rstantools cannot find stan/version.hpp
#97
Comments
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Odd, > sessionInfo()
R version 4.2.0 (2022-04-22)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Monterey 12.5
Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] testpackage_0.0.0.9000
loaded via a namespace (and not attached):
[1] Rcpp_1.0.9 prettyunits_1.1.1 ps_1.7.1 assertthat_0.2.1 rprojroot_2.0.3
[6] digest_0.6.29 utf8_1.2.2 R6_2.5.1 stats4_4.2.0 ggplot2_3.3.6
[11] pillar_1.8.0 rlang_1.0.4 rstudioapi_0.13 whisker_0.4 callr_3.7.1
[16] desc_1.4.1 devtools_2.4.3 stringr_1.4.0 loo_2.5.1 munsell_0.5.0
[21] compiler_4.2.0 xfun_0.31 rstan_2.21.5 pkgconfig_2.0.3 pkgbuild_1.3.1
[26] rstantools_2.2.0 tidyselect_1.1.2 tibble_3.1.8 gridExtra_2.3 roxygen2_7.2.1
[31] codetools_0.2-18 matrixStats_0.62.0 fansi_1.0.3 crayon_1.5.1 dplyr_1.0.9
[36] withr_2.5.0 brio_1.1.3 grid_4.2.0 gtable_0.3.0 lifecycle_1.0.1.9000
[41] DBI_1.1.3 magrittr_2.0.3 StanHeaders_2.21.0-7 scales_1.2.0 RcppParallel_5.1.5
[46] cli_3.3.0 stringi_1.7.8 cachem_1.0.6 fs_1.5.2 remotes_2.4.2
[51] testthat_3.1.4 xml2_1.3.3 ellipsis_0.3.2 generics_0.1.2 vctrs_0.4.1
[56] tools_4.2.0 glue_1.6.2 purrr_0.3.4 processx_3.7.0 pkgload_1.3.0
[61] parallel_4.2.0 fastmap_1.1.0 inline_0.3.19 colorspace_2.0-3 sessioninfo_1.2.2
[66] memoise_2.0.1 knitr_1.39 usethis_2.1.6.9000 |
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Not sure what changed, but the "fatal error: 'stan/version.hpp' file not found" is back in the same version of the RStudio IDE (2022.07.1 Build 554). |
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Compilation succeeds if I manually replace the default package Makevars with the hard-coded Mac-specific one @andrjohns suggested at https://discourse.mc-stan.org/t/compilation-error-with-rstantools-on-mac-os-stan-version-hpp-file-not-found/28624/17 (copied below). Does this provide any clues as to what I can change on my system to make the default package Makevars work? |
|
Yes, the problem is the crossed versions. If you are developing a package
to go to CRAN, then you should use the CRAN version of StanHeaders, rstan,
and anything other dependencies.
…On Thu, May 19, 2022 at 5:18 PM Will Landau ***@***.***> wrote:
I am developing a package with a stan model and using rstantools for
configuration. On my MacBook, R cannot find stan/version.hpp when it
tries to compile the package. I think the file may belong in
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include,
but it is not on my system after installing StanHeaders 2.21.0-7 (either
source or binary) and upgrading to rstan 2.21.5 and rstantools 2.2.0.
list.files("/Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan")
Models like the one below still compile successfully with rstan.
model_code <- "
data {
real y;
}
parameters {
real theta;
}
model {
y ~ normal(theta, 1);
theta ~ normal(0, 1);
}
"
model <- rstan::stan_model(model_code = model_code)
model
#>
#> > model
#> S4 class stanmodel 'f851b51190fe252f738e2d3974c697af' coded as follows:
#>
#> data {
#> real y;
#> }
#> parameters {
#> real theta;
#> }
#> model {
#> y ~ normal(theta, 1);
#> theta ~ normal(0, 1);
#> }
I followed the usual steps to build this model into an R package.
setwd(fs::dir_create(tempfile()))
usethis::create_package("testpackage", open = FALSE)
setwd("testpackage")
roxygen <- c(
"#' @import Rcpp methods",
"#' @importFrom rstan sampling",
"#' @useDynLib testpackage, .registration = TRUE",
"NULL"
)
fs::dir_create("R")
writeLines(roxygen, "R/roxygen.R")
devtools::document()
fs::dir_create(file.path("inst", "stan"))
writeLines(model_code, file.path("inst", "stan", "model.stan"))
rstantools::use_rstan()
install.packages(".", type = "source", repos = NULL)
I ran into this error during compilation when I try to install the package.
In file included from stanExports_model.cc:5:
In file included from ./stanExports_model.h:20:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/stan_fit.hpp:11:10: fatal error:
'stan/version.hpp' file not found
#include <stan/version.hpp>
^~~~~~~~~~~~~~~~~~
14 warnings and 1 error generated.
make: *** [stanExports_model.o] Error 1
ERROR: compilation failed for package ‘testpackage’
* removing ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library/testpackage’
* restoring previous ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library/testpackage’
Warning message:
In install.packages(".", type = "source", repos = NULL) :
installation of package ‘.’ had non-zero exit status
This issue looks similar to #47
<#47>, but it has been long
enough since
https://discourse.mc-stan.org/t/how-to-update-a-package-that-has-stanheaders-and-rstan-in-its-linkingto/6041?u=bgoodri
and
https://discourse.mc-stan.org/t/how-to-update-a-package-that-has-stanheaders-and-rstan-in-its-linkingto-part-ii/6214/4?u=bgoodri
that the package Makevars written by rstantools. And I do not have a
"~/.R/Makevars".
> writeLines(readLines("src/Makevars"))
# Generated by rstantools. Do not edit by hand.
STANHEADERS_SRC = $(shell "$(R_HOME)/bin$(R_ARCH_BIN)/Rscript" -e "message()" -e "cat(system.file('include', 'src', package = 'StanHeaders', mustWork = TRUE))" -e "message()" | grep "StanHeaders")
STANC_FLAGS = $(shell "$(R_HOME)/bin$(R_ARCH_BIN)/Rscript" -e "cat(ifelse(utils::packageVersion('rstan') >= 2.26, '-DUSE_STANC3',''))")
PKG_CPPFLAGS = -I"../inst/include" -I"$(STANHEADERS_SRC)" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error $(STANC_FLAGS)
PKG_CXXFLAGS = $(shell "$(R_HOME)/bin$(R_ARCH_BIN)/Rscript" -e "RcppParallel::CxxFlags()") $(shell "$(R_HOME)/bin$(R_ARCH_BIN)/Rscript" -e "StanHeaders:::CxxFlags()")
PKG_LIBS = $(shell "$(R_HOME)/bin$(R_ARCH_BIN)/Rscript" -e "RcppParallel::RcppParallelLibs()") $(shell "$(R_HOME)/bin$(R_ARCH_BIN)/Rscript" -e "StanHeaders:::LdFlags()")
CXX_STD = CXX14
Complete compilation log
* installing *source* package ‘testpackage’ ...
** using staged installation
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"../inst/include" -I"/Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeader/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppParallel/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include' -I/usr/local/include -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Dense:1:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Core:540:
/Library/Frameworks/R.framework/Versions/4.2/Resources/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 RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Dense:2:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/LU:47:
/Library/Frameworks/R.framework/Versions/4.2/Resources/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 RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Dense:3:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Cholesky:12:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Jacobi:29:
/Library/Frameworks/R.framework/Versions/4.2/Resources/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 RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Dense:3:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Cholesky:43:
/Library/Frameworks/R.framework/Versions/4.2/Resources/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 RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Dense:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/QR:15:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Householder:27:
/Library/Frameworks/R.framework/Versions/4.2/Resources/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 RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Dense:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/QR:48:
/Library/Frameworks/R.framework/Versions/4.2/Resources/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 RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Dense:5:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/SVD:48:
/Library/Frameworks/R.framework/Versions/4.2/Resources/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 RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Dense:6:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Geometry:58:
/Library/Frameworks/R.framework/Versions/4.2/Resources/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 RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/RcppEigenForward.h:30:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Dense:7:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Eigenvalues:58:
/Library/Frameworks/R.framework/Versions/4.2/Resources/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 RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Sparse:26:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/SparseCore:66:
/Library/Frameworks/R.framework/Versions/4.2/Resources/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 RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Sparse:27:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/OrderingMethods:71:
/Library/Frameworks/R.framework/Versions/4.2/Resources/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 RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Sparse:29:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/SparseCholesky:43:
/Library/Frameworks/R.framework/Versions/4.2/Resources/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 RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Sparse:32:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/SparseQR:34:
/Library/Frameworks/R.framework/Versions/4.2/Resources/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 RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Sparse:33:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/IterativeLinearSolvers:46:
/Library/Frameworks/R.framework/Versions/4.2/Resources/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 RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/RcppEigenForward.h:32:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/CholmodSupport:45:
/Library/Frameworks/R.framework/Versions/4.2/Resources/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 RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/RcppEigenForward.h:35:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/unsupported/Eigen/KroneckerProduct:34:
/Library/Frameworks/R.framework/Versions/4.2/Resources/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 RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/RcppEigenForward.h:39:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/unsupported/Eigen/Polynomials:135:
/Library/Frameworks/R.framework/Versions/4.2/Resources/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 RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/RcppEigenForward.h:40:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/unsupported/Eigen/SparseExtra:51:
/Library/Frameworks/R.framework/Versions/4.2/Resources/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
^
18 warnings generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"../inst/include" -I"/Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeader/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppParallel/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include' -I/usr/local/include -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fPIC -Wall -g -O2 -c stanExports_model.cc -o stanExports_model.o
In file included from stanExports_model.cc:5:
In file included from ./stanExports_model.h:20:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Dense:1:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Core:540:
/Library/Frameworks/R.framework/Versions/4.2/Resources/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 stanExports_model.cc:5:
In file included from ./stanExports_model.h:20:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Dense:2:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/LU:47:
/Library/Frameworks/R.framework/Versions/4.2/Resources/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 stanExports_model.cc:5:
In file included from ./stanExports_model.h:20:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Dense:3:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Cholesky:12:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Jacobi:29:
/Library/Frameworks/R.framework/Versions/4.2/Resources/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 stanExports_model.cc:5:
In file included from ./stanExports_model.h:20:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Dense:3:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Cholesky:43:
/Library/Frameworks/R.framework/Versions/4.2/Resources/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 stanExports_model.cc:5:
In file included from ./stanExports_model.h:20:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Dense:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/QR:15:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Householder:27:
/Library/Frameworks/R.framework/Versions/4.2/Resources/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 stanExports_model.cc:5:
In file included from ./stanExports_model.h:20:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Dense:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/QR:48:
/Library/Frameworks/R.framework/Versions/4.2/Resources/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 stanExports_model.cc:5:
In file included from ./stanExports_model.h:20:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Dense:5:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/SVD:48:
/Library/Frameworks/R.framework/Versions/4.2/Resources/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 stanExports_model.cc:5:
In file included from ./stanExports_model.h:20:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Dense:6:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Geometry:58:
/Library/Frameworks/R.framework/Versions/4.2/Resources/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 stanExports_model.cc:5:
In file included from ./stanExports_model.h:20:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Dense:7:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Eigenvalues:58:
/Library/Frameworks/R.framework/Versions/4.2/Resources/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 stanExports_model.cc:5:
In file included from ./stanExports_model.h:20:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Sparse:26:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/SparseCore:66:
/Library/Frameworks/R.framework/Versions/4.2/Resources/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 stanExports_model.cc:5:
In file included from ./stanExports_model.h:20:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Sparse:27:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/OrderingMethods:71:
/Library/Frameworks/R.framework/Versions/4.2/Resources/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 stanExports_model.cc:5:
In file included from ./stanExports_model.h:20:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Sparse:29:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/SparseCholesky:43:
/Library/Frameworks/R.framework/Versions/4.2/Resources/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 stanExports_model.cc:5:
In file included from ./stanExports_model.h:20:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Sparse:32:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/SparseQR:34:
/Library/Frameworks/R.framework/Versions/4.2/Resources/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 stanExports_model.cc:5:
In file included from ./stanExports_model.h:20:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/Sparse:33:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppEigen/include/Eigen/IterativeLinearSolvers:46:
/Library/Frameworks/R.framework/Versions/4.2/Resources/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 stanExports_model.cc:5:
In file included from ./stanExports_model.h:20:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/rstan/include/rstan/stan_fit.hpp:11:10: fatal error:
'stan/version.hpp' file not found
#include <stan/version.hpp>
^~~~~~~~~~~~~~~~~~
14 warnings and 1 error generated.
make: *** [stanExports_model.o] Error 1
ERROR: compilation failed for package ‘testpackage’
* removing ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library/testpackage’
* restoring previous ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library/testpackage’
Warning message:
In install.packages(".", type = "source", repos = NULL) :
installation of package ‘.’ had non-zero exit status
Session info
- Mac OS 12.3.1
- 2018 15-inch MacBook Pro
- Using the Mac Terminal (not RStudio, VSCode, or other IDE).
$ gcc --version
Apple clang version 13.1.6 (clang-1316.0.21.2.5)
Target: x86_64-apple-darwin21.4.0
Thread model: posix
InstalledDir: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin
R version 4.2.0 (2022-04-22)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur/Monterey 10.16
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] testpackage_0.0.0.9000
loaded via a namespace (and not attached):
[1] pillar_1.7.0 compiler_4.2.0 prettyunits_1.1.1 remotes_2.4.2
[5] tools_4.2.0 digest_0.6.29 testthat_3.1.4 pkgbuild_1.3.1
[9] pkgload_1.2.4 memoise_2.0.1 lifecycle_1.0.1 tibble_3.1.7
[13] pkgconfig_2.0.3 rlang_1.0.2 cli_3.3.0 rstudioapi_0.13
[17] xfun_0.31 fastmap_1.1.0 withr_2.5.0 stringr_1.4.0
[21] roxygen2_7.1.2 xml2_1.3.3 knitr_1.39 desc_1.4.1
[25] fs_1.5.2 vctrs_0.4.1 devtools_2.4.3 rprojroot_2.0.3
[29] glue_1.6.2 R6_2.5.1 processx_3.5.3 fansi_1.0.3
[33] sessioninfo_1.2.2 purrr_0.3.4 callr_3.7.0 magrittr_2.0.3
[37] rstantools_2.2.0 ps_1.7.0 ellipsis_0.3.2 usethis_2.1.5
[41] utf8_1.2.2 stringi_1.7.6 cachem_1.0.6 crayon_1.5.1
[45] brio_1.1.3
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I thought so at first, but I reinstalled the current CRAN versions of all the dependencies and I still get the "`stan/version.hpp;' file not found" error from the above reprex in both RStudio and the terminal.
> sessionInfo()
R version 4.2.1 (2022-06-23)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Monterey 12.6
Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets
[6] methods base
other attached packages:
[1] testpackage_0.0.0.9000
loaded via a namespace (and not attached):
[1] Rcpp_1.0.9 prettyunits_1.1.1
[3] ps_1.7.1 assertthat_0.2.1
[5] rprojroot_2.0.3 digest_0.6.29
[7] utf8_1.2.2 mime_0.12
[9] R6_2.5.1 stats4_4.2.1
[11] ggplot2_3.3.6 pillar_1.8.1
[13] rlang_1.0.6 rstudioapi_0.14
[15] miniUI_0.1.1.1 urlchecker_1.0.1
[17] whisker_0.4 callr_3.7.2
[19] desc_1.4.2 devtools_2.4.4
[21] stringr_1.4.1 htmlwidgets_1.5.4
[23] loo_2.5.1 munsell_0.5.0
[25] shiny_1.7.2 compiler_4.2.1
[27] httpuv_1.6.6 xfun_0.33
[29] rstan_2.21.7 pkgconfig_2.0.3
[31] pkgbuild_1.3.1 rstantools_2.2.0
[33] htmltools_0.5.3 tidyselect_1.1.2.9000
[35] tibble_3.1.8 gridExtra_2.3
[37] roxygen2_7.2.1 codetools_0.2-18
[39] matrixStats_0.62.0 fansi_1.0.3
[41] crayon_1.5.1 dplyr_1.0.10
[43] withr_2.5.0 later_1.3.0
[45] grid_4.2.1 xtable_1.8-4
[47] gtable_0.3.1 lifecycle_1.0.2
[49] DBI_1.1.3 magrittr_2.0.3
[51] StanHeaders_2.21.0-7 scales_1.2.1
[53] RcppParallel_5.1.5 cli_3.4.1
[55] stringi_1.7.8 cachem_1.0.6
[57] remotes_2.4.2 fs_1.5.2
[59] promises_1.2.0.1 xml2_1.3.3
[61] ellipsis_0.3.2 generics_0.1.3
[63] vctrs_0.4.1 tools_4.2.1
[65] glue_1.6.2 purrr_0.3.4
[67] pkgload_1.3.0 processx_3.7.0
[69] parallel_4.2.1 fastmap_1.1.0
[71] inline_0.3.19 colorspace_2.0-3
[73] sessioninfo_1.2.2 memoise_2.0.1
[75] knitr_1.40 profvis_0.3.7
[77] usethis_2.1.6.9000 |
|
@andrjohns has helped me a lot in https://discourse.mc-stan.org/t/compilation-error-with-rstantools-on-mac-os-stan-version-hpp-file-not-found/28624/19 to arrive at a hard-coded package |
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I am developing a package with a stan model and using
rstantoolsfor configuration. On my MacBook, R cannot findstan/version.hppwhen it tries to compile the package. I think the file may belong in/Library/Frameworks/R.framework/Versions/4.2/Resources/library/StanHeaders/include, but it is not on my system after installingStanHeaders2.21.0-7 (either source or binary) and upgrading torstan2.21.5 andrstantools2.2.0.Models like the one below still compile successfully with
rstan.I followed the usual steps to build this model into an R package.
I ran into this error during compilation when I try to install the package.
This issue looks similar to #47, but it has been long enough since https://discourse.mc-stan.org/t/how-to-update-a-package-that-has-stanheaders-and-rstan-in-its-linkingto/6041?u=bgoodri and https://discourse.mc-stan.org/t/how-to-update-a-package-that-has-stanheaders-and-rstan-in-its-linkingto-part-ii/6214/4?u=bgoodri that the package
Makevarswritten byrstantools. And I do not have a"~/.R/Makevars".Complete compilation log
Session info
The text was updated successfully, but these errors were encountered: