Error when refreshing page on immutable systems (e.g., NixOS)

[eline-anslot]

The issue #1184 has been closed however the bug seems to still be present.

We came across this problem when running the following R code using the last commit as of today of bslib and version 1.12.1.9 of shiny :

library(shiny)
library(bslib)

ui <- page_fillable(
  # App title ----
  title = "Hello Shiny!",
  # Sidebar panel for inputs ----

  selectizeInput(
    "inSelect",
    "Select input",
    choices = c("Item A", "Item B", "Item C"),
    options = list(create = TRUE, maxItems = 3, placeholder = 'hi there')
  )
)

server <- function(input, output) {}

shinyApp(ui = ui, server = server, options = list(launch.browser = FALSE, port = 6565, host = "0.0.0.0"))

Running this code works but when refreshing the page it returns the following error:

Warning in file.copy(script, dirname(outfile), overwrite = TRUE) :
  problem copying /nix/store/cdg2njsw8vgq14s0rh97zhqx0zfmzqjz-r-shiny/library/shiny/www/shared/selectize//js/selectize.min.js to /tmp/nix-shell.QtkK6m/Rtmp96D4mJ/selectize712f0895bef4f0695ce5aa23269b4ebe/selectize.min.js: Permission denied
Warning in file.copy(script, dirname(outfile), overwrite = TRUE) :
  problem copying /nix/store/cdg2njsw8vgq14s0rh97zhqx0zfmzqjz-r-shiny/library/shiny/www/shared/selectize//accessibility/js/selectize-plugin-a11y.min.js to /tmp/nix-shell.QtkK6m/Rtmp96D4mJ/selectize712f0895bef4f0695ce5aa23269b4ebe/selectize-plugin-a11y.min.js: Permission denied
Warning: Error in bslib::bs_dependency: Failed to copy the following script(s): /nix/store/cdg2njsw8vgq14s0rh97zhqx0zfmzqjz-r-shiny/library/shiny/www/shared/selectize//js/selectize.min.js, /nix/store/cdg2njsw8vgq14s0rh97zhqx0zfmzqjz-r-shiny/library/shiny/www/shared/selectize//accessibility/js/selectize-plugin-a11y.min.js.

Important to know is that we are running the code on NixOS which implies that users have read-only permissions on the file of installed packages.

To reproduce the problem you can find below a flake.nix file:

{
  inputs = {
    utils.url = "github:numtide/flake-utils";
    nixpkgs.url = "github:NixOS/nixpkgs/nixos-25.11";
  };

  outputs = { self, nixpkgs, utils }:
    utils.lib.eachDefaultSystem (system:
      let
        pkgs = import nixpkgs {
          inherit system;
          overlays = [
            (final: prev: {
                rPackages = prev.rPackages.override {
                  overrides = {
                    shiny = prev.rPackages.buildRPackage {
                      name = "shiny";
                      src = prev.fetchFromGitHub {
                        owner = "rstudio";
                        repo = "shiny";
                        rev = "e161f2e4a866c3b3ac1f7d669661786a814641c1";
                        hash = "sha256-ATg8/whRxBzim8JVAvSAcN2hzC8aenGHb9YmHxOEV3M=";
                      };
                      propagatedBuildInputs = with prev.rPackages; 
                      [ final.rPackages.otel 
                        final.rPackages.promises 
                        final.rPackages.bslib
                        cachem
                        cli
                        commonmark fontawesome glue htmltools httpuv jsonlite lifecycle mime sourcetools withr xtable];
                    };
                    bslib = prev.rPackages.buildRPackage {
                      name = "bslib";
                      src = prev.fetchFromGitHub {
                        owner = "rstudio";
                        repo = "bslib";
                        rev = "bc56d8e7671b6c1c41c041b6992e24cf1a4bc05f";
                        hash = "sha256-dhGtf1GRqOBAvn/7abHqnWn9yD+qaj+sfopjnr3tO0s=";
                      };
                      propagatedBuildInputs = prev.rPackages.bslib.propagatedBuildInputs;
                    };
                    promises = prev.rPackages.buildRPackage {
                      name = "promises";
                      src = prev.fetchFromGitHub {
                        owner = "rstudio";
                        repo = "promises";
                        rev = "2f70615f8c38f0b28f1088a08911ce2b1b0aa176";
                        hash = "sha256-gKAtbCE1scwhasQWldh2Cf78zXaXFeLlgeWuCu1GKiY=";
                      };
                      propagatedBuildInputs = prev.rPackages.promises.propagatedBuildInputs ++ [ final.rPackages.otel prev.rPackages.lifecycle ];
                    };
                    otel = prev.rPackages.buildRPackage {
                      name = "otel";
                      src = prev.fetchFromGitHub {
                          owner = "r-lib";
                          repo = "otel";
                          rev = "afc31bc1f4bd177870d44b051ada1d9e4e685346";
                          hash = "sha256-554JJsegzwGfdfUNErAceUX7bzgQimqNxR1oGFKBN40=";
                      };
                      propagatedBuildInputs = prev.rPackages.otel.propagatedBuildInputs;
                    };
                  };
                };
              })
          ];
        };
        rpackages = with pkgs.rPackages; [ shiny ];
        rLocal = (pkgs.rWrapper.override { packages = rpackages; });
      in {
        devShell = pkgs.mkShell {
          packages = with pkgs; [ jq rLocal ];
        };
      });
}

and a Dockerfile:

FROM ubuntu:latest

RUN apt update \
    && apt install -y curl xz-utils \
    && mkdir -m 0755 /nix && chown ubuntu /nix

# Use non root user
USER ubuntu

# Install nix
ENV PATH="/home/ubuntu/.nix-profile/bin:${PATH}"
RUN curl -sL https://nixos.org/nix/install | sh -s -- --no-daemon

# Activate installed nix for user to be able to use nix-shell command
RUN . /home/ubuntu/.nix-profile/etc/profile.d/nix.sh

WORKDIR /home/ubuntu

COPY example.R example.R

COPY flake.nix flake.nix

EXPOSE 6565

CMD nix develop --extra-experimental-features flakes --extra-experimental-features nix-command --command bash -c "Rscript example.R"

Once you have this three files (i.e., example.R with the shiny app code, flake.nix with the package specifications and Dockerfile), you can test as follows:

docker build -t bslibshiny-nixos . && docker run --rm -p 6565:6565 bslibshiny-nixos:latest 

The error does not occur when using fluidPage (shiny) instead of page_fillable (bslib).

Session Info

R version 4.5.1 (2025-06-13)
Platform: x86_64-pc-linux-gnu
Running under: NixOS 25.11 (Xantusia)

Matrix products: default
BLAS/LAPACK: /nix/store/bxzh4js1lrshwlc13cjn86w71jzmdqcz-blas-3/lib/libblas.so.3;  LAPACK version 3.12.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

time zone: NA
tzcode source: system (glibc)

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

other attached packages:
[1] bslib_0.9.0.9002  shiny_1.12.1.9000

loaded via a namespace (and not attached):
 [1] digest_0.6.37       later_1.4.2         R6_2.6.1           
 [4] httpuv_1.6.16       fastmap_1.2.0       magrittr_2.0.3     
 [7] cachem_1.1.0        memoise_2.0.1       htmltools_0.5.8.1  
[10] lifecycle_1.0.4     promises_1.5.0.9000 cli_3.6.5          
[13] xtable_1.8-4        sass_0.4.10         jquerylib_0.1.4    
[16] compiler_4.5.1      tools_4.5.1         mime_0.13          
[19] Rcpp_1.1.0          otel_0.2.0.9000     fs_1.6.6           
[22] jsonlite_2.0.0      rlang_1.1.6 

[gadenbuie]

Thanks for your comment and reproducible example. Would you be open to submitting a pull request to fix this? From the other issue you opened in officer (and the work done here in bslib) it appears that the problem is about tracking down file.copy() calls that need copy.mode = FALSE

[eline-anslot]

I am going to give it a try!

[eline-anslot]

After changing all the file.copy, I noticed that the sass dependency cause some issues when cleaning up (i.e., when closing the shiny app). I opened a PR there as well.