CRAN Package Check Results for Package tidysq

Last updated on 2024-09-12 09:50:47 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.1.3 376.01 78.85 454.86 ERROR
r-devel-linux-x86_64-debian-gcc 1.1.3 233.18 56.60 289.78 ERROR
r-devel-linux-x86_64-fedora-clang 1.1.3 724.09 ERROR
r-devel-linux-x86_64-fedora-gcc 1.1.3 793.44 ERROR
r-devel-windows-x86_64 1.1.3 273.00 137.00 410.00 ERROR
r-patched-linux-x86_64 1.1.3 311.29 78.71 390.00 NOTE
r-release-linux-x86_64 1.1.3 310.23 78.40 388.63 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 1.1.3 370.00 176.00 546.00 OK

Additional issues

noSuggests

Check Details

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’ [15s/17s] 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’ [10s/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-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’ [23s/52s] 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