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### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:peakPantheR.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings peakPantheR_1.22.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/peakPantheR.Rcheck’
* using R version 4.5.1 (2025-06-13)
* 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 ‘peakPantheR/DESCRIPTION’ ... OK
* this is package ‘peakPantheR’ version ‘1.22.0’
* 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 ‘peakPantheR’ 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 whether startup messages can be suppressed ... 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 ... OK
* 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
peakPantheR_ROIStatistics                               20.479  0.313  20.798
outputAnnotationDiagnostic-peakPantheRAnnotation-method 15.711  0.238  15.958
outputAnnotationResult-peakPantheRAnnotation-method     15.131  0.090  15.222
peakPantheR_parallelAnnotation                          15.096  0.080  15.176
EICs-peakPantheRAnnotation-method                       11.695  0.700  12.415
retentionTimeCorrection-peakPantheRAnnotation-method     9.874  0.050   9.925
* 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 failures
  In addition: Warning messages:
  1: In .Internal(gc(verbose, reset, full)) :
    closing unused connection 10 (/tmp/RtmpGhYTyZ/notValidXML.mzML)
  2: In .Internal(gc(verbose, reset, full)) :
    closing unused connection 9 (/tmp/RtmpGhYTyZ/notValidXML.mzML)
  3: In .Internal(gc(verbose, reset, full)) :
    closing unused connection 8 (/tmp/RtmpGhYTyZ/notValidXML.mzML)
  4: In .Internal(gc(verbose, reset, full)) :
    closing unused connection 7 (/tmp/RtmpGhYTyZ/notValidXML.mzML)
  5: In .Internal(gc(verbose, reset, full)) :
    closing unused connection 6 (/home/biocbuild/bbs-3.21-bioc/R/site-library/peakPantheR/extdata/test_fakemzML.mzML)
  6: In .Internal(gc(verbose, reset, full)) :
    closing unused connection 5 (/home/biocbuild/bbs-3.21-bioc/R/site-library/peakPantheR/extdata/test_fakemzML.mzML)
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/peakPantheR.Rcheck/00check.log’
for details.

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### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL peakPantheR
###
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* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘peakPantheR’ ...
** this is package ‘peakPantheR’ version ‘1.22.0’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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 (peakPantheR)

R version 4.5.1 (2025-06-13) -- "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.

> library(testthat)
> library(peakPantheR)

This is peakPantheR version 1.22.0 

> 
> test_check("peakPantheR")
[ FAIL 13 | WARN 1 | SKIP 0 | PASS 1459 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_peakPantheRAnnotation_retentionTimeCorrection-method.R:176:3'): rt correction plot (uROI) ──
<subscriptOutOfBoundsError/error/condition>
Error in `S7::prop(x, "meta")[[i]]`: subscript out of bounds
Backtrace:
    ▆
 1. ├─testthat::expect_equal(...) at test_peakPantheRAnnotation_retentionTimeCorrection-method.R:176:3
 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
 3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
 4. ├─resultCorrected$result$plot[[1]]
 5. └─ggplot2 (local) `[[.ggplot2::gg`(resultCorrected$result$plot, 1)
── Failure ('test_peakPantheR_plotPeakwidth.R:23:3'): plot 3 samples, no color ──
result_3splNoColNoRot$labels$x not equal to "x".
target is NULL, current is character
── Failure ('test_peakPantheR_plotPeakwidth.R:50:3'): plot 3 samples, no color, rotate axis ──
result_3splNoColRot$labels$y not equal to "x".
target is NULL, current is character
── Failure ('test_peakPantheR_plotPeakwidth.R:75:3'): plot 4 samples with color ──
result_4splWithColNoRot$labels$x not equal to "x".
target is NULL, current is character
── Failure ('test_peakPantheR_plotPeakwidth.R:102:3'): plot 4 samples with color, rotate axis ──
result_4splWithColRot$labels$y not equal to "x".
target is NULL, current is character
── Failure ('test_peakPantheR_plotPeakwidth.R:134:3'): sampleColour length warning, peakwidth and rotate and input order message ──
result_plotColourWarning$result$labels$y not equal to "x".
target is NULL, current is character
── Failure ('test_peakPantheR_plotPeakwidth.R:171:3'): missing widthMin, no peakwidth plot ──
result_plotNoWidthMin$result$labels$x not equal to "x".
target is NULL, current is character
── Failure ('test_peakPantheR_plotPeakwidth.R:190:3'): missing widthMax, no peakwidth plot ──
result_plotNoWidthMax$result$labels$x not equal to "x".
target is NULL, current is character
── Failure ('test_peakPantheR_plotPeakwidth.R:209:3'): NA in acquisition time, revert to input order plot ──
result_plotFallBackNAAcqu$result$labels$x not equal to "x".
target is NULL, current is character
── Failure ('test_plotHistogram.R:33:3'): histogram and density, with NA in input ──
result_histoAndDensity$labels$y not equal to "density".
target is NULL, current is character
── Failure ('test_plotHistogram.R:38:3'): histogram and density, with NA in input ──
result_message$messages not equal to `expected_message`.
1/1 mismatches
x[1]: "`stat_bin()` using `bins = 30`. Pick better value `binwidth`."
y[1]: "`stat_bin()` using `bins = 30`. Pick better value with `binwidth`."
── Failure ('test_plotHistogram.R:51:3'): histogram without density ────────────
result_histoNoDensity$labels$y[1] not equal to "count".
target is NULL, current is character
── Failure ('test_plotHistogram.R:72:3'): histogram and density with modified ... (bins) ──
result_histoChangeBins$labels$y not equal to "density".
target is NULL, current is character

[ FAIL 13 | WARN 1 | SKIP 0 | PASS 1459 ]
Error: Test failures
In addition: Warning messages:
1: In .Internal(gc(verbose, reset, full)) :
  closing unused connection 10 (/tmp/RtmpGhYTyZ/notValidXML.mzML)
2: In .Internal(gc(verbose, reset, full)) :
  closing unused connection 9 (/tmp/RtmpGhYTyZ/notValidXML.mzML)
3: In .Internal(gc(verbose, reset, full)) :
  closing unused connection 8 (/tmp/RtmpGhYTyZ/notValidXML.mzML)
4: In .Internal(gc(verbose, reset, full)) :
  closing unused connection 7 (/tmp/RtmpGhYTyZ/notValidXML.mzML)
5: In .Internal(gc(verbose, reset, full)) :
  closing unused connection 6 (/home/biocbuild/bbs-3.21-bioc/R/site-library/peakPantheR/extdata/test_fakemzML.mzML)
6: In .Internal(gc(verbose, reset, full)) :
  closing unused connection 5 (/home/biocbuild/bbs-3.21-bioc/R/site-library/peakPantheR/extdata/test_fakemzML.mzML)
Execution halted