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tidymodels / tidyposterior

Bayesian comparisons of models using resampled statistics
https://tidyposterior.tidymodels.org
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Error when installing tidyposterior from CRAN #49

Closed kamaulindhardt closed 3 years ago

kamaulindhardt commented 3 years ago

< -- ~~~~~~~~~~~~ -->

The problem

ERROR: lazy loading failed for package ‘tidyposterior’

I'm having trouble with ...

Reproducible example

install.packages("tidyposterior") Installing package into ‘/Users/kamaulindhardt_1/Library/R/3.6/library’ (as ‘lib’ is unspecified) also installing the dependency ‘rstanarm’

There are binary versions available but the source versions are later: binary source needs_compilation rstanarm 2.19.2 2.21.1 TRUE tidyposterior 0.0.3 0.1.0 FALSE

Do you want to install from sources the package which needs compilation? (Yes/no/cancel) no trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/rstanarm_2.19.2.tgz' Content type 'application/x-gzip' length 33305501 bytes (31.8 MB)

downloaded 31.8 MB

The downloaded binary packages are in /var/folders/6p/c87kn7652k3bb9lw5j3c2rn00000gp/T//RtmpLkGtyy/downloaded_packages installing the source package ‘tidyposterior’

trying URL 'https://cran.rstudio.com/src/contrib/tidyposterior_0.1.0.tar.gz' Content type 'application/x-gzip' length 233442 bytes (227 KB)

downloaded 227 KB

The downloaded source packages are in ‘/private/var/folders/6p/c87kn7652k3bb9lw5j3c2rn00000gp/T/RtmpLkGtyy/downloaded_packages’

juliasilge commented 3 years ago

namespace ‘rstanarm’ 2.19.2 is being loaded, but >= 2.21.1 is required

Have you tried installing/updating rstanarm?

kamaulindhardt commented 3 years ago

I cannot update rstanarm when I try I get the following crazy error:

> remotes::install_github("tidymodels/tidyposterior")
Downloading GitHub repo tidymodels/tidyposterior@HEAD
These packages have more recent versions available.
It is recommended to update all of them.
Which would you like to update?

1: All                               
2: CRAN packages only                
3: None                              
4: rstanarm (2.19.2 -> 2.21.1) [CRAN]

Enter one or more numbers, or an empty line to skip updates: yes
Enter one or more numbers, or an empty line to skip updates: 1
rstanarm (2.19.2 -> 2.21.1) [CRAN]
Installing 1 packages: rstanarm
Installing package into ‘/Users/kamaulindhardt_1/Library/R/3.6/library’
(as ‘lib’ is unspecified)

  There is a binary version available but the source version is later:
         binary source needs_compilation
rstanarm 2.19.2 2.21.1              TRUE

Do you want to install from sources the package which needs compilation? (Yes/no/cancel) yes
installing the source package ‘rstanarm’

trying URL 'https://cran.rstudio.com/src/contrib/rstanarm_2.21.1.tar.gz'
Content type 'application/x-gzip' length 3548723 bytes (3.4 MB)
==================================================
downloaded 3.4 MB

* installing *source* package ‘rstanarm’ ...
** package ‘rstanarm’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
"/Library/Frameworks/R.framework/Resources/bin/Rscript" -e "source(file.path('..', 'tools', 'make_cc.R')); make_cc(commandArgs(TRUE))" stan_files/bernoulli.stan
Wrote C++ file "stan_files/bernoulli.cc"

clang++ -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"../inst/include" -I"/Users/kamaulindhardt_1/Library/R/3.6/library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -I"/Users/kamaulindhardt_1/Library/R/3.6/library/StanHeaders/include" -I"/Users/kamaulindhardt_1/Library/R/3.6/library/rstan/include" -I"/Users/kamaulindhardt_1/Library/R/3.6/library/BH/include" -I"/Users/kamaulindhardt_1/Library/R/3.6/library/Rcpp/include" -I"/Users/kamaulindhardt_1/Library/R/3.6/library/RcppEigen/include" -I"/Users/kamaulindhardt_1/Library/R/3.6/library/RcppParallel/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include `"/Library/Frameworks/R.framework/Resources/bin/Rscript" -e "RcppParallel::CxxFlags()"` `"/Library/Frameworks/R.framework/Resources/bin/Rscript" -e "StanHeaders:::CxxFlags()"` -fPIC  -Wall -g -O2  -c stan_files/bernoulli.cc -o stan_files/bernoulli.o
In file included from stan_files/bernoulli.cc:3:
In file included from stan_files/bernoulli.hpp:18:
In file included from /Users/kamaulindhardt_1/Library/R/3.6/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Users/kamaulindhardt_1/Library/R/3.6/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
In file included from /Users/kamaulindhardt_1/Library/R/3.6/library/RcppEigen/include/Eigen/Dense:1:
In file included from /Users/kamaulindhardt_1/Library/R/3.6/library/RcppEigen/include/Eigen/Core:540:
/Users/kamaulindhardt_1/Library/R/3.6/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from stan_files/bernoulli.cc:3:
In file included from stan_files/bernoulli.hpp:18:
In file included from /Users/kamaulindhardt_1/Library/R/3.6/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Users/kamaulindhardt_1/Library/R/3.6/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
In file included from /Users/kamaulindhardt_1/Library/R/3.6/library/RcppEigen/include/Eigen/Dense:2:
In file included from /Users/kamaulindhardt_1/Library/R/3.6/library/RcppEigen/include/Eigen/LU:47:
/Users/kamaulindhardt_1/Library/R/3.6/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from stan_files/bernoulli.cc:3:
In file included from stan_files/bernoulli.hpp:18:
In file included from /Users/kamaulindhardt_1/Library/R/3.6/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Users/kamaulindhardt_1/Library/R/3.6/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
In file included from /Users/kamaulindhardt_1/Library/R/3.6/library/RcppEigen/include/Eigen/Dense:3:
In file included from /Users/kamaulindhardt_1/Library/R/3.6/library/RcppEigen/include/Eigen/Cholesky:12:
In file included from /Users/kamaulindhardt_1/Library/R/3.6/library/RcppEigen/include/Eigen/Jacobi:29:
/Users/kamaulindhardt_1/Library/R/3.6/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from stan_files/bernoulli.cc:3:
In file included from stan_files/bernoulli.hpp:18:
In file included from /Users/kamaulindhardt_1/Library/R/3.6/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Users/kamaulindhardt_1/Library/R/3.6/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
In file included from /Users/kamaulindhardt_1/Library/R/3.6/library/RcppEigen/include/Eigen/Dense:3:
In file included from /Users/kamaulindhardt_1/Library/R/3.6/library/RcppEigen/include/Eigen/Cholesky:43:
/Users/kamaulindhardt_1/Library/R/3.6/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from stan_files/bernoulli.cc:3:
In file included from stan_files/bernoulli.hpp:18:
In file included from /Users/kamaulindhardt_1/Library/R/3.6/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Users/kamaulindhardt_1/Library/R/3.6/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
In file included from /Users/kamaulindhardt_1/Library/R/3.6/library/RcppEigen/include/Eigen/Dense:4:
In file included from /Users/kamaulindhardt_1/Library/R/3.6/library/RcppEigen/include/Eigen/QR:15:
In file included from /Users/kamaulindhardt_1/Library/R/3.6/library/RcppEigen/include/Eigen/Householder:27:
/Users/kamaulindhardt_1/Library/R/3.6/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from stan_files/bernoulli.cc:3:
In file included from stan_files/bernoulli.hpp:18:
In file included from /Users/kamaulindhardt_1/Library/R/3.6/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Users/kamaulindhardt_1/Library/R/3.6/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
In file included from /Users/kamaulindhardt_1/Library/R/3.6/library/RcppEigen/include/Eigen/Dense:4:
In file included from /Users/kamaulindhardt_1/Library/R/3.6/library/RcppEigen/include/Eigen/QR:48:
/Users/kamaulindhardt_1/Library/R/3.6/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from stan_files/bernoulli.cc:3:
In file included from stan_files/bernoulli.hpp:18:
In file included from /Users/kamaulindhardt_1/Library/R/3.6/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Users/kamaulindhardt_1/Library/R/3.6/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
In file included from /Users/kamaulindhardt_1/Library/R/3.6/library/RcppEigen/include/Eigen/Dense:5:
In file included from /Users/kamaulindhardt_1/Library/R/3.6/library/RcppEigen/include/Eigen/SVD:48:
/Users/kamaulindhardt_1/Library/R/3.6/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from stan_files/bernoulli.cc:3:
In file included from stan_files/bernoulli.hpp:18:
In file included from /Users/kamaulindhardt_1/Library/R/3.6/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Users/kamaulindhardt_1/Library/R/3.6/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
In file included from /Users/kamaulindhardt_1/Library/R/3.6/library/RcppEigen/include/Eigen/Dense:6:
In file included from /Users/kamaulindhardt_1/Library/R/3.6/library/RcppEigen/include/Eigen/Geometry:58:
/Users/kamaulindhardt_1/Library/R/3.6/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from stan_files/bernoulli.cc:3:
In file included from stan_files/bernoulli.hpp:18:
In file included from /Users/kamaulindhardt_1/Library/R/3.6/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Users/kamaulindhardt_1/Library/R/3.6/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
In file included from /Users/kamaulindhardt_1/Library/R/3.6/library/RcppEigen/include/Eigen/Dense:7:
In file included from /Users/kamaulindhardt_1/Library/R/3.6/library/RcppEigen/include/Eigen/Eigenvalues:58:
/Users/kamaulindhardt_1/Library/R/3.6/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from stan_files/bernoulli.cc:3:
In file included from stan_files/bernoulli.hpp:18:
In file included from /Users/kamaulindhardt_1/Library/R/3.6/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Users/kamaulindhardt_1/Library/R/3.6/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:14:
In file included from /Users/kamaulindhardt_1/Library/R/3.6/library/RcppEigen/include/Eigen/Sparse:26:
In file included from /Users/kamaulindhardt_1/Library/R/3.6/library/RcppEigen/include/Eigen/SparseCore:66:
/Users/kamaulindhardt_1/Library/R/3.6/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from stan_files/bernoulli.cc:3:
In file included from stan_files/bernoulli.hpp:18:
In file included from /Users/kamaulindhardt_1/Library/R/3.6/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Users/kamaulindhardt_1/Library/R/3.6/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:14:
In file included from /Users/kamaulindhardt_1/Library/R/3.6/library/RcppEigen/include/Eigen/Sparse:27:
In file included from /Users/kamaulindhardt_1/Library/R/3.6/library/RcppEigen/include/Eigen/OrderingMethods:71:
/Users/kamaulindhardt_1/Library/R/3.6/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from stan_files/bernoulli.cc:3:
In file included from stan_files/bernoulli.hpp:18:
In file included from /Users/kamaulindhardt_1/Library/R/3.6/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Users/kamaulindhardt_1/Library/R/3.6/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:14:
In file included from /Users/kamaulindhardt_1/Library/R/3.6/library/RcppEigen/include/Eigen/Sparse:29:
In file included from /Users/kamaulindhardt_1/Library/R/3.6/library/RcppEigen/include/Eigen/SparseCholesky:43:
/Users/kamaulindhardt_1/Library/R/3.6/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from stan_files/bernoulli.cc:3:
In file included from stan_files/bernoulli.hpp:18:
In file included from /Users/kamaulindhardt_1/Library/R/3.6/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Users/kamaulindhardt_1/Library/R/3.6/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:14:
In file included from /Users/kamaulindhardt_1/Library/R/3.6/library/RcppEigen/include/Eigen/Sparse:32:
In file included from /Users/kamaulindhardt_1/Library/R/3.6/library/RcppEigen/include/Eigen/SparseQR:34:
/Users/kamaulindhardt_1/Library/R/3.6/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from stan_files/bernoulli.cc:3:
In file included from stan_files/bernoulli.hpp:18:
In file included from /Users/kamaulindhardt_1/Library/R/3.6/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Users/kamaulindhardt_1/Library/R/3.6/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:14:
In file included from /Users/kamaulindhardt_1/Library/R/3.6/library/RcppEigen/include/Eigen/Sparse:33:
In file included from /Users/kamaulindhardt_1/Library/R/3.6/library/RcppEigen/include/Eigen/IterativeLinearSolvers:46:
/Users/kamaulindhardt_1/Library/R/3.6/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from stan_files/bernoulli.cc:3:
In file included from stan_files/bernoulli.hpp:18:
In file included from /Users/kamaulindhardt_1/Library/R/3.6/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Users/kamaulindhardt_1/Library/R/3.6/library/rstan/include/rstan/stan_fit.hpp:22:
In file included from /Users/kamaulindhardt_1/Library/R/3.6/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Users/kamaulindhardt_1/Library/R/3.6/library/RcppEigen/include/RcppEigenForward.h:32:
In file included from /Users/kamaulindhardt_1/Library/R/3.6/library/RcppEigen/include/Eigen/CholmodSupport:45:
/Users/kamaulindhardt_1/Library/R/3.6/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from stan_files/bernoulli.cc:3:
In file included from stan_files/bernoulli.hpp:18:
In file included from /Users/kamaulindhardt_1/Library/R/3.6/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Users/kamaulindhardt_1/Library/R/3.6/library/rstan/include/rstan/stan_fit.hpp:22:
In file included from /Users/kamaulindhardt_1/Library/R/3.6/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Users/kamaulindhardt_1/Library/R/3.6/library/RcppEigen/include/RcppEigenForward.h:35:
In file included from /Users/kamaulindhardt_1/Library/R/3.6/library/RcppEigen/include/unsupported/Eigen/KroneckerProduct:34:
/Users/kamaulindhardt_1/Library/R/3.6/library/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from stan_files/bernoulli.cc:3:
In file included from stan_files/bernoulli.hpp:18:
In file included from /Users/kamaulindhardt_1/Library/R/3.6/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Users/kamaulindhardt_1/Library/R/3.6/library/rstan/include/rstan/stan_fit.hpp:22:
In file included from /Users/kamaulindhardt_1/Library/R/3.6/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Users/kamaulindhardt_1/Library/R/3.6/library/RcppEigen/include/RcppEigenForward.h:39:
In file included from /Users/kamaulindhardt_1/Library/R/3.6/library/RcppEigen/include/unsupported/Eigen/Polynomials:135:
/Users/kamaulindhardt_1/Library/R/3.6/library/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from stan_files/bernoulli.cc:3:
In file included from stan_files/bernoulli.hpp:18:
In file included from /Users/kamaulindhardt_1/Library/R/3.6/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Users/kamaulindhardt_1/Library/R/3.6/library/rstan/include/rstan/stan_fit.hpp:22:
In file included from /Users/kamaulindhardt_1/Library/R/3.6/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Users/kamaulindhardt_1/Library/R/3.6/library/RcppEigen/include/RcppEigenForward.h:40:
In file included from /Users/kamaulindhardt_1/Library/R/3.6/library/RcppEigen/include/unsupported/Eigen/SparseExtra:51:
/Users/kamaulindhardt_1/Library/R/3.6/library/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:14:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
    #pragma clang diagnostic pop
                             ^
In file included from stan_files/bernoulli.cc:3:
In file included from stan_files/bernoulli.hpp:18:
In file included from /Users/kamaulindhardt_1/Library/R/3.6/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Users/kamaulindhardt_1/Library/R/3.6/library/rstan/include/rstan/stan_fit.hpp:35:
In file included from /Users/kamaulindhardt_1/Library/R/3.6/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10:
In file included from /Users/kamaulindhardt_1/Library/R/3.6/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7:
In file included from /Users/kamaulindhardt_1/Library/R/3.6/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4:
In file included from /Users/kamaulindhardt_1/Library/R/3.6/library/StanHeaders/include/stan/math/rev/mat.hpp:12:
In file included from /Users/kamaulindhardt_1/Library/R/3.6/library/StanHeaders/include/stan/math/prim/mat.hpp:283:
/Users/kamaulindhardt_1/Library/R/3.6/library/StanHeaders/include/stan/math/prim/mat/prob/gaussian_dlm_obs_rng.hpp:138:7: warning: unused variable 'n' [-Wunused-variable]
  int n = G.rows();  // number of states
      ^
In file included from stan_files/bernoulli.cc:3:
In file included from stan_files/bernoulli.hpp:18:
In file included from /Users/kamaulindhardt_1/Library/R/3.6/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Users/kamaulindhardt_1/Library/R/3.6/library/rstan/include/rstan/stan_fit.hpp:35:
In file included from /Users/kamaulindhardt_1/Library/R/3.6/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10:
In file included from /Users/kamaulindhardt_1/Library/R/3.6/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7:
In file included from /Users/kamaulindhardt_1/Library/R/3.6/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4:
In file included from /Users/kamaulindhardt_1/Library/R/3.6/library/StanHeaders/include/stan/math/rev/mat.hpp:17:
In file included from /Users/kamaulindhardt_1/Library/R/3.6/library/StanHeaders/include/stan/math/rev/mat/fun/columns_dot_self.hpp:8:
/Users/kamaulindhardt_1/Library/R/3.6/library/StanHeaders/include/stan/math/rev/mat/fun/dot_self.hpp:38:41: warning: all paths through this function will call itself [-Winfinite-recursion]
  inline static double square(double x) { return square(x); }
                                        ^
In file included from stan_files/bernoulli.cc:3:
In file included from stan_files/bernoulli.hpp:18:
In file included from /Users/kamaulindhardt_1/Library/R/3.6/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Users/kamaulindhardt_1/Library/R/3.6/library/rstan/include/rstan/stan_fit.hpp:35:
In file included from /Users/kamaulindhardt_1/Library/R/3.6/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10:
In file included from /Users/kamaulindhardt_1/Library/R/3.6/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7:
In file included from /Users/kamaulindhardt_1/Library/R/3.6/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4:
In file included from /Users/kamaulindhardt_1/Library/R/3.6/library/StanHeaders/include/stan/math/rev/mat.hpp:70:
In file included from /Users/kamaulindhardt_1/Library/R/3.6/library/StanHeaders/include/stan/math/rev/mat/functor/integrate_ode_adams.hpp:5:
/Users/kamaulindhardt_1/Library/R/3.6/library/StanHeaders/include/stan/math/rev/mat/functor/cvodes_integrator.hpp:126:18: warning: unused variable 'coupled_size' [-Wunused-variable]
    const size_t coupled_size = cvodes_data.coupled_ode_.size();
                 ^
In file included from stan_files/bernoulli.cc:3:
In file included from stan_files/bernoulli.hpp:18:
In file included from /Users/kamaulindhardt_1/Library/R/3.6/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Users/kamaulindhardt_1/Library/R/3.6/library/rstan/include/rstan/stan_fit.hpp:35:
In file included from /Users/kamaulindhardt_1/Library/R/3.6/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10:
In file included from /Users/kamaulindhardt_1/Library/R/3.6/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7:
In file included from /Users/kamaulindhardt_1/Library/R/3.6/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4:
In file included from /Users/kamaulindhardt_1/Library/R/3.6/library/StanHeaders/include/stan/math/rev/mat.hpp:6:
In file included from /Users/kamaulindhardt_1/Library/R/3.6/library/StanHeaders/include/stan/math/rev/core.hpp:46:
/Users/kamaulindhardt_1/Library/R/3.6/library/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 stan_files/bernoulli.cc:3:
In file included from stan_files/bernoulli.hpp:18:
In file included from /Users/kamaulindhardt_1/Library/R/3.6/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Users/kamaulindhardt_1/Library/R/3.6/library/rstan/include/rstan/stan_fit.hpp:35:
In file included from /Users/kamaulindhardt_1/Library/R/3.6/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10:
In file included from /Users/kamaulindhardt_1/Library/R/3.6/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7:
In file included from /Users/kamaulindhardt_1/Library/R/3.6/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4:
In file included from /Users/kamaulindhardt_1/Library/R/3.6/library/StanHeaders/include/stan/math/rev/mat.hpp:6:
In file included from /Users/kamaulindhardt_1/Library/R/3.6/library/StanHeaders/include/stan/math/rev/core.hpp:47:
/Users/kamaulindhardt_1/Library/R/3.6/library/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 stan_files/bernoulli.cc:3:
In file included from stan_files/bernoulli.hpp:18:
In file included from /Users/kamaulindhardt_1/Library/R/3.6/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Users/kamaulindhardt_1/Library/R/3.6/library/rstan/include/rstan/stan_fit.hpp:35:
In file included from /Users/kamaulindhardt_1/Library/R/3.6/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10:
In file included from /Users/kamaulindhardt_1/Library/R/3.6/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7:
In file included from /Users/kamaulindhardt_1/Library/R/3.6/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4:
In file included from /Users/kamaulindhardt_1/Library/R/3.6/library/StanHeaders/include/stan/math/rev/mat.hpp:12:
In file included from /Users/kamaulindhardt_1/Library/R/3.6/library/StanHeaders/include/stan/math/prim/mat.hpp:278:
In file included from /Users/kamaulindhardt_1/Library/R/3.6/library/StanHeaders/include/stan/math/prim/mat/prob/dirichlet_log.hpp:5:
/Users/kamaulindhardt_1/Library/R/3.6/library/StanHeaders/include/stan/math/prim/mat/prob/dirichlet_lpmf.hpp:60:9: warning: unused type alias 'T_partials_vec' [-Wunused-local-typedef]
  using T_partials_vec = typename Eigen::Matrix<T_partials_return, -1, 1>;
        ^
In file included from stan_files/bernoulli.cc:3:
In file included from stan_files/bernoulli.hpp:18:
In file included from /Users/kamaulindhardt_1/Library/R/3.6/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Users/kamaulindhardt_1/Library/R/3.6/library/rstan/include/rstan/stan_fit.hpp:35:
In file included from /Users/kamaulindhardt_1/Library/R/3.6/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10:
In file included from /Users/kamaulindhardt_1/Library/R/3.6/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7:
In file included from /Users/kamaulindhardt_1/Library/R/3.6/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4:
In file included from /Users/kamaulindhardt_1/Library/R/3.6/library/StanHeaders/include/stan/math/rev/mat.hpp:12:
In file included from /Users/kamaulindhardt_1/Library/R/3.6/library/StanHeaders/include/stan/math/prim/mat.hpp:328:
In file included from /Users/kamaulindhardt_1/Library/R/3.6/library/StanHeaders/include/stan/math/prim/mat/prob/poisson_log_glm_log.hpp:5:
/Users/kamaulindhardt_1/Library/R/3.6/library/StanHeaders/include/stan/math/prim/mat/prob/poisson_log_glm_lpmf.hpp:52:9: warning: unused type alias 'T_alpha_val' [-Wunused-local-typedef]
  using T_alpha_val = typename std::conditional_t<
        ^
In file included from stan_files/bernoulli.cc:3:
In file included from stan_files/bernoulli.hpp:18:
In file included from /Users/kamaulindhardt_1/Library/R/3.6/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Users/kamaulindhardt_1/Library/R/3.6/library/rstan/include/rstan/stan_fit.hpp:35:
In file included from /Users/kamaulindhardt_1/Library/R/3.6/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10:
In file included from /Users/kamaulindhardt_1/Library/R/3.6/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7:
In file included from /Users/kamaulindhardt_1/Library/R/3.6/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4:
In file included from /Users/kamaulindhardt_1/Library/R/3.6/library/StanHeaders/include/stan/math/rev/mat.hpp:51:
/Users/kamaulindhardt_1/Library/R/3.6/library/StanHeaders/include/stan/math/rev/mat/fun/squared_distance.hpp:27:11: warning: unused type alias 'idx_t' [-Wunused-local-typedef]
    using idx_t = typename index_type<matrix_v>::type;
          ^
/Users/kamaulindhardt_1/Library/R/3.6/library/StanHeaders/include/stan/math/rev/mat/fun/squared_distance.hpp:64:11: warning: unused type alias 'idx_t' [-Wunused-local-typedef]
    using idx_t = typename index_type<matrix_d>::type;
          ^
In file included from stan_files/bernoulli.cc:3:
stan_files/bernoulli.hpp:2651:24: warning: unused typedef 'local_scalar_t__' [-Wunused-local-typedef]
        typedef double local_scalar_t__;
                       ^
make: *** [stan_files/bernoulli.o] Interrupt: 2
make: *** Deleting intermediate file `stan_files/bernoulli.cc'
ERROR: compilation failed for package ‘rstanarm’
* removing ‘/Users/kamaulindhardt_1/Library/R/3.6/library/rstanarm’
* restoring previous ‘/Users/kamaulindhardt_1/Library/R/3.6/library/rstanarm’
kamaulindhardt commented 3 years ago

I also tried installing rstanarm individually.. Its surely seems like the issue is with rstanarm

> install.packages("tidyposterior")
Installing package into ‘/Users/kamaulindhardt_1/Library/R/3.6/library’
(as ‘lib’ is unspecified)
also installing the dependency ‘rstanarm’

  There are binary versions available but
  the source versions are later:
              binary source needs_compilation
rstanarm      2.19.2 2.21.1              TRUE
tidyposterior  0.0.3  0.1.0             FALSE

Do you want to install from sources the package which needs compilation? (Yes/no/cancel) cancel
Error in install.packages : Cancelled by user
> install.packages("rstanarm")
Installing package into ‘/Users/kamaulindhardt_1/Library/R/3.6/library’
(as ‘lib’ is unspecified)

  There is a binary version available but the source version is later:
         binary source needs_compilation
rstanarm 2.19.2 2.21.1              TRUE

Do you want to install from sources the package which needs compilation? (Yes/no/cancel) no
trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/rstanarm_2.19.2.tgz'
Content type 'application/x-gzip' length 33305501 bytes (31.8 MB)
==================================================
downloaded 31.8 MB

The downloaded binary packages are in
    /var/folders/6p/c87kn7652k3bb9lw5j3c2rn00000gp/T//RtmpFmhYGc/downloaded_packages
> library(rstanarm)
Loading required package: Rcpp
rstanarm (Version 2.19.2, packaged: 2019-10-01 20:20:33 UTC)
- Do not expect the default priors to remain the same in future rstanarm versions.
Thus, R scripts should specify priors explicitly, even if they are just the defaults.
- For execution on a local, multicore CPU with excess RAM we recommend calling
options(mc.cores = parallel::detectCores())
- bayesplot theme set to bayesplot::theme_default()
   * Does _not_ affect other ggplot2 plots
   * See ?bayesplot_theme_set for details on theme setting
Warning message:
package ‘Rcpp’ was built under R version 3.6.2 

Restarting R session...

> install.packages("rstanarm")
Installing package into ‘/Users/kamaulindhardt_1/Library/R/3.6/library’
(as ‘lib’ is unspecified)

  There is a binary version available but the source version is later:
         binary source needs_compilation
rstanarm 2.19.2 2.21.1              TRUE

Do you want to install from sources the package which needs compilation? (Yes/no/cancel) yes
installing the source package ‘rstanarm’

trying URL 'https://cran.rstudio.com/src/contrib/rstanarm_2.21.1.tar.gz'
Content type 'application/x-gzip' length 3548723 bytes (3.4 MB)
==================================================
downloaded 3.4 MB

ERROR: failed to lock directory ‘/Users/kamaulindhardt_1/Library/R/3.6/library’ for modifying
Try removing ‘/Users/kamaulindhardt_1/Library/R/3.6/library/00LOCK-rstanarm’
Warning in install.packages :
  installation of package ‘rstanarm’ had non-zero exit status

The downloaded source packages are in
    ‘/private/var/folders/6p/c87kn7652k3bb9lw5j3c2rn00000gp/T/Rtmp8Bbo3q/downloaded_packages’
juliasilge commented 3 years ago

I recommend installing a binary, not from source, for rstanarm, because it can be pretty tricky. It looks like you are using a pretty old version of R at this point, which might be you aren't finding the binary? I am guessing that the package version you need (2.21.1) was never built for the version of R you have (3.6) so it is up to you to build it.

I think you have a couple of options:

kamaulindhardt commented 3 years ago

I will try after updating R. Thanks a lot!

github-actions[bot] commented 3 years ago

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