BioC 3.3: CHECK report for IdMappingAnalysis on zin2

Package: IdMappingAnalysis

Version: 1.16.0

Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings IdMappingAnalysis_1.16.0.tar.gz

StartedAt: 2016-10-13 03:19:25 -0700 (Thu, 13 Oct 2016)

EndedAt: 2016-10-13 03:20:24 -0700 (Thu, 13 Oct 2016)

EllapsedTime: 58.3 seconds

RetCode: 0

Status:  OK

CheckDir: IdMappingAnalysis.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings IdMappingAnalysis_1.16.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.3-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 ‘1.16.0’
* 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
Examples with CPU or elapsed time > 5s
                               user system elapsed
getBootstrap.JointUniquePairs 5.331  0.008   5.341
* 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-3.3-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	0.190	0.004	0.198
Bootstrap	4.635	0.028	4.657
Corr	0.322	0.008	0.327
CorrData	0.041	0.000	0.042
CsvList.merge.Misc	0.002	0.000	0.002
IdMap	0.002	0.004	0.006
IdMapBase	0.002	0.000	0.002
IdMapCounts	0.371	0.000	0.370
IdMapDiff	0.367	0.004	0.371
IdMapDiffCounts	0.228	0.004	0.232
JointIdMap	0.055	0.000	0.054
JointUniquePairs	0.479	0.000	0.479
Mixture	0.32	0.00	0.33
UniquePairs	0.003	0.000	0.002
aligned.IdMapBase	0.005	0.000	0.005
as.IdMap.UniquePairs	0.03	0.00	0.03
as.MultiSet.CorrData	0.487	0.000	0.487
as.UniquePairs.IdMap	0.017	0.000	0.017
as.data.frame.IdMapBase	0.045	0.000	0.045
as.data.frame.JointIdMap	0.041	0.008	0.049
as.list.IdMap	0.01	0.00	0.01
boxplot.JointUniquePairs	0.054	0.000	0.054
byColNames.Subset	0.004	0.000	0.004
byColumn.Subset	0.004	0.000	0.003
byRow.Subset	0.004	0.000	0.004
byRowNames.Subset	0.005	0.000	0.006
clust.Mixture	0.002	0.000	0.001
copy.Display	0.000	0.000	0.001
corr.boxplot.JointUniquePairs	0.071	0.000	0.073
corr.plot.JointUniquePairs	0.038	0.008	0.045
create.Display	0.000	0.000	0.001
create.UniquePairs	0.101	0.004	0.105
diffCounts.plot.JointIdMap	0.375	0.000	0.374
dim.IdMapBase	0.002	0.000	0.001
dimnames.IdMapBase	0.001	0.000	0.002
do.glm.JointUniquePairs	0.015	0.000	0.014
ecdf.plot.JointIdMap	0.178	0.000	0.179
equals.UniquePairs	0.034	0.000	0.034
fisherTransform.DataFilter	0.001	0.000	0.001
fisherTransformInverse.DataFilter	0	0	0
fisherTransformJacobean.DataFilter	0.001	0.000	0.001
getBootstrap.JointUniquePairs	5.331	0.008	5.341
getCompoundEvents.IdMapDiffCounts	0.273	0.000	0.273
getCompoundGroups.IdMapDiffCounts	0.267	0.000	0.266
getCorr.JointUniquePairs	0.037	0.004	0.041
getCorrData.JointUniquePairs	0.043	0.000	0.043
getCorrDataFrame.JointUniquePairs	0.016	0.000	0.016
getCounts.IdMap	0.018	0.000	0.018
getCounts.JointIdMap	0.143	0.000	0.143
getData.Corr	0.001	0.000	0.000
getData.Mixture	0.001	0.000	0.002
getDiff.JointIdMap	0.232	0.000	0.231
getExperimentSet.CorrData	0.069	0.000	0.069
getIdMapList.JointIdMap	0.054	0.000	0.054
getMapNames.JointIdMap	0.046	0.000	0.046
getMapNames.JointUniquePairs	0.002	0.000	0.002
getMatch.UniquePairs	0.037	0.000	0.037
getMatchInfo.JointIdMap	0.048	0.000	0.048
getMatchInfo.JointUniquePairs	0.300	0.000	0.299
getMixture.JointUniquePairs	0.228	0.000	0.228
getSampleNames.CorrData	0.002	0.000	0.002
getStats.IdMapCounts	0.146	0.000	0.146
getStats.Mixture	0.003	0.000	0.002
getUnionIdMap.JointIdMap	0.357	0.000	0.356
getUniquePairs.Corr	0.004	0.000	0.004
getUniquePairs.CorrData	0.005	0.000	0.005
getUniquePairs.JointUniquePairs	0.005	0.000	0.005
interactive.corr.boxplot.JointUniquePairs	0.072	0.000	0.072
interactive.corr.plot.JointUniquePairs	0.045	0.000	0.045
interactive.mixture.boxplot.JointUniquePairs	0.269	0.004	0.272
interactive.mixture.plot.JointUniquePairs	0.233	0.000	0.234
interactive.plot.CorrData	0.041	0.000	0.041
interactive.plot.JointUniquePairs	0.001	0.000	0.000
interleave.Misc	0.001	0.000	0.001
line.loess.Display	0.001	0.000	0.001
line.unsorted.Display	0.001	0.000	0.001
logTen.DataFilter	0.104	0.000	0.104
merge.IdMap	0.566	0.000	0.566
minAvgCountConstraint.DataFilter	0.083	0.000	0.083
minCountConstraint.DataFilter	0.096	0.000	0.096
minCountGroupConstraint.DataFilter	0.137	0.000	0.137
mixture.boxplot.JointUniquePairs	0.234	0.000	0.234
mixture.plot.JointUniquePairs	0.205	0.000	0.214
plot.Bootstrap	0.08	0.00	0.08
plot.Corr	0.049	0.000	0.049
plot.CorrData	0.019	0.000	0.020
plot.IdMapCounts	0.142	0.000	0.141
plot.IdMapDiffCounts	0.473	0.000	0.472
plot.Mixture	0.023	0.000	0.023
primaryIDs.IdMapBase	0.002	0.000	0.003
primaryKey.CorrData	0.002	0.000	0.001
primaryKey.IdMapBase	0.002	0.000	0.002
primaryKey.Mixture	0.001	0.000	0.002
progressMsg.Display	0.001	0.000	0.000
removeNASeries.DataFilter	0.114	0.000	0.114
secondaryKey.CorrData	0.001	0.000	0.001
secondaryKey.IdMapBase	0.002	0.000	0.002
secondaryKey.Mixture	0.000	0.000	0.001
subsetCorr.JointUniquePairs	0.013	0.000	0.012
subsetData.JointUniquePairs	0.008	0.000	0.008
subsetGroups.JointUniquePairs	0.526	0.000	0.525
summary.IdMapDiffCounts	0.285	0.000	0.283
swapKeys.IdMap	0.050	0.000	0.051
swapKeys.UniquePairs	0.018	0.000	0.018
textBoundingBox.Display	0.001	0.000	0.001
to.base.Misc	0.001	0.000	0.001
to.binary.logical.Misc	0.001	0.000	0.001
to.index.expr.Misc	0.001	0.000	0.001
unique.UniquePairs	0.057	0.000	0.056
words.Misc	0.001	0.000	0.001
zoom.pars.Display	0.001	0.000	0.000