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"object 'connectionString' not found" when using argument(s)

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#1

Hi team,
when I ran CodeToRun.R for estimation R package using Databricks database, an error occurred:
ad 1 returns error: “object ‘connectionString’ not found” when using argument(s): list(args = list(connectionDetails = list(dbms = “spark”, extraSettings = NULL, oracleDriver = “thin”, pathToDriver = “c:/temp/jdbcDrivers”, user = function () nrlang::eval_tidy(userExpression). But the ‘connectionString’ has been defined at the beginning. Can someone help me out? Thanks
Best,
Gongliang

#2

Which version of DatabaseConnector are you running?

#3

5.02

#4

I’m pretty sure this problem is solved in the latest version of DatabaseConnector (6.1.0). Could you give that a try?

#5

Hi Dr. Schuemie,
Thank you for your infromation. I updated Databaseconnector, remotes::install_github(“OHDSI/DatabaseConnector”, version = ‘6.1.0’), but another problem raised (see blow). Can you help me fix it? I do appreciate your time and support.

execute(connectionDetails = connectionDetails,

  •     cdmDatabaseSchema = cdmDatabaseSchema,

  •     cohortDatabaseSchema = cohortDatabaseSchema,

  •     cohortTable = cohortTable,

  •     outputFolder = outputFolder,

  •     databaseId = databaseId,

  •     databaseName = databaseName,

  •     databaseDescription = databaseDescription,

  •     verifyDependencies = TRUE,

  •     createCohorts = TRUE,

  •     synthesizePositiveControls = TRUE,

  •     runAnalyses = TRUE,

  •     packageResults = TRUE,

  •     maxCores = maxCores)

Checking whether correct package versions are installed
Error in x$Priority : $ operator is invalid for atomic vectors
In addition: Warning message:
In FUN(X[[i]], …) :
DESCRIPTION file of package ‘DatabaseConnector’ is missing or broken

#6

Error in verifyDependencies() :
Mismatch between required and installed package versions. Did you forget to run renv::restore()?

  • Package rlang version 1.1.0 should be 1.0.1
  • Package glue version 1.6.2 should be 1.6.1
  • Package cli version 3.6.1 should be 3.1.1
  • Package crayon version 1.5.2 should be 1.4.2
  • Package fansi version 1.0.4 should be 1.0.2
  • Package lifecycle version 1.0.3 should be 1.0.1
  • Package magrittr version 2.0.3 should be 2.0.2
  • Package utf8 version 1.2.3 should be 1.2.2
  • Package vctrs version 0.6.1 should be 0.3.8
  • Package bit version 4.0.5 should be 4.0.4
  • Package cpp11 version 0.4.3 should be 0.4.2
  • Package fastmap version 1.1.1 should be 1.1.0
  • Package hms version 1.1.3 should be 1.1.1
  • Package pillar version 1.9.0 should be 1.6.5
  • Package purrr version 1.0.1 should be 0.3.4
  • Package cachem version 1.0.7 should be 1.0.6
  • Package colorspace version 2.1.0 should be 2.0.2
  • Package generics version 0.1.3 should be 0.1.2
  • Package Rcpp version 1.0.10 should be 1.0.8
  • Packag
#7

when I run renv::restore()
get:
Error: target file ‘C:/Users/gxz108/AppData/Local/R/cache/R/renv/library/estimation_study_1_export-2ca07953/R-4.2/x86_64-w64-mingw32/DatabaseConnector’ already exists

#8

Could you try

remove.packages("DatabaseConnector")
renv::purge("DatabaseConnector")

Before running renv::restore()?

#9

Thanks.

t