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###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:lcmsPlot.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings lcmsPlot_0.99.19.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/lcmsPlot.Rcheck’
* using R version 4.6.0 alpha (2026-03-30 r89742)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-04-03 04:47:31 UTC
* checking for file ‘lcmsPlot/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘lcmsPlot’ version ‘0.99.19’
* 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 ‘lcmsPlot’ 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 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
get_XCMSnExp_object_example 24.053  3.325  16.873
lp_rt_diff_plot             16.226  6.025  11.814
lp_total_ion_current        14.253  4.117  10.546
XcmsRawList                 14.326  0.737  15.071
lp_layout                    9.296  1.852  11.005
iterate_plot_batches         8.152  1.117   9.271
lp_get_plot                  5.266  0.421   5.687
lp_mass_trace                5.286  0.376   5.664
next_plot                    4.496  0.577   5.074
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: OK

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### Running command:
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###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL lcmsPlot
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* installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’
* installing *source* package ‘lcmsPlot’ ...
** this is package ‘lcmsPlot’ version ‘0.99.19’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
in method for ‘create_chromatograms’ with signature ‘"DBIConnection","data.frame","list","NULL"’: no definition for class “DBIConnection”
in method for ‘create_chromatograms’ with signature ‘"MChromatograms","data.frame","list","NULL"’: no definition for class “MChromatograms”
in method for ‘create_chromatograms’ with signature ‘"XChromatogram","data.frame","list","NULL"’: no definition for class “XChromatogram”
in method for ‘create_chromatograms’ with signature ‘"XChromatograms","data.frame","list","NULL"’: no definition for class “XChromatograms”
** 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 (lcmsPlot)

R version 4.6.0 alpha (2026-03-30 r89742)
Copyright (C) 2026 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.

> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
> 
> library(testthat)
> library(lcmsPlot)
> 
> test_check("lcmsPlot")
Polarity can not be extracted from netCDF files, please set manually the polarity with the 'polarity' method.

This is xcms version 4.9.2 

Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 635 regions of interest ... OK: 300 found.


This is xcms version 4.9.2 

Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 694 regions of interest ... OK: 312 found.

Sample number 1 used as center sample.
Aligning wt15.CDF against ko15.CDF ... OK

Applying retention time adjustment to the identified chromatographic peaks ... OK
Polarity can not be extracted from netCDF files, please set manually the polarity with the 'polarity' method.
Polarity can not be extracted from netCDF files, please set manually the polarity with the 'polarity' method.

This is xcms version 4.9.2 

Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 635 regions of interest ... OK: 300 found.


This is xcms version 4.9.2 

Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 694 regions of interest ... OK: 312 found.

Polarity can not be extracted from netCDF files, please set manually the polarity with the 'polarity' method.
Polarity can not be extracted from netCDF files, please set manually the polarity with the 'polarity' method.
Polarity can not be extracted from netCDF files, please set manually the polarity with the 'polarity' method.

This is xcms version 4.9.2 

Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 635 regions of interest ... OK: 300 found.


This is xcms version 4.9.2 

Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 694 regions of interest ... OK: 312 found.

[ FAIL 0 | WARN 3 | SKIP 0 | PASS 107 ]

[ FAIL 0 | WARN 3 | SKIP 0 | PASS 107 ]
> 
> proc.time()
   user  system elapsed 
 69.519  15.004  68.260