BioC 3.5: CHECK report for IdMappingAnalysis on malbec2

Package: IdMappingAnalysis

Version: 1.20.0

Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings IdMappingAnalysis_1.20.0.tar.gz

StartedAt: 2017-10-18 00:05:16 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 00:06:15 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 59.1 seconds

RetCode: 0

Status:  OK

CheckDir: IdMappingAnalysis.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings IdMappingAnalysis_1.20.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/IdMappingAnalysis.Rcheck’
* using R version 3.4.2 (2017-09-28)
* 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 ‘1.20.0’
* 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 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-3.5-bioc/meat/IdMappingAnalysis.Rcheck/00check.log’
for details.

* 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)

name	user	system	elapsed
000-LB-.IdMapBase	0.192	0.012	0.205
Bootstrap	4.300	0.008	4.308
Corr	0.232	0.004	0.236
CorrData	0.088	0.000	0.088
CsvList.merge.Misc	0.004	0.000	0.002
IdMap	0.016	0.000	0.016
IdMapBase	0.004	0.000	0.002
IdMapCounts	0.292	0.000	0.294
IdMapDiff	0.264	0.000	0.263
IdMapDiffCounts	0.200	0.000	0.199
JointIdMap	0.044	0.000	0.042
JointUniquePairs	0.524	0.000	0.522
Mixture	0.284	0.000	0.353
UniquePairs	0.000	0.000	0.002
aligned.IdMapBase	0.004	0.000	0.004
as.IdMap.UniquePairs	0.028	0.000	0.029
as.MultiSet.CorrData	0.336	0.000	0.337
as.UniquePairs.IdMap	0.036	0.000	0.037
as.data.frame.IdMapBase	0.136	0.000	0.138
as.data.frame.JointIdMap	0.040	0.000	0.041
as.list.IdMap	0.028	0.000	0.027
boxplot.JointUniquePairs	0.192	0.000	0.191
byColNames.Subset	0.004	0.000	0.003
byColumn.Subset	0.004	0.000	0.003
byRow.Subset	0.004	0.000	0.003
byRowNames.Subset	0.004	0.000	0.004
clust.Mixture	0.000	0.000	0.002
copy.Display	0.000	0.000	0.001
corr.boxplot.JointUniquePairs	0.204	0.004	0.212
corr.plot.JointUniquePairs	0.032	0.000	0.034
create.Display	0	0	0
create.UniquePairs	0.084	0.000	0.087
diffCounts.plot.JointIdMap	0.348	0.000	0.350
dim.IdMapBase	0.000	0.000	0.002
dimnames.IdMapBase	0.000	0.000	0.001
do.glm.JointUniquePairs	0.012	0.000	0.013
ecdf.plot.JointIdMap	0.660	0.004	0.665
equals.UniquePairs	0.036	0.000	0.038
fisherTransform.DataFilter	0.004	0.000	0.000
fisherTransformInverse.DataFilter	0	0	0
fisherTransformJacobean.DataFilter	0	0	0
getBootstrap.JointUniquePairs	3.868	0.008	3.875
getCompoundEvents.IdMapDiffCounts	0.204	0.000	0.201
getCompoundGroups.IdMapDiffCounts	0.208	0.000	0.208
getCorr.JointUniquePairs	0.096	0.000	0.094
getCorrData.JointUniquePairs	0.028	0.000	0.028
getCorrDataFrame.JointUniquePairs	0.016	0.000	0.017
getCounts.IdMap	0.012	0.000	0.012
getCounts.JointIdMap	0.096	0.004	0.100
getData.Corr	0.000	0.000	0.001
getData.Mixture	0.004	0.000	0.001
getDiff.JointIdMap	0.120	0.000	0.122
getExperimentSet.CorrData	0.120	0.004	0.125
getIdMapList.JointIdMap	0.056	0.000	0.057
getMapNames.JointIdMap	0.044	0.000	0.040
getMapNames.JointUniquePairs	0.000	0.000	0.002
getMatch.UniquePairs	0.028	0.004	0.029
getMatchInfo.JointIdMap	0.040	0.000	0.042
getMatchInfo.JointUniquePairs	0.228	0.000	0.229
getMixture.JointUniquePairs	0.148	0.000	0.148
getSampleNames.CorrData	0.004	0.000	0.001
getStats.IdMapCounts	0.164	0.000	0.165
getStats.Mixture	0.004	0.000	0.002
getUnionIdMap.JointIdMap	0.336	0.000	0.338
getUniquePairs.Corr	0.000	0.000	0.003
getUniquePairs.CorrData	0.000	0.000	0.003
getUniquePairs.JointUniquePairs	0.004	0.000	0.003
interactive.corr.boxplot.JointUniquePairs	0.052	0.000	0.048
interactive.corr.plot.JointUniquePairs	0.088	0.000	0.090
interactive.mixture.boxplot.JointUniquePairs	0.176	0.000	0.176
interactive.mixture.plot.JointUniquePairs	0.208	0.000	0.209
interactive.plot.CorrData	0.024	0.000	0.026
interactive.plot.JointUniquePairs	0.004	0.000	0.000
interleave.Misc	0	0	0
line.loess.Display	0	0	0
line.unsorted.Display	0	0	0
logTen.DataFilter	0.14	0.00	0.14
merge.IdMap	0.392	0.000	0.391
minAvgCountConstraint.DataFilter	0.084	0.000	0.084
minCountConstraint.DataFilter	0.084	0.000	0.084
minCountGroupConstraint.DataFilter	0.112	0.000	0.111
mixture.boxplot.JointUniquePairs	0.180	0.000	0.179
mixture.plot.JointUniquePairs	0.148	0.000	0.146
plot.Bootstrap	0.096	0.000	0.098
plot.Corr	0.040	0.000	0.042
plot.CorrData	0.088	0.000	0.087
plot.IdMapCounts	0.168	0.000	0.167
plot.IdMapDiffCounts	0.476	0.000	0.473
plot.Mixture	0.016	0.000	0.017
primaryIDs.IdMapBase	0.004	0.000	0.002
primaryKey.CorrData	0.000	0.000	0.001
primaryKey.IdMapBase	0.000	0.000	0.002
primaryKey.Mixture	0.000	0.000	0.001
progressMsg.Display	0.000	0.000	0.001
removeNASeries.DataFilter	0.092	0.000	0.095
secondaryKey.CorrData	0.000	0.000	0.001
secondaryKey.IdMapBase	0.004	0.000	0.002
secondaryKey.Mixture	0.000	0.000	0.001
subsetCorr.JointUniquePairs	0.020	0.000	0.019
subsetData.JointUniquePairs	0.028	0.000	0.027
subsetGroups.JointUniquePairs	0.572	0.000	0.571
summary.IdMapDiffCounts	0.204	0.000	0.205
swapKeys.IdMap	0.060	0.000	0.057
swapKeys.UniquePairs	0.048	0.000	0.051
textBoundingBox.Display	0	0	0
to.base.Misc	0.000	0.000	0.001
to.binary.logical.Misc	0.004	0.000	0.001
to.index.expr.Misc	0	0	0
unique.UniquePairs	0.04	0.00	0.04
words.Misc	0	0	0
zoom.pars.Display	0.000	0.000	0.001