在R中加载Rstan的问题

Question

我已经安装了Rtan的RStan。安装似乎已成功，但是当我加载该软件包并使用它时，我不断收到错误消息，指示未安装Rstan：

> 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

我有Mac OS.X 10.7.5。 我最近将R升级到3.1.3，并且使用R-studio作为接口。 对于Rstan的安装，我遵循此处的描述： https : //github.com/stan-dev/rstan/wiki/RStan-Mac-OS-X-Prerequisite-Installation-Instructions

我已经通过Apple Developer安装了X代码和命令行工具（Mac OS.X Lion），当我在R中检查是否已正确安装时，收到以下消息：

> 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  

在R中安装Stan时，出现以下消息：

> #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’

然后，我读入rstan： library(rstan)然后得到一条消息，即没有名为Rstan的软件包。

我希望有人能明白为什么Rstan不会为我竞选。

Answer 1

您从未加载过程序包 。 采用

library(rstan)

将程序包加载到当前的R会话中。

Answer 2

加载包裹

require("rstan")

要么

library("rstan")

使用require(rstan)失败，因为它试图从环境中名为rstan的对象中加载并且找不到该对象。 因此，您需要使用反引号。