Closed MansMeg closed 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)
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[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) 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: 0.026165 seconds (Warm-up) # 0.023397 seconds (Sampling) # 0.049562 seconds (Total) SAMPLING FOR MODEL 'example' NOW (CHAIN 3). 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: 0.023488 seconds (Warm-up) # 0.019171 seconds (Sampling) # 0.042659 seconds (Total) SAMPLING FOR MODEL 'example' NOW (CHAIN 4). 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: 0.031504 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). ```*
Not a big deal
bgoodri
commented
9 years ago bgoodri
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)