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###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:peakPantheR.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings peakPantheR_1.22.0.tar.gz
###
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* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/peakPantheR.Rcheck'
* using R version 4.5.1 (2025-06-13 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* 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 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 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                               26.39   0.39   26.82
outputAnnotationDiagnostic-peakPantheRAnnotation-method 18.94   0.14   19.20
peakPantheR_parallelAnnotation                          18.86   0.13   18.99
outputAnnotationResult-peakPantheRAnnotation-method     18.61   0.13   18.74
EICs-peakPantheRAnnotation-method                       15.38   0.83   18.77
retentionTimeCorrection-peakPantheRAnnotation-method    12.30   0.13   12.42
peakPantheR_singleFileSearch                             6.53   0.04    6.58
peakPantheR_quickEIC                                     5.08   0.11    5.19
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 OK
* 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: OK

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###
### Running command:
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###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL peakPantheR
###
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* installing to library 'E:/biocbuild/bbs-3.21-bioc/R/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 ucrt) -- "Great Square Root"
Copyright (C) 2025 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.

> library(testthat)
> library(peakPantheR)

This is peakPantheR version 1.22.0 

> 
> test_check("peakPantheR")
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 1478 ]

[ FAIL 0 | WARN 1 | SKIP 0 | PASS 1478 ]
Warning messages:
1: In .Internal(gc(verbose, reset, full)) :
  closing unused connection 10 (E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp6NoxmG\notValidXML.mzML)
2: In .Internal(gc(verbose, reset, full)) :
  closing unused connection 9 (E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp6NoxmG\notValidXML.mzML)
3: In .Internal(gc(verbose, reset, full)) :
  closing unused connection 8 (E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp6NoxmG\notValidXML.mzML)
4: In .Internal(gc(verbose, reset, full)) :
  closing unused connection 7 (E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp6NoxmG\notValidXML.mzML)
5: In .Internal(gc(verbose, reset, full)) :
  closing unused connection 6 (E:\biocbuild\bbs-3.21-bioc\R\library\peakPantheR\extdata\test_fakemzML.mzML)
6: In .Internal(gc(verbose, reset, full)) :
  closing unused connection 5 (E:\biocbuild\bbs-3.21-bioc\R\library\peakPantheR\extdata\test_fakemzML.mzML)
> 
> proc.time()
   user  system elapsed 
 925.07    7.90 1310.32