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###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:ncRNAtools.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings ncRNAtools_1.21.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/ncRNAtools.Rcheck’
* using R Under development (unstable) (2026-01-15 r89304)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘ncRNAtools/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ncRNAtools’ version ‘1.21.0’
* 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 ‘ncRNAtools’ can be installed ... 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 ... 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 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) flattenDotBracket.Rd:17: Lost braces; missing escapes or markup?
    17 |   "["-"]", "{"-"}", "<"-">", "A"-"a", "B"-"b", "C"-"c" and "D"-"d") to indicate
       |             ^
* 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 files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘ncRNAtools-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: predictAlternativeSecondaryStructures
> ### Title: Predicts alternative secondary structures of a given RNA
> ###   sequence
> ### Aliases: predictAlternativeSecondaryStructures
> 
> ### ** Examples
> 
> # Predict alternative secondary structures of an RNA sequence:
> 
> alternativeStructures <- predictAlternativeSecondaryStructures("AAAGGGGUUUCCC")
Error in strsplit(string, split = split, ...) : non-character argument
Calls: predictAlternativeSecondaryStructures ... sendAlternativeSecondaryStructureQuery -> splitString -> unlist -> strsplit
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 ERROR
Running the tests in ‘tests/runTests.R’ failed.
Last 13 lines of output:
    error in evaluating the argument 'x' in selecting a method for function 'grepl': object of type 'externalptr' is not subsettable
  ERROR in /tmp/RtmpCYVmqk/RLIBS_951d95ee10c94/ncRNAtools/unitTests/test_secondaryStructurePrediction.R: Error while sourcing  /tmp/RtmpCYVmqk/RLIBS_951d95ee10c94/ncRNAtools/unitTests/test_secondaryStructurePrediction.R : Error in strsplit(string, split = split, ...) : non-character argument
  
  Test files with failing tests
  
     test_rnaCentralAccess.R 
       /tmp/RtmpCYVmqk/RLIBS_951d95ee10c94/ncRNAtools/unitTests/test_rnaCentralAccess.R 
  
     test_secondaryStructurePrediction.R 
       /tmp/RtmpCYVmqk/RLIBS_951d95ee10c94/ncRNAtools/unitTests/test_secondaryStructurePrediction.R 
  
  
  Error in BiocGenerics:::testPackage("ncRNAtools") : 
    unit tests failed for package ncRNAtools
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
--- re-building ‘ncRNAtools.Rmd’ using rmarkdown
Warning in eng_r(options) :
  Failed to tidy R code in chunk 'unnamed-chunk-1'. Reason:
Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored.

Warning in eng_r(options) :
  Failed to tidy R code in chunk 'unnamed-chunk-3'. Reason:
Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored.

Warning in eng_r(options) :
  Failed to tidy R code in chunk 'unnamed-chunk-4'. Reason:
Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored.

Warning in eng_r(options) :
  Failed to tidy R code in chunk 'unnamed-chunk-5'. Reason:
Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored.

Warning in eng_r(options) :
  Failed to tidy R code in chunk 'unnamed-chunk-6'. Reason:
Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored.

Warning in eng_r(options) :
  Failed to tidy R code in chunk 'unnamed-chunk-7'. Reason:
Error : The formatR package is required by the chunk option tidy = TRUE but not installed; tidy = TRUE will be ignored.


Quitting from ncRNAtools.Rmd:198-209 [unnamed-chunk-7]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `strsplit()`:
! non-character argument
---
Backtrace:
    ▆
 1. └─ncRNAtools::predictSecondaryStructure(tRNAfragment, "centroidFold")
 2.   └─ncRNAtools:::sendSecondaryStructureQuery(...)
 3.     └─ncRNAtools:::splitString(redirectURL, split = "req_id=")
 4.       ├─base::unlist(strsplit(string, split = split, ...))
 5.       └─base::strsplit(string, split = split, ...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'ncRNAtools.Rmd' failed with diagnostics:
non-character argument
--- failed re-building ‘ncRNAtools.Rmd’

SUMMARY: processing the following file failed:
  ‘ncRNAtools.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE

Status: 3 ERRORs, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.23-bioc/meat/ncRNAtools.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL ncRNAtools
###
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* installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’
* installing *source* package ‘ncRNAtools’ ...
** this is package ‘ncRNAtools’ version ‘1.21.0’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (ncRNAtools)

R Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> BiocGenerics:::testPackage("ncRNAtools")
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: generics

Attaching package: 'generics'

The following objects are masked from 'package:base':

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
    unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:utils':

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: Seqinfo
Error in (function (cond)  : 
  error in evaluating the argument 'x' in selecting a method for function 'grepl': object of type 'externalptr' is not subsettable
Error in strsplit(string, split = split, ...) : non-character argument


RUNIT TEST PROTOCOL -- Wed Feb 18 02:23:44 2026 
*********************************************** 
Number of test functions: 2 
Number of errors: 2 
Number of failures: 0 

 
1 Test Suite : 
ncRNAtools RUnit Tests - 2 test functions, 2 errors, 0 failures
ERROR in /tmp/RtmpCYVmqk/RLIBS_951d95ee10c94/ncRNAtools/unitTests/test_rnaCentralAccess.R: Error while sourcing  /tmp/RtmpCYVmqk/RLIBS_951d95ee10c94/ncRNAtools/unitTests/test_rnaCentralAccess.R : Error in (function (cond)  : 
  error in evaluating the argument 'x' in selecting a method for function 'grepl': object of type 'externalptr' is not subsettable
ERROR in /tmp/RtmpCYVmqk/RLIBS_951d95ee10c94/ncRNAtools/unitTests/test_secondaryStructurePrediction.R: Error while sourcing  /tmp/RtmpCYVmqk/RLIBS_951d95ee10c94/ncRNAtools/unitTests/test_secondaryStructurePrediction.R : Error in strsplit(string, split = split, ...) : non-character argument

Test files with failing tests

   test_rnaCentralAccess.R 
     /tmp/RtmpCYVmqk/RLIBS_951d95ee10c94/ncRNAtools/unitTests/test_rnaCentralAccess.R 

   test_secondaryStructurePrediction.R 
     /tmp/RtmpCYVmqk/RLIBS_951d95ee10c94/ncRNAtools/unitTests/test_secondaryStructurePrediction.R 


Error in BiocGenerics:::testPackage("ncRNAtools") : 
  unit tests failed for package ncRNAtools
Execution halted