Since the current version of rstan (2.18.2) does not produce meaningful error messages if there is an initialization failure (https://github.com/stan-dev/rstan/issues/577) and also swallows all print messages (https://github.com/stan-dev/stan/issues/2737) when using optimizing, I tried to install an older version of stan for debugging a model. I remember that both these things worked at some point.
However, when doing
install_version('rstan','2.15.1',repos='https://www.freestatistics.org/cran/')
I get the errors message
Downloading package from url: https://www.freestatistics.org/cran//src/contrib/Archive/rstan/rstan_2.15.1.tar.gz
Installing rstan
'/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet CMD INSTALL \
'/private/var/folders/lw/kj89878x7ync198n0rbgtc6hgk_515/T/Rtmp4phKG2/devtools3d257e5d29df/rstan' \
--library='/Library/Frameworks/R.framework/Versions/3.5/Resources/library' --install-tests
* installing *source* package ‘rstan’ ...
** package ‘rstan’ successfully unpacked and MD5 sums checked
** libs
clang++ -arch x86_64 -ftemplate-depth-256 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"../inst/include" -I"../inst/include/boost_not_in_BH" -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 -DFUSION_MAX_VECTOR_SIZE=12 -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"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include" -I/usr/local/include -fPIC -Wno-unused-variable -Wno-unused-function -Wno-macro-redefined -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -c chains.cpp -o chains.o
In file included from chains.cpp:19:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/mean.hpp:5:
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:535:
/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 chains.cpp:19:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/mean.hpp:5:
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 chains.cpp:19:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/mean.hpp:5:
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 chains.cpp:19:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/mean.hpp:5:
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 chains.cpp:19:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/mean.hpp:5:
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 chains.cpp:19:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/mean.hpp:5:
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 chains.cpp:19:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/mean.hpp:5:
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 chains.cpp:19:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/mean.hpp:5:
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 chains.cpp:26:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/accumulators/statistics/stats.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/accumulators/statistics_fwd.hpp:12:
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/mpl/print.hpp:52:19: warning: in-class initialization of non-static data member is a C++11 extension [-Wc++11-extensions]
const int m_x = 1 / (sizeof(T) - sizeof(T));
^
In file included from chains.cpp:28:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/lexical_cast.hpp:31:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/lexical_cast/bad_lexical_cast.hpp:28:
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/throw_exception.hpp:70:29: error: no member named 'enable_both' in namespace 'boost::exception_detail'
throw exception_detail::enable_both( e );
~~~~~~~~~~~~~~~~~~^
In file included from chains.cpp:28:
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:44:
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:390:52: note: expanded from macro '_LIBCPP_BEGIN_NAMESPACE_STD'
#define _LIBCPP_BEGIN_NAMESPACE_STD namespace std {inline namespace _LIBCPP_NAMESPACE {
^
In file included from chains.cpp:29:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/random/additive_combine.hpp:27:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/random/linear_congruential.hpp:30:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/random/detail/const_mod.hpp:23:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/random/detail/large_arithmetic.hpp:19:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/random/detail/integer_log2.hpp:19:
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/pending/integer_log2.hpp:7:1: warning: This header is deprecated. Use <boost/integer/integer_log2.hpp> instead. [-W#pragma-messages]
BOOST_HEADER_DEPRECATED("<boost/integer/integer_log2.hpp>");
^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/config/header_deprecated.hpp:23:37: note: expanded from macro 'BOOST_HEADER_DEPRECATED'
# define BOOST_HEADER_DEPRECATED(a) BOOST_PRAGMA_MESSAGE("This header is deprecated. Use " a " instead.")
^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/config/pragma_message.hpp:24:34: note: expanded from macro 'BOOST_PRAGMA_MESSAGE'
# define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x)))
^
<scratch space>:130:2: note: expanded from here
message("This header is deprecated. Use " "<boost/integer/integer_log2.hpp>" " instead.")
^
11 warnings and 1 error generated.
make: *** [chains.o] Error 1
ERROR: compilation failed for package ‘rstan’
* removing ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/rstan’
* restoring previous ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/rstan’
Installation failed: Command failed (1)
The error I find is
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/throw_exception.hpp:70:29: error: no member named 'enable_both' in namespace 'boost::exception_detail' throw exception_detail::enable_both( e );
I understand that this seems to be related to the headers in the BH package but have no clue how to solve this.
-
Operating System
Mac 10.12.6 -
Output of
writeLines(readLines(file.path(Sys.getenv("HOME"), ".R/Makevars")))
CXXFLAGS= -Wno-unused-variable -Wno-unused-function -Wno-macro-redefined -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION
CC=clang
CXX=clang++ -arch x86_64 -ftemplate-depth-256
- Output of
devtools::session_info("rstan")
package * version date source
assertthat 0.2.1 2019-03-21 cran (@0.2.1)
backports 1.1.3 2018-12-14 cran (@1.1.3)
BH 1.69.0-1 2019-01-07 cran (@1.69.0-)
callr 3.2.0 2019-03-15 cran (@3.2.0)
checkmate 1.9.1 2019-01-15 cran (@1.9.1)
cli 1.1.0 2019-03-19 cran (@1.1.0)
colorspace 1.3-2 2016-12-14 CRAN (R 3.5.0)
compiler 3.5.0 2018-04-24 local
crayon 1.3.4 2017-09-16 CRAN (R 3.5.0)
desc 1.2.0 2018-05-01 CRAN (R 3.5.0)
digest 0.6.18 2018-10-10 cran (@0.6.18)
fansi 0.4.0 2018-10-05 cran (@0.4.0)
ggplot2 * 3.1.1 2019-04-07 cran (@3.1.1)
glue 1.2.0 2017-10-29 CRAN (R 3.5.0)
graphics * 3.5.0 2018-04-24 local
grDevices * 3.5.0 2018-04-24 local
grid 3.5.0 2018-04-24 local
gridExtra 2.3 2017-09-09 CRAN (R 3.5.0)
gtable 0.3.0 2019-03-25 cran (@0.3.0)
inline 0.3.15 2018-05-18 CRAN (R 3.5.0)
labeling 0.3 2014-08-23 CRAN (R 3.5.0)
lattice 0.20-35 2017-03-25 CRAN (R 3.5.0)
lazyeval 0.2.2 2019-03-15 cran (@0.2.2)
loo 2.1.0 2019-03-13 cran (@2.1.0)
magrittr 1.5 2014-11-22 CRAN (R 3.5.0)
MASS 7.3-51.4 2019-03-31 CRAN (R 3.5.2)
Matrix 1.2-14 2018-04-13 CRAN (R 3.5.0)
matrixStats 0.54.0 2018-07-23 CRAN (R 3.5.0)
methods * 3.5.0 2018-04-24 local
mgcv 1.8-23 2018-01-21 CRAN (R 3.5.0)
munsell 0.5.0 2018-06-12 CRAN (R 3.5.0)
nlme 3.1-137 2018-04-07 CRAN (R 3.5.0)
parallel 3.5.0 2018-04-24 local
pillar 1.3.1 2018-12-15 cran (@1.3.1)
pkgbuild 1.0.3 2019-03-20 cran (@1.0.3)
pkgconfig 2.0.2 2018-08-16 cran (@2.0.2)
plyr 1.8.4 2016-06-08 CRAN (R 3.5.0)
prettyunits 1.0.2 2015-07-13 CRAN (R 3.5.0)
processx 3.3.0 2019-03-10 cran (@3.3.0)
ps 1.3.0 2018-12-21 cran (@1.3.0)
R6 2.4.0 2019-02-14 cran (@2.4.0)
RColorBrewer 1.1-2 2014-12-07 CRAN (R 3.5.0)
Rcpp 1.0.1 2019-03-17 cran (@1.0.1)
RcppEigen 0.3.3.5.0 2018-11-24 cran (@0.3.3.5)
reshape2 1.4.3 2017-12-11 CRAN (R 3.5.0)
rlang 0.3.4 2019-04-07 cran (@0.3.4)
rprojroot 1.3-2 2018-01-03 CRAN (R 3.5.0)
rstan * 2.18.2 2018-11-07 CRAN (R 3.5.0)
scales 1.0.0 2018-08-09 cran (@1.0.0)
StanHeaders * 2.18.1 2019-01-28 cran (@2.18.1)
stats * 3.5.0 2018-04-24 local
stats4 3.5.0 2018-04-24 local
stringi 1.2.3 2018-06-12 CRAN (R 3.5.0)
stringr 1.3.1 2018-05-10 CRAN (R 3.5.0)
tibble 2.1.1 2019-03-16 cran (@2.1.1)
tools 3.5.0 2018-04-24 local
utf8 1.1.4 2018-05-24 CRAN (R 3.5.0)
utils * 3.5.0 2018-04-24 local
viridisLite 0.3.0 2018-02-01 CRAN (R 3.5.0)
withr 2.1.2 2018-03-15 CRAN (R 3.5.0)