CRAN Package Check Results for Package StanHeaders

Last updated on 2019-07-16 00:48:28 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 2.18.1-10 27.74 353.94 381.68 OK
r-devel-linux-x86_64-debian-gcc 2.18.1-10 16.40 298.03 314.43 OK
r-devel-linux-x86_64-fedora-clang 2.18.1-10 450.54 NOTE
r-devel-linux-x86_64-fedora-gcc 2.18.1-10 518.13 OK
r-devel-windows-ix86+x86_64 2.18.1-10 139.00 549.00 688.00 NOTE
r-patched-linux-x86_64 2.18.1-10 20.22 385.05 405.27 OK
r-patched-solaris-x86 2.18.1-10 572.40 NOTE
r-release-linux-x86_64 2.18.1-10 19.54 378.12 397.66 OK
r-release-windows-ix86+x86_64 2.18.1-10 103.00 408.00 511.00 NOTE
r-release-osx-x86_64 2.18.1-10 WARN
r-oldrel-windows-ix86+x86_64 2.18.1-10 174.00 398.00 572.00 NOTE
r-oldrel-osx-x86_64 2.18.1-10 NOTE

Additional issues

gcc-ASAN

Check Details

Version: 2.18.1-10
Check: installed package size
Result: NOTE
     installed size is 13.3Mb
     sub-directories of 1Mb or more:
     include 10.3Mb
     lib 2.8Mb
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-windows-ix86+x86_64, r-patched-solaris-x86, r-release-windows-ix86+x86_64, r-release-osx-x86_64, r-oldrel-windows-ix86+x86_64, r-oldrel-osx-x86_64

Version: 2.18.1-10
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
    --- re-building ‘stanmath.Rmd’ using rmarkdown
    Warning in engine$weave(file, quiet = quiet, encoding = enc) :
     Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
    Building shared library for Rcpp code chunk...
    In file included from file768f3f652c5c.cpp:4:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/StanHeaders.Rcheck/StanHeaders/include/stan/math/fwd/mat/fun/dot_self.hpp:4:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/StanHeaders.Rcheck/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:4:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/RcppEigen/include/Eigen/Dense:1:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/RcppEigen/include/Eigen/Core:535:
    /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/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 file768f3f652c5c.cpp:4:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/StanHeaders.Rcheck/StanHeaders/include/stan/math/fwd/mat/fun/dot_self.hpp:4:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/StanHeaders.Rcheck/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:4:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/RcppEigen/include/Eigen/Dense:2:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/RcppEigen/include/Eigen/LU:47:
    /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/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 file768f3f652c5c.cpp:4:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/StanHeaders.Rcheck/StanHeaders/include/stan/math/fwd/mat/fun/dot_self.hpp:4:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/StanHeaders.Rcheck/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:4:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/RcppEigen/include/Eigen/Dense:3:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/RcppEigen/include/Eigen/Cholesky:12:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/RcppEigen/include/Eigen/Jacobi:29:
    /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/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 file768f3f652c5c.cpp:4:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/StanHeaders.Rcheck/StanHeaders/include/stan/math/fwd/mat/fun/dot_self.hpp:4:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/StanHeaders.Rcheck/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:4:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/RcppEigen/include/Eigen/Dense:3:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/RcppEigen/include/Eigen/Cholesky:43:
    /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/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 file768f3f652c5c.cpp:4:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/StanHeaders.Rcheck/StanHeaders/include/stan/math/fwd/mat/fun/dot_self.hpp:4:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/StanHeaders.Rcheck/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:4:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/RcppEigen/include/Eigen/Dense:4:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/RcppEigen/include/Eigen/QR:17:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/RcppEigen/include/Eigen/Householder:27:
    /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/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 file768f3f652c5c.cpp:4:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/StanHeaders.Rcheck/StanHeaders/include/stan/math/fwd/mat/fun/dot_self.hpp:4:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/StanHeaders.Rcheck/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:4:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/RcppEigen/include/Eigen/Dense:5:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/RcppEigen/include/Eigen/SVD:48:
    /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/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 file768f3f652c5c.cpp:4:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/StanHeaders.Rcheck/StanHeaders/include/stan/math/fwd/mat/fun/dot_self.hpp:4:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/StanHeaders.Rcheck/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:4:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/RcppEigen/include/Eigen/Dense:6:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/RcppEigen/include/Eigen/Geometry:58:
    /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/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 file768f3f652c5c.cpp:4:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/StanHeaders.Rcheck/StanHeaders/include/stan/math/fwd/mat/fun/dot_self.hpp:4:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/StanHeaders.Rcheck/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:4:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/RcppEigen/include/Eigen/Dense:7:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/RcppEigen/include/Eigen/Eigenvalues:58:
    /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/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 file768f3f652c5c.cpp:6:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/StanHeaders.Rcheck/StanHeaders/include/stan/math.hpp:4:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/StanHeaders.Rcheck/StanHeaders/include/stan/math/rev/mat.hpp:12:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/StanHeaders.Rcheck/StanHeaders/include/stan/math/prim/mat.hpp:109:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/StanHeaders.Rcheck/StanHeaders/include/stan/math/prim/mat/fun/csr_extract_u.hpp:6:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/RcppEigen/include/Eigen/Sparse:26:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/RcppEigen/include/Eigen/SparseCore:66:
    /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/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 file768f3f652c5c.cpp:6:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/StanHeaders.Rcheck/StanHeaders/include/stan/math.hpp:4:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/StanHeaders.Rcheck/StanHeaders/include/stan/math/rev/mat.hpp:12:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/StanHeaders.Rcheck/StanHeaders/include/stan/math/prim/mat.hpp:109:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/StanHeaders.Rcheck/StanHeaders/include/stan/math/prim/mat/fun/csr_extract_u.hpp:6:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/RcppEigen/include/Eigen/Sparse:27:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/RcppEigen/include/Eigen/OrderingMethods:71:
    /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/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 file768f3f652c5c.cpp:6:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/StanHeaders.Rcheck/StanHeaders/include/stan/math.hpp:4:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/StanHeaders.Rcheck/StanHeaders/include/stan/math/rev/mat.hpp:12:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/StanHeaders.Rcheck/StanHeaders/include/stan/math/prim/mat.hpp:109:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/StanHeaders.Rcheck/StanHeaders/include/stan/math/prim/mat/fun/csr_extract_u.hpp:6:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/RcppEigen/include/Eigen/Sparse:29:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/RcppEigen/include/Eigen/SparseCholesky:43:
    /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/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 file768f3f652c5c.cpp:6:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/StanHeaders.Rcheck/StanHeaders/include/stan/math.hpp:4:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/StanHeaders.Rcheck/StanHeaders/include/stan/math/rev/mat.hpp:12:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/StanHeaders.Rcheck/StanHeaders/include/stan/math/prim/mat.hpp:109:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/StanHeaders.Rcheck/StanHeaders/include/stan/math/prim/mat/fun/csr_extract_u.hpp:6:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/RcppEigen/include/Eigen/Sparse:32:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/RcppEigen/include/Eigen/SparseQR:35:
    /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/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 file768f3f652c5c.cpp:6:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/StanHeaders.Rcheck/StanHeaders/include/stan/math.hpp:4:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/StanHeaders.Rcheck/StanHeaders/include/stan/math/rev/mat.hpp:12:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/StanHeaders.Rcheck/StanHeaders/include/stan/math/prim/mat.hpp:109:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/StanHeaders.Rcheck/StanHeaders/include/stan/math/prim/mat/fun/csr_extract_u.hpp:6:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/RcppEigen/include/Eigen/Sparse:33:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/RcppEigen/include/Eigen/IterativeLinearSolvers:46:
    /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/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 file768f3f652c5c.cpp:6:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/StanHeaders.Rcheck/StanHeaders/include/stan/math.hpp:4:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/StanHeaders.Rcheck/StanHeaders/include/stan/math/rev/mat.hpp:12:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/StanHeaders.Rcheck/StanHeaders/include/stan/math/prim/mat.hpp:292:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/StanHeaders.Rcheck/StanHeaders/include/stan/math/prim/mat/prob/dirichlet_rng.hpp:5:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/BH/include/boost/random/gamma_distribution.hpp:25:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/BH/include/boost/random/exponential_distribution.hpp:27:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/BH/include/boost/random/detail/int_float_pair.hpp:26:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/BH/include/boost/random/detail/integer_log2.hpp:19:
    /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/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>");
    ^
    /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/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.")
     ^
    /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/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>:52:2: note: expanded from here
     message("This header is deprecated. Use " "<boost/integer/integer_log2.hpp>" " instead.")
     ^
    In file included from file768f3f652c5c.cpp:8:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/RcppEigen/include/RcppEigen.h:25:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/RcppEigen/include/RcppEigenForward.h:32:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/RcppEigen/include/Eigen/CholmodSupport:45:
    /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/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 file768f3f652c5c.cpp:8:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/RcppEigen/include/RcppEigen.h:25:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/RcppEigen/include/RcppEigenForward.h:35:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/RcppEigen/include/unsupported/Eigen/KroneckerProduct:34:
    /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/RcppEigen/include/unsupported/Eigen/../../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 file768f3f652c5c.cpp:8:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/RcppEigen/include/RcppEigen.h:25:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/RcppEigen/include/RcppEigenForward.h:39:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/RcppEigen/include/unsupported/Eigen/Polynomials:135:
    /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/RcppEigen/include/unsupported/Eigen/../../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 file768f3f652c5c.cpp:8:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/RcppEigen/include/RcppEigen.h:25:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/RcppEigen/include/RcppEigenForward.h:40:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/RcppEigen/include/unsupported/Eigen/SparseExtra:51:
    /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/RcppEigen/include/unsupported/Eigen/../../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 file768f3f652c5c.cpp:5:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/StanHeaders.Rcheck/StanHeaders/include/stan/math/mix/mat/functor/hessian.hpp:6:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/StanHeaders.Rcheck/StanHeaders/include/stan/math/rev/core.hpp:45:
    /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/StanHeaders.Rcheck/StanHeaders/include/stan/math/rev/core/set_zero_all_adjoints.hpp:14:13: warning: unused function 'set_zero_all_adjoints' [-Wunused-function]
    static void set_zero_all_adjoints() {
     ^
    In file included from file768f3f652c5c.cpp:6:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/StanHeaders.Rcheck/StanHeaders/include/stan/math.hpp:4:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/StanHeaders.Rcheck/StanHeaders/include/stan/math/rev/mat.hpp:12:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/StanHeaders.Rcheck/StanHeaders/include/stan/math/prim/mat.hpp:336:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/StanHeaders.Rcheck/StanHeaders/include/stan/math/prim/mat/prob/poisson_log_glm_log.hpp:5:
    /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/StanHeaders.Rcheck/StanHeaders/include/stan/math/prim/mat/prob/poisson_log_glm_lpmf.hpp:64:59: warning: unused typedef 'T_alpha_val' [-Wunused-local-typedef]
     typename partials_return_type<T_alpha>::type>::type T_alpha_val;
     ^
    20 warnings generated.
    Building shared library for Rcpp code chunk...
    In file included from file768f76cd1a48.cpp:4:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/StanHeaders.Rcheck/StanHeaders/include/stan/math.hpp:4:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/StanHeaders.Rcheck/StanHeaders/include/stan/math/rev/mat.hpp:4:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/StanHeaders.Rcheck/StanHeaders/include/stan/math/rev/core.hpp:5:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/StanHeaders.Rcheck/StanHeaders/include/stan/math/rev/core/build_vari_array.hpp:4:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/StanHeaders.Rcheck/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:4:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/RcppEigen/include/Eigen/Dense:1:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/RcppEigen/include/Eigen/Core:535:
    /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/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 file768f76cd1a48.cpp:4:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/StanHeaders.Rcheck/StanHeaders/include/stan/math.hpp:4:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/StanHeaders.Rcheck/StanHeaders/include/stan/math/rev/mat.hpp:4:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/StanHeaders.Rcheck/StanHeaders/include/stan/math/rev/core.hpp:5:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/StanHeaders.Rcheck/StanHeaders/include/stan/math/rev/core/build_vari_array.hpp:4:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/StanHeaders.Rcheck/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:4:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/RcppEigen/include/Eigen/Dense:2:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/RcppEigen/include/Eigen/LU:47:
    /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/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 file768f76cd1a48.cpp:4:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/StanHeaders.Rcheck/StanHeaders/include/stan/math.hpp:4:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/StanHeaders.Rcheck/StanHeaders/include/stan/math/rev/mat.hpp:4:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/StanHeaders.Rcheck/StanHeaders/include/stan/math/rev/core.hpp:5:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/StanHeaders.Rcheck/StanHeaders/include/stan/math/rev/core/build_vari_array.hpp:4:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/StanHeaders.Rcheck/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:4:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/RcppEigen/include/Eigen/Dense:3:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/RcppEigen/include/Eigen/Cholesky:12:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/RcppEigen/include/Eigen/Jacobi:29:
    /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/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 file768f76cd1a48.cpp:4:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/StanHeaders.Rcheck/StanHeaders/include/stan/math.hpp:4:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/StanHeaders.Rcheck/StanHeaders/include/stan/math/rev/mat.hpp:4:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/StanHeaders.Rcheck/StanHeaders/include/stan/math/rev/core.hpp:5:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/StanHeaders.Rcheck/StanHeaders/include/stan/math/rev/core/build_vari_array.hpp:4:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/StanHeaders.Rcheck/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:4:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/RcppEigen/include/Eigen/Dense:3:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/RcppEigen/include/Eigen/Cholesky:43:
    /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/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 file768f76cd1a48.cpp:4:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/StanHeaders.Rcheck/StanHeaders/include/stan/math.hpp:4:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/StanHeaders.Rcheck/StanHeaders/include/stan/math/rev/mat.hpp:4:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/StanHeaders.Rcheck/StanHeaders/include/stan/math/rev/core.hpp:5:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/StanHeaders.Rcheck/StanHeaders/include/stan/math/rev/core/build_vari_array.hpp:4:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/StanHeaders.Rcheck/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:4:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/RcppEigen/include/Eigen/Dense:4:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/RcppEigen/include/Eigen/QR:17:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/RcppEigen/include/Eigen/Householder:27:
    /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/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 file768f76cd1a48.cpp:4:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/StanHeaders.Rcheck/StanHeaders/include/stan/math.hpp:4:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/StanHeaders.Rcheck/StanHeaders/include/stan/math/rev/mat.hpp:4:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/StanHeaders.Rcheck/StanHeaders/include/stan/math/rev/core.hpp:5:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/StanHeaders.Rcheck/StanHeaders/include/stan/math/rev/core/build_vari_array.hpp:4:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/StanHeaders.Rcheck/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:4:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/RcppEigen/include/Eigen/Dense:5:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/RcppEigen/include/Eigen/SVD:48:
    /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/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 file768f76cd1a48.cpp:4:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/StanHeaders.Rcheck/StanHeaders/include/stan/math.hpp:4:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/StanHeaders.Rcheck/StanHeaders/include/stan/math/rev/mat.hpp:4:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/StanHeaders.Rcheck/StanHeaders/include/stan/math/rev/core.hpp:5:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/StanHeaders.Rcheck/StanHeaders/include/stan/math/rev/core/build_vari_array.hpp:4:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/StanHeaders.Rcheck/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:4:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/RcppEigen/include/Eigen/Dense:6:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/RcppEigen/include/Eigen/Geometry:58:
    /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/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 file768f76cd1a48.cpp:4:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/StanHeaders.Rcheck/StanHeaders/include/stan/math.hpp:4:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/StanHeaders.Rcheck/StanHeaders/include/stan/math/rev/mat.hpp:4:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/StanHeaders.Rcheck/StanHeaders/include/stan/math/rev/core.hpp:5:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/StanHeaders.Rcheck/StanHeaders/include/stan/math/rev/core/build_vari_array.hpp:4:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/StanHeaders.Rcheck/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:4:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/RcppEigen/include/Eigen/Dense:7:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/RcppEigen/include/Eigen/Eigenvalues:58:
    /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/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 file768f76cd1a48.cpp:4:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/StanHeaders.Rcheck/StanHeaders/include/stan/math.hpp:4:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/StanHeaders.Rcheck/StanHeaders/include/stan/math/rev/mat.hpp:12:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/StanHeaders.Rcheck/StanHeaders/include/stan/math/prim/mat.hpp:109:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/StanHeaders.Rcheck/StanHeaders/include/stan/math/prim/mat/fun/csr_extract_u.hpp:6:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/RcppEigen/include/Eigen/Sparse:26:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/RcppEigen/include/Eigen/SparseCore:66:
    /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/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 file768f76cd1a48.cpp:4:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/StanHeaders.Rcheck/StanHeaders/include/stan/math.hpp:4:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/StanHeaders.Rcheck/StanHeaders/include/stan/math/rev/mat.hpp:12:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/StanHeaders.Rcheck/StanHeaders/include/stan/math/prim/mat.hpp:109:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/StanHeaders.Rcheck/StanHeaders/include/stan/math/prim/mat/fun/csr_extract_u.hpp:6:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/RcppEigen/include/Eigen/Sparse:27:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/RcppEigen/include/Eigen/OrderingMethods:71:
    /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/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 file768f76cd1a48.cpp:4:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/StanHeaders.Rcheck/StanHeaders/include/stan/math.hpp:4:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/StanHeaders.Rcheck/StanHeaders/include/stan/math/rev/mat.hpp:12:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/StanHeaders.Rcheck/StanHeaders/include/stan/math/prim/mat.hpp:109:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/StanHeaders.Rcheck/StanHeaders/include/stan/math/prim/mat/fun/csr_extract_u.hpp:6:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/RcppEigen/include/Eigen/Sparse:29:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/RcppEigen/include/Eigen/SparseCholesky:43:
    /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/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 file768f76cd1a48.cpp:4:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/StanHeaders.Rcheck/StanHeaders/include/stan/math.hpp:4:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/StanHeaders.Rcheck/StanHeaders/include/stan/math/rev/mat.hpp:12:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/StanHeaders.Rcheck/StanHeaders/include/stan/math/prim/mat.hpp:109:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/StanHeaders.Rcheck/StanHeaders/include/stan/math/prim/mat/fun/csr_extract_u.hpp:6:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/RcppEigen/include/Eigen/Sparse:32:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/RcppEigen/include/Eigen/SparseQR:35:
    /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/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 file768f76cd1a48.cpp:4:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/StanHeaders.Rcheck/StanHeaders/include/stan/math.hpp:4:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/StanHeaders.Rcheck/StanHeaders/include/stan/math/rev/mat.hpp:12:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/StanHeaders.Rcheck/StanHeaders/include/stan/math/prim/mat.hpp:109:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/StanHeaders.Rcheck/StanHeaders/include/stan/math/prim/mat/fun/csr_extract_u.hpp:6:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/RcppEigen/include/Eigen/Sparse:33:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/RcppEigen/include/Eigen/IterativeLinearSolvers:46:
    /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/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 file768f76cd1a48.cpp:4:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/StanHeaders.Rcheck/StanHeaders/include/stan/math.hpp:4:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/StanHeaders.Rcheck/StanHeaders/include/stan/math/rev/mat.hpp:12:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/StanHeaders.Rcheck/StanHeaders/include/stan/math/prim/mat.hpp:292:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/StanHeaders.Rcheck/StanHeaders/include/stan/math/prim/mat/prob/dirichlet_rng.hpp:5:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/BH/include/boost/random/gamma_distribution.hpp:25:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/BH/include/boost/random/exponential_distribution.hpp:27:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/BH/include/boost/random/detail/int_float_pair.hpp:26:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/BH/include/boost/random/detail/integer_log2.hpp:19:
    /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/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>");
    ^
    /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/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.")
     ^
    /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/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>:29:2: note: expanded from here
     message("This header is deprecated. Use " "<boost/integer/integer_log2.hpp>" " instead.")
     ^
    In file included from file768f76cd1a48.cpp:6:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/RcppEigen/include/RcppEigen.h:25:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/RcppEigen/include/RcppEigenForward.h:32:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/RcppEigen/include/Eigen/CholmodSupport:45:
    /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/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 file768f76cd1a48.cpp:6:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/RcppEigen/include/RcppEigen.h:25:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/RcppEigen/include/RcppEigenForward.h:35:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/RcppEigen/include/unsupported/Eigen/KroneckerProduct:34:
    /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/RcppEigen/include/unsupported/Eigen/../../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 file768f76cd1a48.cpp:6:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/RcppEigen/include/RcppEigen.h:25:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/RcppEigen/include/RcppEigenForward.h:39:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/RcppEigen/include/unsupported/Eigen/Polynomials:135:
    /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/RcppEigen/include/unsupported/Eigen/../../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 file768f76cd1a48.cpp:6:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/RcppEigen/include/RcppEigen.h:25:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/RcppEigen/include/RcppEigenForward.h:40:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/RcppEigen/include/unsupported/Eigen/SparseExtra:51:
    /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/RcppEigen/include/unsupported/Eigen/../../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 file768f76cd1a48.cpp:4:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/StanHeaders.Rcheck/StanHeaders/include/stan/math.hpp:4:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/StanHeaders.Rcheck/StanHeaders/include/stan/math/rev/mat.hpp:4:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/StanHeaders.Rcheck/StanHeaders/include/stan/math/rev/core.hpp:45:
    /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/StanHeaders.Rcheck/StanHeaders/include/stan/math/rev/core/set_zero_all_adjoints.hpp:14:13: warning: unused function 'set_zero_all_adjoints' [-Wunused-function]
    static void set_zero_all_adjoints() {
     ^
    In file included from file768f76cd1a48.cpp:4:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/StanHeaders.Rcheck/StanHeaders/include/stan/math.hpp:4:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/StanHeaders.Rcheck/StanHeaders/include/stan/math/rev/mat.hpp:12:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/StanHeaders.Rcheck/StanHeaders/include/stan/math/prim/mat.hpp:336:
    In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/StanHeaders.Rcheck/StanHeaders/include/stan/math/prim/mat/prob/poisson_log_glm_log.hpp:5:
    /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/StanHeaders.Rcheck/StanHeaders/include/stan/math/prim/mat/prob/poisson_log_glm_lpmf.hpp:64:59: warning: unused typedef 'T_alpha_val' [-Wunused-local-typedef]
     typename partials_return_type<T_alpha>::type>::type T_alpha_val;
     ^
    20 warnings generated.
    
     *** caught segfault ***
    address 0x7f9ee6f00000, cause 'memory not mapped'
    
    Traceback:
     1: .Call(<pointer: 0x106cc6db0>, A, y0)
     2: stiff(A, y0)
     3: all.equal(stiff(A, y0), c(0, 0), tol = 1e-08)
     4: eval(expr, envir, enclos)
     5: eval(expr, envir, enclos)
     6: withVisible(eval(expr, envir, enclos))
     7: withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)
     8: handle(ev <- withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler))
     9: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)))
    10: evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos, debug = debug, last = i == length(out), use_try = stop_on_error != 2L, keep_warning = keep_warning, keep_message = keep_message, output_handler = output_handler, include_timing = include_timing)
    11: evaluate::evaluate(...)
    12: evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning), keep_message = !isFALSE(options$message), stop_on_error = if (options$error && options$include) 0L else 2L, output_handler = knit_handlers(options$render, options))
    13: in_dir(input_dir(), evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning), keep_message = !isFALSE(options$message), stop_on_error = if (options$error && options$include) 0L else 2L, output_handler = knit_handlers(options$render, options)))
    14: block_exec(params)
    15: call_block(x)
    16: process_group.block(group)
    17: process_group(group)
    18: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { setwd(wd) cat(res, sep = "\n", file = output %n% "") message("Quitting from lines ", paste(current_lines(i), collapse = "-"), " (", knit_concord$get("infile"), ") ") })
    19: process_file(text, output)
    20: knit(input, text = text, envir = envir, quiet = quiet)
    21: knit2html(..., force_v1 = TRUE)
    22: (if (grepl("\\.[Rr]md$", file)) knit2html_v1 else if (grepl("\\.[Rr]rst$", file)) knit2pandoc else knit)(file, encoding = encoding, quiet = quiet, envir = globalenv(), ...)
    23: vweave(...)
    24: engine$weave(file, quiet = quiet, encoding = enc)
    25: doTryCatch(return(expr), name, parentenv, handler)
    26: tryCatchOne(expr, names, parentenv, handlers[[1L]])
    27: tryCatchList(expr, classes, parentenv, handlers)
    28: tryCatch({ engine$weave(file, quiet = quiet, encoding = enc) setwd(startdir) output <- find_vignette_product(name, by = "weave", engine = engine) if (!have.makefile && vignette_is_tex(output)) { texi2pdf(file = output, clean = FALSE, quiet = quiet) output <- find_vignette_product(name, by = "texi2pdf", engine = engine) } outputs <- c(outputs, output)}, error = function(e) { thisOK <<- FALSE fails <<- c(fails, file) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e)))})
    29: tools:::buildVignettes(dir = "/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/StanHeaders.Rcheck/vign_test/StanHeaders", ser_elibs = "/tmp/RtmpKnOcLm/file741d32e0e0f7.rds")
    An irrecoverable exception occurred. R is aborting now ...
Flavor: r-release-osx-x86_64