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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 ]
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