[skip vbump] upversion v0.6.0 #643
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Example runs more than 5 seconds: Need to fix this. |
Unit Tests Summary 1 files 29 suites 29s ⏱️ Results for commit e76b097. ♻️ This comment has been updated with latest results. |
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There are only two examples in 
Thinking that there's no way around the Any ideas? @insightsengineering/nest-core-dev |
Signed-off-by: Marcin <[email protected]>
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For the example, I can not reproduce locally but we can always wrap into \dontRun tag, or \dontTest |
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MultiAssayExperiment (or MAE in short) is very slow to load, but I think the session should only pay the penalty once, not multiple times. On my computer I got: I didn't profile the examples. It seems like there are some areas to improve beyond the calls to loading the package. The high difference between system and elapsed reminds me of some discussion on mailing lists. I don't recall if they were about parallel computation or something like that. I don't think it will block publication on CRAN, but maybe explaining that loading MAE is the most expensive task could help. |
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@m7pr @llrs-roche Thanks for looking into this, and as discussed, we'll push to CRAN and provide explanation. |
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Got an error under R-devel. Full Failed testshttps://win-builder.r-project.org/qmU6ocnFl9eh/00check.log ══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-SEFilterStates.R:40:3'): constructor accepts a SummarizedExperiment ──
Expected `SEFilterStates$new(data = get_test_data(), dataname = "test")` to run without any errors.
ℹ Actually got a <simpleError> with text:
Package 'BiocGenerics' version 0.50.0 cannot be unloaded:
Error in unloadNamespace(package) : namespace 'BiocGenerics' is imported by 'MultiAssayExperiment', 'IRanges', 'GenomicRanges', 'XVector', 'S4Arrays', 'SparseArray', 'DelayedArray', 'GenomeInfoDb', 'S4Vectors', 'Biobase', 'SummarizedExperiment' so cannot be unloaded
── Error ('test-SEFilterStates.R:50:3'): set_filter_state only accepts `teal_slices` ──
Error in `value[[3L]](cond)`: Package 'BiocGenerics' version 0.50.0 cannot be unloaded:
Error in unloadNamespace(package) : namespace 'BiocGenerics' is imported by 'MultiAssayExperiment', 'IRanges', 'GenomicRanges', 'XVector', 'S4Arrays', 'SparseArray', 'DelayedArray', 'GenomeInfoDb', 'S4Vectors', 'Biobase', 'SummarizedExperiment' so cannot be unloaded
Backtrace:
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1. ├─SEFilterStates$new(data = get_test_data(), dataname = "test") at test-SEFilterStates.R:50:3
2. │ └─teal.slice (local) initialize(...)
3. │ └─checkmate::assert_class(data, "SummarizedExperiment")
4. │ └─checkmate::checkClass(x, classes, ordered, null.ok)
5. └─teal.slice (local) get_test_data()
6. └─base::library(SummarizedExperiment) at test-SEFilterStates.R:2:3
7. └─base::.getRequiredPackages2(...)
8. └─base::library(...)
9. └─base::.getRequiredPackages2(...)
10. └─base::library(...)
11. └─base::tryCatch(...)
12. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
13. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
14. └─value[[3L]](cond)
── Error ('test-SEFilterStates.R:61:3'): set_filter_state arg - ───────────────
Error in `value[[3L]](cond)`: Package 'BiocGenerics' version 0.50.0 cannot be unloaded:
Error in unloadNamespace(package) : namespace 'BiocGenerics' is imported by 'MultiAssayExperiment', 'IRanges', 'GenomicRanges', 'XVector', 'S4Arrays', 'SparseArray', 'DelayedArray', 'GenomeInfoDb', 'S4Vectors', 'Biobase', 'SummarizedExperiment' so cannot be unloaded
Backtrace:
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1. ├─SEFilterStates$new(data = get_test_data(), dataname = "test") at test-SEFilterStates.R:61:3
2. │ └─teal.slice (local) initialize(...)
3. │ └─checkmate::assert_class(data, "SummarizedExperiment")
4. │ └─checkmate::checkClass(x, classes, ordered, null.ok)
5. └─teal.slice (local) get_test_data()
6. └─base::library(SummarizedExperiment) at test-SEFilterStates.R:2:3
7. └─base::.getRequiredPackages2(...)
8. └─base::library(...)
9. └─base::.getRequiredPackages2(...)
10. └─base::library(...)
11. └─base::tryCatch(...)
12. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
13. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
14. └─value[[3L]](cond)
── Error ('test-SEFilterStates.R:76:3'): get_call returns executable subset call ──
Error in `value[[3L]](cond)`: Package 'BiocGenerics' version 0.50.0 cannot be unloaded:
Error in unloadNamespace(package) : namespace 'BiocGenerics' is imported by 'MultiAssayExperiment', 'IRanges', 'GenomicRanges', 'XVector', 'S4Arrays', 'SparseArray', 'DelayedArray', 'GenomeInfoDb', 'S4Vectors', 'Biobase', 'SummarizedExperiment' so cannot be unloaded
Backtrace:
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1. └─teal.slice (local) get_test_data() at test-SEFilterStates.R:76:3
2. └─base::library(SummarizedExperiment) at test-SEFilterStates.R:2:3
3. └─base::.getRequiredPackages2(...)
4. └─base::library(...)
5. └─base::.getRequiredPackages2(...)
6. └─base::library(...)
7. └─base::tryCatch(...)
8. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
9. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
10. └─value[[3L]](cond)
── Error ('test-SEFilterStates.R:104:3'): ui_add returns a message inside a div when data has no rows or no columns ──
Error in `value[[3L]](cond)`: Package 'BiocGenerics' version 0.50.0 cannot be unloaded:
Error in unloadNamespace(package) : namespace 'BiocGenerics' is imported by 'MultiAssayExperiment', 'IRanges', 'GenomicRanges', 'XVector', 'S4Arrays', 'SparseArray', 'DelayedArray', 'GenomeInfoDb', 'S4Vectors', 'Biobase', 'SummarizedExperiment' so cannot be unloaded
Backtrace:
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1. ├─SEFilterStates$new(data = get_test_data(TRUE)[[1]], dataname = "test") at test-SEFilterStates.R:104:3
2. │ └─teal.slice (local) initialize(...)
3. │ └─checkmate::assert_class(data, "SummarizedExperiment")
4. │ └─checkmate::checkClass(x, classes, ordered, null.ok)
5. └─teal.slice (local) get_test_data(TRUE)
6. └─base::library(SummarizedExperiment) at test-SEFilterStates.R:2:3
7. └─base::.getRequiredPackages2(...)
8. └─base::library(...)
9. └─base::.getRequiredPackages2(...)
10. └─base::library(...)
11. └─base::tryCatch(...)
12. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
13. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
14. └─value[[3L]](cond)
[ FAIL 5 | WARN 0 | SKIP 0 | PASS 807 ]
Error: Test failures
Execution halted
The worst-case scenario is skipping the test, but I’d like to investigate further and provide comments in the submission if possible. |
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Out of curiosity, I re-upload the package again to the win-builder and this time everything passed with flying colors.
Package submitted to CRAN and I put these links in the comment. |
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Made it to CRAN |
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@donyunardi those example times are machine dependent, that's why sometimes you get different times on submissions, as they run on various machines |
Fixes #633
eval=requireNamespace("DT", quietly = TRUE)for teal-slice.Rmd