This page was generated on 2018-10-17 08:41:54 -0400 (Wed, 17 Oct 2018).
SwathXtend 2.2.0 Jemma Wu
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
URL: https://git.bioconductor.org/packages/SwathXtend |
Branch: RELEASE_3_7 |
Last Commit: 6ec63fd |
Last Changed Date: 2018-04-30 10:35:40 -0400 (Mon, 30 Apr 2018) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | WARNINGS | | |
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | |
merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
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### Running command:
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### C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SwathXtend.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings SwathXtend_2.2.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/SwathXtend.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'SwathXtend/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'SwathXtend' version '2.2.0'
* 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 whether package 'SwathXtend' can be installed ... OK
* checking installed package size ... NOTE
installed size is 351.7Mb
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 R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 'plot'
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 'plot'
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 'plot'
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 'plot'
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 'plot'
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 'plot'
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 'plot'
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 'plot'
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 plot 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", "plot",
"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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
reliabilityCheckSwath 45.38 2.18 47.79
quantification.accuracy 9.75 0.69 10.50
getFdrBins 3.71 0.50 5.85
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
reliabilityCheckSwath 46.71 2.40 49.31
quantification.accuracy 8.51 0.73 9.33
* 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
'C:/Users/biocbuild/bbs-3.7-bioc/meat/SwathXtend.Rcheck/00check.log'
for details.