Last updated on 2025-11-21 00:49:10 CET.
| Package | ERROR | NOTE | OK |
|---|---|---|---|
| abtest | 13 | ||
| bridgesampling | 2 | 1 | 10 |
Current CRAN status: OK: 13
Current CRAN status: ERROR: 2, NOTE: 1, OK: 10
Version: 1.2-1
Check: tests
Result: ERROR
Running ‘testthat.R’ [9s/11s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> Sys.setenv("R_TESTS" = "")
> library(testthat)
>
> test_check("bridgesampling")
Loading required package: bridgesampling
Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
using C compiler: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’
using SDK: ‘NA’
clang -arch arm64 -std=gnu2x -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o foo.so foo.o -F/Library/Frameworks/R.framework/.. -framework R
ld: library not found for -lSystem
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [foo.so] Error 1
Warning message:
In system2("xcrun", "--show-sdk-version", TRUE, TRUE) :
running command ''xcrun' --show-sdk-version 2>&1' had status 1
make cmd is
make -f '/Library/Frameworks/R.framework/Resources/etc/Makeconf' -f '/Library/Frameworks/R.framework/Resources/share/make/shlib.mk' CXX='$(CXX17) $(CXX17STD)' CXXFLAGS='$(CXX17FLAGS)' CXXPICFLAGS='$(CXX17PICFLAGS)' SHLIB_LDFLAGS='$(SHLIB_CXX17LDFLAGS)' SHLIB_LD='$(SHLIB_CXX17LD)' SHLIB='file15376efcdfdd.so' OBJECTS='file15376efcdfdd.o'
make would use
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/Rcpp/include/" -I"/Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/RcppEigen/include/" -I"/Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/RcppEigen/include/unsupported" -I"/Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/BH/include" -I"/Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/StanHeaders/include/src/" -I"/Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/StanHeaders/include/" -I"/Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/RcppParallel/include/" -I"/Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/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 '/Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/StanHeaders/include/stan/math/prim/fun/Eigen.hpp' -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1 -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c file15376efcdfdd.cpp -o file15376efcdfdd.o
if test "zfile15376efcdfdd.o" != "z"; then \
echo clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L"/Library/Frameworks/R.framework/Resources/lib" -L/opt/R/arm64/lib -o file15376efcdfdd.so file15376efcdfdd.o '/Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/rstan/lib//libStanServices.a' -L'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/StanHeaders/lib/' -lStanHeaders -L'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/RcppParallel/lib/' -ltbb -L/Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/RcppParallel/lib -ltbb -ltbbmalloc -F/Library/Frameworks/R.framework/.. -framework R ; \
clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L"/Library/Frameworks/R.framework/Resources/lib" -L/opt/R/arm64/lib -o file15376efcdfdd.so file15376efcdfdd.o '/Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/rstan/lib//libStanServices.a' -L'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/StanHeaders/lib/' -lStanHeaders -L'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/RcppParallel/lib/' -ltbb -L/Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/RcppParallel/lib -ltbb -ltbbmalloc -F/Library/Frameworks/R.framework/.. -framework R ; \
fi
Saving _problems/test-stan_bridge_sampler_basic-59.R
[ FAIL 2 | WARN 0 | SKIP 19 | PASS 75 ]
══ Skipped tests (19) ══════════════════════════════════════════════════════════
• On CRAN (19): 'test-bridge_sampler_CmdStanMCMC.R:4:3',
'test-bridge_sampler_CmdStanMCMC.R:75:3', 'test-bridge_sampler_Rcpp.R:6:3',
'test-bridge_sampler_Rcpp_parallel.R:6:3',
'test-bridge_sampler_mcmc.list.R:6:3', 'test-bridge_sampler_parallel.R:6:3',
'test-log_posterior_cmdstan.R:4:3', 'test-log_posterior_cmdstan.R:133:3',
'test-nimble_bridge_sampler.R:5:3', 'test-stan_bridge_sampler_basic.R:113:3',
'test-stan_bridge_sampler_bugs.R:65:3',
'test-stan_bridge_sampler_bugs.R:82:3',
'test-stan_bridge_sampler_bugs.R:126:3',
'test-stanreg_bridge_sampler_basic.R:6:3',
'test-stanreg_bridge_sampler_basic.R:26:3',
'test-vignette_example_jags.R:6:3', 'test-vignette_example_nimble.R:6:3',
'test-vignette_example_stan.R:6:3', 'test-vignette_stan_ttest.R:6:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-stan_bridge_sampler_basic.R:57:5'): stan_bridge_sampler ────────
Error in `compileCode(f, code, language = language, verbose = verbose)`: ion 14.0.3 (clang-1403.0.22.14.1)’
using C++17
using SDK: ‘NA’
In file included from <built-in>:1:
In file included from /Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:22:
In file included from /Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/RcppEigen/include/Eigen/Dense:1:
In file included from /Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/RcppEigen/include/Eigen/Core:19:
In file included from /Volumes/Builds/packages/big-sur-arm64/Rlib/4.5/RcppEigen/include/Eigen/src/Core/util/Macros.h:679:
In file included from /Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/cmath:308:
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/math.h:300:15: fatal error: 'math.h' file not found
#include_next <math.h>
^~~~~~~~
1 error generated.
make: *** [file15376efcdfdd.o] Error 1
Warning message:
In system2("xcrun", "--show-sdk-version", TRUE, TRUE) :
running command ''xcrun' --show-sdk-version 2>&1' had status 1
Backtrace:
▆
1. ├─base::suppressWarnings(stan_model(model_code = stancodeH0, model_name = "stanmodel")) at test-stan_bridge_sampler_basic.R:57:5
2. │ └─base::withCallingHandlers(...)
3. └─rstan::stan_model(model_code = stancodeH0, model_name = "stanmodel")
4. └─rstan:::cxxfunctionplus(...)
5. ├─pkgbuild::with_build_tools(...)
6. └─inline::cxxfunction(...)
7. └─inline:::compileCode(f, code, language = language, verbose = verbose)
── Error ('test-stan_bridge_sampler_basic.R:57:5'): stan_bridge_sampler ────────
Error in `sink(type = "output")`: invalid connection
Backtrace:
▆
1. ├─base::suppressWarnings(stan_model(model_code = stancodeH0, model_name = "stanmodel")) at test-stan_bridge_sampler_basic.R:57:5
2. │ └─base::withCallingHandlers(...)
3. └─rstan::stan_model(model_code = stancodeH0, model_name = "stanmodel")
4. └─rstan:::cxxfunctionplus(...)
5. └─base::sink(type = "output")
[ FAIL 2 | WARN 0 | SKIP 19 | PASS 75 ]
Error:
! Test failures.
Execution halted
Flavor: r-release-macos-arm64
Version: 1.2-1
Check: package dependencies
Result: NOTE
Package suggested but not available for checking: ‘cmdstanr’
Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64
Version: 1.2-1
Check: tests
Result: ERROR
Running ‘testthat.R’ [7s/9s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> Sys.setenv("R_TESTS" = "")
> library(testthat)
>
> test_check("bridgesampling")
Loading required package: bridgesampling
Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
using C compiler: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’
using SDK: ‘NA’
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c foo.c -o foo.o
clang -arch arm64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o foo.so foo.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld: framework not found CoreFoundation
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [foo.so] Error 1
make cmd is
make -f '/Library/Frameworks/R.framework/Resources/etc/Makeconf' -f '/Library/Frameworks/R.framework/Resources/share/make/shlib.mk' CXX='$(CXX17) $(CXX17STD)' CXXFLAGS='$(CXX17FLAGS)' CXXPICFLAGS='$(CXX17PICFLAGS)' SHLIB_LDFLAGS='$(SHLIB_CXX17LDFLAGS)' SHLIB_LD='$(SHLIB_CXX17LD)' SHLIB='file71d8666870e5.so' OBJECTS='file71d8666870e5.o'
make would use
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/Rcpp/include/" -I"/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppEigen/include/" -I"/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppEigen/include/unsupported" -I"/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/BH/include" -I"/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/StanHeaders/include/src/" -I"/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/StanHeaders/include/" -I"/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppParallel/include/" -I"/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/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 '/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/StanHeaders/include/stan/math/prim/fun/Eigen.hpp' -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1 -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c file71d8666870e5.cpp -o file71d8666870e5.o
if test "zfile71d8666870e5.o" != "z"; then \
echo clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L"/Library/Frameworks/R.framework/Resources/lib" -L/opt/R/arm64/lib -o file71d8666870e5.so file71d8666870e5.o '/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/rstan/lib//libStanServices.a' -L'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/StanHeaders/lib/' -lStanHeaders -L'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppParallel/lib/' -ltbb -L/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppParallel/lib -ltbb -ltbbmalloc -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation; \
clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L"/Library/Frameworks/R.framework/Resources/lib" -L/opt/R/arm64/lib -o file71d8666870e5.so file71d8666870e5.o '/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/rstan/lib//libStanServices.a' -L'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/StanHeaders/lib/' -lStanHeaders -L'/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppParallel/lib/' -ltbb -L/Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppParallel/lib -ltbb -ltbbmalloc -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation; \
fi
Saving _problems/test-stan_bridge_sampler_basic-59.R
[ FAIL 2 | WARN 0 | SKIP 19 | PASS 75 ]
══ Skipped tests (19) ══════════════════════════════════════════════════════════
• On CRAN (19): 'test-bridge_sampler_CmdStanMCMC.R:4:3',
'test-bridge_sampler_CmdStanMCMC.R:75:3', 'test-bridge_sampler_Rcpp.R:6:3',
'test-bridge_sampler_Rcpp_parallel.R:6:3',
'test-bridge_sampler_mcmc.list.R:6:3', 'test-bridge_sampler_parallel.R:6:3',
'test-log_posterior_cmdstan.R:4:3', 'test-log_posterior_cmdstan.R:133:3',
'test-nimble_bridge_sampler.R:5:3', 'test-stan_bridge_sampler_basic.R:113:3',
'test-stan_bridge_sampler_bugs.R:65:3',
'test-stan_bridge_sampler_bugs.R:82:3',
'test-stan_bridge_sampler_bugs.R:126:3',
'test-stanreg_bridge_sampler_basic.R:6:3',
'test-stanreg_bridge_sampler_basic.R:26:3',
'test-vignette_example_jags.R:6:3', 'test-vignette_example_nimble.R:6:3',
'test-vignette_example_stan.R:6:3', 'test-vignette_stan_ttest.R:6:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-stan_bridge_sampler_basic.R:57:5'): stan_bridge_sampler ────────
Error in `compileCode(f, code, language = language, verbose = verbose)`: using C++ compiler: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’
using C++17
using SDK: ‘NA’
In file included from <built-in>:1:
In file included from /Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:22:
In file included from /Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppEigen/include/Eigen/Dense:1:
In file included from /Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppEigen/include/Eigen/Core:19:
In file included from /Volumes/Builds/packages/big-sur-arm64/Rlib/4.4/RcppEigen/include/Eigen/src/Core/util/Macros.h:679:
In file included from /Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/cmath:308:
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/math.h:300:15: fatal error: 'math.h' file not found
#include_next <math.h>
^~~~~~~~
1 error generated.
make: *** [file71d8666870e5.o] Error 1
Backtrace:
▆
1. ├─base::suppressWarnings(stan_model(model_code = stancodeH0, model_name = "stanmodel")) at test-stan_bridge_sampler_basic.R:57:5
2. │ └─base::withCallingHandlers(...)
3. └─rstan::stan_model(model_code = stancodeH0, model_name = "stanmodel")
4. └─rstan:::cxxfunctionplus(...)
5. ├─pkgbuild::with_build_tools(...)
6. └─inline::cxxfunction(...)
7. └─inline:::compileCode(f, code, language = language, verbose = verbose)
── Error ('test-stan_bridge_sampler_basic.R:57:5'): stan_bridge_sampler ────────
Error in `sink(type = "output")`: invalid connection
Backtrace:
▆
1. ├─base::suppressWarnings(stan_model(model_code = stancodeH0, model_name = "stanmodel")) at test-stan_bridge_sampler_basic.R:57:5
2. │ └─base::withCallingHandlers(...)
3. └─rstan::stan_model(model_code = stancodeH0, model_name = "stanmodel")
4. └─rstan:::cxxfunctionplus(...)
5. └─base::sink(type = "output")
[ FAIL 2 | WARN 0 | SKIP 19 | PASS 75 ]
Error:
! Test failures.
Execution halted
Flavor: r-oldrel-macos-arm64