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  1. Apache Arrow
  2. ARROW-9932

[R] Arrow 1.0.1 R package fails to install on R3.4 over linux

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Details

    • Bug
    • Status: Closed
    • Major
    • Resolution: Duplicate
    • 1.0.1
    • 2.0.0
    • R
    • None
    • R version 3.4.0 (2015-04-16)
      Platform: x86_64-pc-linux-gnu (64-bit)
      Running under: Ubuntu 14.04.5 LTS

    Description

      1. From R (3.4) prompt, we run

      > install.packages("arrow")

      and it seems to succeed.

      2. Next we run:

      > arrow::install_arrow()

      This is the full output:

      Installing package into '/opt/R-3.4.0.mkl/library'
      (as 'lib' is unspecified)
      trying URL 'https://cloud.r-project.org/src/contrib/arrow_1.0.1.tar.gz'
      Content type 'application/x-gzip' length 274865 bytes (268 KB)
      ==================================================
      downloaded 268 KB

      installing source package 'arrow' ...
      ** package 'arrow' successfully unpacked and MD5 sums checked
      *** No C++ binaries found for ubuntu-14.04
      *** Successfully retrieved C++ source
      *** Building C++ libraries
      **** cmake
      Error in dQuote(env_var_list, FALSE) : unused argument (FALSE)
      Calls: build_libarrow -> paste
      Execution halted
      ------------------------- NOTE ---------------------------
      After installation, please run arrow::install_arrow()
      for help installing required runtime libraries
      ---------------------------------------------------------
      ** libs
      g++ -std=gnu++0x -I/opt/R-3.4.0.mkl/lib64/R/include -DNDEBUG -I"/opt/R-3.4.0.mkl/library/Rcpp/include" -I/usr/local/include -fpic -march=x86-64 -O3 -c array.cpp -o array.o
      g++ -std=gnu++0x -I/opt/R-3.4.0.mkl/lib64/R/include -DNDEBUG -I"/opt/R-3.4.0.mkl/library/Rcpp/include" -I/usr/local/include -fpic -march=x86-64 -O3 -c array_from_vector.cpp -o array_from_vector.o
      g++ -std=gnu++0x -I/opt/R-3.4.0.mkl/lib64/R/include -DNDEBUG -I"/opt/R-3.4.0.mkl/library/Rcpp/include" -I/usr/local/include -fpic -march=x86-64 -O3 -c array_to_vector.cpp -o array_to_vector.o
      g++ -std=gnu++0x -I/opt/R-3.4.0.mkl/lib64/R/include -DNDEBUG -I"/opt/R-3.4.0.mkl/library/Rcpp/include" -I/usr/local/include -fpic -march=x86-64 -O3 -c arraydata.cpp -o arraydata.o
      g++ -std=gnu++0x -I/opt/R-3.4.0.mkl/lib64/R/include -DNDEBUG -I"/opt/R-3.4.0.mkl/library/Rcpp/include" -I/usr/local/include -fpic -march=x86-64 -O3 -c arrowExports.cpp -o arrowExports.o
      g++ -std=gnu++0x -I/opt/R-3.4.0.mkl/lib64/R/include -DNDEBUG -I"/opt/R-3.4.0.mkl/library/Rcpp/include" -I/usr/local/include -fpic -march=x86-64 -O3 -c buffer.cpp -o buffer.o
      g++ -std=gnu++0x -I/opt/R-3.4.0.mkl/lib64/R/include -DNDEBUG -I"/opt/R-3.4.0.mkl/library/Rcpp/include" -I/usr/local/include -fpic -march=x86-64 -O3 -c chunkedarray.cpp -o chunkedarray.o
      g++ -std=gnu++0x -I/opt/R-3.4.0.mkl/lib64/R/include -DNDEBUG -I"/opt/R-3.4.0.mkl/library/Rcpp/include" -I/usr/local/include -fpic -march=x86-64 -O3 -c compression.cpp -o compression.o
      g++ -std=gnu++0x -I/opt/R-3.4.0.mkl/lib64/R/include -DNDEBUG -I"/opt/R-3.4.0.mkl/library/Rcpp/include" -I/usr/local/include -fpic -march=x86-64 -O3 -c compute.cpp -o compute.o
      g++ -std=gnu+0x -I/opt/R-3.4.0.mkl/lib64/R/include -DNDEBUG -I"/opt/R-3.4.0.mkl/library/Rcpp/include" -I/usr/local/include -fpic -march=x86-64 -O3 -c csv.cpp -o csv.og+ -std=gnu++0x -I/opt/R-3.4.0.mkl/lib64/R/include -DNDEBUG -I"/opt/R-3.4.0.mkl/library/Rcpp/include" -I/usr/local/include -fpic -march=x86-64 -O3 -c dataset.cpp -o dataset.o
      g++ -std=gnu++0x -I/opt/R-3.4.0.mkl/lib64/R/include -DNDEBUG -I"/opt/R-3.4.0.mkl/library/Rcpp/include" -I/usr/local/include -fpic -march=x86-64 -O3 -c datatype.cpp -o datatype.o
      g++ -std=gnu++0x -I/opt/R-3.4.0.mkl/lib64/R/include -DNDEBUG -I"/opt/R-3.4.0.mkl/library/Rcpp/include" -I/usr/local/include -fpic -march=x86-64 -O3 -c expression.cpp -o expression.o
      g++ -std=gnu++0x -I/opt/R-3.4.0.mkl/lib64/R/include -DNDEBUG -I"/opt/R-3.4.0.mkl/library/Rcpp/include" -I/usr/local/include -fpic -march=x86-64 -O3 -c feather.cpp -o feather.o
      g++ -std=gnu++0x -I/opt/R-3.4.0.mkl/lib64/R/include -DNDEBUG -I"/opt/R-3.4.0.mkl/library/Rcpp/include" -I/usr/local/include -fpic -march=x86-64 -O3 -c field.cpp -o field.o
      g++ -std=gnu++0x -I/opt/R-3.4.0.mkl/lib64/R/include -DNDEBUG -I"/opt/R-3.4.0.mkl/library/Rcpp/include" -I/usr/local/include -fpic -march=x86-64 -O3 -c filesystem.cpp -o filesystem.o
      g++ -std=gnu++0x -I/opt/R-3.4.0.mkl/lib64/R/include -DNDEBUG -I"/opt/R-3.4.0.mkl/library/Rcpp/include" -I/usr/local/include -fpic -march=x86-64 -O3 -c imports.cpp -o imports.o
      g++ -std=gnu++0x -I/opt/R-3.4.0.mkl/lib64/R/include -DNDEBUG -I"/opt/R-3.4.0.mkl/library/Rcpp/include" -I/usr/local/include -fpic -march=x86-64 -O3 -c io.cpp -o io.o
      g++ -std=gnu+0x -I/opt/R-3.4.0.mkl/lib64/R/include -DNDEBUG -I"/opt/R-3.4.0.mkl/library/Rcpp/include" -I/usr/local/include -fpic -march=x86-64 -O3 -c json.cpp -o json.og+ -std=gnu++0x -I/opt/R-3.4.0.mkl/lib64/R/include -DNDEBUG -I"/opt/R-3.4.0.mkl/library/Rcpp/include" -I/usr/local/include -fpic -march=x86-64 -O3 -c memorypool.cpp -o memorypool.o
      g++ -std=gnu++0x -I/opt/R-3.4.0.mkl/lib64/R/include -DNDEBUG -I"/opt/R-3.4.0.mkl/library/Rcpp/include" -I/usr/local/include -fpic -march=x86-64 -O3 -c message.cpp -o message.o
      g++ -std=gnu++0x -I/opt/R-3.4.0.mkl/lib64/R/include -DNDEBUG -I"/opt/R-3.4.0.mkl/library/Rcpp/include" -I/usr/local/include -fpic -march=x86-64 -O3 -c parquet.cpp -o parquet.o
      g++ -std=gnu++0x -I/opt/R-3.4.0.mkl/lib64/R/include -DNDEBUG -I"/opt/R-3.4.0.mkl/library/Rcpp/include" -I/usr/local/include -fpic -march=x86-64 -O3 -c py-to-r.cpp -o py-to-r.o
      g++ -std=gnu++0x -I/opt/R-3.4.0.mkl/lib64/R/include -DNDEBUG -I"/opt/R-3.4.0.mkl/library/Rcpp/include" -I/usr/local/include -fpic -march=x86-64 -O3 -c recordbatch.cpp -o recordbatch.o
      g++ -std=gnu++0x -I/opt/R-3.4.0.mkl/lib64/R/include -DNDEBUG -I"/opt/R-3.4.0.mkl/library/Rcpp/include" -I/usr/local/include -fpic -march=x86-64 -O3 -c recordbatchreader.cpp -o recordbatchreader.o
      g++ -std=gnu++0x -I/opt/R-3.4.0.mkl/lib64/R/include -DNDEBUG -I"/opt/R-3.4.0.mkl/library/Rcpp/include" -I/usr/local/include -fpic -march=x86-64 -O3 -c recordbatchwriter.cpp -o recordbatchwriter.o
      g++ -std=gnu++0x -I/opt/R-3.4.0.mkl/lib64/R/include -DNDEBUG -I"/opt/R-3.4.0.mkl/library/Rcpp/include" -I/usr/local/include -fpic -march=x86-64 -O3 -c scalar.cpp -o scalar.o
      g++ -std=gnu++0x -I/opt/R-3.4.0.mkl/lib64/R/include -DNDEBUG -I"/opt/R-3.4.0.mkl/library/Rcpp/include" -I/usr/local/include -fpic -march=x86-64 -O3 -c schema.cpp -o schema.o
      g++ -std=gnu++0x -I/opt/R-3.4.0.mkl/lib64/R/include -DNDEBUG -I"/opt/R-3.4.0.mkl/library/Rcpp/include" -I/usr/local/include -fpic -march=x86-64 -O3 -c symbols.cpp -o symbols.o
      g++ -std=gnu+0x -I/opt/R-3.4.0.mkl/lib64/R/include -DNDEBUG -I"/opt/R-3.4.0.mkl/library/Rcpp/include" -I/usr/local/include -fpic -march=x86-64 -O3 -c table.cpp -o table.og+ -std=gnu+0x -I/opt/R-3.4.0.mkl/lib64/R/include -DNDEBUG -I"/opt/R-3.4.0.mkl/library/Rcpp/include" -I/usr/local/include -fpic -march=x86-64 -O3 -c threadpool.cpp -o threadpool.og+ -std=gnu++0x -shared -L/opt/R-3.4.0.mkl/lib64/R/lib -L/usr/local/lib64 -o arrow.so array.o array_from_vector.o array_to_vector.o arraydata.o arrowExports.o buffer.o chunkedarray.o compression.o compute.o csv.o dataset.o datatype.o expression.o feather.o field.o filesystem.o imports.o io.o json.o memorypool.o message.o parquet.o py-to-r.o recordbatch.o recordbatchreader.o recordbatchwriter.o scalar.o schema.o symbols.o table.o threadpool.o -L/opt/R-3.4.0.mkl/lib64/R/lib -lR
      installing to /opt/R-3.4.0.mkl/library/arrow/libs** R
      ** inst
      ** preparing package for lazy loading
      ** help
      *** installing help indices
      ** building package indices
      ** installing vignettes** testing if installed package can be loaded
      * DONE (arrow)The downloaded source packages are inThe downloaded source packages are in '/tmp/RtmppBCBzR/downloaded_packages'Please restart R to use the 'arrow' package.

      3. We restart R, and run -

      > arrow::arrow_available()
      [1] FALSE

       

      And indeed all arrow functionality fails:

      {{> x <- arrow::Table$create(data.frame(a=1:2)) }}

      Error in Table__from_dots(dots, schema) :
      Cannot call Table__from_dots(). Please use arrow::install_arrow() to install required runtime libraries.}}

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          is superceded by

          Bug - A problem which impairs or prevents the functions of the product. ARROW-9883 [R] Fix linuxlibs.R install script for R < 3.6

          • Major - Major loss of function.
          • Resolved

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            People

              npr Neal Richardson
              ofek Ofek Shilon
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                Created:
                Updated:
                Resolved: