stan-dev / rstan

RStan, the R interface to Stan
https://mc-stan.org
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Warning at installation (and example run) using R v. 3.2.0 using Mac OSX #169

Closed MansMeg closed 9 years ago

MansMeg commented 9 years ago

I don't know if this is a real problem, but before there where no warning. RStudio Version 0.99.446 Mac OSX 10.10.3 (14D136)

R version 3.2.0 (2015-04-16) -- "Full of Ingredients"
Copyright (C) 2015 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin13.4.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

[Workspace loaded from ~/Dropbox/Doktorandstudier/Forskning/DOLDA/.RData]

> Sys.setenv(MAKEFLAGS = "-j4")
> 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", "RcppEigen"))
+   devtools::install_url("http://cran.r-project.org/src/contrib/Archive/BH/BH_1.55.0-3.tar.gz")
+   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', dependencies = FALSE)
+   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/3.2/Resources/library’
(as ‘lib’ is unspecified)
Error in remove.packages : there is no package called ‘rstan’
trying URL 'http://cran.rstudio.com/bin/macosx/mavericks/contrib/3.2/inline_0.3.14.tgz'
Content type 'application/x-gzip' length 90710 bytes (88 KB)
==================================================
downloaded 88 KB

trying URL 'http://cran.rstudio.com/bin/macosx/mavericks/contrib/3.2/RcppEigen_0.3.2.4.0.tgz'
Content type 'application/x-gzip' length 3900020 bytes (3.7 MB)
==================================================
downloaded 3.7 MB

The downloaded binary packages are in
    /var/folders/nx/psn9dtzd1m19wvf5_cyq2pl40000gn/T//RtmpYfgQwT/downloaded_packages
Downloading package from url: http://cran.r-project.org/src/contrib/Archive/BH/BH_1.55.0-3.tar.gz
Installing BH
'/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file --no-environ --no-save --no-restore  \
  CMD INSTALL  \
  '/private/var/folders/nx/psn9dtzd1m19wvf5_cyq2pl40000gn/T/RtmpYfgQwT/devtools2ca57ed0bc4d/BH'  \
  --library='/Library/Frameworks/R.framework/Versions/3.2/Resources/library' --install-tests 

* installing *source* package ‘BH’ ...
** package ‘BH’ successfully unpacked and MD5 sums checked
** inst
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (BH)
Error in install.packages : Updating loaded packages

Attaching package: ‘Rcpp’

The following object is masked from ‘package:inline’:

    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)
==================================================
downloaded 1.4 MB

* installing *source* package ‘rstan’ ...
** package ‘rstan’ successfully unpacked and MD5 sums checked
** libs
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"../inst/include/stansrc"   -I"../inst/include"  -DBOOST_RESULT_OF_USE_TR1 -DBOOST_NO_DECLTYPE -DBOOST_DISABLE_ASSERTS -ftemplate-depth-256  -Wno-unused-function -Wno-uninitialized -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/RcppEigen/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/BH/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c stanc.cpp -o stanc.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"../inst/include/stansrc"   -I"../inst/include"  -DBOOST_RESULT_OF_USE_TR1 -DBOOST_NO_DECLTYPE -DBOOST_DISABLE_ASSERTS -ftemplate-depth-256  -Wno-unused-function -Wno-uninitialized -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/RcppEigen/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/BH/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c chains.cpp -o chains.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"../inst/include/stansrc"   -I"../inst/include"  -DBOOST_RESULT_OF_USE_TR1 -DBOOST_NO_DECLTYPE -DBOOST_DISABLE_ASSERTS -ftemplate-depth-256  -Wno-unused-function -Wno-uninitialized -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/RcppEigen/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/BH/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c misc.cpp -o misc.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"../inst/include/stansrc"   -I"../inst/include"  -DBOOST_RESULT_OF_USE_TR1 -DBOOST_NO_DECLTYPE -DBOOST_DISABLE_ASSERTS -ftemplate-depth-256  -Wno-unused-function -Wno-uninitialized -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/RcppEigen/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/BH/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c init.cpp -o init.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"../inst/include/stansrc"   -I"../inst/include"  -DBOOST_RESULT_OF_USE_TR1 -DBOOST_NO_DECLTYPE -DBOOST_DISABLE_ASSERTS -ftemplate-depth-256  -Wno-unused-function -Wno-uninitialized -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/RcppEigen/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/BH/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c gm__ast_def.cpp -o gm__ast_def.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"../inst/include/stansrc"   -I"../inst/include"  -DBOOST_RESULT_OF_USE_TR1 -DBOOST_NO_DECLTYPE -DBOOST_DISABLE_ASSERTS -ftemplate-depth-256  -Wno-unused-function -Wno-uninitialized -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/RcppEigen/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/BH/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c gm__grammars__bare_type_grammar_inst.cpp -o gm__grammars__bare_type_grammar_inst.o
In file included from chains.cpp:2:
In file included from ../inst/include/stansrc/stan/math/matrix.hpp:7:
In file included from ../inst/include/stansrc/stan/math/matrix/append_row.hpp:5:
In file included from ../inst/include/stansrc/stan/meta/traits.hpp:11:
In file included from ../inst/include/stansrc/stan/agrad/rev/var.hpp:5:
In file included from ../inst/include/stansrc/stan/agrad/rev/vari.hpp:7:
../inst/include/stansrc/stan/agrad/rev/chainable.hpp:87:17: warning: unused function 'set_zero_all_adjoints' [-Wunused-function]
    static void set_zero_all_adjoints() {
                ^
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"../inst/include/stansrc"   -I"../inst/include"  -DBOOST_RESULT_OF_USE_TR1 -DBOOST_NO_DECLTYPE -DBOOST_DISABLE_ASSERTS -ftemplate-depth-256  -Wno-unused-function -Wno-uninitialized -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/RcppEigen/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/BH/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c gm__grammars__expression07_grammar_inst.cpp -o gm__grammars__expression07_grammar_inst.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"../inst/include/stansrc"   -I"../inst/include"  -DBOOST_RESULT_OF_USE_TR1 -DBOOST_NO_DECLTYPE -DBOOST_DISABLE_ASSERTS -ftemplate-depth-256  -Wno-unused-function -Wno-uninitialized -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/RcppEigen/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/BH/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c gm__grammars__expression_grammar_inst.cpp -o gm__grammars__expression_grammar_inst.o
1 warning generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"../inst/include/stansrc"   -I"../inst/include"  -DBOOST_RESULT_OF_USE_TR1 -DBOOST_NO_DECLTYPE -DBOOST_DISABLE_ASSERTS -ftemplate-depth-256  -Wno-unused-function -Wno-uninitialized -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/RcppEigen/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/BH/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c gm__grammars__functions_grammar_inst.cpp -o gm__grammars__functions_grammar_inst.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"../inst/include/stansrc"   -I"../inst/include"  -DBOOST_RESULT_OF_USE_TR1 -DBOOST_NO_DECLTYPE -DBOOST_DISABLE_ASSERTS -ftemplate-depth-256  -Wno-unused-function -Wno-uninitialized -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/RcppEigen/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/BH/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c gm__grammars__program_grammar_inst.cpp -o gm__grammars__program_grammar_inst.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"../inst/include/stansrc"   -I"../inst/include"  -DBOOST_RESULT_OF_USE_TR1 -DBOOST_NO_DECLTYPE -DBOOST_DISABLE_ASSERTS -ftemplate-depth-256  -Wno-unused-function -Wno-uninitialized -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/RcppEigen/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/BH/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c gm__grammars__statement_2_grammar_inst.cpp -o gm__grammars__statement_2_grammar_inst.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"../inst/include/stansrc"   -I"../inst/include"  -DBOOST_RESULT_OF_USE_TR1 -DBOOST_NO_DECLTYPE -DBOOST_DISABLE_ASSERTS -ftemplate-depth-256  -Wno-unused-function -Wno-uninitialized -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/RcppEigen/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/BH/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c gm__grammars__statement_grammar_inst.cpp -o gm__grammars__statement_grammar_inst.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"../inst/include/stansrc"   -I"../inst/include"  -DBOOST_RESULT_OF_USE_TR1 -DBOOST_NO_DECLTYPE -DBOOST_DISABLE_ASSERTS -ftemplate-depth-256  -Wno-unused-function -Wno-uninitialized -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/RcppEigen/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/BH/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c gm__grammars__term_grammar_inst.cpp -o gm__grammars__term_grammar_inst.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"../inst/include/stansrc"   -I"../inst/include"  -DBOOST_RESULT_OF_USE_TR1 -DBOOST_NO_DECLTYPE -DBOOST_DISABLE_ASSERTS -ftemplate-depth-256  -Wno-unused-function -Wno-uninitialized -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/RcppEigen/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/BH/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c gm__grammars__var_deccls_grammar_inst.cpp -o gm__grammars__var_deccls_grammar_inst.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"../inst/include/stansrc"   -I"../inst/include"  -DBOOST_RESULT_OF_USE_TR1 -DBOOST_NO_DECLTYPE -DBOOST_DISABLE_ASSERTS -ftemplate-depth-256  -Wno-unused-function -Wno-uninitialized -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/RcppEigen/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/BH/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c gm__grammars__whitespace_grammar_inst.cpp -o gm__grammars__whitespace_grammar_inst.o
clang++ -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 -o rstan.so stanc.o chains.o misc.o init.o gm__ast_def.o gm__grammars__bare_type_grammar_inst.o gm__grammars__expression07_grammar_inst.o gm__grammars__expression_grammar_inst.o gm__grammars__functions_grammar_inst.o gm__grammars__program_grammar_inst.o gm__grammars__statement_2_grammar_inst.o gm__grammars__statement_grammar_inst.o gm__grammars__term_grammar_inst.o gm__grammars__var_deccls_grammar_inst.o gm__grammars__whitespace_grammar_inst.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.2/Resources/library/rstan/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 (rstan)

The downloaded source packages are in
    ‘/private/var/folders/nx/psn9dtzd1m19wvf5_cyq2pl40000gn/T/RtmpYfgQwT/downloaded_packages’

Restarting R session...

> install.packages("Rcpp", type = "source")
trying URL 'http://cran.rstudio.com/src/contrib/Rcpp_0.11.6.tar.gz'
Content type 'application/x-gzip' length 2352221 bytes (2.2 MB)
==================================================
downloaded 2.2 MB

* installing *source* package ‘Rcpp’ ...
** package ‘Rcpp’ successfully unpacked and MD5 sums checked
** libs
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include/ -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c Date.cpp -o Date.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include/ -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c Module.cpp -o Module.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include/ -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c Rcpp_init.cpp -o Rcpp_init.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include/ -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c api.cpp -o api.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include/ -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c attributes.cpp -o attributes.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include/ -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c barrier.cpp -o barrier.o
clang++ -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 -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/3.2/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/nx/psn9dtzd1m19wvf5_cyq2pl40000gn/T/Rtmp26iu5l/downloaded_packages’
> 
> schools_dat <- list(J = 8, 
+                     y = c(28,  8, -3,  7, -1,  1, 18, 12),
+                     sigma = c(15, 10, 16, 11,  9, 11, 10, 18))
> fit <- stan(file = 'RScript/example.stan', data = schools_dat, 
+             iter = 1000, chains = 4)

TRANSLATING MODEL 'example' FROM Stan CODE TO C++ CODE NOW.
COMPILING THE C++ CODE FOR MODEL 'example' NOW.
In file included from file2d5819d2c910.cpp:8:
In file included from /Library/Frameworks/R.framework/Versions/3.2/Resources/library/rstan/include//stansrc/stan/model/model_header.hpp:17:
In file included from /Library/Frameworks/R.framework/Versions/3.2/Resources/library/rstan/include//stansrc/stan/agrad/rev.hpp:5:
/Library/Frameworks/R.framework/Versions/3.2/Resources/library/rstan/include//stansrc/stan/agrad/rev/chainable.hpp:87:17: warning: 'static' function 'set_zero_all_adjoints' declared in header file should be declared 'static inline' [-Wunneeded-internal-declaration]
    static void set_zero_all_adjoints() {
                ^
In file included from file2d5819d2c910.cpp:8:
In file included from /Library/Frameworks/R.framework/Versions/3.2/Resources/library/rstan/include//stansrc/stan/model/model_header.hpp:21:
/Library/Frameworks/R.framework/Versions/3.2/Resources/library/rstan/include//stansrc/stan/io/dump.hpp:26:14: warning: function 'product' is not needed and will not be emitted [-Wunneeded-internal-declaration]
      size_t product(std::vector<size_t> dims) {
             ^
2 warnings generated.

SAMPLING FOR MODEL 'example' NOW (CHAIN 1).

Iteration:   1 / 1000 [  0%]  (Warmup)
Iteration: 100 / 1000 [ 10%]  (Warmup)
Iteration: 200 / 1000 [ 20%]  (Warmup)
Iteration: 300 / 1000 [ 30%]  (Warmup)
Iteration: 400 / 1000 [ 40%]  (Warmup)
Iteration: 500 / 1000 [ 50%]  (Warmup)
Iteration: 501 / 1000 [ 50%]  (Sampling)
Iteration: 600 / 1000 [ 60%]  (Sampling)
Iteration: 700 / 1000 [ 70%]  (Sampling)
Iteration: 800 / 1000 [ 80%]  (Sampling)
Iteration: 900 / 1000 [ 90%]  (Sampling)
Iteration: 1000 / 1000 [100%]  (Sampling)
#  Elapsed Time: 0.025 seconds (Warm-up)
#                0.02714 seconds (Sampling)
#                0.05214 seconds (Total)

SAMPLING FOR MODEL 'example' NOW (CHAIN 2).

Iteration:   1 / 1000 [  0%]  (Warmup)
Iteration: 100 / 1000 [ 10%]  (Warmup)
Iteration: 200 / 1000 [ 20%]  (Warmup)
Iteration: 300 / 1000 [ 30%]  (Warmup)
Iteration: 400 / 1000 [ 40%]  (Warmup)
Iteration: 500 / 1000 [ 50%]  (Warmup)
Iteration: 501 / 1000 [ 50%]  (Sampling)
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#  Elapsed Time: 0.026165 seconds (Warm-up)
#                0.023397 seconds (Sampling)
#                0.049562 seconds (Total)

SAMPLING FOR MODEL 'example' NOW (CHAIN 3).

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#  Elapsed Time: 0.023488 seconds (Warm-up)
#                0.019171 seconds (Sampling)
#                0.042659 seconds (Total)

SAMPLING FOR MODEL 'example' NOW (CHAIN 4).

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#  Elapsed Time: 0.031504 seconds (Warm-up)
#                0.02348 seconds (Sampling)
#                0.054984 seconds (Total)

> fit
Inference for Stan model: example.
4 chains, each with iter=1000; warmup=500; thin=1; 
post-warmup draws per chain=500, total post-warmup draws=2000.

          mean se_mean   sd   2.5%   25%   50%   75% 97.5% n_eff Rhat
mu        8.47    0.47 5.97  -1.64  4.85  7.94 11.48 21.61   160 1.03
tau       7.28    0.41 6.16   0.36  2.87  5.83  9.85 23.36   224 1.01
eta[1]    0.41    0.02 0.92  -1.41 -0.17  0.42  1.02  2.25  1416 1.00
eta[2]   -0.03    0.03 0.88  -1.77 -0.61 -0.03  0.52  1.73  1105 1.00
eta[3]   -0.18    0.02 0.95  -2.01 -0.80 -0.21  0.43  1.79  1895 1.00
eta[4]   -0.08    0.03 0.87  -1.73 -0.64 -0.11  0.47  1.69  1097 1.00
eta[5]   -0.37    0.02 0.82  -1.90 -0.91 -0.39  0.13  1.35  1189 1.01
eta[6]   -0.26    0.02 0.87  -1.92 -0.86 -0.28  0.32  1.49  1457 1.00
eta[7]    0.34    0.02 0.84  -1.30 -0.19  0.34  0.89  1.99  1274 1.00
eta[8]    0.06    0.02 0.96  -1.75 -0.63  0.05  0.73  1.85  1641 1.00
theta[1] 12.14    0.50 8.88  -0.82  6.19 10.49 16.48 35.15   313 1.01
theta[2]  7.95    0.15 6.48  -5.18  3.83  7.73 11.89 20.87  1810 1.00
theta[3]  6.31    0.20 7.78 -10.27  2.11  6.34 10.94 22.13  1472 1.00
theta[4]  7.50    0.17 6.59  -5.56  3.58  7.33 11.56 20.53  1592 1.00
theta[5]  4.94    0.16 6.48  -9.77  1.20  5.37  9.13 17.05  1571 1.00
theta[6]  5.84    0.18 7.03  -8.95  2.05  6.23 10.08 18.84  1579 1.00
theta[7] 11.06    0.28 6.99  -0.83  6.29 10.25 15.09 26.14   636 1.00
theta[8]  8.79    0.56 9.11  -8.33  3.80  8.19 13.18 28.45   268 1.01
lp__     -4.68    0.11 2.53 -10.35 -6.28 -4.37 -2.80 -0.53   578 1.01

Samples were drawn using NUTS(diag_e) at Mon Jun 22 09:29:26 2015.
For each parameter, n_eff is a crude measure of effective sample size,
and Rhat is the potential scale reduction factor on split chains (at 
convergence, Rhat=1).
```*
bgoodri commented 9 years ago

Not a big deal