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BioC 3.4: CHECK report for IdMappingAnalysis on zin1

This page was generated on 2016-09-21 03:37:43 -0700 (Wed, 21 Sep 2016).

Package 603/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
IdMappingAnalysis 1.17.0
Alex Lisovich , Roger Day
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/IdMappingAnalysis
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: IdMappingAnalysis
Version: 1.17.0
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings IdMappingAnalysis_1.17.0.tar.gz
StartedAt: 2016-09-20 08:03:51 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 08:04:45 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 54.2 seconds
RetCode: 0
Status:  OK 
CheckDir: IdMappingAnalysis.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings IdMappingAnalysis_1.17.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/IdMappingAnalysis.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 ‘IdMappingAnalysis/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘IdMappingAnalysis’ version ‘1.17.0’
* 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 ‘IdMappingAnalysis’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 ... NOTE
Namespace in Imports field not imported from: ‘Biobase’
  All declared Imports should be used.
Packages in Depends field not imported from:
  ‘R.oo’ ‘rChoiceDialogs’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.onAttach: no visible global function definition for
  ‘packageDescription’
Bootstrap: no visible global function definition for ‘extend’
Bootstrap : FUN: no visible global function definition for ‘cor’
Corr: no visible global function definition for ‘extend’
Corr: no visible global function definition for ‘throw’
Corr: no visible global function definition for ‘cor’
CorrData: no visible global function definition for ‘extend’
CorrData: no visible global function definition for ‘Object’
DataFilter: no visible global function definition for ‘extend’
DataFilter: no visible global function definition for ‘Object’
Display: no visible global function definition for ‘extend’
Display: no visible global function definition for ‘Object’
IdMap: no visible global function definition for ‘throw’
IdMap: no visible global function definition for ‘extend’
IdMapBase: no visible global function definition for ‘throw’
IdMapBase: no visible global function definition for ‘extend’
IdMapBase: no visible global function definition for ‘Object’
IdMapCounts: no visible global function definition for ‘throw’
IdMapCounts: no visible global function definition for ‘extend’
IdMapDiff: no visible global function definition for ‘throw’
IdMapDiff: no visible global function definition for ‘extend’
IdMapDiffCounts: no visible global function definition for ‘extend’
JointIdMap: no visible global function definition for ‘extend’
JointUniquePairs: no visible global function definition for ‘extend’
Misc: no visible global function definition for ‘extend’
Misc: no visible global function definition for ‘Object’
Mixture: no visible global function definition for ‘extend’
Mixture: no visible global function definition for ‘Object’
Mixture: no visible global function definition for ‘density’
Mixture : <anonymous>: no visible global function definition for
  ‘dnorm’
Subset: no visible global function definition for ‘extend’
Subset: no visible global function definition for ‘Object’
UniquePairs: no visible global function definition for ‘throw’
UniquePairs: no visible global function definition for ‘extend’
as.IdMap.UniquePairs: no visible global function definition for
  ‘getName’
as.MultiSet.CorrData: no visible global function definition for ‘new’
as.data.frame.IdMapBase: no visible global function definition for
  ‘getName’
as.data.frame.IdMapBase: no visible global function definition for
  ‘throw’
as.data.frame.IdMapBase: no visible global function definition for ‘as’
as.list.IdMap: no visible global function definition for ‘throw’
boxplot.JointUniquePairs: no visible global function definition for
  ‘par’
boxplot.JointUniquePairs: no visible global function definition for
  ‘axis’
boxplot.JointUniquePairs: no visible global function definition for
  ‘text’
boxplotdataJitter.JointUniquePairs: no visible global function
  definition for ‘par’
copy.Display: no visible global function definition for ‘dev.cur’
copy.Display: no visible global function definition for ‘par’
copy.Display: no visible global function definition for ‘png’
copy.Display: no visible global function definition for ‘jpeg’
copy.Display: no visible global function definition for ‘tiff’
copy.Display: no visible global function definition for ‘bmp’
copy.Display: no visible global function definition for ‘pdf’
copy.Display: no visible global function definition for ‘dev.set’
copy.Display: no visible global function definition for ‘dev.copy’
copy.Display: no visible global function definition for ‘dev.next’
copy.Display: no visible global function definition for ‘dev.off’
corr.boxplot.JointUniquePairs: no visible global function definition
  for ‘boxplot’
corr.boxplot.JointUniquePairs: no visible global function definition
  for ‘abline’
create.Display: no visible global function definition for ‘dev.new’
create.Display: no visible global function definition for ‘par’
diffCounts.plot.JointIdMap: no visible global function definition for
  ‘rselect.list’
diffCounts.plot.JointIdMap: no visible global function definition for
  ‘par’
diffCounts.plot.JointIdMap: no visible global function definition for
  ‘plot’
ecdf.plot.JointIdMap: no visible global function definition for
  ‘rselect.list’
ecdf.plot.JointIdMap: no visible global function definition for ‘par’
ecdf.plot.JointIdMap: no visible global function definition for ‘plot’
fit2clusters: no visible global function definition for ‘rbinom’
fit2clusters: no visible global function definition for ‘rgamma’
fit2clusters: no visible global function definition for ‘rnorm’
fit2clusters: no visible global function definition for ‘dnorm’
fit2clusters: no visible global function definition for ‘plot’
fit2clusters: no visible global function definition for ‘lines’
fit2clusters: no visible global function definition for ‘density’
fit2clusters: no visible global function definition for ‘legend’
fit2clusters: no visible global function definition for ‘par’
getCorr.JointUniquePairs: no visible global function definition for
  ‘equals’
getExperimentSet.CorrData: no visible global function definition for
  ‘throw’
getExperimentSet.CorrData: no visible global function definition for
  ‘new’
getIdMapList.JointIdMap: no visible global function definition for
  ‘throw’
interactive.plot.CorrData: no visible global function definition for
  ‘rselect.list’
interactive.plot.CorrData: no visible global function definition for
  ‘plot’
interactive.plot.JointUniquePairs: no visible global function
  definition for ‘rselect.list’
interactive.plot.JointUniquePairs: no visible global function
  definition for ‘par’
line.loess.Display: no visible global function definition for ‘loess’
line.loess.Display: no visible global function definition for ‘lines’
line.unsorted.Display: no visible global function definition for
  ‘lines’
merge.IdMap: no visible global function definition for ‘getName’
mixture.boxplot.JointUniquePairs: no visible global function definition
  for ‘boxplot’
mixture.boxplot.JointUniquePairs: no visible global function definition
  for ‘abline’
mixture.plot.JointUniquePairs: no visible global function definition
  for ‘plot’
plot.Bootstrap : BootstrapCorr.plot.internal: no visible global
  function definition for ‘par’
plot.Bootstrap : BootstrapCorr.plot.internal: no visible global
  function definition for ‘legend’
plot.Corr: no visible global function definition for ‘density’
plot.Corr: no visible global function definition for ‘plot.new’
plot.Corr: no visible global function definition for ‘plot.window’
plot.Corr: no visible global function definition for ‘axis’
plot.Corr: no visible global function definition for ‘par’
plot.Corr: no visible global function definition for ‘box’
plot.Corr: no visible global function definition for ‘lines’
plot.Corr: no visible global function definition for ‘legend’
plot.Corr: no visible global function definition for ‘abline’
plot.CorrData: no visible global function definition for ‘cor’
plot.CorrData: no visible global function definition for ‘par’
plot.CorrData: no visible global function definition for ‘plot’
plot.CorrData: no visible global function definition for ‘box’
plot.CorrData: no visible global function definition for ‘axis’
plot.CorrData: no visible global function definition for ‘points’
plot.CorrData: no visible global function definition for ‘title’
plot.IdMapCounts: no visible global function definition for ‘plot.new’
plot.IdMapCounts: no visible global function definition for
  ‘plot.window’
plot.IdMapCounts: no visible global function definition for ‘title’
plot.IdMapCounts: no visible global function definition for ‘axis’
plot.IdMapCounts: no visible global function definition for ‘par’
plot.IdMapCounts: no visible global function definition for ‘box’
plot.IdMapCounts: no visible global function definition for ‘ecdf’
plot.IdMapCounts: no visible global function definition for ‘lines’
plot.IdMapCounts: no visible global function definition for ‘legend’
plot.IdMapDiffCounts : plotValGroup: no visible global function
  definition for ‘rect’
plot.IdMapDiffCounts: no visible global function definition for
  ‘plot.new’
plot.IdMapDiffCounts: no visible global function definition for ‘par’
plot.IdMapDiffCounts: no visible global function definition for
  ‘plot.window’
plot.IdMapDiffCounts: no visible global function definition for ‘title’
plot.IdMapDiffCounts: no visible global function definition for ‘axis’
plot.IdMapDiffCounts: no visible global function definition for ‘mtext’
plot.IdMapDiffCounts: no visible global function definition for ‘lines’
plot.IdMapDiffCounts: no visible global function definition for ‘text’
plot.IdMapDiffCounts: no visible global function definition for
  ‘abline’
plot.Mixture: no visible global function definition for ‘plot.new’
plot.Mixture: no visible global function definition for ‘plot.window’
plot.Mixture: no visible global function definition for ‘axis’
plot.Mixture: no visible global function definition for ‘par’
plot.Mixture: no visible global function definition for ‘box’
plot.Mixture: no visible global function definition for ‘lines’
plot.Mixture: no visible global function definition for ‘density’
plot.Mixture: no visible global function definition for ‘rug’
plot.Mixture: no visible global function definition for ‘dnorm’
plot.Mixture : <anonymous>: no visible global function definition for
  ‘dnorm’
plot.Mixture: no visible global function definition for ‘legend’
plot.Mixture: no visible global function definition for ‘abline’
progressMsg.Display: no visible global function definition for
  ‘flush.console’
textBoundingBox.Display: no visible global function definition for
  ‘strwidth’
textBoundingBox.Display: no visible global function definition for
  ‘strheight’
textBoundingBox.Display: no visible global function definition for
  ‘par’
to.index.expr.Misc: no visible global function definition for ‘tail’
unique.UniquePairs: no visible global function definition for ‘getName’
zoom.pars.Display: no visible global function definition for ‘par’
Undefined global functions or variables:
  Object abline as axis bmp box boxplot cor density dev.copy dev.cur
  dev.new dev.next dev.off dev.set dnorm ecdf equals extend
  flush.console getName jpeg legend lines loess mtext new
  packageDescription par pdf plot plot.new plot.window png points
  rbinom rect rgamma rnorm rselect.list rug strheight strwidth tail
  text throw tiff title
Consider adding
  importFrom("grDevices", "bmp", "dev.copy", "dev.cur", "dev.new",
             "dev.next", "dev.off", "dev.set", "jpeg", "pdf", "png",
             "tiff")
  importFrom("graphics", "abline", "axis", "box", "boxplot", "legend",
             "lines", "mtext", "par", "plot", "plot.new", "plot.window",
             "points", "rect", "rug", "strheight", "strwidth", "text",
             "title")
  importFrom("methods", "as", "new")
  importFrom("stats", "cor", "density", "dnorm", "ecdf", "loess",
             "rbinom", "rgamma", "rnorm")
  importFrom("utils", "flush.console", "packageDescription", "tail")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... NOTE
prepare_Rd: DataFilter.Rd:41-42: Dropping empty section \arguments
prepare_Rd: Display.Rd:41-42: Dropping empty section \arguments
prepare_Rd: Misc.Rd:41-42: Dropping empty section \arguments
* 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: 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.4-bioc/meat/IdMappingAnalysis.Rcheck/00check.log’
for details.

IdMappingAnalysis.Rcheck/00install.out:

* installing *source* package ‘IdMappingAnalysis’ ...
** R
** data
*** moving datasets to lazyload DB
** demo
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (IdMappingAnalysis)

IdMappingAnalysis.Rcheck/IdMappingAnalysis-Ex.timings:

nameusersystemelapsed
000-LB-.IdMapBase0.1640.0120.175
Bootstrap4.0760.0124.084
Corr0.2560.0000.256
CorrData0.0320.0040.036
CsvList.merge.Misc0.0000.0000.001
IdMap0.0080.0000.006
IdMapBase0.0000.0000.001
IdMapCounts0.2960.0000.292
IdMapDiff0.3040.0040.308
IdMapDiffCounts0.2280.0040.233
JointIdMap0.0440.0000.046
JointUniquePairs0.4480.0040.449
Mixture0.7720.0000.771
UniquePairs0.0000.0000.002
aligned.IdMapBase0.0040.0000.005
as.IdMap.UniquePairs0.0280.0000.029
as.MultiSet.CorrData0.4280.0040.431
as.UniquePairs.IdMap0.0160.0000.016
as.data.frame.IdMapBase0.0400.0000.041
as.data.frame.JointIdMap0.0400.0040.043
as.list.IdMap0.0080.0000.009
boxplot.JointUniquePairs0.0480.0000.048
byColNames.Subset0.0040.0000.003
byColumn.Subset0.0040.0000.003
byRow.Subset0.0040.0000.004
byRowNames.Subset0.0040.0000.004
clust.Mixture0.0000.0000.002
copy.Display0.0000.0000.001
corr.boxplot.JointUniquePairs0.0600.0000.062
corr.plot.JointUniquePairs0.0400.0040.041
create.Display000
create.UniquePairs0.1000.0000.101
diffCounts.plot.JointIdMap0.3560.0000.358
dim.IdMapBase0.0000.0000.002
dimnames.IdMapBase0.0000.0000.002
do.glm.JointUniquePairs0.0120.0000.012
ecdf.plot.JointIdMap0.1520.0000.151
equals.UniquePairs0.0280.0000.029
fisherTransform.DataFilter0.0040.0000.000
fisherTransformInverse.DataFilter000
fisherTransformJacobean.DataFilter0.0000.0000.001
getBootstrap.JointUniquePairs4.2720.0004.270
getCompoundEvents.IdMapDiffCounts0.2280.0080.237
getCompoundGroups.IdMapDiffCounts0.2440.0040.246
getCorr.JointUniquePairs0.0400.0000.039
getCorrData.JointUniquePairs0.0400.0000.038
getCorrDataFrame.JointUniquePairs0.0120.0000.015
getCounts.IdMap0.0160.0000.017
getCounts.JointIdMap0.1320.0000.132
getData.Corr0.0040.0000.001
getData.Mixture0.0000.0000.002
getDiff.JointIdMap0.2200.0000.217
getExperimentSet.CorrData0.060.000.06
getIdMapList.JointIdMap0.0520.0000.052
getMapNames.JointIdMap0.0480.0000.047
getMapNames.JointUniquePairs0.0000.0000.003
getMatch.UniquePairs0.0400.0000.039
getMatchInfo.JointIdMap0.0480.0000.047
getMatchInfo.JointUniquePairs0.2640.0000.264
getMixture.JointUniquePairs0.4280.0000.428
getSampleNames.CorrData0.0040.0000.001
getStats.IdMapCounts0.1440.0040.147
getStats.Mixture0.0040.0000.003
getUnionIdMap.JointIdMap0.3320.0000.332
getUniquePairs.Corr0.0040.0000.003
getUniquePairs.CorrData0.0040.0000.003
getUniquePairs.JointUniquePairs0.0040.0000.004
interactive.corr.boxplot.JointUniquePairs0.0600.0000.059
interactive.corr.plot.JointUniquePairs0.0400.0000.038
interactive.mixture.boxplot.JointUniquePairs0.4640.0000.462
interactive.mixture.plot.JointUniquePairs0.4280.0040.431
interactive.plot.CorrData0.0320.0000.031
interactive.plot.JointUniquePairs0.0000.0000.001
interleave.Misc0.0000.0000.001
line.loess.Display0.0040.0000.000
line.unsorted.Display000
logTen.DataFilter0.0960.0000.095
merge.IdMap0.5240.0000.522
minAvgCountConstraint.DataFilter0.0800.0000.079
minCountConstraint.DataFilter0.0880.0000.090
minCountGroupConstraint.DataFilter0.1240.0000.125
mixture.boxplot.JointUniquePairs0.4640.0040.466
mixture.plot.JointUniquePairs0.4280.0000.427
plot.Bootstrap0.0760.0000.076
plot.Corr0.0480.0000.046
plot.CorrData0.0200.0000.018
plot.IdMapCounts0.1320.0040.135
plot.IdMapDiffCounts0.4280.0000.429
plot.Mixture0.0240.0000.020
primaryIDs.IdMapBase0.0000.0000.003
primaryKey.CorrData0.0000.0000.001
primaryKey.IdMapBase0.0000.0040.002
primaryKey.Mixture0.0000.0000.001
progressMsg.Display0.0040.0000.000
removeNASeries.DataFilter0.1040.0000.106
secondaryKey.CorrData0.0040.0000.001
secondaryKey.IdMapBase0.0040.0000.002
secondaryKey.Mixture0.0000.0000.001
subsetCorr.JointUniquePairs0.0120.0000.013
subsetData.JointUniquePairs0.0200.0000.018
subsetGroups.JointUniquePairs0.4640.0000.465
summary.IdMapDiffCounts0.2400.0000.241
swapKeys.IdMap0.0440.0000.045
swapKeys.UniquePairs0.0160.0000.016
textBoundingBox.Display000
to.base.Misc0.0000.0000.001
to.binary.logical.Misc0.0040.0000.002
to.index.expr.Misc000
unique.UniquePairs0.0520.0000.051
words.Misc0.0000.0040.001
zoom.pars.Display000