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### Running command:
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###   F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:msPurity.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings msPurity_1.24.0.tar.gz
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* using log directory 'F:/biocbuild/bbs-3.16-bioc/meat/msPurity.Rcheck'
* using R version 4.2.3 (2023-03-15 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'msPurity/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'msPurity' version '1.24.0'
* 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 ... NOTE
Found the following hidden files and directories:
  .travis.yml
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'msPurity' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 19.5Mb
  sub-directories of 1Mb or more:
    extdata  18.8Mb
* 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
Package in Depends field not imported from: 'Rcpp'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
package 'methods' is used but not declared
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
addGenericMS1LookupResults: no visible global function definition for
  'count.fields'
addMetFragResults: no visible global function definition for
  'count.fields'
addSiriusResults: no visible global function definition for
  'count.fields'
assessPuritySingle: no visible binding for global variable 'parallel'
combineAnnotations: no visible binding for global variable
  'compoundDbname'
createDatabase: no visible global function definition for
  'featureValues'
create_database : getxcmsSetObject: no visible global function
  definition for 'sampclass<-'
dimsPredictPuritySingleMz: no visible binding for global variable
  'mtchi'
dimsPredictPuritySingleMz: no visible binding for global variable
  'alli'
dimsPredictPuritySingleMz: no visible binding for global variable
  'mtch'
filterPrecursors: no visible binding for global variable
  'l_speakmetaFiltered'
filterSMeta: no visible binding for global variable 'accession'
filterSMeta: no visible binding for global variable 'inPurity'
filterSMeta: no visible global function definition for 'lower'
filterSMeta: no visible binding for global variable 'polarity'
filterSMeta: no visible binding for global variable 'instrument_type'
filterSMeta: no visible binding for global variable 'instrument'
filterSMeta: no visible binding for global variable 'name.y'
filterSMeta: no visible binding for global variable 'retention_time'
filterSMeta: no visible binding for global variable 'grpid'
filterSMeta: no visible binding for global variable 'pid'
filterSMeta: no visible binding for global variable 'spectrum_type'
flag_remove: no visible global function definition for
  'PeakDensityParam'
flag_remove: no visible global function definition for 'chromPeaks<-'
flag_remove: no visible global function definition for 'chromPeaks'
getScanPeaksSqlite: no visible binding for global variable 'pid'
getScanPeaksSqlite: no visible binding for global variable
  'library_spectra_meta_id'
getScanPeaksSqlite: no visible binding for global variable 'pass_flag'
getScanPeaksSqlite: no visible binding for global variable 'type'
getScanPeaksSqlite: no visible binding for global variable
  'spectraType'
getScanPeaksSqlite: no visible binding for global variable 'ra'
getSmeta: no visible binding for global variable 'pid'
get_topn: no visible binding for global variable 'topn'
matchi: no visible global function definition for 'match_factor'
plotPurity: no visible binding for global variable 'idx'
plotPurity: no visible binding for global variable 'purity'
plotPurity: no visible binding for global variable 'variable'
purityA: no visible binding for global variable 'i'
queryVlibrary: no visible binding for global variable 'precursor_mz'
queryVlibrary: no visible binding for global variable 'retention_time'
queryVlibrarySingle: no visible binding for global variable 'pid'
queryVlibrarySingle: no visible binding for global variable
  'library_spectra_meta_id'
sum_calc_peaklist: no visible global function definition for
  'phenoData'
averageSpectra,purityD: no visible binding for global variable 'i'
subtract,purityD: no visible binding for global variable 'i'
Undefined global functions or variables:
  PeakDensityParam accession alli chromPeaks chromPeaks<-
  compoundDbname count.fields featureValues grpid i idx inPurity
  instrument instrument_type l_speakmetaFiltered
  library_spectra_meta_id lower match_factor mtch mtchi name.y parallel
  pass_flag phenoData pid polarity precursor_mz purity ra
  retention_time sampclass<- spectraType spectrum_type topn type
  variable
Consider adding
  importFrom("utils", "count.fields")
to your NAMESPACE file.
* 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 files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                   user system elapsed
createDatabase                   105.83   1.53  187.11
frag4feature-purityA-method       86.42   0.50  166.11
dimsPredictPurity-purityD-method  31.14   0.67   31.81
combineAnnotations                10.20   0.50   10.74
spectralMatching                   5.26   3.47   18.28
flag_remove                        8.47   0.21   30.80
assessPuritySingle                 7.73   0.15    8.03
groupPeaks-purityD-method          6.80   0.45    7.25
purityA                            7.00   0.14    7.14
subtract-purityD-method            6.50   0.28    6.78
groupPeaksEx                       5.28   0.45    5.74
purityX                            5.02   0.19   23.06
* 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: 4 NOTEs
See
  'F:/biocbuild/bbs-3.16-bioc/meat/msPurity.Rcheck/00check.log'
for details.