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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Structstrings.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Structstrings_1.27.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/Structstrings.Rcheck’
* using R Under development (unstable) (2025-11-04 r88984)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.8
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Structstrings/DESCRIPTION’ ... OK
* this is package ‘Structstrings’ version ‘1.27.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘Structstrings’ can be installed ... OK
* used C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
* used SDK: ‘MacOSX11.3.1.sdk’
* 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 ... 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 whether startup messages can be suppressed ... OK
* checking dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
  ‘Biostrings:::.XStringSet.show_frame_header’
  ‘S4Vectors:::new_SimpleList_from_list’
  See the note in ?`:::` about the use of this operator.
* 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 ... OK
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... INFO
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘Structstrings-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: DotBracketStringSet-io
> ### Title: Reading and writing DotBracketStringSet objects
> ### Aliases: DotBracketStringSet-io readDotBracketStringSet
> ###   writeDotBracketStringSet saveDotBracketStringSet
> 
> ### ** Examples
> 
> data("dbs", package = "Structstrings")
> file <- tempfile()
> # works both since a DotBracketStringSet is a BStringSet
> writeXStringSet(dbs,file)
Error in compatible_seqtypes(from_seqtype, to_seqtype) : 
  seqtype1 %in% .SUPPORTED_SEQTYPES is not TRUE
> writeDotBracketStringSet(dbs,file)
Error in compatible_seqtypes(from_seqtype, to_seqtype) : 
  seqtype1 %in% .SUPPORTED_SEQTYPES is not TRUE
> # to return immediatly a DotBracketStringSet us readDotBracketStringSet()
> dbs2 <- readDotBracketStringSet(file)
Error in .Call2("new_input_filexp", filepath, PACKAGE = "XVector") : 
  cannot open file '/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpEHIjUw/file7f6c5dd1630d'
Calls: readDotBracketStringSet ... lapply -> lapply -> FUN -> new_input_filexp -> .Call2
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  Backtrace:
      ▆
   1. └─Biostrings::BString(db) at test-DotBracketStringSet.R:11:3
   2.   ├─Biostrings:::XString("B", x, start = start, width = nchar)
   3.   └─Biostrings:::XString("B", x, start = start, width = nchar)
   4.     ├─Biostrings::`seqtype<-`(`*tmp*`, value = seqtype)
   5.     └─Biostrings::`seqtype<-`(`*tmp*`, value = seqtype)
   6.       └─Biostrings::get_seqtype_conversion_lookup(from_seqtype, to_seqtype)
   7.         └─Biostrings:::compatible_seqtypes(from_seqtype, to_seqtype)
   8.           └─base::stopifnot(...)
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 136 ]
  Error:
  ! Test failures.
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.23-bioc/meat/Structstrings.Rcheck/00check.log’
for details.