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### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:SwathXtend.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings SwathXtend_2.26.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/SwathXtend.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘SwathXtend/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SwathXtend’ version ‘2.26.0’
* 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 ‘SwathXtend’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 350.2Mb
  sub-directories of 1Mb or more:
    files  350.0Mb
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
reliabilityCheckSwath: warning in venn.diagram(list(seedSwath =
  ds.seed$Peptide, extSwath = ds.ext$Peptide), file = "venn of
  peptide.png", category.names = c("seed", "extended"), fill =
  c("aquamarine1", "chartreuse"), main = paste("Peptides at FDR pass",
  nfdr)): partial argument match of 'file' to 'filename'
reliabilityCheckSwath: warning in venn.diagram(list(seedSwath =
  ds.seed$Protein, extSwath = ds.ext$Protein), file = "venn of
  protein.png", category.names = c("seed", "extended"), fill =
  c("aquamarine1", "chartreuse"), main = paste("Proteins at FDR pass",
  nfdr)): partial argument match of 'file' to 'filename'
alignRTbyHydro: no visible global function definition for ‘as.formula’
alignRTbyHydro: no visible global function definition for ‘lm’
alignRTbyHydro: no visible global function definition for ‘predict’
applyttest : <anonymous>: no visible global function definition for
  ‘t.test’
applyttest : <anonymous>: no visible global function definition for
  ‘na.omit’
applyttestPep : <anonymous>: no visible global function definition for
  ‘na.omit’
applyttestPep: no visible global function definition for ‘aggregate’
applyttestPep : <anonymous>: no visible global function definition for
  ‘t.test’
checkQuality: no visible global function definition for ‘median’
computeRIICor : <anonymous>: no visible global function definition for
  ‘cor’
computeRIICor: no visible global function definition for ‘data’
computeRIICor: no visible global function definition for ‘png’
computeRIICor: no visible global function definition for ‘boxplot’
computeRIICor: no visible global function definition for ‘abline’
computeRIICor: no visible global function definition for ‘dev.off’
computeRTCor: no visible global function definition for ‘cor’
computeRTCor: no visible global function definition for ‘predict’
computeRTCor: no visible global function definition for ‘png’
computeRTCor: no visible global function definition for ‘lines’
computeRTCor: no visible global function definition for ‘lowess’
computeRTCor: no visible global function definition for ‘text’
computeRTCor: no visible global function definition for ‘dev.off’
computeRTCor: no visible global function definition for ‘abline’
computeRTCor: no visible global function definition for ‘axis’
computeRTCor: no visible global function definition for ‘as.formula’
computeRTCor: no visible global function definition for ‘lm’
computeRTCor: no visible global function definition for ‘layout’
computeRTCor: no visible global function definition for ‘resid’
computeRTCor: no visible global function definition for ‘residuals’
cv: no visible global function definition for ‘sd’
cv: no visible global function definition for ‘na.omit’
fdr.crit : <anonymous>: no visible global function definition for
  ‘na.omit’
medianNorm : <anonymous>: no visible global function definition for
  ‘median’
medianNorm : <anonymous>: no visible global function definition for
  ‘na.omit’
mlr: no visible global function definition for ‘na.omit’
mlr: no visible global function definition for ‘hist’
mlr: no visible global function definition for ‘density’
mlr: no visible global function definition for ‘lines’
mlr: no visible global function definition for ‘abline’
mlr: no visible global function definition for ‘text’
mlr: no visible global function definition for ‘segments’
mlrrep: no visible global function definition for ‘na.omit’
normalise: no visible global function definition for ‘aggregate’
outputLib: no visible global function definition for ‘write.table’
parseAccession: no visible global function definition for ‘na.omit’
plotDensities: no visible global function definition for ‘rainbow’
plotDensities: no visible global function definition for ‘density’
plotDensities: no visible global function definition for ‘lines’
plotDensities: no visible global function definition for ‘legend’
plotErrorBarsLines: no visible global function definition for ‘par’
plotErrorBarsLines: no visible global function definition for ‘axis’
plotRIICor : <anonymous>: no visible global function definition for
  ‘cor’
plotRIICor: no visible global function definition for ‘data’
plotRIICor: no visible global function definition for ‘boxplot’
plotRIICor: no visible global function definition for ‘abline’
plotRTCor: no visible global function definition for ‘cor’
plotRTCor: no visible global function definition for ‘predict’
plotRTCor: no visible global function definition for ‘lines’
plotRTCor: no visible global function definition for ‘lowess’
plotRTCor: no visible global function definition for ‘text’
plotRTResd: no visible global function definition for ‘predict’
plotRTResd: no visible global function definition for ‘abline’
plotRTResd: no visible global function definition for ‘axis’
plotRTResd: no visible global function definition for ‘text’
plotRelativeDensities: no visible global function definition for
  ‘rainbow’
plotRelativeDensities: no visible global function definition for
  ‘density’
plotRelativeDensities: no visible global function definition for
  ‘na.omit’
plotRelativeDensities: no visible global function definition for
  ‘abline’
plotRelativeDensities: no visible global function definition for
  ‘lines’
plotStats: no visible global function definition for ‘png’
plotStats: no visible global function definition for ‘layout’
plotStats: no visible global function definition for ‘barplot’
plotStats: no visible global function definition for ‘dev.off’
plotStats: no visible global function definition for ‘density’
plotStats: no visible global function definition for ‘abline’
plotStats: no visible global function definition for ‘aggregate’
plotStats: no visible global function definition for ‘hist’
plotStats: no visible global function definition for ‘par’
predictRT: no visible global function definition for ‘cor’
predictRT: no visible global function definition for ‘lm’
predictRT: no visible global function definition for ‘predict’
quantification.accuracy: no visible global function definition for
  ‘cor’
quantification.accuracy: no visible global function definition for
  ‘median’
readLibFile: no visible global function definition for ‘read.delim2’
reliabilityCheckLibrary: no visible global function definition for
  ‘read.delim’
reliabilityCheckLibrary: no visible global function definition for
  ‘png’
reliabilityCheckLibrary: no visible global function definition for
  ‘barplot’
reliabilityCheckLibrary: no visible global function definition for
  ‘gray’
reliabilityCheckLibrary: no visible global function definition for
  ‘axis’
reliabilityCheckLibrary: no visible global function definition for
  ‘points’
reliabilityCheckLibrary: no visible global function definition for
  ‘mtext’
reliabilityCheckLibrary: no visible global function definition for
  ‘par’
reliabilityCheckLibrary: no visible global function definition for
  ‘legend’
reliabilityCheckLibrary: no visible global function definition for
  ‘dev.off’
reliabilityCheckLibrary: no visible global function definition for
  ‘write.csv’
reliabilityCheckSwath: no visible global function definition for
  ‘flog.threshold’
reliabilityCheckSwath: no visible binding for global variable ‘ERROR’
reliabilityCheckSwath: no visible global function definition for ‘png’
reliabilityCheckSwath: no visible global function definition for
  ‘layout’
reliabilityCheckSwath: no visible global function definition for
  ‘density’
reliabilityCheckSwath: no visible global function definition for
  ‘dev.off’
reliabilityCheckSwath: no visible global function definition for
  ‘gray.colors’
reliabilityCheckSwath: no visible global function definition for ‘par’
reliabilityCheckSwath: no visible global function definition for
  ‘barplot’
reliabilityCheckSwath: no visible global function definition for
  ‘legend’
reliabilityCheckSwath: no visible global function definition for
  ‘terrain.colors’
reliabilityCheckSwath : <anonymous>: no visible global function
  definition for ‘aggregate’
reliabilityCheckSwath: no visible binding for global variable ‘median’
reliabilityCheckSwath: no visible global function definition for
  ‘boxplot’
reliabilityCheckSwath: no visible global function definition for
  ‘write.csv’
selectModel: no visible global function definition for ‘as.formula’
selectModel: no visible global function definition for ‘predict’
selectModel: no visible global function definition for ‘lm’
swath.means: no visible global function definition for ‘aggregate’
swath.means : <anonymous>: no visible global function definition for
  ‘na.omit’
Undefined global functions or variables:
  ERROR abline aggregate as.formula axis barplot boxplot cor data
  density dev.off flog.threshold gray gray.colors hist layout legend
  lines lm lowess median mtext na.omit par png points predict rainbow
  read.delim read.delim2 resid residuals sd segments t.test
  terrain.colors text write.csv write.table
Consider adding
  importFrom("grDevices", "dev.off", "gray", "gray.colors", "png",
             "rainbow", "terrain.colors")
  importFrom("graphics", "abline", "axis", "barplot", "boxplot", "hist",
             "layout", "legend", "lines", "mtext", "par", "points",
             "segments", "text")
  importFrom("stats", "aggregate", "as.formula", "cor", "density", "lm",
             "lowess", "median", "na.omit", "predict", "resid",
             "residuals", "sd", "t.test")
  importFrom("utils", "data", "read.delim", "read.delim2", "write.csv",
             "write.table")
to your NAMESPACE file.
* checking Rd files ... NOTE
prepare_Rd: applyttest.Rd:27-28: Dropping empty section \details
prepare_Rd: applyttest.Rd:36-37: Dropping empty section \note
prepare_Rd: applyttest.Rd:34-35: Dropping empty section \author
prepare_Rd: applyttest.Rd:32-33: Dropping empty section \references
prepare_Rd: applyttestPep.Rd:26-27: Dropping empty section \details
prepare_Rd: applyttestPep.Rd:35-36: Dropping empty section \note
prepare_Rd: applyttestPep.Rd:33-34: Dropping empty section \author
prepare_Rd: applyttestPep.Rd:31-32: Dropping empty section \references
prepare_Rd: coverage.Rd:7-9: Dropping empty section \description
prepare_Rd: coverage.Rd:35-37: Dropping empty section \note
prepare_Rd: coverage.Rd:32-34: Dropping empty section \author
prepare_Rd: coverage.Rd:29-31: Dropping empty section \references
prepare_Rd: coverage.Rd:41-43: Dropping empty section \seealso
prepare_Rd: cv.Rd:7-9: Dropping empty section \description
prepare_Rd: cv.Rd:19-21: Dropping empty section \details
prepare_Rd: cv.Rd:31-33: Dropping empty section \note
prepare_Rd: cv.Rd:28-30: Dropping empty section \author
prepare_Rd: cv.Rd:25-27: Dropping empty section \references
prepare_Rd: cv.Rd:37-39: Dropping empty section \seealso
prepare_Rd: fdr.crit.Rd:7-9: Dropping empty section \description
prepare_Rd: fdr.crit.Rd:19-21: Dropping empty section \details
prepare_Rd: fdr.crit.Rd:22-28: Dropping empty section \value
prepare_Rd: fdr.crit.Rd:35-37: Dropping empty section \note
prepare_Rd: fdr.crit.Rd:32-34: Dropping empty section \author
prepare_Rd: fdr.crit.Rd:29-31: Dropping empty section \references
prepare_Rd: fdr.crit.Rd:41-43: Dropping empty section \seealso
prepare_Rd: getFdrBins.Rd:7-9: Dropping empty section \description
prepare_Rd: getFdrBins.Rd:22-24: Dropping empty section \details
prepare_Rd: getFdrBins.Rd:34-36: Dropping empty section \note
prepare_Rd: getFdrBins.Rd:31-33: Dropping empty section \author
prepare_Rd: getFdrBins.Rd:28-30: Dropping empty section \references
prepare_Rd: getFdrBins.Rd:40-42: Dropping empty section \seealso
prepare_Rd: medianNorm.Rd:17-18: Dropping empty section \details
prepare_Rd: medianNorm.Rd:26-27: Dropping empty section \note
prepare_Rd: medianNorm.Rd:24-25: Dropping empty section \author
prepare_Rd: medianNorm.Rd:22-23: Dropping empty section \references
prepare_Rd: medianNorm.Rd:30-31: Dropping empty section \seealso
prepare_Rd: mlr.Rd:20-21: Dropping empty section \details
prepare_Rd: mlr.Rd:32-33: Dropping empty section \note
prepare_Rd: mlr.Rd:30-31: Dropping empty section \author
prepare_Rd: mlr.Rd:36-37: Dropping empty section \seealso
prepare_Rd: mlrGroup.Rd:20-22: Dropping empty section \details
prepare_Rd: mlrGroup.Rd:31-32: Dropping empty section \note
prepare_Rd: mlrGroup.Rd:29-30: Dropping empty section \author
prepare_Rd: mlrrep.Rd:17-18: Dropping empty section \details
prepare_Rd: mlrrep.Rd:29-30: Dropping empty section \note
prepare_Rd: mlrrep.Rd:27-28: Dropping empty section \author
prepare_Rd: mlrrep.Rd:25-26: Dropping empty section \references
prepare_Rd: plotDensities.Rd:23-24: Dropping empty section \details
prepare_Rd: plotDensities.Rd:32-33: Dropping empty section \note
prepare_Rd: plotDensities.Rd:30-31: Dropping empty section \author
prepare_Rd: plotDensities.Rd:28-29: Dropping empty section \references
prepare_Rd: plotDensities.Rd:37-38: Dropping empty section \seealso
prepare_Rd: plotErrorBarsLines.Rd:35-36: Dropping empty section \details
prepare_Rd: plotErrorBarsLines.Rd:44-45: Dropping empty section \note
prepare_Rd: plotErrorBarsLines.Rd:42-43: Dropping empty section \author
prepare_Rd: plotErrorBarsLines.Rd:40-41: Dropping empty section \references
prepare_Rd: plotRelativeDensities.Rd:26-27: Dropping empty section \details
prepare_Rd: plotRelativeDensities.Rd:35-36: Dropping empty section \note
prepare_Rd: plotRelativeDensities.Rd:33-34: Dropping empty section \author
prepare_Rd: plotRelativeDensities.Rd:31-32: Dropping empty section \references
prepare_Rd: plotRelativeDensities.Rd:38-40: Dropping empty section \seealso
prepare_Rd: quantification.accuracy.Rd:7-9: Dropping empty section \description
prepare_Rd: quantification.accuracy.Rd:36-38: Dropping empty section \details
prepare_Rd: quantification.accuracy.Rd:50-52: Dropping empty section \note
prepare_Rd: quantification.accuracy.Rd:47-49: Dropping empty section \author
prepare_Rd: quantification.accuracy.Rd:44-46: Dropping empty section \references
prepare_Rd: quantification.accuracy.Rd:56-58: Dropping empty section \seealso
prepare_Rd: reliabilityCheckLibrary.Rd:7-9: Dropping empty section \description
prepare_Rd: reliabilityCheckLibrary.Rd:22-24: Dropping empty section \details
prepare_Rd: reliabilityCheckLibrary.Rd:34-36: Dropping empty section \note
prepare_Rd: reliabilityCheckLibrary.Rd:31-33: Dropping empty section \author
prepare_Rd: reliabilityCheckLibrary.Rd:28-30: Dropping empty section \references
prepare_Rd: reliabilityCheckLibrary.Rd:40-42: Dropping empty section \seealso
prepare_Rd: reliabilityCheckSwath.Rd:7-9: Dropping empty section \description
prepare_Rd: reliabilityCheckSwath.Rd:32-34: Dropping empty section \details
prepare_Rd: reliabilityCheckSwath.Rd:46-48: Dropping empty section \note
prepare_Rd: reliabilityCheckSwath.Rd:43-45: Dropping empty section \author
prepare_Rd: reliabilityCheckSwath.Rd:40-42: Dropping empty section \references
prepare_Rd: reliabilityCheckSwath.Rd:52-54: Dropping empty section \seealso
prepare_Rd: swath.means.Rd:7-9: Dropping empty section \description
prepare_Rd: swath.means.Rd:22-24: Dropping empty section \details
prepare_Rd: swath.means.Rd:34-36: Dropping empty section \note
prepare_Rd: swath.means.Rd:31-33: Dropping empty section \author
prepare_Rd: swath.means.Rd:28-30: Dropping empty section \references
prepare_Rd: swath.means.Rd:40-42: Dropping empty section \seealso
* 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 ... NOTE
Rd files without \description:
  ‘coverage.Rd’ ‘cv.Rd’ ‘fdr.crit.Rd’ ‘getFdrBins.Rd’
  ‘quantification.accuracy.Rd’ ‘reliabilityCheckLibrary.Rd’
  ‘reliabilityCheckSwath.Rd’ ‘swath.means.Rd’
* 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
Examples with CPU (user + system) or elapsed time > 5s
                         user system elapsed
reliabilityCheckSwath   26.14  0.336  26.458
quantification.accuracy  5.44  0.336   5.776
* 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: 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/SwathXtend.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL SwathXtend
###
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* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’
* installing *source* package ‘SwathXtend’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (SwathXtend)