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This page was generated on 2025-09-01 11:42 -0400 (Mon, 01 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4824
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4606
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4547
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4579
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 2142/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SwathXtend 2.30.0  (landing page)
Jemma Wu
Snapshot Date: 2025-08-28 13:40 -0400 (Thu, 28 Aug 2025)
git_url: https://git.bioconductor.org/packages/SwathXtend
git_branch: RELEASE_3_21
git_last_commit: 157ffd9
git_last_commit_date: 2025-04-15 10:59:32 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    NA  


CHECK results for SwathXtend on kjohnson1

To the developers/maintainers of the SwathXtend package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SwathXtend.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: SwathXtend
Version: 2.30.0
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_2.30.0.tar.gz
StartedAt: 2025-08-30 14:20:17 -0400 (Sat, 30 Aug 2025)
EndedAt: 2025-08-30 14:22:09 -0400 (Sat, 30 Aug 2025)
EllapsedTime: 111.8 seconds
RetCode: 0
Status:   OK  
CheckDir: SwathXtend.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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_2.30.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/SwathXtend.Rcheck’
* using R version 4.5.1 Patched (2025-06-14 r88325)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SwathXtend/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SwathXtend’ version ‘2.30.0’
* 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 ... INFO
  installed size is 351.5Mb
  sub-directories of 1Mb or more:
    files  351.3Mb
* 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 : <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 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   31.528  2.588  34.655
quantification.accuracy  7.349  0.979   8.411
* 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/SwathXtend.Rcheck/00check.log’
for details.


Installation output

SwathXtend.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL SwathXtend
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’
* installing *source* package ‘SwathXtend’ ...
** this is package ‘SwathXtend’ version ‘2.30.0’
** 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)

Tests output


Example timings

SwathXtend.Rcheck/SwathXtend-Ex.timings

nameusersystemelapsed
applyttest0.2450.0060.251
applyttestPep0.2610.0160.281
buildSpectraLibPair1.2090.0241.243
canonicalFormat0.0150.0020.017
checkQuality0.7770.0290.821
cleanLib0.0160.0000.016
coverage0.0010.0000.000
cv000
fdr.crit1.0740.2301.318
getFdrBins2.9390.5603.566
medianNorm0.0180.0020.021
mlr0.0060.0010.006
mlrGroup0.0180.0030.021
mlrrep0.0170.0050.023
outputLib0.0430.0030.046
plotAll1.4270.0701.507
plotDensities0.1170.0060.128
plotErrorBarsLines0.0030.0000.003
plotRIICor0.1120.0070.123
plotRTCor0.7080.0070.749
plotRTResd0.7090.0150.731
plotRelativeDensities0.0170.0010.017
quantification.accuracy7.3490.9798.411
readLibFile0.0170.0010.018
reliabilityCheckLibrary0.3160.0260.345
reliabilityCheckSwath31.528 2.58834.655
swath.means0.9280.2431.199