Michael,
On Oct 9, 2010, at 5:56 PM, Michael Braun wrote:
> Hi!
>
> I am trying to install rjags on my Mac Pro running OSX 10.6.4, and R 2.11.1
> (which I compiled myself so I could link to the Intel MKL blas, which I
> prefer to other options).
Just FWIW: CRAN R comes with shared BLAS option enabled and allows easy plug-in
of MKL BLAS without the need to re-compile (just use the libRblas.dylib
symlink). Note that MKL BLAS is often slower than ATLAS so if your main goal is
speed I suggest using ATLAS (or vecLib unless you have Nehalem-type Mac Pro) -
it is also easier to handle (both from technical and licensing point of view).
Cheers,
Simon
> I was successfully able to install JAGS 2.1.0 through both the binary
> installer, and compiling from source (I get the same problem either way).
>
> But I would like to use the rjags package. When I do
>
> install.packages("rjags")
>
>
> I get the folliowing output:
>
> * installing *source* package ‘rjags’ ...
> checking for prefix by checking for jags... /usr/local/bin/jags
> checking for g++... g++
> checking for C++ compiler default output file name... a.out
> checking whether the C++ compiler works... yes
> checking whether we are cross compiling... no
> checking for suffix of executables...
> checking for suffix of object files... o
> checking whether we are using the GNU C++ compiler... yes
> checking whether g++ accepts -g... yes
> checking how to run the C++ preprocessor... g++ -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 Console.h usability... yes
> checking Console.h presence... yes
> checking for Console.h... yes
> checking for gcc... gcc
> checking whether we are using the GNU C compiler... yes
> checking whether gcc accepts -g... yes
> checking for gcc option to accept ISO C89... none needed
> checking for jags_version in -ljags... yes
> configure: creating ./config.status
> config.status: creating src/Makevars
> configure: creating ./config.status
> config.status: creating src/Makevars
> config.status: creating R/unix/zzz.R
> ** libs
> *** arch - x86_64
> g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include
> -I/Library/Frameworks/R.framework/Resources/include/x86_64
> -I/usr/local/include/JAGS
> -I/opt/intel/Compiler/11.1/089/Frameworks/mkl/Headers
> -I/Install_Files/MKL_gfortran_interface/include/em64t/lp64 -fPIC -m64
> -msse4.2 -g -O2 -c jags.cc -o jags.o
> g++ -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined
> dynamic_lookup -single_module -multiply_defined suppress
> -L/opt/intel/Compiler/11.1/089/Frameworks/mkl/Libraries/em64t
> -L/Users/braunm/Install_Files/MKL_gfortran_interface/lib/em64t -o rjags.so
> jags.o -lgsl -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -lpthread
> -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework
> -Wl,CoreFoundation
> installing to /Users/braunm/.R/Library/rjags/libs/x86_64
> ** R
> ** data
> ** preparing package for lazy loading
> ** help
> *** installing help indices
> ** building package indices ...
> Error : .onLoad failed in loadNamespace() for 'rjags', details:
> call: dyn.load(file, DLLpath = DLLpath, ...)
> error: unable to load shared library
> '/Users/braunm/.R/Library/rjags/libs/x86_64/rjags.so':
> dlopen(/Users/braunm/.R/Library/rjags/libs/x86_64/rjags.so, 10): Symbol not
> found: _JAGS_NA
> Referenced from: /Users/braunm/.R/Library/rjags/libs/x86_64/rjags.so
> Expected in: flat namespace
> in /Users/braunm/.R/Library/rjags/libs/x86_64/rjags.so
> ERROR: installing package indices failed
> * removing ‘/Users/braunm/.R/Library/rjags’
>
>
> However, when I go to look at the symbols in the jags library, I see
>
> braunm4: /usr/local/lib $ nm libjags.dylib |grep JAGS
> 0000000000098650 S _JAGS_NA
> 0000000000110338 S _JAGS_NAN
> 0000000000110348 S _JAGS_NEGINF
> 0000000000110340 S _JAGS_POSINF
> 000000000000133c t __GLOBAL__I_JAGS_NA
>
> and when I try
>
> braunm4: /usr/local/lib $ nm libjags.a |grep JAGS
> U _JAGS_NA
> U _JAGS_NEGINF
> U _JAGS_NA
> U _JAGS_NA
> 0000000000000060 S _JAGS_NA
> 00000000000000b8 B _JAGS_NAN
> 00000000000000c8 B _JAGS_NEGINF
> 00000000000000c0 B _JAGS_POSINF
> U _JAGS_NA
> U _JAGS_NEGINF
> U _JAGS_POSINF
> U _JAGS_NEGINF
> U _JAGS_POSINF
> U _JAGS_NEGINF
> U _JAGS_NA
> U _JAGS_NEGINF
> U _JAGS_NEGINF
> U _JAGS_NA
> U _JAGS_NEGINF
> U _JAGS_POSINF
>
>
> So the jags libraries (both static and dynamic) are in the standard place,
> and it looks like the symbols rjags.so needs are there as well. So I'm not
> sure what the rjags installer is looking for. Is there perhaps an
> environment variable that I am missing?
>
> Here is my sessionInfo():
>
>> sessionInfo()
> R version 2.11.1 (2010-05-31)
> x86_64-apple-darwin10.4.2
>
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
>
> attached base packages:
> [1] stats grDevices datasets graphics utils methods base
>
> other attached packages:
> [1] xtable_1.5-6 doMC_1.2.1 multicore_0.1-3 foreach_1.3.0
> codetools_0.2-2 iterators_1.0.3 coda_0.13-5 matrixcalc_1.0-1
> lattice_0.18-8 reshape_0.8.3 plyr_1.2.1
> [12] mvtnorm_0.9-92
>
> loaded via a namespace (and not attached):
> [1] grid_2.11.1 tcltk_2.11.1 tools_2.11.1
>
>
> Thanks in advance for your help.
>
> Michael
>
>
>
>
>
>
>
>
> -------------------------------------------
> Michael Braun
> Homer A. Burnell (1928) Career Development Professor,
> and Assistant Professor of Management Science (Marketing Group)
> MIT Sloan School of Management
> 100 Main St.., E62-535
> Cambridge, MA 02139
> bra...@mit.edu
> 617-253-3436
>
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>
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