Hi I’ have a same error too. Even if I tried
install.packages(c("StanHeaders","rstan"),type="source")
It says still
fit <- stan(file='model/model4-5.stan', data=data, seed=1234)
make cmd is
make -f "C:/PROGRA~1/R/R-40~1.3/etc/x64/Makeconf" -f "C:/PROGRA~1/R/R-40~1.3/share/make/winshlib.mk" CXX='$(CXX14) $(CXX14STD)' CXXFLAGS='$(CXX14FLAGS)' CXXPICFLAGS='$(CXX14PICFLAGS)' SHLIB_LDFLAGS='$(SHLIB_CXX14LDFLAGS)' SHLIB_LD='$(SHLIB_CXX14LD)' SHLIB="file28785f8b7742.dll" WIN=64 TCLBIN=64 OBJECTS="file28785f8b7742.o"
make would use
if test "zfile28785f8b7742.o" != "z"; then \
if test -e "file28785f8b7742-win.def"; then \
echo "c:/rtools40/mingw64/bin/"g++ -shared -s -static-libgcc -o file28785f8b7742.dll file28785f8b7742-win.def file28785f8b7742.o "C:/Program Files/R/R-4.0.3/library/rstan/lib/x64/libStanServices.a" -L"C:/Program Files/R/R-4.0.3/library/StanHeaders/libs/x64" -lStanHeaders -L"C:/Program Files/R/R-4.0.3/library/RcppParallel/lib/x64" -ltbb -L"C:/PROGRA~1/R/R-40~1.3/bin/x64" -lR ; \
"c:/rtools40/mingw64/bin/"g++ -shared -s -static-libgcc -o file28785f8b7742.dll file28785f8b7742-win.def file28785f8b7742.o "C:/Program Files/R/R-4.0.3/library/rstan/lib/x64/libStanServices.a" -L"C:/Program Files/R/R-4.0.3/library/StanHeaders/libs/x64" -lStanHeaders -L"C:/Program Files/R/R-4.0.3/library/RcppParallel/lib/x64" -ltbb -L"C:/PROGRA~1/R/R-40~1.3/bin/x64" -lR ; \
else \
echo EXPORTS > tmp.def; \
"c:/rtools40/mingw64/bin/"nm file28785f8b7742.o | sed -n 's/^.* [BCDRT] / /p' | sed -e '/[.]refptr[.]/d' -e '/[.]weak[.]/d' | sed 's/[^ ][^ ]*/"&"/g' >> tmp.def; \
echo "c:/rtools40/mingw64/bin/"g++ -shared -s -static-libgcc -o file28785f8b7742.dll tmp.def file28785f8b7742.o "C:/Program Files/R/R-4.0.3/library/rstan/lib/x64/libStanServices.a" -L"C:/Program Files/R/R-4.0.3/library/StanHeaders/libs/x64" -lStanHeaders -L"C:/Program Files/R/R-4.0.3/library/RcppParallel/lib/x64" -ltbb -L"C:/PROGRA~1/R/R-40~1.3/bin/x64" -lR ; \
"c:/rtools40/mingw64/bin/"g++ -shared -s -static-libgcc -o file28785f8b7742.dll tmp.def file28785f8b7742.o "C:/Program Files/R/R-4.0.3/library/rstan/lib/x64/libStanServices.a" -L"C:/Program Files/R/R-4.0.3/library/StanHeaders/libs/x64" -lStanHeaders -L"C:/Program Files/R/R-4.0.3/library/RcppParallel/lib/x64" -ltbb -L"C:/PROGRA~1/R/R-40~1.3/bin/x64" -lR ; \
rm -f tmp.def; \
fi \
fi
compileCode(f, code, language = language, verbose = verbose) でエラー:
C:/rtools40/mingw64/bin/../lib/gcc/x86_64-w64-mingw32/8.3.0/../../../../x86_64-w64-mingw32/bin/ld.exe: C:/Program Files/R/R-4.0.3/library/rstan/lib/x64/libStanServices.a(stan_fit.o):stan_fit.cpp:(.rdata$_ZZN5boost4math6detail9bessel_j0IeEET_S3_E2P1[_ZZN5boost4math6detail9bessel_j0IeEET_S3_E2P1]+0x0): multiple definition of `boost::math::detail::bessel_j0<long double>(long double)::P1'; file28785f8b7742.o:file28785f8b7742.cpp:(.data$_ZZN5boost4math6detail9bessel_j0IeEET_S3_E2P1[_ZZN5boost4math6detail9bessel_j0IeEET_S3_E2P1]+0x0): first defined hereC:/rtools40/mingw64/bin/../lib/gcc/x86_64-w64-mingw32/8.3.0/../../../../x86_64-w64-mingw32/bin/ld.exe: C:/Program Files/R/R-4.0.3/library/rstan/lib/x64/libStanServices.a(stan_fit.o):stan_fit.cpp:(.rdata$_ZZN5boost4math6detail9bessel_j0IeEET_S3_E2QC[_ZZN5boost4math6detail9bessel_j0IeEET_S3_E2QC]+0x0): multiple definition of `boost::math::detail::bessel_j0<long double>(long double)::QC'; file28785f8b7742.o:file28785f8b7742.cpp:(.d
追加情報: 警告メッセージ:
system(paste(CXX, ARGS), ignore.stdout = TRUE, ignore.stderr = TRUE) で:
'C:/rtools40/usr/mingw_/bin/g++' not found
sink(type = "output") でエラー: コネクションが不正です
I’ll be glad if you could help me.
Can you try running:
remove.packages(c("StanHeaders","rstan"))
Then closing and restarting R, then running:
install.packages(c("StanHeaders","rstan"),type="source")
Thank you so much for your reply. I really appreciate it.
As I proceed your advice. I see a compiling failure of Rstan as follows.
C:/Program Files/R/R-4.0.3/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
failed ************ (Pred::************
^
C:/Program Files/R/R-4.0.3/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
failed ************ (boost::mpl::not_<Pred>::************
The whole compiling message was too long for Rstudio console and I couldn’t get it. But last part is as follows
C:/Program Files/R/R-4.0.3/library/StanHeaders/include/stan/math/rev/core/set_zero_all_adjoints.hpp: At global scope:
C:/Program Files/R/R-4.0.3/library/StanHeaders/include/stan/math/rev/core/set_zero_all_adjoints.hpp:14:13: warning: 'void stan::math::set_zero_all_adjoints()' defined but not used [-Wunused-function]
static void set_zero_all_adjoints() {
^~~~~~~~~~~~~~~~~~~~~
"c:/rtools40/mingw64/bin/"ar -rs ../inst/lib//x64/libStanServices.a stan_fit.o stan_fit_base.o
C:\rtools40\mingw64\bin\ar.exe: ../inst/lib//x64/libStanServices.a を作成しています(generaing)
DLLは生成されませんでした (counldn't generate)
ERROR: compilation failed for package 'rstan'
* removing 'C:/Program Files/R/R-4.0.3/library/rstan'
Warning in install.packages :
installation of package ‘rstan’ had non-zero exit status
I could solve it. Thank you for your help!
By reinstalling R, it was solved. I guess this is caused by my environment.
Hi, face the same problem, I get this error "Error in compileCode(f, code, language = language, verbose = verbose) when I try to run this line of the code :
f_svslagr_incorp ← brm(
formula = m_svslagr_incorp,
prior = prior_svslagr_incorp,
data = d_incl_svslagr_noNAs,
chains = 4,
cores = 4,
warmup = 2000,
iter = 20000,
control = list(adapt_delta = 0.99),
save_pars = save_pars(all = TRUE)
)
p ← pp_check(f_svslagr_incorp, type = “bars”, ndraws = 100)
(p + labs(title = “f_svslagr_incorp”))
The error mssg I get is:
Error in compileCode(f, code, language = language, verbose = verbose) :
C:\rtools42\x86_64-w64-mingw32.static.posix\bin/ld.exe: file653019f55aed.o:file653019f55aed.cpp:(.text$_ZN3tbb8internal26task_scheduler_observer_v3D0Ev[_ZN3tbb8internal26task_scheduler_observer_v3D0Ev]+0x1d): undefined reference to tbb::internal::task_scheduler_observer_v3::observe(bool)'C:\rtools42\x86_64-w64-mingw32.static.posix\bin/ld.exe: file653019f55aed.o:file653019f55aed.cpp:(.text$_ZN3tbb10interface623task_scheduler_observerD1Ev[_ZN3tbb10interface623task_scheduler_observerD1Ev]+0x1d): undefined reference to tbb::internal::task_scheduler_observer_v3::observe(bool)'C:\rtools42\x86_64-w64-mingw32.static.posix\bin/ld.exe: file653019f55aed.o:file653019f55aed.cpp:(.text$_ZN3tbb10interface623task_scheduler_observerD1Ev[_ZN3tbb10interface623task_scheduler_observerD1Ev]+0x3a): undefined reference to `tbb::internal::task_scheduler_observer_v3::observe(bool)'C:\rtools42\x86_64-w64-mingw32.static.posix\bin/ld.exe: file653019f55aed.o:file653019f55aed.cpp:(.text$_ZN3tbb10interface
Error in sink(type = “output”) : invalid connection
I use R4.2.1
It says that the promblem is that R 4.2 is not compatible with the current Rstan, tried the suggested solution, to install the preview of rstan 2.26 using:
install.packages(“StanHeaders”, repos = c(“Repository for distributing (some) stan-dev R packages | r-packages”, getOption(“repos”)))
install.packages(“rstan”, repos = c(“Repository for distributing (some) stan-dev R packages | r-packages”, getOption(“repos”)))
I typed these lines in the code I’m running, at the beginning of the code, and I got the session aborted mssg, I appreciate your help, I’m stuck in this for 5 days so far
thank you
Can you try restarting R, and then only running these lines of code (make sure you copy and paste, rather than typing):
install.packages("StanHeaders", repos = c("https://mc-stan.org/r-packages/", getOption("repos")))
install.packages("rstan", repos = c("https://mc-stan.org/r-packages/", getOption("repos")))
After you run these two lines of code (and no others), does the session abort?
I face the same problem as @sumaya_zoubi and i have followed the steps in the Rstan Getting Started guide. After i ran
install.packages(“StanHeaders”, repos = c(“Repository for distributing (some) stan-dev R packages | r-packages”, getOption(“repos”)))
install.packages(“rstan”, repos = c(“Repository for distributing (some) stan-dev R packages | r-packages”, getOption(“repos”)))
these two lines, the session did not abort.So how can i solve the problem?
Can you be more specific about what the issue is? If the session isn’t aborting, doesn’t that resolve the issue?
but after i ran the example, the error in compileCode(f, code, language = language, verbose = verbose) still came out. And i tried
system(“touch foo.cpp”)
system(“R CMD SHLIB foo.cpp”)
these two lines and got two “[1] 0”
is it the reason of why i had that error?
i use R4.2.1, win11
Can you post the full compileCode error output that you get, as well as the output from:
if (!requireNamespace("devtools")) {
install.packages("devtools")
}
devtools::session_info("rstan")
this is the full compileCode error output:
Error in compileCode(f, code, language = language, verbose = verbose) :
C:\rtools42\x86_64-w64-mingw32.static.posix\bin/ld.exe: file35441cb83cc1.o:file35441cb83cc1.cpp:(.text$_ZN3tbb8internal26task_scheduler_observer_v3D0Ev[_ZN3tbb8internal26task_scheduler_observer_v3D0Ev]+0x1d): undefined reference to `tbb::internal::task_scheduler_observer_v3::observe(bool)'C:\rtools42\x86_64-w64-mingw32.static.posix\bin/ld.exe: file35441cb83cc1.o:file35441cb83cc1.cpp:(.text$_ZN3tbb10interface623task_scheduler_observerD1Ev[_ZN3tbb10interface623task_scheduler_observerD1Ev]+0x1d): undefined reference to `tbb::internal::task_scheduler_observer_v3::observe(bool)'C:\rtools42\x86_64-w64-mingw32.static.posix\bin/ld.exe: file35441cb83cc1.o:file35441cb83cc1.cpp:(.text$_ZN3tbb10interface623task_scheduler_observerD1Ev[_ZN3tbb10interface623task_scheduler_observerD1Ev]+0x3a): undefined reference to `tbb::internal::task_scheduler_observer_v3::observe(bool)'C:\rtools42\x86_64-w64-mingw32.static.posix\bin/ld.exe: file35441cb83cc1.o:file35441cb83cc1.cpp:(.text$_ZN3tbb10interface
and after running two lines:
i got:
devtools::session_info("rstan")
─ Session info ────────────────────────────────────────────────────────
setting value
version R version 4.2.1 (2022-06-23 ucrt)
os Windows 10 x64 (build 22000)
system x86_64, mingw32
ui RStudio
language (EN)
collate Chinese (Simplified)_China.utf8
ctype Chinese (Simplified)_China.utf8
tz Asia/Taipei
date 2022-10-20
rstudio 2022.07.2+576 Spotted Wakerobin (desktop)
pandoc NA
─ Packages ────────────────────────────────────────────────────────────
! package * version date (UTC) lib source
backports 1.4.1 2021-12-13 [1] CRAN (R 4.2.0)
BH 1.78.0-0 2021-12-15 [1] CRAN (R 4.2.0)
callr 3.7.2 2022-08-22 [1] CRAN (R 4.2.1)
checkmate 2.1.0 2022-04-21 [1] CRAN (R 4.2.1)
cli 3.4.1 2022-09-23 [1] CRAN (R 4.2.1)
colorspace 2.0-3 2022-02-21 [1] CRAN (R 4.2.1)
crayon 1.5.2 2022-09-29 [1] CRAN (R 4.2.1)
desc 1.4.2 2022-09-08 [1] CRAN (R 4.2.1)
digest 0.6.29 2021-12-01 [1] CRAN (R 4.2.1)
fansi 1.0.3 2022-03-24 [1] CRAN (R 4.2.1)
farver 2.1.1 2022-07-06 [1] CRAN (R 4.2.1)
ggplot2 * 3.3.6 2022-05-03 [1] CRAN (R 4.2.1)
glue 1.6.2 2022-02-24 [1] CRAN (R 4.2.1)
gridExtra 2.3 2017-09-09 [1] CRAN (R 4.2.1)
gtable 0.3.1 2022-09-01 [1] CRAN (R 4.2.1)
inline 0.3.19 2021-05-31 [1] CRAN (R 4.2.1)
isoband 0.2.6 2022-10-06 [1] CRAN (R 4.2.1)
labeling 0.4.2 2020-10-20 [1] CRAN (R 4.2.0)
lattice 0.20-45 2021-09-22 [1] CRAN (R 4.2.1)
lifecycle 1.0.3 2022-10-07 [1] CRAN (R 4.2.1)
loo 2.5.1 2022-03-24 [1] CRAN (R 4.2.1)
magrittr 2.0.3 2022-03-30 [1] CRAN (R 4.2.1)
MASS 7.3-57 2022-04-22 [1] CRAN (R 4.2.1)
Matrix 1.4-1 2022-03-23 [1] CRAN (R 4.2.1)
matrixStats 0.62.0 2022-04-19 [1] CRAN (R 4.2.1)
mgcv 1.8-40 2022-03-29 [1] CRAN (R 4.2.1)
munsell 0.5.0 2018-06-12 [1] CRAN (R 4.2.1)
nlme 3.1-157 2022-03-25 [1] CRAN (R 4.2.1)
pillar 1.8.1 2022-08-19 [1] CRAN (R 4.2.1)
pkgbuild 1.3.1 2021-12-20 [1] CRAN (R 4.2.1)
pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.2.1)
prettyunits 1.1.1 2020-01-24 [1] CRAN (R 4.2.1)
processx 3.7.0 2022-07-07 [1] CRAN (R 4.2.1)
ps 1.7.1 2022-06-18 [1] CRAN (R 4.2.1)
R6 2.5.1 2021-08-19 [1] CRAN (R 4.2.1)
RColorBrewer 1.1-3 2022-04-03 [1] CRAN (R 4.2.0)
Rcpp 1.0.9 2022-07-08 [1] CRAN (R 4.2.1)
RcppEigen 0.3.3.9.2 2022-04-08 [1] CRAN (R 4.2.1)
D RcppParallel 5.1.5 2022-01-05 [1] CRAN (R 4.2.1)
rlang 1.0.6 2022-09-24 [1] CRAN (R 4.2.1)
rprojroot 2.0.3 2022-04-02 [1] CRAN (R 4.2.1)
rstan * 2.21.7 2022-09-08 [1] CRAN (R 4.2.1)
scales 1.2.1 2022-08-20 [1] CRAN (R 4.2.1)
StanHeaders * 2.21.0-7 2020-12-17 [1] CRAN (R 4.2.1)
tibble 3.1.8 2022-07-22 [1] CRAN (R 4.2.1)
utf8 1.2.2 2021-07-24 [1] CRAN (R 4.2.1)
vctrs 0.4.2 2022-09-29 [1] CRAN (R 4.2.1)
viridisLite 0.4.1 2022-08-22 [1] CRAN (R 4.2.1)
withr 2.5.0 2022-03-03 [1] CRAN (R 4.2.1)
[1] E:/R-4.2.1/library
D ── DLL MD5 mismatch, broken installation.
According that session_info, you haven’t successfully installed the rstan preview. Can you close and restart R, making sure that no packages or objects get loaded, and run:
remove.packages(c("StanHeaders", "rstan"))
install.packages("rstan", repos = c("https://mc-stan.org/r-packages/", getOption("repos")))
And post any errors that you get
there seems to be no error in the output:
> remove.packages(c("StanHeaders", "rstan"))
Removing packages from ‘E:/R-4.2.1/library’
(as ‘lib’ is unspecified)
> install.packages("rstan", repos = c("https://mc-stan.org/r-packages/", getOption("repos")))
also installing the dependency ‘StanHeaders’
trying URL 'https://mc-stan.org/r-packages/bin/windows/contrib/4.2/StanHeaders_2.26.13.zip'
Content type 'application/zip' length 3199156 bytes (3.1 MB)
downloaded 3.1 MB
trying URL 'https://mc-stan.org/r-packages/bin/windows/contrib/4.2/rstan_2.26.13.zip'
Content type 'application/zip' length 2344412 bytes (2.2 MB)
downloaded 2.2 MB
package ‘StanHeaders’ successfully unpacked and MD5 sums checked
package ‘rstan’ successfully unpacked and MD5 sums checked
The downloaded binary packages are in
C:\Users\Administrator\AppData\Local\Temp\RtmpAXULWa\downloaded_packages
Now that the preview has been installed, you should be able to run the example model
There is no error any more! Amazing! Thank you for your patient help!😭
Dear Andrew,
I seem to be having a similar problem. I followed the steps given here to install Rtools, configure the C++ Toolchain, and install RStan:
- but at the step for verifying the RStan installation, I get this error:
Error in compileCode(f, code, language = language, verbose = verbose) :
C:\rtools42\x86_64-w64-mingw32.static.posix\bin/ld.exe: file277864591613.o:file277864591613.cpp:(.text$_ZN3tbb8internal26task_scheduler_observer_v3D0Ev[_ZN3tbb8internal26task_scheduler_observer_v3D0Ev]+0x1d): undefined reference to tbb::internal::task_scheduler_observer_v3::observe(bool)'C:\rtools42\x86_64-w64-mingw32.static.posix\bin/ld.exe: file277864591613.o:file277864591613.cpp:(.text$_ZN3tbb10interface623task_scheduler_observerD1Ev[_ZN3tbb10interface623task_scheduler_observerD1Ev]+0x1d): undefined reference to tbb::internal::task_scheduler_observer_v3::observe(bool)'C:\rtools42\x86_64-w64-mingw32.static.posix\bin/ld.exe: file277864591613.o:file277864591613.cpp:(.text$_ZN3tbb10interface623task_scheduler_observerD1Ev[_ZN3tbb10interface623task_scheduler_observerD1Ev]+0x3a): undefined reference to `tbb::internal::task_scheduler_observer_v3::observe(bool)'C:\rtools42\x86_64-w64-mingw32.static.posix\bin/ld.exe: file277864591613.o:file277864591613.cpp:(.text$_ZN3tbb10interface
Can you please help?