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### Running command:
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###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:ptairMS.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings ptairMS_1.4.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/ptairMS.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ptairMS/DESCRIPTION’ ... OK
* this is package ‘ptairMS’ version ‘1.4.1’
* 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 ‘ptairMS’ can be installed ... WARNING
Found the following significant warnings:
  Warning: undefined slot classes in definition of "ptrRaw": peakList(class "ExpressionSet")
See ‘/home/biocbuild/bbs-3.15-bioc/meat/ptairMS.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 ... OK
* checking R 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 dependencies in R code ... NOTE
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘getCalibrationInfo’ ‘getPeakList’ ‘getPeaksInfo’ ‘getTimeInfo’
  ‘processFileTemporalNominalMass’
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                       user system elapsed
detectPeak           74.975  0.552  75.527
alignSamples         14.827  0.572  15.413
writeEset            14.033  0.088  14.122
annotation           13.423  0.368  13.793
imputeMat            13.262  0.228  13.489
impute               11.990  0.124  12.114
getPeakList          11.053  0.168  11.222
plotTIC               9.689  0.088   9.778
plotFeatures          9.501  0.072   9.573
plot                  9.382  0.128   9.512
setSampleMetadata     8.999  0.036   9.035
updatePtrSet          8.926  0.096   9.022
defineKnots           8.787  0.212   8.999
plotRaw               8.909  0.080   8.989
rmPeakList            8.628  0.064   8.692
changeTimeLimits      8.366  0.048   8.414
plotCalib             8.137  0.088   8.225
resetSampleMetadata   7.886  0.024   7.911
getSampleMetadata     7.667  0.112   7.779
getDirectory          7.442  0.080   7.524
getFileNames          7.295  0.112   7.407
importSampleMetadata  7.310  0.040   7.350
exportSampleMetada    7.065  0.064   7.130
createPtrSet          7.001  0.056   7.067
convert_to_mzML       5.781  0.124   5.897
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.15-bioc/meat/ptairMS.Rcheck/00check.log’
for details.