Hi Iβ 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) γ§γ¨γ©γΌ:
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
θΏ½ε ζ
ε ±: θ¦εγ‘γγ»γΌγΈ:
system(paste(CXX, ARGS), ignore.stdout = TRUE, ignore.stderr = TRUE) γ§:
'C:/rtools40/usr/mingw_/bin/g++' not found
sink(type = "output") γ§γ¨γ©γΌ: γ³γγ―γ·γ§γ³γδΈζ£γ§γ
Iβll 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 couldnβt 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 γδ½ζγγ¦γγΎγ(generaing)
DLLγ―ηζγγγΎγγγ§γγ (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 βrstanβ 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 β 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 β pp_check(f_svslagr_incorp, type = βbarsβ, ndraws = 100)
(p + labs(title = βf_svslagr_incorpβ))
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 = βoutputβ) : 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(βStanHeadersβ, repos = c(βRepository for distributing (some) stan-dev R packages | r-packagesβ, getOption(βreposβ)))
install.packages(βrstanβ, repos = c(βRepository for distributing (some) stan-dev R packages | r-packagesβ, getOption(βreposβ)))
I typed these lines in the code Iβm running, at the beginning of the code, and I got the session aborted mssg, I appreciate your help, Iβm stuck in this for 5 days so far
thank you
1 Like
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(βStanHeadersβ, repos = c(βRepository for distributing (some) stan-dev R packages | r-packagesβ, getOption(βreposβ)))
install.packages(βrstanβ, repos = c(βRepository for distributing (some) stan-dev R packages | r-packagesβ, getOption(βreposβ)))
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 isnβt aborting, doesnβt 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(βtouch foo.cppβ)
system(βR CMD SHLIB foo.cppβ)
these two lines and got two β[1] 0β
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")
β Session info ββββββββββββββββββββββββββββββββββββββββββββββββββββββββ
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
β Packages ββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββ
! 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 ββ DLL MD5 mismatch, broken installation.
According that session_info, you havenβt 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 βE:/R-4.2.1/libraryβ
(as βlibβ is unspecified)
> install.packages("rstan", repos = c("https://mc-stan.org/r-packages/", getOption("repos")))
also installing the dependency βStanHeadersβ
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 βStanHeadersβ successfully unpacked and MD5 sums checked
package βrstanβ 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!π
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?