- using R Under development (unstable) (2025-11-24 r89059)
- using platform: aarch64-apple-darwin23
- R was compiled by
Apple clang version 17.0.0 (clang-1700.3.19.1)
GNU Fortran (GCC) 14.2.0
- running under: macOS Sequoia 15.7.1
- using session charset: UTF-8
- checking for file ‘MetaComp/DESCRIPTION’ ... OK
- this is package ‘MetaComp’ version ‘1.1.2’
- 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 ‘MetaComp’ can be installed ... [1s/1s] OK
See the install log for details.
- checking installed package size ... OK
- checking package 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 ... [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 ... [1s/1s] 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 LazyData ... INFO
'LazyData' is specified without a 'data' directory
- checking examples ... [1s/1s] OK
- checking for unstated dependencies in ‘tests’ ... OK
- checking tests ... [4s/4s] ERROR
Running ‘testthat.R’ [4s/4s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(MetaComp)
>
> test_check("MetaComp")
[1] "gottcha"
[1] "kraken"
Saving _problems/test_load_metaphlan_assignment-14.R
Saving _problems/test_pipeline-37.R
Saving _problems/test_plot_bwa_assignment-31.R
Saving _problems/test_plot_diamond_assignment-31.R
Saving _problems/test_plot_gottcha_assignment-31.R
Saving _problems/test_plot_kraken_assignment-31.R
Saving _problems/test_plot_merged_assignment_b-80.R
Saving _problems/test_plot_merged_assignment_d-80.R
Saving _problems/test_plot_merged_assignment_g-78.R
Saving _problems/test_plot_merged_assignment_g2-78.R
Saving _problems/test_plot_merged_assignment_k-80.R
Saving _problems/test_plot_merged_assignment_m-80.R
Saving _problems/test_plot_merged_assignment_p-81.R
Saving _problems/test_plot_metaphlan_assignment-31.R
Saving _problems/test_plot_pangia_assignment-31.R
[ FAIL 15 | WARN 18 | SKIP 0 | PASS 108 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_load_metaphlan_assignment.R:14:1'): (code run outside of `test_that()`) ──
Error in `matches("LEVEL")`: could not find function "matches"
Backtrace:
▆
1. └─testthat::expect_that(colnames(dat)[1], matches("LEVEL")) at test_load_metaphlan_assignment.R:14:1
── Error ('test_pipeline.R:37:1'): (code run outside of `test_that()`) ─────────
Error in `is_true()`: could not find function "is_true"
Backtrace:
▆
1. └─testthat::expect_that(...) at test_pipeline.R:37:1
── Error ('test_plot_bwa_assignment.R:31:1'): (code run outside of `test_that()`) ──
Error in `is_true()`: could not find function "is_true"
Backtrace:
▆
1. └─testthat::expect_that(file.exists(png_name), is_true()) at test_plot_bwa_assignment.R:31:1
── Error ('test_plot_diamond_assignment.R:31:1'): (code run outside of `test_that()`) ──
Error in `is_true()`: could not find function "is_true"
Backtrace:
▆
1. └─testthat::expect_that(file.exists(png_name), is_true()) at test_plot_diamond_assignment.R:31:1
── Error ('test_plot_gottcha_assignment.R:31:1'): (code run outside of `test_that()`) ──
Error in `is_true()`: could not find function "is_true"
Backtrace:
▆
1. └─testthat::expect_that(file.exists(png_name), is_true()) at test_plot_gottcha_assignment.R:31:1
── Error ('test_plot_kraken_assignment.R:31:1'): (code run outside of `test_that()`) ──
Error in `is_true()`: could not find function "is_true"
Backtrace:
▆
1. └─testthat::expect_that(file.exists(png_name), is_true()) at test_plot_kraken_assignment.R:31:1
── Error ('test_plot_merged_assignment_b.R:80:1'): (code run outside of `test_that()`) ──
Error in `is_true()`: could not find function "is_true"
Backtrace:
▆
1. └─testthat::expect_that(...) at test_plot_merged_assignment_b.R:80:1
── Error ('test_plot_merged_assignment_d.R:80:1'): (code run outside of `test_that()`) ──
Error in `is_true()`: could not find function "is_true"
Backtrace:
▆
1. └─testthat::expect_that(...) at test_plot_merged_assignment_d.R:80:1
── Error ('test_plot_merged_assignment_g.R:78:1'): (code run outside of `test_that()`) ──
Error in `is_true()`: could not find function "is_true"
Backtrace:
▆
1. └─testthat::expect_that(...) at test_plot_merged_assignment_g.R:78:1
── Error ('test_plot_merged_assignment_g2.R:78:1'): (code run outside of `test_that()`) ──
Error in `is_true()`: could not find function "is_true"
Backtrace:
▆
1. └─testthat::expect_that(...) at test_plot_merged_assignment_g2.R:78:1
── Error ('test_plot_merged_assignment_k.R:80:1'): (code run outside of `test_that()`) ──
Error in `is_true()`: could not find function "is_true"
Backtrace:
▆
1. └─testthat::expect_that(...) at test_plot_merged_assignment_k.R:80:1
── Error ('test_plot_merged_assignment_m.R:80:1'): (code run outside of `test_that()`) ──
Error in `is_true()`: could not find function "is_true"
Backtrace:
▆
1. └─testthat::expect_that(...) at test_plot_merged_assignment_m.R:80:1
── Error ('test_plot_merged_assignment_p.R:81:1'): (code run outside of `test_that()`) ──
Error in `is_true()`: could not find function "is_true"
Backtrace:
▆
1. └─testthat::expect_that(...) at test_plot_merged_assignment_p.R:81:1
── Error ('test_plot_metaphlan_assignment.R:31:1'): (code run outside of `test_that()`) ──
Error in `is_true()`: could not find function "is_true"
Backtrace:
▆
1. └─testthat::expect_that(file.exists(png_name), is_true()) at test_plot_metaphlan_assignment.R:31:1
── Error ('test_plot_pangia_assignment.R:31:1'): (code run outside of `test_that()`) ──
Error in `is_true()`: could not find function "is_true"
Backtrace:
▆
1. └─testthat::expect_that(file.exists(png_name), is_true()) at test_plot_pangia_assignment.R:31:1
[ FAIL 15 | WARN 18 | SKIP 0 | PASS 108 ]
Error:
! Test failures.
Execution halted
- checking PDF version of manual ... [1s/1s] OK
- DONE
Status: 1 ERROR
- using check arguments '--no-clean-on-error '