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stan-dev / rstanarm

rstanarm R package for Bayesian applied regression modeling
https://mc-stan.org/rstanarm
GNU General Public License v3.0
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Unable to publish a Shiny App with rstanarm #573

Open edmartraps-l15l opened 2 years ago

edmartraps-l15l commented 2 years ago

Summary:

Whenever I try to deploy a Shiny app with {rstanarm}, it won't publish. It will take a lot of time deploying until it eventually times out. The app works perfectly as intended when running locally. When deploying, the app will get stuck in this point 

Preparing to deploy document...DONE
Uploading bundle for document: 6908182...DONE
Deploying bundle: 6263558 for document: 6908182 ...
Waiting for task: 1214426410
  building: Processing bundle: 6263558
  building: Parsing manifest
  building: Building image: 7300316
  building: Installing system dependencies
  building: Fetching packages
  building: Building package: rstanarm

for a very long time before printing a giant wall of text and, finally, the error message.

Description:

The error I get when deploying ends as follows:

[2022-09-02T17:28:44.241024278+0000] Installing R package: lme4 (1.1-30)
* installing to library '/opt/R/4.2.1/lib/R/library'
* installing *binary* package 'lme4' ...
* DONE (lme4)
[2022-09-02T17:28:45.483821008+0000] Building R package: rstanarm (2.21.3)
/mnt/packages/build /mnt
"/opt/R/4.2.1/lib/R/bin/Rscript" -e "source(file.path('..', 'tools', 'make_cc.R')); make_cc(commandArgs(TRUE))" stan_files/lm.stan
g++ -std=gnu++14 -I"/opt/R/4.2.1/lib/R/include" -DNDEBUG -I"../inst/include" -I"/opt/R/4.2.1/lib/R/library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -I'/opt/R/4.2.1/lib/R/library/StanHeaders/include' -I'/opt/R/4.2.1/lib/R/library/rstan/include' -I'/opt/R/4.2.1/lib/R/library/BH/include' -I'/opt/R/4.2.1/lib/R/library/Rcpp/include' -I'/opt/R/4.2.1/lib/R/library/RcppEigen/include' -I'/opt/R/4.2.1/lib/R/library/RcppParallel/include' -I/usr/local/include  `"/opt/R/4.2.1/lib/R/bin/Rscript" -e "RcppParallel::CxxFlags()"` `"/opt/R/4.2.1/lib/R/bin/Rscript" -e "StanHeaders:::CxxFlags()"` -fpic  -g -O2  -c stan_files/lm.cc -o stan_files/lm.o
"/opt/R/4.2.1/lib/R/bin/Rscript" -e "source(file.path('..', 'tools', 'make_cc.R')); make_cc(commandArgs(TRUE))" stan_files/mvmer.stan
g++ -std=gnu++14 -I"/opt/R/4.2.1/lib/R/include" -DNDEBUG -I"../inst/include" -I"/opt/R/4.2.1/lib/R/library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -I'/opt/R/4.2.1/lib/R/library/StanHeaders/include' -I'/opt/R/4.2.1/lib/R/library/rstan/include' -I'/opt/R/4.2.1/lib/R/library/BH/include' -I'/opt/R/4.2.1/lib/R/library/Rcpp/include' -I'/opt/R/4.2.1/lib/R/library/RcppEigen/include' -I'/opt/R/4.2.1/lib/R/library/RcppParallel/include' -I/usr/local/include  `"/opt/R/4.2.1/lib/R/bin/Rscript" -e "RcppParallel::CxxFlags()"` `"/opt/R/4.2.1/lib/R/bin/Rscript" -e "StanHeaders:::CxxFlags()"` -fpic  -g -O2  -c stan_files/mvmer.cc -o stan_files/mvmer.o
"/opt/R/4.2.1/lib/R/bin/Rscript" -e "source(file.path('..', 'tools', 'make_cc.R')); make_cc(commandArgs(TRUE))" stan_files/binomial.stan
g++ -std=gnu++14 -I"/opt/R/4.2.1/lib/R/include" -DNDEBUG -I"../inst/include" -I"/opt/R/4.2.1/lib/R/library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -I'/opt/R/4.2.1/lib/R/library/StanHeaders/include' -I'/opt/R/4.2.1/lib/R/library/rstan/include' -I'/opt/R/4.2.1/lib/R/library/BH/include' -I'/opt/R/4.2.1/lib/R/library/Rcpp/include' -I'/opt/R/4.2.1/lib/R/library/RcppEigen/include' -I'/opt/R/4.2.1/lib/R/library/RcppParallel/include' -I/usr/local/include  `"/opt/R/4.2.1/lib/R/bin/Rscript" -e "RcppParallel::CxxFlags()"` `"/opt/R/4.2.1/lib/R/bin/Rscript" -e "StanHeaders:::CxxFlags()"` -fpic  -g -O2  -c stan_files/binomial.cc -o stan_files/binomial.o
"/opt/R/4.2.1/lib/R/bin/Rscript" -e "source(file.path('..', 'tools', 'make_cc.R')); make_cc(commandArgs(TRUE))" stan_files/count.stan
g++ -std=gnu++14 -I"/opt/R/4.2.1/lib/R/include" -DNDEBUG -I"../inst/include" -I"/opt/R/4.2.1/lib/R/library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -I'/opt/R/4.2.1/lib/R/library/StanHeaders/include' -I'/opt/R/4.2.1/lib/R/library/rstan/include' -I'/opt/R/4.2.1/lib/R/library/BH/include' -I'/opt/R/4.2.1/lib/R/library/Rcpp/include' -I'/opt/R/4.2.1/lib/R/library/RcppEigen/include' -I'/opt/R/4.2.1/lib/R/library/RcppParallel/include' -I/usr/local/include  `"/opt/R/4.2.1/lib/R/bin/Rscript" -e "RcppParallel::CxxFlags()"` `"/opt/R/4.2.1/lib/R/bin/Rscript" -e "StanHeaders:::CxxFlags()"` -fpic  -g -O2  -c stan_files/count.cc -o stan_files/count.o
"/opt/R/4.2.1/lib/R/bin/Rscript" -e "source(file.path('..', 'tools', 'make_cc.R')); make_cc(commandArgs(TRUE))" stan_files/jm.stan
g++ -std=gnu++14 -I"/opt/R/4.2.1/lib/R/include" -DNDEBUG -I"../inst/include" -I"/opt/R/4.2.1/lib/R/library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -I'/opt/R/4.2.1/lib/R/library/StanHeaders/include' -I'/opt/R/4.2.1/lib/R/library/rstan/include' -I'/opt/R/4.2.1/lib/R/library/BH/include' -I'/opt/R/4.2.1/lib/R/library/Rcpp/include' -I'/opt/R/4.2.1/lib/R/library/RcppEigen/include' -I'/opt/R/4.2.1/lib/R/library/RcppParallel/include' -I/usr/local/include  `"/opt/R/4.2.1/lib/R/bin/Rscript" -e "RcppParallel::CxxFlags()"` `"/opt/R/4.2.1/lib/R/bin/Rscript" -e "StanHeaders:::CxxFlags()"` -fpic  -g -O2  -c stan_files/jm.cc -o stan_files/jm.o
"/opt/R/4.2.1/lib/R/bin/Rscript" -e "source(file.path('..', 'tools', 'make_cc.R')); make_cc(commandArgs(TRUE))" stan_files/bernoulli.stan
g++ -std=gnu++14 -I"/opt/R/4.2.1/lib/R/include" -DNDEBUG -I"../inst/include" -I"/opt/R/4.2.1/lib/R/library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -I'/opt/R/4.2.1/lib/R/library/StanHeaders/include' -I'/opt/R/4.2.1/lib/R/library/rstan/include' -I'/opt/R/4.2.1/lib/R/library/BH/include' -I'/opt/R/4.2.1/lib/R/library/Rcpp/include' -I'/opt/R/4.2.1/lib/R/library/RcppEigen/include' -I'/opt/R/4.2.1/lib/R/library/RcppParallel/include' -I/usr/local/include  `"/opt/R/4.2.1/lib/R/bin/Rscript" -e "RcppParallel::CxxFlags()"` `"/opt/R/4.2.1/lib/R/bin/Rscript" -e "StanHeaders:::CxxFlags()"` -fpic  -g -O2  -c stan_files/bernoulli.cc -o stan_files/bernoulli.o
"/opt/R/4.2.1/lib/R/bin/Rscript" -e "source(file.path('..', 'tools', 'make_cc.R')); make_cc(commandArgs(TRUE))" stan_files/polr.stan
g++ -std=gnu++14 -I"/opt/R/4.2.1/lib/R/include" -DNDEBUG -I"../inst/include" -I"/opt/R/4.2.1/lib/R/library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -I'/opt/R/4.2.1/lib/R/library/StanHeaders/include' -I'/opt/R/4.2.1/lib/R/library/rstan/include' -I'/opt/R/4.2.1/lib/R/library/BH/include' -I'/opt/R/4.2.1/lib/R/library/Rcpp/include' -I'/opt/R/4.2.1/lib/R/library/RcppEigen/include' -I'/opt/R/4.2.1/lib/R/library/RcppParallel/include' -I/usr/local/include  `"/opt/R/4.2.1/lib/R/bin/Rscript" -e "RcppParallel::CxxFlags()"` `"/opt/R/4.2.1/lib/R/bin/Rscript" -e "StanHeaders:::CxxFlags()"` -fpic  -g -O2  -c stan_files/polr.cc -o stan_files/polr.o
"/opt/R/4.2.1/lib/R/bin/Rscript" -e "source(file.path('..', 'tools', 'make_cc.R')); make_cc(commandArgs(TRUE))" stan_files/continuous.stan
g++ -std=gnu++14 -I"/opt/R/4.2.1/lib/R/include" -DNDEBUG -I"../inst/include" -I"/opt/R/4.2.1/lib/R/library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -I'/opt/R/4.2.1/lib/R/library/StanHeaders/include' -I'/opt/R/4.2.1/lib/R/library/rstan/include' -I'/opt/R/4.2.1/lib/R/library/BH/include' -I'/opt/R/4.2.1/lib/R/library/Rcpp/include' -I'/opt/R/4.2.1/lib/R/library/RcppEigen/include' -I'/opt/R/4.2.1/lib/R/library/RcppParallel/include' -I/usr/local/include  `"/opt/R/4.2.1/lib/R/bin/Rscript" -e "RcppParallel::CxxFlags()"` `"/opt/R/4.2.1/lib/R/bin/Rscript" -e "StanHeaders:::CxxFlags()"` -fpic  -g -O2  -c stan_files/continuous.cc -o stan_files/continuous.o
################################# End Task Log ################################# 
Error: Unhandled Exception: Child Task 1214426412 error: Unhandled Exception: HTTP 599: Timeout during request
Execution halted

This isn't the complete error, please let me know if you need the whole wall of text and I'll upload it as soon as I can.

Reproducible Steps:

This simple, reproducible shiny app throws the same error when deploying:

library(shiny)
library(rstanarm)

ui <- fluidPage(
  textInput('text',
            label = 'Ingrese texto:'),
  verbatimTextOutput('textOut')
)

server <- function(input, output, session) {
  output$textOut <- 
    renderText({input$text})
}

shinyApp(ui, server)

This is my sessionInfo:

R version 4.2.1 (2022-06-23)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Monterey 12.5.1

Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] parsnip_1.0.0         recipes_1.0.1         ranger_0.14.1         modelr_0.1.9         
 [5] readxl_1.4.1          stringr_1.4.1         purrr_0.3.4           gridExtra_2.3        
 [9] readr_2.1.2           tidyr_1.2.0           dplyr_1.0.9           ggplot2_3.3.6        
[13] DT_0.23               shinycssloaders_1.0.0 shinyjs_2.1.0         shinyWidgets_0.7.1   
[17] shinydashboard_0.7.2  shiny_1.7.2          

loaded via a namespace (and not attached):
  [1] backports_1.4.1      plyr_1.8.7           igraph_1.3.4         splines_4.2.1       
  [5] crosstalk_1.2.0      listenv_0.8.0        rstantools_2.2.0     inline_0.3.19       
  [9] digest_0.6.29        htmltools_0.5.3      yardstick_1.0.0      rsconnect_0.8.27    
 [13] fansi_1.0.3          magrittr_2.0.3       memoise_2.0.1        tzdb_0.3.0          
 [17] globals_0.15.1       gower_1.0.0          matrixStats_0.62.0   RcppParallel_5.1.5  
 [21] xts_0.12.1           askpass_1.1          hardhat_1.2.0        prettyunits_1.1.1   
 [25] colorspace_2.0-3     xfun_0.32            callr_3.7.2          crayon_1.5.1        
 [29] jsonlite_1.8.0       lme4_1.1-30          survival_3.3-1       zoo_1.8-10          
 [33] glue_1.6.2           gtable_0.3.0         ipred_0.9-13         pkgbuild_1.3.1      
 [37] clipr_0.8.0          rstan_2.21.5         future.apply_1.9.0   scales_1.2.1        
 [41] DBI_1.1.3            miniUI_0.1.1.1       Rcpp_1.0.9           xtable_1.8-4        
 [45] stats4_4.2.1         lava_1.6.10          StanHeaders_2.21.0-7 prodlim_2019.11.13  
 [49] htmlwidgets_1.5.4    threejs_0.3.3        ellipsis_0.3.2       loo_2.5.1           
 [53] pkgconfig_2.0.3      nnet_7.3-17          sass_0.4.2           utf8_1.2.2          
 [57] janitor_2.1.0        tidyselect_1.1.2     rlang_1.0.4          reshape2_1.4.4      
 [61] later_1.3.0          munsell_0.5.0        cellranger_1.1.0     tools_4.2.1         
 [65] cachem_1.0.6         xgboost_1.6.0.1      cli_3.3.0            generics_0.1.3      
 [69] pacman_0.5.1         broom_1.0.0          ggridges_0.5.3       evaluate_0.16       
 [73] fastmap_1.1.0        yaml_2.3.5           processx_3.7.0       knitr_1.40          
 [77] nlme_3.1-157         future_1.27.0        mime_0.12            rstanarm_2.21.3     
 [81] compiler_4.2.1       bayesplot_1.9.0      shinythemes_1.2.0    rstudioapi_0.14     
 [85] curl_4.3.2           tibble_3.1.8         bslib_0.4.0          stringi_1.7.8       
 [89] ps_1.7.1             lattice_0.20-45      Matrix_1.4-1         nloptr_2.0.3        
 [93] markdown_1.1         conflicted_1.1.0     vctrs_0.4.1          pillar_1.8.1        
 [97] lifecycle_1.0.1      jquerylib_0.1.4      data.table_1.14.2    httpuv_1.6.5        
[101] R6_2.5.1             promises_1.2.0.1     parallelly_1.32.1    writexl_1.4.0       
[105] codetools_0.2-18     boot_1.3-28          colourpicker_1.1.1   MASS_7.3-57         
[109] gtools_3.9.3         assertthat_0.2.1     openssl_2.0.2        withr_2.5.0         
[113] shinystan_2.6.0      parallel_4.2.1       hms_1.1.2            grid_4.2.1          
[117] rpart_4.1.16         timeDate_4021.104    minqa_1.2.4          class_7.3-20        
[121] rmarkdown_2.16       snakecase_0.11.0     dbarts_0.9-22        prophet_1.0         
[125] lubridate_1.8.0      base64enc_0.1-3      dygraphs_1.1.1.6