Last updated on 2026-03-05 15:53:53 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.0.2 | 9.64 | 180.20 | 189.84 | OK | |
| r-devel-linux-x86_64-debian-gcc | 1.0.2 | 0.25 | 3.26 | 3.51 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 1.0.2 | 18.00 | 165.07 | 183.07 | ERROR | |
| r-devel-linux-x86_64-fedora-gcc | 1.0.2 | 3.32 | ERROR | |||
| r-devel-macos-arm64 | 1.0.2 | 2.00 | 50.00 | 52.00 | OK | |
| r-devel-windows-x86_64 | 1.0.2 | 13.00 | 220.00 | 233.00 | OK | |
| r-patched-linux-x86_64 | 1.0.2 | 9.11 | 167.00 | 176.11 | OK | |
| r-release-linux-x86_64 | 1.0.2 | 8.75 | 168.42 | 177.17 | OK | |
| r-release-macos-arm64 | 1.0.2 | 4.00 | ERROR | |||
| r-release-macos-x86_64 | 1.0.2 | 7.00 | ERROR | |||
| r-release-windows-x86_64 | 1.0.2 | 12.00 | 216.00 | 228.00 | OK | |
| r-oldrel-macos-arm64 | 1.0.2 | 2.00 | 46.00 | 48.00 | ERROR | |
| r-oldrel-macos-x86_64 | 1.0.2 | 6.00 | 148.00 | 154.00 | ERROR | |
| r-oldrel-windows-x86_64 | 1.0.2 | 15.00 | 189.00 | 204.00 | ERROR |
Version: 1.0.2
Check: package dependencies
Result: ERROR
Packages required but not available: 'rtracklayer', 'ggbio'
See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Flavors: r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-gcc
Version: 1.0.2
Check: tests
Result: ERROR
Running ‘testthat.R’ [14s/38s]
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/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
>
> library(testthat)
> library(PopPsiSeqR)
>
> test_check("PopPsiSeqR")
Saving _problems/test-io-6.R
Saving _problems/test-io-8.R
Saving _problems/test-io-17.R
Saving _problems/test-io-22.R
Saving _problems/test-io-32.R
Saving _problems/test-io-33.R
Saving _problems/test-io-35.R
Saving _problems/test-plot-26.R
Saving _problems/test-plot-27.R
[ FAIL 9 | WARN 3 | SKIP 1 | PASS 3 ]
══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• {rtracklayer} is not installed. (1): 'test-frqshft.R:8:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-io.R:6:3'): merged allele frequencies can be loaded ──────────
Expected `frequencies.bg <- import.freqtbl(merged_frequencies.filename)` not to throw any errors.
Actually got a <packageNotFoundError> with message:
there is no package called 'rtracklayer'
── Error ('test-io.R:8:3'): merged allele frequencies can be loaded ────────────
Error in `eval(code, test_env)`: object 'frequencies.bg' not found
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test-io.R:8:3
2. │ └─testthat::quasi_label(enquo(expected), expected.label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─utils::head(frequencies.bg, n = 1)
── Failure ('test-io.R:17:3'): shifted frequencies can be saved ────────────────
Expected `PopPsiSeqR::export.freqshft(shift2save, shift_frequencies.filename)` not to throw any errors.
Actually got a <packageNotFoundError> with message:
there is no package called 'rtracklayer'
── Failure ('test-io.R:22:3'): shifted frequencies can be saved ────────────────
Expected `correct_hashes` to contain all values in `tools::md5sum(shift_frequencies.filename)[[1]]`.
Actual: "e37492c5b6b3396449ec70e2ae27862a", "8f3feb89facba1da64e34533b8a0b618"
Expected: NA
Missing: NA
── Failure ('test-io.R:32:3'): windowed shifts can be loaded ───────────────────
Expected `windowed_shifts.bg <- import.smvshift(windowed_shifts.filename)` not to throw any errors.
Actually got a <packageNotFoundError> with message:
there is no package called 'rtracklayer'
── Failure ('test-io.R:33:3'): windowed shifts can be loaded ───────────────────
Expected `windowed_shifts.bg <- windowed_shifts.bg %>% as.data.frame()` not to throw any errors.
Actually got a <simpleError> with message:
object 'windowed_shifts.bg' not found
── Error ('test-io.R:35:3'): windowed shifts can be loaded ─────────────────────
Error in `eval(code, test_env)`: object 'windowed_shifts.bg' not found
── Failure ('test-plot.R:26:5'): returns a plot ────────────────────────────────
Expected `mock.plot <- windowedFrequencyShift.plotter(mock_data)` not to throw any errors.
Actually got a <packageNotFoundError> with message:
there is no package called 'ggbio'
── Error ('test-plot.R:27:5'): returns a plot ──────────────────────────────────
Error in `eval(code, test_env)`: object 'mock.plot' not found
Backtrace:
▆
1. ├─testthat::expect_true(ggplot2::is.ggplot(mock.plot@ggplot)) at test-plot.R:27:5
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─ggplot2::is.ggplot(mock.plot@ggplot)
5. └─ggplot2::is_ggplot(x)
6. └─S7::S7_inherits(x, class_ggplot)
[ FAIL 9 | WARN 3 | SKIP 1 | PASS 3 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 1.0.2
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘PopPsiSeq_and_Helpers.Rmd’ using rmarkdown
Quitting from PopPsiSeq_and_Helpers.Rmd:25-36 [setup]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlib_error_package_not_found>
Error in `load_imports()`:
! The packages "rtracklayer" and "ggbio" are required.
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'PopPsiSeq_and_Helpers.Rmd' failed with diagnostics:
The packages "rtracklayer" and "ggbio" are required.
--- failed re-building ‘PopPsiSeq_and_Helpers.Rmd’
SUMMARY: processing the following file failed:
‘PopPsiSeq_and_Helpers.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 1.0.2
Check: package dependencies
Result: ERROR
Package required but not available: ‘ggbio’
See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Flavors: r-release-macos-arm64, r-release-macos-x86_64
Version: 1.0.2
Check: tests
Result: ERROR
Running ‘testthat.R’ [7s/7s]
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/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
>
> library(testthat)
> library(PopPsiSeqR)
>
> test_check("PopPsiSeqR")
Saving _problems/test-plot-26.R
Saving _problems/test-plot-27.R
[ FAIL 2 | WARN 3 | SKIP 0 | PASS 11 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-plot.R:26:5'): returns a plot ────────────────────────────────
Expected `mock.plot <- windowedFrequencyShift.plotter(mock_data)` not to throw any errors.
Actually got a <simpleError> with message:
invalid class "GGbio" object: invalid object for slot "ggplot" in class "GGbio": got class "ggplot2::ggplot", should be or extend class "gg_OR_NULL"
── Error ('test-plot.R:27:5'): returns a plot ──────────────────────────────────
Error in `eval(code, test_env)`: object 'mock.plot' not found
Backtrace:
▆
1. ├─testthat::expect_true(ggplot2::is.ggplot(mock.plot@ggplot)) at test-plot.R:27:5
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─ggplot2::is.ggplot(mock.plot@ggplot)
5. └─ggplot2::is_ggplot(x)
6. └─S7::S7_inherits(x, class_ggplot)
[ FAIL 2 | WARN 3 | SKIP 0 | PASS 11 ]
Error:
! Test failures.
Execution halted
Flavor: r-oldrel-macos-arm64
Version: 1.0.2
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘PopPsiSeq_and_Helpers.Rmd’ using rmarkdown
Quitting from PopPsiSeq_and_Helpers.Rmd:120-124 [unnamed-chunk-7]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `validObject()`:
! invalid class "GGbio" object: invalid object for slot "ggplot" in class "GGbio": got class "ggplot2::ggplot", should be or extend class "gg_OR_NULL"
---
Backtrace:
x
1. +-ggplot2::autoplot(...)
2. \-ggbio::autoplot(...)
3. \-ggbio (local) .local(object, ...)
4. +-BiocGenerics::do.call(ggplot, c(list(data = object), list(aes.res)))
5. +-base::do.call(ggplot, c(list(data = object), list(aes.res)))
6. +-ggplot2 (local) `<fn>`(data = `<GRanges>`, `<ggplt2::>`)
7. \-ggbio:::ggplot.Vector(data = `<GRanges>`, `<ggplt2::>`)
8. \-ggbio::GGbio(gg, data = data)
9. +-BiocGenerics::do.call(...)
10. +-base::do.call(...)
11. \-methods (local) `<fn>`(...)
12. +-methods::initialize(value, ...)
13. \-methods::initialize(value, ...)
14. \-methods::validObject(.Object)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'PopPsiSeq_and_Helpers.Rmd' failed with diagnostics:
invalid class "GGbio" object: invalid object for slot "ggplot" in class "GGbio": got class "ggplot2::ggplot", should be or extend class "gg_OR_NULL"
--- failed re-building ‘PopPsiSeq_and_Helpers.Rmd’
SUMMARY: processing the following file failed:
‘PopPsiSeq_and_Helpers.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64
Version: 1.0.2
Check: tests
Result: ERROR
Running ‘testthat.R’ [17s/22s]
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/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
>
> library(testthat)
> library(PopPsiSeqR)
>
> test_check("PopPsiSeqR")
Saving _problems/test-plot-26.R
Saving _problems/test-plot-27.R
[ FAIL 2 | WARN 3 | SKIP 0 | PASS 11 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-plot.R:26:5'): returns a plot ────────────────────────────────
Expected `mock.plot <- windowedFrequencyShift.plotter(mock_data)` not to throw any errors.
Actually got a <simpleError> with message:
invalid class "GGbio" object: invalid object for slot "ggplot" in class "GGbio": got class "ggplot2::ggplot", should be or extend class "gg_OR_NULL"
── Error ('test-plot.R:27:5'): returns a plot ──────────────────────────────────
Error in `eval(code, test_env)`: object 'mock.plot' not found
Backtrace:
▆
1. ├─testthat::expect_true(ggplot2::is.ggplot(mock.plot@ggplot)) at test-plot.R:27:5
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─ggplot2::is.ggplot(mock.plot@ggplot)
5. └─ggplot2::is_ggplot(x)
6. └─S7::S7_inherits(x, class_ggplot)
[ FAIL 2 | WARN 3 | SKIP 0 | PASS 11 ]
Error:
! Test failures.
Execution halted
Flavor: r-oldrel-macos-x86_64
Version: 1.0.2
Check: tests
Result: ERROR
Running 'testthat.R' [33s]
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/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
>
> library(testthat)
> library(PopPsiSeqR)
>
> test_check("PopPsiSeqR")
Saving _problems/test-plot-26.R
Saving _problems/test-plot-27.R
[ FAIL 2 | WARN 3 | SKIP 0 | PASS 11 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-plot.R:26:5'): returns a plot ────────────────────────────────
Expected `mock.plot <- windowedFrequencyShift.plotter(mock_data)` not to throw any errors.
Actually got a <simpleError> with message:
invalid class "GGbio" object: invalid object for slot "ggplot" in class "GGbio": got class "ggplot2::ggplot", should be or extend class "gg_OR_NULL"
── Error ('test-plot.R:27:5'): returns a plot ──────────────────────────────────
Error in `eval(code, test_env)`: object 'mock.plot' not found
Backtrace:
▆
1. ├─testthat::expect_true(ggplot2::is.ggplot(mock.plot@ggplot)) at test-plot.R:27:5
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─ggplot2::is.ggplot(mock.plot@ggplot)
5. └─ggplot2::is_ggplot(x)
6. └─S7::S7_inherits(x, class_ggplot)
[ FAIL 2 | WARN 3 | SKIP 0 | PASS 11 ]
Error:
! Test failures.
Execution halted
Flavor: r-oldrel-windows-x86_64