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### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:squallms.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings squallms_1.0.0.tar.gz
###
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* using log directory ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/squallms.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘squallms/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘squallms’ version ‘1.0.0’
* 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 ‘squallms’ 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
extractChromMetrics 20.322  0.664  20.983
pickyPCA            16.343  0.029  16.350
logModelFeatQuality 15.732  0.159  15.868
logModelFeatProb    15.394  0.189  15.573
updateXcmsObjFeats  15.271  0.167  15.419
makeXcmsObjFlat     14.658  0.051  14.711
labelFeatsLasso     14.426  0.083  14.515
labelFeatsManual    14.294  0.130  14.433
* 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-3.20-bioc/R/bin/R CMD INSTALL squallms
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* installing to library ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘squallms’ ...
** 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 (squallms)

R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 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(squallms)
> 
> test_check("squallms")
Loading required package: BiocParallel

This is xcms version 4.4.0 


Attaching package: 'xcms'

The following object is masked from 'package:stats':

    sigma


Attaching package: 'dplyr'

The following objects are masked from 'package:xcms':

    collect, groups

The following object is masked from 'package:testthat':

    matches

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union


Attaching package: 'RaMS'

The following object is masked from 'package:dplyr':

    between

Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 198 regions of interest ... OK: 147 found.
Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 232 regions of interest ... OK: 166 found.
Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 218 regions of interest ... OK: 176 found.
Sample number 2 used as center sample.
Aligning LB12HL_AB.mzML.gz against LB12HL_CD.mzML.gz ... OK
Aligning LB12HL_EF.mzML.gz against LB12HL_CD.mzML.gz ... OK
Applying retention time adjustment to the identified chromatographic peaks ... OK
Defining peak areas for filling-in .... OK
Start integrating peak areas from original files
Requesting 57 peaks from LB12HL_AB.mzML.gz ... got 52.
Requesting 46 peaks from LB12HL_CD.mzML.gz ... got 45.
Requesting 41 peaks from LB12HL_EF.mzML.gz ... got 40.
Constructing interpolated data frame
Performing PCA
Logistic model regression coefficients:
(Intercept)     med_cor     med_snr 
 -8.8746254   9.6883921   0.3798715 
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 31 ]
> 
> proc.time()
   user  system elapsed 
 33.980   1.482  35.388