[R-SIG-Mac] problem installing rjags package
Prof Brian Ripley
ripley at stats.ox.ac.uk
Sun Oct 10 08:47:29 CEST 2010
Note your link line has no reference to -ljags. Mine is (for i386,
x86_64 is later on in the output)
g++ -arch i386 -dynamiclib -Wl,-headerpad_max_install_names -undefined
dynamic_lookup -single_module -multiply_defined suppress
-L/usr/local/lib -o rjags.so jags.o -L/usr/local/lib -ljags
-F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework
-Wl,CoreFoundation
with no reference to -lgsl. Also, have you perhaps excluded
/usr/local/lib (the usual place to install JAGS) from the R library
paths?
Have you contacted the maintainer? Although not a Mac user he is very
knowledgable, including about MKL.
On Sat, 9 Oct 2010, 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). 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
> braunm at mit.edu
> 617-253-3436
>
> _______________________________________________
> R-SIG-Mac mailing list
> R-SIG-Mac at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>
--
Brian D. Ripley, ripley at stats.ox.ac.uk
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel: +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UK Fax: +44 1865 272595
More information about the R-SIG-Mac
mailing list