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Microsoft R Open + line breaks during package compilation RRS feed

  • Question

  • For some odd reason, the latest version of Microsoft R Open is failing to compile various packages, because of something (Rcpp I think) that spawns multiple R sessions, and the repeated calls to clear the terminal window are introducing line breaks in the middle of the compiler commands. See example below. There doesn't seem to be a reliable way to completely suppress the verbose startup message, which appears to be causing this error.

    Note the same happens with /opt/microsoft/ropen/4.0.2/lib64/R/bin/R CMD INSTALL as well as /opt/microsoft/ropen/4.0.2/lib64/R/bin/Rscript

    Ideas? Suggestions?

    $ /opt/microsoft/ropen/4.0.2/lib64/R/bin/R -q
    > install.packages('minqa')
    Installing package into ‘/raid/users/g-socsldap/R/x86_64-pc-linux-gnu-library/4.0’
    (as ‘lib’ is unspecified)
      % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                     Dload  Upload   Total   Spent    Left  Speed
    100 53548  100 53548    0     0   247k      0 --:--:-- --:--:-- --:--:--  247k
    Microsoft R Open 4.0.2
    The enhanced R distribution from Microsoft
    Microsoft packages Copyright (C) 2020 Microsoft Corporation
    
    Using the Intel MKL for parallel mathematical computing (using 44 cores).
    
    Default CRAN mirror snapshot taken on 2020-07-16.
    See: https://mran.microsoft.com/.
    
    * installing *source* package ‘minqa’ ...
    ** package ‘minqa’ successfully unpacked and MD5 sums checked
    ** using staged installation
    ** libs
    gfortran   -fpic  -g -O2  -c altmov.f -o altmov.o
    gfortran   -fpic  -g -O2  -c bigden.f -o bigden.o
    gfortran   -fpic  -g -O2  -c biglag.f -o biglag.o
    gfortran   -fpic  -g -O2  -c bobyqa.f -o bobyqa.o
    gfortran   -fpic  -g -O2  -c bobyqb.f -o bobyqb.o
    gfortran   -fpic  -g -O2  -c lagmax.f -o lagmax.o
    g++  -I/opt/microsoft/ropen/4.0.2/lib64/R/include -DNDEBUG  -I'/opt/microsoft/ropen/4.0.2/lib64/R/library/Rcpp/include' -DU_STATIC_IMPLEMENTATION   -fpic  -DU_STATIC_IMPLEMENTATION -O2 -g  -c minqa.cpp -o minqa.o
    gfortran   -fpic  -g -O2  -c newuoa.f -o newuoa.o
    gfortran   -fpic  -g -O2  -c newuob.f -o newuob.o
    gfortran   -fpic  -g -O2  -c prelim.f -o prelim.o
    gfortran   -fpic  -g -O2  -c rescue.f -o rescue.o
    gfortran   -fpic  -g -O2  -c trsapp.f -o trsapp.o
    gfortran   -fpic  -g -O2  -c trsbox.f -o trsbox.o
    gfortran   -fpic  -g -O2  -c trstep.f -o trstep.o
    gfortran   -fpic  -g -O2  -c uobyqa.f -o uobyqa.o
    gfortran   -fpic  -g -O2  -c uobyqb.f -o uobyqb.o
    gfortran   -fpic  -g -O2  -c update.f -o update.o
    gfortran   -fpic  -g -O2  -c updatebobyqa.f -o updatebobyqa.o
    g++ -shared -L/opt/microsoft/ropen/4.0.2/lib64/R/lib -o minqa.so altmov.o bigden.o biglag.o bobyqa.o bobyqb.o lagmax.o minqa.o newuoa.o newuob.o prelim.o rescue.o trsapp.o trsbox.o trstep.o uobyqa.o uobyqb.o update.o updatebobyqa.o Microsoft R Open 4.0.2 The enhanced R distribution from Microsoft Microsoft packages Copyright (C) 2020 Microsoft Corporation Using the Intel MKL for parallel mathematical computing (using 44 cores). Default CRAN mirror snapshot taken on 2020-07-16. See: https://mran.microsoft.com/. -lgfortran -lm -L/opt/microsoft/ropen/4.0.2/lib64/R/lib -lR
    g++: error: Microsoft: No such file or directory
    g++: error: R: No such file or directory
    g++: error: Open: No such file or directory
    g++: error: 4.0.2: No such file or directory
    g++: error: The: No such file or directory
    g++: error: enhanced: No such file or directory
    g++: error: R: No such file or directory
    g++: error: distribution: No such file or directory
    g++: error: from: No such file or directory
    g++: error: Microsoft: No such file or directory
    g++: error: Microsoft: No such file or directory
    g++: error: packages: No such file or directory
    g++: error: Copyright: No such file or directory
    g++: error: (C): No such file or directory
    g++: error: 2020: No such file or directory
    g++: error: Microsoft: No such file or directory
    g++: error: Corporation: No such file or directory
    g++: error: Using: No such file or directory
    g++: error: the: No such file or directory
    g++: error: Intel: No such file or directory
    g++: error: MKL: No such file or directory
    g++: error: for: No such file or directory
    g++: error: parallel: No such file or directory
    g++: error: mathematical: No such file or directory
    g++: error: computing: No such file or directory
    g++: error: (using: No such file or directory
    g++: error: 44: No such file or directory
    g++: error: cores).: No such file or directory
    g++: error: Default: No such file or directory
    g++: error: CRAN: No such file or directory
    g++: error: mirror: No such file or directory
    g++: error: snapshot: No such file or directory
    g++: error: taken: No such file or directory
    g++: error: on: No such file or directory
    g++: error: 2020-07-16.: No such file or directory
    g++: error: See:: No such file or directory
    g++: error: https://mran.microsoft.com/.: No such file or directory
    make: *** [/opt/microsoft/ropen/4.0.2/lib64/R/share/make/shlib.mk:6: minqa.so] Error 1
    ERROR: compilation failed for package ‘minqa’
    * removing ‘/raid/users/g-socsldap/R/x86_64-pc-linux-gnu-library/4.0/minqa’
    
    The downloaded source packages are in
        ‘/tmp/RtmpMlXevk/downloaded_packages’
    Warning message:
    In install.packages("minqa") :
      installation of package ‘minqa’ had non-zero exit status

    Monday, November 16, 2020 10:50 PM

All replies

  • Figured it out. Needed to open R Open using --vanilla:

    /opt/microsoft/ropen/4.0.2/lib64/R/bin/R --vanilla

    Then install the package(s)

    Tuesday, November 17, 2020 6:12 PM