- using R Under development (unstable) (2024-04-29 r86495)
- using platform: x86_64-pc-linux-gnu
- R was compiled by
gcc-13 (Debian 13.2.0-23) 13.2.0
GNU Fortran (Debian 13.2.0-23) 13.2.0
- running under: Debian GNU/Linux trixie/sid
- using session charset: UTF-8
- checking for file ‘CohortCharacteristics/DESCRIPTION’ ... OK
- checking extension type ... Package
- this is package ‘CohortCharacteristics’ version ‘0.1.0’
- 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 serialization versions ... OK
- checking whether package ‘CohortCharacteristics’ can be installed ... OK
See the install log for details.
- 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 ... [1s/2s] 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/2s] 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 ... [14s/24s] OK
- checking Rd files ... [0s/1s] 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 ... 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 ... [1s/2s] OK
- checking for unstated dependencies in ‘tests’ ... OK
- checking tests ... [70s/107s] ERROR
Running ‘spelling.R’ [0s/1s]
Running ‘testthat.R’ [69s/106s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
>
> library(testthat)
> library(CohortCharacteristics)
>
> test_check("CohortCharacteristics")
Starting 2 test processes
[ FAIL 5 | WARN 0 | SKIP 13 | PASS 5 ]
══ Skipped tests (13) ══════════════════════════════════════════════════════════
• On CRAN (12): 'test-plotCharacteristics.R:2:3',
'test-plotLargeScaleCharacteristics.R:3:3', 'test-plotSummarised.R:2:3',
'test-plotSummarised.R:82:3', 'test-plotSummarised.R:179:3',
'test-plotSummarised.R:263:3', 'test-summariseCohortIntersect.R:2:3',
'test-summariseCohortOverlap.R:2:3', 'test-summariseCohortTiming.R:2:3',
'test-summariseLargeScaleCharacteristics.R:2:3',
'test-tableSummarised.R:2:3', 'test-tableSummarised.R:114:3'
• empty test (1): 'test-tableSummarised.R:235:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-summariseCharacteristics.R:76:3'): test summariseCharacteristics ──
Expected `... <- NULL` to run without any errors.
i Actually got a <vctrs_error_subscript_oob> with text:
Can't select columns that don't exist.
x Column `result_type` doesn't exist.
── Error ('test-summariseCharacteristics.R:88:3'): test summariseCharacteristics ──
Error in `eval(code, test_env)`: object 'result' not found
Backtrace:
▆
1. ├─testthat::expect_true(inherits(result, "summarised_result")) at test-summariseCharacteristics.R:88:3
2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─base::inherits(result, "summarised_result")
── Failure ('test-summariseCharacteristics.R:291:3'): test empty cohort ────────
Expected `summariseCharacteristics(...)` to run without any errors.
i Actually got a <vctrs_error_subscript_oob> with text:
Can't select columns that don't exist.
x Column `result_type` doesn't exist.
── Failure ('test-summariseCharacteristics.R:301:3'): test empty cohort ────────
Expected `... <- NULL` to run without any errors.
i Actually got a <vctrs_error_subscript_oob> with text:
Can't select columns that don't exist.
x Column `result_type` doesn't exist.
── Failure ('test-summariseCharacteristics.R:308:3'): test empty cohort ────────
Expected `... <- NULL` to run without any errors.
i Actually got a <vctrs_error_subscript_oob> with text:
Can't select columns that don't exist.
x Column `result_type` doesn't exist.
[ FAIL 5 | WARN 0 | SKIP 13 | PASS 5 ]
Error: Test failures
Execution halted
- checking for unstated dependencies in vignettes ... OK
- checking package vignettes ... OK
- checking re-building of vignette outputs ... [35s/56s] ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘a06_summarisePatientCharacteristics.Rmd’ using rmarkdown
Quitting from lines at lines 27-109 [unnamed-chunk-2] (a06_summarisePatientCharacteristics.Rmd)
Error: processing vignette 'a06_summarisePatientCharacteristics.Rmd' failed with diagnostics:
Can't select columns that don't exist.
✖ Column `result_type` doesn't exist.
--- failed re-building ‘a06_summarisePatientCharacteristics.Rmd’
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
--- re-building ‘a08_summariseCohortOverlap.Rmd’ using rmarkdown
--- finished re-building ‘a08_summariseCohortOverlap.Rmd’
SUMMARY: processing the following file failed:
‘a06_summarisePatientCharacteristics.Rmd’
Error: Vignette re-building failed.
Execution halted
- checking PDF version of manual ... [5s/11s] OK
- checking HTML version of manual ... [1s/2s] OK
- checking for non-standard things in the check directory ... OK
- DONE
Status: 2 ERRORs