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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 ]