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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_1.35.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/basecallQC.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 ‘basecallQC/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘basecallQC’ version ‘1.35.0’
* 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
* 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-3.23-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/4.6-arm64/Resources/library’
* installing *source* package ‘basecallQC’ ...
** this is package ‘basecallQC’ version ‘1.35.0’
** 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 Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-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