Closed ardollam closed 2 years ago
andrjohns
commented
2 years ago Hi Niall,
Is the behaviour different if you pause the dropbox sync before compiling?
Are you able to run the rstan example model?
example(stan_model, package="rstan", run.dontrun=T)
ardollam
commented
2 years ago Dear Andrew:
Thanks so much for the help. I paused Dropbox and tried to run the example model. It generated a lot of text but ultimately did not run. I'm pasting the complete output below, but am putting the error message at the top of it.
Niall
############################################################ Final Error Message ############################################################
Compilation ERROR, function(s)/method(s) not created!
Error in compileCode(f, code, language = language, verbose = verbose) :
C:/Users/Niall Bolger/Dropbox/My PC
(LAPTOP-5APLV4TQ)/Documents/R/win-library/4.1/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:22:56:
required from 'double stan::mcmc::dense_e_metric<Model,
BaseRNG>::T(stan::mcmc::dense_e_point&) [with Model =
model1384485bbe2namespace::model1384485bbe2_; 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> >]'C:/Users/Niall Bolger/Dropbox/My PC
(LAPTOP-5APLV4TQ)/Documents/R/win-library/4.1/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:21:10:
required from hereC:/Users/Niall Bolger/Dropbox/My PC
(LAPTOP-5APLV4TQ)/Documents/R/win-library/4.1/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:55:30:
warning: ignoring attributes on template argument
'Eigen::internal::packet_traits
############################################################ Complete Output ############################################################
example(stan_model, package="rstan", run.dontrun=T) Loading required package: StanHeaders
rstan version 2.26.4 (Stan version 2.26.1)
For execution on a local, multicore CPU with excess RAM we recommend calling
options(mc.cores = parallel::detectCores()).
To avoid recompilation of unchanged Stan programs, we recommend calling
rstan_options(auto_write = TRUE)
For within-chain threading using reduce_sum() or map_rect() Stan
functions,
change threads_per_chain option:
rstan_options(threads_per_chain = 1)
Do not specify '-march=native' in 'LOCAL_CPPFLAGS' or a Makevars file
Attaching package: ‘rstan’
The following object is masked from ‘package:tidyr’:
extractThe following object is masked from ‘package:psych’:
lookupstn_md> stancode <- 'data {real y_mean;} parameters {real y;} model {y ~ normal(y_mean,1);}'
stn_md> mod <- stan_model(model_code = stancode, verbose = TRUE)
TRANSLATING MODEL '' FROM Stan CODE TO C++ CODE NOW. COMPILING THE C++ CODE FOR MODEL 'anon_model' NOW. OS: x86_64, mingw32; rstan: 2.26.4; Rcpp: 1.0.7; inline: 0.3.19
setting environment variables: LOCAL_LIBS = "C:/Users/Niall Bolger/Dropbox/My PC (LAPTOP-5APLV4TQ)/Documents/R/win-library/4.1/rstan/lib/x64/libStanServices.a" -L"C:/Users/Niall Bolger/Dropbox/My PC (LAPTOP-5APLV4TQ)/Documents/R/win-library/4.1/StanHeaders/libs/x64" -lStanHeaders -L"C:/Users/Niall Bolger/Dropbox/My PC (LAPTOP-5APLV4TQ)/Documents/R/win-library/4.1/RcppParallel/lib/x64" -ltbb -LC:\Users\NIALLB~1\Dropbox\MYPC(L~1\DOCUME~1\R\WIN-LI~1\4.1\RCPPPA~1\lib\x64 -ltbb -ltbbmalloc PKG_CPPFLAGS = -I"C:/Users/Niall Bolger/Dropbox/My PC (LAPTOP-5APLV4TQ)/Documents/R/win-library/4.1/Rcpp/include/" -I"C:/Users/Niall Bolger/Dropbox/My PC (LAPTOP-5APLV4TQ)/Documents/R/win-library/4.1/RcppEigen/include/" -I"C:/Users/Niall Bolger/Dropbox/My PC (LAPTOP-5APLV4TQ)/Documents/R/win-library/4.1/RcppEigen/include/unsupported" -I"C:/Users/Niall Bolger/Dropbox/My PC (LAPTOP-5APLV4TQ)/Documents/R/win-library/4.1/BH/include" -I"C:/Users/Niall Bolger/Dropbox/My PC (LAPTOP-5APLV4TQ)/Documents/R/win-library/4.1/StanHeaders/include/src/" -I"C:/Users/Niall Bolger/Dropbox/My PC (LAPTOP-5APLV4TQ)/Documents/R/win-library/4.1/StanHeaders/include/" -I"C:/Users/Niall Bolger/Dropbox/My PC (LAPTOP-5APLV4TQ)/Documents/R/win-library/4.1/RcppParallel/include/" -DRCPP_PARALLEL_USE_TBB=1 -I"C:/Users/Niall Bolger/Dropbox/My PC (LAPTOP-5APLV4TQ)/Documents/R/win-library/4.1/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 -DBOOST_NO_AUTO_PTR -include "C:/Users/Niall Bolger/Dropbox/My PC (LAPTOP-5APLV4TQ)/Documents/R/win-library/4.1/StanHeaders/include/stan/math/prim/fun/Eigen.hpp" -std=c++1y Program source :
1 :
2 : // includes from the plugin
3 : // [[Rcpp::plugins(cpp14)]]
4 :
5 :
6 : // user includes
7 : #include
make would use "C:/rtools40/mingw64/bin/"g++ -std=gnu++14 -I"C:/PROGRA~1/R/R-41~1.2/include" -DNDEBUG -I"C:/Users/Niall Bolger/Dropbox/My PC (LAPTOP-5APLV4TQ)/Documents/R/win-library/4.1/Rcpp/include/" -I"C:/Users/Niall Bolger/Dropbox/My PC (LAPTOP-5APLV4TQ)/Documents/R/win-library/4.1/RcppEigen/include/" -I"C:/Users/Niall Bolger/Dropbox/My PC (LAPTOP-5APLV4TQ)/Documents/R/win-library/4.1/RcppEigen/include/unsupported" -I"C:/Users/Niall Bolger/Dropbox/My PC (LAPTOP-5APLV4TQ)/Documents/R/win-library/4.1/BH/include" -I"C:/Users/Niall Bolger/Dropbox/My PC (LAPTOP-5APLV4TQ)/Documents/R/win-library/4.1/StanHeaders/include/src/" -I"C:/Users/Niall Bolger/Dropbox/My PC (LAPTOP-5APLV4TQ)/Documents/R/win-library/4.1/StanHeaders/include/" -I"C:/Users/Niall Bolger/Dropbox/My PC (LAPTOP-5APLV4TQ)/Documents/R/win-library/4.1/RcppParallel/include/" -DRCPP_PARALLEL_USE_TBB=1 -I"C:/Users/Niall Bolger/Dropbox/My PC (LAPTOP-5APLV4TQ)/Documents/R/win-library/4.1/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 -DBOOST_NO_AUTO_PTR -include "C:/Users/Niall Bolger/Dropbox/My PC (LAPTOP-5APLV4TQ)/Documents/R/win-library/4.1/StanHeaders/include/stan/math/prim/fun/Eigen.hpp" -std=c++1y -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c file138436fe3336.cpp -o file138436fe3336.o if test "zfile138436fe3336.o" != "z"; then \ if test -e "file138436fe3336-win.def"; then \ echo "C:/rtools40/mingw64/bin/"g++ -shared -s -static-libgcc -o file138436fe3336.dll file138436fe3336-win.def file138436fe3336.o "C:/Users/Niall Bolger/Dropbox/My PC (LAPTOP-5APLV4TQ)/Documents/R/win-library/4.1/rstan/lib/x64/libStanServices.a" -L"C:/Users/Niall Bolger/Dropbox/My PC (LAPTOP-5APLV4TQ)/Documents/R/win-library/4.1/StanHeaders/libs/x64" -lStanHeaders -L"C:/Users/Niall Bolger/Dropbox/My PC (LAPTOP-5APLV4TQ)/Documents/R/win-library/4.1/RcppParallel/lib/x64" -ltbb -LC:\Users\NIALLB~1\Dropbox\MYPC(L~1\DOCUME~1\R\WIN-LI~1\4.1\RCPPPA~1\lib\x64 -ltbb -ltbbmalloc -L"C:/PROGRA~1/R/R-41~1.2/bin/x64" -lR ; \ "C:/rtools40/mingw64/bin/"g++ -shared -s -static-libgcc -o file138436fe3336.dll file138436fe3336-win.def file138436fe3336.o "C:/Users/Niall Bolger/Dropbox/My PC (LAPTOP-5APLV4TQ)/Documents/R/win-library/4.1/rstan/lib/x64/libStanServices.a" -L"C:/Users/Niall Bolger/Dropbox/My PC (LAPTOP-5APLV4TQ)/Documents/R/win-library/4.1/StanHeaders/libs/x64" -lStanHeaders -L"C:/Users/Niall Bolger/Dropbox/My PC (LAPTOP-5APLV4TQ)/Documents/R/win-library/4.1/RcppParallel/lib/x64" -ltbb -LC:\Users\NIALLB~1\Dropbox\MYPC(L~1\DOCUME~1\R\WIN-LI~1\4.1\RCPPPA~1\lib\x64 -ltbb -ltbbmalloc -L"C:/PROGRA~1/R/R-41~1.2/bin/x64" -lR ; \ else \ echo EXPORTS > tmp.def; \ "C:/rtools40/mingw64/bin/"nm file138436fe3336.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 file138436fe3336.dll tmp.def file138436fe3336.o "C:/Users/Niall Bolger/Dropbox/My PC (LAPTOP-5APLV4TQ)/Documents/R/win-library/4.1/rstan/lib/x64/libStanServices.a" -L"C:/Users/Niall Bolger/Dropbox/My PC (LAPTOP-5APLV4TQ)/Documents/R/win-library/4.1/StanHeaders/libs/x64" -lStanHeaders -L"C:/Users/Niall Bolger/Dropbox/My PC (LAPTOP-5APLV4TQ)/Documents/R/win-library/4.1/RcppParallel/lib/x64" -ltbb -LC:\Users\NIALLB~1\Dropbox\MYPC(L~1\DOCUME~1\R\WIN-LI~1\4.1\RCPPPA~1\lib\x64 -ltbb -ltbbmalloc -L"C:/PROGRA~1/R/R-41~1.2/bin/x64" -lR ; \ "C:/rtools40/mingw64/bin/"g++ -shared -s -static-libgcc -o file138436fe3336.dll tmp.def file138436fe3336.o "C:/Users/Niall Bolger/Dropbox/My PC (LAPTOP-5APLV4TQ)/Documents/R/win-library/4.1/rstan/lib/x64/libStanServices.a" -L"C:/Users/Niall Bolger/Dropbox/My PC (LAPTOP-5APLV4TQ)/Documents/R/win-library/4.1/StanHeaders/libs/x64" -lStanHeaders -L"C:/Users/Niall Bolger/Dropbox/My PC (LAPTOP-5APLV4TQ)/Documents/R/win-library/4.1/RcppParallel/lib/x64" -ltbb -LC:\Users\NIALLB~1\Dropbox\MYPC(L~1\DOCUME~1\R\WIN-LI~1\4.1\RCPPPA~1\lib\x64 -ltbb -ltbbmalloc -L"C:/PROGRA~1/R/R-41~1.2/bin/x64" -lR ; \ rm -f tmp.def; \ fi \ fi
ERROR(s) during compilation: source code errors or compiler configuration errors!
Program source:
1:
2: // includes from the plugin
3: // [[Rcpp::plugins(cpp14)]]
4:
5:
6: // user includes
7: #include
On Wed, Nov 17, 2021 at 12:29 AM Andrew Johnson @.***> wrote:
Hi Niall,
Is the behaviour different if you pause the dropbox sync before compiling?
Are you able to run the rstan example model?
example(stan_model, package="rstan", run.dontrun=T)
— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/paul-buerkner/brms/issues/1266#issuecomment-971204652, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABNRQEDKKI6XCXPE3VFQIGDUMM4THANCNFSM5IFDX2PA . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.
paul-buerkner
commented
2 years ago I would prefer you ask this question on https://discourse.mc-stan.org/ which is the go to place for brms and Stan related questions.
ardollam
commented
2 years ago I will do that.
On Thu, Nov 18, 2021 at 4:05 AM Paul-Christian Bürkner < @.***> wrote:
I would prefer you ask this question on https://discourse.mc-stan.org/ which is the go to place for brms and Stan related questions.
— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/paul-buerkner/brms/issues/1266#issuecomment-972667847, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABNRQEDE47QUZMJ7AA3COK3UMS6XFANCNFSM5IFDX2PA . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.
ardollam
commented
2 years ago Dear Paul:
I posted my question on https://discourse.mc-stan.org/ seven days ago and have had no response so far. I was wondering if you had any thoughts on my problem. I am currently teaching a graduate statistics course to psychology students at Columbia, and it is a bit embarrassing not to be able to run brm, which I have found to be a great resource.
Sincerely,
Niall Bolger
P.S. In case you need to find it, here is a snippet of my posting
Error in brm compileCode involving RcppEigen? https://discourse.mc-stan.org/t/error-in-brm-compilecode-involving-rcppeigen/25353 Interfaces https://discourse.mc-stan.org/c/interfaces/5brms https://discourse.mc-stan.org/c/interfaces/brms/36 Nov 18 https://discourse.mc-stan.org/t/error-in-brm-compilecode-involving-rcppeigen/25353 1 / 1 Nov 18 7d ago https://discourse.mc-stan.org/t/error-in-brm-compilecode-involving-rcppeigen/25353 https://discourse.mc-stan.org/t/error-in-brm-compilecode-involving-rcppeigen/25353 https://discourse.mc-stan.org/u/ardollam ardollam https://discourse.mc-stan.org/u/ardollam 7d https://discourse.mc-stan.org/t/error-in-brm-compilecode-involving-rcppeigen/25353?u=ardollam
Dear discourse.mc-stan:
I can usually get to the bottom of problems with R packages but this one has me stumped. brm loads okay and accepts commands but quits when it is trying to compile. Below I’m attaching the error messages plus information about my R installation and packages. I have checked to see if the problem has anything to do with Dropbox syncing and it does not.
Sincerely,
Niall Bolger Columbia U.
#####################################################
brm(conformityfscore, data=Moore) Compiling Stan program… make cmd is make -f “C:/PROGRA1/R/R-411.2/etc/x64/Makeconf” -f “C:/PROGRA 1/R/R-41~1.2/share/make/winshlib.mk” CXX=’ (CXX14) (CXX14STD)’ CXXFLAGS=’ (C XX14FLAGS)′CXXPICFLAGS=′ (CXX14PICFLAGS)’ SHLIB_LDFLAGS=’ (SHLIBCXX14LDFLAGS )′SHLIBLD=′ (SHLIB_CXX14LD)’ SHLIB=“file138442045337.dll” WIN=64 TCLBIN=64 OBJECTS=“file138442045337.o”
On Thu, Nov 18, 2021 at 4:05 AM Paul-Christian Bürkner < @.***> wrote:
I would prefer you ask this question on https://discourse.mc-stan.org/ which is the go to place for brms and Stan related questions.
— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/paul-buerkner/brms/issues/1266#issuecomment-972667847, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABNRQEDE47QUZMJ7AA3COK3UMS6XFANCNFSM5IFDX2PA . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.
paul-buerkner
commented
2 years ago I am sorry this error is outside my area of expertise. have you tried using cmdstanr instead of rstan backend?
ardollam @.***> schrieb am Do., 25. Nov. 2021, 13:42:
Dear Paul:
I posted my question on https://discourse.mc-stan.org/ seven days ago and have had no response so far. I was wondering if you had any thoughts on my problem. I am currently teaching a graduate statistics course to psychology students at Columbia, and it is a bit embarrassing not to be able to run brm, which I have found to be a great resource.
Sincerely,
Niall Bolger
P.S. In case you need to find it, here is a snippet of my posting
Error in brm compileCode involving RcppEigen? < https://discourse.mc-stan.org/t/error-in-brm-compilecode-involving-rcppeigen/25353
Interfaces https://discourse.mc-stan.org/c/interfaces/5brms https://discourse.mc-stan.org/c/interfaces/brms/36 Nov 18 < https://discourse.mc-stan.org/t/error-in-brm-compilecode-involving-rcppeigen/25353
1 / 1 Nov 18 7d ago < https://discourse.mc-stan.org/t/error-in-brm-compilecode-involving-rcppeigen/25353
< https://discourse.mc-stan.org/t/error-in-brm-compilecode-involving-rcppeigen/25353
https://discourse.mc-stan.org/u/ardollam ardollam https://discourse.mc-stan.org/u/ardollam 7d < https://discourse.mc-stan.org/t/error-in-brm-compilecode-involving-rcppeigen/25353?u=ardollam
Dear discourse.mc-stan:
I can usually get to the bottom of problems with R packages but this one has me stumped. brm loads okay and accepts commands but quits when it is trying to compile. Below I’m attaching the error messages plus information about my R installation and packages. I have checked to see if the problem has anything to do with Dropbox syncing and it does not.
Sincerely,
Niall Bolger Columbia U.
#####################################################
brm(conformityfscore, data=Moore) Compiling Stan program… make cmd is make -f “C:/PROGRA1/R/R-411.2/etc/x64/Makeconf” -f “C:/PROGRA 1/R/R-41~1.2/share/make/winshlib.mk” CXX=’ (CXX14) (CXX14STD)’ CXXFLAGS=’ (C XX14FLAGS)′CXXPICFLAGS=′ (CXX14PICFLAGS)’ SHLIB_LDFLAGS=’ (SHLIBCXX14LDFLAGS )′SHLIBLD=′ (SHLIB_CXX14LD)’ SHLIB=“file138442045337.dll” WIN=64 TCLBIN=64 OBJECTS=“file138442045337.o”
============================================== Niall Bolger Professor Department of Psychology Columbia University New York, NY 10027 https://columbiacoupleslab.weebly.com/
Bolger & Laurenceau (2013) Intensive Longitudinal Methods: An Introduction to Diary and Experience Sampling Research http://www.intensivelongitudinal.com/
On Thu, Nov 18, 2021 at 4:05 AM Paul-Christian Bürkner < @.***> wrote:
I would prefer you ask this question on https://discourse.mc-stan.org/ which is the go to place for brms and Stan related questions.
— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub < https://github.com/paul-buerkner/brms/issues/1266#issuecomment-972667847>, or unsubscribe < https://github.com/notifications/unsubscribe-auth/ABNRQEDE47QUZMJ7AA3COK3UMS6XFANCNFSM5IFDX2PA
. Triage notifications on the go with GitHub Mobile for iOS < https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675
— You are receiving this because you modified the open/close state. Reply to this email directly, view it on GitHub https://github.com/paul-buerkner/brms/issues/1266#issuecomment-979480212, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADCW2AD6WAVT4PZFQYBHSGDUN2UURANCNFSM5IFDX2PA . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.
ardollam
commented
2 years ago Dear Paul:
Thanks for getting back to me. I will try that. Sorry for bothering you. It sounds like I need to talk to someone who is responsible for stan.
Sincerely,
On Thu, Nov 25, 2021 at 5:12 PM Paul-Christian Bürkner < @.***> wrote:
I am sorry this error is outside my area of expertise. have you tried using cmdstanr instead of rstan backend?
ardollam @.***> schrieb am Do., 25. Nov. 2021, 13:42:
Dear Paul:
I posted my question on https://discourse.mc-stan.org/ seven days ago and have had no response so far. I was wondering if you had any thoughts on my problem. I am currently teaching a graduate statistics course to psychology students at Columbia, and it is a bit embarrassing not to be able to run brm, which I have found to be a great resource.
Sincerely,
Niall Bolger
P.S. In case you need to find it, here is a snippet of my posting
Error in brm compileCode involving RcppEigen? <
https://discourse.mc-stan.org/t/error-in-brm-compilecode-involving-rcppeigen/25353
Interfaces https://discourse.mc-stan.org/c/interfaces/5brms https://discourse.mc-stan.org/c/interfaces/brms/36 Nov 18 <
https://discourse.mc-stan.org/t/error-in-brm-compilecode-involving-rcppeigen/25353
1 / 1 Nov 18 7d ago <
https://discourse.mc-stan.org/t/error-in-brm-compilecode-involving-rcppeigen/25353
<
https://discourse.mc-stan.org/t/error-in-brm-compilecode-involving-rcppeigen/25353
https://discourse.mc-stan.org/u/ardollam ardollam https://discourse.mc-stan.org/u/ardollam 7d <
https://discourse.mc-stan.org/t/error-in-brm-compilecode-involving-rcppeigen/25353?u=ardollam
Dear discourse.mc-stan:
I can usually get to the bottom of problems with R packages but this one has me stumped. brm loads okay and accepts commands but quits when it is trying to compile. Below I’m attaching the error messages plus information about my R installation and packages. I have checked to see if the problem has anything to do with Dropbox syncing and it does not.
Sincerely,
Niall Bolger Columbia U.
#####################################################
brm(conformityfscore, data=Moore) Compiling Stan program… make cmd is make -f “C:/PROGRA1/R/R-411.2/etc/x64/Makeconf” -f “C:/PROGRA 1/R/R-41~1.2/share/make/winshlib.mk” CXX=’ (CXX14) (CXX14STD)’ CXXFLAGS=’ (C XX14FLAGS)′CXXPICFLAGS=′ (CXX14PICFLAGS)’ SHLIB_LDFLAGS=’ (SHLIBCXX14LDFLAGS )′SHLIBLD=′ (SHLIB_CXX14LD)’ SHLIB=“file138442045337.dll” WIN=64 TCLBIN=64 OBJECTS=“file138442045337.o”
============================================== Niall Bolger Professor Department of Psychology Columbia University New York, NY 10027 https://columbiacoupleslab.weebly.com/
Bolger & Laurenceau (2013) Intensive Longitudinal Methods: An Introduction to Diary and Experience Sampling Research http://www.intensivelongitudinal.com/
On Thu, Nov 18, 2021 at 4:05 AM Paul-Christian Bürkner < @.***> wrote:
I would prefer you ask this question on https://discourse.mc-stan.org/ which is the go to place for brms and Stan related questions.
— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub < https://github.com/paul-buerkner/brms/issues/1266#issuecomment-972667847 , or unsubscribe <
https://github.com/notifications/unsubscribe-auth/ABNRQEDE47QUZMJ7AA3COK3UMS6XFANCNFSM5IFDX2PA
. Triage notifications on the go with GitHub Mobile for iOS <
https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675
or Android <
.
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ardollam
commented
2 years ago Dear Paul:
Just a quick update. Your suggestion worked. When I used backend="cmdstanr" my problem went away.
Thank you so much!
On Thu, Nov 25, 2021 at 5:12 PM Paul-Christian Bürkner < @.***> wrote:
I am sorry this error is outside my area of expertise. have you tried using cmdstanr instead of rstan backend?
ardollam @.***> schrieb am Do., 25. Nov. 2021, 13:42:
Dear Paul:
I posted my question on https://discourse.mc-stan.org/ seven days ago and have had no response so far. I was wondering if you had any thoughts on my problem. I am currently teaching a graduate statistics course to psychology students at Columbia, and it is a bit embarrassing not to be able to run brm, which I have found to be a great resource.
Sincerely,
Niall Bolger
P.S. In case you need to find it, here is a snippet of my posting
Error in brm compileCode involving RcppEigen? <
https://discourse.mc-stan.org/t/error-in-brm-compilecode-involving-rcppeigen/25353
Interfaces https://discourse.mc-stan.org/c/interfaces/5brms https://discourse.mc-stan.org/c/interfaces/brms/36 Nov 18 <
https://discourse.mc-stan.org/t/error-in-brm-compilecode-involving-rcppeigen/25353
1 / 1 Nov 18 7d ago <
https://discourse.mc-stan.org/t/error-in-brm-compilecode-involving-rcppeigen/25353
<
https://discourse.mc-stan.org/t/error-in-brm-compilecode-involving-rcppeigen/25353
https://discourse.mc-stan.org/u/ardollam ardollam https://discourse.mc-stan.org/u/ardollam 7d <
https://discourse.mc-stan.org/t/error-in-brm-compilecode-involving-rcppeigen/25353?u=ardollam
Dear discourse.mc-stan:
I can usually get to the bottom of problems with R packages but this one has me stumped. brm loads okay and accepts commands but quits when it is trying to compile. Below I’m attaching the error messages plus information about my R installation and packages. I have checked to see if the problem has anything to do with Dropbox syncing and it does not.
Sincerely,
Niall Bolger Columbia U.
#####################################################
brm(conformityfscore, data=Moore) Compiling Stan program… make cmd is make -f “C:/PROGRA1/R/R-411.2/etc/x64/Makeconf” -f “C:/PROGRA 1/R/R-41~1.2/share/make/winshlib.mk” CXX=’ (CXX14) (CXX14STD)’ CXXFLAGS=’ (C XX14FLAGS)′CXXPICFLAGS=′ (CXX14PICFLAGS)’ SHLIB_LDFLAGS=’ (SHLIBCXX14LDFLAGS )′SHLIBLD=′ (SHLIB_CXX14LD)’ SHLIB=“file138442045337.dll” WIN=64 TCLBIN=64 OBJECTS=“file138442045337.o”
============================================== Niall Bolger Professor Department of Psychology Columbia University New York, NY 10027 https://columbiacoupleslab.weebly.com/
Bolger & Laurenceau (2013) Intensive Longitudinal Methods: An Introduction to Diary and Experience Sampling Research http://www.intensivelongitudinal.com/
On Thu, Nov 18, 2021 at 4:05 AM Paul-Christian Bürkner < @.***> wrote:
I would prefer you ask this question on https://discourse.mc-stan.org/ which is the go to place for brms and Stan related questions.
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or Android <
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Dear Paul:
I can usually get to the bottom of problems with R packages but this one has me stumped. brm loads okay and accepts commands but quits when it is trying to compile. Below I'm attaching the error messages plus information about my R installation and packages. The problem does not seem to be related to rstan specifically, because I can get rstanarm to run fine.
Sincerely,
Niall Bolger Columbia U.
#####################################################
make would use if test "zfile138442045337.o" != "z"; then \ if test -e "file138442045337-win.def"; then \ echo "C:/rtools40/mingw64/bin/"g++ -shared -s -static-libgcc -o file138442045337.dll file138442045337-win.def file138442045337.o "C:/Users/Niall Bolger/Dropbox/My PC (LAPTOP-5APLV4TQ)/Documents/R/win-library/4.1/rstan/lib/x64/libStanServices.a" -L"C:/Users/Niall Bolger/Dropbox/My PC (LAPTOP-5APLV4TQ)/Documents/R/win-library/4.1/StanHeaders/libs/x64" -lStanHeaders -L"C:/Users/Niall Bolger/Dropbox/My PC (LAPTOP-5APLV4TQ)/Documents/R/win-library/4.1/RcppParallel/lib/x64" -ltbb -LC:\Users\NIALLB~1\Dropbox\MYPC(L~1\DOCUME~1\R\WIN-LI~1\4.1\RCPPPA~1\lib\x64 -ltbb -ltbbmalloc -L"C:/PROGRA~1/R/R-41~1.2/bin/x64" -lR ; \ "C:/rtools40/mingw64/bin/"g++ -shared -s -static-libgcc -o file138442045337.dll file138442045337-win.def file138442045337.o "C:/Users/Niall Bolger/Dropbox/My PC (LAPTOP-5APLV4TQ)/Documents/R/win-library/4.1/rstan/lib/x64/libStanServices.a" -L"C:/Users/Niall Bolger/Dropbox/My PC (LAPTOP-5APLV4TQ)/Documents/R/win-library/4.1/StanHeaders/libs/x64" -lStanHeaders -L"C:/Users/Niall Bolger/Dropbox/My PC (LAPTOP-5APLV4TQ)/Documents/R/win-library/4.1/RcppParallel/lib/x64" -ltbb -LC:\Users\NIALLB~1\Dropbox\MYPC(L~1\DOCUME~1\R\WIN-LI~1\4.1\RCPPPA~1\lib\x64 -ltbb -ltbbmalloc -L"C:/PROGRA~1/R/R-41~1.2/bin/x64" -lR ; \ else \ echo EXPORTS > tmp.def; \ "C:/rtools40/mingw64/bin/"nm file138442045337.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 file138442045337.dll tmp.def file138442045337.o "C:/Users/Niall Bolger/Dropbox/My PC (LAPTOP-5APLV4TQ)/Documents/R/win-library/4.1/rstan/lib/x64/libStanServices.a" -L"C:/Users/Niall Bolger/Dropbox/My PC (LAPTOP-5APLV4TQ)/Documents/R/win-library/4.1/StanHeaders/libs/x64" -lStanHeaders -L"C:/Users/Niall Bolger/Dropbox/My PC (LAPTOP-5APLV4TQ)/Documents/R/win-library/4.1/RcppParallel/lib/x64" -ltbb -LC:\Users\NIALLB~1\Dropbox\MYPC(L~1\DOCUME~1\R\WIN-LI~1\4.1\RCPPPA~1\lib\x64 -ltbb -ltbbmalloc -L"C:/PROGRA~1/R/R-41~1.2/bin/x64" -lR ; \ "C:/rtools40/mingw64/bin/"g++ -shared -s -static-libgcc -o file138442045337.dll tmp.def file138442045337.o "C:/Users/Niall Bolger/Dropbox/My PC (LAPTOP-5APLV4TQ)/Documents/R/win-library/4.1/rstan/lib/x64/libStanServices.a" -L"C:/Users/Niall Bolger/Dropbox/My PC (LAPTOP-5APLV4TQ)/Documents/R/win-library/4.1/StanHeaders/libs/x64" -lStanHeaders -L"C:/Users/Niall Bolger/Dropbox/My PC (LAPTOP-5APLV4TQ)/Documents/R/win-library/4.1/RcppParallel/lib/x64" -ltbb -LC:\Users\NIALLB~1\Dropbox\MYPC(L~1\DOCUME~1\R\WIN-LI~1\4.1\RCPPPA~1\lib\x64 -ltbb -ltbbmalloc -L"C:/PROGRA~1/R/R-41~1.2/bin/x64" -lR ; \ rm -f tmp.def; \ fi \ fi Error in compileCode(f, code, language = language, verbose = verbose) : C:/Users/Niall Bolger/Dropbox/My PC (LAPTOP-5APLV4TQ)/Documents/R/win-library/4.1/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:55:30: warning: ignoring attributes on template argument 'Eigen::internal::packet_traits::type' {aka '__vector(2) double'} [-Wignored-attributes] >::type PacketReturnType; ^
~~~sh: -c: line 3: syntax error near unexpected token('sh: -c: line 3:echo "C:/rtools40/mingw64/bin/"g++ -shared -s -static-libgcc -o file138442045337.dll file138442045337-win.def file138442045337.o "C:/Users/Niall Bolger/Dropbox/My PC (LAPTOP-5APLV4TQ)/Documents/R/win-library/4.1/rstan/lib/x64/libStanServices.a" -L"C:/Users/Niall Bolger/Dropbox/My PC (LAPTOP-5APLV4TQ)/Documents/R/win-library/4.1/StanHeaders/libs/x64" -lStanHeaders -L"C:/Users/Niall Bolger/Dropbox/My PC (LAPTOP-5APLV4TQ)/Documents/R/win-library/4.1/RcppParallel/lib/x64" -ltbb -LC:\Users\NIALLB~1\Dropbox\MYPC(L~1\DOCUME~1\R\WIN-LI~ Error in sink(type = "output") : invalid connection######################################### My R installation and packages:
Matrix products: default
locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages: [1] stats graphics grDevices utils datasets methods base
other attached packages: [1] car_3.0-12 carData_3.0-4 brms_2.16.1 Rcpp_1.0.7
loaded via a namespace (and not attached): [1] minqa_1.2.4 colorspace_2.0-2 ellipsis_0.3.2
[4] ggridges_0.5.3 rsconnect_0.8.24 markdown_1.1
[7] base64enc_0.1-3 farver_2.1.0 rstan_2.26.4
[10] DT_0.20 fansi_0.5.0 mvtnorm_1.1-3
[13] bridgesampling_1.1-2 codetools_0.2-18 splines_4.1.2
[16] knitr_1.36 shinythemes_1.2.0 bayesplot_1.8.1
[19] projpred_2.0.2 jsonlite_1.7.2 nloptr_1.2.2.2
[22] shiny_1.7.1 compiler_4.1.2 backports_1.3.0
[25] assertthat_0.2.1 Matrix_1.3-4 fastmap_1.1.0
[28] cli_3.1.0 later_1.3.0 htmltools_0.5.2
[31] prettyunits_1.1.1 tools_4.1.2 igraph_1.2.7
[34] coda_0.19-4 gtable_0.3.0 glue_1.5.0
[37] reshape2_1.4.4 dplyr_1.0.7 posterior_1.1.0
[40] V8_3.4.2 vctrs_0.3.8 nlme_3.1-153
[43] crosstalk_1.2.0 tensorA_0.36.2 xfun_0.28
[46] stringr_1.4.0 ps_1.6.0 lme4_1.1-27.1
[49] mime_0.12 miniUI_0.1.1.1 lifecycle_1.0.1
[52] gtools_3.9.2 MASS_7.3-54 zoo_1.8-9
[55] scales_1.1.1 colourpicker_1.1.1 promises_1.2.0.1
[58] Brobdingnag_1.2-6 parallel_4.1.2 inline_0.3.19
[61] shinystan_2.5.0 gamm4_0.2-6 yaml_2.2.1
[64] curl_4.3.2 gridExtra_2.3 ggplot2_3.3.5
[67] loo_2.4.1 StanHeaders_2.26.4 stringi_1.7.5
[70] dygraphs_1.1.1.6 checkmate_2.0.0 boot_1.3-28
[73] pkgbuild_1.2.0 rlang_0.4.12 pkgconfig_2.0.3
[76] matrixStats_0.61.0 distributional_0.2.2 evaluate_0.14
[79] lattice_0.20-45 purrr_0.3.4 rstantools_2.1.1
[82] htmlwidgets_1.5.4 tidyselect_1.1.1 processx_3.5.2
[85] plyr_1.8.6 magrittr_2.0.1 R6_2.5.1
[88] generics_0.1.1 DBI_1.1.1 pillar_1.6.4
[91] withr_2.4.2 mgcv_1.8-38 xts_0.12.1
[94] abind_1.4-5 tibble_3.1.6 crayon_1.4.2
[97] utf8_1.2.2 rmarkdown_2.11 grid_4.1.2
[100] callr_3.7.0 threejs_0.3.3 digest_0.6.28
[103] xtable_1.8-4 httpuv_1.6.3 RcppParallel_5.1.4
[106] stats4_4.1.2 munsell_0.5.0 shinyjs_2.0.0