• using R Under development (unstable) (2024-09-15 r87152 ucrt)
• using platform: x86_64-w64-mingw32
• R was compiled by     gcc.exe (GCC) 13.2.0     GNU Fortran (GCC) 13.2.0
• running under: Windows Server 2022 x64 (build 20348)
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• checking for file 'tidysq/DESCRIPTION' ... OK
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• this is package 'tidysq' version '1.1.3'
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• used C++ compiler: 'g++.exe (GCC) 13.2.0'
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• checking R files for syntax errors ... OK
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• checking whether the package can be loaded with stated dependencies ... [1s] OK
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• checking R code for possible problems ... [5s] OK
• checking Rd files ... [1s] 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
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• checking pragmas in C/C++ headers and code ... OK
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• checking files in 'vignettes' ... OK
• checking examples ... [2s] 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
• checking for unstated dependencies in 'tests' ... OK
• checking tests ... [13s] 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
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [7s] OK
• checking PDF version of manual ... [23s] OK
• checking HTML version of manual ... [8s] OK
• DONE

Status: 2 ERRORs, 1 NOTE