- using R Under development (unstable) (2026-08-31 r90457 ucrt)
- using platform: x86_64-w64-mingw32
- R was compiled by
gcc.exe (GCC) 14.3.0
GNU Fortran (GCC) 14.3.0
- running under: Windows Server 2022 x64 (build 20348)
- using session charset: UTF-8
* current time: 2026-09-01 12:35:08 UTC
- checking for file 'bonsaiforest/DESCRIPTION' ... OK
- checking extension type ... Package
- this is package 'bonsaiforest' version '0.1.1'
- package encoding: UTF-8
- checking package namespace information ... OK
- checking package dependencies ... OK
- checking if this is a source package ... OK
- checking if there is a namespace ... OK
- checking for hidden files and directories ... OK
- checking for portable file names ... OK
- checking whether package 'bonsaiforest' can be installed ... OK
See the install log for details.
- used C++ compiler: 'g++.exe (GCC) 14.3.0'
- checking installed package size ... INFO
installed size is 9.5Mb
sub-directories of 1Mb or more:
data 7.7Mb
libs 1.2Mb
- checking package directory ... OK
- checking 'build' directory ... OK
- checking DESCRIPTION meta-information ... OK
- checking top-level files ... OK
- checking for left-over files ... OK
- checking index information ... OK
- checking package subdirectories ... OK
- checking code files for non-ASCII characters ... OK
- checking R files for syntax errors ... OK
- checking whether the package can be loaded ... [5s] OK
- checking whether the package can be loaded with stated dependencies ... [4s] OK
- checking whether the package can be unloaded cleanly ... [4s] OK
- checking whether the namespace can be loaded with stated dependencies ... [4s] OK
- checking whether the namespace can be unloaded cleanly ... [5s] OK
- checking loading without being on the library search path ... [5s] OK
- checking use of S3 registration ... OK
- checking dependencies in R code ... OK
- checking S3 generic/method consistency ... OK
- checking replacement functions ... OK
- checking foreign function calls ... OK
- checking R code for possible problems ... [13s] OK
- checking Rd files ... [1s] OK
- checking Rd metadata ... OK
- checking Rd cross-references ... OK
- checking for missing documentation entries ... OK
- checking for code/documentation mismatches ... OK
- checking Rd \usage sections ... OK
- checking Rd contents ... OK
- checking for unstated dependencies in examples ... OK
- checking contents of 'data' directory ... OK
- checking data for non-ASCII characters ... [8s] OK
- checking LazyData ... OK
- checking data for ASCII and uncompressed saves ... OK
- checking line endings in C/C++/Fortran sources/headers ... OK
- checking line endings in Makefiles ... OK
- checking compilation flags in Makevars ... OK
- checking for GNU extensions in Makefiles ... OK
- checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
- checking use of PKG_*FLAGS in Makefiles ... OK
- checking pragmas in C/C++ headers and code ... OK
- checking compiled code ... OK
- checking installed files from 'inst/doc' ... OK
- checking files in 'vignettes' ... OK
- checking examples ... [33s] OK
- checking for unstated dependencies in 'tests' ... OK
- checking tests ... [107s] ERROR
Running 'testthat.R' [107s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
>
> library(testthat)
> library(bonsaiforest)
Attaching package: 'bonsaiforest'
The following object is masked from 'package:testthat':
compare
>
> test_check("bonsaiforest")
Compiling Stan program...
specified C++17
make cmd is
make -f "D:/RCompile/recent/R/etc/x64/Makeconf" -f "D:/RCompile/recent/R/share/make/winshlib.mk" CXX='$(CXX17) $(CXX17STD)' CXXFLAGS='$(CXX17FLAGS)' CXXPICFLAGS='$(CXX17PICFLAGS)' SHLIB_LDFLAGS='$(SHLIB_CXX17LDFLAGS)' SHLIB_LD='$(SHLIB_CXX17LD)' SHLIB="file2084835ca1e43.dll" WIN=64 TCLBIN= OBJECTS="file2084835ca1e43.o"
make would use
make[1]: Entering directory '/d/temp/2026_09_01_01_50_00_22259/RtmpCCvEoF'
g++ -std=gnu++17 -I"D:/RCompile/recent/R/include" -DNDEBUG -I"D:/RCompile/CRANpkg/lib/4.7/Rcpp/include/" -I"D:/temp/2026_09_01_01_50_00_22259/Rtmp6hjLDX/RLIBS_3abd872f61f6e/RcppEigen/include/" -I"D:/temp/2026_09_01_01_50_00_22259/Rtmp6hjLDX/RLIBS_3abd872f61f6e/RcppEigen/include/unsupported" -I"D:/temp/2026_09_01_01_50_00_22259/Rtmp6hjLDX/RLIBS_3abd872f61f6e/BH/include" -I"D:/RCompile/CRANpkg/lib/4.7/StanHeaders/include/src/" -I"D:/RCompile/CRANpkg/lib/4.7/StanHeaders/include/" -I"D:/RCompile/CRANpkg/lib/4.7/RcppParallel/include/" -DRCPP_PARALLEL_USE_TBB=1 -DTBB_INTERFACE_NEW -ID:/RCompile/CRANpkg/lib/4.7/RcppParallel/include -I"D:/RCompile/CRANpkg/lib/4.7/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -DSTAN_THREADS -DUSE_STANC3 -DSTRICT_R_HEADERS -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION -D_HAS_AUTO_PTR_ETC=0 -include "D:/RCompile/CRANpkg/lib/4.7/StanHeaders/include/stan/math/prim/fun/Eigen.hpp" -std=c++1y -I"d:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c file2084835ca1e43.cpp -o file2084835ca1e43.o
if test "zfile2084835ca1e43.o" != "z"; then \
if test -e "file2084835ca1e43-win.def"; then \
echo g++ -shared -s -static-libgcc -o file2084835ca1e43.dll file2084835ca1e43-win.def file2084835ca1e43.o "D:/RCompile/CRANpkg/lib/4.7/rstan/lib/x64/libStanServices.a" -L"D:/RCompile/CRANpkg/lib/4.7/StanHeaders/libs/x64" -lStanHeaders -L"D:/RCompile/CRANpkg/lib/4.7/RcppParallel/lib/x64" -ltbb -LD:/RCompile/CRANpkg/lib/4.7/RcppParallel/libs/x64 -lRcppParallel -LD:/RCompile/CRANpkg/lib/4.7/RcppParallel/lib/x64 -ltbb -ltbbmalloc -L"d:/rtools45/x86_64-w64-mingw32.static.posix/lib/x64" -L"d:/rtools45/x86_64-w64-mingw32.static.posix/lib" -L"D:/RCompile/recent/R/bin/x64" -lR ; \
g++ -shared -s -static-libgcc -o file2084835ca1e43.dll file2084835ca1e43-win.def file2084835ca1e43.o "D:/RCompile/CRANpkg/lib/4.7/rstan/lib/x64/libStanServices.a" -L"D:/RCompile/CRANpkg/lib/4.7/StanHeaders/libs/x64" -lStanHeaders -L"D:/RCompile/CRANpkg/lib/4.7/RcppParallel/lib/x64" -ltbb -LD:/RCompile/CRANpkg/lib/4.7/RcppParallel/libs/x64 -lRcppParallel -LD:/RCompile/CRANpkg/lib/4.7/RcppParallel/lib/x64 -ltbb -ltbbmalloc -L"d:/rtools45/x86_64-w64-mingw32.static.posix/lib/x64" -L"d:/rtools45/x86_64-w64-mingw32.static.posix/lib" -L"D:/RCompile/recent/R/bin/x64" -lR ; \
else \
echo EXPORTS > tmp.def; \
nm file2084835ca1e43.o | sed -n 's/^.* [BCDRT] / /p' | sed -e '/[.]refptr[.]/d' -e '/[.]weak[.]/d' | sed 's/[^ ][^ ]*/"&"/g' >> tmp.def; \
echo g++ -shared -s -static-libgcc -o file2084835ca1e43.dll tmp.def file2084835ca1e43.o "D:/RCompile/CRANpkg/lib/4.7/rstan/lib/x64/libStanServices.a" -L"D:/RCompile/CRANpkg/lib/4.7/StanHeaders/libs/x64" -lStanHeaders -L"D:/RCompile/CRANpkg/lib/4.7/RcppParallel/lib/x64" -ltbb -LD:/RCompile/CRANpkg/lib/4.7/RcppParallel/libs/x64 -lRcppParallel -LD:/RCompile/CRANpkg/lib/4.7/RcppParallel/lib/x64 -ltbb -ltbbmalloc -L"d:/rtools45/x86_64-w64-mingw32.static.posix/lib/x64" -L"d:/rtools45/x86_64-w64-mingw32.static.posix/lib" -L"D:/RCompile/recent/R/bin/x64" -lR ; \
g++ -shared -s -static-libgcc -o file2084835ca1e43.dll tmp.def file2084835ca1e43.o "D:/RCompile/CRANpkg/lib/4.7/rstan/lib/x64/libStanServices.a" -L"D:/RCompile/CRANpkg/lib/4.7/StanHeaders/libs/x64" -lStanHeaders -L"D:/RCompile/CRANpkg/lib/4.7/RcppParallel/lib/x64" -ltbb -LD:/RCompile/CRANpkg/lib/4.7/RcppParallel/libs/x64 -lRcppParallel -LD:/RCompile/CRANpkg/lib/4.7/RcppParallel/lib/x64 -ltbb -ltbbmalloc -L"d:/rtools45/x86_64-w64-mingw32.static.posix/lib/x64" -L"d:/rtools45/x86_64-w64-mingw32.static.posix/lib" -L"D:/RCompile/recent/R/bin/x64" -lR ; \
rm -f tmp.def; \
fi \
fi
make[1]: Leaving directory '/d/temp/2026_09_01_01_50_00_22259/RtmpCCvEoF'
Saving _problems/test-horseshoe-14.R
[ FAIL 2 | WARN 25 | SKIP 12 | PASS 68 ]
══ Skipped tests (12) ══════════════════════════════════════════════════════════
• On CRAN (12): 'test-horseshoe.R:60:3', 'test-plot.R:1:1', 'test-plot.R:6:1',
'test-plot.R:11:1', 'test-plot.R:16:1', 'test-print.R:1:1',
'test-print.R:6:1', 'test-print.R:11:1', 'test-print.R:16:1',
'test-simulation.R:12:1', 'test-simulation.R:19:1', 'test-simulation.R:26:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-horseshoe.R:2:3'): horseshoe outputs the right elements for survival ──
Error in `compileCode(f, code, language = language, verbose = verbose)`: l = model208484f9565de__namespace::model208484f9565de_; BaseRNG = boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned int, 40014, 0, 2147483563>, boost::random::linear_congruential_engine<unsigned int, 40692, 0, 2147483399> >]'
22 | return 0.5 * z.p.transpose() * z.inv_e_metric_ * z.p;
D:/RCompile/CRANpkg/lib/4.7/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:21:0: required from here
21 | double T(dense_e_point& z) {
D:/RCompile/CRANpkg/lib/4.7/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:654:74: warning: ignoring attributes on template argument 'Eigen::internal::packet_traits<double>::type' {aka '__m128d'} [-Wignored-attributes]
654 | return internal::first_aligned<int(unpacket_traits<DefaultPacketType>::alignment),Derived>(m);
| ^~~~~~~~~
make[1]: *** [D:/RCompile/recent/R/etc/x64/Makeconf:304: file2084835ca1e43.o] Error 1
Backtrace:
▆
1. ├─base::suppressWarnings(...) at test-horseshoe.R:2:3
2. │ └─base::withCallingHandlers(...)
3. └─bonsaiforest::horseshoe(...)
4. ├─base::do.call(fit_function, args = list_arguments)
5. └─bonsaiforest (local) `<fn>`(iter = 20, warmup = 10, chains = 1, seed = 0, control = `<named list>`)
6. └─brms::brm(...)
7. └─brms::do_call(compile_model, compile_args)
8. └─brms:::eval2(call, envir = args, enclos = envir)
9. └─base::eval(expr, envir, ...)
10. └─base::eval(expr, envir, ...)
11. └─brms (local) .fun(...)
12. └─brms (local) .compile_model(model, ...)
13. ├─brms:::eval_silent(...)
14. │ └─base::eval(expr, envir)
15. │ └─base::eval(expr, envir)
16. └─brms::do_call(rstan::stan_model, args)
17. └─brms:::eval2(call, envir = args, enclos = envir)
18. └─base::eval(expr, envir, ...)
19. └─base::eval(expr, envir, ...)
20. └─rstan (local) .fun(model_code = .x1)
21. └─rstan:::cxxfunctionplus(...)
22. ├─pkgbuild::with_build_tools(...)
23. │ └─pkgbuild:::withr_with_path(rtools_path(), code)
24. │ └─base::force(code)
25. └─inline::cxxfunction(...)
26. └─inline:::compileCode(f, code, language = language, verbose = verbose)
── Error ('test-horseshoe.R:2:3'): horseshoe outputs the right elements for survival ──
Error in `sink(type = "output")`: invalid connection
Backtrace:
▆
1. ├─base::suppressWarnings(...) at test-horseshoe.R:2:3
2. │ └─base::withCallingHandlers(...)
3. └─bonsaiforest::horseshoe(...)
4. ├─base::do.call(fit_function, args = list_arguments)
5. └─bonsaiforest (local) `<fn>`(iter = 20, warmup = 10, chains = 1, seed = 0, control = `<named list>`)
6. └─brms::brm(...)
7. └─brms::do_call(compile_model, compile_args)
8. └─brms:::eval2(call, envir = args, enclos = envir)
9. └─base::eval(expr, envir, ...)
10. └─base::eval(expr, envir, ...)
11. └─brms (local) .fun(...)
12. └─brms (local) .compile_model(model, ...)
13. ├─brms:::eval_silent(...)
14. │ └─base::eval(expr, envir)
15. │ └─base::eval(expr, envir)
16. └─brms::do_call(rstan::stan_model, args)
17. └─brms:::eval2(call, envir = args, enclos = envir)
18. └─base::eval(expr, envir, ...)
19. └─base::eval(expr, envir, ...)
20. └─rstan (local) .fun(model_code = .x1)
21. └─rstan:::cxxfunctionplus(...)
22. └─base::sink(type = "output")
[ FAIL 2 | WARN 25 | SKIP 12 | PASS 68 ]
Error:
! Test failures.
Execution halted
- checking for unstated dependencies in vignettes ... OK
- checking package vignettes ... OK
- checking re-building of vignette outputs ... [28s] OK
- checking PDF version of manual ... [20s] OK
- checking HTML version of manual ... [2s] OK
- DONE
Status: 1 ERROR