Back to Multiple platform build/check report for BioC 3.15
ABCDEFGHIJKLMNOPQR[S]TUVWXYZ

This page was generated on 2022-10-19 13:20:57 -0400 (Wed, 19 Oct 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.5 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4386
palomino3Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4138
merida1macOS 10.14.6 Mojavex86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4205
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

CHECK results for SwathXtend on nebbiolo1


To the developers/maintainers of the SwathXtend package:
- Please 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 How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1964/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SwathXtend 2.18.0  (landing page)
Jemma Wu
Snapshot Date: 2022-10-18 13:55:19 -0400 (Tue, 18 Oct 2022)
git_url: https://git.bioconductor.org/packages/SwathXtend
git_branch: RELEASE_3_15
git_last_commit: d50b71f
git_last_commit_date: 2022-04-26 11:30:12 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: SwathXtend
Version: 2.18.0
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:SwathXtend.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings SwathXtend_2.18.0.tar.gz
StartedAt: 2022-10-18 22:05:36 -0400 (Tue, 18 Oct 2022)
EndedAt: 2022-10-18 22:06:58 -0400 (Tue, 18 Oct 2022)
EllapsedTime: 81.7 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: SwathXtend.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:SwathXtend.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings SwathXtend_2.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/SwathXtend.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SwathXtend/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SwathXtend’ version ‘2.18.0’
* 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 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 ... 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 ... WARNING
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
checkRd: (5) coverage.Rd:0-51: Must have a \description
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
checkRd: (5) cv.Rd:0-48: Must have a \description
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
checkRd: (5) fdr.crit.Rd:0-63: Must have a \description
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
checkRd: (5) getFdrBins.Rd:0-59: Must have a \description
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
checkRd: (5) quantification.accuracy.Rd:0-79: Must have a \description
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
checkRd: (5) reliabilityCheckLibrary.Rd:0-54: Must have a \description
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
checkRd: (5) reliabilityCheckSwath.Rd:0-64: Must have a \description
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
checkRd: (5) swath.means.Rd:0-60: Must have a \description
* 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
Examples with CPU (user + system) or elapsed time > 5s
                          user system elapsed
reliabilityCheckSwath   27.217  0.404  27.622
quantification.accuracy  5.321  0.268   5.589
* 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: 1 WARNING, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.15-bioc/meat/SwathXtend.Rcheck/00check.log’
for details.



Installation output

SwathXtend.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL SwathXtend
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/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)

Tests output


Example timings

SwathXtend.Rcheck/SwathXtend-Ex.timings

nameusersystemelapsed
applyttest0.1590.0290.187
applyttestPep0.1750.0040.178
buildSpectraLibPair0.9240.0110.940
canonicalFormat0.0080.0040.013
checkQuality0.7790.0080.788
cleanLib0.0120.0000.011
coverage0.0010.0000.000
cv0.0010.0000.000
fdr.crit0.7590.0840.844
getFdrBins1.9560.1682.127
medianNorm0.0130.0000.013
mlr0.0050.0000.005
mlrGroup0.0160.0000.015
mlrrep0.0170.0040.021
outputLib0.0320.0040.036
plotAll1.0680.0161.084
plotDensities0.1300.0000.131
plotErrorBarsLines0.0030.0000.003
plotRIICor0.0790.0040.083
plotRTCor0.6870.0080.695
plotRTResd0.6710.0000.670
plotRelativeDensities0.0160.0000.016
quantification.accuracy5.3210.2685.589
readLibFile0.0110.0000.010
reliabilityCheckLibrary0.4120.0190.433
reliabilityCheckSwath27.217 0.40427.622
swath.means0.7080.0560.765