Last updated on 2026-09-08 13:51:35 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.3.0 | 5.25 | 701.01 | 706.26 | OK | |
| r-devel-linux-x86_64-debian-gcc | 0.3.0 | 3.84 | 641.32 | 645.16 | OK | |
| r-devel-linux-x86_64-fedora-clang | 0.3.0 | 340.98 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 0.3.0 | 529.73 | OK | |||
| r-devel-windows-x86_64 | 0.3.0 | 12.00 | 410.00 | 422.00 | ERROR | |
| r-patched-linux-x86_64 | 0.3.0 | 5.70 | 765.27 | 770.97 | OK | |
| r-release-linux-x86_64 | 0.3.0 | 4.24 | 799.05 | 803.29 | OK | |
| r-release-macos-arm64 | 0.3.0 | 2.00 | 140.00 | 142.00 | OK | |
| r-release-macos-x86_64 | 0.3.0 | 5.00 | 794.00 | 799.00 | OK | |
| r-release-windows-x86_64 | 0.3.0 | 11.00 | 1011.00 | 1022.00 | OK | |
| r-oldrel-macos-arm64 | 0.3.0 | 2.00 | 138.00 | 140.00 | OK | |
| r-oldrel-macos-x86_64 | 0.3.0 | 6.00 | 1404.00 | 1410.00 | OK | |
| r-oldrel-windows-x86_64 | 0.3.0 | 14.00 | 546.00 | 560.00 | ERROR |
Version: 0.3.0
Check: tests
Result: ERROR
Running 'spelling.R' [0s]
Running 'testthat.R' [127s]
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(rbmiUtils)
>
> test_check("rbmiUtils")
Attaching package: 'dplyr'
The following objects are masked from 'package:stats':
filter, lag
The following objects are masked from 'package:base':
intersect, setdiff, setequal, union
v All outcome values are complete -- no missing data to impute.
i You may not need `data_ice` for `rbmi::draws()`.
v All outcome values are complete -- no missing data to impute.
i You may not need `data_ice` for `rbmi::draws()`.
v All outcome values are complete -- no missing data to impute.
i You may not need `data_ice` for `rbmi::draws()`.
v All outcome values are complete -- no missing data to impute.
i You may not need `data_ice` for `rbmi::draws()`.
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="file1f29c35f731ce.dll" WIN=64 TCLBIN= OBJECTS="file1f29c35f731ce.o"
make would use
make[1]: Entering directory '/d/temp/2026_09_07_09_29_56_3012/RtmpaAgpnn'
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_07_09_29_56_3012/RtmpghbPEf/RLIBS_409746b7f4c5d/RcppEigen/include/" -I"D:/temp/2026_09_07_09_29_56_3012/RtmpghbPEf/RLIBS_409746b7f4c5d/RcppEigen/include/unsupported" -I"D:/temp/2026_09_07_09_29_56_3012/RtmpghbPEf/RLIBS_409746b7f4c5d/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 file1f29c35f731ce.cpp -o file1f29c35f731ce.o
if test "zfile1f29c35f731ce.o" != "z"; then \
if test -e "file1f29c35f731ce-win.def"; then \
echo g++ -shared -s -static-libgcc -o file1f29c35f731ce.dll file1f29c35f731ce-win.def file1f29c35f731ce.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 file1f29c35f731ce.dll file1f29c35f731ce-win.def file1f29c35f731ce.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 file1f29c35f731ce.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 file1f29c35f731ce.dll tmp.def file1f29c35f731ce.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 file1f29c35f731ce.dll tmp.def file1f29c35f731ce.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_07_09_29_56_3012/RtmpaAgpnn'
Saving _problems/test-utils-44.R
[ FAIL 2 | WARN 16 | SKIP 2 | PASS 1024 ]
══ Skipped tests (2) ═══════════════════════════════════════════════════════════
• Stanfit mock requires real Stan compilation - tested via integration (1):
'test-describe.R:273:3'
• rbmi::pool() returned empty results for g-computation (df = NA not supported)
(1): 'test-integration.R:279:5'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-utils.R:39:3'): positive test get_imputed_data (from vignettes) ──
Error in `compileCode(f, code, language = language, verbose = verbose)`: ult_namespace::model1f29c4bda56a6_rbmi_MMRM_us_default; 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: file1f29c35f731ce.o] Error 1
Backtrace:
▆
1. ├─rbmi::draws(data = dat, vars = vars, method = method, quiet = TRUE) at test-utils.R:39:3
2. └─rbmi:::draws.bayes(...)
3. └─rbmi:::fit_mcmc(...)
4. └─rbmi:::get_stan_model(covariance = method$covariance, prior_cov = method$prior_cov)
5. └─rstan::stan_model(...)
6. └─rstan:::cxxfunctionplus(...)
7. ├─pkgbuild::with_build_tools(...)
8. │ └─pkgbuild:::withr_with_path(rtools_path(), code)
9. │ └─base::force(code)
10. └─inline::cxxfunction(...)
11. └─inline:::compileCode(f, code, language = language, verbose = verbose)
── Error ('test-utils.R:39:3'): positive test get_imputed_data (from vignettes) ──
Error in `sink(type = "output")`: invalid connection
Backtrace:
▆
1. ├─rbmi::draws(data = dat, vars = vars, method = method, quiet = TRUE) at test-utils.R:39:3
2. └─rbmi:::draws.bayes(...)
3. └─rbmi:::fit_mcmc(...)
4. └─rbmi:::get_stan_model(covariance = method$covariance, prior_cov = method$prior_cov)
5. └─rstan::stan_model(...)
6. └─rstan:::cxxfunctionplus(...)
7. └─base::sink(type = "output")
[ FAIL 2 | WARN 16 | SKIP 2 | PASS 1024 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-windows-x86_64
Version: 0.3.0
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building 'analyse2.Rmd' using rmarkdown
specified C++17
make cmd is
make -f "D:/RCompile/recent/R/etc/x64/Makeconf" -f "D:/RCompile/recent/R/share/make/winshlib.mk" CXX='$(CXX17) $(CXX17STD)' CXXFLAGS='$(CXX17FLAGS)' CXXPICFLAGS='$(CXX17PICFLAGS)' SHLIB_LDFLAGS='$(SHLIB_CXX17LDFLAGS)' SHLIB_LD='$(SHLIB_CXX17LD)' SHLIB="file31da8658d7dd9.dll" WIN=64 TCLBIN= OBJECTS="file31da8658d7dd9.o"
make would use
make[1]: Entering directory '/d/temp/2026_09_07_09_29_56_3012/RtmpUvllHW'
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_07_09_29_56_3012/RtmpghbPEf/RLIBS_409746b7f4c5d/RcppEigen/include/" -I"D:/temp/2026_09_07_09_29_56_3012/RtmpghbPEf/RLIBS_409746b7f4c5d/RcppEigen/include/unsupported" -I"D:/temp/2026_09_07_09_29_56_3012/RtmpghbPEf/RLIBS_409746b7f4c5d/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 file31da8658d7dd9.cpp -o file31da8658d7dd9.o
if test "zfile31da8658d7dd9.o" != "z"; then \
if test -e "file31da8658d7dd9-win.def"; then \
echo g++ -shared -s -static-libgcc -o file31da8658d7dd9.dll file31da8658d7dd9-win.def file31da8658d7dd9.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 file31da8658d7dd9.dll file31da8658d7dd9-win.def file31da8658d7dd9.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 file31da8658d7dd9.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 file31da8658d7dd9.dll tmp.def file31da8658d7dd9.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 file31da8658d7dd9.dll tmp.def file31da8658d7dd9.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_07_09_29_56_3012/RtmpUvllHW'
Quitting from analyse2.Rmd:98-107 [impute]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `sink()`:
! invalid connection
---
Backtrace:
▆
1. ├─rbmi::draws(data = dat, vars = vars, method = method)
2. └─rbmi:::draws.bayes(data = dat, vars = vars, method = method)
3. └─rbmi:::fit_mcmc(...)
4. └─rbmi:::get_stan_model(covariance = method$covariance, prior_cov = method$prior_cov)
5. └─rstan::stan_model(...)
6. └─rstan:::cxxfunctionplus(...)
7. └─base::sink(type = "output")
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'analyse2.Rmd' failed with diagnostics:
invalid connection
--- failed re-building 'analyse2.Rmd'
--- re-building 'data-preparation.Rmd' using rmarkdown
--- finished re-building 'data-preparation.Rmd'
--- re-building 'deriving-endpoints.Rmd' using rmarkdown
--- finished re-building 'deriving-endpoints.Rmd'
--- re-building 'diagnostics.Rmd' using rmarkdown
--- finished re-building 'diagnostics.Rmd'
--- re-building 'efficient-storage.Rmd' using rmarkdown
--- finished re-building 'efficient-storage.Rmd'
--- re-building 'pipeline.Rmd' using rmarkdown
specified C++17
make cmd is
make -f "D:/RCompile/recent/R/etc/x64/Makeconf" -f "D:/RCompile/recent/R/share/make/winshlib.mk" CXX='$(CXX17) $(CXX17STD)' CXXFLAGS='$(CXX17FLAGS)' CXXPICFLAGS='$(CXX17PICFLAGS)' SHLIB_LDFLAGS='$(SHLIB_CXX17LDFLAGS)' SHLIB_LD='$(SHLIB_CXX17LD)' SHLIB="file16c4845036f8b.dll" WIN=64 TCLBIN= OBJECTS="file16c4845036f8b.o"
make would use
make[1]: Entering directory '/d/temp/2026_09_07_09_29_56_3012/RtmpEZkH91'
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_07_09_29_56_3012/RtmpghbPEf/RLIBS_409746b7f4c5d/RcppEigen/include/" -I"D:/temp/2026_09_07_09_29_56_3012/RtmpghbPEf/RLIBS_409746b7f4c5d/RcppEigen/include/unsupported" -I"D:/temp/2026_09_07_09_29_56_3012/RtmpghbPEf/RLIBS_409746b7f4c5d/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 file16c4845036f8b.cpp -o file16c4845036f8b.o
if test "zfile16c4845036f8b.o" != "z"; then \
if test -e "file16c4845036f8b-win.def"; then \
echo g++ -shared -s -static-libgcc -o file16c4845036f8b.dll file16c4845036f8b-win.def file16c4845036f8b.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 file16c4845036f8b.dll file16c4845036f8b-win.def file16c4845036f8b.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 file16c4845036f8b.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 file16c4845036f8b.dll tmp.def file16c4845036f8b.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 file16c4845036f8b.dll tmp.def file16c4845036f8b.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_07_09_29_56_3012/RtmpEZkH91'
Quitting from pipeline.Rmd:160-165 [draws]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `sink()`:
! invalid connection
---
Backtrace:
▆
1. ├─rbmi::draws(data = dat, vars = vars, method = method)
2. └─rbmi:::draws.bayes(data = dat, vars = vars, method = method)
3. └─rbmi:::fit_mcmc(...)
4. └─rbmi:::get_stan_model(covariance = method$covariance, prior_cov = method$prior_cov)
5. └─rstan::stan_model(...)
6. └─rstan:::cxxfunctionplus(...)
7. └─base::sink(type = "output")
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'pipeline.Rmd' failed with diagnostics:
invalid connection
--- failed re-building 'pipeline.Rmd'
SUMMARY: processing the following files failed:
'analyse2.Rmd' 'pipeline.Rmd'
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-windows-x86_64
Version: 0.3.0
Check: tests
Result: ERROR
Running 'spelling.R' [0s]
Running 'testthat.R' [186s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
>
> library(testthat)
> library(rbmiUtils)
>
> test_check("rbmiUtils")
Attaching package: 'dplyr'
The following objects are masked from 'package:stats':
filter, lag
The following objects are masked from 'package:base':
intersect, setdiff, setequal, union
v All outcome values are complete -- no missing data to impute.
i You may not need `data_ice` for `rbmi::draws()`.
v All outcome values are complete -- no missing data to impute.
i You may not need `data_ice` for `rbmi::draws()`.
v All outcome values are complete -- no missing data to impute.
i You may not need `data_ice` for `rbmi::draws()`.
v All outcome values are complete -- no missing data to impute.
i You may not need `data_ice` for `rbmi::draws()`.
make cmd is
make -f "D:/RCompile/recent/R-4.5.3/etc/x64/Makeconf" -f "D:/RCompile/recent/R-4.5.3/share/make/winshlib.mk" CXX='$(CXX17) $(CXX17STD)' CXXFLAGS='$(CXX17FLAGS)' CXXPICFLAGS='$(CXX17PICFLAGS)' SHLIB_LDFLAGS='$(SHLIB_CXX17LDFLAGS)' SHLIB_LD='$(SHLIB_CXX17LD)' SHLIB="filebd2411562bbf.dll" WIN=64 TCLBIN= OBJECTS="filebd2411562bbf.o"
make would use
make[1]: Entering directory '/d/temp/2026_09_07_01_50_00_11199/RtmpCobuqC'
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.5.3/include" -DNDEBUG -I"D:/RCompile/CRANpkg/lib/4.5/Rcpp/include/" -I"D:/temp/2026_09_07_01_50_00_11199/RtmpWI8bYq/RLIBS_72b4c73656a/RcppEigen/include/" -I"D:/temp/2026_09_07_01_50_00_11199/RtmpWI8bYq/RLIBS_72b4c73656a/RcppEigen/include/unsupported" -I"D:/temp/2026_09_07_01_50_00_11199/RtmpWI8bYq/RLIBS_72b4c73656a/BH/include" -I"D:/RCompile/CRANpkg/lib/4.5/StanHeaders/include/src/" -I"D:/RCompile/CRANpkg/lib/4.5/StanHeaders/include/" -I"D:/RCompile/CRANpkg/lib/4.5/RcppParallel/include/" -DRCPP_PARALLEL_USE_TBB=1 -DTBB_INTERFACE_NEW -ID:/RCompile/CRANpkg/lib/4.5/RcppParallel/include -I"D:/RCompile/CRANpkg/lib/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 "D:/RCompile/CRANpkg/lib/4.5/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 filebd2411562bbf.cpp -o filebd2411562bbf.o
if test "zfilebd2411562bbf.o" != "z"; then \
if test -e "filebd2411562bbf-win.def"; then \
echo g++ -shared -s -static-libgcc -o filebd2411562bbf.dll filebd2411562bbf-win.def filebd2411562bbf.o "D:/RCompile/CRANpkg/lib/4.5/rstan/lib/x64/libStanServices.a" -L"D:/RCompile/CRANpkg/lib/4.5/StanHeaders/libs/x64" -lStanHeaders -L"D:/RCompile/CRANpkg/lib/4.5/RcppParallel/lib/x64" -ltbb -LD:/RCompile/CRANpkg/lib/4.5/RcppParallel/libs/x64 -lRcppParallel -LD:/RCompile/CRANpkg/lib/4.5/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-4.5.3/bin/x64" -lR ; \
g++ -shared -s -static-libgcc -o filebd2411562bbf.dll filebd2411562bbf-win.def filebd2411562bbf.o "D:/RCompile/CRANpkg/lib/4.5/rstan/lib/x64/libStanServices.a" -L"D:/RCompile/CRANpkg/lib/4.5/StanHeaders/libs/x64" -lStanHeaders -L"D:/RCompile/CRANpkg/lib/4.5/RcppParallel/lib/x64" -ltbb -LD:/RCompile/CRANpkg/lib/4.5/RcppParallel/libs/x64 -lRcppParallel -LD:/RCompile/CRANpkg/lib/4.5/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-4.5.3/bin/x64" -lR ; \
else \
echo EXPORTS > tmp.def; \
nm filebd2411562bbf.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 filebd2411562bbf.dll tmp.def filebd2411562bbf.o "D:/RCompile/CRANpkg/lib/4.5/rstan/lib/x64/libStanServices.a" -L"D:/RCompile/CRANpkg/lib/4.5/StanHeaders/libs/x64" -lStanHeaders -L"D:/RCompile/CRANpkg/lib/4.5/RcppParallel/lib/x64" -ltbb -LD:/RCompile/CRANpkg/lib/4.5/RcppParallel/libs/x64 -lRcppParallel -LD:/RCompile/CRANpkg/lib/4.5/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-4.5.3/bin/x64" -lR ; \
g++ -shared -s -static-libgcc -o filebd2411562bbf.dll tmp.def filebd2411562bbf.o "D:/RCompile/CRANpkg/lib/4.5/rstan/lib/x64/libStanServices.a" -L"D:/RCompile/CRANpkg/lib/4.5/StanHeaders/libs/x64" -lStanHeaders -L"D:/RCompile/CRANpkg/lib/4.5/RcppParallel/lib/x64" -ltbb -LD:/RCompile/CRANpkg/lib/4.5/RcppParallel/libs/x64 -lRcppParallel -LD:/RCompile/CRANpkg/lib/4.5/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-4.5.3/bin/x64" -lR ; \
rm -f tmp.def; \
fi \
fi
make[1]: Leaving directory '/d/temp/2026_09_07_01_50_00_11199/RtmpCobuqC'
Saving _problems/test-utils-44.R
[ FAIL 2 | WARN 16 | SKIP 2 | PASS 1024 ]
══ Skipped tests (2) ═══════════════════════════════════════════════════════════
• Stanfit mock requires real Stan compilation - tested via integration (1):
'test-describe.R:273:3'
• rbmi::pool() returned empty results for g-computation (df = NA not supported)
(1): 'test-integration.R:279:5'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-utils.R:39:3'): positive test get_imputed_data (from vignettes) ──
Error in `compileCode(f, code, language = language, verbose = verbose)`: namespace::modelbd2449e375a6_rbmi_MMRM_us_default; 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/4.5/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/4.5/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-4.5.3/etc/x64/Makeconf:302: filebd2411562bbf.o] Error 1
Backtrace:
▆
1. ├─rbmi::draws(data = dat, vars = vars, method = method, quiet = TRUE) at test-utils.R:39:3
2. └─rbmi:::draws.bayes(...)
3. └─rbmi:::fit_mcmc(...)
4. └─rbmi:::get_stan_model(covariance = method$covariance, prior_cov = method$prior_cov)
5. └─rstan::stan_model(...)
6. └─rstan:::cxxfunctionplus(...)
7. ├─pkgbuild::with_build_tools(...)
8. │ └─pkgbuild:::withr_with_path(rtools_path(), code)
9. │ └─base::force(code)
10. └─inline::cxxfunction(...)
11. └─inline:::compileCode(f, code, language = language, verbose = verbose)
── Error ('test-utils.R:39:3'): positive test get_imputed_data (from vignettes) ──
Error in `sink(type = "output")`: invalid connection
Backtrace:
▆
1. ├─rbmi::draws(data = dat, vars = vars, method = method, quiet = TRUE) at test-utils.R:39:3
2. └─rbmi:::draws.bayes(...)
3. └─rbmi:::fit_mcmc(...)
4. └─rbmi:::get_stan_model(covariance = method$covariance, prior_cov = method$prior_cov)
5. └─rstan::stan_model(...)
6. └─rstan:::cxxfunctionplus(...)
7. └─base::sink(type = "output")
[ FAIL 2 | WARN 16 | SKIP 2 | PASS 1024 ]
Error:
! Test failures.
Execution halted
Flavor: r-oldrel-windows-x86_64
Version: 0.3.0
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building 'analyse2.Rmd' using rmarkdown
make cmd is
make -f "D:/RCompile/recent/R-4.5.3/etc/x64/Makeconf" -f "D:/RCompile/recent/R-4.5.3/share/make/winshlib.mk" CXX='$(CXX17) $(CXX17STD)' CXXFLAGS='$(CXX17FLAGS)' CXXPICFLAGS='$(CXX17PICFLAGS)' SHLIB_LDFLAGS='$(SHLIB_CXX17LDFLAGS)' SHLIB_LD='$(SHLIB_CXX17LD)' SHLIB="file463c7d9f2b3b.dll" WIN=64 TCLBIN= OBJECTS="file463c7d9f2b3b.o"
make would use
make[1]: Entering directory '/d/temp/2026_09_07_01_50_00_11199/RtmpQ7iBmm'
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.5.3/include" -DNDEBUG -I"D:/RCompile/CRANpkg/lib/4.5/Rcpp/include/" -I"D:/temp/2026_09_07_01_50_00_11199/RtmpWI8bYq/RLIBS_72b4c73656a/RcppEigen/include/" -I"D:/temp/2026_09_07_01_50_00_11199/RtmpWI8bYq/RLIBS_72b4c73656a/RcppEigen/include/unsupported" -I"D:/temp/2026_09_07_01_50_00_11199/RtmpWI8bYq/RLIBS_72b4c73656a/BH/include" -I"D:/RCompile/CRANpkg/lib/4.5/StanHeaders/include/src/" -I"D:/RCompile/CRANpkg/lib/4.5/StanHeaders/include/" -I"D:/RCompile/CRANpkg/lib/4.5/RcppParallel/include/" -DRCPP_PARALLEL_USE_TBB=1 -DTBB_INTERFACE_NEW -ID:/RCompile/CRANpkg/lib/4.5/RcppParallel/include -I"D:/RCompile/CRANpkg/lib/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 "D:/RCompile/CRANpkg/lib/4.5/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 file463c7d9f2b3b.cpp -o file463c7d9f2b3b.o
if test "zfile463c7d9f2b3b.o" != "z"; then \
if test -e "file463c7d9f2b3b-win.def"; then \
echo g++ -shared -s -static-libgcc -o file463c7d9f2b3b.dll file463c7d9f2b3b-win.def file463c7d9f2b3b.o "D:/RCompile/CRANpkg/lib/4.5/rstan/lib/x64/libStanServices.a" -L"D:/RCompile/CRANpkg/lib/4.5/StanHeaders/libs/x64" -lStanHeaders -L"D:/RCompile/CRANpkg/lib/4.5/RcppParallel/lib/x64" -ltbb -LD:/RCompile/CRANpkg/lib/4.5/RcppParallel/libs/x64 -lRcppParallel -LD:/RCompile/CRANpkg/lib/4.5/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-4.5.3/bin/x64" -lR ; \
g++ -shared -s -static-libgcc -o file463c7d9f2b3b.dll file463c7d9f2b3b-win.def file463c7d9f2b3b.o "D:/RCompile/CRANpkg/lib/4.5/rstan/lib/x64/libStanServices.a" -L"D:/RCompile/CRANpkg/lib/4.5/StanHeaders/libs/x64" -lStanHeaders -L"D:/RCompile/CRANpkg/lib/4.5/RcppParallel/lib/x64" -ltbb -LD:/RCompile/CRANpkg/lib/4.5/RcppParallel/libs/x64 -lRcppParallel -LD:/RCompile/CRANpkg/lib/4.5/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-4.5.3/bin/x64" -lR ; \
else \
echo EXPORTS > tmp.def; \
nm file463c7d9f2b3b.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 file463c7d9f2b3b.dll tmp.def file463c7d9f2b3b.o "D:/RCompile/CRANpkg/lib/4.5/rstan/lib/x64/libStanServices.a" -L"D:/RCompile/CRANpkg/lib/4.5/StanHeaders/libs/x64" -lStanHeaders -L"D:/RCompile/CRANpkg/lib/4.5/RcppParallel/lib/x64" -ltbb -LD:/RCompile/CRANpkg/lib/4.5/RcppParallel/libs/x64 -lRcppParallel -LD:/RCompile/CRANpkg/lib/4.5/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-4.5.3/bin/x64" -lR ; \
g++ -shared -s -static-libgcc -o file463c7d9f2b3b.dll tmp.def file463c7d9f2b3b.o "D:/RCompile/CRANpkg/lib/4.5/rstan/lib/x64/libStanServices.a" -L"D:/RCompile/CRANpkg/lib/4.5/StanHeaders/libs/x64" -lStanHeaders -L"D:/RCompile/CRANpkg/lib/4.5/RcppParallel/lib/x64" -ltbb -LD:/RCompile/CRANpkg/lib/4.5/RcppParallel/libs/x64 -lRcppParallel -LD:/RCompile/CRANpkg/lib/4.5/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-4.5.3/bin/x64" -lR ; \
rm -f tmp.def; \
fi \
fi
make[1]: Leaving directory '/d/temp/2026_09_07_01_50_00_11199/RtmpQ7iBmm'
Quitting from analyse2.Rmd:98-107 [impute]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `sink()`:
! invalid connection
---
Backtrace:
▆
1. ├─rbmi::draws(data = dat, vars = vars, method = method)
2. └─rbmi:::draws.bayes(data = dat, vars = vars, method = method)
3. └─rbmi:::fit_mcmc(...)
4. └─rbmi:::get_stan_model(covariance = method$covariance, prior_cov = method$prior_cov)
5. └─rstan::stan_model(...)
6. └─rstan:::cxxfunctionplus(...)
7. └─base::sink(type = "output")
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'analyse2.Rmd' failed with diagnostics:
invalid connection
--- failed re-building 'analyse2.Rmd'
--- re-building 'data-preparation.Rmd' using rmarkdown
--- finished re-building 'data-preparation.Rmd'
--- re-building 'deriving-endpoints.Rmd' using rmarkdown
--- finished re-building 'deriving-endpoints.Rmd'
--- re-building 'diagnostics.Rmd' using rmarkdown
--- finished re-building 'diagnostics.Rmd'
--- re-building 'efficient-storage.Rmd' using rmarkdown
--- finished re-building 'efficient-storage.Rmd'
--- re-building 'pipeline.Rmd' using rmarkdown
make cmd is
make -f "D:/RCompile/recent/R-4.5.3/etc/x64/Makeconf" -f "D:/RCompile/recent/R-4.5.3/share/make/winshlib.mk" CXX='$(CXX17) $(CXX17STD)' CXXFLAGS='$(CXX17FLAGS)' CXXPICFLAGS='$(CXX17PICFLAGS)' SHLIB_LDFLAGS='$(SHLIB_CXX17LDFLAGS)' SHLIB_LD='$(SHLIB_CXX17LD)' SHLIB="fileb9b4581c2a95.dll" WIN=64 TCLBIN= OBJECTS="fileb9b4581c2a95.o"
make would use
make[1]: Entering directory '/d/temp/2026_09_07_01_50_00_11199/RtmpOKr6av'
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.5.3/include" -DNDEBUG -I"D:/RCompile/CRANpkg/lib/4.5/Rcpp/include/" -I"D:/temp/2026_09_07_01_50_00_11199/RtmpWI8bYq/RLIBS_72b4c73656a/RcppEigen/include/" -I"D:/temp/2026_09_07_01_50_00_11199/RtmpWI8bYq/RLIBS_72b4c73656a/RcppEigen/include/unsupported" -I"D:/temp/2026_09_07_01_50_00_11199/RtmpWI8bYq/RLIBS_72b4c73656a/BH/include" -I"D:/RCompile/CRANpkg/lib/4.5/StanHeaders/include/src/" -I"D:/RCompile/CRANpkg/lib/4.5/StanHeaders/include/" -I"D:/RCompile/CRANpkg/lib/4.5/RcppParallel/include/" -DRCPP_PARALLEL_USE_TBB=1 -DTBB_INTERFACE_NEW -ID:/RCompile/CRANpkg/lib/4.5/RcppParallel/include -I"D:/RCompile/CRANpkg/lib/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 "D:/RCompile/CRANpkg/lib/4.5/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 fileb9b4581c2a95.cpp -o fileb9b4581c2a95.o
if test "zfileb9b4581c2a95.o" != "z"; then \
if test -e "fileb9b4581c2a95-win.def"; then \
echo g++ -shared -s -static-libgcc -o fileb9b4581c2a95.dll fileb9b4581c2a95-win.def fileb9b4581c2a95.o "D:/RCompile/CRANpkg/lib/4.5/rstan/lib/x64/libStanServices.a" -L"D:/RCompile/CRANpkg/lib/4.5/StanHeaders/libs/x64" -lStanHeaders -L"D:/RCompile/CRANpkg/lib/4.5/RcppParallel/lib/x64" -ltbb -LD:/RCompile/CRANpkg/lib/4.5/RcppParallel/libs/x64 -lRcppParallel -LD:/RCompile/CRANpkg/lib/4.5/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-4.5.3/bin/x64" -lR ; \
g++ -shared -s -static-libgcc -o fileb9b4581c2a95.dll fileb9b4581c2a95-win.def fileb9b4581c2a95.o "D:/RCompile/CRANpkg/lib/4.5/rstan/lib/x64/libStanServices.a" -L"D:/RCompile/CRANpkg/lib/4.5/StanHeaders/libs/x64" -lStanHeaders -L"D:/RCompile/CRANpkg/lib/4.5/RcppParallel/lib/x64" -ltbb -LD:/RCompile/CRANpkg/lib/4.5/RcppParallel/libs/x64 -lRcppParallel -LD:/RCompile/CRANpkg/lib/4.5/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-4.5.3/bin/x64" -lR ; \
else \
echo EXPORTS > tmp.def; \
nm fileb9b4581c2a95.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 fileb9b4581c2a95.dll tmp.def fileb9b4581c2a95.o "D:/RCompile/CRANpkg/lib/4.5/rstan/lib/x64/libStanServices.a" -L"D:/RCompile/CRANpkg/lib/4.5/StanHeaders/libs/x64" -lStanHeaders -L"D:/RCompile/CRANpkg/lib/4.5/RcppParallel/lib/x64" -ltbb -LD:/RCompile/CRANpkg/lib/4.5/RcppParallel/libs/x64 -lRcppParallel -LD:/RCompile/CRANpkg/lib/4.5/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-4.5.3/bin/x64" -lR ; \
g++ -shared -s -static-libgcc -o fileb9b4581c2a95.dll tmp.def fileb9b4581c2a95.o "D:/RCompile/CRANpkg/lib/4.5/rstan/lib/x64/libStanServices.a" -L"D:/RCompile/CRANpkg/lib/4.5/StanHeaders/libs/x64" -lStanHeaders -L"D:/RCompile/CRANpkg/lib/4.5/RcppParallel/lib/x64" -ltbb -LD:/RCompile/CRANpkg/lib/4.5/RcppParallel/libs/x64 -lRcppParallel -LD:/RCompile/CRANpkg/lib/4.5/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-4.5.3/bin/x64" -lR ; \
rm -f tmp.def; \
fi \
fi
make[1]: Leaving directory '/d/temp/2026_09_07_01_50_00_11199/RtmpOKr6av'
Quitting from pipeline.Rmd:160-165 [draws]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `sink()`:
! invalid connection
---
Backtrace:
▆
1. ├─rbmi::draws(data = dat, vars = vars, method = method)
2. └─rbmi:::draws.bayes(data = dat, vars = vars, method = method)
3. └─rbmi:::fit_mcmc(...)
4. └─rbmi:::get_stan_model(covariance = method$covariance, prior_cov = method$prior_cov)
5. └─rstan::stan_model(...)
6. └─rstan:::cxxfunctionplus(...)
7. └─base::sink(type = "output")
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'pipeline.Rmd' failed with diagnostics:
invalid connection
--- failed re-building 'pipeline.Rmd'
SUMMARY: processing the following files failed:
'analyse2.Rmd' 'pipeline.Rmd'
Error: Vignette re-building failed.
Execution halted
Flavor: r-oldrel-windows-x86_64