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stan-dev / rstanarm

rstanarm R package for Bayesian applied regression modeling
https://mc-stan.org/rstanarm
GNU General Public License v3.0
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R 3.2.3 Crashes on OS X 10.11.3 when loading rstanarm #63

Closed rubgb closed 8 years ago

rubgb commented 8 years ago

Hi there, every time I try to load the rstanarm library R crashes. Below is a copy of the message:

**[R.app GUI 1.66 (7060) x86_64-apple-darwin13.4.0]

library(rstanarm) Loading required package: Rcpp

* caught segfault * address 0x18, cause 'memory not mapped'

Traceback: 1: dyn.load(file, DLLpath = DLLpath, ...) 2: library.dynam(lib, package, package.lib) 3: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) 4: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]), from = package) 5: loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) 6: asNamespace(ns) 7: namespaceImportFrom(ns, loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]), i[[2L]], from = package) 8: loadNamespace(package, c(which.lib.loc, lib.loc)) 9: doTryCatch(return(expr), name, parentenv, handler) 10: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 11: tryCatchList(expr, classes, parentenv, handlers) 12: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call)[1L] prefix <- paste("Error in", dcall, ": ") LONG <- 75L msg <- conditionMessage(e) sm <- strsplit(msg, "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && identical(getOption("show.error.messages"), TRUE)) { cat(msg, file = stderr()) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))}) 13: try({ ns <- loadNamespace(package, c(which.lib.loc, lib.loc)) env <- attachNamespace(ns, pos = pos, deps)}) 14: library(rstanarm) ** Any suggestions? Many thanks in advance, Rube

jgabry commented 8 years ago

Hmm, is this the version installed from CRAN or from GitHub?

bgoodri commented 8 years ago

Things like that have usually been some sort of incompatibility between the versions of Rcpp and rstanarm.

rubgb commented 8 years ago

I'm using Rcpp 0.12.3 and rstanarm 2.9.0-1. They were both installed from CRAN

bgoodri commented 8 years ago

Does it work if you do

install.packages("rstanarm", type = "source") # requires Xcode
rubgb commented 8 years ago

Unfortunately it doesn't work.Here's the complete output after executing the command:

 * caught segfault * address 0x18, cause 'memory not mapped'

Traceback:  1: dyn.load(file, DLLpath = DLLpath, ...)  2: library.dynam(lib, package, package.lib)  3: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])  4: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()),     versionCheck = vI[[i]]), from = package)  5: loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])  6: asNamespace(ns)  7: namespaceImportFrom(ns, loadNamespace(j <- i[[1L]], c(lib.loc,     .libPaths()), versionCheck = vI[[j]]), i[[2L]], from = package)  8: loadNamespace(name)  9: doTryCatch(return(expr), name, parentenv, handler) 10: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 11: tryCatchList(expr, classes, parentenv, handlers) 12: tryCatch(loadNamespace(name), error = function(e) {    warning(gettextf("namespace %s is not available and has been replaced\nby .GlobalEnv when processing object %s",         sQuote(name)[1L], sQuote(where)), domain = NA, call. = FALSE,         immediate. = TRUE)    .GlobalEnv}) 13: ..getNamespace(c("rstanarm", "2.8.9"), "example_model") 14: load(zfile, envir = envir) 15: utils::data(list = f, package = package, lib.loc = lib.loc, envir = dataEnv) 16: data2LazyLoadDB(pkg_name, lib, compress = data_compress) 17: doTryCatch(return(expr), name, parentenv, handler) 18: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 19: tryCatchList(expr, classes, parentenv, handlers) 20: tryCatch(expr, error = function(e) {    call <- conditionCall(e)    if (!is.null(call)) {        if (identical(call[[1L]], quote(doTryCatch)))             call <- sys.call(-4L)        dcall <- deparse(call)[1L]        prefix <- paste("Error in", dcall, ": ")        LONG <- 75L        msg <- conditionMessage(e)        sm <- strsplit(msg, "\n")[[1L]]        w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")        if (is.na(w))             w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],                 type = "b")        if (w > LONG)             prefix <- paste0(prefix, "\n  ")    }    else prefix <- "Error : "    msg <- paste0(prefix, conditionMessage(e), "\n")    .Internal(seterrmessage(msg[1L]))    if (!silent && identical(getOption("show.error.messages"),         TRUE)) {        cat(msg, file = stderr())        .Internal(printDeferredWarnings())    }    invisible(structure(msg, class = "try-error", condition = e))}) 21: try(data2LazyLoadDB(pkg_name, lib, compress = data_compress)) 22: do_install_source(pkg_name, instdir, pkg, desc) 23: do_install(pkg) 24: tools:::.install_packages() aborting ... /Library/Frameworks/R.framework/Resources/bin/INSTALL: line 34: 10128 Done                    echo 'tools:::.install_packages()'      10129 Segmentation fault: 11  | R_DEFAULT_PACKAGES= LC_COLLATE=C "${R_HOME}/bin/R" $myArgs --slave --args ${args} Warning in install.packages :   installation of package ‘rstanarm’ had non-zero exit status

On Saturday, January 30, 2016 10:44 AM, bgoodri <notifications@github.com> wrote:

Does it work if you doinstall.packages("rstanarm", type = "source") # requires Xcode — Reply to this email directly or view it on GitHub.

bgoodri commented 8 years ago

Hmm. It seems that you have some extra linker options being invoked in

clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined
dynamic_lookup -single_module -multiply_defined suppress
-L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o
rstanarm.so Modules.o -F/Library/Frameworks/R.framework/.. -framework R
-Wl,-framework -Wl,CoreFoundation
installing to
/Library/Frameworks/R.framework/Versions/3.2/Resources/library/rstanarm/libs

Are these specified in your ~/.R/Makevars file?

On Sat, Jan 30, 2016 at 3:38 AM, rubgb notifications@github.com wrote:

Unfortunately it doesn't work.Here's the complete output after executing the command:

  • installing source package ‘rstanarm’ ... * package ‘rstanarm’ successfully unpacked and MD5 sums checked * libs clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -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 -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/StanHeaders/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/rstan/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/RcppEigen/include" -fPIC -Wall -mtune=core2 -g -O2 -c Modules.cpp -o Modules.o In file included from Modules.cpp:3: In file included from ./include/models.hpp:21: In file included from /Library/Frameworks/R.framework/Versions/3.2/Resources/library/rstan/include/rstan/rstaninc.hpp:3: In file included from /Library/Frameworks/R.framework/Versions/3.2/Resources/library/rstan/include/rstan/stan_fit.hpp:18: In file included from /Library/Frameworks/R.framework/Versions/3.2/Resources/library/StanHeaders/include/src/stan/model/util.hpp:7: In file included from /Library/Frameworks/R.framework/Versions/3.2/Resources/library/StanHeaders/include/stan/math/rev/mat/fun/grad.hpp:6: In file included from /Library/Frameworks/R.framework/Versions/3.2/Resources/library/StanHeaders/include/stan/math/rev/mat/fun/Eigen_NumTraits.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/3.2/Resources/library/StanHeaders/include/stan/math/rev/core.hpp:42: /Library/Frameworks/R.framework/Versions/3.2/Resources/library/StanHeaders/include/stan/math/rev/core/set_zero_all_adjoints.hpp:14:17: warning: 'static' function 'set_zero_all_adjoints' declared in header file should be declared 'static inline' [-Wunneeded-internal-declaration] static void set_zero_all_adjoints() { ^ In file included from Modules.cpp:3: In file included from ./include/models.hpp:21: In file included from /Library/Frameworks/R.framework/Versions/3.2/Resources/library/rstan/include/rstan/rstaninc.hpp:3: In file included from /Library/Frameworks/R.framework/Versions/3.2/Resources/library/rstan/include/rstan/stan_fit.hpp:18: In file included from /Library/Frameworks/R.framework/Versions/3.2/Resources/library/StanHeaders/include/src/stan/model/util.hpp:7: In file included from /Library/Frameworks/R.framework/Versions/3.2/Resources/library/StanHeaders/include/stan/math/rev/mat/fun/grad.hpp:6: In file included from /Library/Frameworks/R.framework/Versions/3.2/Resources/library/StanHeaders/include/stan/math/rev/mat/fun/Eigen_NumTraits.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/3.2/Resources/library/StanHeaders/include/stan/math/rev/core.hpp:43: /Library/Frameworks/R.framework/Versions/3.2/Resources/library/StanHeaders/include/stan/math/rev/core/set_zero_all_adjoints_nested.hpp:16:17: warning: 'static' function 'set_zero_all_adjoints_nested' declared in header file should be declared 'static inline' [-Wunneeded-internal-declaration] static void set_zero_all_adjoints_nested() { ^ In file included from Modules.cpp:3: In file included from ./include/models.hpp:21: In file included from /Library/Frameworks/R.framework/Versions/3.2/Resources/library/rstan/include/rstan/rstaninc.hpp:3: In file included from /Library/Frameworks/R.framework/Versions/3.2/Resources/library/rstan/include/rstan/stan_fit.hpp:83: In file included from /Library/Frameworks/R.framework/Versions/3.2/Resources/library/StanHeaders/include/src/stan/variational/advi.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/3.2/Resources/library/StanHeaders/include/stan/math.hpp:99: /Library/Frameworks/R.framework/Versions/3.2/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/autocorrelation.hpp:19:14: warning: function 'fft_next_good_size' is not needed and will not be emitted [-Wunneeded-internal-declaration] size_t fft_next_good_size(size_t N) { ^ In file included from Modules.cpp:3: In file included from ./include/models.hpp:21: In file included from /Library/Frameworks/R.framework/Versions/3.2/Resources/library/rstan/include/rstan/rstaninc.hpp:3: In file included from /Library/Frameworks/R.framework/Versions/3.2/Resources/library/rstan/include/rstan/stan_fit.hpp:83: In file included from /Library/Frameworks/R.framework/Versions/3.2/Resources/library/StanHeaders/include/src/stan/variational/advi.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/3.2/Resources/library/StanHeaders/include/stan/math.hpp:65: In file included from /Library/Frameworks/R.framework/Versions/3.2/Resources/library/StanHeaders/include/stan/math/prim/arr/functor/integrate_ode.hpp:12: In file included from /Library/Frameworks/R.framework/Versions/3.2/Resources/library/BH/include/boost/numeric/odeint.hpp:61: In file included from /Library/Frameworks/R.framework/Versions/3.2/Resources/library/BH/include/boost/numeric/odeint/util/multi_array_adaption.hpp:29: In file included from /Library/Frameworks/R.framework/Versions/3.2/Resources/library/BH/include/boost/multi_array.hpp:21: In file included from /Library/Frameworks/R.framework/Versions/3.2/Resources/library/BH/include/boost/multi_array/base.hpp:28: /Library/Frameworks/R.framework/Versions/3.2/Resources/library/BH/include/boost/multi_array/concept_checks.hpp:42:43: warning: unused typedef 'index_range' [-Wunused-local-typedef] typedef typename Array::index_range index_range; ^ /Library/Frameworks/R.framework/Versions/3.2/Resources/library/BH/include/boost/multi_array/concept_checks.hpp:43:37: warning: unused typedef 'index' [-Wunused-local-typedef] typedef typename Array::index index; ^ /Library/Frameworks/R.framework/Versions/3.2/Resources/library/BH/include/boost/multi_array/concept_checks.hpp:53:43: warning: unused typedef 'index_range' [-Wunused-local-typedef] typedef typename Array::index_range index_range; ^ /Library/Frameworks/R.framework/Versions/3.2/Resources/library/BH/include/boost/multi_array/concept_checks.hpp:54:37: warning: unused typedef 'index' [-Wunused-local-typedef] typedef typename Array::index index; ^ In file included from Modules.cpp:3: In file included from ./include/models.hpp:21: In file included from /Library/Frameworks/R.framework/Versions/3.2/Resources/library/rstan/include/rstan/rstaninc.hpp:3: In file included from /Library/Frameworks/R.framework/Versions/3.2/Resources/library/rstan/include/rstan/stan_fit.hpp:83: In file included from /Library/Frameworks/R.framework/Versions/3.2/Resources/library/StanHeaders/include/src/stan/variational/advi.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/3.2/Resources/library/StanHeaders/include/stan/math.hpp:80: /Library/Frameworks/R.framework/Versions/3.2/Resources/library/StanHeaders/include/stan/math/prim/mat/err/check_positive_ordered.hpp:39:67: warning: unused typedef 'size_type' [-Wunused-local-typedef] typedef typename index_type<Matrix<T_y, Dynamic, 1> >::type size_type; ^ In file included from Modules.cpp:3: ./include/models.hpp:335:28: warning: unused typedef 'fun_return_scalar_t' [-Wunused-local-typedef] typedef fun_scalar_t fun_return_scalar_t; ^ ./include/models.hpp:2633:28: warning: unused typedef 'fun_return_scalar_t' [-Wunused-local-typedef] typedef fun_scalar_t fun_return_scalar_t; ^ ./include/models.hpp:4806:28: warning: unused typedef 'fun_return_scalar_t' [-Wunused-local-typedef] typedef fun_scalar_t fun_return_scalar_t; ^ ./include/models.hpp:7500:28: warning: unused typedef 'fun_return_scalar_t' [-Wunused-local-typedef] typedef fun_scalar_t fun_return_scalar_t; ^ 12 warnings generated. clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o rstanarm.so Modules.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/3.2/Resources/library/rstanarm/libs * R * data *\ moving datasets to lazyload DB

    * caught segfault * address 0x18, cause 'memory not mapped'

Traceback: 1: dyn.load(file, DLLpath = DLLpath, ...) 2: library.dynam(lib, package, package.lib) 3: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) 4: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]), from = package) 5: loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) 6: asNamespace(ns) 7: namespaceImportFrom(ns, loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]), i[[2L]], from = package) 8: loadNamespace(name) 9: doTryCatch(return(expr), name, parentenv, handler) 10: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 11: tryCatchList(expr, classes, parentenv, handlers) 12: tryCatch(loadNamespace(name), error = function(e) { warning(gettextf("namespace %s is not available and has been replaced\nby .GlobalEnv when processing object %s", sQuote(name)[1L], sQuote(where)), domain = NA, call. = FALSE, immediate. = TRUE) .GlobalEnv}) 13: ..getNamespace(c("rstanarm", "2.8.9"), "example_model") 14: load(zfile, envir = envir) 15: utils::data(list = f, package = package, lib.loc = lib.loc, envir = dataEnv) 16: data2LazyLoadDB(pkg_name, lib, compress = data_compress) 17: doTryCatch(return(expr), name, parentenv, handler) 18: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 19: tryCatchList(expr, classes, parentenv, handlers) 20: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call)[1L] prefix <- paste("Error in", dcall, ": ") LONG <- 75L msg <- conditionMessage(e) sm <- strsplit(msg, "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && identical(getOption("show.error.messages"), TRUE)) { cat(msg, file = stderr()) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))}) 21: try(data2LazyLoadDB(pkg_name, lib, compress = data_compress)) 22: do_install_source(pkg_name, instdir, pkg, desc) 23: do_install(pkg) 24: tools:::.install_packages() aborting ... /Library/Frameworks/R.framework/Resources/bin/INSTALL: line 34: 10128 Done echo 'tools:::.install_packages()' 10129 Segmentation fault: 11 | R_DEFAULT_PACKAGES= LC_COLLATE=C "${R_HOME}/bin/R" $myArgs --slave --args ${args} Warning in install.packages : installation of package ‘rstanarm’ had non-zero exit status

On Saturday, January 30, 2016 10:44 AM, bgoodri notifications@github.com wrote:

Does it work if you doinstall.packages("rstanarm", type = "source") # requires Xcode

— Reply to this email directly or view it on GitHub.

— Reply to this email directly or view it on GitHub https://github.com/stan-dev/rstanarm/issues/63#issuecomment-177103158.

rubgb commented 8 years ago

No they're not. In my makevar file there only 2 lines: CC=clang CXX=clang++

On Saturday, January 30, 2016 9:04 PM, bgoodri <notifications@github.com> wrote:

Hmm. It seems that you have some extra linker options being invoked in

clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined
dynamic_lookup -single_module -multiply_defined suppress
-L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o
rstanarm.so Modules.o -F/Library/Frameworks/R.framework/.. -framework R
-Wl,-framework -Wl,CoreFoundation
installing to
/Library/Frameworks/R.framework/Versions/3.2/Resources/library/rstanarm/libs

Are these specified in your ~/.R/Makevars file?

On Sat, Jan 30, 2016 at 3:38 AM, rubgb notifications@github.com wrote:

Unfortunately it doesn't work.Here's the complete output after executing the command:

  • installing source package ‘rstanarm’ ... * package ‘rstanarm’ successfully unpacked and MD5 sums checked * libs clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -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 -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/StanHeaders/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/rstan/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/RcppEigen/include" -fPIC -Wall -mtune=core2 -g -O2 -c Modules.cpp -o Modules.o In file included from Modules.cpp:3: In file included from ./include/models.hpp:21: In file included from /Library/Frameworks/R.framework/Versions/3.2/Resources/library/rstan/include/rstan/rstaninc.hpp:3: In file included from /Library/Frameworks/R.framework/Versions/3.2/Resources/library/rstan/include/rstan/stan_fit.hpp:18: In file included from /Library/Frameworks/R.framework/Versions/3.2/Resources/library/StanHeaders/include/src/stan/model/util.hpp:7: In file included from /Library/Frameworks/R.framework/Versions/3.2/Resources/library/StanHeaders/include/stan/math/rev/mat/fun/grad.hpp:6: In file included from /Library/Frameworks/R.framework/Versions/3.2/Resources/library/StanHeaders/include/stan/math/rev/mat/fun/Eigen_NumTraits.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/3.2/Resources/library/StanHeaders/include/stan/math/rev/core.hpp:42: /Library/Frameworks/R.framework/Versions/3.2/Resources/library/StanHeaders/include/stan/math/rev/core/set_zero_all_adjoints.hpp:14:17: warning: 'static' function 'set_zero_all_adjoints' declared in header file should be declared 'static inline' [-Wunneeded-internal-declaration] static void set_zero_all_adjoints() { ^ In file included from Modules.cpp:3: In file included from ./include/models.hpp:21: In file included from /Library/Frameworks/R.framework/Versions/3.2/Resources/library/rstan/include/rstan/rstaninc.hpp:3: In file included from /Library/Frameworks/R.framework/Versions/3.2/Resources/library/rstan/include/rstan/stan_fit.hpp:18: In file included from /Library/Frameworks/R.framework/Versions/3.2/Resources/library/StanHeaders/include/src/stan/model/util.hpp:7: In file included from /Library/Frameworks/R.framework/Versions/3.2/Resources/library/StanHeaders/include/stan/math/rev/mat/fun/grad.hpp:6: In file included from /Library/Frameworks/R.framework/Versions/3.2/Resources/library/StanHeaders/include/stan/math/rev/mat/fun/Eigen_NumTraits.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/3.2/Resources/library/StanHeaders/include/stan/math/rev/core.hpp:43: /Library/Frameworks/R.framework/Versions/3.2/Resources/library/StanHeaders/include/stan/math/rev/core/set_zero_all_adjoints_nested.hpp:16:17: warning: 'static' function 'set_zero_all_adjoints_nested' declared in header file should be declared 'static inline' [-Wunneeded-internal-declaration] static void set_zero_all_adjoints_nested() { ^ In file included from Modules.cpp:3: In file included from ./include/models.hpp:21: In file included from /Library/Frameworks/R.framework/Versions/3.2/Resources/library/rstan/include/rstan/rstaninc.hpp:3: In file included from /Library/Frameworks/R.framework/Versions/3.2/Resources/library/rstan/include/rstan/stan_fit.hpp:83: In file included from /Library/Frameworks/R.framework/Versions/3.2/Resources/library/StanHeaders/include/src/stan/variational/advi.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/3.2/Resources/library/StanHeaders/include/stan/math.hpp:99: /Library/Frameworks/R.framework/Versions/3.2/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/autocorrelation.hpp:19:14: warning: function 'fft_next_good_size' is not needed and will not be emitted [-Wunneeded-internal-declaration] size_t fft_next_good_size(size_t N) { ^ In file included from Modules.cpp:3: In file included from ./include/models.hpp:21: In file included from /Library/Frameworks/R.framework/Versions/3.2/Resources/library/rstan/include/rstan/rstaninc.hpp:3: In file included from /Library/Frameworks/R.framework/Versions/3.2/Resources/library/rstan/include/rstan/stan_fit.hpp:83: In file included from /Library/Frameworks/R.framework/Versions/3.2/Resources/library/StanHeaders/include/src/stan/variational/advi.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/3.2/Resources/library/StanHeaders/include/stan/math.hpp:65: In file included from /Library/Frameworks/R.framework/Versions/3.2/Resources/library/StanHeaders/include/stan/math/prim/arr/functor/integrate_ode.hpp:12: In file included from /Library/Frameworks/R.framework/Versions/3.2/Resources/library/BH/include/boost/numeric/odeint.hpp:61: In file included from /Library/Frameworks/R.framework/Versions/3.2/Resources/library/BH/include/boost/numeric/odeint/util/multi_array_adaption.hpp:29: In file included from /Library/Frameworks/R.framework/Versions/3.2/Resources/library/BH/include/boost/multi_array.hpp:21: In file included from /Library/Frameworks/R.framework/Versions/3.2/Resources/library/BH/include/boost/multi_array/base.hpp:28: /Library/Frameworks/R.framework/Versions/3.2/Resources/library/BH/include/boost/multi_array/concept_checks.hpp:42:43: warning: unused typedef 'index_range' [-Wunused-local-typedef] typedef typename Array::index_range index_range; ^ /Library/Frameworks/R.framework/Versions/3.2/Resources/library/BH/include/boost/multi_array/concept_checks.hpp:43:37: warning: unused typedef 'index' [-Wunused-local-typedef] typedef typename Array::index index; ^ /Library/Frameworks/R.framework/Versions/3.2/Resources/library/BH/include/boost/multi_array/concept_checks.hpp:53:43: warning: unused typedef 'index_range' [-Wunused-local-typedef] typedef typename Array::index_range index_range; ^ /Library/Frameworks/R.framework/Versions/3.2/Resources/library/BH/include/boost/multi_array/concept_checks.hpp:54:37: warning: unused typedef 'index' [-Wunused-local-typedef] typedef typename Array::index index; ^ In file included from Modules.cpp:3: In file included from ./include/models.hpp:21: In file included from /Library/Frameworks/R.framework/Versions/3.2/Resources/library/rstan/include/rstan/rstaninc.hpp:3: In file included from /Library/Frameworks/R.framework/Versions/3.2/Resources/library/rstan/include/rstan/stan_fit.hpp:83: In file included from /Library/Frameworks/R.framework/Versions/3.2/Resources/library/StanHeaders/include/src/stan/variational/advi.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/3.2/Resources/library/StanHeaders/include/stan/math.hpp:80: /Library/Frameworks/R.framework/Versions/3.2/Resources/library/StanHeaders/include/stan/math/prim/mat/err/check_positive_ordered.hpp:39:67: warning: unused typedef 'size_type' [-Wunused-local-typedef] typedef typename index_type<Matrix<T_y, Dynamic, 1> >::type size_type; ^ In file included from Modules.cpp:3: ./include/models.hpp:335:28: warning: unused typedef 'fun_return_scalar_t' [-Wunused-local-typedef] typedef fun_scalar_t fun_return_scalar_t; ^ ./include/models.hpp:2633:28: warning: unused typedef 'fun_return_scalar_t' [-Wunused-local-typedef] typedef fun_scalar_t fun_return_scalar_t; ^ ./include/models.hpp:4806:28: warning: unused typedef 'fun_return_scalar_t' [-Wunused-local-typedef] typedef fun_scalar_t fun_return_scalar_t; ^ ./include/models.hpp:7500:28: warning: unused typedef 'fun_return_scalar_t' [-Wunused-local-typedef] typedef fun_scalar_t fun_return_scalar_t; ^ 12 warnings generated. clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o rstanarm.so Modules.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/3.2/Resources/library/rstanarm/libs * R * data *\ moving datasets to lazyload DB

* caught segfault * address 0x18, cause 'memory not mapped'

Traceback: 1: dyn.load(file, DLLpath = DLLpath, ...) 2: library.dynam(lib, package, package.lib) 3: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) 4: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]), from = package) 5: loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) 6: asNamespace(ns) 7: namespaceImportFrom(ns, loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]), i[[2L]], from = package) 8: loadNamespace(name) 9: doTryCatch(return(expr), name, parentenv, handler) 10: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 11: tryCatchList(expr, classes, parentenv, handlers) 12: tryCatch(loadNamespace(name), error = function(e) { warning(gettextf("namespace %s is not available and has been replaced\nby .GlobalEnv when processing object %s", sQuote(name)[1L], sQuote(where)), domain = NA, call. = FALSE, immediate. = TRUE) .GlobalEnv}) 13: ..getNamespace(c("rstanarm", "2.8.9"), "example_model") 14: load(zfile, envir = envir) 15: utils::data(list = f, package = package, lib.loc = lib.loc, envir = dataEnv) 16: data2LazyLoadDB(pkg_name, lib, compress = data_compress) 17: doTryCatch(return(expr), name, parentenv, handler) 18: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 19: tryCatchList(expr, classes, parentenv, handlers) 20: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call)[1L] prefix <- paste("Error in", dcall, ": ") LONG <- 75L msg <- conditionMessage(e) sm <- strsplit(msg, "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && identical(getOption("show.error.messages"), TRUE)) { cat(msg, file = stderr()) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))}) 21: try(data2LazyLoadDB(pkg_name, lib, compress = data_compress)) 22: do_install_source(pkg_name, instdir, pkg, desc) 23: do_install(pkg) 24: tools:::.install_packages() aborting ... /Library/Frameworks/R.framework/Resources/bin/INSTALL: line 34: 10128 Done echo 'tools:::.install_packages()' 10129 Segmentation fault: 11 | R_DEFAULT_PACKAGES= LC_COLLATE=C "${R_HOME}/bin/R" $myArgs --slave --args ${args} Warning in install.packages : installation of package ‘rstanarm’ had non-zero exit status

On Saturday, January 30, 2016 10:44 AM, bgoodri notifications@github.com wrote:

Does it work if you doinstall.packages("rstanarm", type = "source") # requires Xcode

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— Reply to this email directly or view it on GitHub https://github.com/stan-dev/rstanarm/issues/63#issuecomment-177103158.

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bgoodri commented 8 years ago

Can you run any models with just rstan? For example,

library(rstan)
stan_demo("blocker", chains = 1)