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### Running command:
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###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:hdxmsqc.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings hdxmsqc_1.0.1.tar.gz
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* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/hdxmsqc.Rcheck'
* using R version 4.4.1 (2024-06-14 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'hdxmsqc/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'hdxmsqc' version '1.0.1'
* 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 whether package 'hdxmsqc' can be installed ... OK
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
chargeCorrelationHdx: no visible global function definition for 'assay'
chargeCorrelationHdx: no visible binding for global variable 'x'
chargeCorrelationHdx: no visible binding for global variable 'z'
chargeCorrelationHdx: no visible binding for global variable 'peptide'
chargeCorrelationHdx: no visible binding for global variable 'y'
compatibleUptake: no visible global function definition for 'rowData'
compatibleUptake: no visible global function definition for 'assay'
computeMassError: no visible global function definition for 'rowData'
computeMassError: no visible global function definition for 'assay'
computeMonotoneStats: no visible global function definition for 'assay'
computeMonotoneStats: no visible binding for global variable 'x'
computeMonotoneStats: no visible binding for global variable 'y'
imTimeOutlier: no visible global function definition for 'rowData'
imTimeOutlier: no visible global function definition for 'rowMedians'
imTimeOutlier: no visible binding for global variable 'Experiment'
imTimeOutlier: no visible binding for global variable 'IMS_shift'
intensityOutliers: no visible global function definition for 'rowData'
isMissingAtRandom: no visible global function definition for 'assay'
isMissingAtRandom: no visible global function definition for 'rowData'
plotImTimeOutlier: no visible binding for global variable 'Experiment'
plotImTimeOutlier: no visible binding for global variable 'IMS_shift'
plotImTimeOutlier: no visible global function definition for
  'brewer.pal'
plotIntensityOutliers: no visible binding for global variable 'x'
plotIntensityOutliers: no visible binding for global variable 'y'
plotIntensityOutliers: no visible binding for global variable 'outlier'
plotIntensityOutliers: no visible global function definition for
  'brewer.pal'
plotMassError: no visible binding for global variable 'x'
plotMassError: no visible binding for global variable 'y'
plotMassError: no visible global function definition for 'brewer.pal'
plotMissing: no visible global function definition for 'assay'
plotMissing: no visible global function definition for 'pheatmap'
plotMissing: no visible global function definition for 'brewer.pal'
plotMonotoneStat : <anonymous>: no visible binding for global variable
  'x'
plotMonotoneStat : <anonymous>: no visible binding for global variable
  'y'
plotMonotoneStat : <anonymous>: no visible binding for global variable
  'outlier'
plotMonotoneStat : <anonymous>: no visible global function definition
  for 'brewer.pal'
plotrTimeOutliers: no visible binding for global variable 'Experiment'
plotrTimeOutliers: no visible binding for global variable 'RT_shift'
plotrTimeOutliers: no visible global function definition for
  'brewer.pal'
processHDE: no visible binding for global variable 'Deut.Time'
processHDE: no visible binding for global variable 'Sequence'
processHDE: no visible binding for global variable 'Protein.State'
processHDE: no visible binding for global variable 'Charge'
qualityControl: no visible global function definition for 'rowData'
rTimeOutliers: no visible global function definition for 'rowData'
rTimeOutliers: no visible global function definition for 'rowMedians'
rTimeOutliers: no visible binding for global variable 'Experiment'
rTimeOutliers: no visible binding for global variable 'RT_shift'
replicateCorrelation: no visible global function definition for 'assay'
replicateCorrelation: no visible binding for global variable 'x'
replicateCorrelation: no visible binding for global variable 'y'
replicateOutlier: no visible global function definition for 'assay'
replicateOutlier: no visible binding for global variable 'x'
replicateOutlier: no visible binding for global variable 'y'
spectraSimilarity: no visible global function definition for 'bpparam'
spectraSimilarity: no visible binding for global variable 'timepoints'
spectraSimilarity: no visible binding for global variable 'Sequence'
spectraSimilarity: no visible global function definition for 'bplapply'
spectraSimilarity: no visible global function definition for
  'spectraData'
spectraSimilarity: no visible binding for global variable 'Charge'
spectraSimilarity: no visible binding for global variable 'DeutTime'
Undefined global functions or variables:
  Charge Deut.Time DeutTime Experiment IMS_shift Protein.State RT_shift
  Sequence assay bplapply bpparam brewer.pal outlier peptide pheatmap
  rowData rowMedians spectraData timepoints x y z
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
* 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: 1 NOTE
See
  'F:/biocbuild/bbs-3.19-bioc/meat/hdxmsqc.Rcheck/00check.log'
for details.