##############################################################################
##############################################################################
###
### 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_0.99.17.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/lcmsPlot.Rcheck’
* using R Under development (unstable) (2026-03-05 r89546)
* 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 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-03-11 04:30:38 UTC
* checking for file ‘lcmsPlot/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘lcmsPlot’ version ‘0.99.17’
* 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 ... NOTE
ms_header,RawrrReader: no visible binding for global variable ‘rawfile’
Undefined global functions or variables:
  rawfile
* 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 35.217  4.551  29.924
lp_rt_diff_plot             17.966  5.622  13.089
lp_total_ion_current        13.824  3.665   9.201
lp_layout                    9.054  1.849  10.771
iterate_plot_batches         9.304  0.985  10.291
lp_rt_line                   6.516  1.369   7.885
lp_mass_trace                5.341  0.580   5.920
lp_get_plot                  5.368  0.532   5.903
lp_grid                      4.696  0.380   5.079
* 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.23-bioc/meat/lcmsPlot.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL lcmsPlot
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’
* installing *source* package ‘lcmsPlot’ ...
** this is package ‘lcmsPlot’ version ‘0.99.17’
** 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 (lcmsPlot)

R Under development (unstable) (2026-03-05 r89546) -- "Unsuffered Consequences"
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.
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 99 ]

[ FAIL 0 | WARN 3 | SKIP 0 | PASS 99 ]
> 
> proc.time()
   user  system elapsed 
 60.315  11.306  63.187