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Trouble installing on HPC cluster#31
@yiyangphd

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@yiyangphd
yiyangphd
opened on Mar 28, 2021

Updated 03/29/2021: was able to install the package using the following commands:
wget --no-check-certificate https://github.com/zhengxwen/gdsfmt/tarball/master -O gdsfmt_latest.tar.gz
R CMD INSTALL gdsfmt_latest.tar.gz
Hope this helps anyone having the same issue.

Dear Dr. Zheng,

I was able to install the package "gdsfmt" on my own computer but was not able to do so on our university's computing cluster. I have enclosed the error messages:

  • installing source package 'gdsfmt' ...
    ** using staged installation
    ** libs
    g++ -std=gnu++11 -I"/nfs/apps/R/3.6.0/lib64/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -fpic -g -O2 -c R_CoreArray.cpp -o R_CoreArray.o
    g++ -std=gnu++11 -I"/nfs/apps/R/3.6.0/lib64/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -fpic -g -O2 -c gdsfmt.cpp -o gdsfmt.o
    g++ -std=gnu++11 -I"/nfs/apps/R/3.6.0/lib64/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -fpic -g -O2 -c digest.cpp -o digest.o
    g++ -std=gnu++11 -I"/nfs/apps/R/3.6.0/lib64/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -fpic -g -O2 -c CoreArray/CoreArray.cpp -o CoreArray/CoreArray.o
    g++ -std=gnu++11 -I"/nfs/apps/R/3.6.0/lib64/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -fpic -g -O2 -c CoreArray/dAllocator.cpp -o CoreArray/dAllocator.o
    g++ -std=gnu++11 -I"/nfs/apps/R/3.6.0/lib64/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -fpic -g -O2 -c CoreArray/dAny.cpp -o CoreArray/dAny.o
    g++ -std=gnu++11 -I"/nfs/apps/R/3.6.0/lib64/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -fpic -g -O2 -c CoreArray/dBase.cpp -o CoreArray/dBase.o
    g++ -std=gnu++11 -I"/nfs/apps/R/3.6.0/lib64/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -fpic -g -O2 -c CoreArray/dBitGDS.cpp -o CoreArray/dBitGDS.o
    g++ -std=gnu++11 -I"/nfs/apps/R/3.6.0/lib64/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -fpic -g -O2 -c CoreArray/dEndian.cpp -o CoreArray/dEndian.o
    g++ -std=gnu++11 -I"/nfs/apps/R/3.6.0/lib64/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -fpic -g -O2 -c CoreArray/dFile.cpp -o CoreArray/dFile.o
    g++ -std=gnu++11 -I"/nfs/apps/R/3.6.0/lib64/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -fpic -g -O2 -c CoreArray/dParallel.cpp -o CoreArray/dParallel.o
    gcc -std=gnu99 -I"/nfs/apps/R/3.6.0/lib64/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -fpic -g -O2 -c CoreArray/dParallel_Ext.c -o CoreArray/dParallel_Ext.o
    g++ -std=gnu++11 -I"/nfs/apps/R/3.6.0/lib64/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -fpic -g -O2 -c CoreArray/dPlatform.cpp -o CoreArray/dPlatform.o
    g++ -std=gnu++11 -I"/nfs/apps/R/3.6.0/lib64/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -fpic -g -O2 -c CoreArray/dRealGDS.cpp -o CoreArray/dRealGDS.o
    g++ -std=gnu++11 -I"/nfs/apps/R/3.6.0/lib64/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -fpic -g -O2 -c CoreArray/dSerial.cpp -o CoreArray/dSerial.o
    g++ -std=gnu++11 -I"/nfs/apps/R/3.6.0/lib64/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -fpic -g -O2 -c CoreArray/dStrGDS.cpp -o CoreArray/dStrGDS.o
    g++ -std=gnu++11 -I"/nfs/apps/R/3.6.0/lib64/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -fpic -g -O2 -c CoreArray/dStream.cpp -o CoreArray/dStream.o
    g++ -std=gnu++11 -I"/nfs/apps/R/3.6.0/lib64/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -fpic -g -O2 -c CoreArray/dStruct.cpp -o CoreArray/dStruct.o
    g++ -std=gnu++11 -I"/nfs/apps/R/3.6.0/lib64/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -fpic -g -O2 -c CoreArray/dVLIntGDS.cpp -o CoreArray/dVLIntGDS.o
    gcc -std=gnu99 -I"/nfs/apps/R/3.6.0/lib64/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -fpic -g -O2 -c ZLIB/adler32.c -o ZLIB/adler32.o
    gcc -std=gnu99 -I"/nfs/apps/R/3.6.0/lib64/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -fpic -g -O2 -c ZLIB/compress.c -o ZLIB/compress.o
    gcc -std=gnu99 -I"/nfs/apps/R/3.6.0/lib64/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -fpic -g -O2 -c ZLIB/crc32.c -o ZLIB/crc32.o
    gcc -std=gnu99 -I"/nfs/apps/R/3.6.0/lib64/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -fpic -g -O2 -c ZLIB/deflate.c -o ZLIB/deflate.o
    gcc -std=gnu99 -I"/nfs/apps/R/3.6.0/lib64/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -fpic -g -O2 -c ZLIB/infback.c -o ZLIB/infback.o
    gcc -std=gnu99 -I"/nfs/apps/R/3.6.0/lib64/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -fpic -g -O2 -c ZLIB/inffast.c -o ZLIB/inffast.o
    gcc -std=gnu99 -I"/nfs/apps/R/3.6.0/lib64/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -fpic -g -O2 -c ZLIB/inflate.c -o ZLIB/inflate.o
    gcc -std=gnu99 -I"/nfs/apps/R/3.6.0/lib64/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -fpic -g -O2 -c ZLIB/inftrees.c -o ZLIB/inftrees.o
    gcc -std=gnu99 -I"/nfs/apps/R/3.6.0/lib64/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -fpic -g -O2 -c ZLIB/trees.c -o ZLIB/trees.o
    gcc -std=gnu99 -I"/nfs/apps/R/3.6.0/lib64/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -fpic -g -O2 -c ZLIB/uncompr.c -o ZLIB/uncompr.o
    gcc -std=gnu99 -I"/nfs/apps/R/3.6.0/lib64/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -fpic -g -O2 -c ZLIB/zutil.c -o ZLIB/zutil.o
    gcc -std=gnu99 -I"/nfs/apps/R/3.6.0/lib64/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -fpic -g -O2 -c LZ4/lz4.c -o LZ4/lz4.o
    gcc -std=gnu99 -I"/nfs/apps/R/3.6.0/lib64/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -fpic -g -O2 -c LZ4/lz4hc.c -o LZ4/lz4hc.o
    gcc -std=gnu99 -I"/nfs/apps/R/3.6.0/lib64/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -fpic -g -O2 -c LZ4/lz4frame.c -o LZ4/lz4frame.o
    gcc -std=gnu99 -I"/nfs/apps/R/3.6.0/lib64/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -fpic -g -O2 -c LZ4/xxhash.c -o LZ4/xxhash.o
    cd XZ && tar -xzf xz-5.2.3.tar.gz
    cd XZ/xz-5.2.3 &&
    ./configure CC="gcc -std=gnu99" CPP="gcc -std=gnu99 -E" CXX="g++ -std=gnu++11" CXXCPP="g++ -std=gnu++11 -E" --build=""
    --with-pic --enable-silent-rules --quiet --disable-xz > /dev/null
    cd XZ/xz-5.2.3/src/liblzma && make
    make[1]: Entering directory /tmp/269292.1.int.q/RtmpZXKb9P/R.INSTALL85751e980379/gdsfmt/src/XZ/xz-5.2.3/src/liblzma' Making all in api make[2]: Entering directory /tmp/269292.1.int.q/RtmpZXKb9P/R.INSTALL85751e980379/gdsfmt/src/XZ/xz-5.2.3/src/liblzma/api'
    make[2]: Nothing to be done for all'. make[2]: Leaving directory /tmp/269292.1.int.q/RtmpZXKb9P/R.INSTALL85751e980379/gdsfmt/src/XZ/xz-5.2.3/src/liblzma/api'
    make[2]: Entering directory `/tmp/269292.1.int.q/RtmpZXKb9P/R.INSTALL85751e980379/gdsfmt/src/XZ/xz-5.2.3/src/liblzma'
    CC liblzma_la-tuklib_physmem.lo
    CC liblzma_la-tuklib_cpucores.lo
    CC liblzma_la-common.lo
    CC liblzma_la-block_util.lo
    CC liblzma_la-easy_preset.lo
    CC liblzma_la-filter_common.lo
    CC liblzma_la-hardware_physmem.lo
    CC liblzma_la-index.lo
    CC liblzma_la-stream_flags_common.lo
    CC liblzma_la-vli_size.lo
    CC liblzma_la-hardware_cputhreads.lo
    CC liblzma_la-alone_encoder.lo
    CC liblzma_la-block_buffer_encoder.lo
    CC liblzma_la-block_encoder.lo
    CC liblzma_la-block_header_encoder.lo
    CC liblzma_la-easy_buffer_encoder.lo
    CC liblzma_la-easy_encoder.lo
    CC liblzma_la-easy_encoder_memusage.lo
    CC liblzma_la-filter_buffer_encoder.lo
    CC liblzma_la-filter_encoder.lo
    CC liblzma_la-filter_flags_encoder.lo
    CC liblzma_la-index_encoder.lo
    CC liblzma_la-stream_buffer_encoder.lo
    CC liblzma_la-stream_encoder.lo
    CC liblzma_la-stream_flags_encoder.lo
    Hangup
    make[2]: *** wait: No child processes. Stop.
    make[2]: *** Waiting for unfinished jobs....
    make[2]: *** wait: No child processes. Stop.
    make[1]: *** wait: No child processes. Stop.
    make[1]: *** Waiting for unfinished jobs....
    make[1]: *** wait: No child processes. Stop.
    make: *** wait: No child processes. Stop.
    make: *** Waiting for unfinished jobs....
    make: *** wait: No child processes. Stop.

Updated 03/29/2021:
Switched to R/4.0.3 and still wasn't able to install the package. The error messages are as follows:

  • installing source package 'gdsfmt' ...
    ** using staged installation
    ** libs
    g++ -std=gnu++11 -I"/nfs/apps/R/4.0.3/lib64/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -fpic -g -O2 -c R_CoreArray.cpp -o R_CoreArray.o
    g++ -std=gnu++11 -I"/nfs/apps/R/4.0.3/lib64/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -fpic -g -O2 -c gdsfmt.cpp -o gdsfmt.o
    g++ -std=gnu++11 -I"/nfs/apps/R/4.0.3/lib64/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -fpic -g -O2 -c digest.cpp -o digest.o
    g++ -std=gnu++11 -I"/nfs/apps/R/4.0.3/lib64/R/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -fpic -g -O2 -c CoreArray/CoreArray.cpp -o CoreArray/CoreArray.o
    make: *** wait: No child processes. Stop.
    make: *** Waiting for unfinished jobs....
    make: *** wait: No child processes. Stop.

Would you by any chance happen to know the meaning of these messages and perhaps how to install this package?

Thanks a lot in advance!

Sincerely,

Ian

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