Last updated on 2026-03-08 05:50:18 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 4.0.2 | 10.65 | 318.49 | 329.14 | OK | |
| r-devel-linux-x86_64-debian-gcc | 4.0.2 | 9.22 | 221.14 | 230.36 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 4.0.2 | 19.00 | 486.07 | 505.07 | OK | |
| r-devel-linux-x86_64-fedora-gcc | 4.0.2 | 18.00 | 492.01 | 510.01 | OK | |
| r-devel-macos-arm64 | 4.0.2 | 3.00 | 86.00 | 89.00 | OK | |
| r-devel-windows-x86_64 | 4.0.2 | 14.00 | 304.00 | 318.00 | OK | |
| r-patched-linux-x86_64 | 4.0.2 | 10.61 | 310.47 | 321.08 | OK | |
| r-release-linux-x86_64 | 4.0.2 | 9.63 | 304.54 | 314.17 | OK | |
| r-release-macos-arm64 | 4.0.2 | 3.00 | 102.00 | 105.00 | OK | |
| r-release-macos-x86_64 | 4.0.2 | 9.00 | 680.00 | 689.00 | OK | |
| r-release-windows-x86_64 | 4.0.2 | 14.00 | 305.00 | 319.00 | OK | |
| r-oldrel-macos-arm64 | 4.0.2 | 3.00 | 104.00 | 107.00 | OK | |
| r-oldrel-macos-x86_64 | 4.0.2 | 9.00 | 534.00 | 543.00 | OK | |
| r-oldrel-windows-x86_64 | 4.0.2 | 20.00 | 382.00 | 402.00 | OK |
Version: 4.0.2
Check: tests
Result: ERROR
Running ‘testthat.R’ [122s/158s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat);
> library(ApplyPolygenicScore);
>
> test_check('ApplyPolygenicScore');
Input data passed validation
Input data passed validation
Saving _problems/test-pgs-statistics-371.R
Skipping test for >12 PGS columns as 'scales' package is available and will be used.
Saving _problems/test-pgs-statistics-559.R
Saving _problems/test-plotting-136.R
Saving _problems/test-plotting-431.R
Saving _problems/test-plotting-741.R
[1] "springgreen3"
[1] "darkturquoise"
[1] "springgreen3"
[1] "darkturquoise"
Saving _problems/test-plotting-995.R
[ FAIL 6 | WARN 87 | SKIP 0 | PASS 625 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-pgs-statistics.R:363:9'): analyze.pgs.binary.predictiveness validates binary phenotype columns ──
Error in `basename(x)`: a character vector argument expected
Backtrace:
▆
1. ├─testthat::expect_warning(...) at test-pgs-statistics.R:363:9
2. │ └─testthat:::expect_condition_matching_(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. └─ApplyPolygenicScore::analyze.pgs.binary.predictiveness(...)
8. └─BoutrosLab.plotting.general::create.multipanelplot(...)
9. └─BoutrosLab.plotting.general:::get.legend.height(...)
10. └─tools::file_ext(filename)
11. ├─base::ifelse(...)
12. ├─base::grepl("^(.*[^.]+.*)[.]([[:alnum:]]+)$", basename(x))
13. │ └─base::is.factor(x)
14. └─base::basename(x)
── Error ('test-pgs-statistics.R:552:9'): analyze.pgs.binary.predictiveness correctly formats outputs ──
Error in `basename(x)`: a character vector argument expected
Backtrace:
▆
1. └─ApplyPolygenicScore::analyze.pgs.binary.predictiveness(...) at test-pgs-statistics.R:552:9
2. └─BoutrosLab.plotting.general::create.multipanelplot(...)
3. └─BoutrosLab.plotting.general:::get.legend.height(...)
4. └─tools::file_ext(filename)
5. ├─base::ifelse(...)
6. ├─base::grepl("^(.*[^.]+.*)[.]([[:alnum:]]+)$", basename(x))
7. │ └─base::is.factor(x)
8. └─base::basename(x)
── Error ('test-plotting.R:132:9'): create.pgs.density.plot runs with no error with basic inputs ──
Error in `basename(x)`: a character vector argument expected
Backtrace:
▆
1. └─ApplyPolygenicScore::create.pgs.density.plot(...) at test-plotting.R:132:9
2. └─BoutrosLab.plotting.general::create.multipanelplot(...)
3. └─BoutrosLab.plotting.general:::get.legend.height(...)
4. └─tools::file_ext(filename)
5. ├─base::ifelse(...)
6. ├─base::grepl("^(.*[^.]+.*)[.]([[:alnum:]]+)$", basename(x))
7. │ └─base::is.factor(x)
8. └─base::basename(x)
── Error ('test-plotting.R:426:9'): create.pgs.with.continuous.phenotype.plot runs with no error with basic inputs ──
Error in `basename(x)`: a character vector argument expected
Backtrace:
▆
1. └─ApplyPolygenicScore::create.pgs.with.continuous.phenotype.plot(...) at test-plotting.R:426:9
2. └─BoutrosLab.plotting.general::create.multipanelplot(...)
3. └─BoutrosLab.plotting.general:::get.legend.height(...)
4. └─tools::file_ext(filename)
5. ├─base::ifelse(...)
6. ├─base::grepl("^(.*[^.]+.*)[.]([[:alnum:]]+)$", basename(x))
7. │ └─base::is.factor(x)
8. └─base::basename(x)
── Error ('test-plotting.R:737:9'): create.pgs.rank.plot runs with no error with basic inputs ──
Error in `basename(x)`: a character vector argument expected
Backtrace:
▆
1. └─ApplyPolygenicScore::create.pgs.rank.plot(...) at test-plotting.R:737:9
2. └─BoutrosLab.plotting.general::create.multipanelplot(...)
3. └─BoutrosLab.plotting.general:::get.legend.height(...)
4. └─tools::file_ext(filename)
5. ├─base::ifelse(...)
6. ├─base::grepl("^(.*[^.]+.*)[.]([[:alnum:]]+)$", basename(x))
7. │ └─base::is.factor(x)
8. └─base::basename(x)
── Error ('test-plotting.R:991:9'): create.pgs.boxplot runs with no error with basic inputs ──
Error in `basename(x)`: a character vector argument expected
Backtrace:
▆
1. └─ApplyPolygenicScore::create.pgs.boxplot(...) at test-plotting.R:991:9
2. └─BoutrosLab.plotting.general::create.multipanelplot(...)
3. └─BoutrosLab.plotting.general:::get.legend.height(...)
4. └─tools::file_ext(filename)
5. ├─base::ifelse(...)
6. ├─base::grepl("^(.*[^.]+.*)[.]([[:alnum:]]+)$", basename(x))
7. │ └─base::is.factor(x)
8. └─base::basename(x)
[ FAIL 6 | WARN 87 | SKIP 0 | PASS 625 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc