none
Error during package installation of SVD on R server RRS feed

  • Question

  • I do not know whether it is Microsoft R open issue, or R Server Problem, but from the error log, it seems that it is an issue of LAPACK libraries which comes with R Installation.

    Error log:

     install.packages("svd")
    Installing package into ‘/home/hdinsight/R/x86_64-pc-linux-gnu-library/3.2’
    (as ‘lib’ is unspecified)
      % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                     Dload  Upload   Total   Spent    Left  Speed
      0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0100 84147  100 84147    0     0   113k      0 --:--:-- --:--:-- --:--:--  113k
    * installing *source* package ‘svd’ ...
    ** package ‘svd’ successfully unpacked and MD5 sums checked
    ** libs
    gcc -std=gnu99 -I/usr/lib64/microsoft-r/8.0/lib64/R/include -DNDEBUG  -I/usr/local/include   -I../inst/include -fpic  -g -O2 -DU_STATIC_IMPLEMENTATION  -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/microsoft-r/8.0/lib64/R/include -DNDEBUG  -I/usr/local/include   -I../inst/include -fpic  -g -O2 -DU_STATIC_IMPLEMENTATION  -c propack/propack_svd.c -o propack/propack_svd.o
    gcc -std=gnu99 -I/usr/lib64/microsoft-r/8.0/lib64/R/include -DNDEBUG  -I/usr/local/include   -I../inst/include -fpic  -g -O2 -DU_STATIC_IMPLEMENTATION  -c trlan/dsort2.c -o trlan/dsort2.o
    gcc -std=gnu99 -I/usr/lib64/microsoft-r/8.0/lib64/R/include -DNDEBUG  -I/usr/local/include   -I../inst/include -fpic  -g -O2 -DU_STATIC_IMPLEMENTATION  -c trlan/dstqrb.c -o trlan/dstqrb.o
    gcc -std=gnu99 -I/usr/lib64/microsoft-r/8.0/lib64/R/include -DNDEBUG  -I/usr/local/include   -I../inst/include -fpic  -g -O2 -DU_STATIC_IMPLEMENTATION  -c trlan/trlcore.c -o trlan/trlcore.o
    gcc -std=gnu99 -I/usr/lib64/microsoft-r/8.0/lib64/R/include -DNDEBUG  -I/usr/local/include   -I../inst/include -fpic  -g -O2 -DU_STATIC_IMPLEMENTATION  -c trlan/trlaux.c -o trlan/trlaux.o
    gcc -std=gnu99 -I/usr/lib64/microsoft-r/8.0/lib64/R/include -DNDEBUG  -I/usr/local/include   -I../inst/include -fpic  -g -O2 -DU_STATIC_IMPLEMENTATION  -c trlan/trlan.c -o trlan/trlan.o
    gcc -std=gnu99 -I/usr/lib64/microsoft-r/8.0/lib64/R/include -DNDEBUG  -I/usr/local/include   -I../inst/include -fpic  -g -O2 -DU_STATIC_IMPLEMENTATION  -c trlan/trl_comm_none.c -o trlan/trl_comm_none.o
    gcc -std=gnu99 -I/usr/lib64/microsoft-r/8.0/lib64/R/include -DNDEBUG  -I/usr/local/include   -I../inst/include -fpic  -g -O2 -DU_STATIC_IMPLEMENTATION  -c trlan/trlmap.c -o trlan/trlmap.o
    gcc -std=gnu99 -I/usr/lib64/microsoft-r/8.0/lib64/R/include -DNDEBUG  -I/usr/local/include   -I../inst/include -fpic  -g -O2 -DU_STATIC_IMPLEMENTATION  -c trlan/restart.c -o trlan/restart.o
    gcc -std=gnu99 -I/usr/lib64/microsoft-r/8.0/lib64/R/include -DNDEBUG  -I/usr/local/include   -I../inst/include -fpic  -g -O2 -DU_STATIC_IMPLEMENTATION  -c trlan/trlan_R.c -o trlan/trlan_R.o
    gcc -std=gnu99 -shared -L/usr/lib64/microsoft-r/8.0/lib64/R/lib -L/usr/local/lib64 -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/trlan_R.o -L/usr/lib64/microsoft-r/8.0/lib64/R/lib -lRlapack -L/usr/lib64/microsoft-r/8.0/lib64/R/lib -lRblas -lgfortran -lm -L/usr/lib64/microsoft-r/8.0/lib64/R/lib -lR
    installing to /home/hdinsight/R/x86_64-pc-linux-gnu-library/3.2/svd/libs
    ** R
    ** inst
    ** preparing package for lazy loading
    ** 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 '/home/hdinsight/R/x86_64-pc-linux-gnu-library/3.2/svd/libs/svd.so':
      /home/hdinsight/R/x86_64-pc-linux-gnu-library/3.2/svd/libs/svd.so: undefined symbol: lsame_
    Error: loading failed
    Execution halted
    ERROR: loading failed
    * removing ‘/home/hdinsight/R/x86_64-pc-linux-gnu-library/3.2/svd’
    Warning in install.packages :
      installation of package ‘svd’ had non-zero exit Status
    

    Can you please answer how to fix this issue? if not than who should ideally be responsible for this?

    I have seen some Forum Solutions, and most of the times "Symbol not found" errors often occur from simply not linking the correct libraries.

    I am able to install and load SVD package on Linux Gnu 64 bit with R 3.2 Version, as well as on Windows. I have the Installation log of the same. I can provide it if needed.

    Thanks for your help in advance.

    Wednesday, February 1, 2017 12:31 PM

Answers

  • Hi,

    It seems that you are using R Server cluster 8.0, and the Linux dependency libs are somewhat messed up.

    Can you use a R Server on HDInsight 9.0 cluster instead? I just tried and it is working fine.

    Feel free to drop me an email at xiaoyzhu at Microsoft dot com and I can help link to the relevant folks if possible.

    • Marked as answer by AyKumar Thursday, February 2, 2017 10:39 AM
    Thursday, February 2, 2017 5:13 AM

All replies

  • Hi,

    It seems that you are using R Server cluster 8.0, and the Linux dependency libs are somewhat messed up.

    Can you use a R Server on HDInsight 9.0 cluster instead? I just tried and it is working fine.

    Feel free to drop me an email at xiaoyzhu at Microsoft dot com and I can help link to the relevant folks if possible.

    • Marked as answer by AyKumar Thursday, February 2, 2017 10:39 AM
    Thursday, February 2, 2017 5:13 AM
  • Thanks Mr. Zhu, it solved the problem.

    We just checked it ourselves as well.

    Thanks also for such a quick reply.

    I will mark your suggestion as an answer, and close this thread.

    Have a nice day.

    Thursday, February 2, 2017 10:39 AM