rstanarm
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Published
20 hours ago •
stan-dev
stan-dev
Unable to publish a Shiny App with rstanarm
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
