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mran version of qdap package installs on Windows but not Mac RRS feed

  • Question

  • I am trying to install the qdap package on a Macbook Air.  I am using a fresh install of Microsoft Open R and Rstudio.  The results of sessionInfo() are given here:

    > sessionInfo()
    R version 3.3.1 (2016-06-21)
    Platform: x86_64-apple-darwin15.0.0 (64-bit)
    Running under: OS X 10.11.6 (El Capitan)
    
    locale:
    [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
    
    attached base packages:
    [1] stats     graphics  grDevices utils     datasets  methods  
    [7] base     
    
    loaded via a namespace (and not attached):
    [1] RevoUtils_10.0.1 tools_3.3.1    

    When I try to install the qdap package I get the standard output given below.  The first problem that I find is the line saying: 

    In doTryCatch(return(expr), name, parentenv, handler) :  unable to load shared object '/Library/Frameworks/R.framework/Resources/modules//R_X11.so'

    But, if I open Terminal I find that /Library/Frameworks/R.framework/Resources/modules/R_X11.so exists.

    The next problem that I find is that it is expecting some library that doesn't (and maybe shouldn't-at least not in the specified directory) exist on my machine: '-L/private/var/root/jenkins/workspace/External-R-3.3.1/vendor/build/lib'

    Further, there is the following problems with it trying to call gcc and gfortran, both of which are installed on my machine but not in the directories that the package installer is looking in.

    If instead I do a fresh install of Microsoft R open and Rstudio on a borrowed Windows 10 computer qdap installs correctly.

    Does anyone have a suggestion as to what to do in order to get this package to install correctly?

    > install.packages("qdap", dependencies = TRUE)
    Installing package into ‘/Users/booger/Library/R/3.3/library’
    (as ‘lib’ is unspecified)
    also installing the dependencies ‘slam’, ‘igraph’, ‘tm’, ‘wordcloud’
    
    trying URL 'https://mran.revolutionanalytics.com/snapshot/2016-07-01/src/contrib/slam_0.1-35.tar.gz'
    Content type 'application/octet-stream' length 47123 bytes (46 KB)
    ==================================================
    downloaded 46 KB
    
    trying URL 'https://mran.revolutionanalytics.com/snapshot/2016-07-01/src/contrib/igraph_1.0.1.tar.gz'
    Content type 'application/octet-stream' length 3328353 bytes (3.2 MB)
    ==================================================
    downloaded 3.2 MB
    
    trying URL 'https://mran.revolutionanalytics.com/snapshot/2016-07-01/src/contrib/tm_0.6-2.tar.gz'
    Content type 'application/octet-stream' length 511060 bytes (499 KB)
    ==================================================
    downloaded 499 KB
    
    trying URL 'https://mran.revolutionanalytics.com/snapshot/2016-07-01/src/contrib/wordcloud_2.5.tar.gz'
    Content type 'application/octet-stream' length 40861 bytes (39 KB)
    ==================================================
    downloaded 39 KB
    
    trying URL 'https://mran.revolutionanalytics.com/snapshot/2016-07-01/src/contrib/qdap_2.2.5.tar.gz'
    Content type 'application/octet-stream' length 2475423 bytes (2.4 MB)
    ==================================================
    downloaded 2.4 MB
    
    Warning message:
    In doTryCatch(return(expr), name, parentenv, handler) :
      unable to load shared object '/Library/Frameworks/R.framework/Resources/modules//R_X11.so':
      dlopen(/Library/Frameworks/R.framework/Resources/modules//R_X11.so, 6): Symbol not found: _CGBitmapContextCreate
      Referenced from: /Library/Frameworks/R.framework/Resources/modules//R_X11.so
      Expected in: flat namespace
     in /Library/Frameworks/R.framework/Resources/modules//R_X11.so
    * installing *source* package ‘slam’ ...
    ** package ‘slam’ successfully unpacked and MD5 sums checked
    ** libs
    clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/private/var/root/jenkins/workspace/External-R-3.3.1/vendor/build/include -DU_STATIC_IMPLEMENTATION -Wall -mtune=core2 -g -O2 -I/opt/X11/include    -fPIC  -I/private/var/root/jenkins/workspace/External-R-3.3.1/vendor/build/include -DU_STATIC_IMPLEMENTATION -Wall -mtune=core2 -g -O2 -I/opt/X11/include -framework CoreFoundation -framework CoreGraphics -framework CoreText  -c apply.c -o apply.o
    clang: warning: -framework CoreFoundation: 'linker' input unused
    clang: warning: -framework CoreGraphics: 'linker' input unused
    clang: warning: -framework CoreText: 'linker' input unused
    clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/private/var/root/jenkins/workspace/External-R-3.3.1/vendor/build/include -DU_STATIC_IMPLEMENTATION -Wall -mtune=core2 -g -O2 -I/opt/X11/include    -fPIC  -I/private/var/root/jenkins/workspace/External-R-3.3.1/vendor/build/include -DU_STATIC_IMPLEMENTATION -Wall -mtune=core2 -g -O2 -I/opt/X11/include -framework CoreFoundation -framework CoreGraphics -framework CoreText  -c grouped.c -o grouped.o
    clang: warning: -framework CoreFoundation: 'linker' input unused
    clang: warning: -framework CoreGraphics: 'linker' input unused
    clang: warning: -framework CoreText: 'linker' input unused
    clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/private/var/root/jenkins/workspace/External-R-3.3.1/vendor/build/include -DU_STATIC_IMPLEMENTATION -Wall -mtune=core2 -g -O2 -I/opt/X11/include    -fPIC  -I/private/var/root/jenkins/workspace/External-R-3.3.1/vendor/build/include -DU_STATIC_IMPLEMENTATION -Wall -mtune=core2 -g -O2 -I/opt/X11/include -framework CoreFoundation -framework CoreGraphics -framework CoreText  -c sparse.c -o sparse.o
    clang: warning: -framework CoreFoundation: 'linker' input unused
    clang: warning: -framework CoreGraphics: 'linker' input unused
    clang: warning: -framework CoreText: 'linker' input unused
    clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/private/var/root/jenkins/workspace/External-R-3.3.1/vendor/build/include -DU_STATIC_IMPLEMENTATION -Wall -mtune=core2 -g -O2 -I/opt/X11/include    -fPIC  -I/private/var/root/jenkins/workspace/External-R-3.3.1/vendor/build/include -DU_STATIC_IMPLEMENTATION -Wall -mtune=core2 -g -O2 -I/opt/X11/include -framework CoreFoundation -framework CoreGraphics -framework CoreText  -c util.c -o util.o
    clang: warning: -framework CoreFoundation: 'linker' input unused
    clang: warning: -framework CoreGraphics: 'linker' input unused
    clang: warning: -framework CoreText: 'linker' input unused
    clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/private/var/root/jenkins/workspace/External-R-3.3.1/vendor/build/lib -o slam.so apply.o grouped.o sparse.o util.o -framework Accelerate -L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3/x86_64 -L/usr/local/lib/x86_64 -L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3 -L/usr/local/lib -lgfortran -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
    ld: warning: directory not found for option '-L/private/var/root/jenkins/workspace/External-R-3.3.1/vendor/build/lib'
    ld: warning: directory not found for option '-L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3/x86_64'
    ld: warning: directory not found for option '-L/usr/local/lib/x86_64'
    ld: warning: directory not found for option '-L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3'
    ld: library not found for -lgfortran
    clang: error: linker command failed with exit code 1 (use -v to see invocation)
    make: *** [slam.so] Error 1
    ERROR: compilation failed for package ‘slam’
    * removing ‘/Users/booger/Library/R/3.3/library/slam’
    Warning in install.packages :
      installation of package ‘slam’ had non-zero exit status
    Warning message:
    In doTryCatch(return(expr), name, parentenv, handler) :
      unable to load shared object '/Library/Frameworks/R.framework/Resources/modules//R_X11.so':
      dlopen(/Library/Frameworks/R.framework/Resources/modules//R_X11.so, 6): Symbol not found: _CGBitmapContextCreate
      Referenced from: /Library/Frameworks/R.framework/Resources/modules//R_X11.so
      Expected in: flat namespace
     in /Library/Frameworks/R.framework/Resources/modules//R_X11.so
    * installing *source* package ‘igraph’ ...
    ** package ‘igraph’ successfully unpacked and MD5 sums checked
    checking for gcc... clang
    checking whether the C compiler works... yes
    checking for C compiler default output file name... a.out
    checking for suffix of executables... 
    checking whether we are cross compiling... no
    checking for suffix of object files... o
    checking whether we are using the GNU C compiler... yes
    checking whether clang accepts -g... yes
    checking for clang option to accept ISO C89... none needed
    checking whether we are using the GNU Fortran compiler... no
    checking whether gfortran -arch x86_64 accepts -g... no
    checking whether we are using the GNU C++ compiler... yes
    checking whether clang++ accepts -g... yes
    checking how to run the C++ preprocessor... clang++ -E
    checking for rintf... yes
    checking for finite... yes
    checking for expm1... yes
    checking for rint... yes
    checking for log2... yes
    checking for logbl... yes
    checking for snprintf... yes
    checking for log1p... yes
    checking for round... yes
    checking for fmin... yes
    checking for stpcpy... yes
    checking how to run the C preprocessor... clang -E
    checking for grep that handles long lines and -e... /usr/bin/grep
    checking for egrep... /usr/bin/grep -E
    checking for ANSI C header files... yes
    checking for sys/types.h... yes
    checking for sys/stat.h... yes
    checking for stdlib.h... yes
    checking for string.h... yes
    checking for memory.h... yes
    checking for strings.h... yes
    checking for inttypes.h... yes
    checking for stdint.h... yes
    checking for unistd.h... yes
    checking whether stpcpy is declared... yes
    checking sys/times.h usability... yes
    checking sys/times.h presence... yes
    checking for sys/times.h... yes
    checking net/if.h usability... yes
    checking net/if.h presence... yes
    checking for net/if.h... yes
    checking netinet/in.h usability... yes
    checking netinet/in.h presence... yes
    checking for netinet/in.h... yes
    checking net/if_dl.h usability... yes
    checking net/if_dl.h presence... yes
    checking for net/if_dl.h... yes
    checking sys/sockio.h usability... yes
    checking sys/sockio.h presence... yes
    checking for sys/sockio.h... yes
    checking sys/un.h usability... yes
    checking sys/un.h presence... yes
    checking for sys/un.h... yes
    checking sys/socket.h usability... yes
    checking sys/socket.h presence... yes
    checking for sys/socket.h... yes
    checking sys/ioctl.h usability... yes
    checking sys/ioctl.h presence... yes
    checking for sys/ioctl.h... yes
    checking sys/time.h usability... yes
    checking sys/time.h presence... yes
    checking for sys/time.h... yes
    checking sys/file.h usability... yes
    checking sys/file.h presence... yes
    checking for sys/file.h... yes
    checking for struct sockaddr.sa_len... yes
    checking for xml2-config... /usr/bin/xml2-config
    checking for xmlSAXUserParseFile in -lxml2... yes
    checking libxml/parser.h usability... yes
    checking libxml/parser.h presence... yes
    checking for libxml/parser.h... yes
    checking for __gmpz_add in -lgmp... no
    configure: creating ./config.status
    config.status: creating src/Makevars.tmp
    config.status: creating src/Makevars
    config.status: creating src/config.h
    ** libs
    gfortran -arch x86_64   -fPIC  -g -O2  -c AMD/Source/amd.f -o AMD/Source/amd.o
    make: gfortran: No such file or directory
    make: *** [AMD/Source/amd.o] Error 1
    ERROR: compilation failed for package ‘igraph’
    * removing ‘/Users/booger/Library/R/3.3/library/igraph’
    Warning in install.packages :
      installation of package ‘igraph’ had non-zero exit status
    Warning message:
    In doTryCatch(return(expr), name, parentenv, handler) :
      unable to load shared object '/Library/Frameworks/R.framework/Resources/modules//R_X11.so':
      dlopen(/Library/Frameworks/R.framework/Resources/modules//R_X11.so, 6): Symbol not found: _CGBitmapContextCreate
      Referenced from: /Library/Frameworks/R.framework/Resources/modules//R_X11.so
      Expected in: flat namespace
     in /Library/Frameworks/R.framework/Resources/modules//R_X11.so
    ERROR: dependency ‘slam’ is not available for package ‘tm’
    * removing ‘/Users/booger/Library/R/3.3/library/tm’
    Warning in install.packages :
      installation of package ‘tm’ had non-zero exit status
    Warning message:
    In doTryCatch(return(expr), name, parentenv, handler) :
      unable to load shared object '/Library/Frameworks/R.framework/Resources/modules//R_X11.so':
      dlopen(/Library/Frameworks/R.framework/Resources/modules//R_X11.so, 6): Symbol not found: _CGBitmapContextCreate
      Referenced from: /Library/Frameworks/R.framework/Resources/modules//R_X11.so
      Expected in: flat namespace
     in /Library/Frameworks/R.framework/Resources/modules//R_X11.so
    ERROR: dependency ‘slam’ is not available for package ‘wordcloud’
    * removing ‘/Users/booger/Library/R/3.3/library/wordcloud’
    Warning in install.packages :
      installation of package ‘wordcloud’ had non-zero exit status
    Warning message:
    In doTryCatch(return(expr), name, parentenv, handler) :
      unable to load shared object '/Library/Frameworks/R.framework/Resources/modules//R_X11.so':
      dlopen(/Library/Frameworks/R.framework/Resources/modules//R_X11.so, 6): Symbol not found: _CGBitmapContextCreate
      Referenced from: /Library/Frameworks/R.framework/Resources/modules//R_X11.so
      Expected in: flat namespace
     in /Library/Frameworks/R.framework/Resources/modules//R_X11.so
    ERROR: dependencies ‘igraph’, ‘tm’, ‘wordcloud’ are not available for package ‘qdap’
    * removing ‘/Users/booger/Library/R/3.3/library/qdap’
    Warning in install.packages :
      installation of package ‘qdap’ had non-zero exit status
    
    The downloaded source packages are in
    	‘/private/var/folders/xq/th6sk4bj0_l02c93zqpnmyw80000gn/T/RtmphZqJD4/downloaded_packages’


    Thursday, October 6, 2016 12:12 AM

All replies

  • I have it working.  One of my friends noted that I needed to run the command

    chmod 777 /Library/Frameworks/R.framework/Resources/modules//R_X11.so

    The other thing that I found that I needed to do is install gfortran using the package installer located here:

    https://cran.fhcrc.org

    Thursday, October 6, 2016 10:59 PM