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> devtools::test()
ℹ Testing bambu
✔ | F W S OK | Context
✔ | 2 | bambu-processReads_utilityConstructReadClasses [1.7s]
⠏ | 0 | bambu-processReads_utilityConstructReadClasses [1] "Line 85"
[1] "Line 90"
[14:58:31] WARNING: src/learner.cc:553:
If you are loading a serialized model (like pickle in Python, RDS in R) generated by
older XGBoost, please export the model by calling `Booster.save_model` from that version
first, then load it back in current version. See:
https://xgboost.readthedocs.io/en/latest/tutorials/saving_model.html
for more details about differences between saving model and serializing.
[14:58:31] WARNING: src/learner.cc:553:
If you are loading a serialized model (like pickle in Python, RDS in R) generated by
older XGBoost, please export the model by calling `Booster.save_model` from that version
first, then load it back in current version. See:
https://xgboost.readthedocs.io/en/latest/tutorials/saving_model.html
for more details about differences between saving model and serializing.
[14:58:31] WARNING: src/learner.cc:553:
If you are loading a serialized model (like pickle in Python, RDS in R) generated by
older XGBoost, please export the model by calling `Booster.save_model` from that version
first, then load it back in current version. See:
https://xgboost.readthedocs.io/en/latest/tutorials/saving_model.html
for more details about differences between saving model and serializing.
[14:58:31] WARNING: src/learner.cc:553:
If you are loading a serialized model (like pickle in Python, RDS in R) generated by
older XGBoost, please export the model by calling `Booster.save_model` from that version
first, then load it back in current version. See:
https://xgboost.readthedocs.io/en/latest/tutorials/saving_model.html
for more details about differences between saving model and serializing.
[14:58:36] WARNING: src/learner.cc:553:
If you are loading a serialized model (like pickle in Python, RDS in R) generated by
older XGBoost, please export the model by calling `Booster.save_model` from that version
first, then load it back in current version. See:
https://xgboost.readthedocs.io/en/latest/tutorials/saving_model.html
for more details about differences between saving model and serializing.
[14:58:36] WARNING: src/learner.cc:553:
If you are loading a serialized model (like pickle in Python, RDS in R) generated by
older XGBoost, please export the model by calling `Booster.save_model` from that version
first, then load it back in current version. See:
https://xgboost.readthedocs.io/en/latest/tutorials/saving_model.html
for more details about differences between saving model and serializing.
⠋ | 1 | bambu-processReads_utilityConstructReadClasses [1] "Line 85"
[1] "Line 90"
⠴ | 3 3 | bambu-processReads_utilityConstructReadClasses [1] "Line 85"
[1] "Line 90"
⠏ | 5 5 | bambu-processReads_utilityConstructReadClasses [1] "Line 85"
[1] "Line 90"
✔ | 8 9 | bambu-processReads_utilityConstructReadClasses [86.0s]
─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Warning (test_bambu_arguments.R:28:5): reads are correctly assigned to transcripts
Returning more (or less) than 1 row per `summarise()` group was deprecated in dplyr 1.1.0.
ℹ Please use `reframe()` instead.
ℹ When switching from `summarise()` to `reframe()`, remember that `reframe()` always returns an ungrouped data frame and
adjust accordingly.
Backtrace:
1. bambu::bambu(...)
at test_bambu_arguments.R:28:4
10. dplyr:::summarise.grouped_df(...)
11. dplyr:::summarise_deprecate_variable_size()
Warning (test_bambu_arguments.R:28:5): reads are correctly assigned to transcripts
Each row in `x` is expected to match at most 1 row in `y`.
ℹ Row 16 of `x` matches multiple rows.
ℹ If multiple matches are expected, set `multiple = "all"` to silence this warning.
Backtrace:
1. bambu::bambu(...)
at test_bambu_arguments.R:28:4
47. dplyr (local) `<fn>`(`<vctrs___>`)
48. dplyr:::rethrow_warning_join_matches_multiple(cnd, error_call)
49. dplyr:::warn_join(...)
50. dplyr:::warn_dplyr(...)
Warning (test_bambu_arguments.R:28:5): reads are correctly assigned to transcripts
Each row in `x` is expected to match at most 1 row in `y`.
ℹ Row 2 of `x` matches multiple rows.
ℹ If multiple matches are expected, set `multiple = "all"` to silence this warning.
Backtrace:
1. bambu::bambu(...)
at test_bambu_arguments.R:28:4
49. dplyr (local) `<fn>`(`<vctrs___>`)
50. dplyr:::rethrow_warning_join_matches_multiple(cnd, error_call)
51. dplyr:::warn_join(...)
52. dplyr:::warn_dplyr(...)
Warning (test_bambu_arguments.R:40:5): returnDistTable returns the correct distTable
Each row in `x` is expected to match at most 1 row in `y`.
ℹ Row 16 of `x` matches multiple rows.
ℹ If multiple matches are expected, set `multiple = "all"` to silence this warning.
Backtrace:
1. bambu::bambu(...)
at test_bambu_arguments.R:40:4
47. dplyr (local) `<fn>`(`<vctrs___>`)
48. dplyr:::rethrow_warning_join_matches_multiple(cnd, error_call)
49. dplyr:::warn_join(...)
50. dplyr:::warn_dplyr(...)
Warning (test_bambu_arguments.R:40:5): returnDistTable returns the correct distTable
Each row in `x` is expected to match at most 1 row in `y`.
ℹ Row 2 of `x` matches multiple rows.
ℹ If multiple matches are expected, set `multiple = "all"` to silence this warning.
Backtrace:
1. bambu::bambu(...)
at test_bambu_arguments.R:40:4
49. dplyr (local) `<fn>`(`<vctrs___>`)
50. dplyr:::rethrow_warning_join_matches_multiple(cnd, error_call)
51. dplyr:::warn_join(...)
52. dplyr:::warn_dplyr(...)
Warning (test_bambu_arguments.R:52:5): low Memory mode does not change results
Returning more (or less) than 1 row per `summarise()` group was deprecated in dplyr 1.1.0.
ℹ Please use `reframe()` instead.
ℹ When switching from `summarise()` to `reframe()`, remember that `reframe()` always returns an ungrouped data frame and
adjust accordingly.
Backtrace:
1. bambu::bambu(...)
at test_bambu_arguments.R:52:4
10. dplyr:::summarise.grouped_df(...)
11. dplyr:::summarise_deprecate_variable_size()
Warning (test_bambu_arguments.R:52:5): low Memory mode does not change results
Each row in `x` is expected to match at most 1 row in `y`.
ℹ Row 16 of `x` matches multiple rows.
ℹ If multiple matches are expected, set `multiple = "all"` to silence this warning.
Backtrace:
1. bambu::bambu(...)
at test_bambu_arguments.R:52:4
47. dplyr (local) `<fn>`(`<vctrs___>`)
48. dplyr:::rethrow_warning_join_matches_multiple(cnd, error_call)
49. dplyr:::warn_join(...)
50. dplyr:::warn_dplyr(...)
Warning (test_bambu_arguments.R:52:5): low Memory mode does not change results
Each row in `x` is expected to match at most 1 row in `y`.
ℹ Row 2 of `x` matches multiple rows.
ℹ If multiple matches are expected, set `multiple = "all"` to silence this warning.
Backtrace:
1. bambu::bambu(...)
at test_bambu_arguments.R:52:4
49. dplyr (local) `<fn>`(`<vctrs___>`)
50. dplyr:::rethrow_warning_join_matches_multiple(cnd, error_call)
51. dplyr:::warn_join(...)
52. dplyr:::warn_dplyr(...)
─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
✔ | 17 | annotate splice overlap by distance [6.1s]
⠏ | 0 | Isoform reconstruction [1] "Line 85"
✖ | 1 2 5 | Isoform reconstruction [13.9s]
─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Error (test_isore.R:15:5): junction identification and isore.constructReadClasses completes successfully
Error in `h(simpleError(msg, call))`: erreur d'�valuation de l'argument 'value' lors de la s�lection d'une m�thode pour la fonction 'unsplit' : erreur d'�valuation de l'argument 'x' lors de la s�lection d'une m�thode pour la fonction 'extractAt' : subscript contains invalid names
Backtrace:
1. bambu:::isore.constructJunctionTables(...)
at test_isore.R:15:4
23. base::.handleSimpleError(...)
24. base (local) h(simpleError(msg, call))
Warning (test_isore.R:51:5): isore.combineTranscriptCandidates completes successfully
Returning more (or less) than 1 row per `summarise()` group was deprecated in dplyr 1.1.0.
ℹ Please use `reframe()` instead.
ℹ When switching from `summarise()` to `reframe()`, remember that `reframe()` always returns an ungrouped data frame and
adjust accordingly.
Backtrace:
1. bambu:::isore.combineTranscriptCandidates(...)
at test_isore.R:51:4
8. dplyr:::summarise.grouped_df(...)
9. dplyr:::summarise_deprecate_variable_size()
Warning (test_isore.R:63:5): isore.combineTranscriptCandidates completes successfully
Returning more (or less) than 1 row per `summarise()` group was deprecated in dplyr 1.1.0.
ℹ Please use `reframe()` instead.
ℹ When switching from `summarise()` to `reframe()`, remember that `reframe()` always returns an ungrouped data frame and
adjust accordingly.
Backtrace:
1. bambu:::isore.combineTranscriptCandidates(...)
at test_isore.R:63:4
8. dplyr:::summarise.grouped_df(...)
9. dplyr:::summarise_deprecate_variable_size()
─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
✖ | 2 0 | Visualization of estimates [0.6s]
─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Error (test_plotBambu.R:12:5): visualization for transcript expression is successful
<packageNotFoundError/error/condition>
Error in `loadNamespace(x)`: aucun package nommé ‘circlize’ n'est trouvé
Backtrace:
1. testthat::expect_is(...)
at test_plotBambu.R:12:4
6. base::loadNamespace(x)
at bambu/R/plotBambu_utilityFunctions.R:118:4
7. base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
8. base (local) withOneRestart(expr, restarts[[1L]])
9. base (local) doWithOneRestart(return(expr), restart)
Error (test_plotBambu.R:32:5): visualization for gene expression is successful
<packageNotFoundError/error/condition>
Error in `loadNamespace(x)`: aucun package nommé ‘circlize’ n'est trouvé
Backtrace:
1. testthat::expect_is(...)
at test_plotBambu.R:32:4
6. base::loadNamespace(x)
at bambu/R/plotBambu_utilityFunctions.R:118:4
7. base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
8. base (local) withOneRestart(expr, restarts[[1L]])
9. base (local) doWithOneRestart(return(expr), restart)
─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
✔ | 14 | Prepare annotations [9.7s]
⠦ | 8 19 | Isoform quantification [1] "Line 85"
[1] "Line 90"
| | 0%[1] "Line 85"
[1] "Line 90"
|======================================================== | 50%[1] "Line 85"
[1] "Line 90"
|===============================================================================================================| 100%
|===============================================================================================================| 100%
⠇ | 15 24 | Isoform quantification [1] "Line 85"
[1] "Line 90"
| | 0%[1] "Line 85"
[1] "Line 90"
|======================================================== | 50%[1] "Line 85"
[1] "Line 90"
|===============================================================================================================| 100%
|===============================================================================================================| 100%
✔ | 30 32 | Isoform quantification [125.7s]
─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Warning (test_quant.R:12:5): generic function of isoform quantification of data.table is list of 2
Each row in `x` is expected to match at most 1 row in `y`.
ℹ Row 5 of `x` matches multiple rows.
ℹ If multiple matches are expected, set `multiple = "all"` to silence this warning.
Backtrace:
1. BiocGenerics::lapply(...)
at test_quant.R:12:4
23. dplyr (local) `<fn>`(`<vctrs___>`)
24. dplyr:::rethrow_warning_join_matches_multiple(cnd, error_call)
25. dplyr:::warn_join(...)
26. dplyr:::warn_dplyr(...)
Warning (test_quant.R:12:5): generic function of isoform quantification of data.table is list of 2
Each row in `x` is expected to match at most 1 row in `y`.
ℹ Row 1 of `x` matches multiple rows.
ℹ If multiple matches are expected, set `multiple = "all"` to silence this warning.
Backtrace:
1. BiocGenerics::lapply(...)
at test_quant.R:12:4
23. dplyr (local) `<fn>`(`<vctrs___>`)
24. dplyr:::rethrow_warning_join_matches_multiple(cnd, error_call)
25. dplyr:::warn_join(...)
26. dplyr:::warn_dplyr(...)
Warning (test_quant.R:12:5): generic function of isoform quantification of data.table is list of 2
Each row in `x` is expected to match at most 1 row in `y`.
ℹ Row 1 of `x` matches multiple rows.
ℹ If multiple matches are expected, set `multiple = "all"` to silence this warning.
Backtrace:
1. BiocGenerics::lapply(...)
at test_quant.R:12:4
23. dplyr (local) `<fn>`(`<vctrs___>`)
24. dplyr:::rethrow_warning_join_matches_multiple(cnd, error_call)
25. dplyr:::warn_join(...)
26. dplyr:::warn_dplyr(...)
Warning (test_quant.R:12:5): generic function of isoform quantification of data.table is list of 2
Each row in `x` is expected to match at most 1 row in `y`.
ℹ Row 5 of `x` matches multiple rows.
ℹ If multiple matches are expected, set `multiple = "all"` to silence this warning.
Backtrace:
1. BiocGenerics::lapply(...)
at test_quant.R:12:4
23. dplyr (local) `<fn>`(`<vctrs___>`)
24. dplyr:::rethrow_warning_join_matches_multiple(cnd, error_call)
25. dplyr:::warn_join(...)
26. dplyr:::warn_dplyr(...)
Warning (test_quant.R:21:5): generic function of isoform quantification of data.table is list of 2
Each row in `x` is expected to match at most 1 row in `y`.
ℹ Row 5 of `x` matches multiple rows.
ℹ If multiple matches are expected, set `multiple = "all"` to silence this warning.
Backtrace:
1. BiocGenerics::lapply(...)
at test_quant.R:21:4
23. dplyr (local) `<fn>`(`<vctrs___>`)
24. dplyr:::rethrow_warning_join_matches_multiple(cnd, error_call)
25. dplyr:::warn_join(...)
26. dplyr:::warn_dplyr(...)
Warning (test_quant.R:21:5): generic function of isoform quantification of data.table is list of 2
Each row in `x` is expected to match at most 1 row in `y`.
ℹ Row 1 of `x` matches multiple rows.
ℹ If multiple matches are expected, set `multiple = "all"` to silence this warning.
Backtrace:
1. BiocGenerics::lapply(...)
at test_quant.R:21:4
23. dplyr (local) `<fn>`(`<vctrs___>`)
24. dplyr:::rethrow_warning_join_matches_multiple(cnd, error_call)
25. dplyr:::warn_join(...)
26. dplyr:::warn_dplyr(...)
Warning (test_quant.R:21:5): generic function of isoform quantification of data.table is list of 2
Each row in `x` is expected to match at most 1 row in `y`.
ℹ Row 1 of `x` matches multiple rows.
ℹ If multiple matches are expected, set `multiple = "all"` to silence this warning.
Backtrace:
1. BiocGenerics::lapply(...)
at test_quant.R:21:4
23. dplyr (local) `<fn>`(`<vctrs___>`)
24. dplyr:::rethrow_warning_join_matches_multiple(cnd, error_call)
25. dplyr:::warn_join(...)
26. dplyr:::warn_dplyr(...)
Warning (test_quant.R:21:5): generic function of isoform quantification of data.table is list of 2
Each row in `x` is expected to match at most 1 row in `y`.
ℹ Row 5 of `x` matches multiple rows.
ℹ If multiple matches are expected, set `multiple = "all"` to silence this warning.
Backtrace:
1. BiocGenerics::lapply(...)
at test_quant.R:21:4
23. dplyr (local) `<fn>`(`<vctrs___>`)
24. dplyr:::rethrow_warning_join_matches_multiple(cnd, error_call)
25. dplyr:::warn_join(...)
26. dplyr:::warn_dplyr(...)
Warning (test_quant.R:57:5): bambu (isoform quantification of bam file) produces expected output
Returning more (or less) than 1 row per `summarise()` group was deprecated in dplyr 1.1.0.
ℹ Please use `reframe()` instead.
ℹ When switching from `summarise()` to `reframe()`, remember that `reframe()` always returns an ungrouped data frame and
adjust accordingly.
Backtrace:
1. bambu::bambu(reads = test.bam, annotations = annotations, genome = fa.file)
at test_quant.R:57:4
10. dplyr:::summarise.grouped_df(...)
11. dplyr:::summarise_deprecate_variable_size()
Warning (test_quant.R:57:5): bambu (isoform quantification of bam file) produces expected output
Each row in `x` is expected to match at most 1 row in `y`.
ℹ Row 16 of `x` matches multiple rows.
ℹ If multiple matches are expected, set `multiple = "all"` to silence this warning.
Backtrace:
1. bambu::bambu(reads = test.bam, annotations = annotations, genome = fa.file)
at test_quant.R:57:4
47. dplyr (local) `<fn>`(`<vctrs___>`)
48. dplyr:::rethrow_warning_join_matches_multiple(cnd, error_call)
49. dplyr:::warn_join(...)
50. dplyr:::warn_dplyr(...)
Warning (test_quant.R:57:5): bambu (isoform quantification of bam file) produces expected output
Each row in `x` is expected to match at most 1 row in `y`.
ℹ Row 2 of `x` matches multiple rows.
ℹ If multiple matches are expected, set `multiple = "all"` to silence this warning.
Backtrace:
1. bambu::bambu(reads = test.bam, annotations = annotations, genome = fa.file)
at test_quant.R:57:4
49. dplyr (local) `<fn>`(`<vctrs___>`)
50. dplyr:::rethrow_warning_join_matches_multiple(cnd, error_call)
51. dplyr:::warn_join(...)
52. dplyr:::warn_dplyr(...)
Warning (test_quant.R:63:5): bambu (isoform quantification of bam file) produces expected output
Each row in `x` is expected to match at most 1 row in `y`.
ℹ Row 16 of `x` matches multiple rows.
ℹ If multiple matches are expected, set `multiple = "all"` to silence this warning.
Backtrace:
1. bambu::bambu(...)
at test_quant.R:63:4
47. dplyr (local) `<fn>`(`<vctrs___>`)
48. dplyr:::rethrow_warning_join_matches_multiple(cnd, error_call)
49. dplyr:::warn_join(...)
50. dplyr:::warn_dplyr(...)
Warning (test_quant.R:63:5): bambu (isoform quantification of bam file) produces expected output
Each row in `x` is expected to match at most 1 row in `y`.
ℹ Row 2 of `x` matches multiple rows.
ℹ If multiple matches are expected, set `multiple = "all"` to silence this warning.
Backtrace:
1. bambu::bambu(...)
at test_quant.R:63:4
49. dplyr (local) `<fn>`(`<vctrs___>`)
50. dplyr:::rethrow_warning_join_matches_multiple(cnd, error_call)
51. dplyr:::warn_join(...)
52. dplyr:::warn_dplyr(...)
Warning (test_quant.R:63:5): bambu (isoform quantification of bam file) produces expected output
Each row in `x` is expected to match at most 1 row in `y`.
ℹ Row 16 of `x` matches multiple rows.
ℹ If multiple matches are expected, set `multiple = "all"` to silence this warning.
Backtrace:
1. bambu::bambu(...)
at test_quant.R:63:4
47. dplyr (local) `<fn>`(`<vctrs___>`)
48. dplyr:::rethrow_warning_join_matches_multiple(cnd, error_call)
49. dplyr:::warn_join(...)
50. dplyr:::warn_dplyr(...)
Warning (test_quant.R:63:5): bambu (isoform quantification of bam file) produces expected output
Each row in `x` is expected to match at most 1 row in `y`.
ℹ Row 2 of `x` matches multiple rows.
ℹ If multiple matches are expected, set `multiple = "all"` to silence this warning.
Backtrace:
1. bambu::bambu(...)
at test_quant.R:63:4
49. dplyr (local) `<fn>`(`<vctrs___>`)
50. dplyr:::rethrow_warning_join_matches_multiple(cnd, error_call)
51. dplyr:::warn_join(...)
52. dplyr:::warn_dplyr(...)
Warning (test_quant.R:96:5): bambu (isoform quantification of bam file and save readClassFiles) produces expected output
Returning more (or less) than 1 row per `summarise()` group was deprecated in dplyr 1.1.0.
ℹ Please use `reframe()` instead.
ℹ When switching from `summarise()` to `reframe()`, remember that `reframe()` always returns an ungrouped data frame and
adjust accordingly.
Backtrace:
1. bambu::bambu(reads = test.bam, annotations = gr, genome = fa.file)
at test_quant.R:96:4
10. dplyr:::summarise.grouped_df(...)
11. dplyr:::summarise_deprecate_variable_size()
Warning (test_quant.R:96:5): bambu (isoform quantification of bam file and save readClassFiles) produces expected output
Each row in `x` is expected to match at most 1 row in `y`.
ℹ Row 16 of `x` matches multiple rows.
ℹ If multiple matches are expected, set `multiple = "all"` to silence this warning.
Backtrace:
1. bambu::bambu(reads = test.bam, annotations = gr, genome = fa.file)
at test_quant.R:96:4
47. dplyr (local) `<fn>`(`<vctrs___>`)
48. dplyr:::rethrow_warning_join_matches_multiple(cnd, error_call)
49. dplyr:::warn_join(...)
50. dplyr:::warn_dplyr(...)
Warning (test_quant.R:96:5): bambu (isoform quantification of bam file and save readClassFiles) produces expected output
Each row in `x` is expected to match at most 1 row in `y`.
ℹ Row 2 of `x` matches multiple rows.
ℹ If multiple matches are expected, set `multiple = "all"` to silence this warning.
Backtrace:
1. bambu::bambu(reads = test.bam, annotations = gr, genome = fa.file)
at test_quant.R:96:4
49. dplyr (local) `<fn>`(`<vctrs___>`)
50. dplyr:::rethrow_warning_join_matches_multiple(cnd, error_call)
51. dplyr:::warn_join(...)
52. dplyr:::warn_dplyr(...)
Warning (test_quant.R:103:5): bambu (isoform quantification of bam file and save readClassFiles) produces expected output
Returning more (or less) than 1 row per `summarise()` group was deprecated in dplyr 1.1.0.
ℹ Please use `reframe()` instead.
ℹ When switching from `summarise()` to `reframe()`, remember that `reframe()` always returns an ungrouped data frame and
adjust accordingly.
Backtrace:
1. bambu::bambu(...)
at test_quant.R:103:4
10. dplyr:::summarise.grouped_df(...)
11. dplyr:::summarise_deprecate_variable_size()
Warning (test_quant.R:103:5): bambu (isoform quantification of bam file and save readClassFiles) produces expected output
Each row in `x` is expected to match at most 1 row in `y`.
ℹ Row 16 of `x` matches multiple rows.
ℹ If multiple matches are expected, set `multiple = "all"` to silence this warning.
Backtrace:
1. bambu::bambu(...)
at test_quant.R:103:4
47. dplyr (local) `<fn>`(`<vctrs___>`)
48. dplyr:::rethrow_warning_join_matches_multiple(cnd, error_call)
49. dplyr:::warn_join(...)
50. dplyr:::warn_dplyr(...)
Warning (test_quant.R:103:5): bambu (isoform quantification of bam file and save readClassFiles) produces expected output
Each row in `x` is expected to match at most 1 row in `y`.
ℹ Row 2 of `x` matches multiple rows.
ℹ If multiple matches are expected, set `multiple = "all"` to silence this warning.
Backtrace:
1. bambu::bambu(...)
at test_quant.R:103:4
49. dplyr (local) `<fn>`(`<vctrs___>`)
50. dplyr:::rethrow_warning_join_matches_multiple(cnd, error_call)
51. dplyr:::warn_join(...)
52. dplyr:::warn_dplyr(...)
Warning (test_quant.R:103:5): bambu (isoform quantification of bam file and save readClassFiles) produces expected output
Each row in `x` is expected to match at most 1 row in `y`.
ℹ Row 16 of `x` matches multiple rows.
ℹ If multiple matches are expected, set `multiple = "all"` to silence this warning.
Backtrace:
1. bambu::bambu(...)
at test_quant.R:103:4
47. dplyr (local) `<fn>`(`<vctrs___>`)
48. dplyr:::rethrow_warning_join_matches_multiple(cnd, error_call)
49. dplyr:::warn_join(...)
50. dplyr:::warn_dplyr(...)
Warning (test_quant.R:103:5): bambu (isoform quantification of bam file and save readClassFiles) produces expected output
Each row in `x` is expected to match at most 1 row in `y`.
ℹ Row 2 of `x` matches multiple rows.
ℹ If multiple matches are expected, set `multiple = "all"` to silence this warning.
Backtrace:
1. bambu::bambu(...)
at test_quant.R:103:4
49. dplyr (local) `<fn>`(`<vctrs___>`)
50. dplyr:::rethrow_warning_join_matches_multiple(cnd, error_call)
51. dplyr:::warn_join(...)
52. dplyr:::warn_dplyr(...)
Warning (test_quant.R:125:5): bambu (isoform quantification of saved readClassFiles) produces expected output
Returning more (or less) than 1 row per `summarise()` group was deprecated in dplyr 1.1.0.
ℹ Please use `reframe()` instead.
ℹ When switching from `summarise()` to `reframe()`, remember that `reframe()` always returns an ungrouped data frame and
adjust accordingly.
Backtrace:
1. bambu::bambu(...)
at test_quant.R:125:4
10. dplyr:::summarise.grouped_df(...)
11. dplyr:::summarise_deprecate_variable_size()
Warning (test_quant.R:125:5): bambu (isoform quantification of saved readClassFiles) produces expected output
Each row in `x` is expected to match at most 1 row in `y`.
ℹ Row 16 of `x` matches multiple rows.
ℹ If multiple matches are expected, set `multiple = "all"` to silence this warning.
Backtrace:
1. bambu::bambu(...)
at test_quant.R:125:4
47. dplyr (local) `<fn>`(`<vctrs___>`)
48. dplyr:::rethrow_warning_join_matches_multiple(cnd, error_call)
49. dplyr:::warn_join(...)
50. dplyr:::warn_dplyr(...)
Warning (test_quant.R:125:5): bambu (isoform quantification of saved readClassFiles) produces expected output
Each row in `x` is expected to match at most 1 row in `y`.
ℹ Row 2 of `x` matches multiple rows.
ℹ If multiple matches are expected, set `multiple = "all"` to silence this warning.
Backtrace:
1. bambu::bambu(...)
at test_quant.R:125:4
49. dplyr (local) `<fn>`(`<vctrs___>`)
50. dplyr:::rethrow_warning_join_matches_multiple(cnd, error_call)
51. dplyr:::warn_join(...)
52. dplyr:::warn_dplyr(...)
Warning (test_quant.R:133:5): bambu (isoform quantification of saved readClassFiles) produces expected output
Each row in `x` is expected to match at most 1 row in `y`.
ℹ Row 16 of `x` matches multiple rows.
ℹ If multiple matches are expected, set `multiple = "all"` to silence this warning.
Backtrace:
1. bambu::bambu(...)
at test_quant.R:133:4
47. dplyr (local) `<fn>`(`<vctrs___>`)
48. dplyr:::rethrow_warning_join_matches_multiple(cnd, error_call)
49. dplyr:::warn_join(...)
50. dplyr:::warn_dplyr(...)
Warning (test_quant.R:133:5): bambu (isoform quantification of saved readClassFiles) produces expected output
Each row in `x` is expected to match at most 1 row in `y`.
ℹ Row 2 of `x` matches multiple rows.
ℹ If multiple matches are expected, set `multiple = "all"` to silence this warning.
Backtrace:
1. bambu::bambu(...)
at test_quant.R:133:4
49. dplyr (local) `<fn>`(`<vctrs___>`)
50. dplyr:::rethrow_warning_join_matches_multiple(cnd, error_call)
51. dplyr:::warn_join(...)
52. dplyr:::warn_dplyr(...)
Warning (test_quant.R:133:5): bambu (isoform quantification of saved readClassFiles) produces expected output
Each row in `x` is expected to match at most 1 row in `y`.
ℹ Row 16 of `x` matches multiple rows.
ℹ If multiple matches are expected, set `multiple = "all"` to silence this warning.
Backtrace:
1. bambu::bambu(...)
at test_quant.R:133:4
47. dplyr (local) `<fn>`(`<vctrs___>`)
48. dplyr:::rethrow_warning_join_matches_multiple(cnd, error_call)
49. dplyr:::warn_join(...)
50. dplyr:::warn_dplyr(...)
Warning (test_quant.R:133:5): bambu (isoform quantification of saved readClassFiles) produces expected output
Each row in `x` is expected to match at most 1 row in `y`.
ℹ Row 2 of `x` matches multiple rows.
ℹ If multiple matches are expected, set `multiple = "all"` to silence this warning.
Backtrace:
1. bambu::bambu(...)
at test_quant.R:133:4
49. dplyr (local) `<fn>`(`<vctrs___>`)
50. dplyr:::rethrow_warning_join_matches_multiple(cnd, error_call)
51. dplyr:::warn_join(...)
52. dplyr:::warn_dplyr(...)
─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
✔ | 8 | Generate GTF file from summarizedExperiment object [3.8s]
✖ | 2 18 | txRange, full length transcript prediction [6.5s]
─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Error (test_scoreRC.R:9:5): txRange generates a gene and transcript score
Error in `h(simpleError(msg, call))`: erreur d'�valuation de l'argument 'value' lors de la s�lection d'une m�thode pour la fonction 'unsplit' : erreur d'�valuation de l'argument 'x' lors de la s�lection d'une m�thode pour la fonction 'extractAt' : subscript contains invalid names
Backtrace:
1. bambu:::scoreReadClasses(...)
at test_scoreRC.R:9:4
23. base::.handleSimpleError(...)
24. base (local) h(simpleError(msg, call))
Error (test_scoreRC.R:51:5): countPolyATerminals
Error in `h(simpleError(msg, call))`: erreur d'�valuation de l'argument 'value' lors de la s�lection d'une m�thode pour la fonction 'unsplit' : erreur d'�valuation de l'argument 'x' lors de la s�lection d'une m�thode pour la fonction 'extractAt' : subscript contains invalid names
Backtrace:
1. bambu:::countPolyATerminals(...)
at test_scoreRC.R:51:4
22. base::.handleSimpleError(...)
23. base (local) h(simpleError(msg, call))
─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
✔ | 8 | Gene quantification [1.0s]
✔ | 2 | XGBoost functionality [3.5s]
══ Results ══════════════════════════════════════════════════════════════════════════════════════════════════════════════
Duration: 275.3 s
[ FAIL 5 | WARN 40 | SKIP 0 | PASS 115 ]Editor is loading...