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Compilation ERROR, function(s)/method(s) not created! #527

Closed yhwhu2008 closed 6 years ago

yhwhu2008 commented 6 years ago

Summary:

Cannot compile rstan.

Description:

I tried the 8schools example of rstan: [https://cran.r-project.org/web/packages/rstan/vignettes/rstan.html#typical-workflow] and ran into problems.

Reproducible Steps:

schools_data <- list(J = 8, y = c(28, 8, -3, 7, -1, 1, 18, 12), sigma = c(15, 10, 16, 11, 9, 11, 10, 18))

library(rstan) fit1 <- stan( file = "8schools.stan", # Stan program data = schools_data, # named list of data chains = 4, # number of Markov chains warmup = 1000, # number of warmup iterations per chain iter = 2000, # total number of iterations per chain cores = 2, # number of cores (using 2 just for the vignette) refresh = 1000 # show progress every 'refresh' iterations )

Current Output:

Error in compileCode(f, code, language = language, verbose = verbose) : Compilation ERROR, function(s)/method(s) not created! In file included from C:/Program Files/R/R-3.4.0/library/BH/include/boost/config.hpp:39:0, from C:/Program Files/R/R-3.4.0/library/BH/include/boost/math/tools/config.hpp:13, from C:/Program Files/R/R-3.4.0/library/StanHeaders/include/stan/math/rev/core/var.hpp:7, from C:/Program Files/R/R-3.4.0/library/StanHeaders/include/stan/math/rev/core/gevv_vvv_vari.hpp:5, from C:/Program Files/R/R-3.4.0/library/StanHeaders/include/stan/math/rev/core.hpp:12, from C:/Program Files/R/R-3.4.0/library/StanHeaders/include/stan/math/rev/mat.hpp:4, from C:/Program Files/R/R-3.4.0/library/StanHeaders/include/stan/math.hpp:4, from C:/Program Files/R/R-3.4.0/library/StanHeaders/include/src/stan/model/model_header.hpp:4, from file2fcc6cb655ab.cpp:8: C:/Program Files/R/R-3.4.0/library/BH/include/boost/config/comp In addition: Warning messages: 1: In readLines(file, warn = TRUE) : incomplete final line found on 'C:\Users\kgvp043\Documents\8schools.stan' 2: running command 'C:/PROGRA~1/R/R-34~1.0/bin/x64/R CMD SHLIB file2fcc6cb655ab.cpp 2> file2fcc6cb655ab.cpp.err.txt' had status 1

Expected Output:

If applicable, the output you expected from RStan.

RStan Version:

2.17.3

R Version:

3.4.0

Operating System:

win10

bgoodri commented 6 years ago

It looks as if you do not have the C++ toolchain installed correctly. Does it work if you do the test from the wiki?

fx <- inline::cxxfunction( signature(x = "integer", y = "numeric" ) , '

return ScalarReal( INTEGER(x)[0] * REAL(y)[0] ) ;' )

fx( 2L, 5 ) # should be 10

On Thu, May 17, 2018 at 2:07 PM, yhwhu2008 notifications@github.com wrote:

Summary:

Cannot compile rstan. Description:

I tried the 8schools example of rstan: [https://cran.r-project.org/ web/packages/rstan/vignettes/rstan.html#typical-workflow] and ran into problems. Reproducible Steps:

schools_data <- list(J = 8, y = c(28, 8, -3, 7, -1, 1, 18, 12), sigma = c(15, 10, 16, 11, 9, 11, 10, 18))

library(rstan) fit1 <- stan( file = "8schools.stan", # Stan program data = schools_data, # named list of data chains = 4, # number of Markov chains warmup = 1000, # number of warmup iterations per chain iter = 2000, # total number of iterations per chain cores = 2, # number of cores (using 2 just for the vignette) refresh = 1000 # show progress every 'refresh' iterations ) Current Output:

Error in compileCode(f, code, language = language, verbose = verbose) : Compilation ERROR, function(s)/method(s) not created! In file included from C:/Program Files/R/R-3.4.0/library/BH/include/boost/config.hpp:39:0, from C:/Program Files/R/R-3.4.0/library/BH/include/boost/math/tools/ config.hpp:13, from C:/Program Files/R/R-3.4.0/library/StanHeaders/include/stan/math/ rev/core/var.hpp:7, from C:/Program Files/R/R-3.4.0/library/StanHeaders/include/stan/math/ rev/core/gevv_vvv_vari.hpp:5, from C:/Program Files/R/R-3.4.0/library/StanHeaders/include/stan/math/ rev/core.hpp:12, from C:/Program Files/R/R-3.4.0/library/StanHeaders/include/stan/math/ rev/mat.hpp:4, from C:/Program Files/R/R-3.4.0/library/StanHeaders/include/stan/math. hpp:4, from C:/Program Files/R/R-3.4.0/library/StanHeaders/include/src/stan/ model/model_header.hpp:4, from file2fcc6cb655ab.cpp:8: C:/Program Files/R/R-3.4.0/library/BH/include/boost/config/comp In addition: Warning messages: 1: In readLines(file, warn = TRUE) : incomplete final line found on 'C:\Users\kgvp043\Documents\8schools.stan' 2: running command 'C:/PROGRA1/R/R-341.0/bin/x64/R CMD SHLIB file2fcc6cb655ab.cpp 2> file2fcc6cb655ab.cpp.err.txt' had status 1 Expected Output:

If applicable, the output you expected from RStan. RStan Version:

The version of RStan you are running (e.g., from packageVersion("rstan")) R Version:

2.17.3 Operating System:

win10

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yhwhu2008 commented 6 years ago

Hi, I solved this problem by using R 3.3.3 and rtools 33. But I have another issue now. I tried to use "torsten" and ran the example codes. But it's like the functions in torsten cannot be used.

library("rstan") modelName = 'TwoCptModel' data <- read_rdump(file.path(modelDir, paste0(modelName,".data.R"))) init <- function(){ list(CL = exp(rnorm(1, log(10), 0.2)), Q = exp(rnorm(1, log(20), 0.2)), V1 = exp(rnorm(1, log(70), 0.2)), V2 = exp(rnorm(1, log(70), 0.2)), ka = exp(rnorm(1, log(2), 0.2)), ke0 = exp(rnorm(1,log(1),0.2)), EC50 = exp(rnorm(1,log(100),0.2)), sigma = 0.5, sigmaResp = 20) } parametersToPlot <- c("CL", "Q", "V1", "V2", "ka", "sigma")

otherRVs <- c("cObsPred")

parameters <- c(parametersToPlot, otherRVs) parametersToPlot <- c("lp__", parametersToPlot)

nChains <- 4 nPost <- 1000 ## Number of post-warm-up samples per chain after thinning nBurn <- 1000 ## Number of warm-up samples per chain after thinning nThin <- 1 nIter <- (nBurn + nPost) nThin nBurnin <- nBurn nThin

fit <- stan(file = file.path(modelDir, paste(modelName, ".stan", sep = "")), data = data, pars = parameters, iter = nIter, warmup = nBurnin, thin = nThin, init = init, chains = nChains, cores = min(nChains, parallel::detectCores()))

And I have the following output:

SYNTAX ERROR, MESSAGE(S) FROM PARSER:

No matches for:

PKModelTwoCpt(real[], real[], real[], real[], int[], int[], int[], int[], real[], real[], real[])

Function PKModelTwoCpt not found. error in 'model3b0c610a18a3_TwoCptModel' at line 69, column 21

67: // compartment at each event.
68: x = PKModelTwoCpt(time, amt, rate, ii, evid, cmt, addl, ss,
69: theta, biovar, tlag);
                        ^
70:

Error in stanc(file = file, model_code = model_code, model_name = model_name, : failed to parse Stan model 'TwoCptModel' due to the above error. In addition: Warning message: In readLines(file, warn = TRUE) : incomplete final line found on ''

bgoodri commented 6 years ago

Torsten is not included in rstan or StanHeaders.

danrawly commented 6 years ago

Hi @bgoodri, I have the same error as the original post, so have tried to run your line of test code and get an error, could you help?

fx <- inline::cxxfunction( signature(x = "integer", y = "numeric" ) , '

  • return ScalarReal( INTEGER(x)[0] * REAL(y)[0] ) ;' ) In file included from fileb397678dcb48.cpp:3: In file included from /Library/Frameworks/R.framework/Resources/include/R.h:47: In file included from /usr/local/clang4/bin/../include/c++/v1/cstdlib:86: /usr/local/clang4/bin/../include/c++/v1/stdlib.h:94:15: fatal error: 'stdlib.h' file not found

    include_next

    ^~~~~~ 1 error generated. make: *** [fileb397678dcb48.o] Error 1

ERROR(s) during compilation: source code errors or compiler configuration errors!

Program source: 1: 2: // includes from the plugin 3: #include <R.h> 4: #include 5: #include <R_ext/Error.h> 6: 7: 8: // user includes 9: 10: 11: // declarations 12: extern "C" { 13: SEXP fileb397678dcb48( SEXP x, SEXP y) ; 14: } 15: 16: // definition 17: 18: SEXP fileb397678dcb48( SEXP x, SEXP y ){ 19: 20: 21: return ScalarReal( INTEGER(x)[0] * REAL(y)[0] ) ; 22: Rf_warning("your C++ program does not return anything"); 23: return R_NilValue ; 24: } 25: 26: Error in compileCode(f, code, language = language, verbose = verbose) : Compilation ERROR, function(s)/method(s) not created! In file included from fileb397678dcb48.cpp:3: In file included from /Library/Frameworks/R.framework/Resources/include/R.h:47: In file included from /usr/local/clang4/bin/../include/c++/v1/cstdlib:86: /usr/local/clang4/bin/../include/c++/v1/stdlib.h:94:15: fatal error: 'stdlib.h' file not found

include_next 

          ^~~~~~~~~~

1 error generated. make: *** [fileb397678dcb48.o] Error 1 In addition: Warning message: running command '/Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB fileb397678dcb48.cpp 2> fileb397678dcb48.cpp.err.txt' had status 1

What should I do next?

bgoodri commented 6 years ago

What is contained in the file ~/.R/Makevars ?

On Mon, Aug 6, 2018 at 5:29 PM Daniel Rawlings notifications@github.com wrote:

Hi @bgoodri https://github.com/bgoodri, I have the same error as the original post, so have tried to run your line of test code and get an error, could you help?

fx <- inline::cxxfunction( signature(x = "integer", y = "numeric" ) , '

-

                      return ScalarReal( INTEGER(x)[0] * REAL(y)[0] ) ;' )

In file included from fileb397678dcb48.cpp:3: In file included from /Library/Frameworks/R.framework/Resources/include/R.h:47: In file included from /usr/local/clang4/bin/../include/c++/v1/cstdlib:86: /usr/local/clang4/bin/../include/c++/v1/stdlib.h:94:15: fatal error: 'stdlib.h' file not found

include_next

^~~~~~ 1 error generated. make: *** [fileb397678dcb48.o] Error 1

ERROR(s) during compilation: source code errors or compiler configuration errors!

Program source: 1: 2: // includes from the plugin 3: #include <R.h> 4: #include 5: #include <R_ext/Error.h> 6: 7: 8: // user includes 9: 10: 11: // declarations 12: extern "C" { 13: SEXP fileb397678dcb48( SEXP x, SEXP y) ; 14: } 15: 16: // definition 17: 18: SEXP fileb397678dcb48( SEXP x, SEXP y ){ 19: 20: 21: return ScalarReal( INTEGER(x)[0] * REAL(y)[0] ) ; 22: Rf_warning("your C++ program does not return anything"); 23: return R_NilValue ; 24: } 25: 26: Error in compileCode(f, code, language = language, verbose = verbose) : Compilation ERROR, function(s)/method(s) not created! In file included from fileb397678dcb48.cpp:3: In file included from /Library/Frameworks/R.framework/Resources/include/R.h:47: In file included from /usr/local/clang4/bin/../include/c++/v1/cstdlib:86: /usr/local/clang4/bin/../include/c++/v1/stdlib.h:94:15: fatal error: 'stdlib.h' file not found

include_next

^~~~~~ 1 error generated. make: *** [fileb397678dcb48.o] Error 1 In addition: Warning message: running command '/Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB fileb397678dcb48.cpp 2> fileb397678dcb48.cpp.err.txt' had status 1

What should I do next?

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danrawly commented 6 years ago

The following text is in the file:

The following statements are required to use the clang4 binary

CC=/usr/local/clang4/bin/clang CXX=/usr/local/clang4/bin/clang++ CXX1X=/usr/local/clang4/bin/clang++ CXX98=/usr/local/clang4/bin/clang++ CXX11=/usr/local/clang4/bin/clang++ CXX14=/usr/local/clang4/bin/clang++ CXX17=/usr/local/clang4/bin/clang++ LDFLAGS=-L/usr/local/clang4/lib

End clang4 inclusion statements

The following statement changes the Fortran linking path

FLIBS=-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin16/6.3.0

End Fortran linking path statement

cimentadaj commented 6 years ago

I was receiving exactly the same error you have and just reinstalled clang in terminal with xcode-select --install and 

fx <- inline::cxxfunction( signature(x = "integer", y = "numeric" ) , '
    return ScalarReal( INTEGER(x)[0] * REAL(y)[0] ) ;
' )

fx( 2L, 5 ) # should be 10

was able to ran seamlessly.

MattMalis commented 6 years ago

I have the same problem from the original post. The test:

fx <- inline::cxxfunction( signature(x = "integer", y = "numeric" ) , '

    return ScalarReal( INTEGER(x)[0] * REAL(y)[0] ) ;' )
fx( 2L, 5 )

does return 10. Does anyone have a solution that can make rstan work?

bgoodri commented 6 years ago

What is your error message? I suspect it is slightly different from the one in the OP.

On Thu, Oct 11, 2018 at 1:09 PM MattMalis notifications@github.com wrote:

I have the same problem from the original post. The test:

fx <- inline::cxxfunction( signature(x = "integer", y = "numeric" ) , '

return ScalarReal( INTEGER(x)[0] * REAL(y)[0] ) ;' ) fx( 2L, 5 )

does return 10. Does anyone have a solution that can make rstan work?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/stan-dev/rstan/issues/527#issuecomment-429039412, or mute the thread https://github.com/notifications/unsubscribe-auth/ADOrqiqguVVXalOlUa1AS4F8ZshEAxLpks5uj3tjgaJpZM4UDhzC .

MattMalis commented 6 years ago

For the full reproducible example:

> rm(list=ls())
> library(rstan)
> set.seed(12345)
> p = 0.4
> N = 15
> (y <- rbinom(n = N, size = 1, prob = p))
 [1] 1 1 1 1 0 0 0 0 1 1 0 0 1 0 0
> modstring <- '
+ data {
+   int<lower=0> N ;
+   int<lower=0, upper=1> y[N] ;
+ }
+ 
+ parameters {
+   real<lower=0,upper=1> theta;
+ }
+ 
+ model {
+   theta ~ beta(1, 1) ;
+   y ~ bernoulli(theta) ;
+ }
+ '
> modfit <- rstan::stan(model_code = modstring, data = list(N = N, y = y),
+                chains = 3, iter = 5000, warmup = 1000, thin = 1, seed = 12345)
In file included from file337116bc25.cpp:8:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/src/stan/model/model_header.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math/rev/core.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math/rev/core/autodiffstackstorage.hpp:4:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math/memory/stack_alloc.hpp:145:10: warning: 'auto' type specifier is a C++11 extension [-Wc++11-extensions]
    for (auto& block : blocks_)
         ^
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math/memory/stack_alloc.hpp:145:22: warning: range-based for loop is a C++11 extension [-Wc++11-extensions]
    for (auto& block : blocks_)
                     ^
In file included from file337116bc25.cpp:8:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/src/stan/model/model_header.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math/rev/core.hpp:4:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math/rev/core/autodiffstackstorage.hpp:47:69: warning: deleted function definitions are a C++11 extension [-Wc++11-extensions]
    AutodiffStackStorage &operator=(const AutodiffStackStorage &) = delete;
                                                                    ^
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math/rev/core/autodiffstackstorage.hpp:60:30: warning: deleted function definitions are a C++11 extension [-Wc++11-extensions]
  AutodiffStackSingleton() = delete;
                             ^
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math/rev/core/autodiffstackstorage.hpp:61:71: warning: deleted function definitions are a C++11 extension [-Wc++11-extensions]
  explicit AutodiffStackSingleton(AutodiffStackSingleton_t const &) = delete;
                                                                      ^
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math/rev/core/autodiffstackstorage.hpp:62:73: warning: deleted function definitions are a C++11 extension [-Wc++11-extensions]
  AutodiffStackSingleton &operator=(const AutodiffStackSingleton_t &) = delete;
                                                                        ^
In file included from file337116bc25.cpp:8:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/src/stan/model/model_header.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math/rev/core.hpp:12:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math/rev/core/gevv_vvv_vari.hpp:5:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math/rev/core/var.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include/boost/math/tools/config.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include/boost/config.hpp:39:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include/boost/config/compiler/clang.hpp:200:11: warning: 'BOOST_NO_CXX11_RVALUE_REFERENCES' macro redefined [-Wmacro-redefined]
#  define BOOST_NO_CXX11_RVALUE_REFERENCES
          ^
<command line>:6:9: note: previous definition is here
#define BOOST_NO_CXX11_RVALUE_REFERENCES 1
        ^
In file included from file337116bc25.cpp:8:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/src/stan/model/model_header.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math/rev/core.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math/rev/core/matrix_vari.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math/rev/mat/fun/Eigen_NumTraits.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/Dense:1:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/Core:531:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from file337116bc25.cpp:8:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/src/stan/model/model_header.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math/rev/core.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math/rev/core/matrix_vari.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math/rev/mat/fun/Eigen_NumTraits.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/Dense:2:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/LU:47:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from file337116bc25.cpp:8:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/src/stan/model/model_header.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math/rev/core.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math/rev/core/matrix_vari.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math/rev/mat/fun/Eigen_NumTraits.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/Dense:3:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/Cholesky:12:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/Jacobi:29:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from file337116bc25.cpp:8:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/src/stan/model/model_header.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math/rev/core.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math/rev/core/matrix_vari.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math/rev/mat/fun/Eigen_NumTraits.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/Dense:3:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/Cholesky:43:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from file337116bc25.cpp:8:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/src/stan/model/model_header.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math/rev/core.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math/rev/core/matrix_vari.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math/rev/mat/fun/Eigen_NumTraits.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/Dense:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/QR:17:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/Householder:27:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from file337116bc25.cpp:8:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/src/stan/model/model_header.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math/rev/core.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math/rev/core/matrix_vari.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math/rev/mat/fun/Eigen_NumTraits.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/Dense:5:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/SVD:48:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from file337116bc25.cpp:8:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/src/stan/model/model_header.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math/rev/core.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math/rev/core/matrix_vari.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math/rev/mat/fun/Eigen_NumTraits.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/Dense:6:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/Geometry:58:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from file337116bc25.cpp:8:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/src/stan/model/model_header.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math/rev/core.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math/rev/core/matrix_vari.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math/rev/mat/fun/Eigen_NumTraits.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/Dense:7:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/Eigenvalues:58:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from file337116bc25.cpp:8:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/src/stan/model/model_header.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math/rev/core.hpp:36:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math/rev/core/operator_unary_plus.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math/prim/scal/fun/constants.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include/boost/math/constants/constants.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include/boost/math/tools/convert_from_string.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include/boost/lexical_cast.hpp:32:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include/boost/lexical_cast/try_lexical_convert.hpp:42:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include/boost/lexical_cast/detail/converter_lexical.hpp:52:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include/boost/container/container_fwd.hpp:61:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include/boost/container/detail/std_fwd.hpp:27:1: warning: inline namespaces are a C++11 feature [-Wc++11-inline-namespace]
BOOST_MOVE_STD_NS_BEG
^
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include/boost/move/detail/std_ns_begin.hpp:18:34: note: expanded from macro 'BOOST_MOVE_STD_NS_BEG'
   #define BOOST_MOVE_STD_NS_BEG _LIBCPP_BEGIN_NAMESPACE_STD
                                 ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:399:52: note: expanded from macro '_LIBCPP_BEGIN_NAMESPACE_STD'
#define _LIBCPP_BEGIN_NAMESPACE_STD namespace std {inline namespace _LIBCPP_NAMESPACE {
                                                   ^
In file included from file337116bc25.cpp:8:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/src/stan/model/model_header.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math/rev/core.hpp:42:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math/rev/core/recover_memory.hpp:25:8: warning: 'auto' type specifier is a C++11 extension [-Wc++11-extensions]
  for (auto &x : ChainableStack::instance().var_alloc_stack_) {
       ^
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math/rev/core/recover_memory.hpp:25:16: warning: range-based for loop is a C++11 extension [-Wc++11-extensions]
  for (auto &x : ChainableStack::instance().var_alloc_stack_) {
               ^
In file included from file337116bc25.cpp:8:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/src/stan/model/model_header.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math/rev/core.hpp:44:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math/rev/core/set_zero_all_adjoints.hpp:15:8: warning: 'auto' type specifier is a C++11 extension [-Wc++11-extensions]
  for (auto &x : ChainableStack::instance().var_stack_)
       ^
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math/rev/core/set_zero_all_adjoints.hpp:15:16: warning: range-based for loop is a C++11 extension [-Wc++11-extensions]
  for (auto &x : ChainableStack::instance().var_stack_)
               ^
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math/rev/core/set_zero_all_adjoints.hpp:17:8: warning: 'auto' type specifier is a C++11 extension [-Wc++11-extensions]
  for (auto &x : ChainableStack::instance().var_nochain_stack_)
       ^
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math/rev/core/set_zero_all_adjoints.hpp:17:16: warning: range-based for loop is a C++11 extension [-Wc++11-extensions]
  for (auto &x : ChainableStack::instance().var_nochain_stack_)
               ^
In file included from file337116bc25.cpp:8:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/src/stan/model/model_header.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:12:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math/prim/mat.hpp:22:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math/prim/mat/meta/operands_and_partials.hpp:19:59: error: expected expression
class ops_partials_edge<ViewElt, Eigen::Matrix<Op, R, C>> {
                                                          ^
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math/prim/mat/meta/operands_and_partials.hpp:35:2: error: expected a type
};
 ^
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math/prim/mat/meta/operands_and_partials.hpp:38:70: error: expected expression
class ops_partials_edge<ViewElt, std::vector<Eigen::Matrix<Op, R, C>>> {
                                                                     ^
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math/prim/mat/meta/operands_and_partials.hpp:38:72: error: expected a type
class ops_partials_edge<ViewElt, std::vector<Eigen::Matrix<Op, R, C>>> {
                                                                       ^
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math/prim/mat/meta/operands_and_partials.hpp:53:2: error: expected a type
};
 ^
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math/prim/mat/meta/operands_and_partials.hpp:56:60: error: a space is required between consecutive right angle brackets (use '> >')
class ops_partials_edge<ViewElt, std::vector<std::vector<Op>>> {
                                                           ^~
                                                           > > 
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math/prim/mat/meta/operands_and_partials.hpp:58:68: error: a space is required between consecutive right angle brackets (use '> >')
  typedef empty_broadcast_array<ViewElt, std::vector<std::vector<Op>>>
                                                                   ^~
                                                                   > > 
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math/prim/mat/meta/operands_and_partials.hpp:61:63: error: a space is required between consecutive right angle brackets (use '> >')
  empty_broadcast_array<partials_t, std::vector<std::vector<Op>>> partials_vec_;
                                                              ^~
                                                              > > 
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math/prim/mat/meta/operands_and_partials.hpp:63:62: error: a space is required between consecutive right angle brackets (use '> >')
  explicit ops_partials_edge(const std::vector<std::vector<Op>> ops) {}
                                                             ^~
                                                             > >
In file included from file337116bc25.cpp:8:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/src/stan/model/model_header.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:12:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math/prim/mat.hpp:96:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/csr_extract_u.hpp:6:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/Sparse:26:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/SparseCore:66:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from file337116bc25.cpp:8:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/src/stan/model/model_header.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:12:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math/prim/mat.hpp:96:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/csr_extract_u.hpp:6:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/Sparse:27:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/OrderingMethods:71:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from file337116bc25.cpp:8:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/src/stan/model/model_header.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:12:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math/prim/mat.hpp:96:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/csr_extract_u.hpp:6:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/Sparse:29:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/SparseCholesky:43:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from file337116bc25.cpp:8:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/src/stan/model/model_header.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:12:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math/prim/mat.hpp:96:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/csr_extract_u.hpp:6:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/Sparse:32:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/SparseQR:35:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from file337116bc25.cpp:8:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/src/stan/model/model_header.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:12:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math/prim/mat.hpp:96:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/csr_extract_u.hpp:6:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/Sparse:33:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/IterativeLinearSolvers:46:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from file337116bc25.cpp:8:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/src/stan/model/model_header.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:12:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math/prim/mat.hpp:99:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/csr_matrix_times_vector.hpp:91:14: warning: range-based for loop is a C++11 extension [-Wc++11-extensions]
  for (int i : v)
             ^
In file included from file337116bc25.cpp:8:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/src/stan/model/model_header.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:12:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math/prim/mat.hpp:100:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/csr_to_dense_matrix.hpp:48:14: warning: range-based for loop is a C++11 extension [-Wc++11-extensions]
  for (int i : v)
             ^
In file included from file337116bc25.cpp:8:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/src/stan/model/model_header.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:12:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math/prim/mat.hpp:156:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/log_mix.hpp:178:26: error: expected expression
              .unaryExpr([](T_partials_return x) { return exp(x); });
                         ^
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/log_mix.hpp:262:24: error: expected expression
            .unaryExpr([](T_partials_return x) { return exp(x); });
                       ^
In file included from file337116bc25.cpp:8:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/src/stan/model/model_header.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:12:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math/prim/mat.hpp:161:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/matrix_exp.hpp:5:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/matrix_exp_2x2.hpp:21:13: warning: alias declarations are a C++11 extension [-Wc++11-extensions]
  using T = typename Mtype::Scalar;
            ^
In file included from file337116bc25.cpp:8:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/src/stan/model/model_header.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:12:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math/prim/mat.hpp:162:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/matrix_exp_multiply.hpp:5:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/matrix_exp_action_handler.hpp:20:10: error: unknown type name 'constexpr'
  static constexpr int p_max = 8;
         ^
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/matrix_exp_action_handler.hpp:20:20: error: expected member name or ';' after declaration specifiers
  static constexpr int p_max = 8;
  ~~~~~~~~~~~~~~~~ ^
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/matrix_exp_action_handler.hpp:21:10: error: unknown type name 'constexpr'
  static constexpr int m_max = 55;
         ^
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/matrix_exp_action_handler.hpp:21:20: error: expected member name or ';' after declaration specifiers
  static constexpr int m_max = 55;
  ~~~~~~~~~~~~~~~~ ^
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/matrix_exp_action_handler.hpp:22:10: error: unknown type name 'constexpr'
  static constexpr double tol = 1.1e-16;
         ^
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/matrix_exp_action_handler.hpp:22:20: error: expected member name or ';' after declaration specifiers
  static constexpr double tol = 1.1e-16;
  ~~~~~~~~~~~~~~~~ ^
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/matrix_exp_action_handler.hpp:25:29: error: function definition does not declare parameters
  const std::vector<double> theta_m_single_precision{
                            ^
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/matrix_exp_action_handler.hpp:28:29: error: function definition does not declare parameters
  const std::vector<double> theta_m_double_precision{
                            ^
fatal error: too many errors emitted, stopping now [-ferror-limit=]
30 warnings and 20 errors generated.
make: *** [file337116bc25.o] Error 1

ERROR(s) during compilation: source code errors or compiler configuration errors!

Program source:
  1: 
  2: // includes from the plugin
  3: 
  4: 
  5: // user includes
  6: #define STAN__SERVICES__COMMAND_HPP// Code generated by Stan version 2.17.0
  7: 
  8: #include <stan/model/model_header.hpp>
  9: 
 10: namespace model33733471a68_29d68658bae2087c6157562fc6a3f1bb_namespace {
 11: 
 12: using std::istream;
 13: using std::string;
 14: using std::stringstream;
 15: using std::vector;
 16: using stan::io::dump;
 17: using stan::math::lgamma;
 18: using stan::model::prob_grad;
 19: using namespace stan::math;
 20: 
 21: typedef Eigen::Matrix<double,Eigen::Dynamic,1> vector_d;
 22: typedef Eigen::Matrix<double,1,Eigen::Dynamic> row_vector_d;
 23: typedef Eigen::Matrix<double,Eigen::Dynamic,Eigen::Dynamic> matrix_d;
 24: 
 25: static int current_statement_begin__;
 26: 
 27: stan::io::program_reader prog_reader__() {
 28:     stan::io::program_reader reader;
 29:     reader.add_event(0, 0, "start", "model33733471a68_29d68658bae2087c6157562fc6a3f1bb");
 30:     reader.add_event(14, 14, "end", "model33733471a68_29d68658bae2087c6157562fc6a3f1bb");
 31:     return reader;
 32: }
 33: 
 34: class model33733471a68_29d68658bae2087c6157562fc6a3f1bb : public prob_grad {
 35: private:
 36:     int N;
 37:     vector<int> y;
 38: public:
 39:     model33733471a68_29d68658bae2087c6157562fc6a3f1bb(stan::io::var_context& context__,
 40:         std::ostream* pstream__ = 0)
 41:         : prob_grad(0) {
 42:         ctor_body(context__, 0, pstream__);
 43:     }
 44: 
 45:     model33733471a68_29d68658bae2087c6157562fc6a3f1bb(stan::io::var_context& context__,
 46:         unsigned int random_seed__,
 47:         std::ostream* pstream__ = 0)
 48:         : prob_grad(0) {
 49:         ctor_body(context__, random_seed__, pstream__);
 50:     }
 51: 
 52:     void ctor_body(stan::io::var_context& context__,
 53:                    unsigned int random_seed__,
 54:                    std::ostream* pstream__) {
 55:         boost::ecuyer1988 base_rng__ =
 56:           stan::services::util::create_rng(random_seed__, 0);
 57:         (void) base_rng__;  // suppress unused var warning
 58: 
 59:         current_statement_begin__ = -1;
 60: 
 61:         static const char* function__ = "model33733471a68_29d68658bae2087c6157562fc6a3f1bb_namespace::model33733471a68_29d68658bae2087c6157562fc6a3f1bb";
 62:         (void) function__;  // dummy to suppress unused var warning
 63:         size_t pos__;
 64:         (void) pos__;  // dummy to suppress unused var warning
 65:         std::vector<int> vals_i__;
 66:         std::vector<double> vals_r__;
 67:         double DUMMY_VAR__(std::numeric_limits<double>::quiet_NaN());
 68:         (void) DUMMY_VAR__;  // suppress unused var warning
 69: 
 70:         // initialize member variables
 71:         try {
 72:             current_statement_begin__ = 3;
 73:             context__.validate_dims("data initialization", "N", "int", context__.to_vec());
 74:             N = int(0);
 75:             vals_i__ = context__.vals_i("N");
 76:             pos__ = 0;
 77:             N = vals_i__[pos__++];
 78:             current_statement_begin__ = 4;
 79:             validate_non_negative_index("y", "N", N);
 80:             context__.validate_dims("data initialization", "y", "int", context__.to_vec(N));
 81:             validate_non_negative_index("y", "N", N);
 82:             y = std::vector<int>(N,int(0));
 83:             vals_i__ = context__.vals_i("y");
 84:             pos__ = 0;
 85:             size_t y_limit_0__ = N;
 86:             for (size_t i_0__ = 0; i_0__ < y_limit_0__; ++i_0__) {
 87:                 y[i_0__] = vals_i__[pos__++];
 88:             }
 89: 
 90:             // validate, data variables
 91:             current_statement_begin__ = 3;
 92:             check_greater_or_equal(function__,"N",N,0);
 93:             current_statement_begin__ = 4;
 94:             for (int k0__ = 0; k0__ < N; ++k0__) {
 95:                 check_greater_or_equal(function__,"y[k0__]",y[k0__],0);
 96:                 check_less_or_equal(function__,"y[k0__]",y[k0__],1);
 97:             }
 98:             // initialize data variables
 99: 
100: 
101:             // validate transformed data
102: 
103:             // validate, set parameter ranges
104:             num_params_r__ = 0U;
105:             param_ranges_i__.clear();
106:             current_statement_begin__ = 8;
107:             ++num_params_r__;
108:         } catch (const std::exception& e) {
109:             stan::lang::rethrow_located(e, current_statement_begin__, prog_reader__());
110:             // Next line prevents compiler griping about no return
111:             throw std::runtime_error("*** IF YOU SEE THIS, PLEASE REPORT A BUG ***");
112:         }
113:     }
114: 
115:     ~model33733471a68_29d68658bae2087c6157562fc6a3f1bb() { }
116: 
117: 
118:     void transform_inits(const stan::io::var_context& context__,
119:                          std::vector<int>& params_i__,
120:                          std::vector<double>& params_r__,
121:                          std::ostream* pstream__) const {
122:         stan::io::writer<double> writer__(params_r__,params_i__);
123:         size_t pos__;
124:         (void) pos__; // dummy call to supress warning
125:         std::vector<double> vals_r__;
126:         std::vector<int> vals_i__;
127: 
128:         if (!(context__.contains_r("theta")))
129:             throw std::runtime_error("variable theta missing");
130:         vals_r__ = context__.vals_r("theta");
131:         pos__ = 0U;
132:         context__.validate_dims("initialization", "theta", "double", context__.to_vec());
133:         double theta(0);
134:         theta = vals_r__[pos__++];
135:         try {
136:             writer__.scalar_lub_unconstrain(0,1,theta);
137:         } catch (const std::exception& e) { 
138:             throw std::runtime_error(std::string("Error transforming variable theta: ") + e.what());
139:         }
140: 
141:         params_r__ = writer__.data_r();
142:         params_i__ = writer__.data_i();
143:     }
144: 
145:     void transform_inits(const stan::io::var_context& context,
146:                          Eigen::Matrix<double,Eigen::Dynamic,1>& params_r,
147:                          std::ostream* pstream__) const {
148:       std::vector<double> params_r_vec;
149:       std::vector<int> params_i_vec;
150:       transform_inits(context, params_i_vec, params_r_vec, pstream__);
151:       params_r.resize(params_r_vec.size());
152:       for (int i = 0; i < params_r.size(); ++i)
153:         params_r(i) = params_r_vec[i];
154:     }
155: 
156: 
157:     template <bool propto__, bool jacobian__, typename T__>
158:     T__ log_prob(vector<T__>& params_r__,
159:                  vector<int>& params_i__,
160:                  std::ostream* pstream__ = 0) const {
161: 
162:         T__ DUMMY_VAR__(std::numeric_limits<double>::quiet_NaN());
163:         (void) DUMMY_VAR__;  // suppress unused var warning
164: 
165:         T__ lp__(0.0);
166:         stan::math::accumulator<T__> lp_accum__;
167: 
168:         try {
169:             // model parameters
170:             stan::io::reader<T__> in__(params_r__,params_i__);
171: 
172:             T__ theta;
173:             (void) theta;  // dummy to suppress unused var warning
174:             if (jacobian__)
175:                 theta = in__.scalar_lub_constrain(0,1,lp__);
176:             else
177:                 theta = in__.scalar_lub_constrain(0,1);
178: 
179: 
180:             // transformed parameters
181: 
182: 
183: 
184:             // validate transformed parameters
185: 
186:             const char* function__ = "validate transformed params";
187:             (void) function__;  // dummy to suppress unused var warning
188: 
189:             // model body
190: 
191:             current_statement_begin__ = 12;
192:             lp_accum__.add(beta_log<propto__>(theta, 1, 1));
193:             current_statement_begin__ = 13;
194:             lp_accum__.add(bernoulli_log<propto__>(y, theta));
195: 
196:         } catch (const std::exception& e) {
197:             stan::lang::rethrow_located(e, current_statement_begin__, prog_reader__());
198:             // Next line prevents compiler griping about no return
199:             throw std::runtime_error("*** IF YOU SEE THIS, PLEASE REPORT A BUG ***");
200:         }
201: 
202:         lp_accum__.add(lp__);
203:         return lp_accum__.sum();
204: 
205:     } // log_prob()
206: 
207:     template <bool propto, bool jacobian, typename T_>
208:     T_ log_prob(Eigen::Matrix<T_,Eigen::Dynamic,1>& params_r,
209:                std::ostream* pstream = 0) const {
210:       std::vector<T_> vec_params_r;
211:       vec_params_r.reserve(params_r.size());
212:       for (int i = 0; i < params_r.size(); ++i)
213:         vec_params_r.push_back(params_r(i));
214:       std::vector<int> vec_params_i;
215:       return log_prob<propto,jacobian,T_>(vec_params_r, vec_params_i, pstream);
216:     }
217: 
218: 
219:     void get_param_names(std::vector<std::string>& names__) const {
220:         names__.resize(0);
221:         names__.push_back("theta");
222:     }
223: 
224: 
225:     void get_dims(std::vector<std::vector<size_t> >& dimss__) const {
226:         dimss__.resize(0);
227:         std::vector<size_t> dims__;
228:         dims__.resize(0);
229:         dimss__.push_back(dims__);
230:     }
231: 
232:     template <typename RNG>
233:     void write_array(RNG& base_rng__,
234:                      std::vector<double>& params_r__,
235:                      std::vector<int>& params_i__,
236:                      std::vector<double>& vars__,
237:                      bool include_tparams__ = true,
238:                      bool include_gqs__ = true,
239:                      std::ostream* pstream__ = 0) const {
240:         vars__.resize(0);
241:         stan::io::reader<double> in__(params_r__,params_i__);
242:         static const char* function__ = "model33733471a68_29d68658bae2087c6157562fc6a3f1bb_namespace::write_array";
243:         (void) function__;  // dummy to suppress unused var warning
244:         // read-transform, write parameters
245:         double theta = in__.scalar_lub_constrain(0,1);
246:         vars__.push_back(theta);
247: 
248:         if (!include_tparams__) return;
249:         // declare and define transformed parameters
250:         double lp__ = 0.0;
251:         (void) lp__;  // dummy to suppress unused var warning
252:         stan::math::accumulator<double> lp_accum__;
253: 
254:         double DUMMY_VAR__(std::numeric_limits<double>::quiet_NaN());
255:         (void) DUMMY_VAR__;  // suppress unused var warning
256: 
257:         try {
258: 
259: 
260: 
261:             // validate transformed parameters
262: 
263:             // write transformed parameters
264: 
265:             if (!include_gqs__) return;
266:             // declare and define generated quantities
267: 
268: 
269: 
270:             // validate generated quantities
271: 
272:             // write generated quantities
273:         } catch (const std::exception& e) {
274:             stan::lang::rethrow_located(e, current_statement_begin__, prog_reader__());
275:             // Next line prevents compiler griping about no return
276:             throw std::runtime_error("*** IF YOU SEE THIS, PLEASE REPORT A BUG ***");
277:         }
278:     }
279: 
280:     template <typename RNG>
281:     void write_array(RNG& base_rng,
282:                      Eigen::Matrix<double,Eigen::Dynamic,1>& params_r,
283:                      Eigen::Matrix<double,Eigen::Dynamic,1>& vars,
284:                      bool include_tparams = true,
285:                      bool include_gqs = true,
286:                      std::ostream* pstream = 0) const {
287:       std::vector<double> params_r_vec(params_r.size());
288:       for (int i = 0; i < params_r.size(); ++i)
289:         params_r_vec[i] = params_r(i);
290:       std::vector<double> vars_vec;
291:       std::vector<int> params_i_vec;
292:       write_array(base_rng,params_r_vec,params_i_vec,vars_vec,include_tparams,include_gqs,pstream);
293:       vars.resize(vars_vec.size());
294:       for (int i = 0; i < vars.size(); ++i)
295:         vars(i) = vars_vec[i];
296:     }
297: 
298:     static std::string model_name() {
299:         return "model33733471a68_29d68658bae2087c6157562fc6a3f1bb";
300:     }
301: 
302: 
303:     void constrained_param_names(std::vector<std::string>& param_names__,
304:                                  bool include_tparams__ = true,
305:                                  bool include_gqs__ = true) const {
306:         std::stringstream param_name_stream__;
307:         param_name_stream__.str(std::string());
308:         param_name_stream__ << "theta";
309:         param_names__.push_back(param_name_stream__.str());
310: 
311:         if (!include_gqs__ && !include_tparams__) return;
312: 
313:         if (!include_gqs__) return;
314:     }
315: 
316: 
317:     void unconstrained_param_names(std::vector<std::string>& param_names__,
318:                                    bool include_tparams__ = true,
319:                                    bool include_gqs__ = true) const {
320:         std::stringstream param_name_stream__;
321:         param_name_stream__.str(std::string());
322:         param_name_stream__ << "theta";
323:         param_names__.push_back(param_name_stream__.str());
324: 
325:         if (!include_gqs__ && !include_tparams__) return;
326: 
327:         if (!include_gqs__) return;
328:     }
329: 
330: }; // model
331: 
332: }
333: 
334: typedef model33733471a68_29d68658bae2087c6157562fc6a3f1bb_namespace::model33733471a68_29d68658bae2087c6157562fc6a3f1bb stan_model;
335: 
336: #include <rstan/rstaninc.hpp>
337: /**
338:  * Define Rcpp Module to expose stan_fit's functions to R.
339:  */
340: RCPP_MODULE(stan_fit4model33733471a68_29d68658bae2087c6157562fc6a3f1bb_mod){
341:   Rcpp::class_<rstan::stan_fit<model33733471a68_29d68658bae2087c6157562fc6a3f1bb_namespace::model33733471a68_29d68658bae2087c6157562fc6a3f1bb,
342:                boost::random::ecuyer1988> >("stan_fit4model33733471a68_29d68658bae2087c6157562fc6a3f1bb")
343:     // .constructor<Rcpp::List>()
344:     .constructor<SEXP, SEXP, SEXP>()
345:     // .constructor<SEXP, SEXP>()
346:     .method("call_sampler",
347:             &rstan::stan_fit<model33733471a68_29d68658bae2087c6157562fc6a3f1bb_namespace::model33733471a68_29d68658bae2087c6157562fc6a3f1bb, boost::random::ecuyer1988>::call_sampler)
348:     .method("param_names",
349:             &rstan::stan_fit<model33733471a68_29d68658bae2087c6157562fc6a3f1bb_namespace::model33733471a68_29d68658bae2087c6157562fc6a3f1bb, boost::random::ecuyer1988>::param_names)
350:     .method("param_names_oi",
351:             &rstan::stan_fit<model33733471a68_29d68658bae2087c6157562fc6a3f1bb_namespace::model33733471a68_29d68658bae2087c6157562fc6a3f1bb, boost::random::ecuyer1988>::param_names_oi)
352:     .method("param_fnames_oi",
353:             &rstan::stan_fit<model33733471a68_29d68658bae2087c6157562fc6a3f1bb_namespace::model33733471a68_29d68658bae2087c6157562fc6a3f1bb, boost::random::ecuyer1988>::param_fnames_oi)
354:     .method("param_dims",
355:             &rstan::stan_fit<model33733471a68_29d68658bae2087c6157562fc6a3f1bb_namespace::model33733471a68_29d68658bae2087c6157562fc6a3f1bb, boost::random::ecuyer1988>::param_dims)
356:     .method("param_dims_oi",
357:             &rstan::stan_fit<model33733471a68_29d68658bae2087c6157562fc6a3f1bb_namespace::model33733471a68_29d68658bae2087c6157562fc6a3f1bb, boost::random::ecuyer1988>::param_dims_oi)
358:     .method("update_param_oi",
359:             &rstan::stan_fit<model33733471a68_29d68658bae2087c6157562fc6a3f1bb_namespace::model33733471a68_29d68658bae2087c6157562fc6a3f1bb, boost::random::ecuyer1988>::update_param_oi)
360:     .method("param_oi_tidx",
361:             &rstan::stan_fit<model33733471a68_29d68658bae2087c6157562fc6a3f1bb_namespace::model33733471a68_29d68658bae2087c6157562fc6a3f1bb, boost::random::ecuyer1988>::param_oi_tidx)
362:     .method("grad_log_prob",
363:             &rstan::stan_fit<model33733471a68_29d68658bae2087c6157562fc6a3f1bb_namespace::model33733471a68_29d68658bae2087c6157562fc6a3f1bb, boost::random::ecuyer1988>::grad_log_prob)
364:     .method("log_prob",
365:             &rstan::stan_fit<model33733471a68_29d68658bae2087c6157562fc6a3f1bb_namespace::model33733471a68_29d68658bae2087c6157562fc6a3f1bb, boost::random::ecuyer1988>::log_prob)
366:     .method("unconstrain_pars",
367:             &rstan::stan_fit<model33733471a68_29d68658bae2087c6157562fc6a3f1bb_namespace::model33733471a68_29d68658bae2087c6157562fc6a3f1bb, boost::random::ecuyer1988>::unconstrain_pars)
368:     .method("constrain_pars",
369:             &rstan::stan_fit<model33733471a68_29d68658bae2087c6157562fc6a3f1bb_namespace::model33733471a68_29d68658bae2087c6157562fc6a3f1bb, boost::random::ecuyer1988>::constrain_pars)
370:     .method("num_pars_unconstrained",
371:             &rstan::stan_fit<model33733471a68_29d68658bae2087c6157562fc6a3f1bb_namespace::model33733471a68_29d68658bae2087c6157562fc6a3f1bb, boost::random::ecuyer1988>::num_pars_unconstrained)
372:     .method("unconstrained_param_names",
373:             &rstan::stan_fit<model33733471a68_29d68658bae2087c6157562fc6a3f1bb_namespace::model33733471a68_29d68658bae2087c6157562fc6a3f1bb, boost::random::ecuyer1988>::unconstrained_param_names)
374:     .method("constrained_param_names",
375:             &rstan::stan_fit<model33733471a68_29d68658bae2087c6157562fc6a3f1bb_namespace::model33733471a68_29d68658bae2087c6157562fc6a3f1bb, boost::random::ecuyer1988>::constrained_param_names)
376:     ;
377: }
378: 
379: // declarations
380: extern "C" {
381: SEXP file337116bc25( ) ;
382: }
383: 
384: // definition
385: 
386: SEXP file337116bc25(  ){
387:  return Rcpp::wrap("29d68658bae2087c6157562fc6a3f1bb");
388: }
389: 
390: 
Error in compileCode(f, code, language = language, verbose = verbose) : 
  Compilation ERROR, function(s)/method(s) not created! In file included from file337116bc25.cpp:8:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/src/stan/model/model_header.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math/rev/core.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math/rev/core/autodiffstackstorage.hpp:4:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/StanHeaders/include/stan/math/memory/stack_alloc.hpp:145:10: warning: 'auto' type specifier is a C++11 extension [-Wc++11-extensions]
    for (auto& block
In addition: Warning messages:
1: In stan_model(file, model_name = model_name, model_code = model_code,  :
  StanHeaders version is ahead of rstan version; update to latest rstan
2: running command '/Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB file337116bc25.cpp 2> file337116bc25.cpp.err.txt' had status 1
bgoodri commented 6 years ago

At the moment, you are going to need to first call

Sys.setenv(USE_CXX14 = 1)

once before calling anything that compiles a Stan model.

MattMalis commented 6 years ago

Looks like that worked. Thank you so much! Can you explain what that did/why it was necessary?

bgoodri commented 6 years ago

Not on a PG-13 website. It won't be necessary once rstan 2.18.1 is approved by CRAN.

On Thu, Oct 11, 2018 at 3:04 PM MattMalis notifications@github.com wrote:

Looks like that worked. Thank you so much! Can you explain what that did/why it was necessary?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/stan-dev/rstan/issues/527#issuecomment-429080830, or mute the thread https://github.com/notifications/unsubscribe-auth/ADOrqpfW2JPtD77XcINqSHACLupW1HGEks5uj5ZHgaJpZM4UDhzC .

fsolt commented 6 years ago

I'm sad to report that I had similar issues, resolved by calling Sys.setenv(USE_CXX14 = 1), still after installing rstan 2.18.1.

bgoodri commented 6 years ago

@fsolt Can you give an example and list your setup? In rstan 2.18.1 it is calling Sys.setenv(USE_CXX14 = 1) internally so I don't know why the user would need to do that in advance.

fsolt commented 6 years ago

Hmm. Matt's example works fine. I'm running MacOS 10.14 (Mojave), R 3.5.1, rstan 2.18.1; a new install after wiping my HD yesterday and starting fresh.

I'm trying to rebuild my DCPO package, which I've been doing with devtools::install('.', local=FALSE).

> devtools::install('.', local=FALSE)
Installing DCPO
'/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file --no-environ --no-save  \
  --no-restore --quiet CMD build '/Users/fredsolt/Documents/Projects/DCPO' --no-resave-data  \
  --no-manual --no-build-vignettes 

* checking for file ‘/Users/fredsolt/Documents/Projects/DCPO/DESCRIPTION’ ... OK
* preparing ‘DCPO’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
Removed empty directory ‘DCPO/dev’
Removed empty directory ‘DCPO/vignettes’
* looking to see if a ‘data/datalist’ file should be added
* building ‘DCPO_0.1.0.9000.tar.gz’

'/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file --no-environ --no-save  \
  --no-restore --quiet CMD INSTALL  \
  '/private/var/folders/6b/krhmytd940z1m52c1z_2dw4w0000gn/T/Rtmp2HzPT8/DCPO_0.1.0.9000.tar.gz'  \
  --library='/Library/Frameworks/R.framework/Versions/3.5/Resources/library' --install-tests 

* installing *source* package ‘DCPO’ ...
** libs
"/Library/Frameworks/R.framework/Resources/bin/Rscript" -e "source(file.path('..', 'tools', 'make_cc.R')); make_cc(commandArgs(TRUE))" stan_files/dcpo.stan
DIAGNOSTIC(S) FROM PARSER:
Info: left-hand side variable (name=beta) occurs on right-hand side of assignment, causing inefficient deep copy to avoid aliasing.
Info: left-hand side variable (name=theta) occurs on right-hand side of assignment, causing inefficient deep copy to avoid aliasing.

Wrote C++ file "stan_files/dcpo.cc"
clang++ -arch x86_64 -ftemplate-depth-256 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"../inst/include" -I"`"/Library/Frameworks/R.framework/Resources/bin/Rscript" --vanilla -e "cat(system.file('include', 'src', package = 'StanHeaders'))"`" -DBOOST_RESULT_OF_USE_TR1 -DBOOST_NO_DECLTYPE -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/rstan/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppEigen/include" -I/usr/local/include   -fPIC  -O3 -mtune=native -march=native -Wno-unused-variable -Wno-unused-function -c stan_files/dcpo.cc -o stan_files/dcpo.o
In file included from stan_files/dcpo.cc:3:
In file included from stan_files/dcpo.hpp:18:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/rstan/include/rstan/stan_fit.hpp:20:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/rstan/include/rstan/stan_args.hpp:12:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/lexical_cast.hpp:32:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/lexical_cast/try_lexical_convert.hpp:42:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/lexical_cast/detail/converter_lexical.hpp:52:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/container/container_fwd.hpp:61:
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/container/detail/std_fwd.hpp:27:1: warning: inline namespaces are a C++11 feature [-Wc++11-inline-namespace]
BOOST_MOVE_STD_NS_BEG
^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/move/detail/std_ns_begin.hpp:18:34: note: expanded from macro 'BOOST_MOVE_STD_NS_BEG'
   #define BOOST_MOVE_STD_NS_BEG _LIBCPP_BEGIN_NAMESPACE_STD
                                 ^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/__config:445:52: note: expanded from macro '_LIBCPP_BEGIN_NAMESPACE_STD'
#define _LIBCPP_BEGIN_NAMESPACE_STD namespace std {inline namespace _LIBCPP_NAMESPACE {
                                                   ^
In file included from stan_files/dcpo.cc:3:
In file included from stan_files/dcpo.hpp:18:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/rstan/include/rstan/stan_fit.hpp:34:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/rev/core.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/rev/core/autodiffstackstorage.hpp:4:
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/memory/stack_alloc.hpp:145:10: warning: 'auto' type specifier is a C++11 extension [-Wc++11-extensions]
    for (auto& block : blocks_)
         ^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/memory/stack_alloc.hpp:145:22: warning: range-based for loop is a C++11 extension [-Wc++11-extensions]
    for (auto& block : blocks_)
                     ^
In file included from stan_files/dcpo.cc:3:
In file included from stan_files/dcpo.hpp:18:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/rstan/include/rstan/stan_fit.hpp:34:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/rev/core.hpp:4:
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/rev/core/autodiffstackstorage.hpp:47:69: warning: deleted function definitions are a C++11 extension [-Wc++11-extensions]
    AutodiffStackStorage &operator=(const AutodiffStackStorage &) = delete;
                                                                    ^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/rev/core/autodiffstackstorage.hpp:60:30: warning: deleted function definitions are a C++11 extension [-Wc++11-extensions]
  AutodiffStackSingleton() = delete;
                             ^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/rev/core/autodiffstackstorage.hpp:61:71: warning: deleted function definitions are a C++11 extension [-Wc++11-extensions]
  explicit AutodiffStackSingleton(AutodiffStackSingleton_t const &) = delete;
                                                                      ^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/rev/core/autodiffstackstorage.hpp:62:73: warning: deleted function definitions are a C++11 extension [-Wc++11-extensions]
  AutodiffStackSingleton &operator=(const AutodiffStackSingleton_t &) = delete;
                                                                        ^
In file included from stan_files/dcpo.cc:3:
In file included from stan_files/dcpo.hpp:18:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/rstan/include/rstan/stan_fit.hpp:34:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/rev/core.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/rev/core/matrix_vari.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/rev/mat/fun/Eigen_NumTraits.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppEigen/include/Eigen/Dense:1:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppEigen/include/Eigen/Core:531:
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from stan_files/dcpo.cc:3:
In file included from stan_files/dcpo.hpp:18:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/rstan/include/rstan/stan_fit.hpp:34:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/rev/core.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/rev/core/matrix_vari.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/rev/mat/fun/Eigen_NumTraits.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppEigen/include/Eigen/Dense:2:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppEigen/include/Eigen/LU:47:
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from stan_files/dcpo.cc:3:
In file included from stan_files/dcpo.hpp:18:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/rstan/include/rstan/stan_fit.hpp:34:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/rev/core.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/rev/core/matrix_vari.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/rev/mat/fun/Eigen_NumTraits.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppEigen/include/Eigen/Dense:3:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppEigen/include/Eigen/Cholesky:12:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppEigen/include/Eigen/Jacobi:29:
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from stan_files/dcpo.cc:3:
In file included from stan_files/dcpo.hpp:18:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/rstan/include/rstan/stan_fit.hpp:34:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/rev/core.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/rev/core/matrix_vari.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/rev/mat/fun/Eigen_NumTraits.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppEigen/include/Eigen/Dense:3:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppEigen/include/Eigen/Cholesky:43:
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from stan_files/dcpo.cc:3:
In file included from stan_files/dcpo.hpp:18:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/rstan/include/rstan/stan_fit.hpp:34:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/rev/core.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/rev/core/matrix_vari.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/rev/mat/fun/Eigen_NumTraits.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppEigen/include/Eigen/Dense:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppEigen/include/Eigen/QR:17:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppEigen/include/Eigen/Householder:27:
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from stan_files/dcpo.cc:3:
In file included from stan_files/dcpo.hpp:18:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/rstan/include/rstan/stan_fit.hpp:34:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/rev/core.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/rev/core/matrix_vari.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/rev/mat/fun/Eigen_NumTraits.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppEigen/include/Eigen/Dense:5:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppEigen/include/Eigen/SVD:48:
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from stan_files/dcpo.cc:3:
In file included from stan_files/dcpo.hpp:18:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/rstan/include/rstan/stan_fit.hpp:34:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/rev/core.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/rev/core/matrix_vari.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/rev/mat/fun/Eigen_NumTraits.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppEigen/include/Eigen/Dense:6:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppEigen/include/Eigen/Geometry:58:
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from stan_files/dcpo.cc:3:
In file included from stan_files/dcpo.hpp:18:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/rstan/include/rstan/stan_fit.hpp:34:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/rev/core.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/rev/core/matrix_vari.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/rev/mat/fun/Eigen_NumTraits.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppEigen/include/Eigen/Dense:7:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppEigen/include/Eigen/Eigenvalues:58:
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from stan_files/dcpo.cc:3:
In file included from stan_files/dcpo.hpp:18:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/rstan/include/rstan/stan_fit.hpp:34:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/rev/core.hpp:42:
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/rev/core/recover_memory.hpp:25:8: warning: 'auto' type specifier is a C++11 extension [-Wc++11-extensions]
  for (auto &x : ChainableStack::instance().var_alloc_stack_) {
       ^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/rev/core/recover_memory.hpp:25:16: warning: range-based for loop is a C++11 extension [-Wc++11-extensions]
  for (auto &x : ChainableStack::instance().var_alloc_stack_) {
               ^
In file included from stan_files/dcpo.cc:3:
In file included from stan_files/dcpo.hpp:18:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/rstan/include/rstan/stan_fit.hpp:34:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/rev/core.hpp:44:
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/rev/core/set_zero_all_adjoints.hpp:15:8: warning: 'auto' type specifier is a C++11 extension [-Wc++11-extensions]
  for (auto &x : ChainableStack::instance().var_stack_)
       ^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/rev/core/set_zero_all_adjoints.hpp:15:16: warning: range-based for loop is a C++11 extension [-Wc++11-extensions]
  for (auto &x : ChainableStack::instance().var_stack_)
               ^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/rev/core/set_zero_all_adjoints.hpp:17:8: warning: 'auto' type specifier is a C++11 extension [-Wc++11-extensions]
  for (auto &x : ChainableStack::instance().var_nochain_stack_)
       ^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/rev/core/set_zero_all_adjoints.hpp:17:16: warning: range-based for loop is a C++11 extension [-Wc++11-extensions]
  for (auto &x : ChainableStack::instance().var_nochain_stack_)
               ^
In file included from stan_files/dcpo.cc:3:
In file included from stan_files/dcpo.hpp:18:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/rstan/include/rstan/stan_fit.hpp:34:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:12:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/prim/mat.hpp:22:
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/prim/mat/meta/operands_and_partials.hpp:19:59: error: expected expression
class ops_partials_edge<ViewElt, Eigen::Matrix<Op, R, C>> {
                                                          ^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/prim/mat/meta/operands_and_partials.hpp:35:2: error: expected a type
};
 ^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/prim/mat/meta/operands_and_partials.hpp:38:70: error: expected expression
class ops_partials_edge<ViewElt, std::vector<Eigen::Matrix<Op, R, C>>> {
                                                                     ^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/prim/mat/meta/operands_and_partials.hpp:38:72: error: expected a type
class ops_partials_edge<ViewElt, std::vector<Eigen::Matrix<Op, R, C>>> {
                                                                       ^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/prim/mat/meta/operands_and_partials.hpp:53:2: error: expected a type
};
 ^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/prim/mat/meta/operands_and_partials.hpp:56:60: error: a space is required between consecutive right angle brackets (use '> >')
class ops_partials_edge<ViewElt, std::vector<std::vector<Op>>> {
                                                           ^~
                                                           > > 
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/prim/mat/meta/operands_and_partials.hpp:58:68: error: a space is required between consecutive right angle brackets (use '> >')
  typedef empty_broadcast_array<ViewElt, std::vector<std::vector<Op>>>
                                                                   ^~
                                                                   > > 
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/prim/mat/meta/operands_and_partials.hpp:61:63: error: a space is required between consecutive right angle brackets (use '> >')
  empty_broadcast_array<partials_t, std::vector<std::vector<Op>>> partials_vec_;
                                                              ^~
                                                              > > 
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/prim/mat/meta/operands_and_partials.hpp:63:62: error: a space is required between consecutive right angle brackets (use '> >')
  explicit ops_partials_edge(const std::vector<std::vector<Op>> ops) {}
                                                             ^~
                                                             > >
In file included from stan_files/dcpo.cc:3:
In file included from stan_files/dcpo.hpp:18:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/rstan/include/rstan/stan_fit.hpp:34:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:12:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/prim/mat.hpp:96:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/csr_extract_u.hpp:6:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppEigen/include/Eigen/Sparse:26:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppEigen/include/Eigen/SparseCore:66:
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from stan_files/dcpo.cc:3:
In file included from stan_files/dcpo.hpp:18:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/rstan/include/rstan/stan_fit.hpp:34:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:12:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/prim/mat.hpp:96:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/csr_extract_u.hpp:6:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppEigen/include/Eigen/Sparse:27:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppEigen/include/Eigen/OrderingMethods:71:
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from stan_files/dcpo.cc:3:
In file included from stan_files/dcpo.hpp:18:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/rstan/include/rstan/stan_fit.hpp:34:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:12:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/prim/mat.hpp:96:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/csr_extract_u.hpp:6:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppEigen/include/Eigen/Sparse:29:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppEigen/include/Eigen/SparseCholesky:43:
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from stan_files/dcpo.cc:3:
In file included from stan_files/dcpo.hpp:18:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/rstan/include/rstan/stan_fit.hpp:34:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:12:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/prim/mat.hpp:96:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/csr_extract_u.hpp:6:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppEigen/include/Eigen/Sparse:32:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppEigen/include/Eigen/SparseQR:35:
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from stan_files/dcpo.cc:3:
In file included from stan_files/dcpo.hpp:18:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/rstan/include/rstan/stan_fit.hpp:34:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:12:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/prim/mat.hpp:96:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/csr_extract_u.hpp:6:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppEigen/include/Eigen/Sparse:33:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppEigen/include/Eigen/IterativeLinearSolvers:46:
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from stan_files/dcpo.cc:3:
In file included from stan_files/dcpo.hpp:18:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/rstan/include/rstan/stan_fit.hpp:34:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:12:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/prim/mat.hpp:99:
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/csr_matrix_times_vector.hpp:91:14: warning: range-based for loop is a C++11 extension [-Wc++11-extensions]
  for (int i : v)
             ^
In file included from stan_files/dcpo.cc:3:
In file included from stan_files/dcpo.hpp:18:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/rstan/include/rstan/stan_fit.hpp:34:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:12:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/prim/mat.hpp:100:
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/csr_to_dense_matrix.hpp:48:14: warning: range-based for loop is a C++11 extension [-Wc++11-extensions]
  for (int i : v)
             ^
In file included from stan_files/dcpo.cc:3:
In file included from stan_files/dcpo.hpp:18:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/rstan/include/rstan/stan_fit.hpp:34:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:12:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/prim/mat.hpp:156:
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/log_mix.hpp:178:26: error: expected expression
              .unaryExpr([](T_partials_return x) { return exp(x); });
                         ^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/log_mix.hpp:262:24: error: expected expression
            .unaryExpr([](T_partials_return x) { return exp(x); });
                       ^
In file included from stan_files/dcpo.cc:3:
In file included from stan_files/dcpo.hpp:18:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/rstan/include/rstan/stan_fit.hpp:34:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:12:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/prim/mat.hpp:161:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/matrix_exp.hpp:5:
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/matrix_exp_2x2.hpp:21:13: warning: alias declarations are a C++11 extension [-Wc++11-extensions]
  using T = typename Mtype::Scalar;
            ^
In file included from stan_files/dcpo.cc:3:
In file included from stan_files/dcpo.hpp:18:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/rstan/include/rstan/stan_fit.hpp:34:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:12:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/prim/mat.hpp:162:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/matrix_exp_multiply.hpp:5:
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/matrix_exp_action_handler.hpp:20:10: error: unknown type name 'constexpr'
  static constexpr int p_max = 8;
         ^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/matrix_exp_action_handler.hpp:20:20: error: expected member name or ';' after declaration specifiers
  static constexpr int p_max = 8;
  ~~~~~~~~~~~~~~~~ ^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/matrix_exp_action_handler.hpp:21:10: error: unknown type name 'constexpr'
  static constexpr int m_max = 55;
         ^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/matrix_exp_action_handler.hpp:21:20: error: expected member name or ';' after declaration specifiers
  static constexpr int m_max = 55;
  ~~~~~~~~~~~~~~~~ ^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/matrix_exp_action_handler.hpp:22:10: error: unknown type name 'constexpr'
  static constexpr double tol = 1.1e-16;
         ^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/matrix_exp_action_handler.hpp:22:20: error: expected member name or ';' after declaration specifiers
  static constexpr double tol = 1.1e-16;
  ~~~~~~~~~~~~~~~~ ^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/matrix_exp_action_handler.hpp:25:29: error: function definition does not declare parameters
  const std::vector<double> theta_m_single_precision{
                            ^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/matrix_exp_action_handler.hpp:28:29: error: function definition does not declare parameters
  const std::vector<double> theta_m_double_precision{
                            ^
fatal error: too many errors emitted, stopping now [-ferror-limit=]
29 warnings and 20 errors generated.
make: *** [stan_files/dcpo.o] Error 1
rm stan_files/dcpo.cc
ERROR: compilation failed for package ‘DCPO’
* removing ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/DCPO’
* restoring previous ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/DCPO’
Error: Command failed (1)

But, OTOH, this works fine:

> Sys.setenv(USE_CXX14 = 1)
> devtools::install('.', local=FALSE)
Installing DCPO
'/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file --no-environ --no-save  \
  --no-restore --quiet CMD build '/Users/fredsolt/Documents/Projects/DCPO' --no-resave-data  \
  --no-manual --no-build-vignettes 

* checking for file ‘/Users/fredsolt/Documents/Projects/DCPO/DESCRIPTION’ ... OK
* preparing ‘DCPO’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
Removed empty directory ‘DCPO/dev’
Removed empty directory ‘DCPO/vignettes’
* looking to see if a ‘data/datalist’ file should be added
* building ‘DCPO_0.1.0.9000.tar.gz’

'/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file --no-environ --no-save  \
  --no-restore --quiet CMD INSTALL  \
  '/private/var/folders/6b/krhmytd940z1m52c1z_2dw4w0000gn/T/Rtmp2HzPT8/DCPO_0.1.0.9000.tar.gz'  \
  --library='/Library/Frameworks/R.framework/Versions/3.5/Resources/library' --install-tests 

* installing *source* package ‘DCPO’ ...
** libs
"/Library/Frameworks/R.framework/Resources/bin/Rscript" -e "source(file.path('..', 'tools', 'make_cc.R')); make_cc(commandArgs(TRUE))" stan_files/dcpo.stan
DIAGNOSTIC(S) FROM PARSER:
Info: left-hand side variable (name=beta) occurs on right-hand side of assignment, causing inefficient deep copy to avoid aliasing.
Info: left-hand side variable (name=theta) occurs on right-hand side of assignment, causing inefficient deep copy to avoid aliasing.

Wrote C++ file "stan_files/dcpo.cc"
clang++ -arch x86_64 -ftemplate-depth-256 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"../inst/include" -I"`"/Library/Frameworks/R.framework/Resources/bin/Rscript" --vanilla -e "cat(system.file('include', 'src', package = 'StanHeaders'))"`" -DBOOST_RESULT_OF_USE_TR1 -DBOOST_NO_DECLTYPE -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/rstan/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppEigen/include" -I/usr/local/include   -fPIC  -O3 -mtune=native -march=native -Wno-unused-variable -Wno-unused-function  -Wno-macro-redefined -Wno-unknown-pragmas -c stan_files/dcpo.cc -o stan_files/dcpo.o
"/Library/Frameworks/R.framework/Resources/bin/Rscript" -e "source(file.path('..', 'tools', 'make_cc.R')); make_cc(commandArgs(TRUE))" stan_files/dcpo_as_dv.stan
DIAGNOSTIC(S) FROM PARSER:
Info: left-hand side variable (name=minmax_count) occurs on right-hand side of assignment, causing inefficient deep copy to avoid aliasing.
Info: left-hand side variable (name=beta) occurs on right-hand side of assignment, causing inefficient deep copy to avoid aliasing.
Info: left-hand side variable (name=theta) occurs on right-hand side of assignment, causing inefficient deep copy to avoid aliasing.
Info (non-fatal):
Left-hand side of sampling statement (~) may contain a non-linear transform of a parameter or local variable.
If it does, you need to include a target += statement with the log absolute determinant of the Jacobian of the transform.
Left-hand-side of sampling statement:
    theta ~ normal(...)
Info: left-hand side variable (name=lambda) occurs on right-hand side of assignment, causing inefficient deep copy to avoid aliasing.

Wrote C++ file "stan_files/dcpo_as_dv.cc"
clang++ -arch x86_64 -ftemplate-depth-256 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"../inst/include" -I"`"/Library/Frameworks/R.framework/Resources/bin/Rscript" --vanilla -e "cat(system.file('include', 'src', package = 'StanHeaders'))"`" -DBOOST_RESULT_OF_USE_TR1 -DBOOST_NO_DECLTYPE -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/rstan/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppEigen/include" -I/usr/local/include   -fPIC  -O3 -mtune=native -march=native -Wno-unused-variable -Wno-unused-function  -Wno-macro-redefined -Wno-unknown-pragmas -c stan_files/dcpo_as_dv.cc -o stan_files/dcpo_as_dv.o
clang++ -arch x86_64 -ftemplate-depth-256 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"../inst/include" -I"`"/Library/Frameworks/R.framework/Resources/bin/Rscript" --vanilla -e "cat(system.file('include', 'src', package = 'StanHeaders'))"`" -DBOOST_RESULT_OF_USE_TR1 -DBOOST_NO_DECLTYPE -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/rstan/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppEigen/include" -I/usr/local/include   -fPIC  -O3 -mtune=native -march=native -Wno-unused-variable -Wno-unused-function  -Wno-macro-redefined -Wno-unknown-pragmas -c init.cpp -o init.o
clang++ -arch x86_64 -ftemplate-depth-256 -std=gnu++14 -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 DCPO.so stan_files/dcpo.o stan_files/dcpo_as_dv.o init.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
rm stan_files/dcpo_as_dv.cc stan_files/dcpo.cc
installing to /Library/Frameworks/R.framework/Versions/3.5/Resources/library/DCPO/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
DIAGNOSTIC(S) FROM PARSER:
Info: left-hand side variable (name=beta) occurs on right-hand side of assignment, causing inefficient deep copy to avoid aliasing.
Info: left-hand side variable (name=theta) occurs on right-hand side of assignment, causing inefficient deep copy to avoid aliasing.

DIAGNOSTIC(S) FROM PARSER:
Info: left-hand side variable (name=minmax_count) occurs on right-hand side of assignment, causing inefficient deep copy to avoid aliasing.
Info: left-hand side variable (name=beta) occurs on right-hand side of assignment, causing inefficient deep copy to avoid aliasing.
Info: left-hand side variable (name=theta) occurs on right-hand side of assignment, causing inefficient deep copy to avoid aliasing.
Info (non-fatal):
Left-hand side of sampling statement (~) may contain a non-linear transform of a parameter or local variable.
If it does, you need to include a target += statement with the log absolute determinant of the Jacobian of the transform.
Left-hand-side of sampling statement:
    theta ~ normal(...)
Info: left-hand side variable (name=lambda) occurs on right-hand side of assignment, causing inefficient deep copy to avoid aliasing.

** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (DCPO)
bgoodri commented 6 years ago

@fsolt You need to follow https://discourse.mc-stan.org/t/how-to-update-a-package-that-has-stanheaders-and-rstan-in-its-linkingto/6041?u=bgoodri I contacted the maintainers of all the packages using Stan that I was aware of but I guess DCOP is not on CRAN yet.

fsolt commented 6 years ago

Right, it's still in development. Thanks for your help!

fsolt commented 6 years ago

Crud. Now it complains that it doesn't find 'Rcpp.h':

> devtools::install('.', local=FALSE)
Installing DCPO
'/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file --no-environ --no-save --no-restore  \
  --quiet CMD build '/Users/fredsolt/Documents/Projects/DCPO' --no-resave-data --no-manual  \
  --no-build-vignettes 

* checking for file ‘/Users/fredsolt/Documents/Projects/DCPO/DESCRIPTION’ ... OK
* preparing ‘DCPO’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
Removed empty directory ‘DCPO/dev’
Removed empty directory ‘DCPO/vignettes’
* looking to see if a ‘data/datalist’ file should be added
* building ‘DCPO_0.1.0.9000.tar.gz’

'/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file --no-environ --no-save --no-restore  \
  --quiet CMD INSTALL  \
  '/private/var/folders/6b/krhmytd940z1m52c1z_2dw4w0000gn/T/RtmpGXEjNy/DCPO_0.1.0.9000.tar.gz'  \
  --library='/Library/Frameworks/R.framework/Versions/3.5/Resources/library' --install-tests 

* installing *source* package ‘DCPO’ ...
** libs
"/Library/Frameworks/R.framework/Resources/bin/Rscript" -e "source(file.path('..', 'tools', 'make_cc.R')); make_cc(commandArgs(TRUE))" stan_files/dcpo.stan
DIAGNOSTIC(S) FROM PARSER:
Info: left-hand side variable (name=beta) occurs on right-hand side of assignment, causing inefficient deep copy to avoid aliasing.
Info: left-hand side variable (name=theta) occurs on right-hand side of assignment, causing inefficient deep copy to avoid aliasing.

Wrote C++ file "stan_files/dcpo.cc"
clang++ -arch x86_64 -ftemplate-depth-256 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"../inst/include" -I"`"/Library/Frameworks/R.framework/Resources/bin/Rscript" --vanilla -e "cat(system.file('include', 'src', package = 'StanHeaders'))"`" -DBOOST_RESULT_OF_USE_TR1 -DBOOST_NO_DECLTYPE -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include" -I/usr/local/include   -fPIC  -O3 -mtune=native -march=native -Wno-unused-variable -Wno-unused-function  -Wno-macro-redefined -Wno-unknown-pragmas -c stan_files/dcpo.cc -o stan_files/dcpo.o
stan_files/dcpo.cc:1:10: fatal error: 'Rcpp.h' file not found
#include <Rcpp.h>
         ^~~~~~~~
1 error generated.
make: *** [stan_files/dcpo.o] Error 1
rm stan_files/dcpo.cc
ERROR: compilation failed for package ‘DCPO’
* removing ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/DCPO’
* restoring previous ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/DCPO’
Error: Command failed (1)
bgoodri commented 6 years ago

devtools::install_github("fsolt/DCPO") does not work for me because it eventually says

Error : Please provide username and/or password.
Error : unable to load R code in package ‘DCPO’

but clang++ -arch x86_64 -ftemplate-depth-256 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"../inst/include" -I""/Library/Frameworks/R.framework/Resources/bin/Rscript" --vanilla -e "cat(system.file('include', 'src', package = 'StanHeaders'))"" -DBOOST_RESULT_OF_USE_TR1 -DBOOST_NO_DECLTYPE -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include" -I/usr/local/include -fPIC -O3 -mtune=native -march=native -Wno-unused-variable -Wno-unused-function -Wno-macro-redefined -Wno-unknown-pragmas -c stan_files/dcpo.cc -o stan_files/dcpo.o is supposed to have a -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" in it, which it supposed to have according to your src/Makevars file. Are you working off a version that has unpushed commits?

fsolt commented 6 years ago

IDK why it would demand a password; it's a public repo.

But whoops, yes, pushing is always helpful. It's up to date now.

bgoodri commented 6 years ago

In the LinkingTo section of the DESCRIPTION file, you need commas after each of the packages except the last one. Like this:

LinkingTo:
  StanHeaders (>= 2.18.0),
  rstan (>= 2.18.1),
  BH (>= 1.66.0-1), 
  Rcpp (>= 0.12.0),
  RcppEigen (>= 0.3.3.4.0)
bgoodri commented 6 years ago

And I think the password thing comes from this line https://github.com/fsolt/DCPO/blob/master/R/get_data.R#L207

fsolt commented 6 years ago

For the love of . . .

Yes, the missing commas were the problem.

fsolt commented 6 years ago

Thanks, too, for the heads-up re get_data.R. I'll have to get that figured out and squared away before it goes on CRAN, I guess.

Again, I really appreciate your help!