Last updated on 2024-04-20 03:52:56 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.1.1 | 0.54 | 2.24 | 2.78 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 1.1.1 | OK | ||||
| r-devel-linux-x86_64-fedora-clang | 1.1.1 | 869.86 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 1.1.1 | 877.80 | OK | |||
| r-prerel-macos-arm64 | 1.1.1 | 241.00 | OK | |||
| r-prerel-macos-x86_64 | 1.1.1 | 506.00 | OK | |||
| r-prerel-windows-x86_64 | 1.1.1 | 63.00 | 411.00 | 474.00 | OK | |
| r-patched-linux-x86_64 | 1.1.1 | 48.46 | 589.05 | 637.51 | OK | |
| r-release-linux-x86_64 | 1.1.1 | 51.84 | 595.73 | 647.57 | OK | |
| r-release-macos-arm64 | 1.1.1 | 12.00 | ERROR | |||
| r-release-macos-x86_64 | 1.1.1 | 6.00 | ERROR | |||
| r-release-windows-x86_64 | 1.1.1 | 81.00 | 555.00 | 636.00 | OK | |
| r-oldrel-macos-arm64 | 1.1.0 | 215.00 | NOTE | |||
| r-oldrel-windows-x86_64 | 1.1.0 | 56.00 | 375.00 | 431.00 | ERROR |
Version: 1.1.1
Check: package dependencies
Result: ERROR
Packages required but not available: 'GSEABase', 'GSVA', 'singscore'
See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Flavor: r-devel-linux-x86_64-debian-clang
Version: 1.1.1
Check: package dependencies
Result: ERROR
Package required but not available: ‘GSVA’
See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Flavors: r-release-macos-arm64, r-release-macos-x86_64
Version: 1.1.0
Check: LazyData
Result: NOTE
'LazyData' is specified without a 'data' directory
Flavors: r-oldrel-macos-arm64, r-oldrel-windows-x86_64
Version: 1.1.0
Check: tests
Result: ERROR
Running 'testthat.R' [27s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
> library(testthat)
> library(clustermole)
>
> test_check("clustermole")
[ FAIL 5 | WARN 7 | SKIP 0 | PASS 29 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-enrichment.R:30:3'): clustermole_enrichment() human input default method ──
<defunctError/error/condition>
Error: useNames = NA is defunct. Instead, specify either useNames = TRUE or useNames = FALSE.
Backtrace:
▆
1. └─clustermole::clustermole_enrichment(expr_mat = log_cpm_mat, species = "hs") at test-enrichment.R:30:3
2. └─clustermole:::get_scores(...)
3. ├─GSVA::gsva(...)
4. └─GSVA::gsva(...)
5. └─GSVA (local) .local(expr, gset.idx.list, ...)
6. └─GSVA:::.filterFeatures(expr, method)
7. ├─DelayedMatrixStats::rowSds(expr)
8. └─DelayedMatrixStats::rowSds(expr)
9. └─MatrixGenerics (local) .local(x, rows, cols, na.rm, center, ..., useNames = useNames)
10. └─matrixStats::rowSds(...)
11. └─matrixStats::rowVars(...)
12. └─matrixStats:::deprecatedUseNamesNA()
13. └─base::.Defunct(...)
── Error ('test-enrichment.R:38:3'): clustermole_enrichment() human input gsva method ──
<defunctError/error/condition>
Error: useNames = NA is defunct. Instead, specify either useNames = TRUE or useNames = FALSE.
Backtrace:
▆
1. └─clustermole::clustermole_enrichment(...) at test-enrichment.R:38:3
2. └─clustermole:::get_scores(...)
3. ├─GSVA::gsva(...)
4. └─GSVA::gsva(...)
5. └─GSVA (local) .local(expr, gset.idx.list, ...)
6. └─GSVA:::.filterFeatures(expr, method)
7. ├─DelayedMatrixStats::rowSds(expr)
8. └─DelayedMatrixStats::rowSds(expr)
9. └─MatrixGenerics (local) .local(x, rows, cols, na.rm, center, ..., useNames = useNames)
10. └─matrixStats::rowSds(...)
11. └─matrixStats::rowVars(...)
12. └─matrixStats:::deprecatedUseNamesNA()
13. └─base::.Defunct(...)
── Error ('test-enrichment.R:46:3'): clustermole_enrichment() human input ssgsea method ──
<defunctError/error/condition>
Error: useNames = NA is defunct. Instead, specify either useNames = TRUE or useNames = FALSE.
Backtrace:
▆
1. └─clustermole::clustermole_enrichment(...) at test-enrichment.R:46:3
2. └─clustermole:::get_scores(...)
3. ├─GSVA::gsva(...)
4. └─GSVA::gsva(...)
5. └─GSVA (local) .local(expr, gset.idx.list, ...)
6. └─GSVA:::.filterFeatures(expr, method)
7. ├─DelayedMatrixStats::rowSds(expr)
8. └─DelayedMatrixStats::rowSds(expr)
9. └─MatrixGenerics (local) .local(x, rows, cols, na.rm, center, ..., useNames = useNames)
10. └─matrixStats::rowSds(...)
11. └─matrixStats::rowVars(...)
12. └─matrixStats:::deprecatedUseNamesNA()
13. └─base::.Defunct(...)
── Error ('test-enrichment.R:62:3'): clustermole_enrichment() human input all combined method ──
<defunctError/error/condition>
Error: useNames = NA is defunct. Instead, specify either useNames = TRUE or useNames = FALSE.
Backtrace:
▆
1. └─clustermole::clustermole_enrichment(...) at test-enrichment.R:62:3
2. └─clustermole:::get_scores(...)
3. ├─GSVA::gsva(...)
4. └─GSVA::gsva(...)
5. └─GSVA (local) .local(expr, gset.idx.list, ...)
6. └─GSVA:::.filterFeatures(expr, method)
7. ├─DelayedMatrixStats::rowSds(expr)
8. └─DelayedMatrixStats::rowSds(expr)
9. └─MatrixGenerics (local) .local(x, rows, cols, na.rm, center, ..., useNames = useNames)
10. └─matrixStats::rowSds(...)
11. └─matrixStats::rowVars(...)
12. └─matrixStats:::deprecatedUseNamesNA()
13. └─base::.Defunct(...)
── Error ('test-enrichment.R:76:3'): clustermole_enrichment() mouse input ──────
<defunctError/error/condition>
Error: useNames = NA is defunct. Instead, specify either useNames = TRUE or useNames = FALSE.
Backtrace:
▆
1. └─clustermole::clustermole_enrichment(expr_mat = log_cpm_mat, species = "mm") at test-enrichment.R:76:3
2. └─clustermole:::get_scores(...)
3. ├─GSVA::gsva(...)
4. └─GSVA::gsva(...)
5. └─GSVA (local) .local(expr, gset.idx.list, ...)
6. └─GSVA:::.filterFeatures(expr, method)
7. ├─DelayedMatrixStats::rowSds(expr)
8. └─DelayedMatrixStats::rowSds(expr)
9. └─MatrixGenerics (local) .local(x, rows, cols, na.rm, center, ..., useNames = useNames)
10. └─matrixStats::rowSds(...)
11. └─matrixStats::rowVars(...)
12. └─matrixStats:::deprecatedUseNamesNA()
13. └─base::.Defunct(...)
[ FAIL 5 | WARN 7 | SKIP 0 | PASS 29 ]
Error: Test failures
Execution halted
Flavor: r-oldrel-windows-x86_64