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### Running command:
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###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:ptairMS.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings ptairMS_1.14.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/ptairMS.Rcheck’
* using R version 4.4.3 (2025-02-28)
* 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 24.04.2 LTS
* using session charset: UTF-8
* checking for file ‘ptairMS/DESCRIPTION’ ... OK
* this is package ‘ptairMS’ version ‘1.14.0’
* 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++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* 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           78.979  0.564  79.548
writeEset            15.610  0.072  15.683
imputeMat            14.900  0.077  14.979
alignSamples         14.008  0.281  14.314
impute               13.448  0.058  13.505
annotation           12.970  0.178  13.148
getPeakList          13.001  0.060  13.061
convert_to_mzML      11.215  0.406  11.621
plot                 11.354  0.065  11.419
resetSampleMetadata  10.083  0.012  10.094
plotTIC               9.897  0.018   9.915
plotFeatures          9.757  0.103   9.861
plotRaw               9.710  0.043   9.754
defineKnots           9.582  0.147   9.728
plotCalib             9.325  0.031   9.357
updatePtrSet          9.258  0.015   9.273
setSampleMetadata     9.227  0.026   9.253
rmPeakList            8.920  0.009   8.929
getDirectory          8.809  0.020   8.829
importSampleMetadata  8.657  0.018   8.675
getSampleMetadata     8.602  0.017   8.620
createPtrSet          8.223  0.162   8.401
exportSampleMetada    8.108  0.166   8.274
changeTimeLimits      8.075  0.066   8.141
getFileNames          7.938  0.042   7.980
* 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 re-building of vignette outputs ... OK
* 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.