Last updated on 2024-09-19 00:49:59 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.1.3 | 373.37 | 77.92 | 451.29 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 1.1.3 | 230.86 | 55.82 | 286.68 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 1.1.3 | 689.55 | ERROR | |||
| r-devel-linux-x86_64-fedora-gcc | 1.1.3 | 793.44 | ERROR | |||
| r-devel-windows-x86_64 | 1.1.3 | 252.00 | 131.00 | 383.00 | ERROR | |
| r-patched-linux-x86_64 | 1.1.3 | 312.88 | 78.51 | 391.39 | NOTE | |
| r-release-linux-x86_64 | 1.1.3 | 300.54 | 77.92 | 378.46 | NOTE | |
| r-release-macos-arm64 | 1.1.3 | 192.00 | NOTE | |||
| r-release-macos-x86_64 | 1.1.3 | 189.00 | NOTE | |||
| r-release-windows-x86_64 | 1.1.3 | 262.00 | 138.00 | 400.00 | NOTE | |
| r-oldrel-macos-arm64 | 1.1.3 | 267.00 | NOTE | |||
| r-oldrel-macos-x86_64 | 1.1.3 | 464.00 | NOTE | |||
| r-oldrel-windows-x86_64 | 1.1.3 | 363.00 | 173.00 | 536.00 | OK |
Version: 1.1.3
Check: Rd files
Result: NOTE
checkRd: (-1) get_tidysq_options.Rd:37: Lost braces
37 | \item tidysq_pillar_max_width [code{integer(1)}]\cr
| ^
checkRd: (-1) read_fasta.Rd:54-55: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) read_fasta.Rd:56: Lost braces in \itemize; \value handles \item{}{} directly
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64, r-patched-linux-x86_64, r-release-linux-x86_64, r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64
Version: 1.1.3
Check: examples
Result: ERROR
Running examples in ‘tidysq-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ==.sq
> ### Title: Compare sq objects
> ### Aliases: ==.sq
>
> ### ** Examples
>
> # Creating objects to work on:
> sq_dna_1 <- sq(c("ACTGCTG", "CTTAGA", "CCCT", "CTGAATGT"),
+ alphabet = "dna_bsc")
> sq_dna_2 <- sq(c("ACTGCTG", "CTTAGA", "CCCT", "CTGAATGT"),
+ alphabet = "dna_bsc")
> sq_dna_3 <- sq(c("ACTGCTG", "CTTAGA", "GGAA"),
+ alphabet = "dna_bsc")
> sq_dna_4 <- sq(c("ACTGCTG", "CTTAGA", "CCCT", "GTNANN"),
+ alphabet = "dna_ext")
> sq_ami_1 <- sq(c("ACTGCTG", "NIKAAR", "CCCT", "CTGAATGT"),
+ alphabet = "ami_bsc")
> sq_unt <- sq(c("AHSNLVSCTK$SH%&VS", "YQTVKA&#BSKJGY",
+ "CCCT", "AVYI#VSV&*DVGDJCFA"))
>
> # Comparing sq object with an object of the same length:
> sq_dna_1 == sq_dna_2
[1] TRUE TRUE TRUE TRUE
> sq_dna_1 == c("ACTGCTG", "CTTAGA", "CCCT", "CTGAATGT")
[1] TRUE TRUE TRUE TRUE
>
> # Cannot compare sq objects of different lengths:
> ## Not run:
> ##D sq_dna_1 == sq_dna_3
> ##D sq_dna_1 == c("AAA", "CCC")
> ## End(Not run)
>
> # Unless comparing sq object with scalar value:
> sq_dna_1 == "CTTAGA"
[1] FALSE TRUE FALSE FALSE
>
> # It's possible to compare basic and extended types:
> sq_dna_1 == sq_dna_4
[1] TRUE TRUE TRUE FALSE
>
> # Mixing DNA, RNA and amino acid types throws an error, however:
> ## Not run:
> ##D sq_dna_1 == sq_ami_1
> ## End(Not run)
>
> # On the other hand, unt sq is acceptable everywhere:
> sq_dna_1 == sq_unt
Error in `vec_c()`:
! Can't combine `..1` <tidysq alphabet> and `..2` <tidysq alphabet>.
✖ Some attributes are incompatible.
ℹ The author of the class should implement vctrs methods.
ℹ See <https://vctrs.r-lib.org/reference/faq-error-incompatible-attributes.html>.
Backtrace:
▆
1. ├─tidysq:::`==.sq`(sq_dna_1, sq_unt)
2. │ └─vctrs::vec_equal(e1, e2)
3. │ └─vctrs:::vec_cast_common_params(!!!args, .to = .ptype)
4. │ └─vctrs:::vec_cast_common_opts(...)
5. │ └─vctrs (local) `<fn>`()
6. │ └─tidysq:::vec_ptype2.sq_dna_bsc.sq_unt(...)
7. │ ├─tidysq:::sq_ptype(union(alphabet(x), alphabet(y)), "unt")
8. │ │ ├─vctrs::new_list_of(...)
9. │ │ │ └─vctrs:::new_list_of0(x = x, ptype = ptype, ..., class = class)
10. │ │ │ └─vctrs::new_vctr(x, ..., ptype = ptype, class = c(class, "vctrs_list_of"))
11. │ │ └─tidysq:::sq_alphabet(str_alphabet, type)
12. │ │ └─vctrs::new_vctr(alph, type = type, class = c("sq_alphabet", "character"))
13. │ │ └─rlang::is_vector(.data)
14. │ └─base::union(alphabet(x), alphabet(y))
15. │ ├─base::c(x, y[match(y, x, 0L) == 0L])
16. │ └─vctrs:::c.vctrs_vctr(x, y[match(y, x, 0L) == 0L])
17. │ └─vctrs::vec_c(...)
18. └─vctrs (local) `<fn>`()
19. └─vctrs::vec_default_ptype2(...)
20. ├─base::withRestarts(...)
21. │ └─base (local) withOneRestart(expr, restarts[[1L]])
22. │ └─base (local) doWithOneRestart(return(expr), restart)
23. └─vctrs::stop_incompatible_type(...)
24. └─vctrs:::stop_incompatible(...)
25. └─vctrs:::stop_vctrs(...)
26. └─rlang::abort(message, class = c(class, "vctrs_error"), ..., call = call)
Execution halted
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc
Version: 1.1.3
Check: tests
Result: ERROR
Running ‘spelling.R’ [0s/0s]
Running ‘testthat.R’ [14s/16s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(tidysq)
Attaching package: 'tidysq'
The following object is masked from 'package:base':
paste
>
> test_check("tidysq")
[ FAIL 4 | WARN 0 | SKIP 1 | PASS 789 ]
══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• warning handling on C++ side is poorly implemented (1):
'test-warnings.R:39:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-concatenate.R:93:3'): c() generalizes any standard type and untyped sequences to unt sq ──
<vctrs_error_ptype2/vctrs_error_incompatible_type/vctrs_error_incompatible/vctrs_error/rlang_error/error/condition>
Error in `vec_c(...)`: Can't combine `..1` <tidysq alphabet> and `..2` <tidysq alphabet>.
x Some attributes are incompatible.
i The author of the class should implement vctrs methods.
i See <https://vctrs.r-lib.org/reference/faq-error-incompatible-attributes.html>.
Backtrace:
▆
1. ├─testthat::expect_vector(...) at test-concatenate.R:93:3
2. │ └─testthat::quasi_label(enquo(object), arg = "object")
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─base::c(sq_dna_bsc, sq_unt, sq_dna_bsc)
5. ├─vctrs:::c.vctrs_vctr(sq_dna_bsc, sq_unt, sq_dna_bsc)
6. │ └─vctrs::vec_c(...)
7. │ └─vctrs (local) `<fn>`()
8. │ └─tidysq:::vec_ptype2.sq_dna_bsc.sq_unt(...)
9. │ ├─tidysq:::sq_ptype(union(alphabet(x), alphabet(y)), "unt")
10. │ │ ├─vctrs::new_list_of(...)
11. │ │ │ └─vctrs:::new_list_of0(x = x, ptype = ptype, ..., class = class)
12. │ │ │ └─vctrs::new_vctr(x, ..., ptype = ptype, class = c(class, "vctrs_list_of"))
13. │ │ └─tidysq:::sq_alphabet(str_alphabet, type)
14. │ │ └─vctrs::new_vctr(alph, type = type, class = c("sq_alphabet", "character"))
15. │ │ └─rlang::is_vector(.data)
16. │ └─base::union(alphabet(x), alphabet(y))
17. │ ├─base::c(x, y[match(y, x, 0L) == 0L])
18. │ └─vctrs:::c.vctrs_vctr(x, y[match(y, x, 0L) == 0L])
19. │ └─vctrs::vec_c(...)
20. └─vctrs (local) `<fn>`()
21. └─vctrs::vec_default_ptype2(...)
22. ├─base::withRestarts(...)
23. │ └─base (local) withOneRestart(expr, restarts[[1L]])
24. │ └─base (local) doWithOneRestart(return(expr), restart)
25. └─vctrs::stop_incompatible_type(...)
26. └─vctrs:::stop_incompatible(...)
27. └─vctrs:::stop_vctrs(...)
28. └─rlang::abort(message, class = c(class, "vctrs_error"), ..., call = call)
── Error ('test-concatenate.R:114:3'): c() on any standard type and untyped sequences return correct value ──
<vctrs_error_ptype2/vctrs_error_incompatible_type/vctrs_error_incompatible/vctrs_error/rlang_error/error/condition>
Error in `vec_c(...)`: Can't combine `..1` <tidysq alphabet> and `..2` <tidysq alphabet>.
x Some attributes are incompatible.
i The author of the class should implement vctrs methods.
i See <https://vctrs.r-lib.org/reference/faq-error-incompatible-attributes.html>.
Backtrace:
▆
1. ├─testthat::expect_identical(...) at test-concatenate.R:114:3
2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─base::c(sq_dna_bsc, sq_unt, sq_dna_bsc)
5. ├─vctrs:::c.vctrs_vctr(sq_dna_bsc, sq_unt, sq_dna_bsc)
6. │ └─vctrs::vec_c(...)
7. │ └─vctrs (local) `<fn>`()
8. │ └─tidysq:::vec_ptype2.sq_dna_bsc.sq_unt(...)
9. │ ├─tidysq:::sq_ptype(union(alphabet(x), alphabet(y)), "unt")
10. │ │ ├─vctrs::new_list_of(...)
11. │ │ │ └─vctrs:::new_list_of0(x = x, ptype = ptype, ..., class = class)
12. │ │ │ └─vctrs::new_vctr(x, ..., ptype = ptype, class = c(class, "vctrs_list_of"))
13. │ │ └─tidysq:::sq_alphabet(str_alphabet, type)
14. │ │ └─vctrs::new_vctr(alph, type = type, class = c("sq_alphabet", "character"))
15. │ │ └─rlang::is_vector(.data)
16. │ └─base::union(alphabet(x), alphabet(y))
17. │ ├─base::c(x, y[match(y, x, 0L) == 0L])
18. │ └─vctrs:::c.vctrs_vctr(x, y[match(y, x, 0L) == 0L])
19. │ └─vctrs::vec_c(...)
20. └─vctrs (local) `<fn>`()
21. └─vctrs::vec_default_ptype2(...)
22. ├─base::withRestarts(...)
23. │ └─base (local) withOneRestart(expr, restarts[[1L]])
24. │ └─base (local) doWithOneRestart(return(expr), restart)
25. └─vctrs::stop_incompatible_type(...)
26. └─vctrs:::stop_incompatible(...)
27. └─vctrs:::stop_vctrs(...)
28. └─rlang::abort(message, class = c(class, "vctrs_error"), ..., call = call)
── Error ('test-paste.R:29:3'): paste() finds common prototype for all arguments (recycling length 1 vectors if necessary) ──
<vctrs_error_ptype2/vctrs_error_incompatible_type/vctrs_error_incompatible/vctrs_error/rlang_error/error/condition>
Error in `vec_c(...)`: Can't combine `..1` <tidysq alphabet> and `..2` <tidysq alphabet>.
x Some attributes are incompatible.
i The author of the class should implement vctrs methods.
i See <https://vctrs.r-lib.org/reference/faq-error-incompatible-attributes.html>.
Backtrace:
▆
1. ├─testthat::expect_vector(...) at test-paste.R:29:3
2. │ └─testthat::quasi_label(enquo(object), arg = "object")
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─tidysq::paste(sq_dna_1, sq_unt_3, sq_dna_2)
5. ├─tidysq:::paste.sq(sq_dna_1, sq_unt_3, sq_dna_2)
6. │ ├─tidysq:::CPP_paste(vec_cast_common(...), NA_letter)
7. │ └─vctrs::vec_cast_common(...)
8. │ └─vctrs (local) `<fn>`()
9. │ └─tidysq:::vec_ptype2.sq_dna_bsc.sq_unt(...)
10. │ ├─tidysq:::sq_ptype(union(alphabet(x), alphabet(y)), "unt")
11. │ │ ├─vctrs::new_list_of(...)
12. │ │ │ └─vctrs:::new_list_of0(x = x, ptype = ptype, ..., class = class)
13. │ │ │ └─vctrs::new_vctr(x, ..., ptype = ptype, class = c(class, "vctrs_list_of"))
14. │ │ └─tidysq:::sq_alphabet(str_alphabet, type)
15. │ │ └─vctrs::new_vctr(alph, type = type, class = c("sq_alphabet", "character"))
16. │ │ └─rlang::is_vector(.data)
17. │ └─base::union(alphabet(x), alphabet(y))
18. │ ├─base::c(x, y[match(y, x, 0L) == 0L])
19. │ └─vctrs:::c.vctrs_vctr(x, y[match(y, x, 0L) == 0L])
20. │ └─vctrs::vec_c(...)
21. └─vctrs (local) `<fn>`()
22. └─vctrs::vec_default_ptype2(...)
23. ├─base::withRestarts(...)
24. │ └─base (local) withOneRestart(expr, restarts[[1L]])
25. │ └─base (local) doWithOneRestart(return(expr), restart)
26. └─vctrs::stop_incompatible_type(...)
27. └─vctrs:::stop_incompatible(...)
28. └─vctrs:::stop_vctrs(...)
29. └─rlang::abort(message, class = c(class, "vctrs_error"), ..., call = call)
── Error ('test-paste.R:57:3'): paste() correctly merges sq objects of different types and alphabets ──
<vctrs_error_ptype2/vctrs_error_incompatible_type/vctrs_error_incompatible/vctrs_error/rlang_error/error/condition>
Error in `vec_c(...)`: Can't combine `..1` <tidysq alphabet> and `..2` <tidysq alphabet>.
x Some attributes are incompatible.
i The author of the class should implement vctrs methods.
i See <https://vctrs.r-lib.org/reference/faq-error-incompatible-attributes.html>.
Backtrace:
▆
1. ├─testthat::expect_identical(...) at test-paste.R:57:3
2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─tidysq::paste(sq_dna_1, sq_unt_3, sq_dna_2)
5. ├─tidysq:::paste.sq(sq_dna_1, sq_unt_3, sq_dna_2)
6. │ ├─tidysq:::CPP_paste(vec_cast_common(...), NA_letter)
7. │ └─vctrs::vec_cast_common(...)
8. │ └─vctrs (local) `<fn>`()
9. │ └─tidysq:::vec_ptype2.sq_dna_bsc.sq_unt(...)
10. │ ├─tidysq:::sq_ptype(union(alphabet(x), alphabet(y)), "unt")
11. │ │ ├─vctrs::new_list_of(...)
12. │ │ │ └─vctrs:::new_list_of0(x = x, ptype = ptype, ..., class = class)
13. │ │ │ └─vctrs::new_vctr(x, ..., ptype = ptype, class = c(class, "vctrs_list_of"))
14. │ │ └─tidysq:::sq_alphabet(str_alphabet, type)
15. │ │ └─vctrs::new_vctr(alph, type = type, class = c("sq_alphabet", "character"))
16. │ │ └─rlang::is_vector(.data)
17. │ └─base::union(alphabet(x), alphabet(y))
18. │ ├─base::c(x, y[match(y, x, 0L) == 0L])
19. │ └─vctrs:::c.vctrs_vctr(x, y[match(y, x, 0L) == 0L])
20. │ └─vctrs::vec_c(...)
21. └─vctrs (local) `<fn>`()
22. └─vctrs::vec_default_ptype2(...)
23. ├─base::withRestarts(...)
24. │ └─base (local) withOneRestart(expr, restarts[[1L]])
25. │ └─base (local) doWithOneRestart(return(expr), restart)
26. └─vctrs::stop_incompatible_type(...)
27. └─vctrs:::stop_incompatible(...)
28. └─vctrs:::stop_vctrs(...)
29. └─rlang::abort(message, class = c(class, "vctrs_error"), ..., call = call)
[ FAIL 4 | WARN 0 | SKIP 1 | PASS 789 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 1.1.3
Check: tests
Result: ERROR
Running ‘spelling.R’ [0s/0s]
Running ‘testthat.R’ [9s/10s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(tidysq)
Attaching package: 'tidysq'
The following object is masked from 'package:base':
paste
>
> test_check("tidysq")
[ FAIL 4 | WARN 0 | SKIP 1 | PASS 789 ]
══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• warning handling on C++ side is poorly implemented (1):
'test-warnings.R:39:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-concatenate.R:93:3'): c() generalizes any standard type and untyped sequences to unt sq ──
<vctrs_error_ptype2/vctrs_error_incompatible_type/vctrs_error_incompatible/vctrs_error/rlang_error/error/condition>
Error in `vec_c(...)`: Can't combine `..1` <tidysq alphabet> and `..2` <tidysq alphabet>.
x Some attributes are incompatible.
i The author of the class should implement vctrs methods.
i See <https://vctrs.r-lib.org/reference/faq-error-incompatible-attributes.html>.
Backtrace:
▆
1. ├─testthat::expect_vector(...) at test-concatenate.R:93:3
2. │ └─testthat::quasi_label(enquo(object), arg = "object")
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─base::c(sq_dna_bsc, sq_unt, sq_dna_bsc)
5. ├─vctrs:::c.vctrs_vctr(sq_dna_bsc, sq_unt, sq_dna_bsc)
6. │ └─vctrs::vec_c(...)
7. │ └─vctrs (local) `<fn>`()
8. │ └─tidysq:::vec_ptype2.sq_dna_bsc.sq_unt(...)
9. │ ├─tidysq:::sq_ptype(union(alphabet(x), alphabet(y)), "unt")
10. │ │ ├─vctrs::new_list_of(...)
11. │ │ │ └─vctrs:::new_list_of0(x = x, ptype = ptype, ..., class = class)
12. │ │ │ └─vctrs::new_vctr(x, ..., ptype = ptype, class = c(class, "vctrs_list_of"))
13. │ │ └─tidysq:::sq_alphabet(str_alphabet, type)
14. │ │ └─vctrs::new_vctr(alph, type = type, class = c("sq_alphabet", "character"))
15. │ │ └─rlang::is_vector(.data)
16. │ └─base::union(alphabet(x), alphabet(y))
17. │ ├─base::c(x, y[match(y, x, 0L) == 0L])
18. │ └─vctrs:::c.vctrs_vctr(x, y[match(y, x, 0L) == 0L])
19. │ └─vctrs::vec_c(...)
20. └─vctrs (local) `<fn>`()
21. └─vctrs::vec_default_ptype2(...)
22. ├─base::withRestarts(...)
23. │ └─base (local) withOneRestart(expr, restarts[[1L]])
24. │ └─base (local) doWithOneRestart(return(expr), restart)
25. └─vctrs::stop_incompatible_type(...)
26. └─vctrs:::stop_incompatible(...)
27. └─vctrs:::stop_vctrs(...)
28. └─rlang::abort(message, class = c(class, "vctrs_error"), ..., call = call)
── Error ('test-concatenate.R:114:3'): c() on any standard type and untyped sequences return correct value ──
<vctrs_error_ptype2/vctrs_error_incompatible_type/vctrs_error_incompatible/vctrs_error/rlang_error/error/condition>
Error in `vec_c(...)`: Can't combine `..1` <tidysq alphabet> and `..2` <tidysq alphabet>.
x Some attributes are incompatible.
i The author of the class should implement vctrs methods.
i See <https://vctrs.r-lib.org/reference/faq-error-incompatible-attributes.html>.
Backtrace:
▆
1. ├─testthat::expect_identical(...) at test-concatenate.R:114:3
2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─base::c(sq_dna_bsc, sq_unt, sq_dna_bsc)
5. ├─vctrs:::c.vctrs_vctr(sq_dna_bsc, sq_unt, sq_dna_bsc)
6. │ └─vctrs::vec_c(...)
7. │ └─vctrs (local) `<fn>`()
8. │ └─tidysq:::vec_ptype2.sq_dna_bsc.sq_unt(...)
9. │ ├─tidysq:::sq_ptype(union(alphabet(x), alphabet(y)), "unt")
10. │ │ ├─vctrs::new_list_of(...)
11. │ │ │ └─vctrs:::new_list_of0(x = x, ptype = ptype, ..., class = class)
12. │ │ │ └─vctrs::new_vctr(x, ..., ptype = ptype, class = c(class, "vctrs_list_of"))
13. │ │ └─tidysq:::sq_alphabet(str_alphabet, type)
14. │ │ └─vctrs::new_vctr(alph, type = type, class = c("sq_alphabet", "character"))
15. │ │ └─rlang::is_vector(.data)
16. │ └─base::union(alphabet(x), alphabet(y))
17. │ ├─base::c(x, y[match(y, x, 0L) == 0L])
18. │ └─vctrs:::c.vctrs_vctr(x, y[match(y, x, 0L) == 0L])
19. │ └─vctrs::vec_c(...)
20. └─vctrs (local) `<fn>`()
21. └─vctrs::vec_default_ptype2(...)
22. ├─base::withRestarts(...)
23. │ └─base (local) withOneRestart(expr, restarts[[1L]])
24. │ └─base (local) doWithOneRestart(return(expr), restart)
25. └─vctrs::stop_incompatible_type(...)
26. └─vctrs:::stop_incompatible(...)
27. └─vctrs:::stop_vctrs(...)
28. └─rlang::abort(message, class = c(class, "vctrs_error"), ..., call = call)
── Error ('test-paste.R:29:3'): paste() finds common prototype for all arguments (recycling length 1 vectors if necessary) ──
<vctrs_error_ptype2/vctrs_error_incompatible_type/vctrs_error_incompatible/vctrs_error/rlang_error/error/condition>
Error in `vec_c(...)`: Can't combine `..1` <tidysq alphabet> and `..2` <tidysq alphabet>.
x Some attributes are incompatible.
i The author of the class should implement vctrs methods.
i See <https://vctrs.r-lib.org/reference/faq-error-incompatible-attributes.html>.
Backtrace:
▆
1. ├─testthat::expect_vector(...) at test-paste.R:29:3
2. │ └─testthat::quasi_label(enquo(object), arg = "object")
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─tidysq::paste(sq_dna_1, sq_unt_3, sq_dna_2)
5. ├─tidysq:::paste.sq(sq_dna_1, sq_unt_3, sq_dna_2)
6. │ ├─tidysq:::CPP_paste(vec_cast_common(...), NA_letter)
7. │ └─vctrs::vec_cast_common(...)
8. │ └─vctrs (local) `<fn>`()
9. │ └─tidysq:::vec_ptype2.sq_dna_bsc.sq_unt(...)
10. │ ├─tidysq:::sq_ptype(union(alphabet(x), alphabet(y)), "unt")
11. │ │ ├─vctrs::new_list_of(...)
12. │ │ │ └─vctrs:::new_list_of0(x = x, ptype = ptype, ..., class = class)
13. │ │ │ └─vctrs::new_vctr(x, ..., ptype = ptype, class = c(class, "vctrs_list_of"))
14. │ │ └─tidysq:::sq_alphabet(str_alphabet, type)
15. │ │ └─vctrs::new_vctr(alph, type = type, class = c("sq_alphabet", "character"))
16. │ │ └─rlang::is_vector(.data)
17. │ └─base::union(alphabet(x), alphabet(y))
18. │ ├─base::c(x, y[match(y, x, 0L) == 0L])
19. │ └─vctrs:::c.vctrs_vctr(x, y[match(y, x, 0L) == 0L])
20. │ └─vctrs::vec_c(...)
21. └─vctrs (local) `<fn>`()
22. └─vctrs::vec_default_ptype2(...)
23. ├─base::withRestarts(...)
24. │ └─base (local) withOneRestart(expr, restarts[[1L]])
25. │ └─base (local) doWithOneRestart(return(expr), restart)
26. └─vctrs::stop_incompatible_type(...)
27. └─vctrs:::stop_incompatible(...)
28. └─vctrs:::stop_vctrs(...)
29. └─rlang::abort(message, class = c(class, "vctrs_error"), ..., call = call)
── Error ('test-paste.R:57:3'): paste() correctly merges sq objects of different types and alphabets ──
<vctrs_error_ptype2/vctrs_error_incompatible_type/vctrs_error_incompatible/vctrs_error/rlang_error/error/condition>
Error in `vec_c(...)`: Can't combine `..1` <tidysq alphabet> and `..2` <tidysq alphabet>.
x Some attributes are incompatible.
i The author of the class should implement vctrs methods.
i See <https://vctrs.r-lib.org/reference/faq-error-incompatible-attributes.html>.
Backtrace:
▆
1. ├─testthat::expect_identical(...) at test-paste.R:57:3
2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─tidysq::paste(sq_dna_1, sq_unt_3, sq_dna_2)
5. ├─tidysq:::paste.sq(sq_dna_1, sq_unt_3, sq_dna_2)
6. │ ├─tidysq:::CPP_paste(vec_cast_common(...), NA_letter)
7. │ └─vctrs::vec_cast_common(...)
8. │ └─vctrs (local) `<fn>`()
9. │ └─tidysq:::vec_ptype2.sq_dna_bsc.sq_unt(...)
10. │ ├─tidysq:::sq_ptype(union(alphabet(x), alphabet(y)), "unt")
11. │ │ ├─vctrs::new_list_of(...)
12. │ │ │ └─vctrs:::new_list_of0(x = x, ptype = ptype, ..., class = class)
13. │ │ │ └─vctrs::new_vctr(x, ..., ptype = ptype, class = c(class, "vctrs_list_of"))
14. │ │ └─tidysq:::sq_alphabet(str_alphabet, type)
15. │ │ └─vctrs::new_vctr(alph, type = type, class = c("sq_alphabet", "character"))
16. │ │ └─rlang::is_vector(.data)
17. │ └─base::union(alphabet(x), alphabet(y))
18. │ ├─base::c(x, y[match(y, x, 0L) == 0L])
19. │ └─vctrs:::c.vctrs_vctr(x, y[match(y, x, 0L) == 0L])
20. │ └─vctrs::vec_c(...)
21. └─vctrs (local) `<fn>`()
22. └─vctrs::vec_default_ptype2(...)
23. ├─base::withRestarts(...)
24. │ └─base (local) withOneRestart(expr, restarts[[1L]])
25. │ └─base (local) doWithOneRestart(return(expr), restart)
26. └─vctrs::stop_incompatible_type(...)
27. └─vctrs:::stop_incompatible(...)
28. └─vctrs:::stop_vctrs(...)
29. └─rlang::abort(message, class = c(class, "vctrs_error"), ..., call = call)
[ FAIL 4 | WARN 0 | SKIP 1 | PASS 789 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.1.3
Check: examples
Result: ERROR
Running examples in ‘tidysq-Ex.R’ failed
The error most likely occurred in:
> ### Name: ==.sq
> ### Title: Compare sq objects
> ### Aliases: ==.sq
>
> ### ** Examples
>
> # Creating objects to work on:
> sq_dna_1 <- sq(c("ACTGCTG", "CTTAGA", "CCCT", "CTGAATGT"),
+ alphabet = "dna_bsc")
> sq_dna_2 <- sq(c("ACTGCTG", "CTTAGA", "CCCT", "CTGAATGT"),
+ alphabet = "dna_bsc")
> sq_dna_3 <- sq(c("ACTGCTG", "CTTAGA", "GGAA"),
+ alphabet = "dna_bsc")
> sq_dna_4 <- sq(c("ACTGCTG", "CTTAGA", "CCCT", "GTNANN"),
+ alphabet = "dna_ext")
> sq_ami_1 <- sq(c("ACTGCTG", "NIKAAR", "CCCT", "CTGAATGT"),
+ alphabet = "ami_bsc")
> sq_unt <- sq(c("AHSNLVSCTK$SH%&VS", "YQTVKA&#BSKJGY",
+ "CCCT", "AVYI#VSV&*DVGDJCFA"))
>
> # Comparing sq object with an object of the same length:
> sq_dna_1 == sq_dna_2
[1] TRUE TRUE TRUE TRUE
> sq_dna_1 == c("ACTGCTG", "CTTAGA", "CCCT", "CTGAATGT")
[1] TRUE TRUE TRUE TRUE
>
> # Cannot compare sq objects of different lengths:
> ## Not run:
> ##D sq_dna_1 == sq_dna_3
> ##D sq_dna_1 == c("AAA", "CCC")
> ## End(Not run)
>
> # Unless comparing sq object with scalar value:
> sq_dna_1 == "CTTAGA"
[1] FALSE TRUE FALSE FALSE
>
> # It's possible to compare basic and extended types:
> sq_dna_1 == sq_dna_4
[1] TRUE TRUE TRUE FALSE
>
> # Mixing DNA, RNA and amino acid types throws an error, however:
> ## Not run:
> ##D sq_dna_1 == sq_ami_1
> ## End(Not run)
>
> # On the other hand, unt sq is acceptable everywhere:
> sq_dna_1 == sq_unt
Error in `vec_c()`:
! Can't combine `..1` <tidysq alphabet> and `..2` <tidysq alphabet>.
✖ Some attributes are incompatible.
ℹ The author of the class should implement vctrs methods.
ℹ See <https://vctrs.r-lib.org/reference/faq-error-incompatible-attributes.html>.
Backtrace:
▆
1. ├─tidysq:::`==.sq`(sq_dna_1, sq_unt)
2. │ └─vctrs::vec_equal(e1, e2)
3. │ └─vctrs:::vec_cast_common_params(!!!args, .to = .ptype)
4. │ └─vctrs:::vec_cast_common_opts(...)
5. │ └─vctrs (local) `<fn>`()
6. │ └─tidysq:::vec_ptype2.sq_dna_bsc.sq_unt(...)
7. │ ├─tidysq:::sq_ptype(union(alphabet(x), alphabet(y)), "unt")
8. │ │ ├─vctrs::new_list_of(...)
9. │ │ │ └─vctrs:::new_list_of0(x = x, ptype = ptype, ..., class = class)
10. │ │ │ └─vctrs::new_vctr(x, ..., ptype = ptype, class = c(class, "vctrs_list_of"))
11. │ │ └─tidysq:::sq_alphabet(str_alphabet, type)
12. │ │ └─vctrs::new_vctr(alph, type = type, class = c("sq_alphabet", "character"))
13. │ │ └─rlang::is_vector(.data)
14. │ └─base::union(alphabet(x), alphabet(y))
15. │ ├─base::c(x, y[match(y, x, 0L) == 0L])
16. │ └─vctrs:::c.vctrs_vctr(x, y[match(y, x, 0L) == 0L])
17. │ └─vctrs::vec_c(...)
18. └─vctrs (local) `<fn>`()
19. └─vctrs::vec_default_ptype2(...)
20. ├─base::withRestarts(...)
21. │ └─base (local) withOneRestart(expr, restarts[[1L]])
22. │ └─base (local) doWithOneRestart(return(expr), restart)
23. └─vctrs::stop_incompatible_type(...)
24. └─vctrs:::stop_incompatible(...)
25. └─vctrs:::stop_vctrs(...)
26. └─rlang::abort(message, class = c(class, "vctrs_error"), ..., call = call)
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64
Version: 1.1.3
Check: tests
Result: ERROR
Running ‘spelling.R’
Running ‘testthat.R’ [21s/25s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(tidysq)
Attaching package: 'tidysq'
The following object is masked from 'package:base':
paste
>
> test_check("tidysq")
[ FAIL 4 | WARN 0 | SKIP 1 | PASS 789 ]
══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• warning handling on C++ side is poorly implemented (1):
'test-warnings.R:39:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-concatenate.R:93:3'): c() generalizes any standard type and untyped sequences to unt sq ──
<vctrs_error_ptype2/vctrs_error_incompatible_type/vctrs_error_incompatible/vctrs_error/rlang_error/error/condition>
Error in `vec_c(...)`: Can't combine `..1` <tidysq alphabet> and `..2` <tidysq alphabet>.
x Some attributes are incompatible.
i The author of the class should implement vctrs methods.
i See <https://vctrs.r-lib.org/reference/faq-error-incompatible-attributes.html>.
Backtrace:
▆
1. ├─testthat::expect_vector(...) at test-concatenate.R:93:3
2. │ └─testthat::quasi_label(enquo(object), arg = "object")
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─base::c(sq_dna_bsc, sq_unt, sq_dna_bsc)
5. ├─vctrs:::c.vctrs_vctr(sq_dna_bsc, sq_unt, sq_dna_bsc)
6. │ └─vctrs::vec_c(...)
7. │ └─vctrs (local) `<fn>`()
8. │ └─tidysq:::vec_ptype2.sq_dna_bsc.sq_unt(...)
9. │ ├─tidysq:::sq_ptype(union(alphabet(x), alphabet(y)), "unt")
10. │ │ ├─vctrs::new_list_of(...)
11. │ │ │ └─vctrs:::new_list_of0(x = x, ptype = ptype, ..., class = class)
12. │ │ │ └─vctrs::new_vctr(x, ..., ptype = ptype, class = c(class, "vctrs_list_of"))
13. │ │ └─tidysq:::sq_alphabet(str_alphabet, type)
14. │ │ └─vctrs::new_vctr(alph, type = type, class = c("sq_alphabet", "character"))
15. │ │ └─rlang::is_vector(.data)
16. │ └─base::union(alphabet(x), alphabet(y))
17. │ ├─base::c(x, y[match(y, x, 0L) == 0L])
18. │ └─vctrs:::c.vctrs_vctr(x, y[match(y, x, 0L) == 0L])
19. │ └─vctrs::vec_c(...)
20. └─vctrs (local) `<fn>`()
21. └─vctrs::vec_default_ptype2(...)
22. ├─base::withRestarts(...)
23. │ └─base (local) withOneRestart(expr, restarts[[1L]])
24. │ └─base (local) doWithOneRestart(return(expr), restart)
25. └─vctrs::stop_incompatible_type(...)
26. └─vctrs:::stop_incompatible(...)
27. └─vctrs:::stop_vctrs(...)
28. └─rlang::abort(message, class = c(class, "vctrs_error"), ..., call = call)
── Error ('test-concatenate.R:114:3'): c() on any standard type and untyped sequences return correct value ──
<vctrs_error_ptype2/vctrs_error_incompatible_type/vctrs_error_incompatible/vctrs_error/rlang_error/error/condition>
Error in `vec_c(...)`: Can't combine `..1` <tidysq alphabet> and `..2` <tidysq alphabet>.
x Some attributes are incompatible.
i The author of the class should implement vctrs methods.
i See <https://vctrs.r-lib.org/reference/faq-error-incompatible-attributes.html>.
Backtrace:
▆
1. ├─testthat::expect_identical(...) at test-concatenate.R:114:3
2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─base::c(sq_dna_bsc, sq_unt, sq_dna_bsc)
5. ├─vctrs:::c.vctrs_vctr(sq_dna_bsc, sq_unt, sq_dna_bsc)
6. │ └─vctrs::vec_c(...)
7. │ └─vctrs (local) `<fn>`()
8. │ └─tidysq:::vec_ptype2.sq_dna_bsc.sq_unt(...)
9. │ ├─tidysq:::sq_ptype(union(alphabet(x), alphabet(y)), "unt")
10. │ │ ├─vctrs::new_list_of(...)
11. │ │ │ └─vctrs:::new_list_of0(x = x, ptype = ptype, ..., class = class)
12. │ │ │ └─vctrs::new_vctr(x, ..., ptype = ptype, class = c(class, "vctrs_list_of"))
13. │ │ └─tidysq:::sq_alphabet(str_alphabet, type)
14. │ │ └─vctrs::new_vctr(alph, type = type, class = c("sq_alphabet", "character"))
15. │ │ └─rlang::is_vector(.data)
16. │ └─base::union(alphabet(x), alphabet(y))
17. │ ├─base::c(x, y[match(y, x, 0L) == 0L])
18. │ └─vctrs:::c.vctrs_vctr(x, y[match(y, x, 0L) == 0L])
19. │ └─vctrs::vec_c(...)
20. └─vctrs (local) `<fn>`()
21. └─vctrs::vec_default_ptype2(...)
22. ├─base::withRestarts(...)
23. │ └─base (local) withOneRestart(expr, restarts[[1L]])
24. │ └─base (local) doWithOneRestart(return(expr), restart)
25. └─vctrs::stop_incompatible_type(...)
26. └─vctrs:::stop_incompatible(...)
27. └─vctrs:::stop_vctrs(...)
28. └─rlang::abort(message, class = c(class, "vctrs_error"), ..., call = call)
── Error ('test-paste.R:29:3'): paste() finds common prototype for all arguments (recycling length 1 vectors if necessary) ──
<vctrs_error_ptype2/vctrs_error_incompatible_type/vctrs_error_incompatible/vctrs_error/rlang_error/error/condition>
Error in `vec_c(...)`: Can't combine `..1` <tidysq alphabet> and `..2` <tidysq alphabet>.
x Some attributes are incompatible.
i The author of the class should implement vctrs methods.
i See <https://vctrs.r-lib.org/reference/faq-error-incompatible-attributes.html>.
Backtrace:
▆
1. ├─testthat::expect_vector(...) at test-paste.R:29:3
2. │ └─testthat::quasi_label(enquo(object), arg = "object")
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─tidysq::paste(sq_dna_1, sq_unt_3, sq_dna_2)
5. ├─tidysq:::paste.sq(sq_dna_1, sq_unt_3, sq_dna_2)
6. │ ├─tidysq:::CPP_paste(vec_cast_common(...), NA_letter)
7. │ └─vctrs::vec_cast_common(...)
8. │ └─vctrs (local) `<fn>`()
9. │ └─tidysq:::vec_ptype2.sq_dna_bsc.sq_unt(...)
10. │ ├─tidysq:::sq_ptype(union(alphabet(x), alphabet(y)), "unt")
11. │ │ ├─vctrs::new_list_of(...)
12. │ │ │ └─vctrs:::new_list_of0(x = x, ptype = ptype, ..., class = class)
13. │ │ │ └─vctrs::new_vctr(x, ..., ptype = ptype, class = c(class, "vctrs_list_of"))
14. │ │ └─tidysq:::sq_alphabet(str_alphabet, type)
15. │ │ └─vctrs::new_vctr(alph, type = type, class = c("sq_alphabet", "character"))
16. │ │ └─rlang::is_vector(.data)
17. │ └─base::union(alphabet(x), alphabet(y))
18. │ ├─base::c(x, y[match(y, x, 0L) == 0L])
19. │ └─vctrs:::c.vctrs_vctr(x, y[match(y, x, 0L) == 0L])
20. │ └─vctrs::vec_c(...)
21. └─vctrs (local) `<fn>`()
22. └─vctrs::vec_default_ptype2(...)
23. ├─base::withRestarts(...)
24. │ └─base (local) withOneRestart(expr, restarts[[1L]])
25. │ └─base (local) doWithOneRestart(return(expr), restart)
26. └─vctrs::stop_incompatible_type(...)
27. └─vctrs:::stop_incompatible(...)
28. └─vctrs:::stop_vctrs(...)
29. └─rlang::abort(message, class = c(class, "vctrs_error"), ..., call = call)
── Error ('test-paste.R:57:3'): paste() correctly merges sq objects of different types and alphabets ──
<vctrs_error_ptype2/vctrs_error_incompatible_type/vctrs_error_incompatible/vctrs_error/rlang_error/error/condition>
Error in `vec_c(...)`: Can't combine `..1` <tidysq alphabet> and `..2` <tidysq alphabet>.
x Some attributes are incompatible.
i The author of the class should implement vctrs methods.
i See <https://vctrs.r-lib.org/reference/faq-error-incompatible-attributes.html>.
Backtrace:
▆
1. ├─testthat::expect_identical(...) at test-paste.R:57:3
2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─tidysq::paste(sq_dna_1, sq_unt_3, sq_dna_2)
5. ├─tidysq:::paste.sq(sq_dna_1, sq_unt_3, sq_dna_2)
6. │ ├─tidysq:::CPP_paste(vec_cast_common(...), NA_letter)
7. │ └─vctrs::vec_cast_common(...)
8. │ └─vctrs (local) `<fn>`()
9. │ └─tidysq:::vec_ptype2.sq_dna_bsc.sq_unt(...)
10. │ ├─tidysq:::sq_ptype(union(alphabet(x), alphabet(y)), "unt")
11. │ │ ├─vctrs::new_list_of(...)
12. │ │ │ └─vctrs:::new_list_of0(x = x, ptype = ptype, ..., class = class)
13. │ │ │ └─vctrs::new_vctr(x, ..., ptype = ptype, class = c(class, "vctrs_list_of"))
14. │ │ └─tidysq:::sq_alphabet(str_alphabet, type)
15. │ │ └─vctrs::new_vctr(alph, type = type, class = c("sq_alphabet", "character"))
16. │ │ └─rlang::is_vector(.data)
17. │ └─base::union(alphabet(x), alphabet(y))
18. │ ├─base::c(x, y[match(y, x, 0L) == 0L])
19. │ └─vctrs:::c.vctrs_vctr(x, y[match(y, x, 0L) == 0L])
20. │ └─vctrs::vec_c(...)
21. └─vctrs (local) `<fn>`()
22. └─vctrs::vec_default_ptype2(...)
23. ├─base::withRestarts(...)
24. │ └─base (local) withOneRestart(expr, restarts[[1L]])
25. │ └─base (local) doWithOneRestart(return(expr), restart)
26. └─vctrs::stop_incompatible_type(...)
27. └─vctrs:::stop_incompatible(...)
28. └─vctrs:::stop_vctrs(...)
29. └─rlang::abort(message, class = c(class, "vctrs_error"), ..., call = call)
[ FAIL 4 | WARN 0 | SKIP 1 | PASS 789 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 1.1.3
Check: tests
Result: ERROR
Running ‘spelling.R’
Running ‘testthat.R’ [22s/28s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(tidysq)
Attaching package: 'tidysq'
The following object is masked from 'package:base':
paste
>
> test_check("tidysq")
[ FAIL 4 | WARN 0 | SKIP 1 | PASS 789 ]
══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• warning handling on C++ side is poorly implemented (1):
'test-warnings.R:39:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-concatenate.R:93:3'): c() generalizes any standard type and untyped sequences to unt sq ──
<vctrs_error_ptype2/vctrs_error_incompatible_type/vctrs_error_incompatible/vctrs_error/rlang_error/error/condition>
Error in `vec_c(...)`: Can't combine `..1` <tidysq alphabet> and `..2` <tidysq alphabet>.
x Some attributes are incompatible.
i The author of the class should implement vctrs methods.
i See <https://vctrs.r-lib.org/reference/faq-error-incompatible-attributes.html>.
Backtrace:
▆
1. ├─testthat::expect_vector(...) at test-concatenate.R:93:3
2. │ └─testthat::quasi_label(enquo(object), arg = "object")
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─base::c(sq_dna_bsc, sq_unt, sq_dna_bsc)
5. ├─vctrs:::c.vctrs_vctr(sq_dna_bsc, sq_unt, sq_dna_bsc)
6. │ └─vctrs::vec_c(...)
7. │ └─vctrs (local) `<fn>`()
8. │ └─tidysq:::vec_ptype2.sq_dna_bsc.sq_unt(...)
9. │ ├─tidysq:::sq_ptype(union(alphabet(x), alphabet(y)), "unt")
10. │ │ ├─vctrs::new_list_of(...)
11. │ │ │ └─vctrs:::new_list_of0(x = x, ptype = ptype, ..., class = class)
12. │ │ │ └─vctrs::new_vctr(x, ..., ptype = ptype, class = c(class, "vctrs_list_of"))
13. │ │ └─tidysq:::sq_alphabet(str_alphabet, type)
14. │ │ └─vctrs::new_vctr(alph, type = type, class = c("sq_alphabet", "character"))
15. │ │ └─rlang::is_vector(.data)
16. │ └─base::union(alphabet(x), alphabet(y))
17. │ ├─base::c(x, y[match(y, x, 0L) == 0L])
18. │ └─vctrs:::c.vctrs_vctr(x, y[match(y, x, 0L) == 0L])
19. │ └─vctrs::vec_c(...)
20. └─vctrs (local) `<fn>`()
21. └─vctrs::vec_default_ptype2(...)
22. ├─base::withRestarts(...)
23. │ └─base (local) withOneRestart(expr, restarts[[1L]])
24. │ └─base (local) doWithOneRestart(return(expr), restart)
25. └─vctrs::stop_incompatible_type(...)
26. └─vctrs:::stop_incompatible(...)
27. └─vctrs:::stop_vctrs(...)
28. └─rlang::abort(message, class = c(class, "vctrs_error"), ..., call = call)
── Error ('test-concatenate.R:114:3'): c() on any standard type and untyped sequences return correct value ──
<vctrs_error_ptype2/vctrs_error_incompatible_type/vctrs_error_incompatible/vctrs_error/rlang_error/error/condition>
Error in `vec_c(...)`: Can't combine `..1` <tidysq alphabet> and `..2` <tidysq alphabet>.
x Some attributes are incompatible.
i The author of the class should implement vctrs methods.
i See <https://vctrs.r-lib.org/reference/faq-error-incompatible-attributes.html>.
Backtrace:
▆
1. ├─testthat::expect_identical(...) at test-concatenate.R:114:3
2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─base::c(sq_dna_bsc, sq_unt, sq_dna_bsc)
5. ├─vctrs:::c.vctrs_vctr(sq_dna_bsc, sq_unt, sq_dna_bsc)
6. │ └─vctrs::vec_c(...)
7. │ └─vctrs (local) `<fn>`()
8. │ └─tidysq:::vec_ptype2.sq_dna_bsc.sq_unt(...)
9. │ ├─tidysq:::sq_ptype(union(alphabet(x), alphabet(y)), "unt")
10. │ │ ├─vctrs::new_list_of(...)
11. │ │ │ └─vctrs:::new_list_of0(x = x, ptype = ptype, ..., class = class)
12. │ │ │ └─vctrs::new_vctr(x, ..., ptype = ptype, class = c(class, "vctrs_list_of"))
13. │ │ └─tidysq:::sq_alphabet(str_alphabet, type)
14. │ │ └─vctrs::new_vctr(alph, type = type, class = c("sq_alphabet", "character"))
15. │ │ └─rlang::is_vector(.data)
16. │ └─base::union(alphabet(x), alphabet(y))
17. │ ├─base::c(x, y[match(y, x, 0L) == 0L])
18. │ └─vctrs:::c.vctrs_vctr(x, y[match(y, x, 0L) == 0L])
19. │ └─vctrs::vec_c(...)
20. └─vctrs (local) `<fn>`()
21. └─vctrs::vec_default_ptype2(...)
22. ├─base::withRestarts(...)
23. │ └─base (local) withOneRestart(expr, restarts[[1L]])
24. │ └─base (local) doWithOneRestart(return(expr), restart)
25. └─vctrs::stop_incompatible_type(...)
26. └─vctrs:::stop_incompatible(...)
27. └─vctrs:::stop_vctrs(...)
28. └─rlang::abort(message, class = c(class, "vctrs_error"), ..., call = call)
── Error ('test-paste.R:29:3'): paste() finds common prototype for all arguments (recycling length 1 vectors if necessary) ──
<vctrs_error_ptype2/vctrs_error_incompatible_type/vctrs_error_incompatible/vctrs_error/rlang_error/error/condition>
Error in `vec_c(...)`: Can't combine `..1` <tidysq alphabet> and `..2` <tidysq alphabet>.
x Some attributes are incompatible.
i The author of the class should implement vctrs methods.
i See <https://vctrs.r-lib.org/reference/faq-error-incompatible-attributes.html>.
Backtrace:
▆
1. ├─testthat::expect_vector(...) at test-paste.R:29:3
2. │ └─testthat::quasi_label(enquo(object), arg = "object")
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─tidysq::paste(sq_dna_1, sq_unt_3, sq_dna_2)
5. ├─tidysq:::paste.sq(sq_dna_1, sq_unt_3, sq_dna_2)
6. │ ├─tidysq:::CPP_paste(vec_cast_common(...), NA_letter)
7. │ └─vctrs::vec_cast_common(...)
8. │ └─vctrs (local) `<fn>`()
9. │ └─tidysq:::vec_ptype2.sq_dna_bsc.sq_unt(...)
10. │ ├─tidysq:::sq_ptype(union(alphabet(x), alphabet(y)), "unt")
11. │ │ ├─vctrs::new_list_of(...)
12. │ │ │ └─vctrs:::new_list_of0(x = x, ptype = ptype, ..., class = class)
13. │ │ │ └─vctrs::new_vctr(x, ..., ptype = ptype, class = c(class, "vctrs_list_of"))
14. │ │ └─tidysq:::sq_alphabet(str_alphabet, type)
15. │ │ └─vctrs::new_vctr(alph, type = type, class = c("sq_alphabet", "character"))
16. │ │ └─rlang::is_vector(.data)
17. │ └─base::union(alphabet(x), alphabet(y))
18. │ ├─base::c(x, y[match(y, x, 0L) == 0L])
19. │ └─vctrs:::c.vctrs_vctr(x, y[match(y, x, 0L) == 0L])
20. │ └─vctrs::vec_c(...)
21. └─vctrs (local) `<fn>`()
22. └─vctrs::vec_default_ptype2(...)
23. ├─base::withRestarts(...)
24. │ └─base (local) withOneRestart(expr, restarts[[1L]])
25. │ └─base (local) doWithOneRestart(return(expr), restart)
26. └─vctrs::stop_incompatible_type(...)
27. └─vctrs:::stop_incompatible(...)
28. └─vctrs:::stop_vctrs(...)
29. └─rlang::abort(message, class = c(class, "vctrs_error"), ..., call = call)
── Error ('test-paste.R:57:3'): paste() correctly merges sq objects of different types and alphabets ──
<vctrs_error_ptype2/vctrs_error_incompatible_type/vctrs_error_incompatible/vctrs_error/rlang_error/error/condition>
Error in `vec_c(...)`: Can't combine `..1` <tidysq alphabet> and `..2` <tidysq alphabet>.
x Some attributes are incompatible.
i The author of the class should implement vctrs methods.
i See <https://vctrs.r-lib.org/reference/faq-error-incompatible-attributes.html>.
Backtrace:
▆
1. ├─testthat::expect_identical(...) at test-paste.R:57:3
2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─tidysq::paste(sq_dna_1, sq_unt_3, sq_dna_2)
5. ├─tidysq:::paste.sq(sq_dna_1, sq_unt_3, sq_dna_2)
6. │ ├─tidysq:::CPP_paste(vec_cast_common(...), NA_letter)
7. │ └─vctrs::vec_cast_common(...)
8. │ └─vctrs (local) `<fn>`()
9. │ └─tidysq:::vec_ptype2.sq_dna_bsc.sq_unt(...)
10. │ ├─tidysq:::sq_ptype(union(alphabet(x), alphabet(y)), "unt")
11. │ │ ├─vctrs::new_list_of(...)
12. │ │ │ └─vctrs:::new_list_of0(x = x, ptype = ptype, ..., class = class)
13. │ │ │ └─vctrs::new_vctr(x, ..., ptype = ptype, class = c(class, "vctrs_list_of"))
14. │ │ └─tidysq:::sq_alphabet(str_alphabet, type)
15. │ │ └─vctrs::new_vctr(alph, type = type, class = c("sq_alphabet", "character"))
16. │ │ └─rlang::is_vector(.data)
17. │ └─base::union(alphabet(x), alphabet(y))
18. │ ├─base::c(x, y[match(y, x, 0L) == 0L])
19. │ └─vctrs:::c.vctrs_vctr(x, y[match(y, x, 0L) == 0L])
20. │ └─vctrs::vec_c(...)
21. └─vctrs (local) `<fn>`()
22. └─vctrs::vec_default_ptype2(...)
23. ├─base::withRestarts(...)
24. │ └─base (local) withOneRestart(expr, restarts[[1L]])
25. │ └─base (local) doWithOneRestart(return(expr), restart)
26. └─vctrs::stop_incompatible_type(...)
27. └─vctrs:::stop_incompatible(...)
28. └─vctrs:::stop_vctrs(...)
29. └─rlang::abort(message, class = c(class, "vctrs_error"), ..., call = call)
[ FAIL 4 | WARN 0 | SKIP 1 | PASS 789 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 1.1.3
Check: tests
Result: ERROR
Running 'spelling.R' [0s]
Running 'testthat.R' [13s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
> library(testthat)
> library(tidysq)
Attaching package: 'tidysq'
The following object is masked from 'package:base':
paste
>
> test_check("tidysq")
[ FAIL 4 | WARN 0 | SKIP 1 | PASS 789 ]
══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• warning handling on C++ side is poorly implemented (1):
'test-warnings.R:39:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-concatenate.R:93:3'): c() generalizes any standard type and untyped sequences to unt sq ──
<vctrs_error_ptype2/vctrs_error_incompatible_type/vctrs_error_incompatible/vctrs_error/rlang_error/error/condition>
Error in `vec_c(...)`: Can't combine `..1` <tidysq alphabet> and `..2` <tidysq alphabet>.
x Some attributes are incompatible.
i The author of the class should implement vctrs methods.
i See <https://vctrs.r-lib.org/reference/faq-error-incompatible-attributes.html>.
Backtrace:
▆
1. ├─testthat::expect_vector(...) at test-concatenate.R:93:3
2. │ └─testthat::quasi_label(enquo(object), arg = "object")
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─base::c(sq_dna_bsc, sq_unt, sq_dna_bsc)
5. ├─vctrs:::c.vctrs_vctr(sq_dna_bsc, sq_unt, sq_dna_bsc)
6. │ └─vctrs::vec_c(...)
7. │ └─vctrs (local) `<fn>`()
8. │ └─tidysq:::vec_ptype2.sq_dna_bsc.sq_unt(...)
9. │ ├─tidysq:::sq_ptype(union(alphabet(x), alphabet(y)), "unt")
10. │ │ ├─vctrs::new_list_of(...)
11. │ │ │ └─vctrs:::new_list_of0(x = x, ptype = ptype, ..., class = class)
12. │ │ │ └─vctrs::new_vctr(x, ..., ptype = ptype, class = c(class, "vctrs_list_of"))
13. │ │ └─tidysq:::sq_alphabet(str_alphabet, type)
14. │ │ └─vctrs::new_vctr(alph, type = type, class = c("sq_alphabet", "character"))
15. │ │ └─rlang::is_vector(.data)
16. │ └─base::union(alphabet(x), alphabet(y))
17. │ ├─base::c(x, y[match(y, x, 0L) == 0L])
18. │ └─vctrs:::c.vctrs_vctr(x, y[match(y, x, 0L) == 0L])
19. │ └─vctrs::vec_c(...)
20. └─vctrs (local) `<fn>`()
21. └─vctrs::vec_default_ptype2(...)
22. ├─base::withRestarts(...)
23. │ └─base (local) withOneRestart(expr, restarts[[1L]])
24. │ └─base (local) doWithOneRestart(return(expr), restart)
25. └─vctrs::stop_incompatible_type(...)
26. └─vctrs:::stop_incompatible(...)
27. └─vctrs:::stop_vctrs(...)
28. └─rlang::abort(message, class = c(class, "vctrs_error"), ..., call = call)
── Error ('test-concatenate.R:114:3'): c() on any standard type and untyped sequences return correct value ──
<vctrs_error_ptype2/vctrs_error_incompatible_type/vctrs_error_incompatible/vctrs_error/rlang_error/error/condition>
Error in `vec_c(...)`: Can't combine `..1` <tidysq alphabet> and `..2` <tidysq alphabet>.
x Some attributes are incompatible.
i The author of the class should implement vctrs methods.
i See <https://vctrs.r-lib.org/reference/faq-error-incompatible-attributes.html>.
Backtrace:
▆
1. ├─testthat::expect_identical(...) at test-concatenate.R:114:3
2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─base::c(sq_dna_bsc, sq_unt, sq_dna_bsc)
5. ├─vctrs:::c.vctrs_vctr(sq_dna_bsc, sq_unt, sq_dna_bsc)
6. │ └─vctrs::vec_c(...)
7. │ └─vctrs (local) `<fn>`()
8. │ └─tidysq:::vec_ptype2.sq_dna_bsc.sq_unt(...)
9. │ ├─tidysq:::sq_ptype(union(alphabet(x), alphabet(y)), "unt")
10. │ │ ├─vctrs::new_list_of(...)
11. │ │ │ └─vctrs:::new_list_of0(x = x, ptype = ptype, ..., class = class)
12. │ │ │ └─vctrs::new_vctr(x, ..., ptype = ptype, class = c(class, "vctrs_list_of"))
13. │ │ └─tidysq:::sq_alphabet(str_alphabet, type)
14. │ │ └─vctrs::new_vctr(alph, type = type, class = c("sq_alphabet", "character"))
15. │ │ └─rlang::is_vector(.data)
16. │ └─base::union(alphabet(x), alphabet(y))
17. │ ├─base::c(x, y[match(y, x, 0L) == 0L])
18. │ └─vctrs:::c.vctrs_vctr(x, y[match(y, x, 0L) == 0L])
19. │ └─vctrs::vec_c(...)
20. └─vctrs (local) `<fn>`()
21. └─vctrs::vec_default_ptype2(...)
22. ├─base::withRestarts(...)
23. │ └─base (local) withOneRestart(expr, restarts[[1L]])
24. │ └─base (local) doWithOneRestart(return(expr), restart)
25. └─vctrs::stop_incompatible_type(...)
26. └─vctrs:::stop_incompatible(...)
27. └─vctrs:::stop_vctrs(...)
28. └─rlang::abort(message, class = c(class, "vctrs_error"), ..., call = call)
── Error ('test-paste.R:29:3'): paste() finds common prototype for all arguments (recycling length 1 vectors if necessary) ──
<vctrs_error_ptype2/vctrs_error_incompatible_type/vctrs_error_incompatible/vctrs_error/rlang_error/error/condition>
Error in `vec_c(...)`: Can't combine `..1` <tidysq alphabet> and `..2` <tidysq alphabet>.
x Some attributes are incompatible.
i The author of the class should implement vctrs methods.
i See <https://vctrs.r-lib.org/reference/faq-error-incompatible-attributes.html>.
Backtrace:
▆
1. ├─testthat::expect_vector(...) at test-paste.R:29:3
2. │ └─testthat::quasi_label(enquo(object), arg = "object")
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─tidysq::paste(sq_dna_1, sq_unt_3, sq_dna_2)
5. ├─tidysq:::paste.sq(sq_dna_1, sq_unt_3, sq_dna_2)
6. │ ├─tidysq:::CPP_paste(vec_cast_common(...), NA_letter)
7. │ └─vctrs::vec_cast_common(...)
8. │ └─vctrs (local) `<fn>`()
9. │ └─tidysq:::vec_ptype2.sq_dna_bsc.sq_unt(...)
10. │ ├─tidysq:::sq_ptype(union(alphabet(x), alphabet(y)), "unt")
11. │ │ ├─vctrs::new_list_of(...)
12. │ │ │ └─vctrs:::new_list_of0(x = x, ptype = ptype, ..., class = class)
13. │ │ │ └─vctrs::new_vctr(x, ..., ptype = ptype, class = c(class, "vctrs_list_of"))
14. │ │ └─tidysq:::sq_alphabet(str_alphabet, type)
15. │ │ └─vctrs::new_vctr(alph, type = type, class = c("sq_alphabet", "character"))
16. │ │ └─rlang::is_vector(.data)
17. │ └─base::union(alphabet(x), alphabet(y))
18. │ ├─base::c(x, y[match(y, x, 0L) == 0L])
19. │ └─vctrs:::c.vctrs_vctr(x, y[match(y, x, 0L) == 0L])
20. │ └─vctrs::vec_c(...)
21. └─vctrs (local) `<fn>`()
22. └─vctrs::vec_default_ptype2(...)
23. ├─base::withRestarts(...)
24. │ └─base (local) withOneRestart(expr, restarts[[1L]])
25. │ └─base (local) doWithOneRestart(return(expr), restart)
26. └─vctrs::stop_incompatible_type(...)
27. └─vctrs:::stop_incompatible(...)
28. └─vctrs:::stop_vctrs(...)
29. └─rlang::abort(message, class = c(class, "vctrs_error"), ..., call = call)
── Error ('test-paste.R:57:3'): paste() correctly merges sq objects of different types and alphabets ──
<vctrs_error_ptype2/vctrs_error_incompatible_type/vctrs_error_incompatible/vctrs_error/rlang_error/error/condition>
Error in `vec_c(...)`: Can't combine `..1` <tidysq alphabet> and `..2` <tidysq alphabet>.
x Some attributes are incompatible.
i The author of the class should implement vctrs methods.
i See <https://vctrs.r-lib.org/reference/faq-error-incompatible-attributes.html>.
Backtrace:
▆
1. ├─testthat::expect_identical(...) at test-paste.R:57:3
2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─tidysq::paste(sq_dna_1, sq_unt_3, sq_dna_2)
5. ├─tidysq:::paste.sq(sq_dna_1, sq_unt_3, sq_dna_2)
6. │ ├─tidysq:::CPP_paste(vec_cast_common(...), NA_letter)
7. │ └─vctrs::vec_cast_common(...)
8. │ └─vctrs (local) `<fn>`()
9. │ └─tidysq:::vec_ptype2.sq_dna_bsc.sq_unt(...)
10. │ ├─tidysq:::sq_ptype(union(alphabet(x), alphabet(y)), "unt")
11. │ │ ├─vctrs::new_list_of(...)
12. │ │ │ └─vctrs:::new_list_of0(x = x, ptype = ptype, ..., class = class)
13. │ │ │ └─vctrs::new_vctr(x, ..., ptype = ptype, class = c(class, "vctrs_list_of"))
14. │ │ └─tidysq:::sq_alphabet(str_alphabet, type)
15. │ │ └─vctrs::new_vctr(alph, type = type, class = c("sq_alphabet", "character"))
16. │ │ └─rlang::is_vector(.data)
17. │ └─base::union(alphabet(x), alphabet(y))
18. │ ├─base::c(x, y[match(y, x, 0L) == 0L])
19. │ └─vctrs:::c.vctrs_vctr(x, y[match(y, x, 0L) == 0L])
20. │ └─vctrs::vec_c(...)
21. └─vctrs (local) `<fn>`()
22. └─vctrs::vec_default_ptype2(...)
23. ├─base::withRestarts(...)
24. │ └─base (local) withOneRestart(expr, restarts[[1L]])
25. │ └─base (local) doWithOneRestart(return(expr), restart)
26. └─vctrs::stop_incompatible_type(...)
27. └─vctrs:::stop_incompatible(...)
28. └─vctrs:::stop_vctrs(...)
29. └─rlang::abort(message, class = c(class, "vctrs_error"), ..., call = call)
[ FAIL 4 | WARN 0 | SKIP 1 | PASS 789 ]
Error: Test failures
Execution halted
Flavor: r-devel-windows-x86_64
Version: 1.1.3
Check: installed package size
Result: NOTE
installed size is 43.5Mb
sub-directories of 1Mb or more:
libs 42.7Mb
Flavors: r-release-macos-arm64, r-release-macos-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64