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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:basecallQC.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings basecallQC_1.34.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/basecallQC.Rcheck’
* using R version 4.5.2 (2025-10-31)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘basecallQC/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘basecallQC’ version ‘1.34.0’
* 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 ‘basecallQC’ 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) BCL2FastQparams.Rd:39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) BCL2FastQparams.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) BCL2FastQparams.Rd:41-42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) basecallQC.Rd:39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) basecallQC.Rd:40-42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) basecallQC.Rd:43-44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) basecallQC.Rd:45-46: Lost braces in \itemize; meant \describe ?
checkRd: (-1) basecallQC.Rd:47-48: Lost braces in \itemize; meant \describe ?
checkRd: (-1) basecallQC.Rd:49-50: Lost braces in \itemize; meant \describe ?
checkRd: (-1) basecallQC.Rd:51-52: Lost braces in \itemize; meant \describe ?
checkRd: (-1) interOpsReport.Rd:32-33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) interOpsReport.Rd:34-37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) interOpsReport.Rd:38-41: Lost braces in \itemize; meant \describe ?
* 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
reportBCL             19.879  0.400  22.018
demuxBarplot          13.785  0.095  14.711
baseCallMetrics       12.623  0.416  14.462
passFilterTileplot    12.404  0.059  13.027
summaryDemuxTable     12.280  0.054  13.069
passFilterBoxplot     12.155  0.058  12.698
summaryConvStatsTable 12.119  0.072  12.826
demuxBoxplot          12.009  0.083  12.648
passFilterBar         12.019  0.046  12.868
makeFQTable           11.998  0.059  13.757
basecallQC            11.969  0.082  12.668
* 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:
  ── Error ('test_Run4.R:14:1'): (code run outside of `test_that()`) ─────────────
  Error in `is_true()`: could not find function "is_true"
  Backtrace:
      ▆
   1. └─testthat::expect_that(...) at test_Run4.R:14:1
  ── Error ('test_Run5.R:14:1'): (code run outside of `test_that()`) ─────────────
  Error in `is_true()`: could not find function "is_true"
  Backtrace:
      ▆
   1. └─testthat::expect_that(...) at test_Run5.R:14:1
  
  [ FAIL 5 | WARN 42 | SKIP 0 | PASS 0 ]
  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: 1 ERROR, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.22-bioc/meat/basecallQC.Rcheck/00check.log’
for details.

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL basecallQC
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘basecallQC’ ...
** this is package ‘basecallQC’ version ‘1.34.0’
** 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 (basecallQC)

R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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.

> library(testthat)
> library(basecallQC)
Loading required package: rmarkdown
Loading required package: knitr
Loading required package: prettydoc
Loading required package: yaml
> 
> test_check("basecallQC")
Saving _problems/test_Run1-13.R
Saving _problems/test_Run2-16.R
Saving _problems/test_Run3-17.R
Saving _problems/test_Run4-17.R
Saving _problems/test_Run5-17.R
[ FAIL 5 | WARN 42 | SKIP 0 | PASS 0 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_Run1.R:11:1'): (code run outside of `test_that()`) ─────────────
Error in `is_true()`: could not find function "is_true"
Backtrace:
    ▆
 1. └─testthat::expect_that(class(plot)[2] == "ggplot", is_true()) at test_Run1.R:11:1
── Error ('test_Run2.R:13:1'): (code run outside of `test_that()`) ─────────────
Error in `is_true()`: could not find function "is_true"
Backtrace:
    ▆
 1. └─testthat::expect_that(...) at test_Run2.R:13:1
── Error ('test_Run3.R:14:1'): (code run outside of `test_that()`) ─────────────
Error in `is_true()`: could not find function "is_true"
Backtrace:
    ▆
 1. └─testthat::expect_that(...) at test_Run3.R:14:1
── Error ('test_Run4.R:14:1'): (code run outside of `test_that()`) ─────────────
Error in `is_true()`: could not find function "is_true"
Backtrace:
    ▆
 1. └─testthat::expect_that(...) at test_Run4.R:14:1
── Error ('test_Run5.R:14:1'): (code run outside of `test_that()`) ─────────────
Error in `is_true()`: could not find function "is_true"
Backtrace:
    ▆
 1. └─testthat::expect_that(...) at test_Run5.R:14:1

[ FAIL 5 | WARN 42 | SKIP 0 | PASS 0 ]
Error:
! Test failures.
Execution halted