R 用の RStan をインストールしました。インストールは成功したようですが、パッケージをロードして使用すると、Rstan がインストールされていないことを示すエラー メッセージが表示され続けます。
> source("http://mc-stan.org/rstan/stan.R")
> fit <- stan("7b Class.stan", data=list(N=1187, J=J, y=earn, height=height, male=male, edu=ed, cluster=cluster), iter=1000, chains=4)
Fejl i packageDescription("rstan")$Date :
$ operator is invalid for atomic vectors
In addition: Advarselsbesked:
In packageDescription("rstan") : no package 'rstan' was found
Mac OS.X 10.7.5 を使用しています。最近、R を 3.1.3 にアップグレードし、R-studio をインターフェイスとして使用しています。Rstan のインストールについては、こちらの説明に従いました: https://github.com/stan-dev/rstan/wiki/RStan-Mac-OS-X-Prerequisite-Installation-Instructions
X コードとコマンド ライン ツール (Mac OS.X Lion) を Apple Developer からインストールしました。R が正しくインストールされているかどうかを確認すると、次のメッセージが表示されます。
> system('clang++ -v')
Apple LLVM version 4.2 (clang-425.0.28) (based on LLVM 3.2svn)
Target: x86_64-apple-darwin11.4.2
Thread model: posix
Stan を R にインストールすると、次のメッセージが表示されます。
> #Install STAN - https://github.com/stan-dev/rstan/wiki/RStan-Getting-Started
> ###Step 1 - Set numbers of processes to uge
> Sys.setenv(MAKEFLAGS = "-j4")
> ###Step 2 - Run the script
> source('http://mc-stan.org/rstan/install.R', echo = TRUE, max.deparse.length = 2000)
> install_rstan <- function() {
+ on.exit(Sys.unsetenv("R_MAKEVARS_USER"))
+ on.exit(Sys.unsetenv("R_MAKEVARS_SITE"), add = TRUE)
+
+ try(remove.packages("rstan"), silent = TRUE)
+ Sys.setenv(R_MAKEVARS_USER = "foobar")
+ Sys.setenv(R_MAKEVARS_SITE = "foobar")
+ install.packages(c("inline", "BH", "RcppEigen"))
+ install.packages("Rcpp", type = "source")
+ library(inline)
+ library(Rcpp)
+ src <- '
+ std::vector<std::string> s;
+ s.push_back("hello");
+ s.push_back("world");
+ return Rcpp::wrap(s);
+ '
+ hellofun <- cxxfunction(body = src, includes = '', plugin = 'Rcpp', verbose = FALSE)
+ test <- try(hellofun())
+ if(inherits(test, "try-error")) stop("hello world failed; ask for help on Rcpp list")
+
+ options(repos = c(getOption("repos"),
+ rstan = "http://rstan.org/repo/"))
+ install.packages("rstan", type = 'source')
+ library(rstan)
+ set_cppo("fast")
+ if (any(grepl("^darwin", R.version$os, ignore.case = TRUE))) {
+ cat('\nCC=clang', 'CXX=clang++ -arch x86_64 -ftemplate-depth-256',
+ file = "~/.R/Makevars", sep = "\n", append = TRUE)
+ }
+ return(invisible(NULL))
+ }
> install_rstan()
Removing package from ‘/Library/Frameworks/R.framework/Versions/3.1/Resources/library’
(as ‘lib’ is unspecified)
Error in remove.packages : there is no package called ‘rstan’
trying URL 'http://cran.rstudio.com/bin/macosx/contrib/3.1/inline_0.3.13.tgz'
Content type 'application/x-gzip' length 78503 bytes (76 KB)
opened URL
==================================================
downloaded 76 KB
trying URL 'http://cran.rstudio.com/bin/macosx/contrib/3.1/BH_1.55.0-3.tgz'
Content type 'application/x-gzip' length 7455235 bytes (7.1 MB)
opened URL
==================================================
downloaded 7.1 MB
trying URL 'http://cran.rstudio.com/bin/macosx/contrib/3.1/RcppEigen_0.3.2.4.0.tgz'
Content type 'application/x-gzip' length 3335332 bytes (3.2 MB)
opened URL
==================================================
downloaded 3.2 MB
The downloaded binary packages are in
/var/folders/0x/zkhg5kyd7j3199jkj76v9p340000gn/T//Rtmpk2CfrS/downloaded_packages
Error in install.packages : Updating loaded packages
Attaching package: ‘inline’
The following object is masked from ‘package:Rcpp’:
registerPlugin
trying URL 'http://rstan.org/repo/src/contrib/rstan_2.6.0.tar.gz'
Content type 'application/x-gzip' length 1423850 bytes (1.4 MB)
opened URL
==================================================
downloaded 1.4 MB
ERROR: failed to lock directory ‘/Library/Frameworks/R.framework/Versions/3.1/Resources/library’ for modifying
Try removing ‘/Library/Frameworks/R.framework/Versions/3.1/Resources/library/00LOCK-rstan’
Warning in install.packages :
installation of package ‘rstan’ had non-zero exit status
The downloaded source packages are in
‘/private/var/folders/0x/zkhg5kyd7j3199jkj76v9p340000gn/T/Rtmpk2CfrS/downloaded_packages’
Fejl i library(rstan) : there is no package called ‘rstan’
Called from: top level
Restarting R session...
> install.packages("Rcpp", type = "source")
trying URL 'http://cran.rstudio.com/src/contrib/Rcpp_0.11.5.tar.gz'
Content type 'application/x-gzip' length 2353791 bytes (2.2 MB)
opened URL
==================================================
downloaded 2.2 MB
* installing *source* package ‘Rcpp’ ...
** package ‘Rcpp’ successfully unpacked and MD5 sums checked
** libs
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include" -fPIC -mtune=core2 -g -O2 -c Date.cpp -o Date.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include" -fPIC -mtune=core2 -g -O2 -c Module.cpp -o Module.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include" -fPIC -mtune=core2 -g -O2 -c Rcpp_init.cpp -o Rcpp_init.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include" -fPIC -mtune=core2 -g -O2 -c api.cpp -o api.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include" -fPIC -mtune=core2 -g -O2 -c attributes.cpp -o attributes.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include" -fPIC -mtune=core2 -g -O2 -c barrier.cpp -o barrier.o
llvm-g++-4.2 -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -L/usr/local/lib -o Rcpp.so Date.o Module.o Rcpp_init.o api.o attributes.o barrier.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (Rcpp)
The downloaded source packages are in
‘/private/var/folders/0x/zkhg5kyd7j3199jkj76v9p340000gn/T/RtmpZSUb93/downloaded_packages’
次に rstan: を読み込んでみると、Rstanlibrary(rstan)というパッケージがないというメッセージが表示されます。
Rstan が私のために立候補しない理由を誰かが理解してくれることを願っています。