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### Running command:
###
###   E:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ncRNAtools.install-out.txt --library=E:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings ncRNAtools_1.14.0.tar.gz
###
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* using log directory 'E:/biocbuild/bbs-3.19-bioc/meat/ncRNAtools.Rcheck'
* using R version 4.4.1 (2024-06-14 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'ncRNAtools/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ncRNAtools' version '1.14.0'
* 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 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 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                      user system elapsed
predictAlternativeSecondaryStructures 0.13   0.01   16.70
rnaCentralTextSearch                  0.03   0.00    6.39
* 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:
  1 Test Suite : 
  ncRNAtools RUnit Tests - 1 test function, 1 error, 0 failures
  ERROR in E:/biocbuild/bbs-3.19-bioc/tmpdir/RtmpUzv2WO/RLIBS_1e7201f082049/ncRNAtools/unitTests/test_rnaCentralAccess.R: Error while sourcing  E:/biocbuild/bbs-3.19-bioc/tmpdir/RtmpUzv2WO/RLIBS_1e7201f082049/ncRNAtools/unitTests/test_rnaCentralAccess.R : Error in checkTrue(grepl("^URS", rnaCentralTextSearch("HOTAIR")[1])) : 
    Test not TRUE
  
  
  Test files with failing tests
  
     test_rnaCentralAccess.R 
       E:/biocbuild/bbs-3.19-bioc/tmpdir/RtmpUzv2WO/RLIBS_1e7201f082049/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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 NOTE
See
  'E:/biocbuild/bbs-3.19-bioc/meat/ncRNAtools.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   E:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL ncRNAtools
###
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* installing to library 'E:/biocbuild/bbs-3.19-bioc/R/library'
* installing *source* package 'ncRNAtools' ...
** 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 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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

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, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply,
    union, 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

Attaching package: 'IRanges'

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

    windows

Loading required package: GenomeInfoDb
No encoding supplied: defaulting to UTF-8.
Error in checkTrue(grepl("^URS", rnaCentralTextSearch("HOTAIR")[1])) : 
  Test not TRUE

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


RUNIT TEST PROTOCOL -- Thu Oct 17 03:59:41 2024 
*********************************************** 
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 E:/biocbuild/bbs-3.19-bioc/tmpdir/RtmpUzv2WO/RLIBS_1e7201f082049/ncRNAtools/unitTests/test_rnaCentralAccess.R: Error while sourcing  E:/biocbuild/bbs-3.19-bioc/tmpdir/RtmpUzv2WO/RLIBS_1e7201f082049/ncRNAtools/unitTests/test_rnaCentralAccess.R : Error in checkTrue(grepl("^URS", rnaCentralTextSearch("HOTAIR")[1])) : 
  Test not TRUE


Test files with failing tests

   test_rnaCentralAccess.R 
     E:/biocbuild/bbs-3.19-bioc/tmpdir/RtmpUzv2WO/RLIBS_1e7201f082049/ncRNAtools/unitTests/test_rnaCentralAccess.R 


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