PatientLevelPrediction
PatientLevelPrediction copied to clipboard
Shiny App crashes after attempting to viewPlp report
Describe the bug
After successfully loading a patient-level prediction (PLP) evaluation using the loadPlpResult
function, attempting to view the report in the Shiny App results in two different behaviors:
- Shiny App opens and then closes abruptly.
- When accessing the Shiny App through a web browser, clicking the "View Report" option within the "Actions" section results in a blank gray screen.
The error from the R console is:
Listening on http://127.0.0.1:6603
Warning: Ignoring explicitly provided widget ID "resultDataFiltered"; Shiny doesn't use themWarning: Ignoring explicitly provided widget ID "resultDataFiltered"; Shiny doesn't use themWarning: Error in .make_numeric_version: invalid non-character version specification 'x' (type: double) 4: shiny::runApp
3: ShinyAppBuilder::viewShiny [/private/var/folders/1b/3plyy51n7yq4l71722c2xvl80000gn/T/RtmpEasC7f/R.INSTALL1224721efe5df/OHDSI-ShinyAppBuilder-9360b5f/R/ViewShiny.R#138]
2: viewPlps [/private/var/folders/1b/3plyy51n7yq4l71722c2xvl80000gn/T/RtmpawxSw7/R.INSTALL57313205f01d/PatientLevelPrediction/R/ViewShinyPlp.R#168]
1: viewPlp [/private/var/folders/1b/3plyy51n7yq4l71722c2xvl80000gn/T/RtmpawxSw7/R.INSTALL57313205f01d/PatientLevelPrediction/R/ViewShinyPlp.R#71]
Set up (please run in R "sessionInfo()" and copy the output here):
> sessionInfo()
R version 4.4.1 (2024-06-14)
Platform: aarch64-apple-darwin20
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.12.0
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
time zone: Europe/Berlin
tzcode source: internal
attached base packages:
[1] stats graphics grDevices datasets utils methods base
other attached packages:
[1] shiny_1.9.1 memuse_4.2-3 ResultModelManager_0.5.11 R6_2.5.1 PatientLevelPrediction_6.3.9 FeatureExtraction_3.7.1
[7] Andromeda_0.6.6 dplyr_1.1.4 DatabaseConnector_6.3.2
loaded via a namespace (and not attached):
[1] tidyselect_1.2.1 viridisLite_0.4.2 blob_1.2.4 fastmap_1.2.0 lazyeval_0.2.2 promises_1.3.0 digest_0.6.37 mime_0.12
[9] lifecycle_1.0.4 processx_3.8.4 RSQLite_2.3.7 magrittr_2.0.3 compiler_4.4.1 rlang_1.1.4 sass_0.4.9 tools_4.4.1
[17] utf8_1.2.4 yaml_2.3.10 data.table_1.16.2 knitr_1.48 htmlwidgets_1.6.4 bit_4.5.0 xgboost_1.7.8.1 withr_3.0.1
[25] purrr_1.0.2 shinyWidgets_0.8.7 grid_4.4.1 fansi_1.0.6 xtable_1.8-4 colorspace_2.1-1 ggplot2_3.5.1 scales_1.3.0
[33] cli_3.6.3 crayon_1.5.3 rmarkdown_2.28 generics_0.1.3 rstudioapi_0.17.0 httr_1.4.7 tzdb_0.4.0 DBI_1.2.3
[41] cachem_1.1.0 drat_0.2.4 ShinyAppBuilder_3.1.0 vctrs_0.6.5 Matrix_1.7-0 jsonlite_1.8.9 tippy_0.1.0 hms_1.1.3
[49] bit64_4.5.2 ParallelLogger_3.3.1 crosstalk_1.2.1 plotly_4.10.4 fontawesome_0.5.2 jquerylib_0.1.4 tidyr_1.3.1 glue_1.8.0
[57] reactR_0.6.1 ps_1.8.0 rJava_1.0-11 gtable_0.3.5 later_1.3.2 shinycssloaders_1.1.0 shinydashboard_0.7.2 pool_1.0.4
[65] munsell_0.5.1 tibble_3.2.1 pillar_1.9.0 htmltools_0.5.8.1 reactable_0.4.4 dbplyr_2.5.0 evaluate_1.0.1 lattice_0.22-6
[73] readr_2.1.5 backports_1.5.0 OhdsiShinyModules_3.1.0 memoise_2.0.1 renv_1.0.7 httpuv_1.6.15 bslib_0.8.0 Rcpp_1.0.13
[81] checkmate_2.3.2 SqlRender_1.19.0 xfun_0.48 pkgconfig_2.0.3
To Reproduce
The code:
library(FeatureExtraction)
library(PatientLevelPrediction)
library(ResultModelManager)
outputFolder = "~/My path ot the model"
gmbResult = loadPlpResult(file.path(outputFolder, '1', 'plpResult'))
viewPlp(gmbResult)
In the Shiny app or the web browser:
- Navigate to the prediction section
- Select the target, outcome cohort, click "Generate Report"
- Select "View Report" from the "Actions" section.
PLP Log File The "PLP Log File" doesn't apply in this case.
Additional context
This issue occurs when attempting to view a previously loaded PLP evaluation, not when running the PatientLevelPrediction
package directly.