CRAN Package Check Results for Package rstan

Last updated on 2020-04-25 01:53:16 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 2.19.3 709.05 788.21 1497.26 NOTE
r-devel-linux-x86_64-debian-gcc 2.19.3 615.14 605.22 1220.36 NOTE
r-devel-linux-x86_64-fedora-clang 2.19.3 1875.35 NOTE
r-devel-linux-x86_64-fedora-gcc 2.19.3 2111.19 NOTE
r-devel-windows-ix86+x86_64 2.19.3 1749.00 673.00 2422.00 NOTE
r-patched-linux-x86_64 2.19.3 714.67 746.88 1461.55 NOTE
r-patched-osx-x86_64 2.19.3 WARN
r-patched-solaris-x86 2.19.3 1694.30 NOTE
r-release-linux-x86_64 2.19.3 701.98 736.97 1438.95 NOTE
r-release-windows-ix86+x86_64 2.19.3 1779.00 689.00 2468.00 NOTE
r-release-osx-x86_64 2.19.3 NOTE
r-oldrel-windows-ix86+x86_64 2.19.3 1337.00 773.00 2110.00 NOTE
r-oldrel-osx-x86_64 2.19.3 NOTE

Check Details

Version: 2.19.3
Check: for GNU extensions in Makefiles
Result: NOTE
    GNU make is a SystemRequirements.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-ix86+x86_64, r-patched-linux-x86_64, r-patched-osx-x86_64, r-patched-solaris-x86, r-release-linux-x86_64, r-release-windows-ix86+x86_64, r-release-osx-x86_64, r-oldrel-windows-ix86+x86_64, r-oldrel-osx-x86_64

Version: 2.19.3
Check: installed package size
Result: NOTE
     installed size is 191.6Mb
     sub-directories of 1Mb or more:
     libs 188.8Mb
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-windows-ix86+x86_64, r-patched-osx-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: 2.19.3
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
    --- re-building ‘SBC.Rmd’ using rmarkdown
    Creating a 'stanmodel' object beta_binomial
    dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
     Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
     Expected in: /usr/lib/libSystem.B.dylib
    
    dyld: Symbol not found: ____chkstk_darwin
     Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
     Expected in: /usr/lib/libSystem.B.dylib
    
    Error: processing vignette 'SBC.Rmd' failed with diagnostics:
    pandoc document conversion failed with error 6
    --- failed re-building ‘SBC.Rmd’
    
    --- re-building ‘external.Rmd’ using rmarkdown
    dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
     Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
     Expected in: /usr/lib/libSystem.B.dylib
    
    dyld: Symbol not found: ____chkstk_darwin
     Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
     Expected in: /usr/lib/libSystem.B.dylib
    
    Error: processing vignette 'external.Rmd' failed with diagnostics:
    pandoc document conversion failed with error 6
    --- failed re-building ‘external.Rmd’
    
    --- re-building ‘rstan.Rmd’ using rmarkdown
    In file included from <built-in>:1:
    In file included from /Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.0/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:4:
    In file included from /Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.0/RcppEigen/include/Eigen/Dense:1:
    In file included from /Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.0/RcppEigen/include/Eigen/Core:535:
    /Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.0/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 <built-in>:1:
    In file included from /Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.0/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:4:
    In file included from /Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.0/RcppEigen/include/Eigen/Dense:2:
    In file included from /Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.0/RcppEigen/include/Eigen/LU:47:
    /Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.0/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 <built-in>:1:
    In file included from /Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.0/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:4:
    In file included from /Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.0/RcppEigen/include/Eigen/Dense:3:
    In file included from /Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.0/RcppEigen/include/Eigen/Cholesky:12:
    In file included from /Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.0/RcppEigen/include/Eigen/Jacobi:29:
    /Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.0/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 <built-in>:1:
    In file included from /Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.0/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:4:
    In file included from /Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.0/RcppEigen/include/Eigen/Dense:3:
    In file included from /Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.0/RcppEigen/include/Eigen/Cholesky:43:
    /Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.0/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 <built-in>:1:
    In file included from /Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.0/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:4:
    In file included from /Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.0/RcppEigen/include/Eigen/Dense:4:
    In file included from /Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.0/RcppEigen/include/Eigen/QR:17:
    In file included from /Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.0/RcppEigen/include/Eigen/Householder:27:
    /Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.0/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 <built-in>:1:
    In file included from /Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.0/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:4:
    In file included from /Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.0/RcppEigen/include/Eigen/Dense:5:
    In file included from /Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.0/RcppEigen/include/Eigen/SVD:48:
    /Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.0/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 <built-in>:1:
    In file included from /Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.0/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:4:
    In file included from /Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.0/RcppEigen/include/Eigen/Dense:6:
    In file included from /Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.0/RcppEigen/include/Eigen/Geometry:58:
    /Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.0/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 <built-in>:1:
    In file included from /Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.0/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:4:
    In file included from /Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.0/RcppEigen/include/Eigen/Dense:7:
    In file included from /Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.0/RcppEigen/include/Eigen/Eigenvalues:58:
    /Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.0/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 file1335b46ab23df.cpp:8:
    In file included from /Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.0/RcppEigen/include/RcppEigen.h:25:
    In file included from /Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.0/RcppEigen/include/RcppEigenForward.h:31:
    In file included from /Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.0/RcppEigen/include/Eigen/Sparse:26:
    In file included from /Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.0/RcppEigen/include/Eigen/SparseCore:66:
    /Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.0/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 file1335b46ab23df.cpp:8:
    In file included from /Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.0/RcppEigen/include/RcppEigen.h:25:
    In file included from /Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.0/RcppEigen/include/RcppEigenForward.h:31:
    In file included from /Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.0/RcppEigen/include/Eigen/Sparse:27:
    In file included from /Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.0/RcppEigen/include/Eigen/OrderingMethods:71:
    /Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.0/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 file1335b46ab23df.cpp:8:
    In file included from /Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.0/RcppEigen/include/RcppEigen.h:25:
    In file included from /Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.0/RcppEigen/include/RcppEigenForward.h:31:
    In file included from /Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.0/RcppEigen/include/Eigen/Sparse:29:
    In file included from /Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.0/RcppEigen/include/Eigen/SparseCholesky:43:
    /Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.0/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 file1335b46ab23df.cpp:8:
    In file included from /Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.0/RcppEigen/include/RcppEigen.h:25:
    In file included from /Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.0/RcppEigen/include/RcppEigenForward.h:31:
    In file included from /Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.0/RcppEigen/include/Eigen/Sparse:32:
    In file included from /Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.0/RcppEigen/include/Eigen/SparseQR:35:
    /Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.0/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 file1335b46ab23df.cpp:8:
    In file included from /Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.0/RcppEigen/include/RcppEigen.h:25:
    In file included from /Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.0/RcppEigen/include/RcppEigenForward.h:31:
    In file included from /Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.0/RcppEigen/include/Eigen/Sparse:33:
    In file included from /Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.0/RcppEigen/include/Eigen/IterativeLinearSolvers:46:
    /Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.0/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 file1335b46ab23df.cpp:8:
    In file included from /Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.0/RcppEigen/include/RcppEigen.h:25:
    In file included from /Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.0/RcppEigen/include/RcppEigenForward.h:32:
    In file included from /Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.0/RcppEigen/include/Eigen/CholmodSupport:45:
    /Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.0/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 file1335b46ab23df.cpp:8:
    In file included from /Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.0/RcppEigen/include/RcppEigen.h:25:
    In file included from /Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.0/RcppEigen/include/RcppEigenForward.h:35:
    In file included from /Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.0/RcppEigen/include/unsupported/Eigen/KroneckerProduct:34:
    /Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.0/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 file1335b46ab23df.cpp:8:
    In file included from /Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.0/RcppEigen/include/RcppEigen.h:25:
    In file included from /Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.0/RcppEigen/include/RcppEigenForward.h:39:
    In file included from /Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.0/RcppEigen/include/unsupported/Eigen/Polynomials:135:
    /Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.0/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 file1335b46ab23df.cpp:8:
    In file included from /Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.0/RcppEigen/include/RcppEigen.h:25:
    In file included from /Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.0/RcppEigen/include/RcppEigenForward.h:40:
    In file included from /Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.0/RcppEigen/include/unsupported/Eigen/SparseExtra:51:
    /Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.0/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 file1335b46ab23df.cpp:11:
    In file included from /Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.0/StanHeaders/include/src/stan/model/standalone_functions_header.hpp:4:
    In file included from /Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.0/StanHeaders/include/stan/math.hpp:4:
    In file included from /Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.0/StanHeaders/include/stan/math/rev/mat.hpp:4:
    In file included from /Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.0/StanHeaders/include/stan/math/rev/core.hpp:45:
    /Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.0/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 file1335b46ab23df.cpp:11:
    In file included from /Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.0/StanHeaders/include/src/stan/model/standalone_functions_header.hpp:4:
    In file included from /Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.0/StanHeaders/include/stan/math.hpp:4:
    In file included from /Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.0/StanHeaders/include/stan/math/rev/mat.hpp:4:
    In file included from /Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.0/StanHeaders/include/stan/math/rev/core.hpp:46:
    /Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.0/StanHeaders/include/stan/math/rev/core/set_zero_all_adjoints_nested.hpp:17:13: 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 file1335b46ab23df.cpp:11:
    In file included from /Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.0/StanHeaders/include/src/stan/model/standalone_functions_header.hpp:4:
    In file included from /Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.0/StanHeaders/include/stan/math.hpp:4:
    In file included from /Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.0/StanHeaders/include/stan/math/rev/mat.hpp:12:
    In file included from /Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.0/StanHeaders/include/stan/math/prim/mat.hpp:336:
    In file included from /Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.0/StanHeaders/include/stan/math/prim/mat/prob/poisson_log_glm_log.hpp:5:
    /Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.0/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.
    ld: warning: text-based stub file /System/Library/Frameworks//CoreFoundation.framework/CoreFoundation.tbd and library file /System/Library/Frameworks//CoreFoundation.framework/CoreFoundation are out of sync. Falling back to library file for linking.
    dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
     Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
     Expected in: /usr/lib/libSystem.B.dylib
    
    dyld: Symbol not found: ____chkstk_darwin
     Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
     Expected in: /usr/lib/libSystem.B.dylib
    
    Error: processing vignette 'rstan.Rmd' failed with diagnostics:
    pandoc document conversion failed with error 6
    --- failed re-building ‘rstan.Rmd’
    
    --- re-building ‘stanfit-objects.Rmd’ using rmarkdown
    dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
     Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
     Expected in: /usr/lib/libSystem.B.dylib
    
    dyld: Symbol not found: ____chkstk_darwin
     Referenced from: /usr/local/bin/pandoc (which was built for Mac OS X 10.15)
     Expected in: /usr/lib/libSystem.B.dylib
    
    Error: processing vignette 'stanfit-objects.Rmd' failed with diagnostics:
    pandoc document conversion failed with error 6
    --- failed re-building ‘stanfit-objects.Rmd’
    
    SUMMARY: processing the following files failed:
     ‘SBC.Rmd’ ‘external.Rmd’ ‘rstan.Rmd’ ‘stanfit-objects.Rmd’
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-patched-osx-x86_64