• using R Under development (unstable) (2024-12-25 r87466)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     Debian clang version 19.1.6 (1)     Debian flang-new version 19.1.6 (1)
• running under: Debian GNU/Linux trixie/sid
• using session charset: UTF-8
• checking for file ‘tidysq/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘tidysq’ version ‘1.2.2’
• 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 executable files ... OK
• checking for hidden files and directories ... OK
• checking for portable file names ... OK
• checking for sufficient/correct file permissions ... OK
• checking serialization versions ... OK
• checking whether package ‘tidysq’ can be installed ... OK See the install log for details.
• used C++ compiler: ‘Debian clang version 19.1.6 (1)’
• checking C++ specification ... OK
• checking package directory ... OK
• checking for future file timestamps ... 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/2s] OK
• checking whether the package can be loaded with stated dependencies ... [1s/1s] OK
• checking whether the package can be unloaded cleanly ... [1s/1s] OK
• checking whether the namespace can be loaded with stated dependencies ... [1s/1s] OK
• checking whether the namespace can be unloaded cleanly ... [1s/2s] OK
• checking loading without being on the library search path ... [1s/2s] OK
• checking whether startup messages can be suppressed ... [1s/2s] 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 ... [10s/14s] OK
• checking Rd files ... [1s/1s] OK
• checking Rd metadata ... OK
• checking Rd line widths ... 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 use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK
• checking pragmas in C/C++ headers and code ... OK
• checking compilation flags used ... OK
• checking compiled code ... OK
• checking installed files from ‘inst/doc’ ... OK
• checking files in ‘vignettes’ ... OK
• checking examples ... [8s/10s] OK Examples with CPU (user + system) or elapsed time > 5s            user system elapsed export_sq 4.182 0.294 5.135
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [14s/18s] ERROR   Running ‘spelling.R’ [0s/0s]   Running ‘testthat.R’ [14s/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 6 | WARN 0 | SKIP 1 | PASS 812 ]      ══ Skipped tests (1) ═══════════════════════════════════════════════════════════   • warning handling on C++ side is poorly implemented (1):     'test-warnings.R:39:3'      ══ Failed tests ════════════════════════════════════════════════════════════════   ── Failure ('test-sq.R:48:3'): sq() returns object with alphabet attribute that contains existing letters for unt and atp options ──   alphabet(sq(str_atp, alphabet = atp_alph)) (`actual`) and `atp_alph` (`expected`) don't have the same values.   * Only in `actual`: NA      ── Failure ('test-sq.R:52:3'): sq() returns object with alphabet attribute that contains existing letters for unt and atp options ──   alphabet(sq(str_unt, alphabet = "unt")) (`actual`) and obtain_alphabet(str_unt) (`expected`) don't have the same values.   * Only in `actual`: NA   * Only in `expected`: NA      ── Failure ('test-sq.R:56:3'): sq() returns object with alphabet attribute that contains existing letters for unt and atp options ──   alphabet(sq(str_unt, alphabet = "unt", NA_letter = "?")) (`actual`) and obtain_alphabet(str_unt, NA_letter = "?") (`expected`) don't have the same values.   * Only in `actual`: NA   * Only in `expected`: NA      ── Failure ('test-sq.R:60:3'): sq() returns object with alphabet attribute that contains existing letters for unt and atp options ──   alphabet(sq(str_unt, alphabet = "unt", NA_letter = "(?)")) (`actual`) and obtain_alphabet(str_unt, NA_letter = "(?)") (`expected`) don't have the same values.   * Only in `actual`: NA   * Only in `expected`: NA      ── Failure ('test-substitute_letters.R:23:3'): substitute_letters() returns an object with trimmed alphabet attribute ──   alphabet(substitute_letters(sq_dna, c(T = "B"))) (`actual`) and c("A", "C", "G", "B", "-") (`expected`) don't have the same values.   * Only in `actual`: NA      ── Failure ('test-substitute_letters.R:27:3'): substitute_letters() returns an object with trimmed alphabet attribute ──   alphabet(...) (`actual`) and setdiff(...) (`expected`) don't have the same values.   * Only in `actual`: NA         [ FAIL 6 | WARN 0 | SKIP 1 | PASS 812 ]   Error: Test failures   Execution halted
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [6s/10s] OK
• checking PDF version of manual ... [8s/11s] OK
• checking HTML version of manual ... [2s/4s] OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: 1 ERROR