Fix integration test failures

[danielinteractive]

Integration test failed

* using log directory ‘/builds/nest/automation/systems-integration-tests/teal.modules.hermes.Rcheck’
* using R version 4.2.2 Patched (2022-11-10 r83330)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--ignore-vignettes’
* checking for file ‘teal.modules.hermes/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘teal.modules.hermes’ version ‘0.1.4.9014’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘teal.modules.hermes’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... SKIPPED
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > pkg_name <- "teal.modules.hermes"
  > library(pkg_name, character.only = TRUE)
  Loading required package: ggplot2
  Loading required package: shiny
  Loading required package: teal
  Loading required package: teal.data
  Loading required package: teal.slice
  Loading required package: teal.transform
  Loading required package: magrittr

  You are using teal version 0.13.0.9008

  Attaching package: 'teal'

  The following object is masked from 'package:teal.slice':

      teal_slices

  Attaching package: 'teal.modules.hermes'

  The following object is masked from 'package:teal':

      validate_n_levels

  > testthat::test_check(pkg_name)

  Attaching package: 'testthat'

  The following objects are masked from 'package:magrittr':

      equals, is_less_than, not

  Error received while setting inputs: Unable to find input binding for element with id teal-main_ui-root-samplevarspec_example-module-facet_var-sample_var
      x
   1. \-app$set_inputs(`:=`(!!ns("facet_var-sample_var"), "AGE18")) at test-sampleVarSpec.R:189:2
   2.   \-shinytest2:::app_set_inputs(...)
  Error received while setting inputs: Unable to find input binding for element with id teal-main_ui-filter_panel-add_MAE_filter-subjects-var_to_add
      x
   1. \-app$set_inputs(...) at test-scatterplot.R:67:2
   2.   \-shinytest2:::app_set_inputs(...)
  [ FAIL 11 | WARN 3 | SKIP 0 | PASS 87 ]

  ══ Warnings ════════════════════════════════════════════════════════════════════
  ── Warning ('test-scatterplot.R:83:3'): scatterplot module works as expected in the test app ──
  Adding new file snapshot: 'tests/testthat/_snaps/linux-4.2/scatterplot-001.png'
  ── Warning ('test-volcanoplot.R:48:3'): volcanoplot module works as expected in the test app ──
  Adding new file snapshot: 'tests/testthat/_snaps/linux-4.2/volcanoplot-001.png'
  ── Warning ('test-volcanoplot.R:53:3'): volcanoplot module works as expected in the test app ──
  Adding new file snapshot: 'tests/testthat/_snaps/linux-4.2/volcanoplot-002.png'

  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-adtteSpec.R:187:3'): adtteSpecServer module works as expected in the test app ──
  Error in `app_initialize(self, private, app_dir = app_dir, ..., load_timeout = load_timeout, 
      timeout = timeout, wait = wait, expect_values_screenshot_args = expect_values_screenshot_args, 
      screenshot_args = screenshot_args, check_names = check_names, 
      name = name, variant = variant, view = view, height = height, 
      width = width, seed = seed, clean_logs = clean_logs, shiny_args = shiny_args, 
      render_args = render_args, options = options)`: Cannot find shiny port number. Error lines found:
  Loading required package: shiny
  Loading required package: ggplot2
  Loading required package: teal
  Loading required package: teal.data
  Loading required package: teal.slice
  Loading required package: teal.transform
  Loading required package: magrittr

  You are using teal version 0.13.0.9008

  Attaching package: ‘teal’

  The following object is masked from ‘package:teal.slice’:

      teal_slices

  Attaching package: ‘teal.modules.hermes’

  The following object is masked from ‘package:teal’:

      validate_n_levels

  i You can inspect the failed AppDriver object via `rlang::last_error()$app`
  i AppDriver logs:
  {shinytest2} R info   03:03:13.12 Start AppDriver initialization
  {shinytest2} R info   03:03:13.12 Starting Shiny app
  {shinytest2} R info   03:03:28.40 Error while initializing AppDriver:
                                    Cannot find shiny port number. Error lines found:
                                    Loading required package: shiny
                                    Loading required package: ggplot2
                                    Loading required package: teal
                                    Loading required package: teal.data
                                    Loading required package: teal.slice
                                    Loading required package: teal.transform
                                    Loading required package: magrittr

                                    You are using teal version 0.13.0.9008

                                    Attaching package: ‘teal’

                                    The following object is masked from ‘package:teal.slice’:

                                        teal_slices

                                    Attaching package: ‘teal.modules.hermes’

                                    The following object is masked from ‘package:teal’:

                                        validate_n_levels
  {shiny}      R stderr ----------- Loading required package: shiny
  {shiny}      R stderr ----------- Loading required package: ggplot2
  {shiny}      R stderr ----------- Loading required package: teal
  {shiny}      R stderr ----------- Loading required package: teal.data
  {shiny}      R stderr ----------- Loading required package: teal.slice
  {shiny}      R stderr ----------- Loading required package: teal.transform
  {shiny}      R stderr ----------- Loading required package: magrittr
  {shiny}      R stderr ----------- 
  {shiny}      R stderr ----------- You are using teal version 0.13.0.9008
  {shiny}      R stderr ----------- 
  {shiny}      R stderr ----------- Attaching package: ‘teal’
  {shiny}      R stderr ----------- 
  {shiny}      R stderr ----------- The following object is masked from ‘package:teal.slice’:
  {shiny}      R stderr ----------- 
  {shiny}      R stderr -----------     teal_slices
  {shiny}      R stderr ----------- 
  {shiny}      R stderr ----------- 
  {shiny}      R stderr ----------- Attaching package: ‘teal.modules.hermes’
  {shiny}      R stderr ----------- 
  {shiny}      R stderr ----------- The following object is masked from ‘package:teal’:
  {shiny}      R stderr ----------- 
  {shiny}      R stderr -----------     validate_n_levels
  {shiny}      R stderr ----------- 

  Caused by error in `app_start_shiny()`:
  ! Cannot find shiny port number. Error lines found:
  Loading required package: shiny
  Loading required package: ggplot2
  Loading required package: teal
  Loading required package: teal.data
  Loading required package: teal.slice
  Loading required package: teal.transform
  Loading required package: magrittr

  You are using teal version 0.13.0.9008

  Attaching package: ‘teal’

  The following object is masked from ‘package:teal.slice’:

      teal_slices

  Attaching package: ‘teal.modules.hermes’

  The following object is masked from ‘package:teal’:

      validate_n_levels
  ── Error ('test-assaySpec.R:17:3'): assaySpecServer module works as expected in the test app ──
  Error in `app_initialize(self, private, app_dir = app_dir, ..., load_timeout = load_timeout, 
      timeout = timeout, wait = wait, expect_values_screenshot_args = expect_values_screenshot_args, 
      screenshot_args = screenshot_args, check_names = check_names, 
      name = name, variant = variant, view = view, height = height, 
      width = width, seed = seed, clean_logs = clean_logs, shiny_args = shiny_args, 
      render_args = render_args, options = options)`: Cannot find shiny port number. Error lines found:
  Loading required package: shiny
  Loading required package: ggplot2
  Loading required package: teal
  Loading required package: teal.data
  Loading required package: teal.slice
  Loading required package: teal.transform
  Loading required package: magrittr

  You are using teal version 0.13.0.9008

  Attaching package: ‘teal’

  The following object is masked from ‘package:teal.slice’:

      teal_slices

  Attaching package: ‘teal.modules.hermes’

  The following object is masked from ‘package:teal’:

      validate_n_levels

  i You can inspect the failed AppDriver object via `rlang::last_error()$app`
  i AppDriver logs:
  {shinytest2} R info   03:03:31.63 Start AppDriver initialization
  {shinytest2} R info   03:03:31.63 Starting Shiny app
  {shinytest2} R info   03:03:46.82 Error while initializing AppDriver:
                                    Cannot find shiny port number. Error lines found:
                                    Loading required package: shiny
                                    Loading required package: ggplot2
                                    Loading required package: teal
                                    Loading required package: teal.data
                                    Loading required package: teal.slice
                                    Loading required package: teal.transform
                                    Loading required package: magrittr

                                    You are using teal version 0.13.0.9008

                                    Attaching package: ‘teal’

                                    The following object is masked from ‘package:teal.slice’:

                                        teal_slices

                                    Attaching package: ‘teal.modules.hermes’

                                    The following object is masked from ‘package:teal’:

                                        validate_n_levels
  {shiny}      R stderr ----------- Loading required package: shiny
  {shiny}      R stderr ----------- Loading required package: ggplot2
  {shiny}      R stderr ----------- Loading required package: teal
  {shiny}      R stderr ----------- Loading required package: teal.data
  {shiny}      R stderr ----------- Loading required package: teal.slice
  {shiny}      R stderr ----------- Loading required package: teal.transform
  {shiny}      R stderr ----------- Loading required package: magrittr
  {shiny}      R stderr ----------- 
  {shiny}      R stderr ----------- You are using teal version 0.13.0.9008
  {shiny}      R stderr ----------- 
  {shiny}      R stderr ----------- Attaching package: ‘teal’
  {shiny}      R stderr ----------- 
  {shiny}      R stderr ----------- The following object is masked from ‘package:teal.slice’:
  {shiny}      R stderr ----------- 
  {shiny}      R stderr -----------     teal_slices
  {shiny}      R stderr ----------- 
  {shiny}      R stderr ----------- 
  {shiny}      R stderr ----------- Attaching package: ‘teal.modules.hermes’
  {shiny}      R stderr ----------- 
  {shiny}      R stderr ----------- The following object is masked from ‘package:teal’:
  {shiny}      R stderr ----------- 
  {shiny}      R stderr -----------     validate_n_levels
  {shiny}      R stderr ----------- 

  Caused by error in `app_start_shiny()`:
  ! Cannot find shiny port number. Error lines found:
  Loading required package: shiny
  Loading required package: ggplot2
  Loading required package: teal
  Loading required package: teal.data
  Loading required package: teal.slice
  Loading required package: teal.transform
  Loading required package: magrittr

  You are using teal version 0.13.0.9008

  Attaching package: ‘teal’

  The following object is masked from ‘package:teal.slice’:

      teal_slices

  Attaching package: ‘teal.modules.hermes’

  The following object is masked from ‘package:teal’:

      validate_n_levels
  ── Error ('test-barplot.R:29:3'): barplot module works as expected in the test app ──
  Error in `app_initialize(self, private, app_dir = app_dir, ..., load_timeout = load_timeout, 
      timeout = timeout, wait = wait, expect_values_screenshot_args = expect_values_screenshot_args, 
      screenshot_args = screenshot_args, check_names = check_names, 
      name = name, variant = variant, view = view, height = height, 
      width = width, seed = seed, clean_logs = clean_logs, shiny_args = shiny_args, 
      render_args = render_args, options = options)`: Cannot find shiny port number. Error lines found:
  Loading required package: shiny
  Loading required package: ggplot2
  Loading required package: teal
  Loading required package: teal.data
  Loading required package: teal.slice
  Loading required package: teal.transform
  Loading required package: magrittr

  You are using teal version 0.13.0.9008

  Attaching package: ‘teal’

  The following object is masked from ‘package:teal.slice’:

      teal_slices

  Attaching package: ‘teal.modules.hermes’

  The following object is masked from ‘package:teal’:

      validate_n_levels

  i You can inspect the failed AppDriver object via `rlang::last_error()$app`
  i AppDriver logs:
  {shinytest2} R info   03:03:50.11 Start AppDriver initialization
  {shinytest2} R info   03:03:50.11 Starting Shiny app
  {shinytest2} R info   03:04:05.31 Error while initializing AppDriver:
                                    Cannot find shiny port number. Error lines found:
                                    Loading required package: shiny
                                    Loading required package: ggplot2
                                    Loading required package: teal
                                    Loading required package: teal.data
                                    Loading required package: teal.slice
                                    Loading required package: teal.transform
                                    Loading required package: magrittr

                                    You are using teal version 0.13.0.9008

                                    Attaching package: ‘teal’

                                    The following object is masked from ‘package:teal.slice’:

                                        teal_slices

                                    Attaching package: ‘teal.modules.hermes’

                                    The following object is masked from ‘package:teal’:

                                        validate_n_levels
  {shiny}      R stderr ----------- Loading required package: shiny
  {shiny}      R stderr ----------- Loading required package: ggplot2
  {shiny}      R stderr ----------- Loading required package: teal
  {shiny}      R stderr ----------- Loading required package: teal.data
  {shiny}      R stderr ----------- Loading required package: teal.slice
  {shiny}      R stderr ----------- Loading required package: teal.transform
  {shiny}      R stderr ----------- Loading required package: magrittr
  {shiny}      R stderr ----------- 
  {shiny}      R stderr ----------- You are using teal version 0.13.0.9008
  {shiny}      R stderr ----------- 
  {shiny}      R stderr ----------- Attaching package: ‘teal’
  {shiny}      R stderr ----------- 
  {shiny}      R stderr ----------- The following object is masked from ‘package:teal.slice’:
  {shiny}      R stderr ----------- 
  {shiny}      R stderr -----------     teal_slices
  {shiny}      R stderr ----------- 
  {shiny}      R stderr ----------- 
  {shiny}      R stderr ----------- Attaching package: ‘teal.modules.hermes’
  {shiny}      R stderr ----------- 
  {shiny}      R stderr ----------- The following object is masked from ‘package:teal’:
  {shiny}      R stderr ----------- 
  {shiny}      R stderr -----------     validate_n_levels
  {shiny}      R stderr ----------- 

  Caused by error in `app_start_shiny()`:
  ! Cannot find shiny port number. Error lines found:
  Loading required package: shiny
  Loading required package: ggplot2
  Loading required package: teal
  Loading required package: teal.data
  Loading required package: teal.slice
  Loading required package: teal.transform
  Loading required package: magrittr

  You are using teal version 0.13.0.9008

  Attaching package: ‘teal’

  The following object is masked from ‘package:teal.slice’:

      teal_slices

  Attaching package: ‘teal.modules.hermes’

  The following object is masked from ‘package:teal’:

      validate_n_levels
  ── Error ('test-boxplot.R:25:3'): boxplot module works as expected in the test app ──
  Error in `app_initialize(self, private, app_dir = app_dir, ..., load_timeout = load_timeout, 
      timeout = timeout, wait = wait, expect_values_screenshot_args = expect_values_screenshot_args, 
      screenshot_args = screenshot_args, check_names = check_names, 
      name = name, variant = variant, view = view, height = height, 
      width = width, seed = seed, clean_logs = clean_logs, shiny_args = shiny_args, 
      render_args = render_args, options = options)`: Cannot find shiny port number. Error lines found:
  Loading required package: shiny
  Loading required package: ggplot2
  Loading required package: teal
  Loading required package: teal.data
  Loading required package: teal.slice
  Loading required package: teal.transform
  Loading required package: magrittr

  You are using teal version 0.13.0.9008

  Attaching package: ‘teal’

  The following object is masked from ‘package:teal.slice’:

      teal_slices

  Attaching package: ‘teal.modules.hermes’

  The following object is masked from ‘package:teal’:

      validate_n_levels

  i You can inspect the failed AppDriver object via `rlang::last_error()$app`
  i AppDriver logs:
  {shinytest2} R info   03:04:08.84 Start AppDriver initialization
  {shinytest2} R info   03:04:08.84 Starting Shiny app
  {shinytest2} R info   03:04:24.11 Error while initializing AppDriver:
                                    Cannot find shiny port number. Error lines found:
                                    Loading required package: shiny
                                    Loading required package: ggplot2
                                    Loading required package: teal
                                    Loading required package: teal.data
                                    Loading required package: teal.slice
                                    Loading required package: teal.transform
                                    Loading required package: magrittr

                                    You are using teal version 0.13.0.9008

                                    Attaching package: ‘teal’

                                    The following object is masked from ‘package:teal.slice’:

                                        teal_slices

                                    Attaching package: ‘teal.modules.hermes’

                                    The following object is masked from ‘package:teal’:

                                        validate_n_levels
  {shiny}      R stderr ----------- Loading required package: shiny
  {shiny}      R stderr ----------- Loading required package: ggplot2
  {shiny}      R stderr ----------- Loading required package: teal
  {shiny}      R stderr ----------- Loading required package: teal.data
  {shiny}      R stderr ----------- Loading required package: teal.slice
  {shiny}      R stderr ----------- Loading required package: teal.transform
  {shiny}      R stderr ----------- Loading required package: magrittr
  {shiny}      R stderr ----------- 
  {shiny}      R stderr ----------- You are using teal version 0.13.0.9008
  {shiny}      R stderr ----------- 
  {shiny}      R stderr ----------- Attaching package: ‘teal’
  {shiny}      R stderr ----------- 
  {shiny}      R stderr ----------- The following object is masked from ‘package:teal.slice’:
  {shiny}      R stderr ----------- 
  {shiny}      R stderr -----------     teal_slices
  {shiny}      R stderr ----------- 
  {shiny}      R stderr ----------- 
  {shiny}      R stderr ----------- Attaching package: ‘teal.modules.hermes’
  {shiny}      R stderr ----------- 
  {shiny}      R stderr ----------- The following object is masked from ‘package:teal’:
  {shiny}      R stderr ----------- 
  {shiny}      R stderr -----------     validate_n_levels
  {shiny}      R stderr ----------- 

  Caused by error in `app_start_shiny()`:
  ! Cannot find shiny port number. Error lines found:
  Loading required package: shiny
  Loading required package: ggplot2
  Loading required package: teal
  Loading required package: teal.data
  Loading required package: teal.slice
  Loading required package: teal.transform
  Loading required package: magrittr

  You are using teal version 0.13.0.9008

  Attaching package: ‘teal’

  The following object is masked from ‘package:teal.slice’:

      teal_slices

  Attaching package: ‘teal.modules.hermes’

  The following object is masked from ‘package:teal’:

      validate_n_levels
  ── Error ('test-experimentSpec.R:92:3'): experimentSpec module works as expected in the test app ──
  Error in `app_initialize(self, private, app_dir = app_dir, ..., load_timeout = load_timeout, 
      timeout = timeout, wait = wait, expect_values_screenshot_args = expect_values_screenshot_args, 
      screenshot_args = screenshot_args, check_names = check_names, 
      name = name, variant = variant, view = view, height = height, 
      width = width, seed = seed, clean_logs = clean_logs, shiny_args = shiny_args, 
      render_args = render_args, options = options)`: Cannot find shiny port number. Error lines found:
  Loading required package: shiny
  Loading required package: ggplot2
  Loading required package: teal
  Loading required package: teal.data
  Loading required package: teal.slice
  Loading required package: teal.transform
  Loading required package: magrittr

  You are using teal version 0.13.0.9008

  Attaching package: ‘teal’

  The following object is masked from ‘package:teal.slice’:

      teal_slices

  Attaching package: ‘teal.modules.hermes’

  The following object is masked from ‘package:teal’:

      validate_n_levels

  i You can inspect the failed AppDriver object via `rlang::last_error()$app`
  i AppDriver logs:
  {shinytest2} R info   03:04:27.52 Start AppDriver initialization
  {shinytest2} R info   03:04:27.52 Starting Shiny app
  {shinytest2} R info   03:04:42.73 Error while initializing AppDriver:
                                    Cannot find shiny port number. Error lines found:
                                    Loading required package: shiny
                                    Loading required package: ggplot2
                                    Loading required package: teal
                                    Loading required package: teal.data
                                    Loading required package: teal.slice
                                    Loading required package: teal.transform
                                    Loading required package: magrittr

                                    You are using teal version 0.13.0.9008

                                    Attaching package: ‘teal’

                                    The following object is masked from ‘package:teal.slice’:

                                        teal_slices

                                    Attaching package: ‘teal.modules.hermes’

                                    The following object is masked from ‘package:teal’:

                                        validate_n_levels
  {shiny}      R stderr ----------- Loading required package: shiny
  {shiny}      R stderr ----------- Loading required package: ggplot2
  {shiny}      R stderr ----------- Loading required package: teal
  {shiny}      R stderr ----------- Loading required package: teal.data
  {shiny}      R stderr ----------- Loading required package: teal.slice
  {shiny}      R stderr ----------- Loading required package: teal.transform
  {shiny}      R stderr ----------- Loading required package: magrittr
  {shiny}      R stderr ----------- 
  {shiny}      R stderr ----------- You are using teal version 0.13.0.9008
  {shiny}      R stderr ----------- 
  {shiny}      R stderr ----------- Attaching package: ‘teal’
  {shiny}      R stderr ----------- 
  {shiny}      R stderr ----------- The following object is masked from ‘package:teal.slice’:
  {shiny}      R stderr ----------- 
  {shiny}      R stderr -----------     teal_slices
  {shiny}      R stderr ----------- 
  {shiny}      R stderr ----------- 
  {shiny}      R stderr ----------- Attaching package: ‘teal.modules.hermes’
  {shiny}      R stderr ----------- 
  {shiny}      R stderr ----------- The following object is masked from ‘package:teal’:
  {shiny}      R stderr ----------- 
  {shiny}      R stderr -----------     validate_n_levels
  {shiny}      R stderr ----------- 

  Caused by error in `app_start_shiny()`:
  ! Cannot find shiny port number. Error lines found:
  Loading required package: shiny
  Loading required package: ggplot2
  Loading required package: teal
  Loading required package: teal.data
  Loading required package: teal.slice
  Loading required package: teal.transform
  Loading required package: magrittr

  You are using teal version 0.13.0.9008

  Attaching package: ‘teal’

  The following object is masked from ‘package:teal.slice’:

      teal_slices

  Attaching package: ‘teal.modules.hermes’

  The following object is masked from ‘package:teal’:

      validate_n_levels
  ── Error ('test-forest.R:29:3'): forest_tte module works as expected in the test app ──
  Error in `app_initialize(self, private, app_dir = app_dir, ..., load_timeout = load_timeout, 
      timeout = timeout, wait = wait, expect_values_screenshot_args = expect_values_screenshot_args, 
      screenshot_args = screenshot_args, check_names = check_names, 
      name = name, variant = variant, view = view, height = height, 
      width = width, seed = seed, clean_logs = clean_logs, shiny_args = shiny_args, 
      render_args = render_args, options = options)`: Cannot find shiny port number. Error lines found:
  Loading required package: shiny
  Loading required package: ggplot2
  Loading required package: teal
  Loading required package: teal.data
  Loading required package: teal.slice
  Loading required package: teal.transform
  Loading required package: magrittr

  You are using teal version 0.13.0.9008

  Attaching package: ‘teal’

  The following object is masked from ‘package:teal.slice’:

      teal_slices

  Attaching package: ‘teal.modules.hermes’

  The following object is masked from ‘package:teal’:

      validate_n_levels

  i You can inspect the failed AppDriver object via `rlang::last_error()$app`
  i AppDriver logs:
  {shinytest2} R info   03:04:45.33 Start AppDriver initialization
  {shinytest2} R info   03:04:45.33 Starting Shiny app
  {shinytest2} R info   03:05:00.51 Error while initializing AppDriver:
                                    Cannot find shiny port number. Error lines found:
                                    Loading required package: shiny
                                    Loading required package: ggplot2
                                    Loading required package: teal
                                    Loading required package: teal.data
                                    Loading required package: teal.slice
                                    Loading required package: teal.transform
                                    Loading required package: magrittr

                                    You are using teal version 0.13.0.9008

                                    Attaching package: ‘teal’

                                    The following object is masked from ‘package:teal.slice’:

                                        teal_slices

                                    Attaching package: ‘teal.modules.hermes’

                                    The following object is masked from ‘package:teal’:

                                        validate_n_levels
  {shiny}      R stderr ----------- Loading required package: shiny
  {shiny}      R stderr ----------- Loading required package: ggplot2
  {shiny}      R stderr ----------- Loading required package: teal
  {shiny}      R stderr ----------- Loading required package: teal.data
  {shiny}      R stderr ----------- Loading required package: teal.slice
  {shiny}      R stderr ----------- Loading required package: teal.transform
  {shiny}      R stderr ----------- Loading required package: magrittr
  {shiny}      R stderr ----------- 
  {shiny}      R stderr ----------- You are using teal version 0.13.0.9008
  {shiny}      R stderr ----------- 
  {shiny}      R stderr ----------- Attaching package: ‘teal’
  {shiny}      R stderr ----------- 
  {shiny}      R stderr ----------- The following object is masked from ‘package:teal.slice’:
  {shiny}      R stderr ----------- 
  {shiny}      R stderr -----------     teal_slices
  {shiny}      R stderr ----------- 
  {shiny}      R stderr ----------- 
  {shiny}      R stderr ----------- Attaching package: ‘teal.modules.hermes’
  {shiny}      R stderr ----------- 
  {shiny}      R stderr ----------- The following object is masked from ‘package:teal’:
  {shiny}      R stderr ----------- 
  {shiny}      R stderr -----------     validate_n_levels
  {shiny}      R stderr ----------- 

  Caused by error in `app_start_shiny()`:
  ! Cannot find shiny port number. Error lines found:
  Loading required package: shiny
  Loading required package: ggplot2
  Loading required package: teal
  Loading required package: teal.data
  Loading required package: teal.slice
  Loading required package: teal.transform
  Loading required package: magrittr

  You are using teal version 0.13.0.9008

  Attaching package: ‘teal’

  The following object is masked from ‘package:teal.slice’:

      teal_slices

  Attaching package: ‘teal.modules.hermes’

  The following object is masked from ‘package:teal’:

      validate_n_levels
  ── Error ('test-geneSpec.R:41:3'): geneSpec module works as expected in the test app ──
  Error in `app_initialize(self, private, app_dir = app_dir, ..., load_timeout = load_timeout, 
      timeout = timeout, wait = wait, expect_values_screenshot_args = expect_values_screenshot_args, 
      screenshot_args = screenshot_args, check_names = check_names, 
      name = name, variant = variant, view = view, height = height, 
      width = width, seed = seed, clean_logs = clean_logs, shiny_args = shiny_args, 
      render_args = render_args, options = options)`: Cannot find shiny port number. Error lines found:
  Loading required package: shiny
  Loading required package: ggplot2
  Loading required package: teal
  Loading required package: teal.data
  Loading required package: teal.slice
  Loading required package: teal.transform
  Loading required package: magrittr

  You are using teal version 0.13.0.9008

  Attaching package: ‘teal’

  The following object is masked from ‘package:teal.slice’:

      teal_slices

  Attaching package: ‘teal.modules.hermes’

  The following object is masked from ‘package:teal’:

      validate_n_levels

  i You can inspect the failed AppDriver object via `rlang::last_error()$app`
  i AppDriver logs:
  {shinytest2} R info   03:05:02.84 Start AppDriver initialization
  {shinytest2} R info   03:05:02.84 Starting Shiny app
  {shinytest2} R info   03:05:18.04 Error while initializing AppDriver:
                                    Cannot find shiny port number. Error lines found:
                                    Loading required package: shiny
                                    Loading required package: ggplot2
                                    Loading required package: teal
                                    Loading required package: teal.data
                                    Loading required package: teal.slice
                                    Loading required package: teal.transform
                                    Loading required package: magrittr

                                    You are using teal version 0.13.0.9008

                                    Attaching package: ‘teal’

                                    The following object is masked from ‘package:teal.slice’:

                                        teal_slices

                                    Attaching package: ‘teal.modules.hermes’

                                    The following object is masked from ‘package:teal’:

                                        validate_n_levels
  {shiny}      R stderr ----------- Loading required package: shiny
  {shiny}      R stderr ----------- Loading required package: ggplot2
  {shiny}      R stderr ----------- Loading required package: teal
  {shiny}      R stderr ----------- Loading required package: teal.data
  {shiny}      R stderr ----------- Loading required package: teal.slice
  {shiny}      R stderr ----------- Loading required package: teal.transform
  {shiny}      R stderr ----------- Loading required package: magrittr
  {shiny}      R stderr ----------- 
  {shiny}      R stderr ----------- You are using teal version 0.13.0.9008
  {shiny}      R stderr ----------- 
  {shiny}      R stderr ----------- Attaching package: ‘teal’
  {shiny}      R stderr ----------- 
  {shiny}      R stderr ----------- The following object is masked from ‘package:teal.slice’:
  {shiny}      R stderr ----------- 
  {shiny}      R stderr -----------     teal_slices
  {shiny}      R stderr ----------- 
  {shiny}      R stderr ----------- 
  {shiny}      R stderr ----------- Attaching package: ‘teal.modules.hermes’
  {shiny}      R stderr ----------- 
  {shiny}      R stderr ----------- The following object is masked from ‘package:teal’:
  {shiny}      R stderr ----------- 
  {shiny}      R stderr -----------     validate_n_levels
  {shiny}      R stderr ----------- 

  Caused by error in `app_start_shiny()`:
  ! Cannot find shiny port number. Error lines found:
  Loading required package: shiny
  Loading required package: ggplot2
  Loading required package: teal
  Loading required package: teal.data
  Loading required package: teal.slice
  Loading required package: teal.transform
  Loading required package: magrittr

  You are using teal version 0.13.0.9008

  Attaching package: ‘teal’

  The following object is masked from ‘package:teal.slice’:

      teal_slices

  Attaching package: ‘teal.modules.hermes’

  The following object is masked from ‘package:teal’:

      validate_n_levels
  ── Error ('test-km.R:30:3'): km module works as expected in the test app ───────
  Error in `app_initialize(self, private, app_dir = app_dir, ..., load_timeout = load_timeout, 
      timeout = timeout, wait = wait, expect_values_screenshot_args = expect_values_screenshot_args, 
      screenshot_args = screenshot_args, check_names = check_names, 
      name = name, variant = variant, view = view, height = height, 
      width = width, seed = seed, clean_logs = clean_logs, shiny_args = shiny_args, 
      render_args = render_args, options = options)`: Cannot find shiny port number. Error lines found:
  Loading required package: shiny
  Loading required package: ggplot2
  Loading required package: teal
  Loading required package: teal.data
  Loading required package: teal.slice
  Loading required package: teal.transform
  Loading required package: magrittr

  You are using teal version 0.13.0.9008

  Attaching package: ‘teal’

  The following object is masked from ‘package:teal.slice’:

      teal_slices

  Attaching package: ‘teal.modules.hermes’

  The following object is masked from ‘package:teal’:

      validate_n_levels

  i You can inspect the failed AppDriver object via `rlang::last_error()$app`
  i AppDriver logs:
  {shinytest2} R info   03:05:20.93 Start AppDriver initialization
  {shinytest2} R info   03:05:20.93 Starting Shiny app
  {shinytest2} R info   03:05:36.11 Error while initializing AppDriver:
                                    Cannot find shiny port number. Error lines found:
                                    Loading required package: shiny
                                    Loading required package: ggplot2
                                    Loading required package: teal
                                    Loading required package: teal.data
                                    Loading required package: teal.slice
                                    Loading required package: teal.transform
                                    Loading required package: magrittr

                                    You are using teal version 0.13.0.9008

                                    Attaching package: ‘teal’

                                    The following object is masked from ‘package:teal.slice’:

                                        teal_slices

                                    Attaching package: ‘teal.modules.hermes’

                                    The following object is masked from ‘package:teal’:

                                        validate_n_levels
  {shiny}      R stderr ----------- Loading required package: shiny
  {shiny}      R stderr ----------- Loading required package: ggplot2
  {shiny}      R stderr ----------- Loading required package: teal
  {shiny}      R stderr ----------- Loading required package: teal.data
  {shiny}      R stderr ----------- Loading required package: teal.slice
  {shiny}      R stderr ----------- Loading required package: teal.transform
  {shiny}      R stderr ----------- Loading required package: magrittr
  {shiny}      R stderr ----------- 
  {shiny}      R stderr ----------- You are using teal version 0.13.0.9008
  {shiny}      R stderr ----------- 
  {shiny}      R stderr ----------- Attaching package: ‘teal’
  {shiny}      R stderr ----------- 
  {shiny}      R stderr ----------- The following object is masked from ‘package:teal.slice’:
  {shiny}      R stderr ----------- 
  {shiny}      R stderr -----------     teal_slices
  {shiny}      R stderr ----------- 
  {shiny}      R stderr ----------- 
  {shiny}      R stderr ----------- Attaching package: ‘teal.modules.hermes’
  {shiny}      R stderr ----------- 
  {shiny}      R stderr ----------- The following object is masked from ‘package:teal’:
  {shiny}      R stderr ----------- 
  {shiny}      R stderr -----------     validate_n_levels
  {shiny}      R stderr ----------- 

  Caused by error in `app_start_shiny()`:
  ! Cannot find shiny port number. Error lines found:
  Loading required package: shiny
  Loading required package: ggplot2
  Loading required package: teal
  Loading required package: teal.data
  Loading required package: teal.slice
  Loading required package: teal.transform
  Loading required package: magrittr

  You are using teal version 0.13.0.9008

  Attaching package: ‘teal’

  The following object is masked from ‘package:teal.slice’:

      teal_slices

  Attaching package: ‘teal.modules.hermes’

  The following object is masked from ‘package:teal’:

      validate_n_levels
  ── Error ('test-pca.R:24:3'): pca module works as expected in the test app ─────
  Error in `app_initialize(self, private, app_dir = app_dir, ..., load_timeout = load_timeout, 
      timeout = timeout, wait = wait, expect_values_screenshot_args = expect_values_screenshot_args, 
      screenshot_args = screenshot_args, check_names = check_names, 
      name = name, variant = variant, view = view, height = height, 
      width = width, seed = seed, clean_logs = clean_logs, shiny_args = shiny_args, 
      render_args = render_args, options = options)`: Cannot find shiny port number. Error lines found:
  Loading required package: shiny
  Loading required package: ggplot2
  Loading required package: teal
  Loading required package: teal.data
  Loading required package: teal.slice
  Loading required package: teal.transform
  Loading required package: magrittr

  You are using teal version 0.13.0.9008

  Attaching package: ‘teal’

  The following object is masked from ‘package:teal.slice’:

      teal_slices

  Attaching package: ‘teal.modules.hermes’

  The following object is masked from ‘package:teal’:

      validate_n_levels

  i You can inspect the failed AppDriver object via `rlang::last_error()$app`
  i AppDriver logs:
  {shinytest2} R info   03:05:39.11 Start AppDriver initialization
  {shinytest2} R info   03:05:39.11 Starting Shiny app
  {shinytest2} R info   03:05:54.31 Error while initializing AppDriver:
                                    Cannot find shiny port number. Error lines found:
                                    Loading required package: shiny
                                    Loading required package: ggplot2
                                    Loading required package: teal
                                    Loading required package: teal.data
                                    Loading required package: teal.slice
                                    Loading required package: teal.transform
                                    Loading required package: magrittr

                                    You are using teal version 0.13.0.9008

                                    Attaching package: ‘teal’

                                    The following object is masked from ‘package:teal.slice’:

                                        teal_slices

                                    Attaching package: ‘teal.modules.hermes’

                                    The following object is masked from ‘package:teal’:

                                        validate_n_levels
  {shiny}      R stderr ----------- Loading required package: shiny
  {shiny}      R stderr ----------- Loading required package: ggplot2
  {shiny}      R stderr ----------- Loading required package: teal
  {shiny}      R stderr ----------- Loading required package: teal.data
  {shiny}      R stderr ----------- Loading required package: teal.slice
  {shiny}      R stderr ----------- Loading required package: teal.transform
  {shiny}      R stderr ----------- Loading required package: magrittr
  {shiny}      R stderr ----------- 
  {shiny}      R stderr ----------- You are using teal version 0.13.0.9008
  {shiny}      R stderr ----------- 
  {shiny}      R stderr ----------- Attaching package: ‘teal’
  {shiny}      R stderr ----------- 
  {shiny}      R stderr ----------- The following object is masked from ‘package:teal.slice’:
  {shiny}      R stderr ----------- 
  {shiny}      R stderr -----------     teal_slices
  {shiny}      R stderr ----------- 
  {shiny}      R stderr ----------- 
  {shiny}      R stderr ----------- Attaching package: ‘teal.modules.hermes’
  {shiny}      R stderr ----------- 
  {shiny}      R stderr ----------- The following object is masked from ‘package:teal’:
  {shiny}      R stderr ----------- 
  {shiny}      R stderr -----------     validate_n_levels
  {shiny}      R stderr ----------- 

  Caused by error in `app_start_shiny()`:
  ! Cannot find shiny port number. Error lines found:
  Loading required package: shiny
  Loading required package: ggplot2
  Loading required package: teal
  Loading required package: teal.data
  Loading required package: teal.slice
  Loading required package: teal.transform
  Loading required package: magrittr

  You are using teal version 0.13.0.9008

  Attaching package: ‘teal’

  The following object is masked from ‘package:teal.slice’:

      teal_slices

  Attaching package: ‘teal.modules.hermes’

  The following object is masked from ‘package:teal’:

      validate_n_levels
  ── Error ('test-quality.R:26:3'): quality module works as expected in the test app ──
  Error in `app_initialize(self, private, app_dir = app_dir, ..., load_timeout = load_timeout, 
      timeout = timeout, wait = wait, expect_values_screenshot_args = expect_values_screenshot_args, 
      screenshot_args = screenshot_args, check_names = check_names, 
      name = name, variant = variant, view = view, height = height, 
      width = width, seed = seed, clean_logs = clean_logs, shiny_args = shiny_args, 
      render_args = render_args, options = options)`: Cannot find shiny port number. Error lines found:
  Loading required package: shiny
  Loading required package: ggplot2
  Loading required package: teal
  Loading required package: teal.data
  Loading required package: teal.slice
  Loading required package: teal.transform
  Loading required package: magrittr

  You are using teal version 0.13.0.9008

  Attaching package: ‘teal’

  The following object is masked from ‘package:teal.slice’:

      teal_slices

  Attaching package: ‘teal.modules.hermes’

  The following object is masked from ‘package:teal’:

      validate_n_levels

  i You can inspect the failed AppDriver object via `rlang::last_error()$app`
  i AppDriver logs:
  {shinytest2} R info   03:05:56.80 Start AppDriver initialization
  {shinytest2} R info   03:05:56.80 Starting Shiny app
  {shinytest2} R info   03:06:11.94 Error while initializing AppDriver:
                                    Cannot find shiny port number. Error lines found:
                                    Loading required package: shiny
                                    Loading required package: ggplot2
                                    Loading required package: teal
                                    Loading required package: teal.data
                                    Loading required package: teal.slice
                                    Loading required package: teal.transform
                                    Loading required package: magrittr

                                    You are using teal version 0.13.0.9008

                                    Attaching package: ‘teal’

                                    The following object is masked from ‘package:teal.slice’:

                                        teal_slices

                                    Attaching package: ‘teal.modules.hermes’

                                    The following object is masked from ‘package:teal’:

                                        validate_n_levels
  {shiny}      R stderr ----------- Loading required package: shiny
  {shiny}      R stderr ----------- Loading required package: ggplot2
  {shiny}      R stderr ----------- Loading required package: teal
  {shiny}      R stderr ----------- Loading required package: teal.data
  {shiny}      R stderr ----------- Loading required package: teal.slice
  {shiny}      R stderr ----------- Loading required package: teal.transform
  {shiny}      R stderr ----------- Loading required package: magrittr
  {shiny}      R stderr ----------- 
  {shiny}      R stderr ----------- You are using teal version 0.13.0.9008
  {shiny}      R stderr ----------- 
  {shiny}      R stderr ----------- Attaching package: ‘teal’
  {shiny}      R stderr ----------- 
  {shiny}      R stderr ----------- The following object is masked from ‘package:teal.slice’:
  {shiny}      R stderr ----------- 
  {shiny}      R stderr -----------     teal_slices
  {shiny}      R stderr ----------- 
  {shiny}      R stderr ----------- 
  {shiny}      R stderr ----------- Attaching package: ‘teal.modules.hermes’
  {shiny}      R stderr ----------- 
  {shiny}      R stderr ----------- The following object is masked from ‘package:teal’:
  {shiny}      R stderr ----------- 
  {shiny}      R stderr -----------     validate_n_levels
  {shiny}      R stderr ----------- 

  Caused by error in `app_start_shiny()`:
  ! Cannot find shiny port number. Error lines found:
  Loading required package: shiny
  Loading required package: ggplot2
  Loading required package: teal
  Loading required package: teal.data
  Loading required package: teal.slice
  Loading required package: teal.transform
  Loading required package: magrittr

  You are using teal version 0.13.0.9008

  Attaching package: ‘teal’

  The following object is masked from ‘package:teal.slice’:

      teal_slices

  Attaching package: ‘teal.modules.hermes’

  The following object is masked from ‘package:teal’:

      validate_n_levels
  ── Error ('test-sampleVarSpec.R:197:3'): sampleVarSpec module works as expected in the test app ──
  Error in `app_find_node_id(self, private, input = input, output = output, 
      selector = selector)`: Cannot find HTML element with selector #teal-main_ui-root-samplevarspec_example-module-facet_var-levels_button.shiny-bound-input
  Backtrace:
      ▆
   1. └─app$click(ns("facet_var-levels_button")) at test-sampleVarSpec.R:197:2
   2.   └─shinytest2:::app_click(...)
   3.     └─shinytest2:::app_find_node_id(self, private, input = input, output = output, selector = selector)
   4.       └─shinytest2:::app_abort(...)
   5.         └─rlang::abort(..., app = self, call = call)

  [ FAIL 11 | WARN 3 | SKIP 0 | PASS 87 ]
  Error: Test failures
  Execution halted
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR
See
  ‘/builds/nest/automation/systems-integration-tests/teal.modules.hermes.Rcheck/00check.log’
for details.

[danielinteractive]

@gogonzo has teal.modules.hermes received teal filter panel updates already or not yet? just to understand if part of the failures could come from yet to be done adaptation

[gogonzo]

Hi Daniel, I'm checking this out