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List: r-sig-mac
Subject: Re: [R-SIG-Mac] problem installing rjags package
From: Michael Braun <braunm () mit ! edu>
Date: 2010-10-12 15:19:24
Message-ID: AADE68A5-2C79-4A05-897E-7719C63D00DB () mit ! edu
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Thanks, Simon:
I do have a Nehalem Mac Pro, and I've found MKL to be much faster than vecLib. I saw \
in one of the manuals that one could point R to another BLAS. But I wasn't sure what \
to do with MKL because of their "layering" approach to linking. So if I point \
libRblas to something else, how to I tell the link which of the multiple libraries I \
need?
And since we are now straying away from the original topic about JAGS, let me know if \
you prefer that I start another thread. I do try to follow the posting guide as best \
I can.
Michael
On Oct 12, 2010, at 9:10 AM, Simon Urbanek wrote:
> 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
> > braunm@mit.edu
> > 617-253-3436
> >
> > _______________________________________________
> > R-SIG-Mac mailing list
> > R-SIG-Mac@stat.math.ethz.ch
> > https://stat.ethz.ch/mailman/listinfo/r-sig-mac
> >
> >
>
-------------------------------------------
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@mit.edu
617-253-3436
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