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### Running command:
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###   /home/biocbuild/R/R/bin/R CMD check --install=check:ptairMS.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings ptairMS_1.13.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/ptairMS.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14)
    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 ‘1.13.0’
* 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-3.20-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 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 ... 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           124.834  0.415 125.531
imputeMat             26.159  0.116  26.330
writeEset             25.695  0.068  25.818
alignSamples          24.869  0.232  25.229
impute                23.930  0.116  24.096
getPeakList           22.773  0.059  22.885
annotation            22.355  0.127  22.532
plot                  18.914  0.087  19.040
plotRaw               17.666  0.124  17.827
plotTIC               17.635  0.091  17.765
setSampleMetadata     17.412  0.112  17.560
plotFeatures          17.422  0.092  17.552
plotCalib             17.244  0.136  17.418
defineKnots           16.983  0.092  17.113
importSampleMetadata  16.893  0.104  17.034
resetSampleMetadata   16.802  0.056  16.890
updatePtrSet          16.222  0.076  16.333
getSampleMetadata     16.096  0.100  16.232
getDirectory          16.045  0.116  16.194
getFileNames          15.795  0.076  15.901
rmPeakList            15.740  0.072  15.841
exportSampleMetada    15.282  0.052  15.367
convert_to_mzML       14.762  0.347  15.136
changeTimeLimits      14.847  0.060  14.939
createPtrSet          13.144  0.112  13.348
* 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: 2 WARNINGs, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/ptairMS.Rcheck/00check.log’
for details.