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Getting error when installing R packages using SSH R Terminal RRS feed

  • Question

  • Hi All,

    I have created HdInsight R server cluster, now trying to install few R packages to run R query.

    I badly stuck from last 3 days, I have given the full access on below path using given command

    sudo chmod  777 /usr/lib64/microsoft-r/3.3/lib64/R/library


    Thankx &amp; regards, Vipin <g class="gr_ gr_14 gr-alert gr_spell gr_inline_cards gr_run_anim ContextualSpelling ins-del multiReplace" data-gr-id="14" id="14">jha</g> MCP


    • Edited by Vipin jha Monday, September 10, 2018 3:22 PM error
    Monday, September 10, 2018 3:21 PM

All replies

  • Can you paste the console output from your R session as text below?

    The included screenshot is too small to read....

    Thanks!

    Monday, September 10, 2018 3:48 PM

  • Thankx &amp; regards, Vipin jha MCP

    Monday, September 10, 2018 4:59 PM
  • I/usr/lib64/microsoft-r/3.3/lib64/R/include -DNDEBUG -DR_BUILD -DU_STATIC_IMPLEMENTATION -I"/usr/lib64/microsoft-r/3.3/lib64/R/library/Rcpp/include"      -c AAA_check_cpp11.cpp -o AAA_check_cpp11.o
    sh: I/usr/lib64/microsoft-r/3.3/lib64/R/include: No such file or directory
    /usr/lib64/microsoft-r/3.3/lib64/R/etc/Makeconf:141: recipe for target 'AAA_check_cpp11.o' failed
    make: [AAA_check_cpp11.o] Error 127 (ignored)
    I/usr/lib64/microsoft-r/3.3/lib64/R/include -DNDEBUG -DR_BUILD -DU_STATIC_IMPLEMENTATION -I"/usr/lib64/microsoft-r/3.3/lib64/R/library/Rcpp/include"      -c Data.cpp -o Data.o
    sh: I/usr/lib64/microsoft-r/3.3/lib64/R/include: No such file or directory
    /usr/lib64/microsoft-r/3.3/lib64/R/etc/Makeconf:141: recipe for target 'Data.o' failed
    make: [Data.o] Error 127 (ignored)
    I/usr/lib64/microsoft-r/3.3/lib64/R/include -DNDEBUG -DR_BUILD -DU_STATIC_IMPLEMENTATION -I"/usr/lib64/microsoft-r/3.3/lib64/R/library/Rcpp/include"      -c DataChar.cpp -o DataChar.o
    sh: I/usr/lib64/microsoft-r/3.3/lib64/R/include: No such file or directory
    /usr/lib64/microsoft-r/3.3/lib64/R/etc/Makeconf:141: recipe for target 'DataChar.o' failed
    make: [DataChar.o] Error 127 (ignored)
    I/usr/lib64/microsoft-r/3.3/lib64/R/include -DNDEBUG -DR_BUILD -DU_STATIC_IMPLEMENTATION -I"/usr/lib64/microsoft-r/3.3/lib64/R/library/Rcpp/include"      -c DataDouble.cpp -o DataDouble.o
    sh: I/usr/lib64/microsoft-r/3.3/lib64/R/include: No such file or directory
    /usr/lib64/microsoft-r/3.3/lib64/R/etc/Makeconf:141: recipe for target 'DataDouble.o' failed
    make: [DataDouble.o] Error 127 (ignored)
    I/usr/lib64/microsoft-r/3.3/lib64/R/include -DNDEBUG -DR_BUILD -DU_STATIC_IMPLEMENTATION -I"/usr/lib64/microsoft-r/3.3/lib64/R/library/Rcpp/include"      -c DataFloat.cpp -o DataFloat.o
    sh: I/usr/lib64/microsoft-r/3.3/lib64/R/include: No such file or directory
    /usr/lib64/microsoft-r/3.3/lib64/R/etc/Makeconf:141: recipe for target 'DataFloat.o' failed
    make: [DataFloat.o] Error 127 (ignored)
    I/usr/lib64/microsoft-r/3.3/lib64/R/include -DNDEBUG -DR_BUILD -DU_STATIC_IMPLEMENTATION -I"/usr/lib64/microsoft-r/3.3/lib64/R/library/Rcpp/include"      -c Forest.cpp -o Forest.o
    sh: I/usr/lib64/microsoft-r/3.3/lib64/R/include: No such file or directory
    /usr/lib64/microsoft-r/3.3/lib64/R/etc/Makeconf:141: recipe for target 'Forest.o' failed
    make: [Forest.o] Error 127 (ignored)
    I/usr/lib64/microsoft-r/3.3/lib64/R/include -DNDEBUG -DR_BUILD -DU_STATIC_IMPLEMENTATION -I"/usr/lib64/microsoft-r/3.3/lib64/R/library/Rcpp/include"      -c ForestClassification.cpp -o ForestClassification.o
    sh: I/usr/lib64/microsoft-r/3.3/lib64/R/include: No such file or directory
    /usr/lib64/microsoft-r/3.3/lib64/R/etc/Makeconf:141: recipe for target 'ForestClassification.o' failed
    make: [ForestClassification.o] Error 127 (ignored)
    I/usr/lib64/microsoft-r/3.3/lib64/R/include -DNDEBUG -DR_BUILD -DU_STATIC_IMPLEMENTATION -I"/usr/lib64/microsoft-r/3.3/lib64/R/library/Rcpp/include"      -c ForestProbability.cpp -o ForestProbability.o
    sh: I/usr/lib64/microsoft-r/3.3/lib64/R/include: No such file or directory
    /usr/lib64/microsoft-r/3.3/lib64/R/etc/Makeconf:141: recipe for target 'ForestProbability.o' failed
    make: [ForestProbability.o] Error 127 (ignored)
    I/usr/lib64/microsoft-r/3.3/lib64/R/include -DNDEBUG -DR_BUILD -DU_STATIC_IMPLEMENTATION -I"/usr/lib64/microsoft-r/3.3/lib64/R/library/Rcpp/include"      -c ForestRegression.cpp -o ForestRegression.o
    sh: I/usr/lib64/microsoft-r/3.3/lib64/R/include: No such file or directory
    /usr/lib64/microsoft-r/3.3/lib64/R/etc/Makeconf:141: recipe for target 'ForestRegression.o' failed
    make: [ForestRegression.o] Error 127 (ignored)
    I/usr/lib64/microsoft-r/3.3/lib64/R/include -DNDEBUG -DR_BUILD -DU_STATIC_IMPLEMENTATION -I"/usr/lib64/microsoft-r/3.3/lib64/R/library/Rcpp/include"      -c ForestSurvival.cpp -o ForestSurvival.o
    sh: I/usr/lib64/microsoft-r/3.3/lib64/R/include: No such file or directory
    /usr/lib64/microsoft-r/3.3/lib64/R/etc/Makeconf:141: recipe for target 'ForestSurvival.o' failed
    make: [ForestSurvival.o] Error 127 (ignored)
    I/usr/lib64/microsoft-r/3.3/lib64/R/include -DNDEBUG -DR_BUILD -DU_STATIC_IMPLEMENTATION -I"/usr/lib64/microsoft-r/3.3/lib64/R/library/Rcpp/include"      -c RcppExports.cpp -o RcppExports.o
    sh: I/usr/lib64/microsoft-r/3.3/lib64/R/include: No such file or directory
    /usr/lib64/microsoft-r/3.3/lib64/R/etc/Makeconf:141: recipe for target 'RcppExports.o' failed
    make: [RcppExports.o] Error 127 (ignored)
    I/usr/lib64/microsoft-r/3.3/lib64/R/include -DNDEBUG -DR_BUILD -DU_STATIC_IMPLEMENTATION -I"/usr/lib64/microsoft-r/3.3/lib64/R/library/Rcpp/include"      -c Tree.cpp -o Tree.o
    sh: I/usr/lib64/microsoft-r/3.3/lib64/R/include: No such file or directory
    /usr/lib64/microsoft-r/3.3/lib64/R/etc/Makeconf:141: recipe for target 'Tree.o' failed
    make: [Tree.o] Error 127 (ignored)
    I/usr/lib64/microsoft-r/3.3/lib64/R/include -DNDEBUG -DR_BUILD -DU_STATIC_IMPLEMENTATION -I"/usr/lib64/microsoft-r/3.3/lib64/R/library/Rcpp/include"      -c TreeClassification.cpp -o TreeClassification.o
    sh: I/usr/lib64/microsoft-r/3.3/lib64/R/include: No such file or directory
    /usr/lib64/microsoft-r/3.3/lib64/R/etc/Makeconf:141: recipe for target 'TreeClassification.o' failed
    make: [TreeClassification.o] Error 127 (ignored)
    I/usr/lib64/microsoft-r/3.3/lib64/R/include -DNDEBUG -DR_BUILD -DU_STATIC_IMPLEMENTATION -I"/usr/lib64/microsoft-r/3.3/lib64/R/library/Rcpp/include"      -c TreeProbability.cpp -o TreeProbability.o
    sh: I/usr/lib64/microsoft-r/3.3/lib64/R/include: No such file or directory
    /usr/lib64/microsoft-r/3.3/lib64/R/etc/Makeconf:141: recipe for target 'TreeProbability.o' failed
    make: [TreeProbability.o] Error 127 (ignored)
    I/usr/lib64/microsoft-r/3.3/lib64/R/include -DNDEBUG -DR_BUILD -DU_STATIC_IMPLEMENTATION -I"/usr/lib64/microsoft-r/3.3/lib64/R/library/Rcpp/include"      -c TreeRegression.cpp -o TreeRegression.o
    sh: I/usr/lib64/microsoft-r/3.3/lib64/R/include: No such file or directory
    /usr/lib64/microsoft-r/3.3/lib64/R/etc/Makeconf:141: recipe for target 'TreeRegression.o' failed
    make: [TreeRegression.o] Error 127 (ignored)
    I/usr/lib64/microsoft-r/3.3/lib64/R/include -DNDEBUG -DR_BUILD -DU_STATIC_IMPLEMENTATION -I"/usr/lib64/microsoft-r/3.3/lib64/R/library/Rcpp/include"      -c TreeSurvival.cpp -o TreeSurvival.o
    sh: I/usr/lib64/microsoft-r/3.3/lib64/R/include: No such file or directory
    /usr/lib64/microsoft-r/3.3/lib64/R/etc/Makeconf:141: recipe for target 'TreeSurvival.o' failed
    make: [TreeSurvival.o] Error 127 (ignored)
    I/usr/lib64/microsoft-r/3.3/lib64/R/include -DNDEBUG -DR_BUILD -DU_STATIC_IMPLEMENTATION -I"/usr/lib64/microsoft-r/3.3/lib64/R/library/Rcpp/include"      -c rangerCpp.cpp -o rangerCpp.o
    sh: I/usr/lib64/microsoft-r/3.3/lib64/R/include: No such file or directory
    /usr/lib64/microsoft-r/3.3/lib64/R/etc/Makeconf:141: recipe for target 'rangerCpp.o' failed
    make: [rangerCpp.o] Error 127 (ignored)
    I/usr/lib64/microsoft-r/3.3/lib64/R/include -DNDEBUG -DR_BUILD -DU_STATIC_IMPLEMENTATION -I"/usr/lib64/microsoft-r/3.3/lib64/R/library/Rcpp/include"      -c utility.cpp -o utility.o
    sh: I/usr/lib64/microsoft-r/3.3/lib64/R/include: No such file or directory
    /usr/lib64/microsoft-r/3.3/lib64/R/etc/Makeconf:141: recipe for target 'utility.o' failed
    make: [utility.o] Error 127 (ignored)
    -shared -L/usr/lib64/microsoft-r/3.3/lib64/R/lib -o ranger.so AAA_check_cpp11.o Data.o DataChar.o DataDouble.o DataFloat.o Forest.o ForestClassification.o ForestProbability.o ForestRegression.o ForestSurvival.o RcppExports.o Tree.o TreeClassification.o TreeProbability.o TreeRegression.o TreeSurvival.o rangerCpp.o utility.o -L/usr/lib64/microsoft-r/3.3/lib64/R/lib -lR
    sh: line 2: -shared: command not found
    /usr/lib64/microsoft-r/3.3/lib64/R/share/make/shlib.mk:6: recipe for target 'ranger.so' failed
    make: *** [ranger.so] Error 127
    ERROR: compilation failed for package ‘ranger’
    * removing ‘/usr/lib64/microsoft-r/3.3/lib64/R/library/ranger’
    Warning in install.packages :
      installation of package ‘ranger’ had non-zero exit status
    ERROR: dependency ‘ranger’ is not available for package ‘Boruta’
    * removing ‘/usr/lib64/microsoft-r/3.3/lib64/R/library/Boruta’
    Warning in install.packages :
      installation of package ‘Boruta’ had non-zero exit status
    
    The downloaded source packages are in
    	‘/tmp/RtmpgI2Lx5/downloaded_packages’
    Updating HTML index of packages in '.Library'
    Making 'packages.html' ... done

    Thankx &amp; regards, Vipin jha MCP

    Tuesday, September 11, 2018 5:42 AM
  • This looks like the same problem outlined in the following GitHub discussion:

    https://github.com/rstudio/tensorflow/issues/57

    You might try the same fix tried there:

    Adding these flags to my Makeconf allowed the installation to complete.
    /usr/lib64/microsoft-r/3.3/lib64/R/etc/Makeconf:

    CXX1X=gcc -std=c++0x
    CXX1XSTD=-std=c++0x -fPIC

    Hope this helps.

    Tuesday, September 11, 2018 3:59 PM