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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ptairMS.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ptairMS_1.12.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/ptairMS.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ptairMS/DESCRIPTION’ ... OK
* this is package ‘ptairMS’ version ‘1.12.0’
* 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 ‘/Users/biocbuild/bbs-3.19-bioc/meat/ptairMS.Rcheck/00install.out’ for details.
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* 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 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           94.259  3.490  98.663
writeEset            18.340  0.714  19.264
imputeMat            16.847  0.817  17.833
alignSamples         16.678  0.919  17.789
impute               16.045  0.710  16.910
getPeakList          15.026  0.657  15.841
annotation           14.596  0.629  15.381
convert_to_mzML      13.144  0.681  13.938
plotTIC              12.485  0.479  13.073
plot                 12.221  0.524  12.854
setSampleMetadata    11.814  0.435  12.388
plotRaw              11.634  0.569  12.329
plotCalib            11.604  0.515  12.231
plotFeatures         11.552  0.530  12.239
updatePtrSet         11.606  0.450  12.184
resetSampleMetadata  11.440  0.416  11.970
defineKnots          10.863  0.436  11.393
rmPeakList           10.695  0.414  11.236
getSampleMetadata     9.987  0.425  10.521
exportSampleMetada    9.791  0.441  10.332
importSampleMetadata  9.176  0.405   9.667
getDirectory          9.000  0.449   9.691
getFileNames          9.020  0.407   9.514
changeTimeLimits      8.972  0.377   9.417
createPtrSet          8.722  0.554   9.372
* 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
  ‘/Users/biocbuild/bbs-3.19-bioc/meat/ptairMS.Rcheck/00check.log’
for details.