* using log directory 'd:/Rcompile/CRANpkg/local/4.5/tidysq.Rcheck' * using R Under development (unstable) (2024-09-21 r87186 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) * using session charset: UTF-8 * checking for file 'tidysq/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'tidysq' version '1.1.3' * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking whether package 'tidysq' can be installed ... OK * used C++ compiler: 'g++.exe (GCC) 13.2.0' * checking C++ specification ... OK * checking installed package size ... OK * checking package directory ... OK * checking 'build' directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... [1s] OK * checking whether the package can be loaded with stated dependencies ... [1s] OK * checking whether the package can be unloaded cleanly ... [1s] OK * checking whether the namespace can be loaded with stated dependencies ... [1s] OK * checking whether the namespace can be unloaded cleanly ... [1s] OK * checking loading without being on the library search path ... [1s] OK * checking whether startup messages can be suppressed ... [1s] OK * checking use of S3 registration ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * 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 * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking R/sysdata.rda ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking compilation flags in Makevars ... OK * checking for GNU extensions in Makefiles ... OK * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... OK * checking pragmas in C/C++ headers and code ... OK * checking compiled code ... OK * checking installed files from 'inst/doc' ... OK * checking files in 'vignettes' ... OK * checking examples ... [2s] ERROR Running examples in 'tidysq-Ex.R' failed The error most likely occurred in: > ### Name: ==.sq > ### Title: Compare sq objects > ### Aliases: ==.sq > > ### ** Examples > > # Creating objects to work on: > sq_dna_1 <- sq(c("ACTGCTG", "CTTAGA", "CCCT", "CTGAATGT"), + alphabet = "dna_bsc") > sq_dna_2 <- sq(c("ACTGCTG", "CTTAGA", "CCCT", "CTGAATGT"), + alphabet = "dna_bsc") > sq_dna_3 <- sq(c("ACTGCTG", "CTTAGA", "GGAA"), + alphabet = "dna_bsc") > sq_dna_4 <- sq(c("ACTGCTG", "CTTAGA", "CCCT", "GTNANN"), + alphabet = "dna_ext") > sq_ami_1 <- sq(c("ACTGCTG", "NIKAAR", "CCCT", "CTGAATGT"), + alphabet = "ami_bsc") > sq_unt <- sq(c("AHSNLVSCTK$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` and `..2` . ✖ Some attributes are incompatible. ℹ The author of the class should implement vctrs methods. ℹ See . 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) ``() 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) ``() 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 ... [14s] 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 ── Error in `vec_c(...)`: Can't combine `..1` and `..2` . x Some attributes are incompatible. i The author of the class should implement vctrs methods. i See . 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) ``() 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) ``() 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 ── Error in `vec_c(...)`: Can't combine `..1` and `..2` . x Some attributes are incompatible. i The author of the class should implement vctrs methods. i See . 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) ``() 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) ``() 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) ── Error in `vec_c(...)`: Can't combine `..1` and `..2` . x Some attributes are incompatible. i The author of the class should implement vctrs methods. i See . 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) ``() 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) ``() 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 ── Error in `vec_c(...)`: Can't combine `..1` and `..2` . x Some attributes are incompatible. i The author of the class should implement vctrs methods. i See . 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) ``() 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) ``() 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 ... [22s] OK * checking HTML version of manual ... [8s] OK * DONE Status: 2 ERRORs, 1 NOTE