Last updated on 2026-10-17 08:50:27 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.3.0 | 5.60 | 889.01 | 894.61 | OK | |
| r-devel-linux-x86_64-debian-gcc | 0.3.0 | 4.00 | 940.78 | 944.78 | OK | |
| r-devel-linux-x86_64-fedora-clang | 0.3.0 | 346.34 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 0.3.0 | 512.40 | OK | |||
| r-devel-windows-x86_64 | 0.3.0 | 13.00 | 428.00 | 441.00 | ERROR | |
| r-patched-linux-x86_64 | 0.3.0 | 6.44 | 963.67 | 970.11 | OK | |
| r-release-linux-x86_64 | 0.3.0 | 4.61 | 937.86 | 942.47 | 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 | 13.00 | 407.00 | 420.00 | ERROR | |
| 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 | 16.00 | 530.00 | 546.00 | ERROR |
Version: 0.3.0
Check: tests
Result: ERROR
Running 'spelling.R' [0s]
Running 'testthat.R' [138s]
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="file53ad878ee1bad.dll" WIN=64 TCLBIN= OBJECTS="file53ad878ee1bad.o"
make would use
make[1]: Entering directory '/d/temp/2026_10_15_10_16_52_18621/RtmpMtQeN5'
g++ -std=gnu++17 -I"D:/RCompile/recent/R/include" -DNDEBUG -I"D:/RCompile/CRANpkg/lib/4.7/Rcpp/include/" -I"D:/temp/2026_10_15_10_16_52_18621/RtmpIhfto8/RLIBS_61df06516c79/RcppEigen/include/" -I"D:/temp/2026_10_15_10_16_52_18621/RtmpIhfto8/RLIBS_61df06516c79/RcppEigen/include/unsupported" -I"D:/temp/2026_10_15_10_16_52_18621/RtmpIhfto8/RLIBS_61df06516c79/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 file53ad878ee1bad.cpp -o file53ad878ee1bad.o
if test "zfile53ad878ee1bad.o" != "z"; then \
if test -e "file53ad878ee1bad-win.def"; then \
echo g++ -shared -s -static-libgcc -o file53ad878ee1bad.dll file53ad878ee1bad-win.def file53ad878ee1bad.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 file53ad878ee1bad.dll file53ad878ee1bad-win.def file53ad878ee1bad.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 file53ad878ee1bad.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 file53ad878ee1bad.dll tmp.def file53ad878ee1bad.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 file53ad878ee1bad.dll tmp.def file53ad878ee1bad.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_10_15_10_16_52_18621/RtmpMtQeN5'
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::model53ad87f461135_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: file53ad878ee1bad.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="file923469f67b8.dll" WIN=64 TCLBIN= OBJECTS="file923469f67b8.o"
make would use
make[1]: Entering directory '/d/temp/2026_10_15_10_16_52_18621/RtmpA9t3gJ'
g++ -std=gnu++17 -I"D:/RCompile/recent/R/include" -DNDEBUG -I"D:/RCompile/CRANpkg/lib/4.7/Rcpp/include/" -I"D:/temp/2026_10_15_10_16_52_18621/RtmpIhfto8/RLIBS_61df06516c79/RcppEigen/include/" -I"D:/temp/2026_10_15_10_16_52_18621/RtmpIhfto8/RLIBS_61df06516c79/RcppEigen/include/unsupported" -I"D:/temp/2026_10_15_10_16_52_18621/RtmpIhfto8/RLIBS_61df06516c79/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 file923469f67b8.cpp -o file923469f67b8.o
if test "zfile923469f67b8.o" != "z"; then \
if test -e "file923469f67b8-win.def"; then \
echo g++ -shared -s -static-libgcc -o file923469f67b8.dll file923469f67b8-win.def file923469f67b8.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 file923469f67b8.dll file923469f67b8-win.def file923469f67b8.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 file923469f67b8.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 file923469f67b8.dll tmp.def file923469f67b8.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 file923469f67b8.dll tmp.def file923469f67b8.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_10_15_10_16_52_18621/RtmpA9t3gJ'
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="file10cd855027cbc.dll" WIN=64 TCLBIN= OBJECTS="file10cd855027cbc.o"
make would use
make[1]: Entering directory '/d/temp/2026_10_15_10_16_52_18621/RtmpmoufSA'
g++ -std=gnu++17 -I"D:/RCompile/recent/R/include" -DNDEBUG -I"D:/RCompile/CRANpkg/lib/4.7/Rcpp/include/" -I"D:/temp/2026_10_15_10_16_52_18621/RtmpIhfto8/RLIBS_61df06516c79/RcppEigen/include/" -I"D:/temp/2026_10_15_10_16_52_18621/RtmpIhfto8/RLIBS_61df06516c79/RcppEigen/include/unsupported" -I"D:/temp/2026_10_15_10_16_52_18621/RtmpIhfto8/RLIBS_61df06516c79/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 file10cd855027cbc.cpp -o file10cd855027cbc.o
if test "zfile10cd855027cbc.o" != "z"; then \
if test -e "file10cd855027cbc-win.def"; then \
echo g++ -shared -s -static-libgcc -o file10cd855027cbc.dll file10cd855027cbc-win.def file10cd855027cbc.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 file10cd855027cbc.dll file10cd855027cbc-win.def file10cd855027cbc.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 file10cd855027cbc.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 file10cd855027cbc.dll tmp.def file10cd855027cbc.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 file10cd855027cbc.dll tmp.def file10cd855027cbc.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_10_15_10_16_52_18621/RtmpmoufSA'
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$prior_cov)
5. └─rstan::stan_model(...)
6. └─rstan:::cxxfunctionplus(...)
7. └─base::sink(type = "output")
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'pipeline.Rmd' failed with diagnostics:
invalid connection
--- failed re-building 'pipeline.Rmd'
SUMMARY: processing the following files failed:
'analyse2.Rmd' 'pipeline.Rmd'
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-windows-x86_64
Version: 0.3.0
Check: tests
Result: ERROR
Running 'spelling.R' [0s]
Running 'testthat.R' [128s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
>
> library(testthat)
> library(rbmiUtils)
>
> test_check("rbmiUtils")
Attaching package: 'dplyr'
The following objects are masked from 'package:stats':
filter, lag
The following objects are masked from 'package:base':
intersect, setdiff, setequal, union
v All outcome values are complete -- no missing data to impute.
i You may not need `data_ice` for `rbmi::draws()`.
v All outcome values are complete -- no missing data to impute.
i You may not need `data_ice` for `rbmi::draws()`.
v All outcome values are complete -- no missing data to impute.
i You may not need `data_ice` for `rbmi::draws()`.
v All outcome values are complete -- no missing data to impute.
i You may not need `data_ice` for `rbmi::draws()`.
specified C++17
make cmd is
make -f "D:/RCompile/recent/R-4.6.1/etc/x64/Makeconf" -f "D:/RCompile/recent/R-4.6.1/share/make/winshlib.mk" CXX='$(CXX17) $(CXX17STD)' CXXFLAGS='$(CXX17FLAGS)' CXXPICFLAGS='$(CXX17PICFLAGS)' SHLIB_LDFLAGS='$(SHLIB_CXX17LDFLAGS)' SHLIB_LD='$(SHLIB_CXX17LD)' SHLIB="file6a2b425713f9b.dll" WIN=64 TCLBIN= OBJECTS="file6a2b425713f9b.o"
make would use
make[1]: Entering directory '/d/temp/2026_10_14_01_50_00_30378/RtmpQFazju'
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.6.1/include" -DNDEBUG -I"D:/RCompile/CRANpkg/lib/4.6/Rcpp/include/" -I"D:/temp/2026_10_14_01_50_00_30378/RtmpoNfcdy/RLIBS_1bbf4310366b0/RcppEigen/include/" -I"D:/temp/2026_10_14_01_50_00_30378/RtmpoNfcdy/RLIBS_1bbf4310366b0/RcppEigen/include/unsupported" -I"D:/temp/2026_10_14_01_50_00_30378/RtmpoNfcdy/RLIBS_1bbf4310366b0/BH/include" -I"D:/RCompile/CRANpkg/lib/4.6/StanHeaders/include/src/" -I"D:/RCompile/CRANpkg/lib/4.6/StanHeaders/include/" -I"D:/RCompile/CRANpkg/lib/4.6/RcppParallel/include/" -DRCPP_PARALLEL_USE_TBB=1 -DTBB_INTERFACE_NEW -ID:/RCompile/CRANpkg/lib/4.6/RcppParallel/include -I"D:/RCompile/CRANpkg/lib/4.6/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/4.6/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 file6a2b425713f9b.cpp -o file6a2b425713f9b.o
if test "zfile6a2b425713f9b.o" != "z"; then \
if test -e "file6a2b425713f9b-win.def"; then \
echo g++ -shared -s -static-libgcc -o file6a2b425713f9b.dll file6a2b425713f9b-win.def file6a2b425713f9b.o "D:/RCompile/CRANpkg/lib/4.6/rstan/lib/x64/libStanServices.a" -L"D:/RCompile/CRANpkg/lib/4.6/StanHeaders/libs/x64" -lStanHeaders -L"D:/RCompile/CRANpkg/lib/4.6/RcppParallel/lib/x64" -ltbb -LD:/RCompile/CRANpkg/lib/4.6/RcppParallel/libs/x64 -lRcppParallel -LD:/RCompile/CRANpkg/lib/4.6/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-4.6.1/bin/x64" -lR ; \
g++ -shared -s -static-libgcc -o file6a2b425713f9b.dll file6a2b425713f9b-win.def file6a2b425713f9b.o "D:/RCompile/CRANpkg/lib/4.6/rstan/lib/x64/libStanServices.a" -L"D:/RCompile/CRANpkg/lib/4.6/StanHeaders/libs/x64" -lStanHeaders -L"D:/RCompile/CRANpkg/lib/4.6/RcppParallel/lib/x64" -ltbb -LD:/RCompile/CRANpkg/lib/4.6/RcppParallel/libs/x64 -lRcppParallel -LD:/RCompile/CRANpkg/lib/4.6/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-4.6.1/bin/x64" -lR ; \
else \
echo EXPORTS > tmp.def; \
nm file6a2b425713f9b.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 file6a2b425713f9b.dll tmp.def file6a2b425713f9b.o "D:/RCompile/CRANpkg/lib/4.6/rstan/lib/x64/libStanServices.a" -L"D:/RCompile/CRANpkg/lib/4.6/StanHeaders/libs/x64" -lStanHeaders -L"D:/RCompile/CRANpkg/lib/4.6/RcppParallel/lib/x64" -ltbb -LD:/RCompile/CRANpkg/lib/4.6/RcppParallel/libs/x64 -lRcppParallel -LD:/RCompile/CRANpkg/lib/4.6/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-4.6.1/bin/x64" -lR ; \
g++ -shared -s -static-libgcc -o file6a2b425713f9b.dll tmp.def file6a2b425713f9b.o "D:/RCompile/CRANpkg/lib/4.6/rstan/lib/x64/libStanServices.a" -L"D:/RCompile/CRANpkg/lib/4.6/StanHeaders/libs/x64" -lStanHeaders -L"D:/RCompile/CRANpkg/lib/4.6/RcppParallel/lib/x64" -ltbb -LD:/RCompile/CRANpkg/lib/4.6/RcppParallel/libs/x64 -lRcppParallel -LD:/RCompile/CRANpkg/lib/4.6/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-4.6.1/bin/x64" -lR ; \
rm -f tmp.def; \
fi \
fi
make[1]: Leaving directory '/d/temp/2026_10_14_01_50_00_30378/RtmpQFazju'
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)`: amespace::model6a2b47e2351e_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/4.6/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/4.6/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-4.6.1/etc/x64/Makeconf:304: file6a2b425713f9b.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$prior_cov)
5. └─rstan::stan_model(...)
6. └─rstan:::cxxfunctionplus(...)
7. └─base::sink(type = "output")
[ FAIL 2 | WARN 16 | SKIP 2 | PASS 1024 ]
Error:
! Test failures.
Execution halted
Flavor: r-release-windows-x86_64
Version: 0.3.0
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building 'analyse2.Rmd' using rmarkdown
specified C++17
make cmd is
make -f "D:/RCompile/recent/R-4.6.1/etc/x64/Makeconf" -f "D:/RCompile/recent/R-4.6.1/share/make/winshlib.mk" CXX='$(CXX17) $(CXX17STD)' CXXFLAGS='$(CXX17FLAGS)' CXXPICFLAGS='$(CXX17PICFLAGS)' SHLIB_LDFLAGS='$(SHLIB_CXX17LDFLAGS)' SHLIB_LD='$(SHLIB_CXX17LD)' SHLIB="file5509c12495b82.dll" WIN=64 TCLBIN= OBJECTS="file5509c12495b82.o"
make would use
make[1]: Entering directory '/d/temp/2026_10_14_01_50_00_30378/RtmpoHestN'
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.6.1/include" -DNDEBUG -I"D:/RCompile/CRANpkg/lib/4.6/Rcpp/include/" -I"D:/temp/2026_10_14_01_50_00_30378/RtmpoNfcdy/RLIBS_1bbf4310366b0/RcppEigen/include/" -I"D:/temp/2026_10_14_01_50_00_30378/RtmpoNfcdy/RLIBS_1bbf4310366b0/RcppEigen/include/unsupported" -I"D:/temp/2026_10_14_01_50_00_30378/RtmpoNfcdy/RLIBS_1bbf4310366b0/BH/include" -I"D:/RCompile/CRANpkg/lib/4.6/StanHeaders/include/src/" -I"D:/RCompile/CRANpkg/lib/4.6/StanHeaders/include/" -I"D:/RCompile/CRANpkg/lib/4.6/RcppParallel/include/" -DRCPP_PARALLEL_USE_TBB=1 -DTBB_INTERFACE_NEW -ID:/RCompile/CRANpkg/lib/4.6/RcppParallel/include -I"D:/RCompile/CRANpkg/lib/4.6/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/4.6/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 file5509c12495b82.cpp -o file5509c12495b82.o
if test "zfile5509c12495b82.o" != "z"; then \
if test -e "file5509c12495b82-win.def"; then \
echo g++ -shared -s -static-libgcc -o file5509c12495b82.dll file5509c12495b82-win.def file5509c12495b82.o "D:/RCompile/CRANpkg/lib/4.6/rstan/lib/x64/libStanServices.a" -L"D:/RCompile/CRANpkg/lib/4.6/StanHeaders/libs/x64" -lStanHeaders -L"D:/RCompile/CRANpkg/lib/4.6/RcppParallel/lib/x64" -ltbb -LD:/RCompile/CRANpkg/lib/4.6/RcppParallel/libs/x64 -lRcppParallel -LD:/RCompile/CRANpkg/lib/4.6/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-4.6.1/bin/x64" -lR ; \
g++ -shared -s -static-libgcc -o file5509c12495b82.dll file5509c12495b82-win.def file5509c12495b82.o "D:/RCompile/CRANpkg/lib/4.6/rstan/lib/x64/libStanServices.a" -L"D:/RCompile/CRANpkg/lib/4.6/StanHeaders/libs/x64" -lStanHeaders -L"D:/RCompile/CRANpkg/lib/4.6/RcppParallel/lib/x64" -ltbb -LD:/RCompile/CRANpkg/lib/4.6/RcppParallel/libs/x64 -lRcppParallel -LD:/RCompile/CRANpkg/lib/4.6/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-4.6.1/bin/x64" -lR ; \
else \
echo EXPORTS > tmp.def; \
nm file5509c12495b82.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 file5509c12495b82.dll tmp.def file5509c12495b82.o "D:/RCompile/CRANpkg/lib/4.6/rstan/lib/x64/libStanServices.a" -L"D:/RCompile/CRANpkg/lib/4.6/StanHeaders/libs/x64" -lStanHeaders -L"D:/RCompile/CRANpkg/lib/4.6/RcppParallel/lib/x64" -ltbb -LD:/RCompile/CRANpkg/lib/4.6/RcppParallel/libs/x64 -lRcppParallel -LD:/RCompile/CRANpkg/lib/4.6/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-4.6.1/bin/x64" -lR ; \
g++ -shared -s -static-libgcc -o file5509c12495b82.dll tmp.def file5509c12495b82.o "D:/RCompile/CRANpkg/lib/4.6/rstan/lib/x64/libStanServices.a" -L"D:/RCompile/CRANpkg/lib/4.6/StanHeaders/libs/x64" -lStanHeaders -L"D:/RCompile/CRANpkg/lib/4.6/RcppParallel/lib/x64" -ltbb -LD:/RCompile/CRANpkg/lib/4.6/RcppParallel/libs/x64 -lRcppParallel -LD:/RCompile/CRANpkg/lib/4.6/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-4.6.1/bin/x64" -lR ; \
rm -f tmp.def; \
fi \
fi
make[1]: Leaving directory '/d/temp/2026_10_14_01_50_00_30378/RtmpoHestN'
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$prior_cov)
5. └─rstan::stan_model(...)
6. └─rstan:::cxxfunctionplus(...)
7. └─base::sink(type = "output")
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'analyse2.Rmd' failed with diagnostics:
invalid connection
--- failed re-building 'analyse2.Rmd'
--- re-building 'data-preparation.Rmd' using rmarkdown
--- finished re-building 'data-preparation.Rmd'
--- re-building 'deriving-endpoints.Rmd' using rmarkdown
--- finished re-building 'deriving-endpoints.Rmd'
--- re-building 'diagnostics.Rmd' using rmarkdown
--- finished re-building 'diagnostics.Rmd'
--- re-building 'efficient-storage.Rmd' using rmarkdown
--- finished re-building 'efficient-storage.Rmd'
--- re-building 'pipeline.Rmd' using rmarkdown
specified C++17
make cmd is
make -f "D:/RCompile/recent/R-4.6.1/etc/x64/Makeconf" -f "D:/RCompile/recent/R-4.6.1/share/make/winshlib.mk" CXX='$(CXX17) $(CXX17STD)' CXXFLAGS='$(CXX17FLAGS)' CXXPICFLAGS='$(CXX17PICFLAGS)' SHLIB_LDFLAGS='$(SHLIB_CXX17LDFLAGS)' SHLIB_LD='$(SHLIB_CXX17LD)' SHLIB="file22c286fca5300.dll" WIN=64 TCLBIN= OBJECTS="file22c286fca5300.o"
make would use
make[1]: Entering directory '/d/temp/2026_10_14_01_50_00_30378/Rtmpye64j1'
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.6.1/include" -DNDEBUG -I"D:/RCompile/CRANpkg/lib/4.6/Rcpp/include/" -I"D:/temp/2026_10_14_01_50_00_30378/RtmpoNfcdy/RLIBS_1bbf4310366b0/RcppEigen/include/" -I"D:/temp/2026_10_14_01_50_00_30378/RtmpoNfcdy/RLIBS_1bbf4310366b0/RcppEigen/include/unsupported" -I"D:/temp/2026_10_14_01_50_00_30378/RtmpoNfcdy/RLIBS_1bbf4310366b0/BH/include" -I"D:/RCompile/CRANpkg/lib/4.6/StanHeaders/include/src/" -I"D:/RCompile/CRANpkg/lib/4.6/StanHeaders/include/" -I"D:/RCompile/CRANpkg/lib/4.6/RcppParallel/include/" -DRCPP_PARALLEL_USE_TBB=1 -DTBB_INTERFACE_NEW -ID:/RCompile/CRANpkg/lib/4.6/RcppParallel/include -I"D:/RCompile/CRANpkg/lib/4.6/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/4.6/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 file22c286fca5300.cpp -o file22c286fca5300.o
if test "zfile22c286fca5300.o" != "z"; then \
if test -e "file22c286fca5300-win.def"; then \
echo g++ -shared -s -static-libgcc -o file22c286fca5300.dll file22c286fca5300-win.def file22c286fca5300.o "D:/RCompile/CRANpkg/lib/4.6/rstan/lib/x64/libStanServices.a" -L"D:/RCompile/CRANpkg/lib/4.6/StanHeaders/libs/x64" -lStanHeaders -L"D:/RCompile/CRANpkg/lib/4.6/RcppParallel/lib/x64" -ltbb -LD:/RCompile/CRANpkg/lib/4.6/RcppParallel/libs/x64 -lRcppParallel -LD:/RCompile/CRANpkg/lib/4.6/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-4.6.1/bin/x64" -lR ; \
g++ -shared -s -static-libgcc -o file22c286fca5300.dll file22c286fca5300-win.def file22c286fca5300.o "D:/RCompile/CRANpkg/lib/4.6/rstan/lib/x64/libStanServices.a" -L"D:/RCompile/CRANpkg/lib/4.6/StanHeaders/libs/x64" -lStanHeaders -L"D:/RCompile/CRANpkg/lib/4.6/RcppParallel/lib/x64" -ltbb -LD:/RCompile/CRANpkg/lib/4.6/RcppParallel/libs/x64 -lRcppParallel -LD:/RCompile/CRANpkg/lib/4.6/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-4.6.1/bin/x64" -lR ; \
else \
echo EXPORTS > tmp.def; \
nm file22c286fca5300.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 file22c286fca5300.dll tmp.def file22c286fca5300.o "D:/RCompile/CRANpkg/lib/4.6/rstan/lib/x64/libStanServices.a" -L"D:/RCompile/CRANpkg/lib/4.6/StanHeaders/libs/x64" -lStanHeaders -L"D:/RCompile/CRANpkg/lib/4.6/RcppParallel/lib/x64" -ltbb -LD:/RCompile/CRANpkg/lib/4.6/RcppParallel/libs/x64 -lRcppParallel -LD:/RCompile/CRANpkg/lib/4.6/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-4.6.1/bin/x64" -lR ; \
g++ -shared -s -static-libgcc -o file22c286fca5300.dll tmp.def file22c286fca5300.o "D:/RCompile/CRANpkg/lib/4.6/rstan/lib/x64/libStanServices.a" -L"D:/RCompile/CRANpkg/lib/4.6/StanHeaders/libs/x64" -lStanHeaders -L"D:/RCompile/CRANpkg/lib/4.6/RcppParallel/lib/x64" -ltbb -LD:/RCompile/CRANpkg/lib/4.6/RcppParallel/libs/x64 -lRcppParallel -LD:/RCompile/CRANpkg/lib/4.6/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-4.6.1/bin/x64" -lR ; \
rm -f tmp.def; \
fi \
fi
make[1]: Leaving directory '/d/temp/2026_10_14_01_50_00_30378/Rtmpye64j1'
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$prior_cov)
5. └─rstan::stan_model(...)
6. └─rstan:::cxxfunctionplus(...)
7. └─base::sink(type = "output")
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'pipeline.Rmd' failed with diagnostics:
invalid connection
--- failed re-building 'pipeline.Rmd'
SUMMARY: processing the following files failed:
'analyse2.Rmd' 'pipeline.Rmd'
Error: Vignette re-building failed.
Execution halted
Flavor: r-release-windows-x86_64
Version: 0.3.0
Check: tests
Result: ERROR
Running 'spelling.R' [0s]
Running 'testthat.R' [180s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
>
> library(testthat)
> library(rbmiUtils)
>
> test_check("rbmiUtils")
Attaching package: 'dplyr'
The following objects are masked from 'package:stats':
filter, lag
The following objects are masked from 'package:base':
intersect, setdiff, setequal, union
v All outcome values are complete -- no missing data to impute.
i You may not need `data_ice` for `rbmi::draws()`.
v All outcome values are complete -- no missing data to impute.
i You may not need `data_ice` for `rbmi::draws()`.
v All outcome values are complete -- no missing data to impute.
i You may not need `data_ice` for `rbmi::draws()`.
v All outcome values are complete -- no missing data to impute.
i You may not need `data_ice` for `rbmi::draws()`.
make cmd is
make -f "D:/RCompile/recent/R-4.5.3/etc/x64/Makeconf" -f "D:/RCompile/recent/R-4.5.3/share/make/winshlib.mk" CXX='$(CXX17) $(CXX17STD)' CXXFLAGS='$(CXX17FLAGS)' CXXPICFLAGS='$(CXX17PICFLAGS)' SHLIB_LDFLAGS='$(SHLIB_CXX17LDFLAGS)' SHLIB_LD='$(SHLIB_CXX17LD)' SHLIB="file28a3853197904.dll" WIN=64 TCLBIN= OBJECTS="file28a3853197904.o"
make would use
make[1]: Entering directory '/d/temp/2026_10_14_01_50_00_30378/Rtmpeu3OMF'
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_10_14_01_50_00_30378/RtmpCGn4Bq/RLIBS_549c0680866e4/RcppEigen/include/" -I"D:/temp/2026_10_14_01_50_00_30378/RtmpCGn4Bq/RLIBS_549c0680866e4/RcppEigen/include/unsupported" -I"D:/temp/2026_10_14_01_50_00_30378/RtmpCGn4Bq/RLIBS_549c0680866e4/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 file28a3853197904.cpp -o file28a3853197904.o
if test "zfile28a3853197904.o" != "z"; then \
if test -e "file28a3853197904-win.def"; then \
echo g++ -shared -s -static-libgcc -o file28a3853197904.dll file28a3853197904-win.def file28a3853197904.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 file28a3853197904.dll file28a3853197904-win.def file28a3853197904.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 file28a3853197904.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 file28a3853197904.dll tmp.def file28a3853197904.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 file28a3853197904.dll tmp.def file28a3853197904.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_10_14_01_50_00_30378/Rtmpeu3OMF'
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)`: mespace::model28a3870775b93_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: file28a3853197904.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="file511c8cfe75cb.dll" WIN=64 TCLBIN= OBJECTS="file511c8cfe75cb.o"
make would use
make[1]: Entering directory '/d/temp/2026_10_14_01_50_00_30378/RtmpGcHTJX'
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_10_14_01_50_00_30378/RtmpCGn4Bq/RLIBS_549c0680866e4/RcppEigen/include/" -I"D:/temp/2026_10_14_01_50_00_30378/RtmpCGn4Bq/RLIBS_549c0680866e4/RcppEigen/include/unsupported" -I"D:/temp/2026_10_14_01_50_00_30378/RtmpCGn4Bq/RLIBS_549c0680866e4/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 file511c8cfe75cb.cpp -o file511c8cfe75cb.o
if test "zfile511c8cfe75cb.o" != "z"; then \
if test -e "file511c8cfe75cb-win.def"; then \
echo g++ -shared -s -static-libgcc -o file511c8cfe75cb.dll file511c8cfe75cb-win.def file511c8cfe75cb.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 file511c8cfe75cb.dll file511c8cfe75cb-win.def file511c8cfe75cb.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 file511c8cfe75cb.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 file511c8cfe75cb.dll tmp.def file511c8cfe75cb.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 file511c8cfe75cb.dll tmp.def file511c8cfe75cb.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_10_14_01_50_00_30378/RtmpGcHTJX'
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="file560c065057c71.dll" WIN=64 TCLBIN= OBJECTS="file560c065057c71.o"
make would use
make[1]: Entering directory '/d/temp/2026_10_14_01_50_00_30378/Rtmp04ZAay'
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_10_14_01_50_00_30378/RtmpCGn4Bq/RLIBS_549c0680866e4/RcppEigen/include/" -I"D:/temp/2026_10_14_01_50_00_30378/RtmpCGn4Bq/RLIBS_549c0680866e4/RcppEigen/include/unsupported" -I"D:/temp/2026_10_14_01_50_00_30378/RtmpCGn4Bq/RLIBS_549c0680866e4/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 file560c065057c71.cpp -o file560c065057c71.o
if test "zfile560c065057c71.o" != "z"; then \
if test -e "file560c065057c71-win.def"; then \
echo g++ -shared -s -static-libgcc -o file560c065057c71.dll file560c065057c71-win.def file560c065057c71.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 file560c065057c71.dll file560c065057c71-win.def file560c065057c71.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 file560c065057c71.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 file560c065057c71.dll tmp.def file560c065057c71.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 file560c065057c71.dll tmp.def file560c065057c71.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_10_14_01_50_00_30378/Rtmp04ZAay'
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