Hi all,
Thanks for your help (Whit especially) on various things.
After a fair bit of effort I got rccpbugs installed on my
Mac 10.7 in R.app. Here's my setup:
> sessionInfo()
R version 2.14.1 (2011-12-22)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
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 grDevices utils datasets graphics
methods base
other attached packages:
[1] rcppbugs_0.1.0 RcppArmadillo_0.3.0.2 Rcpp_0.9.10
inline_0.3.8
loaded via a namespace (and not attached):
[1] compiler_2.14.1 tools_2.14.1
The basic steps:
1. Install dependencies
install.packages("Rcpp")
install.packages("inline")
2. (I updated Xcode to 3.2 and installed the Command Line
Tools, I doubt the details of this matter though.)
3. The default compiler on Mac OS X 10.7 is gcc4.2.
However, rcppbugs needs gcc4.6. I got gcc4.6 to install by
following the directions here:
http://solarianprogrammer.com/2011/12/01/compiling-gcc-4-6-2-on-mac-osx-lion/
If you want to try gcc4.7, the instructions are here, but
Whit recommends against it for now:
http://solarianprogrammer.com/2012/02/20/living-on-the-edge-building-gcc-4-7-on-mac-osx-lion/
In my case, I installed gcc46 and the 3 dependencies in
(root)/my_gcc rather than $HOME/my_gcc. After installing
the dependencies, I configured and maked the gcc46 install
as follows:
In Terminal (not R):
========================
cd /Users/nickm/Downloads/z_installed_good/gcc47/
502 ls
503 gunzip -c mpc-0.9.tar.gz | tar xopf -
504 gunzip -c mpfr-3.1.0.tar.gz | tar xopf -
505 gunzip -c gmp-5.0.5.tar.gz | tar xopf -
506 gunzip -c gmp-5.0.5.tar.bz2 | tar xopf -
507 tar jxf gmp-5.0.5.tar.bz2
508 ls
509 cd gmp*
510 mkdir build
511 cd build
514 ../configure --prefix=/my_gcc
515 make
516 make install
517 cd ..
518 cd ..
519 cd mpfr*
520 mkdir build
521 cd build
522 ../configure --prefix=/my_gcc --with-gmp=/my_gcc
523 pwd
524 make
525 make install
526 cd ..
527 cd ..
528 cd mpc*
529 mkdir build
530 cd build
532 ../configure --prefix=/my_gcc --with-gmp=/my_gcc
--with-mpfr=/my_gcc
533 make
534 make install
535 cd ..
536 cd ..
537 ls
548 cd /Users/nickm/Downloads/z_installed_good/gcc46/
549 ls
550 gunzip -c gcc-4.6.3.tar.gz | tar xopf -
560 cd gcc*
561 ls
562 mkdir build
563 cd build
564 ls
565 ../configure --prefix=/my_gcc
--enable-checking-release --with-gmp=/my_gcc
--with-mpfr=/my_gcc --enable-languages=c,c++,fortran
--program-suffix=46
566 make -j 4
567 ls
568 cd bin
569 make install
570 history
========================
4. Now we have gcc 4.6.3 installed as /my_gcc/gcc46, and
also g++46 (R uses g++ by default), but R CMD INSTALL
doesn't know where to find it. Solution:
4a. First we make gcc46 the default gcc:
# g++
# Change symbolic linkage:
cd /usr/bin
rm g++; ln -s /my_gcc/bin/g++46 /usr/bin/g++
(To turn it back later, we can do this)
# Change it back
cd /usr/bin
rm g++; ln -s /usr/bin/llvm-g++-4.2 /usr/bin/g++
4b. Now when we run R CMD INSTALL, it uses the correct g++,
but for whatever reason, with gcc 4.6 the "-arch x86_64"
flag is not recognized, so this throws an error when you
attempt to install.
The default settings for the command-line R CMD INSTALL (and
R CMD SHLIB) commands are stored in something like
$R_HOME/etc/Makeconf. You can figure it out exactly with
R.home:
# Return the R Home Directory
#
http://stat.ethz.ch/R-manual/R-patched/library/base/html/Rhome.html
In R:
R.home(component="home")
# "/Library/Frameworks/R.framework/Resources"
#
# Find the Makeconf file (default Make settings)
# cd /Library/Frameworks/R.framework/Resources/etc/x86_64/
#
In my case, the Makeconf file was at:
/Library/Frameworks/R.framework/Resources/etc/x86_64/Makeconf
4c. The variables specifying the compiler are:
CXX
SHLIB_CXXLD
They can be changed from their defaults by editing Makeconf:
/Library/Frameworks/R.framework/Resources/etc/x86_64/Makeconf
Or, more easily/properly by creating a Makevars file in
$HOME/.R/Makevars
# The Makevars file should be stored at:
# $HOME/.R/Makevars
I did the latter.
5. The Makevars file:
$Home/.R/Makevars
/Users/nickm/.R/Makevars
==============================
# THIS IS THE MANUALLY-CREATED Makevars file WHICH LETS YOU
CUSTOMIZE
# R CMD INSTALL and R CMD SHLIB compiler flags more easily
than you
# would by modifying the Makeconf default file directly.
#
# (On this machine, Makeconf default file is at:
# /Library/Frameworks/R.framework/Resources/etc/x86_64/Makeconf
# )
#
# The Makevars file should be stored at:
# $HOME/.R/Makevars
#
#
# default for R 2.14 on Mac OS X 10.7 is to use gcc --> gcc4.2
# but we want to use gcc4.6, which doesn't use the -arch
(architecture) tags
#
# So, edit that environment variable for R CMD INSTALL and R
CMD SHLIB
#
# CXX - the compiler for each code file
#CXX=g++ -arch x86_64
CXX=g++ -std=c++0x
# SHLIB_CXXLD - maybe this is the linker? - YEP
#SHLIB_CXXLD = g++ -arch x86_64
SHLIB_CXXLD = g++ -std=c++0x
==============================
6. Now we are ready for rcppbugs. Download and unzip the
source from here:
http://cran.r-project.org/web/packages/rcppbugs/index.html
7. In R:
===================
# Install from source, after changing compiler to g++46 and
modifying Makevars:
packagepath =
"/Users/nickm/Desktop/__projects/__BayArea/_detection_probability/_RcppBUGS/rcppbugs"
libpath = "/Library/Frameworks/R.framework/Resources/library/"
install.packages(c(packagepath), libpath, NULL,
type='source', INSTALL_opts=c("--no-multiarch"))
cmd = paste("R CMD INSTALL --preclean --no-multiarch
--library=", libpath, " ", packagepath, sep="")
system(cmd)
===================
The --no-multiarch flag was needed because otherwise R on
Mac OS X attempts to also compile for PPC or i386
architecture or something, and I didn't want to figure that out.
8. Test code:
====================================
?run.model
# Example code from run.model
NR <- 1e2L
NC <- 2L
y <- matrix(rnorm(NR,1) + 10,nr=NR,nc=1L)
X <- matrix(nr=NR,nc=NC)
X[,1] <- 1
X[,2] <- y + rnorm(NR)/2 - 10
## RCppBugs Model
b <- mcmc.normal(rnorm(NC),mu=0,tau=0.0001)
tau.y <- mcmc.gamma(sd(as.vector(y)),alpha=0.1,beta=0.1)
y.hat <- linear(X,b)
y.lik <- mcmc.normal(y,mu=y.hat,tau=tau.y,observed=TRUE)
m <- create.model(b, tau.y, y.hat, y.lik)
runtime <- system.time(ans <- run.model(m, iterations=1e2L,
burn=1e2L, adapt=1e3L, thin=10L))
print(get.ar(ans))
print(apply(ans[["b"]],2,mean))
====================================
Done!
Nick
PS:
STUFF THAT DIDN'T WORK, BUT WHICH MIGHT BE HANDY TO GOOGLE
FOR OTHERS WHO HIT MY ERROR MESSAGES:
ERRORS TRYING TO COMPILE cppbugs code (the precursor of
rcppbugs) with the wrong compilers etc.; many of these are
the product of attempting to compile with g++4.2, although I
never got g++4.6 or 4.7 to work either, could be the -std
flag was wrong or something. I got similar error messages
with rcppbugs early on before I switched compilers.
============
(very long, see next message)
============
LEFT OUT THE --no-multiarch FLAG
=========================
install.packages(c(packagepath),
"/Library/Frameworks/R.framework/Resources/library/", NULL,
type='source')
* installing *source* package ‘rcppbugs’ ...
files src/Makevars, src/Makevars.win,
src/cppbugs/cppbugs/mcmc.bernoulli.hpp,
src/cppbugs/cppbugs/mcmc.beta.hpp,
src/cppbugs/cppbugs/mcmc.binomial.hpp,
src/cppbugs/cppbugs/mcmc.gamma.hpp,
src/cppbugs/cppbugs/mcmc.model.hpp,
src/cppbugs/cppbugs/mcmc.multivariate.normal.hpp,
src/cppbugs/cppbugs/mcmc.normal.hpp,
src/cppbugs/cppbugs/mcmc.stochastic.hpp,
src/cppbugs/cppbugs/mcmc.uniform.hpp, src/r.mcmc.model.h
have the wrong MD5 checksums
** libs
*** arch - i386
g++ -std=c++0x
-I/Library/Frameworks/R.framework/Resources/include
-I/Library/Frameworks/R.framework/Resources/include/i386
-I/usr/local/include
-I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Rcpp/include"
-I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/RcppArmadillo/include"
-I/opt/local/include -I./cppbugs -fPIC -g -O2 -c
interface.cpp -o interface.o
g++ -std=c++0x
-I/Library/Frameworks/R.framework/Resources/include
-I/Library/Frameworks/R.framework/Resources/include/i386
-I/usr/local/include
-I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Rcpp/include"
-I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/RcppArmadillo/include"
-I/opt/local/include -I./cppbugs -fPIC -g -O2 -c
raw.address.cpp -o raw.address.o
g++ -arch i386 -dynamiclib -Wl,-headerpad_max_install_names
-undefined dynamic_lookup -single_module -multiply_defined
suppress -L/usr/local/lib -o rcppbugs.so helpers.o
interface.o raw.address.o
/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Rcpp/lib/i386/libRcpp.a
-L/Library/Frameworks/R.framework/Resources/lib/i386
-lRlapack
-L/Library/Frameworks/R.framework/Resources/lib/i386 -lRblas
-lgfortran -F/Library/Frameworks/R.framework/.. -framework R
-Wl,-framework -Wl,CoreFoundation
g++: error: i386: No such file or directory
g++: error: unrecognized option ‘-arch’
make: *** [rcppbugs.so] Error 1
ERROR: compilation failed for package ‘rcppbugs’
* removing
‘/Library/Frameworks/R.framework/Versions/2.14/Resources/library/rcppbugs’
Warning message:
In install.packages(c(packagepath),
"/Library/Frameworks/R.framework/Resources/library/", :
installation of package
‘/Users/nickm/Desktop/__projects/__BayArea/_detection_probability/_RcppBUGS/rcppbugs’
had non-zero exit status
=========================
CXX CHANGED, BUT NOT SHLIB_CXXLD:
====================
system(cmd)
* installing *source* package ‘rcppbugs’ ...
files src/Makevars, src/Makevars.win,
src/cppbugs/cppbugs/mcmc.bernoulli.hpp,
src/cppbugs/cppbugs/mcmc.beta.hpp,
src/cppbugs/cppbugs/mcmc.binomial.hpp,
src/cppbugs/cppbugs/mcmc.gamma.hpp,
src/cppbugs/cppbugs/mcmc.model.hpp,
src/cppbugs/cppbugs/mcmc.multivariate.normal.hpp,
src/cppbugs/cppbugs/mcmc.normal.hpp,
src/cppbugs/cppbugs/mcmc.stochastic.hpp,
src/cppbugs/cppbugs/mcmc.uniform.hpp, src/r.mcmc.model.h
have the wrong MD5 checksums
** libs
*** arch - x86_64
g++ -std=c++0x
-I/Library/Frameworks/R.framework/Resources/include
-I/Library/Frameworks/R.framework/Resources/include/x86_64
-I/usr/local/include
-I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Rcpp/include"
-I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/RcppArmadillo/include"
-I/opt/local/include -I./cppbugs -fPIC -g -O2 -c
helpers.cpp -o helpers.o
g++ -std=c++0x
-I/Library/Frameworks/R.framework/Resources/include
-I/Library/Frameworks/R.framework/Resources/include/x86_64
-I/usr/local/include
-I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Rcpp/include"
-I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/RcppArmadillo/include"
-I/opt/local/include -I./cppbugs -fPIC -g -O2 -c
interface.cpp -o interface.o
g++ -std=c++0x
-I/Library/Frameworks/R.framework/Resources/include
-I/Library/Frameworks/R.framework/Resources/include/x86_64
-I/usr/local/include
-I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Rcpp/include"
-I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/RcppArmadillo/include"
-I/opt/local/include -I./cppbugs -fPIC -g -O2 -c
raw.address.cpp -o raw.address.o
g++ -arch x86_64 -dynamiclib
-Wl,-headerpad_max_install_names -undefined dynamic_lookup
-single_module -multiply_defined suppress -L/usr/local/lib
-o rcppbugs.so helpers.o interface.o raw.address.o
/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Rcpp/lib/x86_64/libRcpp.a
-L/Library/Frameworks/R.framework/Resources/lib/x86_64
-lRlapack
-L/Library/Frameworks/R.framework/Resources/lib/x86_64
-lRblas -lgfortran -F/Library/Frameworks/R.framework/..
-framework R -Wl,-framework -Wl,CoreFoundation
g++: error: x86_64: No such file or directory
g++: error: unrecognized option ‘-arch’
make: *** [rcppbugs.so] Error 1
ERROR: compilation failed for package ‘rcppbugs’
* removing
‘/Library/Frameworks/R.framework/Versions/2.14/Resources/library/rcppbugs’
====================
--
====================================================
Nicholas J. Matzke
Ph.D. Candidate, Graduate Student Researcher
Huelsenbeck Lab
Center for Theoretical Evolutionary Genomics
4151 VLSB (Valley Life Sciences Building)
Department of Integrative Biology
University of California, Berkeley
Graduate Student Instructor, IB200B
Principles of Phylogenetics: Ecology and Evolution
http://ib.berkeley.edu/courses/ib200b/
http://phylo.wikidot.com/
Lab websites:
http://ib.berkeley.edu/people/lab_detail.php?lab=54
http://fisher.berkeley.edu/cteg/hlab.html
Dept. personal page:
http://ib.berkeley.edu/people/students/person_detail.php?person=370
Lab personal page:
http://fisher.berkeley.edu/cteg/members/matzke.html
Lab phone: 510-643-6299
Dept. fax: 510-643-6264
Cell phone: 510-301-0179
Email: [email protected]
Mailing address:
Department of Integrative Biology
1005 Valley Life Sciences Building #3140
Berkeley, CA 94720-3140
-----------------------------------------------------
"[W]hen people thought the earth was flat, they were wrong.
When people thought the earth was spherical, they were
wrong. But if you think that thinking the earth is spherical
is just as wrong as thinking the earth is flat, then your
view is wronger than both of them put together."
Isaac Asimov (1989). "The Relativity of Wrong." The
Skeptical Inquirer, 14(1), 35-44. Fall 1989.
http://chem.tufts.edu/AnswersInScience/RelativityofWrong.htm
====================================================
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