############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SwathXtend.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SwathXtend_2.28.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/SwathXtend.Rcheck’ * using R version 4.4.2 (2024-10-31) * 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 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘SwathXtend/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘SwathXtend’ version ‘2.28.0’ * 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 362.6Mb sub-directories of 1Mb or more: files 362.3Mb * 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 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 : : no visible global function definition for ‘t.test’ applyttest : : no visible global function definition for ‘na.omit’ applyttestPep : : no visible global function definition for ‘na.omit’ applyttestPep: no visible global function definition for ‘aggregate’ applyttestPep : : no visible global function definition for ‘t.test’ checkQuality: no visible global function definition for ‘median’ computeRIICor : : 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 : : no visible global function definition for ‘na.omit’ medianNorm : : no visible global function definition for ‘median’ medianNorm : : 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 : : 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 : : 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 : : 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 sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed reliabilityCheckSwath 64.479 4.704 78.801 quantification.accuracy 12.621 2.773 17.682 getFdrBins 3.810 1.471 6.232 * 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: 4 NOTEs See ‘/Users/biocbuild/bbs-3.20-bioc/meat/SwathXtend.Rcheck/00check.log’ for details.