- using R version 4.3.3 (2024-02-29)
- using platform: aarch64-apple-darwin20 (64-bit)
- R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
- running under: macOS Ventura 13.4
- using session charset: UTF-8
- checking for file ‘OhdsiReportGenerator/DESCRIPTION’ ... OK
- checking extension type ... Package
- this is package ‘OhdsiReportGenerator’ version ‘1.0.1’
- package encoding: UTF-8
- 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 ‘OhdsiReportGenerator’ can be installed ... [2s/2s] OK
See the install log for details.
- checking installed package size ... OK
- checking package directory ... 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 R files for non-ASCII characters ... OK
- checking R files for syntax errors ... OK
- checking whether the package can be loaded ... [0s/0s] OK
- checking whether the package can be loaded with stated dependencies ... [0s/0s] OK
- checking whether the package can be unloaded cleanly ... [0s/0s] OK
- checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK
- checking whether the namespace can be unloaded cleanly ... [0s/0s] OK
- checking loading without being on the library search path ... [0s/0s] 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 ... [2s/2s] OK
- checking Rd files ... [0s/0s] OK
- checking Rd metadata ... OK
- 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 installed files from ‘inst/doc’ ... OK
- checking files in ‘vignettes’ ... OK
- checking examples ... [4s/4s] ERROR
Running examples in ‘OhdsiReportGenerator-Ex.R’ failed
The error most likely occurred in:
> ### Name: kableDark
> ### Title: output a nicely formatted html table
> ### Aliases: kableDark
>
> ### ** Examples
>
> kableDark(
+ data = data.frame(a=1,b=4),
+ caption = 'A made up table to demonstrate this function',
+ position = 'h'
+ )
Closing database connection
Closing database connection
Closing database connection
Closing database connection
Closing database connection
Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) :
there is no package called ‘systemfonts’
Calls: kableDark ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Closing database connection
Closing database connection
Closing database connection
Closing database connection
- checking for unstated dependencies in ‘tests’ ... OK
- checking tests ... [6s/5s] ERROR
Running ‘testthat.R’ [6s/5s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> test_check("OhdsiReportGenerator")
Loading required package: OhdsiReportGenerator
Connecting using SQLite driver
[ FAIL 2 | WARN 1 | SKIP 2 | PASS 384 ]
══ Skipped tests (2) ═══════════════════════════════════════════════════════════
• empty test (1): 'test-Helpers.R:89:1'
• skip prediction report due to odd linux error (1):
'test-PredictionReport.R:5:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-Generate.R:10:3'): generatePresentationMultiple ────────────────
Error in `find_quarto()`: Quarto command-line tools path not found!
Please make sure you have installed and added Quarto to your PATH or set the
QUARTO_PATH environment variable.
Backtrace:
▆
1. └─OhdsiReportGenerator::generatePresentationMultiple(...) at test-Generate.R:10:3
2. └─quarto::quarto_render(...)
3. └─quarto:::find_quarto()
4. └─cli::cli_abort(quarto_not_found_msg)
5. └─rlang::abort(...)
── Error ('test-Helpers.R:105:1'): kableDark ───────────────────────────────────
<packageNotFoundError/error/condition>
Error in `loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])`: there is no package called 'systemfonts'
Backtrace:
▆
1. ├─OhdsiReportGenerator::kableDark(...) at test-Helpers.R:105:1
2. │ └─... %>% ...
3. └─base::loadNamespace(x)
4. ├─base::namespaceImportFrom(...)
5. │ └─base::asNamespace(ns)
6. └─base::loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
7. ├─base::namespaceImportFrom(...)
8. │ └─base::asNamespace(ns)
9. └─base::loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
10. └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
11. └─base (local) withOneRestart(expr, restarts[[1L]])
12. └─base (local) doWithOneRestart(return(expr), restart)
[ FAIL 2 | WARN 1 | SKIP 2 | PASS 384 ]
Error: Test failures
Execution halted
Closing database connection
- checking for unstated dependencies in vignettes ... OK
- checking package vignettes in ‘inst/doc’ ... OK
- checking re-building of vignette outputs ... [10s/39s] OK
- checking PDF version of manual ... [5s/5s] OK
- DONE
Status: 2 ERRORs
- using check arguments '--no-clean-on-error '