack_svd.o

    gcc -std=gnu99 -I/usr/lib64/MRO-3.2.4/R-3.2.4/lib/R/include -DNDEBUG  -I/usr/local/include   -I../inst/include -fpic  -g -O2  -c trlan/dsort2.c -o trlan/dsort2.o

    gcc -std=gnu99 -I/usr/lib64/MRO-3.2.4/R-3.2.4/lib/R/include -DNDEBUG  -I/usr/local/include   -I../inst/include -fpic  -g -O2  -c trlan/dstqrb.c -o trlan/dstqrb.o

    gcc -std=gnu99 -I/usr/lib64/MRO-3.2.4/R-3.2.4/lib/R/include -DNDEBUG  -I/usr/local/include   -I../inst/include -fpic  -g -O2  -c trlan/trlcore.c -o trlan/trlcore.o

    gcc -std=gnu99 -I/usr/lib64/MRO-3.2.4/R-3.2.4/lib/R/include -DNDEBUG  -I/usr/local/include   -I../inst/include -fpic  -g -O2  -c trlan/trlaux.c -o trlan/trlaux.o

    gcc -std=gnu99 -I/usr/lib64/MRO-3.2.4/R-3.2.4/lib/R/include -DNDEBUG  -I/usr/local/include   -I../inst/include -fpic  -g -O2  -c trlan/trlan.c -o trlan/trlan.o

    gcc -std=gnu99 -I/usr/lib64/MRO-3.2.4/R-3.2.4/lib/R/include -DNDEBUG  -I/usr/local/include   -I../inst/include -fpic  -g -O2  -c trlan/trl_comm_none.c -o trlan/trl_comm_none.o

    gcc -std=gnu99 -I/usr/lib64/MRO-3.2.4/R-3.2.4/lib/R/include -DNDEBUG  -I/usr/local/include   -I../inst/include -fpic  -g -O2  -c trlan/trlmap.c -o trlan/trlmap.o

    gcc -std=gnu99 -I/usr/lib64/MRO-3.2.4/R-3.2.4/lib/R/include -DNDEBUG  -I/usr/local/include   -I../inst/include -fpic  -g -O2  -c trlan/restart.c -o trlan/restart.o

    gcc -std=gnu99 -I/usr/lib64/MRO-3.2.4/R-3.2.4/lib/R/include -DNDEBUG  -I/usr/local/include   -I../inst/include -fpic  -g -O2  -c trlan/ztrl_comm_none.c -o trlan/ztrl_comm_none.o

    gcc -std=gnu99 -I/usr/lib64/MRO-3.2.4/R-3.2.4/lib/R/include -DNDEBUG  -I/usr/local/include   -I../inst/include -fpic  -g -O2  -c trlan/ztrlan.c -o trlan/ztrlan.o

    gcc -std=gnu99 -I/usr/lib64/MRO-3.2.4/R-3.2.4/lib/R/include -DNDEBUG  -I/usr/local/include   -I../inst/include -fpic  -g -O2  -c trlan/ztrlcore.c -o trlan/ztrlcore.o

    gcc -std=gnu99 -I/usr/lib64/MRO-3.2.4/R-3.2.4/lib/R/include -DNDEBUG  -I/usr/local/include   -I../inst/include -fpic  -g -O2  -c trlan/ztrlaux.c -o trlan/ztrlaux.o

    gcc -std=gnu99 -I/usr/lib64/MRO-3.2.4/R-3.2.4/lib/R/include -DNDEBUG  -I/usr/local/include   -I../inst/include -fpic  -g -O2  -c trlan/zdaxpy.c -o trlan/zdaxpy.o

    gcc -std=gnu99 -I/usr/lib64/MRO-3.2.4/R-3.2.4/lib/R/include -DNDEBUG  -I/usr/local/include   -I../inst/include -fpic  -g -O2  -c trlan/zdgemv.c -o trlan/zdgemv.o

    gcc -std=gnu99 -I/usr/lib64/MRO-3.2.4/R-3.2.4/lib/R/include -DNDEBUG  -I/usr/local/include   -I../inst/include -fpic  -g -O2  -c trlan/trlan_R.c -o trlan/trlan_R.o

    gcc -std=gnu99 -I/usr/lib64/MRO-3.2.4/R-3.2.4/lib/R/include -DNDEBUG  -I/usr/local/include   -I../inst/include -fpic  -g -O2  -c trlan/ztrlan_R.c -o trlan/ztrlan_R.o

    gcc -std=gnu99 -shared -L/usr/lib64/MRO-3.2.4/R-3.2.4/lib/R/lib -L/usr/local/lib -o svd.so extmat.o propack/dlansvd_irl.o propack/printstat.o propack/second.o propack/propack_svd.o trlan/dsort2.o trlan/dstqrb.o trlan/trlcore.o trlan/trlaux.o trlan/trlan.o trlan/trl_comm_none.o trlan/trlmap.o trlan/restart.o trlan/ztrl_comm_none.o trlan/ztrlan.o trlan/ztrlcore.o trlan/ztrlaux.o trlan/zdaxpy.o trlan/zdgemv.o trlan/trlan_R.o trlan/ztrlan_R.o -L/usr/lib64/MRO-3.2.4/R-3.2.4/lib/R/lib -lRlapack -L/usr/lib64/MRO-3.2.4/R-3.2.4/lib/R/lib -lRblas -lgfortran -lm -lquadmath -L/usr/lib64/MRO-3.2.4/R-3.2.4/lib/R/lib -lR

    installing to /usr/lib64/MRO-3.2.4/R-3.2.4/lib/R/library/svd/libs

    ** R

    ** inst

    ** preparing package for lazy loading

    Creating a generic function for ‘as.matrix’ from package ‘base’ in package ‘svd’

    Creating a generic function for ‘as.array’ from package ‘base’ in package ‘svd’

    Creating a generic function for ‘as.vector’ from package ‘base’ in package ‘svd’

    Creating a generic function for ‘t’ from package ‘base’ in package ‘svd’

    Creating a generic function for ‘crossprod’ from package ‘base’ in package ‘svd’

    Creating a generic function for ‘tcrossprod’ from package ‘base’ in package ‘svd’

    ** help

    *** installing help indices

    ** building package indices

    ** testing if installed package can be loaded

    Error in dyn.load(file, DLLpath = DLLpath, ...) :

      unable to load shared object '/usr/lib64/MRO-3.2.4/R-3.2.4/lib/R/library/svd/libs/svd.so':

      /usr/lib64/MRO-3.2.4/R-3.2.4/lib/R/library/svd/libs/svd.so: undefined symbol: lsame_

    Error: loading failed

    Execution halted

    ERROR: loading failed

    * removing ‘/usr/lib64/MRO-3.2.4/R-3.2.4/lib/R/library/svd’

    Thursday, May 12, 2016 6:31 PM

All replies

  • After discussing this issue with the author of the SVD library, it seems that R Open's LAPACK implementation does not provide all functions which are available normally (e.g. lsame).  Is anyone else running into an issue with LAPACK functions, and if so, is there anything I can do to contribute to a fix?

    Thanks in advance

    Monday, May 16, 2016 7:52 PM
  • This works perfectly fine for me in Windows, so I'm sorry you're having trouble using Linux.

    I'll ask one of our tech experts to take a look.

    Tuesday, May 17, 2016 2:11 PM
  • Thank you for having someone look into this problem.  I am using the build for Ubuntu 14.04.

    Tuesday, May 17, 2016 4:43 PM
  • FYI.  The problem exists on the 3.2.5 build as well.  Thanks for looking into this.
    Tuesday, May 24, 2016 6:51 PM
  • Hi,

    I am getting the same error as of writing this Response. Have you found a Solution or Workaround? I thought of changing to EMD + hht packages in R to do the Job of SVD, but Output is not always as desired.

     

    Friday, January 20, 2017 10:49 AM