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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:squallms.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings squallms_1.1.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/squallms.Rcheck’
* using R Under development (unstable) (2024-11-24 r87369)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘squallms/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘squallms’ version ‘1.1.0’
* 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 ... WARNING
Found the following significant warnings:
  Warning: program compiled against libxml 212 using older 211
See ‘/home/biocbuild/bbs-3.21-bioc/meat/squallms.Rcheck/00install.out’ for details.
* 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 ...Warning: program compiled against libxml 212 using older 211
 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 ... NOTE
Warning: program compiled against libxml 212 using older 211

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Warning: program compiled against libxml 212 using older 211
* checking S3 generic/method consistency ... WARNING
Warning: program compiled against libxml 212 using older 211
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
* checking replacement functions ... WARNING
Warning: program compiled against libxml 212 using older 211
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
* checking foreign function calls ... NOTE
Warning: program compiled against libxml 212 using older 211
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... NOTE
Warning: program compiled against libxml 212 using older 211
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Warning: program compiled against libxml 212 using older 211
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... WARNING
Warning: program compiled against libxml 212 using older 211
Warning: program compiled against libxml 212 using older 211
Warning: program compiled against libxml 212 using older 211
* checking Rd \usage sections ... NOTE
Warning: program compiled against libxml 212 using older 211
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 33.076  0.421  35.739
logModelFeatQuality 26.796  0.188  28.460
logModelFeatProb    26.504  0.121  27.887
updateXcmsObjFeats  25.587  0.146  30.404
pickyPCA            24.744  0.164  26.997
labelFeatsManual    24.313  0.057  25.397
labelFeatsLasso     23.899  0.420  25.181
makeXcmsObjFlat     23.728  0.108  28.710
* 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: 5 WARNINGs, 5 NOTEs
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/squallms.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL squallms
###
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* installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library’
* installing *source* package ‘squallms’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Warning: program compiled against libxml 212 using older 211
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: program compiled against libxml 212 using older 211
** testing if installed package can be loaded from final location
Warning: program compiled against libxml 212 using older 211
** testing if installed package keeps a record of temporary installation path
* DONE (squallms)

R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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)
Warning: program compiled against libxml 212 using older 211
> 
> test_check("squallms")
Loading required package: BiocParallel

This is xcms version 4.5.2 


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 
 60.894   1.336  64.927