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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:ncRNAtools.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings ncRNAtools_1.19.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/ncRNAtools.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* 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 ‘1.19.0’
* 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: rnaCentralGenomicCoordinatesSearch
> ### Title: Retrieves annotated non-coding RNA in a set of genomic ranges
> ### Aliases: rnaCentralGenomicCoordinatesSearch
> 
> ### ** Examples
> 
> # Generate a GRanges object with 2 genomic ranges specifying coordinates of
> # the human genome:
> 
> genomicCoordinates <- GenomicRanges::GRanges(seqnames=S4Vectors::Rle(c("chr3", "chr4")),
+ ranges=IRanges::IRanges(rep(39745816, 2), rep(39847679, 2)))
> 
> # Retrieve known annotated non-coding RNA present in the specified genomic
> # ranges:
> 
> knownNonCodingRNA <- rnaCentralGenomicCoordinatesSearch(genomicCoordinates, "Homo sapiens")
No encoding supplied: defaulting to UTF-8.
Error in FUN(X[[i]], ...) : 
  object of type 'externalptr' is not subsettable
Calls: rnaCentralGenomicCoordinatesSearch -> grepl -> is.factor -> unlist -> lapply
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
                                       user system elapsed
predictAlternativeSecondaryStructures 0.106  0.051  18.081
* 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 /tmp/Rtmpingz0U/RLIBS_23c0f32bdf8cd9/ncRNAtools/unitTests/test_rnaCentralAccess.R: Error while sourcing  /tmp/Rtmpingz0U/RLIBS_23c0f32bdf8cd9/ncRNAtools/unitTests/test_rnaCentralAccess.R : Error in checkEquals("URS000075C808_9606", rnaCentralRetrieveEntry("URS000075C808_9606")$rnaCentralID) : 
    Modes: character, NULL
  Lengths: 1, 0
  target is character, current is NULL
  
  
  Test files with failing tests
  
     test_rnaCentralAccess.R 
       /tmp/Rtmpingz0U/RLIBS_23c0f32bdf8cd9/ncRNAtools/unitTests/test_rnaCentralAccess.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.


Quitting from ncRNAtools.Rmd:163-178 [unnamed-chunk-6]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `FUN()`:
! object of type 'externalptr' is not subsettable
---
Backtrace:
    ▆
 1. └─ncRNAtools::rnaCentralGenomicCoordinatesSearch(...)
 2.   ├─base::grepl("^URS", unlist(lapply(parsedResult, `[`, "external_name")))
 3.   │ └─base::is.factor(x)
 4.   ├─base::unlist(lapply(parsedResult, `[`, "external_name"))
 5.   └─base::lapply(parsedResult, `[`, "external_name")
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'ncRNAtools.Rmd' failed with diagnostics:
object of type 'externalptr' is not subsettable
--- 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-3.22-bioc/meat/ncRNAtools.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL ncRNAtools
###
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* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘ncRNAtools’ ...
** this is package ‘ncRNAtools’ version ‘1.19.0’
** 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 version 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"
Copyright (C) 2025 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
No encoding supplied: defaulting to UTF-8.
Error in checkEquals("URS000075C808_9606", rnaCentralRetrieveEntry("URS000075C808_9606")$rnaCentralID) : 
  Modes: character, NULL
Lengths: 1, 0
target is character, current is NULL

Secondary structure prediction completed.
Secondary structure prediction completed.
No alternative structures were found. 
            Returning canonical structure.


RUNIT TEST PROTOCOL -- Tue Sep 23 02:22:27 2025 
*********************************************** 
Number of test functions: 1 
Number of errors: 1 
Number of failures: 0 

 
1 Test Suite : 
ncRNAtools RUnit Tests - 1 test function, 1 error, 0 failures
ERROR in /tmp/Rtmpingz0U/RLIBS_23c0f32bdf8cd9/ncRNAtools/unitTests/test_rnaCentralAccess.R: Error while sourcing  /tmp/Rtmpingz0U/RLIBS_23c0f32bdf8cd9/ncRNAtools/unitTests/test_rnaCentralAccess.R : Error in checkEquals("URS000075C808_9606", rnaCentralRetrieveEntry("URS000075C808_9606")$rnaCentralID) : 
  Modes: character, NULL
Lengths: 1, 0
target is character, current is NULL


Test files with failing tests

   test_rnaCentralAccess.R 
     /tmp/Rtmpingz0U/RLIBS_23c0f32bdf8cd9/ncRNAtools/unitTests/test_rnaCentralAccess.R 


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