Build/check report for BioC 3.22 - CHECK results for MAIT on nebbiolo2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.3 LTS)	x86_64	4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"	4889
Click on any hostname to see more info about the system (e.g. compilers) () as reported by 'uname -p', except on Windows and Mac OS X*

CHECK results for MAIT on nebbiolo2

To the developers/maintainers of the MAIT package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MAIT.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results

Summary

Package: MAIT

Version: 1.44.0

Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:MAIT.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings MAIT_1.44.0.tar.gz

StartedAt: 2026-02-10 01:25:45 -0500 (Tue, 10 Feb 2026)

EndedAt: 2026-02-10 01:35:06 -0500 (Tue, 10 Feb 2026)

EllapsedTime: 560.6 seconds

RetCode: 0

Status: OK

CheckDir: MAIT.Rcheck

Warnings: 0

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:MAIT.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings MAIT_1.44.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/MAIT.Rcheck’
* using R version 4.5.2 (2025-10-31)
* 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 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘MAIT/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MAIT’ version ‘1.44.0’
* 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 ‘MAIT’ 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 ... NOTE
'library' or 'require' call to ‘rgl’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
Biotransformations: no visible global function definition for ‘data’
Biotransformations: no visible binding for global variable ‘MAITtables’
Biotransformations: no visible global function definition for
  ‘read.csv’
Biotransformations: no visible global function definition for
  ‘read.csv2’
PLSDA: no visible global function definition for ‘predict’
Validation: no visible global function definition for ‘predict’
Validation: no visible global function definition for ‘sd’
Validation: no visible global function definition for ‘rainbow’
Validation: no visible global function definition for ‘png’
Validation: no visible global function definition for ‘boxplot’
Validation: no visible global function definition for ‘legend’
Validation: no visible global function definition for ‘title’
Validation: no visible global function definition for ‘dev.off’
Validation: no visible binding for global variable ‘sd’
computeSpectra: no visible global function definition for ‘cor’
identifyMetabolites: no visible global function definition for ‘data’
identifyMetabolites: no visible binding for global variable
  ‘MAITtables’
identifyMetabolites: no visible global function definition for
  ‘read.csv’
identifyMetabolites: no visible global function definition for
  ‘write.table’
metaboliteTable: no visible global function definition for
  ‘write.table’
peakAggregation: no visible global function definition for
  ‘write.table’
peakAnnotation: no visible global function definition for ‘data’
peakAnnotation: no visible binding for global variable ‘MAITtables’
peakAnnotation: no visible global function definition for ‘read.csv2’
plotBoxplot: no visible global function definition for ‘png’
plotBoxplot: no visible global function definition for ‘boxplot’
plotBoxplot: no visible global function definition for ‘title’
plotBoxplot: no visible global function definition for ‘dev.off’
plotHeatmap: no visible global function definition for ‘p.adjust’
plotHeatmap : distCor: no visible global function definition for
  ‘as.dist’
plotHeatmap : distCor: no visible global function definition for ‘cor’
plotHeatmap : hclustWard: no visible global function definition for
  ‘hclust’
plotHeatmap: no visible global function definition for
  ‘colorRampPalette’
plotHeatmap: no visible global function definition for ‘png’
plotHeatmap: no visible global function definition for ‘legend’
plotHeatmap: no visible global function definition for ‘dev.off’
plotPCA: no visible global function definition for ‘prcomp’
plotPCA: no visible global function definition for ‘png’
plotPCA: no visible global function definition for ‘legend’
plotPCA: no visible global function definition for ‘dev.off’
plotPLS: no visible global function definition for ‘png’
plotPLS: no visible global function definition for ‘legend’
plotPLS: no visible global function definition for ‘dev.off’
sigPeaksTable: no visible global function definition for ‘p.adjust’
sigPeaksTable: no visible global function definition for ‘aggregate’
sigPeaksTable: no visible binding for global variable ‘median’
sigPeaksTable: no visible global function definition for ‘write.csv’
spectralAnova: no visible global function definition for ‘lm’
spectralAnova: no visible global function definition for ‘anova’
spectralAnova: no visible global function definition for ‘p.adjust’
spectralFUN: no visible global function definition for ‘p.adjust’
spectralKruskal: no visible global function definition for
  ‘kruskal.test’
spectralKruskal: no visible global function definition for ‘p.adjust’
spectralTStudent: no visible global function definition for ‘lm’
spectralTStudent: no visible global function definition for ‘t.test’
spectralTStudent: no visible global function definition for ‘p.adjust’
spectralWelch: no visible global function definition for ‘lm’
spectralWelch: no visible global function definition for ‘t.test’
spectralWelch: no visible global function definition for ‘p.adjust’
spectralWilcox: no visible global function definition for ‘lm’
spectralWilcox: no visible global function definition for ‘wilcox.test’
spectralWilcox: no visible global function definition for ‘p.adjust’
writeExcelTable: no visible global function definition for ‘write.csv’
writeParameterTable: no visible global function definition for
  ‘write.csv’
Undefined global functions or variables:
  MAITtables aggregate anova as.dist boxplot colorRampPalette cor data
  dev.off hclust kruskal.test legend lm median p.adjust png prcomp
  predict rainbow read.csv read.csv2 sd t.test title wilcox.test
  write.csv write.table
Consider adding
  importFrom("grDevices", "colorRampPalette", "dev.off", "png",
             "rainbow")
  importFrom("graphics", "boxplot", "legend", "title")
  importFrom("stats", "aggregate", "anova", "as.dist", "cor", "hclust",
             "kruskal.test", "lm", "median", "p.adjust", "prcomp",
             "predict", "sd", "t.test", "wilcox.test")
  importFrom("utils", "data", "read.csv", "read.csv2", "write.csv",
             "write.table")
to your NAMESPACE file.
* checking Rd files ... NOTE
checkRd: (-1) classes.Rd:5: Lost braces
     5 | Function \code{classes} extracts the class names of a link{MAIT-class} object as a vector. 
       |                                                           ^
checkRd: (-1) parameters.Rd:5: Lost braces
     5 | Function \code{parameters} extracts the slot link{MAIT.Parameters-class} of a \code{\link{MAIT-class}} object. This class contains all the parameters that have been used in the previous functions. Typing a summary of this object, a matrix version of the parameters is obtained.
       |                                                  ^
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  MAIT-class.Rd: xsAnnotate
  MAIT.FeatureData-class.Rd: xsAnnotate
  MAIT.FeatureInfo-class.Rd: xsAnnotate
  MAIT.PhenoData-class.Rd: xsAnnotate
  MAIT.RawData-class.Rd: xsAnnotate
  MAIT.Validation-class.Rd: xsAnnotate
  peakAnnotation.Rd: xsAnnotate, groupCorr, xsAnnotate-class
  rawData.Rd: xsAnnotate, xsAnnotate-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                      user system elapsed
ovClassifRatio      12.386  0.371  12.757
Validation          11.562  0.717  12.268
classifRatioClasses 11.498  0.603  12.101
ovClassifRatioTable 10.846  0.099  10.945
parameters          10.690  0.064  10.754
* 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: 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/MAIT.Rcheck/00check.log’
for details.

Installation output

MAIT.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL MAIT
###
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* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘MAIT’ ...
** this is package ‘MAIT’ version ‘1.44.0’
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for ‘scores’ in package ‘MAIT’
Creating a new generic function for ‘loadings’ in package ‘MAIT’
** 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 (MAIT)

Tests output

Example timings

MAIT.Rcheck/MAIT-Ex.timings

name	user	system	elapsed
Biotransformations	0.759	0.120	0.880
LSDResults	0.704	0.033	0.737
MAITbuilder	0.017	0.000	0.017
Validation	11.562	0.717	12.268
classNum	0.004	0.000	0.004
classes	0.003	0.001	0.004
classifRatioClasses	11.498	0.603	12.101
featureID	0.677	0.026	0.703
featureInfo	0.692	0.074	0.765
featureSigID	0.667	0.059	0.725
getScoresTable	0.692	0.010	0.702
identifyMetabolites	1.120	0.024	1.144
loadings	1.279	0.031	1.310
metaboliteTable	1.117	0.008	1.124
method	0.002	0.001	0.003
model	1.278	0.008	1.286
models	0.722	0.003	0.724
ovClassifRatio	12.386	0.371	12.757
ovClassifRatioTable	10.846	0.099	10.945
parameters	10.690	0.064	10.754
pcaLoadings	0.682	0.002	0.685
pcaModel	0.780	0.017	0.798
pcaScores	0.679	0.006	0.685
peakAggregation	0.006	0.001	0.007
peakAnnotation	0	0	0
plotBoxplot	0.823	0.000	0.822
plotHeatmap	2.337	0.050	2.357
plotPCA	0.717	0.008	0.725
plotPLS	1.146	0.028	1.174
plsLoadings	1.175	0.039	1.215
plsModel	1.159	0.017	1.177
plsScores	1.168	0.032	1.200
pvalues	0.665	0.028	0.694
pvaluesCorrection	0.647	0.001	0.648
rawData	0.003	0.000	0.003
resultsPath	0.667	0.007	0.673
sampleProcessing	0	0	0
scores	1.218	0.023	1.241
sigPeaksTable	0.761	0.008	0.769
spectralSigFeatures	0.662	0.000	0.662