Fix R-check notes

[ginberg]

── R CMD build ─────────────────────────────────────────────────────────────────

• checking for file 'D:\a\CohortDiagnostics\CohortDiagnostics/DESCRIPTION' ... OK
• preparing 'CohortDiagnostics':
• checking DESCRIPTION meta-information ... OK
• installing the package to build vignettes
• creating vignettes ... OK
• compacting vignettes and other PDF files
  compacted 'CreatingAStudyPackage.pdf' from 258Kb to 50Kb
  compacted 'DatabaseModeInDiagnosticsExplorer.pdf' from 207Kb to 34Kb
  compacted 'RunningCohortDiagnostics.pdf' from 219Kb to 46Kb
  compacted 'ViewingResultsUsingDiagnosticsExplorer.pdf' from 364Kb to 84Kb
  compacted 'WhatIsCohortDiagnostics.pdf' from 126Kb to 17Kb
• checking for LF line-endings in source and make files and shell scripts
• checking for empty or unneeded directories
• building 'CohortDiagnostics_3.4.1.tar.gz'

── R CMD check ─────────────────────────────────────────────────────────────────

• using log directory 'D:/a/CohortDiagnostics/CohortDiagnostics/check/CohortDiagnostics.Rcheck'
• using R version 4.4.0 (2024-04-24 ucrt)
• using platform: x86_64-w64-mingw32
• R was compiled by
  gcc.exe (GCC) 13.2.0
  GNU Fortran (GCC) 13.2.0
• running under: Windows Server 2022 x64 (build 20348)
• using session charset: UTF-8
• using options '--no-manual --as-cran'
• checking for file 'CohortDiagnostics/DESCRIPTION' ... OK
• checking extension type ... Package
• this is package 'CohortDiagnostics' version '3.4.1'
• package encoding: UTF-8
• checking package namespace information ... OK
• checking package dependencies ... NOTE
  Imports includes 33 non-default packages.
  Importing from so many packages makes the package vulnerable to any of
  them becoming unavailable. Move as many as possible to Suggests and
  use conditionally.
• 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 whether package 'CohortDiagnostics' can be installed ... NOTE
  Found the following notes/warnings:
  Non-staged installation was used
  See 'D:/a/CohortDiagnostics/CohortDiagnostics/check/CohortDiagnostics.Rcheck/00install.out' for details.
• checking installed package size ... OK
• checking package directory ... OK
• checking for future file timestamps ... OK
• checking 'build' 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 code 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 ... NOTE
  Namespaces in Imports field not imported from:
  'Eunomia' 'OhdsiShinyModules' 'ROhdsiWebApi' 'RSQLite' 'knitr'
  'testthat' 'withr'
  All declared Imports should be used.
  Unexported object imported by a ':::' call: 'FeatureExtraction:::createEmptyCovariateData'
  See the note in ?::: about the use of this operator.
• checking S3 generic/method consistency ... OK
• checking replacement functions ... OK
• checking foreign function calls ... OK
• checking R code for possible problems ... [11s] NOTE
  getCohortCharacteristics: warning in getDbCovariateData(connection =
  connection, oracleTempSchema = tempEmulationSchema, cdmDatabaseSchema
  = cdmDatabaseSchema, cohortDatabaseSchema = cohortDatabaseSchema,
  cdmVersion = cdmVersion, cohortTable = cohortTable, cohortId =
  cohortIds, covariateSettings = covariateSettings, aggregated = TRUE):
  partial argument match of 'cohortId' to 'cohortIds'
  executeCohortCharacterization: no visible binding for global variable
  'cohortId'
  getCohortCharacteristics: no visible binding for global variable
  'sumValue'
  getCohortCharacteristics: no visible binding for global variable 'p'
  getCohortCharacteristics: no visible binding for global variable
  'timeId'
  getCohortCharacteristics: no visible global function definition for
  'if_else'
  getCohortCharacteristics: no visible binding for global variable
  'averageValue'
  getCohortCharacteristics: no visible binding for global variable
  'standardDeviation'
  getCohortCharacteristics: no visible binding for global variable
  'cohortDefinitionId'
  getDbCovariateData : hasData: no visible global function definition for
  'count'
  getDbCovariateData : hasData: no visible global function definition for
  'pull'
  getDbDefaultCovariateData: no visible global function definition for
  'createEmptyCovariateData'
  getDbDefaultCovariateData: no visible binding for global variable
  'cohortId'
  Undefined global functions or variables:
  averageValue cohortDefinitionId cohortId count
  createEmptyCovariateData if_else p pull standardDeviation sumValue
  timeId
• checking Rd files ... OK
• checking Rd metadata ... OK
• checking Rd line widths ... NOTE
  Rd file 'executeDiagnosticsCdm.Rd':
  \examples lines wider than 100 characters:
  cohortDefinitionSet <- CDMConnector::readCohortSet(system.file("cohorts", package = "CohortDiagnostics"))
  These lines will be truncated in the PDF manual.
• 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 sizes of PDF files under 'inst/doc' ... OK
• checking installed files from 'inst/doc' ... OK
• checking files in 'vignettes' ... OK
• checking examples ... OK
• checking for unstated dependencies in 'tests' ... OK
• checking tests ...
  Running 'testOracle.R'
  Running 'testPostgres.R'
  Running 'testRedshift.R'
  Running 'testSqlServer.R'
  Running 'testSqlite.R' [20m]
  [20m] OK
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [15s] OK
• checking for non-standard things in the check directory ... OK
• checking for detritus in the temp directory ... OK
• DONE
  Status: 5 NOTEs
  See
  'D:/a/CohortDiagnostics/CohortDiagnostics/check/CohortDiagnostics.Rcheck/00check.log'
  for details.