Last updated on 2025-02-24 19:50:36 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 2.1.0 | 2.56 | 74.17 | 76.73 | OK | |
| r-devel-linux-x86_64-debian-gcc | 2.1.0 | 2.01 | 34.84 | 36.85 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 2.1.0 | 78.66 | ERROR | |||
| r-devel-linux-x86_64-fedora-gcc | 2.1.0 | 91.92 | ERROR | |||
| r-devel-macos-arm64 | 2.1.0 | 41.00 | OK | |||
| r-devel-macos-x86_64 | 2.1.0 | 92.00 | OK | |||
| r-devel-windows-x86_64 | 2.1.0 | 3.00 | 84.00 | 87.00 | OK | |
| r-patched-linux-x86_64 | 2.1.0 | 2.62 | 68.01 | 70.63 | OK | |
| r-release-linux-x86_64 | 2.1.0 | 2.44 | 68.81 | 71.25 | OK | |
| r-release-macos-arm64 | 2.1.0 | 57.00 | OK | |||
| r-release-macos-x86_64 | 2.1.0 | 14.00 | ERROR | |||
| r-release-windows-x86_64 | 2.1.0 | 5.00 | 83.00 | 88.00 | OK | |
| r-oldrel-macos-arm64 | 2.1.0 | 9.00 | ERROR | |||
| r-oldrel-macos-x86_64 | 2.1.0 | 10.00 | ERROR | |||
| r-oldrel-windows-x86_64 | 2.1.0 | 0.00 | 9.00 | 9.00 | ERROR |
Version: 2.1.0
Check: examples
Result: ERROR
Running examples in ‘kmeRs-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: kmeRs_heatmap
> ### Title: K-mer similarity score heatmap
> ### Aliases: kmeRs_heatmap
>
> ### ** Examples
>
> # Use RColorBrewer to generate a figure similar to publication
> library(RColorBrewer)
> h.palette <- rev(brewer.pal(9, "YlGnBu"))
> q0 <- c("GATTACA", "ACAGATT", "GAATTAC", "GAAATCT", "CTATAGA", "GTACATA", "AACGATT")
> example <- kmeRs_similarity_matrix(q0, submat = "BLOSUM62")
Error in h(simpleError(msg, call)) :
error in evaluating the argument 'x' in selecting a method for function 'score': 'recursive' must be a length-1 vector
Calls: kmeRs_similarity_matrix ... mpi.XStringSet.pairwiseAlignment -> XStringSet.pairwiseAlignment -> array -> unlist
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 2.1.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [4s/5s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
>
> library(testthat)
> library(kmeRs)
>
> test_check("kmeRs")
[ FAIL 7 | WARN 0 | SKIP 0 | PASS 0 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-kmeRs_heatmap.R:5:3'): Generate similarity matrix and display as a heatmap ──
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'x' in selecting a method for function 'score': 'recursive' must be a length-1 vector
Backtrace:
▆
1. ├─kmeRs::kmeRs_similarity_matrix(q = kmers_given, submat = "BLOSUM62") at test-kmeRs_heatmap.R:5:3
2. │ ├─base::as.vector(...)
3. │ └─base::sapply(...)
4. │ └─base::lapply(X = X, FUN = FUN, ...)
5. │ └─kmeRs (local) FUN(X[[i]], ...)
6. │ ├─BiocGenerics::score(...)
7. │ └─kmeRs:::kmeRs_twoSeqSim(...)
8. │ ├─pwalign::pairwiseAlignment(...)
9. │ └─pwalign::pairwiseAlignment(...)
10. │ └─pwalign (local) .local(pattern, subject, ...)
11. │ └─pwalign:::mpi.XStringSet.pairwiseAlignment(...)
12. │ └─pwalign:::XStringSet.pairwiseAlignment(...)
13. │ ├─base::array(...)
14. │ └─base::unlist(substitutionMatrix, substitutionMatrix)
15. │ └─base::stop("'recursive' must be a length-1 vector")
16. └─base::.handleSimpleError(...)
17. └─base (local) h(simpleError(msg, call))
── Error ('test-kmeRs_score.R:5:3'): Generate similarity matrix for given k-mers ──
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'x' in selecting a method for function 'score': 'recursive' must be a length-1 vector
Backtrace:
▆
1. ├─kmeRs::kmeRs_similarity_matrix(...) at test-kmeRs_score.R:5:3
2. │ ├─base::as.vector(...)
3. │ └─base::sapply(...)
4. │ └─base::lapply(X = X, FUN = FUN, ...)
5. │ └─kmeRs (local) FUN(X[[i]], ...)
6. │ ├─BiocGenerics::score(...)
7. │ └─kmeRs:::kmeRs_twoSeqSim(...)
8. │ ├─pwalign::pairwiseAlignment(...)
9. │ └─pwalign::pairwiseAlignment(...)
10. │ └─pwalign (local) .local(pattern, subject, ...)
11. │ └─pwalign:::mpi.XStringSet.pairwiseAlignment(...)
12. │ └─pwalign:::XStringSet.pairwiseAlignment(...)
13. │ ├─base::array(...)
14. │ └─base::unlist(substitutionMatrix, substitutionMatrix)
15. │ └─base::stop("'recursive' must be a length-1 vector")
16. └─base::.handleSimpleError(...)
17. └─base (local) h(simpleError(msg, call))
── Error ('test-kmeRs_show_alignment.R:3:3'): multiplication works ─────────────
Error in `unlist(substitutionMatrix, substitutionMatrix)`: 'recursive' must be a length-1 vector
Backtrace:
▆
1. └─kmeRs::kmeRs_show_alignment(...) at test-kmeRs_show_alignment.R:3:3
2. └─kmeRs:::kmeRs_twoSeqSim(...)
3. ├─pwalign::pairwiseAlignment(...)
4. └─pwalign::pairwiseAlignment(...)
5. └─pwalign (local) .local(pattern, subject, ...)
6. └─pwalign:::mpi.XStringSet.pairwiseAlignment(...)
7. └─pwalign:::XStringSet.pairwiseAlignment(...)
8. ├─base::array(...)
9. └─base::unlist(substitutionMatrix, substitutionMatrix)
── Error ('test-kmeRs_similarity_matrix.R:3:3'): Generate BLOSUM62 matrix ──────
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'x' in selecting a method for function 'score': 'recursive' must be a length-1 vector
Backtrace:
▆
1. ├─testthat::expect_true(is.data.frame(kmeRs_similarity_matrix(submat = "BLOSUM62"))) at test-kmeRs_similarity_matrix.R:3:3
2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─base::is.data.frame(kmeRs_similarity_matrix(submat = "BLOSUM62"))
5. ├─kmeRs::kmeRs_similarity_matrix(submat = "BLOSUM62")
6. │ ├─base::as.vector(...)
7. │ └─base::sapply(...)
8. │ └─base::lapply(X = X, FUN = FUN, ...)
9. │ └─kmeRs (local) FUN(X[[i]], ...)
10. │ ├─BiocGenerics::score(...)
11. │ └─kmeRs:::kmeRs_twoSeqSim(...)
12. │ ├─pwalign::pairwiseAlignment(...)
13. │ └─pwalign::pairwiseAlignment(...)
14. │ └─pwalign (local) .local(pattern, subject, ...)
15. │ └─pwalign:::mpi.XStringSet.pairwiseAlignment(...)
16. │ └─pwalign:::XStringSet.pairwiseAlignment(...)
17. │ ├─base::array(...)
18. │ └─base::unlist(substitutionMatrix, substitutionMatrix)
19. │ └─base::stop("'recursive' must be a length-1 vector")
20. └─base::.handleSimpleError(...)
21. └─base (local) h(simpleError(msg, call))
── Error ('test-kmeRs_similarity_matrix.R:10:3'): Generate similarity matrix for given k-mer ──
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'x' in selecting a method for function 'score': 'recursive' must be a length-1 vector
Backtrace:
▆
1. ├─kmeRs::kmeRs_similarity_matrix(...) at test-kmeRs_similarity_matrix.R:10:3
2. │ ├─base::as.vector(...)
3. │ └─base::sapply(...)
4. │ └─base::lapply(X = X, FUN = FUN, ...)
5. │ └─kmeRs (local) FUN(X[[i]], ...)
6. │ ├─BiocGenerics::score(...)
7. │ └─kmeRs:::kmeRs_twoSeqSim(...)
8. │ ├─pwalign::pairwiseAlignment(...)
9. │ └─pwalign::pairwiseAlignment(...)
10. │ └─pwalign (local) .local(pattern, subject, ...)
11. │ └─pwalign:::mpi.XStringSet.pairwiseAlignment(...)
12. │ └─pwalign:::XStringSet.pairwiseAlignment(...)
13. │ ├─base::array(...)
14. │ └─base::unlist(substitutionMatrix, substitutionMatrix)
15. │ └─base::stop("'recursive' must be a length-1 vector")
16. └─base::.handleSimpleError(...)
17. └─base (local) h(simpleError(msg, call))
── Error ('test-kmeRs_similarity_matrix.R:19:3'): Generate similarity matrix for given k-mers ──
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'x' in selecting a method for function 'score': 'recursive' must be a length-1 vector
Backtrace:
▆
1. ├─kmeRs::kmeRs_similarity_matrix(q = kmers_given, submat = "BLOSUM62") at test-kmeRs_similarity_matrix.R:19:3
2. │ ├─base::as.vector(...)
3. │ └─base::sapply(...)
4. │ └─base::lapply(X = X, FUN = FUN, ...)
5. │ └─kmeRs (local) FUN(X[[i]], ...)
6. │ ├─BiocGenerics::score(...)
7. │ └─kmeRs:::kmeRs_twoSeqSim(...)
8. │ ├─pwalign::pairwiseAlignment(...)
9. │ └─pwalign::pairwiseAlignment(...)
10. │ └─pwalign (local) .local(pattern, subject, ...)
11. │ └─pwalign:::mpi.XStringSet.pairwiseAlignment(...)
12. │ └─pwalign:::XStringSet.pairwiseAlignment(...)
13. │ ├─base::array(...)
14. │ └─base::unlist(substitutionMatrix, substitutionMatrix)
15. │ └─base::stop("'recursive' must be a length-1 vector")
16. └─base::.handleSimpleError(...)
17. └─base (local) h(simpleError(msg, call))
── Error ('test-kmeRs_statistics.R:5:3'): Calculate basic statistics for the matrix ──
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'x' in selecting a method for function 'score': 'recursive' must be a length-1 vector
Backtrace:
▆
1. ├─kmeRs::kmeRs_similarity_matrix(q = kmers_given, submat = "BLOSUM62") at test-kmeRs_statistics.R:5:3
2. │ ├─base::as.vector(...)
3. │ └─base::sapply(...)
4. │ └─base::lapply(X = X, FUN = FUN, ...)
5. │ └─kmeRs (local) FUN(X[[i]], ...)
6. │ ├─BiocGenerics::score(...)
7. │ └─kmeRs:::kmeRs_twoSeqSim(...)
8. │ ├─pwalign::pairwiseAlignment(...)
9. │ └─pwalign::pairwiseAlignment(...)
10. │ └─pwalign (local) .local(pattern, subject, ...)
11. │ └─pwalign:::mpi.XStringSet.pairwiseAlignment(...)
12. │ └─pwalign:::XStringSet.pairwiseAlignment(...)
13. │ ├─base::array(...)
14. │ └─base::unlist(substitutionMatrix, substitutionMatrix)
15. │ └─base::stop("'recursive' must be a length-1 vector")
16. └─base::.handleSimpleError(...)
17. └─base (local) h(simpleError(msg, call))
[ FAIL 7 | WARN 0 | SKIP 0 | PASS 0 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 2.1.0
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘Introduction_to_kmeRs_package.Rmd’ using rmarkdown
Quitting from lines 40-44 [unnamed-chunk-2] (Introduction_to_kmeRs_package.Rmd)
Error: processing vignette 'Introduction_to_kmeRs_package.Rmd' failed with diagnostics:
error in evaluating the argument 'x' in selecting a method for function 'score': 'recursive' must be a length-1 vector
--- failed re-building ‘Introduction_to_kmeRs_package.Rmd’
SUMMARY: processing the following file failed:
‘Introduction_to_kmeRs_package.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 2.1.0
Check: examples
Result: ERROR
Running examples in ‘kmeRs-Ex.R’ failed
The error most likely occurred in:
> ### Name: kmeRs_heatmap
> ### Title: K-mer similarity score heatmap
> ### Aliases: kmeRs_heatmap
>
> ### ** Examples
>
> # Use RColorBrewer to generate a figure similar to publication
> library(RColorBrewer)
> h.palette <- rev(brewer.pal(9, "YlGnBu"))
> q0 <- c("GATTACA", "ACAGATT", "GAATTAC", "GAAATCT", "CTATAGA", "GTACATA", "AACGATT")
> example <- kmeRs_similarity_matrix(q0, submat = "BLOSUM62")
Error in h(simpleError(msg, call)) :
error in evaluating the argument 'x' in selecting a method for function 'score': 'recursive' must be of length 1
Calls: kmeRs_similarity_matrix ... mpi.XStringSet.pairwiseAlignment -> XStringSet.pairwiseAlignment -> array -> unlist
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Version: 2.1.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [9s/21s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
>
> library(testthat)
> library(kmeRs)
>
> test_check("kmeRs")
[ FAIL 7 | WARN 0 | SKIP 0 | PASS 0 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-kmeRs_heatmap.R:5:3'): Generate similarity matrix and display as a heatmap ──
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'x' in selecting a method for function 'score': 'recursive' must be of length 1
Backtrace:
▆
1. ├─kmeRs::kmeRs_similarity_matrix(q = kmers_given, submat = "BLOSUM62") at test-kmeRs_heatmap.R:5:3
2. │ ├─base::as.vector(...)
3. │ └─base::sapply(...)
4. │ └─base::lapply(X = X, FUN = FUN, ...)
5. │ └─kmeRs (local) FUN(X[[i]], ...)
6. │ ├─BiocGenerics::score(...)
7. │ └─kmeRs:::kmeRs_twoSeqSim(...)
8. │ ├─pwalign::pairwiseAlignment(...)
9. │ └─pwalign::pairwiseAlignment(...)
10. │ └─pwalign (local) .local(pattern, subject, ...)
11. │ └─pwalign:::mpi.XStringSet.pairwiseAlignment(...)
12. │ └─pwalign:::XStringSet.pairwiseAlignment(...)
13. │ ├─base::array(...)
14. │ └─base::unlist(substitutionMatrix, substitutionMatrix)
15. │ └─base::stop("'recursive' must be of length 1")
16. └─base::.handleSimpleError(...)
17. └─base (local) h(simpleError(msg, call))
── Error ('test-kmeRs_score.R:5:3'): Generate similarity matrix for given k-mers ──
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'x' in selecting a method for function 'score': 'recursive' must be of length 1
Backtrace:
▆
1. ├─kmeRs::kmeRs_similarity_matrix(...) at test-kmeRs_score.R:5:3
2. │ ├─base::as.vector(...)
3. │ └─base::sapply(...)
4. │ └─base::lapply(X = X, FUN = FUN, ...)
5. │ └─kmeRs (local) FUN(X[[i]], ...)
6. │ ├─BiocGenerics::score(...)
7. │ └─kmeRs:::kmeRs_twoSeqSim(...)
8. │ ├─pwalign::pairwiseAlignment(...)
9. │ └─pwalign::pairwiseAlignment(...)
10. │ └─pwalign (local) .local(pattern, subject, ...)
11. │ └─pwalign:::mpi.XStringSet.pairwiseAlignment(...)
12. │ └─pwalign:::XStringSet.pairwiseAlignment(...)
13. │ ├─base::array(...)
14. │ └─base::unlist(substitutionMatrix, substitutionMatrix)
15. │ └─base::stop("'recursive' must be of length 1")
16. └─base::.handleSimpleError(...)
17. └─base (local) h(simpleError(msg, call))
── Error ('test-kmeRs_show_alignment.R:3:3'): multiplication works ─────────────
Error in `unlist(substitutionMatrix, substitutionMatrix)`: 'recursive' must be of length 1
Backtrace:
▆
1. └─kmeRs::kmeRs_show_alignment(...) at test-kmeRs_show_alignment.R:3:3
2. └─kmeRs:::kmeRs_twoSeqSim(...)
3. ├─pwalign::pairwiseAlignment(...)
4. └─pwalign::pairwiseAlignment(...)
5. └─pwalign (local) .local(pattern, subject, ...)
6. └─pwalign:::mpi.XStringSet.pairwiseAlignment(...)
7. └─pwalign:::XStringSet.pairwiseAlignment(...)
8. ├─base::array(...)
9. └─base::unlist(substitutionMatrix, substitutionMatrix)
── Error ('test-kmeRs_similarity_matrix.R:3:3'): Generate BLOSUM62 matrix ──────
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'x' in selecting a method for function 'score': 'recursive' must be of length 1
Backtrace:
▆
1. ├─testthat::expect_true(is.data.frame(kmeRs_similarity_matrix(submat = "BLOSUM62"))) at test-kmeRs_similarity_matrix.R:3:3
2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─base::is.data.frame(kmeRs_similarity_matrix(submat = "BLOSUM62"))
5. ├─kmeRs::kmeRs_similarity_matrix(submat = "BLOSUM62")
6. │ ├─base::as.vector(...)
7. │ └─base::sapply(...)
8. │ └─base::lapply(X = X, FUN = FUN, ...)
9. │ └─kmeRs (local) FUN(X[[i]], ...)
10. │ ├─BiocGenerics::score(...)
11. │ └─kmeRs:::kmeRs_twoSeqSim(...)
12. │ ├─pwalign::pairwiseAlignment(...)
13. │ └─pwalign::pairwiseAlignment(...)
14. │ └─pwalign (local) .local(pattern, subject, ...)
15. │ └─pwalign:::mpi.XStringSet.pairwiseAlignment(...)
16. │ └─pwalign:::XStringSet.pairwiseAlignment(...)
17. │ ├─base::array(...)
18. │ └─base::unlist(substitutionMatrix, substitutionMatrix)
19. │ └─base::stop("'recursive' must be of length 1")
20. └─base::.handleSimpleError(...)
21. └─base (local) h(simpleError(msg, call))
── Error ('test-kmeRs_similarity_matrix.R:10:3'): Generate similarity matrix for given k-mer ──
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'x' in selecting a method for function 'score': 'recursive' must be of length 1
Backtrace:
▆
1. ├─kmeRs::kmeRs_similarity_matrix(...) at test-kmeRs_similarity_matrix.R:10:3
2. │ ├─base::as.vector(...)
3. │ └─base::sapply(...)
4. │ └─base::lapply(X = X, FUN = FUN, ...)
5. │ └─kmeRs (local) FUN(X[[i]], ...)
6. │ ├─BiocGenerics::score(...)
7. │ └─kmeRs:::kmeRs_twoSeqSim(...)
8. │ ├─pwalign::pairwiseAlignment(...)
9. │ └─pwalign::pairwiseAlignment(...)
10. │ └─pwalign (local) .local(pattern, subject, ...)
11. │ └─pwalign:::mpi.XStringSet.pairwiseAlignment(...)
12. │ └─pwalign:::XStringSet.pairwiseAlignment(...)
13. │ ├─base::array(...)
14. │ └─base::unlist(substitutionMatrix, substitutionMatrix)
15. │ └─base::stop("'recursive' must be of length 1")
16. └─base::.handleSimpleError(...)
17. └─base (local) h(simpleError(msg, call))
── Error ('test-kmeRs_similarity_matrix.R:19:3'): Generate similarity matrix for given k-mers ──
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'x' in selecting a method for function 'score': 'recursive' must be of length 1
Backtrace:
▆
1. ├─kmeRs::kmeRs_similarity_matrix(q = kmers_given, submat = "BLOSUM62") at test-kmeRs_similarity_matrix.R:19:3
2. │ ├─base::as.vector(...)
3. │ └─base::sapply(...)
4. │ └─base::lapply(X = X, FUN = FUN, ...)
5. │ └─kmeRs (local) FUN(X[[i]], ...)
6. │ ├─BiocGenerics::score(...)
7. │ └─kmeRs:::kmeRs_twoSeqSim(...)
8. │ ├─pwalign::pairwiseAlignment(...)
9. │ └─pwalign::pairwiseAlignment(...)
10. │ └─pwalign (local) .local(pattern, subject, ...)
11. │ └─pwalign:::mpi.XStringSet.pairwiseAlignment(...)
12. │ └─pwalign:::XStringSet.pairwiseAlignment(...)
13. │ ├─base::array(...)
14. │ └─base::unlist(substitutionMatrix, substitutionMatrix)
15. │ └─base::stop("'recursive' must be of length 1")
16. └─base::.handleSimpleError(...)
17. └─base (local) h(simpleError(msg, call))
── Error ('test-kmeRs_statistics.R:5:3'): Calculate basic statistics for the matrix ──
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'x' in selecting a method for function 'score': 'recursive' must be of length 1
Backtrace:
▆
1. ├─kmeRs::kmeRs_similarity_matrix(q = kmers_given, submat = "BLOSUM62") at test-kmeRs_statistics.R:5:3
2. │ ├─base::as.vector(...)
3. │ └─base::sapply(...)
4. │ └─base::lapply(X = X, FUN = FUN, ...)
5. │ └─kmeRs (local) FUN(X[[i]], ...)
6. │ ├─BiocGenerics::score(...)
7. │ └─kmeRs:::kmeRs_twoSeqSim(...)
8. │ ├─pwalign::pairwiseAlignment(...)
9. │ └─pwalign::pairwiseAlignment(...)
10. │ └─pwalign (local) .local(pattern, subject, ...)
11. │ └─pwalign:::mpi.XStringSet.pairwiseAlignment(...)
12. │ └─pwalign:::XStringSet.pairwiseAlignment(...)
13. │ ├─base::array(...)
14. │ └─base::unlist(substitutionMatrix, substitutionMatrix)
15. │ └─base::stop("'recursive' must be of length 1")
16. └─base::.handleSimpleError(...)
17. └─base (local) h(simpleError(msg, call))
[ FAIL 7 | WARN 0 | SKIP 0 | PASS 0 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 2.1.0
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘Introduction_to_kmeRs_package.Rmd’ using rmarkdown
Quitting from lines 40-44 [unnamed-chunk-2] (Introduction_to_kmeRs_package.Rmd)
Error: processing vignette 'Introduction_to_kmeRs_package.Rmd' failed with diagnostics:
error in evaluating the argument 'x' in selecting a method for function 'score': 'recursive' must be of length 1
--- failed re-building ‘Introduction_to_kmeRs_package.Rmd’
SUMMARY: processing the following file failed:
‘Introduction_to_kmeRs_package.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Version: 2.1.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [9s/20s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
>
> library(testthat)
> library(kmeRs)
>
> test_check("kmeRs")
[ FAIL 7 | WARN 0 | SKIP 0 | PASS 0 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-kmeRs_heatmap.R:5:3'): Generate similarity matrix and display as a heatmap ──
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'x' in selecting a method for function 'score': 'recursive' must be of length 1
Backtrace:
▆
1. ├─kmeRs::kmeRs_similarity_matrix(q = kmers_given, submat = "BLOSUM62") at test-kmeRs_heatmap.R:5:3
2. │ ├─base::as.vector(...)
3. │ └─base::sapply(...)
4. │ └─base::lapply(X = X, FUN = FUN, ...)
5. │ └─kmeRs (local) FUN(X[[i]], ...)
6. │ ├─BiocGenerics::score(...)
7. │ └─kmeRs:::kmeRs_twoSeqSim(...)
8. │ ├─pwalign::pairwiseAlignment(...)
9. │ └─pwalign::pairwiseAlignment(...)
10. │ └─pwalign (local) .local(pattern, subject, ...)
11. │ └─pwalign:::mpi.XStringSet.pairwiseAlignment(...)
12. │ └─pwalign:::XStringSet.pairwiseAlignment(...)
13. │ ├─base::array(...)
14. │ └─base::unlist(substitutionMatrix, substitutionMatrix)
15. │ └─base::stop("'recursive' must be of length 1")
16. └─base::.handleSimpleError(...)
17. └─base (local) h(simpleError(msg, call))
── Error ('test-kmeRs_score.R:5:3'): Generate similarity matrix for given k-mers ──
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'x' in selecting a method for function 'score': 'recursive' must be of length 1
Backtrace:
▆
1. ├─kmeRs::kmeRs_similarity_matrix(...) at test-kmeRs_score.R:5:3
2. │ ├─base::as.vector(...)
3. │ └─base::sapply(...)
4. │ └─base::lapply(X = X, FUN = FUN, ...)
5. │ └─kmeRs (local) FUN(X[[i]], ...)
6. │ ├─BiocGenerics::score(...)
7. │ └─kmeRs:::kmeRs_twoSeqSim(...)
8. │ ├─pwalign::pairwiseAlignment(...)
9. │ └─pwalign::pairwiseAlignment(...)
10. │ └─pwalign (local) .local(pattern, subject, ...)
11. │ └─pwalign:::mpi.XStringSet.pairwiseAlignment(...)
12. │ └─pwalign:::XStringSet.pairwiseAlignment(...)
13. │ ├─base::array(...)
14. │ └─base::unlist(substitutionMatrix, substitutionMatrix)
15. │ └─base::stop("'recursive' must be of length 1")
16. └─base::.handleSimpleError(...)
17. └─base (local) h(simpleError(msg, call))
── Error ('test-kmeRs_show_alignment.R:3:3'): multiplication works ─────────────
Error in `unlist(substitutionMatrix, substitutionMatrix)`: 'recursive' must be of length 1
Backtrace:
▆
1. └─kmeRs::kmeRs_show_alignment(...) at test-kmeRs_show_alignment.R:3:3
2. └─kmeRs:::kmeRs_twoSeqSim(...)
3. ├─pwalign::pairwiseAlignment(...)
4. └─pwalign::pairwiseAlignment(...)
5. └─pwalign (local) .local(pattern, subject, ...)
6. └─pwalign:::mpi.XStringSet.pairwiseAlignment(...)
7. └─pwalign:::XStringSet.pairwiseAlignment(...)
8. ├─base::array(...)
9. └─base::unlist(substitutionMatrix, substitutionMatrix)
── Error ('test-kmeRs_similarity_matrix.R:3:3'): Generate BLOSUM62 matrix ──────
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'x' in selecting a method for function 'score': 'recursive' must be of length 1
Backtrace:
▆
1. ├─testthat::expect_true(is.data.frame(kmeRs_similarity_matrix(submat = "BLOSUM62"))) at test-kmeRs_similarity_matrix.R:3:3
2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─base::is.data.frame(kmeRs_similarity_matrix(submat = "BLOSUM62"))
5. ├─kmeRs::kmeRs_similarity_matrix(submat = "BLOSUM62")
6. │ ├─base::as.vector(...)
7. │ └─base::sapply(...)
8. │ └─base::lapply(X = X, FUN = FUN, ...)
9. │ └─kmeRs (local) FUN(X[[i]], ...)
10. │ ├─BiocGenerics::score(...)
11. │ └─kmeRs:::kmeRs_twoSeqSim(...)
12. │ ├─pwalign::pairwiseAlignment(...)
13. │ └─pwalign::pairwiseAlignment(...)
14. │ └─pwalign (local) .local(pattern, subject, ...)
15. │ └─pwalign:::mpi.XStringSet.pairwiseAlignment(...)
16. │ └─pwalign:::XStringSet.pairwiseAlignment(...)
17. │ ├─base::array(...)
18. │ └─base::unlist(substitutionMatrix, substitutionMatrix)
19. │ └─base::stop("'recursive' must be of length 1")
20. └─base::.handleSimpleError(...)
21. └─base (local) h(simpleError(msg, call))
── Error ('test-kmeRs_similarity_matrix.R:10:3'): Generate similarity matrix for given k-mer ──
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'x' in selecting a method for function 'score': 'recursive' must be of length 1
Backtrace:
▆
1. ├─kmeRs::kmeRs_similarity_matrix(...) at test-kmeRs_similarity_matrix.R:10:3
2. │ ├─base::as.vector(...)
3. │ └─base::sapply(...)
4. │ └─base::lapply(X = X, FUN = FUN, ...)
5. │ └─kmeRs (local) FUN(X[[i]], ...)
6. │ ├─BiocGenerics::score(...)
7. │ └─kmeRs:::kmeRs_twoSeqSim(...)
8. │ ├─pwalign::pairwiseAlignment(...)
9. │ └─pwalign::pairwiseAlignment(...)
10. │ └─pwalign (local) .local(pattern, subject, ...)
11. │ └─pwalign:::mpi.XStringSet.pairwiseAlignment(...)
12. │ └─pwalign:::XStringSet.pairwiseAlignment(...)
13. │ ├─base::array(...)
14. │ └─base::unlist(substitutionMatrix, substitutionMatrix)
15. │ └─base::stop("'recursive' must be of length 1")
16. └─base::.handleSimpleError(...)
17. └─base (local) h(simpleError(msg, call))
── Error ('test-kmeRs_similarity_matrix.R:19:3'): Generate similarity matrix for given k-mers ──
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'x' in selecting a method for function 'score': 'recursive' must be of length 1
Backtrace:
▆
1. ├─kmeRs::kmeRs_similarity_matrix(q = kmers_given, submat = "BLOSUM62") at test-kmeRs_similarity_matrix.R:19:3
2. │ ├─base::as.vector(...)
3. │ └─base::sapply(...)
4. │ └─base::lapply(X = X, FUN = FUN, ...)
5. │ └─kmeRs (local) FUN(X[[i]], ...)
6. │ ├─BiocGenerics::score(...)
7. │ └─kmeRs:::kmeRs_twoSeqSim(...)
8. │ ├─pwalign::pairwiseAlignment(...)
9. │ └─pwalign::pairwiseAlignment(...)
10. │ └─pwalign (local) .local(pattern, subject, ...)
11. │ └─pwalign:::mpi.XStringSet.pairwiseAlignment(...)
12. │ └─pwalign:::XStringSet.pairwiseAlignment(...)
13. │ ├─base::array(...)
14. │ └─base::unlist(substitutionMatrix, substitutionMatrix)
15. │ └─base::stop("'recursive' must be of length 1")
16. └─base::.handleSimpleError(...)
17. └─base (local) h(simpleError(msg, call))
── Error ('test-kmeRs_statistics.R:5:3'): Calculate basic statistics for the matrix ──
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'x' in selecting a method for function 'score': 'recursive' must be of length 1
Backtrace:
▆
1. ├─kmeRs::kmeRs_similarity_matrix(q = kmers_given, submat = "BLOSUM62") at test-kmeRs_statistics.R:5:3
2. │ ├─base::as.vector(...)
3. │ └─base::sapply(...)
4. │ └─base::lapply(X = X, FUN = FUN, ...)
5. │ └─kmeRs (local) FUN(X[[i]], ...)
6. │ ├─BiocGenerics::score(...)
7. │ └─kmeRs:::kmeRs_twoSeqSim(...)
8. │ ├─pwalign::pairwiseAlignment(...)
9. │ └─pwalign::pairwiseAlignment(...)
10. │ └─pwalign (local) .local(pattern, subject, ...)
11. │ └─pwalign:::mpi.XStringSet.pairwiseAlignment(...)
12. │ └─pwalign:::XStringSet.pairwiseAlignment(...)
13. │ ├─base::array(...)
14. │ └─base::unlist(substitutionMatrix, substitutionMatrix)
15. │ └─base::stop("'recursive' must be of length 1")
16. └─base::.handleSimpleError(...)
17. └─base (local) h(simpleError(msg, call))
[ FAIL 7 | WARN 0 | SKIP 0 | PASS 0 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 2.1.0
Check: package dependencies
Result: ERROR
Package required but not available: ‘pwalign’
See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Flavors: r-release-macos-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64