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### Running command:
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###   /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:ptairMS.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings ptairMS_1.10.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/ptairMS.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ptairMS/DESCRIPTION’ ... OK
* this is package ‘ptairMS’ version ‘1.10.0’
* 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 ‘ptairMS’ can be installed ... WARNING
Found the following significant warnings:
  Warning: replacing previous import ‘Biobase::cache’ by ‘bit64::cache’ when loading ‘ptairMS’
See ‘/home/biocbuild/bbs-3.18-bioc/meat/ptairMS.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++ (GCC) 10.3.1’
* 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 loading without being on the library search path ... OK
* checking dependencies in R code ... WARNING
'::' or ':::' imports not declared from:
  ‘htmlwidgets’ ‘plyr’
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’ ‘tofToMz’
* 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           124.414  0.966 125.627
alignSamples          25.630  0.408  26.138
imputeMat             25.862  0.056  25.975
writeEset             24.771  0.083  24.897
annotation            23.931  0.180  24.162
getPeakList           23.040  0.112  23.198
impute                22.987  0.111  23.143
plot                  18.656  0.088  18.805
plotTIC               18.018  0.143  18.197
plotFeatures          17.746  0.092  17.876
plotRaw               17.657  0.108  17.840
plotCalib             16.563  0.096  16.697
updatePtrSet          16.277  0.116  16.420
resetSampleMetadata   16.227  0.129  16.383
setSampleMetadata     16.261  0.084  16.373
rmPeakList            16.126  0.042  16.197
defineKnots           15.920  0.071  16.037
importSampleMetadata  15.798  0.096  15.926
changeTimeLimits      15.705  0.103  15.839
getSampleMetadata     15.550  0.044  15.624
getFileNames          15.508  0.056  15.597
exportSampleMetada    15.439  0.111  15.583
getDirectory          15.161  0.064  15.252
createPtrSet          12.260  0.127  12.480
convert_to_mzML        7.920  0.144   8.078
* 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: 2 WARNINGs, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/ptairMS.Rcheck/00check.log’
for details.