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MRAN 3.4.1 causing error in installing openair package RRS feed

  • Question

  • I've been using the openair package with MRAN 3.4 without difficulties. I recently upgraded to MRAN 3.4.1 and trying to run openair results in an error. See below for an attempt to install openair.

    I've been using the openair package with MRAN 3.4 without difficulties. I recently upgraded to MRAN 3.4.1 and trying to run openair results in an error. See below for an attempt to install openair.

    > install_github('davidcarslaw/openair')
    ...

    Installing openair
    '/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet CMD INSTALL  \
      '/private/var/folders/bv/881_rsvd2kv83c13yywwc_xh0000gn/T/Rtmpz6778s/devtoolscf5234a1e7d/davidcarslaw-openair-b782399'  \
      --library='/Users/gcn/Library/R/3.4/library' --install-tests 

    * installing *source* package ‘openair’ ...
    ** libs
    clang-omp++ -fopenmp -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Users/gcn/Library/R/3.4/library/Rcpp/include" -DU_STATIC_IMPLEMENTATION -Wall -mtune=core2 -g -O2 -I/opt/X11/include   -fPIC  -g -O3 -Wall -pedantic -mtune=native -std=c++11 -c cluster.cpp -o cluster.o
    clang-omp -fopenmp -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Users/gcn/Library/R/3.4/library/Rcpp/include" -DU_STATIC_IMPLEMENTATION -Wall -mtune=core2 -g -O2 -I/opt/X11/include   -fPIC  -g -O3 -Wall -pedantic -mtune=native  -std=gnu99 -c init.c -o init.o
    init.c:26:2: warning: no newline at end of file [-Wnewline-eof]
    }
     ^
    1 warning generated.
    clang-omp++ -fopenmp -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Users/gcn/Library/R/3.4/library/Rcpp/include" -DU_STATIC_IMPLEMENTATION -Wall -mtune=core2 -g -O2 -I/opt/X11/include   -fPIC  -g -O3 -Wall -pedantic -mtune=native -std=c++11 -c rolling.cpp -o rolling.o
    clang-omp++ -fopenmp -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/clang4/lib -o openair.so cluster.o init.o rolling.o -framework Accelerate -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
    ld: warning: directory not found for option '-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0'
    installing to /Users/gcn/Library/R/3.4/library/openair/libs
    ** R
    ** data
    *** moving datasets to lazyload DB
    ** inst
    ** byte-compile and prepare package for lazy loading
    Error in dyn.load(file, DLLpath = DLLpath, ...) : 
      unable to load shared object '/Library/Frameworks/R.framework/Versions/3.4.1-MRO/Resources/library/Matrix/libs/Matrix.so':
      dlopen(/Library/Frameworks/R.framework/Versions/3.4.1-MRO/Resources/library/Matrix/libs/Matrix.so, 6): Library not loaded: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib
      Referenced from: /Library/Frameworks/R.framework/Versions/3.4.1-MRO/Resources/library/Matrix/libs/Matrix.so
      Reason: image not found
    ERROR: lazy loading failed for package ‘openair’


    • Edited by JerryN1 Thursday, September 21, 2017 10:31 PM
    Thursday, September 21, 2017 10:30 PM

All replies

  • MRO 3.4.1 on the Mac (like CRAN R 3.4.1 on the Mac) uses a new compiler <g class="gr_ gr_5 gr-alert gr_spell gr_inline_cards gr_run_anim ContextualSpelling ins-del" data-gr-id="5" id="5">tool chain</g>—clang 4 with <g class="gr_ gr_6 gr-alert gr_spell gr_inline_cards gr_run_anim ContextualSpelling ins-del multiReplace" data-gr-id="6" id="6">gfortran</g> 6.1. Installing packages from source requires the user to have this new toolchain installed, and it appears from the error messages that you do not have this. This is a change and we ran into this as well. 

    Here is a link you can get it from - 

    https://mran.westus2.cloudapp.azure.com/snapshot/2017-09-01/bin/macosx/tools/

    Friday, September 22, 2017 12:10 AM
  • I installed the new fortran. I am now at fortran 4.2.3. Unfortunately I still have a problem. See below

    > install_github('davidcarslaw/openair')
    Downloading GitHub repo davidcarslaw/openair@master
    from URL https://api.github.com/repos/davidcarslaw/openair/zipball/master
    Installing openair
    '/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet CMD INSTALL  \
      '/private/var/folders/bv/881_rsvd2kv83c13yywwc_xh0000gn/T/RtmpFU4M1T/devtools12abf7da93151/davidcarslaw-openair-b782399'  \
      --library='/Users/gcn/Library/R/3.4/library' --install-tests 

    * installing *source* package ‘openair’ ...
    ** libs
    clang-omp++ -fopenmp -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Users/gcn/Library/R/3.4/library/Rcpp/include" -DU_STATIC_IMPLEMENTATION -Wall -mtune=core2 -g -O2 -I/opt/X11/include   -fPIC  -g -O3 -Wall -pedantic -mtune=native -std=c++11 -c cluster.cpp -o cluster.o
    clang-omp -fopenmp -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Users/gcn/Library/R/3.4/library/Rcpp/include" -DU_STATIC_IMPLEMENTATION -Wall -mtune=core2 -g -O2 -I/opt/X11/include   -fPIC  -g -O3 -Wall -pedantic -mtune=native  -std=gnu99 -c init.c -o init.o
    init.c:26:2: warning: no newline at end of file [-Wnewline-eof]
    }
     ^
    1 warning generated.
    clang-omp++ -fopenmp -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Users/gcn/Library/R/3.4/library/Rcpp/include" -DU_STATIC_IMPLEMENTATION -Wall -mtune=core2 -g -O2 -I/opt/X11/include   -fPIC  -g -O3 -Wall -pedantic -mtune=native -std=c++11 -c rolling.cpp -o rolling.o
    clang-omp++ -fopenmp -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/clang4/lib -o openair.so cluster.o init.o rolling.o -framework Accelerate -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
    ld: warning: directory not found for option '-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0'
    installing to /Users/gcn/Library/R/3.4/library/openair/libs
    ** R
    ** data
    *** moving datasets to lazyload DB
    ** inst
    ** byte-compile and prepare package for lazy loading
    Error in dyn.load(file, DLLpath = DLLpath, ...) : 
      unable to load shared object '/Users/gcn/Library/R/3.4/library/hexbin/libs/hexbin.so':
      dlopen(/Users/gcn/Library/R/3.4/library/hexbin/libs/hexbin.so, 6): Symbol not found: ___addtf3
      Referenced from: /usr/local/lib/libquadmath.0.dylib
      Expected in: /usr/local/lib/libgcc_s.1.dylib
     in /usr/local/lib/libquadmath.0.dylib
    ERROR: lazy loading failed for package ‘openair’
    * removing ‘/Users/gcn/Library/R/3.4/library/openair’
    Installation failed: Command failed (1)

    Friday, September 22, 2017 2:49 PM
  • I have now installed gfortran 6.1 and clang4. I now get the following output, ending in an error having to do with unable to load shared object '/Users/gcn/Library/R/3.4/library/hexbin/libs/hexbin.so 

    Downloading GitHub repo davidcarslaw/openair@master
    from URL https://api.github.com/repos/davidcarslaw/openair/zipball/master
    Installing openair
    '/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet CMD INSTALL  \
      '/private/var/folders/bv/881_rsvd2kv83c13yywwc_xh0000gn/T/RtmppZYfhl/devtools36bf517ad9/davidcarslaw-openair-b782399'  \
      --library='/Users/gcn/Library/R/3.4/library' --install-tests 

    * installing *source* package ‘openair’ ...
    ** libs
    /usr/local/clang4/bin/clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Users/gcn/Library/R/3.4/library/Rcpp/include" -DU_STATIC_IMPLEMENTATION -Wall -mtune=core2 -g -O2 -I/opt/X11/include   -fPIC  -DU_STATIC_IMPLEMENTATION -Wall -mtune=core2 -g -O2 -I/opt/X11/include  -c cluster.cpp -o cluster.o
    /usr/local/clang4/bin/clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Users/gcn/Library/R/3.4/library/Rcpp/include" -DU_STATIC_IMPLEMENTATION -Wall -mtune=core2 -g -O2 -I/opt/X11/include   -fPIC  -g -O3 -Wall -pedantic -mtune=native  -std=gnu99 -c init.c -o init.o
    init.c:26:2: warning: no newline at end of file [-Wnewline-eof]
    }
     ^
    1 warning generated.
    /usr/local/clang4/bin/clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Users/gcn/Library/R/3.4/library/Rcpp/include" -DU_STATIC_IMPLEMENTATION -Wall -mtune=core2 -g -O2 -I/opt/X11/include   -fPIC  -DU_STATIC_IMPLEMENTATION -Wall -mtune=core2 -g -O2 -I/opt/X11/include  -c rolling.cpp -o rolling.o
    /usr/local/clang4/bin/clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/clang4/lib -o openair.so cluster.o init.o rolling.o -framework Accelerate -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
    installing to /Users/gcn/Library/R/3.4/library/openair/libs
    ** R
    ** data
    *** moving datasets to lazyload DB
    ** inst
    ** byte-compile and prepare package for lazy loading
    Error in dyn.load(file, DLLpath = DLLpath, ...) : 
      unable to load shared object '/Users/gcn/Library/R/3.4/library/hexbin/libs/hexbin.so':
      dlopen(/Users/gcn/Library/R/3.4/library/hexbin/libs/hexbin.so, 6): Symbol not found: ___addtf3
      Referenced from: /usr/local/lib/libquadmath.0.dylib
      Expected in: /usr/local/lib/libgcc_s.1.dylib
     in /usr/local/lib/libquadmath.0.dylib
    ERROR: lazy loading failed for package ‘openair’
    * removing ‘/Users/gcn/Library/R/3.4/library/openair’
    Installation failed: Command failed (1)

    Friday, September 22, 2017 4:50 PM
  • Are you sure that you don't have a old version of the hexbin package installed on your system?

    I would try removing that with the 'remove.packages()' function, then try installing hexbin by itself, followed by the 'openair' package - it did work for me when I tried it with MRO 3.4.1 on Mac OS-X Sierra.

    Steve Weller

    Monday, October 2, 2017 11:15 PM
  • Tried that. I now have hexbin version 1.27.1. Openair binary installed but when I try to load the library I get errors. Here are the messages from the installation process from the CRAN repository. I'll tried compiling from source from GitHub without success? Does it matter that the Rcpp on my computer is compiled for R version 3.4.2 but I'm using MRAN R version 3.4.1?

    > install.packages("openair")
    Installing package into ‘/Users/gcn/Library/R/3.4/library’
    (as ‘lib’ is unspecified)
    trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.4/openair_2.1-5.tgz'
    Content type 'application/x-gzip' length 2749885 bytes (2.6 MB)
    ==================================================
    downloaded 2.6 MB


    The downloaded binary packages are in
    /var/folders/bv/881_rsvd2kv83c13yywwc_xh0000gn/T//RtmpVfDAWZ/downloaded_packages
    > library(openair)
    Error: package or namespace load failed for ‘openair’ in dyn.load(file, DLLpath = DLLpath, ...):
     unable to load shared object '/Library/Frameworks/R.framework/Versions/3.4.1-MRO/Resources/library/Matrix/libs/Matrix.so':
      dlopen(/Library/Frameworks/R.framework/Versions/3.4.1-MRO/Resources/library/Matrix/libs/Matrix.so, 6): Library not loaded: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib
      Referenced from: /Library/Frameworks/R.framework/Versions/3.4.1-MRO/Resources/library/Matrix/libs/Matrix.so
      Reason: image not found


    Thursday, October 5, 2017 5:47 PM