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BioC 3.4: CHECK report for SwathXtend on zin1

This page was generated on 2016-09-21 03:40:39 -0700 (Wed, 21 Sep 2016).

Package 1183/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SwathXtend 1.1.0
Jemma Wu
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/SwathXtend
Last Changed Rev: 117081 / Revision: 121152
Last Changed Date: 2016-05-03 14:30:44 -0700 (Tue, 03 May 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: SwathXtend
Version: 1.1.0
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings SwathXtend_1.1.0.tar.gz
StartedAt: 2016-09-20 13:11:12 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 13:11:42 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 29.9 seconds
RetCode: 0
Status:  OK 
CheckDir: SwathXtend.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings SwathXtend_1.1.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/SwathXtend.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘1.1.0’
* 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 ... OK
* 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 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
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’
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’
readLibFile: no visible global function definition for ‘read.delim2’
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’
Undefined global functions or variables:
  abline aggregate as.formula axis barplot boxplot cor data density
  dev.off hist layout legend lines lm lowess median na.omit par plot
  png predict rainbow read.delim2 resid residuals segments t.test text
  write.table
Consider adding
  importFrom("grDevices", "dev.off", "png", "rainbow")
  importFrom("graphics", "abline", "axis", "barplot", "boxplot", "hist",
             "layout", "legend", "lines", "par", "plot", "segments",
             "text")
  importFrom("stats", "aggregate", "as.formula", "cor", "density", "lm",
             "lowess", "median", "na.omit", "predict", "resid",
             "residuals", "t.test")
  importFrom("utils", "data", "read.delim2", "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: 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
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.4-bioc/meat/SwathXtend.Rcheck/00check.log’
for details.


SwathXtend.Rcheck/00install.out:

* installing *source* package ‘SwathXtend’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (SwathXtend)

SwathXtend.Rcheck/SwathXtend-Ex.timings:

nameusersystemelapsed
applyttest0.2400.0000.237
applyttestPep0.2760.0000.278
buildSpectraLibPair1.7720.0001.774
canonicalFormat0.0160.0040.017
checkQuality1.4640.0001.475
cleanLib0.0200.0000.018
medianNorm0.0120.0000.011
mlr0.0080.0000.008
mlrGroup0.0200.0000.019
mlrrep0.0240.0000.024
outputLib0.0520.0000.050
plotAll2.1240.0042.145
plotDensities0.1520.0000.153
plotErrorBarsLines0.0000.0040.003
plotRIICor0.1360.0000.137
plotRTCor1.2560.0041.264
plotRTResd1.280.001.28
plotRelativeDensities0.0240.0000.025
readLibFile0.0120.0040.019