* using log directory ‘/srv/hornik/tmp/CRAN/ResultModelManager.Rcheck’
* using R Under development (unstable) (2024-07-10 r86888)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 18.1.8 (1+b1)
    Debian flang-new version 18.1.8 (1+b1)
* running under: Debian GNU/Linux trixie/sid
* using session charset: UTF-8
* checking for file ‘ResultModelManager/DESCRIPTION’ ... OK
* this is package ‘ResultModelManager’ version ‘0.5.8’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [3s/4s] NOTE
Maintainer: ‘Jamie Gilbert <gilbert@ohdsi.org>’

New submission

Possibly misspelled words in DESCRIPTION:
  OHDSI (6:59)

Found the following (possibly) invalid URLs:
  URL: https://codecov.io/github/OHDSI/ResultModelManager?branch=main (moved to https://app.codecov.io/github/OHDSI/ResultModelManager?branch=main)
    From: README.md
    Status: 301
    Message: Moved Permanently
For content that is 'Moved Permanently', please change http to https,
add trailing slashes, or replace the old by the new URL.
* 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 ‘ResultModelManager’ can be installed ... [5s/5s] OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking ‘build’ directory ... WARNING
Output(s) listed in 'build/vignette.rds' but not in package:
  ‘inst/doc/UsingAnExportManager.pdf’
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... NOTE
Non-standard file/directory found at top level:
  ‘sql’
* 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 ... [1s/1s] OK
* checking whether the package can be loaded with stated dependencies ... [1s/1s] OK
* checking whether the package can be unloaded cleanly ... [1s/1s] OK
* checking whether the namespace can be loaded with stated dependencies ... [1s/1s] OK
* checking whether the namespace can be unloaded cleanly ... [1s/1s] OK
* checking loading without being on the library search path ... [1s/1s] OK
* checking use of S3 registration ... 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 ... [6s/5s] NOTE
Found if() conditions comparing class() to string:
File ‘ResultModelManager/R/DataModel.R’: if (class(pkValuesInDb[[columnName]]) == "integer") ...
File ‘ResultModelManager/R/DataModel.R’: if (class(chunk[[columnName]]) == "integer") ...
File ‘ResultModelManager/R/DataModel.R’: if (class(pkValuesInDb[[columnName]]) == "character") ...
Use inherits() (or maybe is()) instead.
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Undocumented arguments in Rd file 'formatChunk.Rd'
  ‘pkValuesInDb’ ‘chunk’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 ... [1s/1s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [6s/6s] OK
  Running ‘testthat.R’ [6s/6s]
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... WARNING
Failed to locate ‘weave’ output file ‘UsingAnExportManager.pdf’ or ‘UsingAnExportManager.html’ for vignette with name ‘UsingAnExportManager’ and engine ‘knitr::rmarkdown’. The following files exist in working directory ‘/srv/hornik/tmp/CRAN/ResultModelManager.Rcheck/00_pkg_src/ResultModelManager/inst/doc’: ‘CreatingMigrations.R’ (1264 bytes), ‘CreatingMigrations.Rmd’ (6670 bytes), ‘CreatingMigrations.pdf’ (254883 bytes), ‘PackageDesign.R’ (1647 bytes), ‘PackageDesign.Rmd’ (10645 bytes), ‘PackageDesign.pdf’ (234406 bytes), ‘UploadFunctionality.R’ (1407 bytes), ‘UploadFunctionality.Rmd’ (4379 bytes), ‘UploadFunctionality.pdf’ (210148 bytes), ‘UsingAnExportManager.R’ (3405 bytes), ‘UsingAnExportManager.Rmd’ (5436 bytes), ‘UsingAnexportManager.pdf’ (221609 bytes), ‘UsingConnectionHandlers.R’ (826 bytes), ‘UsingConnectionHandlers.Rmd’ (2197 bytes), ‘UsingConnectionHandlers.pdf’ (186791 bytes), ‘UsingQueryNamespaces.R’ (2030 bytes), ‘UsingQueryNamespaces.Rmd’ (3341 bytes), ‘UsingQueryNamespaces.pdf’ (212347 bytes)
Package vignette without corresponding single PDF/HTML:
  ‘UsingAnExportManager.Rmd’
* checking re-building of vignette outputs ... [15s/15s] OK
* checking PDF version of manual ... [3s/3s] OK
* checking HTML version of manual ... [1s/1s] OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 3 WARNINGs, 3 NOTEs