std::bad_function_call
vflorelo opened this issue · 6 comments
Incident
Whenever me or my team try to use a shiny app, rstudio-server crashes and restarts the session, the behaviour is similar if we try to run any shiny app from the command line, which shows the following error
terminate called after throwing an instance of 'std::bad_function_call'
what(): bad_function_call
Aborted
We are using Ubuntu 22.04, we noticed the incident started after updating all packages on 2024-06-30, but the bug might have been there previously. At the time, we were running R v4.3.2 and rstudio-server 2024.04.2-764.
We then updated R to v4.4.1, R was installed from source with the following flags for configure:
--enable-R-shlib--with-tcltk
Except for system dependencies, none of the R packages were installed using apt or dpkg.
System details
Output of sessionInfo():
R version 4.4.1 (2024-06-14)
Platform: x86_64-pc-linux-gnu
Running under: Ubuntu 22.04.4 LTS
Matrix products: default
BLAS: /usr/local/lib/R/lib/libRblas.so
LAPACK: /usr/local/lib/R/lib/libRlapack.so; LAPACK version 3.12.0
locale:
[1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8
[5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8
[7] LC_PAPER=en_GB.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
time zone: Europe/London
tzcode source: system (glibc)
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] compiler_4.4.1
Example application
#!/usr/local/bin/R
library("shiny")
shiny::devmode(TRUE)
ui <- fluidPage("Hello, world!")
server <- function(input, output, session) {}
shinyApp(ui, server)Mitigation attempts
- We tried updating R to the newest version
- We tried updating shiny to the newest version
- We tried updating rstudio to the newest version
- We tried installing shiny from source
No errors were reported in any of the above
Googling "shiny" + "bad_function_call" did not return any significant results
Any help or pointers are greatly appreciated.
Hi @vflorelo, thanks for the report. It sounds like this might be an rstudio-server issue, but I'm not sure. Can you also include the output from devtools::session_info() in your issue? That function gives more information about your environment and the version of RStudio being used.
Dear @gadenbuie
Thank you very much for your promptly reply.
Here's the output of devtools::session_info()
> devtools::session_info()
─ Session info ────────────────────────────────────────────────────────────────────────────────────────────────────────
setting value
version R version 4.4.1 (2024-06-14)
os Ubuntu 22.04.4 LTS
system x86_64, linux-gnu
ui RStudio
language (EN)
collate en_GB.UTF-8
ctype en_GB.UTF-8
tz Europe/London
date 2024-07-10
rstudio 2024.04.2+764 Chocolate Cosmos (server)
pandoc 2.9.2.1 @ /usr/bin/pandoc
─ Packages ────────────────────────────────────────────────────────────────────────────────────────────────────────────
package * version date (UTC) lib source
cachem 1.1.0 2024-05-16 [1] CRAN (R 4.4.1)
cli 3.6.3 2024-06-21 [1] CRAN (R 4.4.1)
devtools 2.4.5 2022-10-11 [1] CRAN (R 4.4.1)
digest 0.6.36 2024-06-23 [1] CRAN (R 4.4.1)
ellipsis 0.3.2 2021-04-29 [1] CRAN (R 4.4.1)
fastmap 1.2.0 2024-05-15 [1] CRAN (R 4.4.1)
fs 1.6.4 2024-04-25 [1] CRAN (R 4.4.1)
glue 1.7.0 2024-01-09 [1] CRAN (R 4.4.1)
htmltools 0.5.8.1 2024-04-04 [1] CRAN (R 4.4.1)
htmlwidgets 1.6.4 2023-12-06 [1] CRAN (R 4.4.1)
httpuv 1.6.15 2024-03-26 [1] CRAN (R 4.4.1)
later 1.3.2 2023-12-06 [1] CRAN (R 4.4.1)
lifecycle 1.0.4 2023-11-07 [1] CRAN (R 4.4.1)
magrittr 2.0.3 2022-03-30 [1] CRAN (R 4.4.1)
memoise 2.0.1 2021-11-26 [1] CRAN (R 4.4.1)
mime 0.12 2021-09-28 [1] CRAN (R 4.4.1)
miniUI 0.1.1.1 2018-05-18 [1] CRAN (R 4.4.1)
pkgbuild 1.4.4 2024-03-17 [1] CRAN (R 4.4.1)
pkgload 1.4.0 2024-06-28 [1] CRAN (R 4.4.1)
profvis 0.3.8 2023-05-02 [1] CRAN (R 4.4.1)
promises 1.3.0 2024-04-05 [1] CRAN (R 4.4.1)
purrr 1.0.2 2023-08-10 [1] CRAN (R 4.4.1)
R6 2.5.1 2021-08-19 [1] CRAN (R 4.4.1)
Rcpp * 1.0.12 2024-01-09 [1] CRAN (R 4.4.1)
remotes 2.5.0 2024-03-17 [1] CRAN (R 4.4.1)
rlang 1.1.4 2024-06-04 [1] CRAN (R 4.4.1)
rstudioapi 0.16.0 2024-03-24 [1] CRAN (R 4.4.1)
sessioninfo 1.2.2 2021-12-06 [1] CRAN (R 4.4.1)
shiny 1.8.1.1 2024-04-02 [1] CRAN (R 4.4.1)
stringi 1.8.4 2024-05-06 [1] CRAN (R 4.4.1)
stringr 1.5.1 2023-11-14 [1] CRAN (R 4.4.1)
urlchecker 1.0.1 2021-11-30 [1] CRAN (R 4.4.1)
usethis 2.2.3 2024-02-19 [1] CRAN (R 4.4.1)
vctrs 0.6.5 2023-12-01 [1] CRAN (R 4.4.1)
xtable 1.8-4 2019-04-21 [1] CRAN (R 4.4.1)
[1] /usr/local/lib/R/site-library
[2] /usr/local/lib/R/library
──────────────────────────────────────────────────────────────────────────────
Noteworthy, the shiny error also happens when I call the program from the R command line (outside rstudio) or if I execute it as a script with Rscript
Thank you again for your support
Noteworthy, the shiny error also happens when I call the program from the R command line (outside rstudio) or if I execute it as a script with Rscript
Oh interesting, that is noteworthy. I tried to reproduce the issue with Ubuntu via rocker, but couldn't. In the mitigation attempts section you mention "updating R to the newest version". Was that also installed from source? Can you install R from apt?
I think I figured out what happened.
Timeline:
- I removed my R installation from source.
- I installed R 4.4.1 and shiny v1.5.0+dfsg-2 using apt. No errors whatsoever.
- I ran
BiocManager::install()as root and shiny broke again. - I removed everything and started from scratch again
- I launched an infinite loop starting and stopping a simple shiny app, so that when the problematic package was installed, I was able to catch it
Since apt puts the installed packages in /usr/lib/R/site-packages, but BiocManager::install() and install.packages() place them in /usr/local/lib/R/site-packages, it was easy, but time consuming to find the problematic package.
The culprit: httpuv, the version installed when running install.packages("httpuv") (1.6.15) results in shiny complaining about the bad_function_call, whereas the version installed with apt (1.6.5+dfsg-1) works fine. I repeated this to make sure httpuv was the problematic package.
This bug(?) might be out of shiny's scope, so it might be worth closing this issue, but still worth checking if updates to httpuv cause similar issues to other users.
Thank you for your pointers and your help.
Best wishes. Vic.
httpuv, the version installed when running
install.packages("httpuv")(1.6.15) results in shiny complaining about thebad_function_call, whereas the version installed with apt (1.6.5+dfsg-1) works fine. I repeated this to make sure httpuv was the problematic package.
Two interesting things stand out to me here. First httpuv 1.6.5 is relatively old (released Jan 2022). And second the +dfsg-1 suffix seems like an indication that the person who packaged httpuv for Ubuntu (really Debian) modified the package in some way, likely to avoid the issues you've encountered. It took me a bit of searching, but I found the repository where the apt package versions live: https://salsa.debian.org/r-pkg-team/r-cran-httpuv.
I guess my recommendation would be to install httpuv via apt if possible.