* using log directory ‘/data/gannet/ripley/R/packages/tests-Suggests/tidysq.Rcheck’
* using R Under development (unstable) (2024-04-19 r86451)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc-13 (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Fedora Linux 36 (Workstation Edition)
* using session charset: UTF-8
* using option ‘--no-stop-on-test-error’
* 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 executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘tidysq’ can be installed ... [702s/295s] OK
* used C++ compiler: ‘g++-13 (GCC) 13.2.0’
* checking C++ specification ... OK
  Not all R platforms support C++17
* 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 ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... 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 ... OK
* checking Rd files ... 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 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 ... ERROR
Running examples in ‘tidysq-Ex.R’ failed
The error most likely occurred in:

> ### Name: export_sq
> ### Title: Export sq objects into other formats
> ### Aliases: export_sq
> 
> ### ** Examples
> 
> # DNA and amino acid sequences can be exported to most packages
> sq_ami <- sq(c("MVVGL", "LAVPP"), alphabet = "ami_bsc")
> export_sq(sq_ami, "ape::AAbin")
Error in export_sq.sq_ami_bsc(sq_ami, "ape::AAbin") : 
  Assertion on '"ape"' failed: you need to install 'ape' package.
Calls: export_sq ... export_sq.sq_ami_bsc -> assert_package_installed -> <Anonymous> -> mstop
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘spelling.R’
  Running ‘testthat.R’
 ERROR
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 8 | WARN 0 | SKIP 1 | PASS 571 ]
  
  ══ Skipped tests (1) ═══════════════════════════════════════════════════════════
  • warning handling on C++ side is poorly implemented (1):
    'test-warnings.R:39:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-casting.R:49:3'): (code run outside of `test_that()`) ──────────
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'Biostrings'
  Backtrace:
      ▆
   1. ├─base::suppressWarnings(...) at test-casting.R:48:1
   2. │ └─base::withCallingHandlers(...)
   3. └─base::loadNamespace(x) at test-casting.R:49:3
   4.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   5.     └─base (local) withOneRestart(expr, restarts[[1L]])
   6.       └─base (local) doWithOneRestart(return(expr), restart)
  ── Error ('test-find_motifs.R:157:3'): 'start' and 'end' columns have values between 1 and length(sequence) ──
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'purrr'
  Backtrace:
      ▆
   1. └─base::loadNamespace(x) at test-find_motifs.R:157:3
   2.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   3.     └─base (local) withOneRestart(expr, restarts[[1L]])
   4.       └─base (local) doWithOneRestart(return(expr), restart)
  ── Error ('test-find_motifs.R:197:3'): index columns can be used to retrieve found subsequence from original sequence ──
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'purrr'
  Backtrace:
      ▆
   1. └─base::loadNamespace(x) at test-find_motifs.R:197:3
   2.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   3.     └─base (local) withOneRestart(expr, restarts[[1L]])
   4.       └─base (local) doWithOneRestart(return(expr), restart)
  ── Error ('test-pkg-Biostrings.R:29:1'): (code run outside of `test_that()`) ───
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'Biostrings'
  Backtrace:
      ▆
   1. └─base::loadNamespace(x) at test-pkg-Biostrings.R:29:1
   2.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   3.     └─base (local) withOneRestart(expr, restarts[[1L]])
   4.       └─base (local) doWithOneRestart(return(expr), restart)
  ── Error ('test-pkg-ape.R:12:1'): (code run outside of `test_that()`) ──────────
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'ape'
  Backtrace:
      ▆
   1. └─base::loadNamespace(x) at test-pkg-ape.R:12:1
   2.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   3.     └─base (local) withOneRestart(expr, restarts[[1L]])
   4.       └─base (local) doWithOneRestart(return(expr), restart)
  ── Error ('test-pkg-bioseq.R:15:1'): (code run outside of `test_that()`) ───────
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'bioseq'
  Backtrace:
      ▆
   1. └─base::loadNamespace(x) at test-pkg-bioseq.R:15:1
   2.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   3.     └─base (local) withOneRestart(expr, restarts[[1L]])
   4.       └─base (local) doWithOneRestart(return(expr), restart)
  ── Error ('test-pkg-seqinr.R:8:31'): (code run outside of `test_that()`) ───────
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'seqinr'
  Backtrace:
      ▆
   1. ├─base::lapply(str_dna, function(x) seqinr::as.SeqFastadna(seqinr::s2c(x))) at test-pkg-seqinr.R:8:1
   2. │ └─tidysq (local) FUN(X[[i]], ...)
   3. └─base::loadNamespace(x) at test-pkg-seqinr.R:8:31
   4.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   5.     └─base (local) withOneRestart(expr, restarts[[1L]])
   6.       └─base (local) doWithOneRestart(return(expr), restart)
  ── Error ('test-random_sq.R:31:3'): using sd argument of random_sq() doesn't generate negative-length sequences ──
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'mockr'
  Backtrace:
      ▆
   1. └─base::loadNamespace(x) at test-random_sq.R:31:3
   2.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   3.     └─base (local) withOneRestart(expr, restarts[[1L]])
   4.       └─base (local) doWithOneRestart(return(expr), restart)
  
  [ FAIL 8 | WARN 0 | SKIP 1 | PASS 571 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* checking HTML version of manual ... OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE

Status: 2 ERRORs, 1 NOTE
See
  ‘/data/gannet/ripley/R/packages/tests-Suggests/tidysq.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 5:56.42, 718.19 + 42.91