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I ran cohort diagnostics and have a folder with csv files.
I created the merged sqlite zip file.
Then I ran
CohortDiagnostics::launchDiagnosticsExplorer(here::here("MergedCohortDiagnosticsData.sqlite"))
and get the following error.
Error in DatabaseConnector::getTableNames(connectionHandler$getConnection(), : Pool, R6 connection not supported
I'm using the latest release of the Hades packages.
To reproduce this error I created a minimal reprex. These are the lines in the shiny module that cause the error.
remotes::install_github("OHDSI/DatabaseConnector") #> Skipping install of 'DatabaseConnector' from a github remote, the SHA1 (bee58a31) has not changed since last install. #> Use `force = TRUE` to force installation remotes::install_github("OHDSI/ResultModelManager") #> Skipping install of 'ResultModelManager' from a github remote, the SHA1 (ad706b43) has not changed since last install. #> Use `force = TRUE` to force installation connectionDetails <- DatabaseConnector::createConnectionDetails("sqlite", server = ":memory:") connectionHandler <- ResultModelManager::PooledConnectionHandler$new(connectionDetails) #> Using DatabaseConnector jdbc driver. #> Initalizing pooled connection #> Connecting using SQLite driver DatabaseConnector::getTableNames(connectionHandler$getConnection(), databaseSchema = "main") #> Error in `DatabaseConnector::getTableNames()`: #> ! Pool, R6 connection not supported connectionHandler$closeConnection() sessionInfo() #> R version 4.3.1 (2023-06-16) #> Platform: aarch64-apple-darwin20 (64-bit) #> Running under: macOS Sonoma 14.0 #> #> Matrix products: default #> BLAS: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRblas.0.dylib #> LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0 #> #> 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/Amsterdam #> tzcode source: internal #> #> attached base packages: #> [1] stats graphics grDevices utils datasets methods base #> #> loaded via a namespace (and not attached): #> [1] styler_1.10.3 utf8_1.2.4 generics_0.1.3 #> [4] RSQLite_2.3.6 hms_1.1.3 digest_0.6.35 #> [7] magrittr_2.0.3 evaluate_0.23 fastmap_1.1.1 #> [10] blob_1.2.4 R.oo_1.26.0 DatabaseConnector_6.3.2 #> [13] R.cache_0.16.0 R.utils_2.12.3 backports_1.5.0 #> [16] DBI_1.2.2 purrr_1.0.2 fansi_1.0.6 #> [19] cli_3.6.2 rlang_1.1.4 R.methodsS3_1.8.2 #> [22] bit64_4.0.5 reprex_2.1.0 remotes_2.5.0 #> [25] withr_3.0.0 cachem_1.0.8 yaml_2.3.8 #> [28] tools_4.3.1 ParallelLogger_3.3.0 tzdb_0.4.0 #> [31] memoise_2.0.1 checkmate_2.3.1 dplyr_1.1.4 #> [34] SqlRender_1.18.1 curl_5.2.1 vctrs_0.6.5 #> [37] R6_2.5.1 lifecycle_1.0.4 pool_1.0.3 #> [40] fs_1.6.4 bit_4.0.5 ResultModelManager_0.5.8 #> [43] pkgconfig_2.0.3 rJava_1.0-11 pillar_1.9.0 #> [46] later_1.3.2 glue_1.7.0 Rcpp_1.0.12 #> [49] xfun_0.43 tibble_3.2.1 tidyselect_1.2.1 #> [52] rstudioapi_0.16.0 knitr_1.45 htmltools_0.5.8.1 #> [55] rmarkdown_2.26 readr_2.1.5 compiler_4.3.1
Created on 2024-06-18 with reprex v2.1.0
references in the code:
Connection handler is created here: https://github.com/OHDSI/CohortDiagnostics/blob/03c40ab06832a329f2c904fbd686a0596ea9af6f/inst/shiny/DiagnosticsExplorer/global.R#L82
getTableNames is called here: https://github.com/OHDSI/OhdsiShinyModules/blob/42f5bb42c731fd9ff1a9c96bb68b624fd357ba78/R/cohort-diagnostics-main.R#L27C3-L29C16
The error comes from the line above which is why I thought the issue should be in OhdsiShinyModules.
The text was updated successfully, but these errors were encountered:
No branches or pull requests
I ran cohort diagnostics and have a folder with csv files.
I created the merged sqlite zip file.
Then I ran
CohortDiagnostics::launchDiagnosticsExplorer(here::here("MergedCohortDiagnosticsData.sqlite"))
and get the following error.
I'm using the latest release of the Hades packages.
To reproduce this error I created a minimal reprex. These are the lines in the shiny module that cause the error.
Created on 2024-06-18 with reprex v2.1.0
references in the code:
Connection handler is created here:
https://github.com/OHDSI/CohortDiagnostics/blob/03c40ab06832a329f2c904fbd686a0596ea9af6f/inst/shiny/DiagnosticsExplorer/global.R#L82
getTableNames is called here:
https://github.com/OHDSI/OhdsiShinyModules/blob/42f5bb42c731fd9ff1a9c96bb68b624fd357ba78/R/cohort-diagnostics-main.R#L27C3-L29C16
The error comes from the line above which is why I thought the issue should be in OhdsiShinyModules.
The text was updated successfully, but these errors were encountered: