BioC 3.5: CHECK report for IdMappingAnalysis on toluca2

Package: IdMappingAnalysis

Version: 1.19.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings IdMappingAnalysis_1.19.0.tar.gz

StartedAt: 2017-04-23 05:23:55 -0400 (Sun, 23 Apr 2017)

EndedAt: 2017-04-23 05:25:22 -0400 (Sun, 23 Apr 2017)

EllapsedTime: 87.2 seconds

RetCode: 0

Status:  OK

CheckDir: IdMappingAnalysis.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings IdMappingAnalysis_1.19.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/IdMappingAnalysis.Rcheck’
* using R Under development (unstable) (2017-02-15 r72187)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.19.0’
* 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 6.488  0.071   6.658
Bootstrap                     6.418  0.092   6.566
* 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
  ‘/Users/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	0.224	0.015	0.239
Bootstrap	6.418	0.092	6.566
Corr	0.417	0.013	0.450
CorrData	0.140	0.002	0.145
CsvList.merge.Misc	0.003	0.000	0.002
IdMap	0.028	0.001	0.028
IdMapBase	0.002	0.000	0.001
IdMapCounts	0.414	0.009	0.429
IdMapDiff	0.450	0.005	0.457
IdMapDiffCounts	0.403	0.006	0.411
JointIdMap	0.124	0.002	0.126
JointUniquePairs	0.682	0.004	0.694
Mixture	0.239	0.002	0.242
UniquePairs	0.003	0.000	0.003
aligned.IdMapBase	0.007	0.000	0.007
as.IdMap.UniquePairs	0.045	0.000	0.045
as.MultiSet.CorrData	0.525	0.005	0.535
as.UniquePairs.IdMap	0.024	0.000	0.025
as.data.frame.IdMapBase	0.291	0.005	0.296
as.data.frame.JointIdMap	0.060	0.004	0.064
as.list.IdMap	0.050	0.000	0.052
boxplot.JointUniquePairs	0.159	0.002	0.161
byColNames.Subset	0.004	0.001	0.005
byColumn.Subset	0.004	0.000	0.004
byRow.Subset	0.005	0.000	0.005
byRowNames.Subset	0.007	0.000	0.007
clust.Mixture	0.002	0.000	0.002
copy.Display	0.001	0.000	0.000
corr.boxplot.JointUniquePairs	0.357	0.001	0.362
corr.plot.JointUniquePairs	0.050	0.001	0.054
create.Display	0.001	0.000	0.001
create.UniquePairs	0.136	0.001	0.138
diffCounts.plot.JointIdMap	0.565	0.001	0.574
dim.IdMapBase	0.002	0.000	0.002
dimnames.IdMapBase	0.002	0.000	0.002
do.glm.JointUniquePairs	0.016	0.000	0.015
ecdf.plot.JointIdMap	1.072	0.013	1.096
equals.UniquePairs	0.062	0.000	0.065
fisherTransform.DataFilter	0.001	0.000	0.000
fisherTransformInverse.DataFilter	0	0	0
fisherTransformJacobean.DataFilter	0	0	0
getBootstrap.JointUniquePairs	6.488	0.071	6.658
getCompoundEvents.IdMapDiffCounts	0.384	0.002	0.395
getCompoundGroups.IdMapDiffCounts	0.491	0.006	0.511
getCorr.JointUniquePairs	0.161	0.002	0.164
getCorrData.JointUniquePairs	0.047	0.001	0.049
getCorrDataFrame.JointUniquePairs	0.020	0.001	0.021
getCounts.IdMap	0.02	0.00	0.02
getCounts.JointIdMap	0.151	0.001	0.153
getData.Corr	0.001	0.000	0.001
getData.Mixture	0.002	0.001	0.002
getDiff.JointIdMap	0.211	0.002	0.215
getExperimentSet.CorrData	0.223	0.004	0.227
getIdMapList.JointIdMap	0.067	0.000	0.068
getMapNames.JointIdMap	0.066	0.003	0.069
getMapNames.JointUniquePairs	0.002	0.001	0.003
getMatch.UniquePairs	0.052	0.002	0.054
getMatchInfo.JointIdMap	0.058	0.001	0.064
getMatchInfo.JointUniquePairs	0.328	0.002	0.330
getMixture.JointUniquePairs	0.139	0.002	0.142
getSampleNames.CorrData	0.002	0.000	0.003
getStats.IdMapCounts	0.257	0.004	0.262
getStats.Mixture	0.003	0.000	0.003
getUnionIdMap.JointIdMap	0.513	0.007	0.525
getUniquePairs.Corr	0.005	0.000	0.005
getUniquePairs.CorrData	0.005	0.000	0.006
getUniquePairs.JointUniquePairs	0.005	0.000	0.005
interactive.corr.boxplot.JointUniquePairs	0.076	0.002	0.080
interactive.corr.plot.JointUniquePairs	0.125	0.005	0.136
interactive.mixture.boxplot.JointUniquePairs	0.187	0.006	0.195
interactive.mixture.plot.JointUniquePairs	0.244	0.007	0.253
interactive.plot.CorrData	0.037	0.001	0.038
interactive.plot.JointUniquePairs	0.000	0.000	0.001
interleave.Misc	0	0	0
line.loess.Display	0.001	0.001	0.001
line.unsorted.Display	0.001	0.000	0.001
logTen.DataFilter	0.088	0.005	0.095
merge.IdMap	0.769	0.010	0.789
minAvgCountConstraint.DataFilter	0.118	0.004	0.124
minCountConstraint.DataFilter	0.109	0.004	0.113
minCountGroupConstraint.DataFilter	0.168	0.005	0.175
mixture.boxplot.JointUniquePairs	0.206	0.003	0.212
mixture.plot.JointUniquePairs	0.139	0.001	0.143
plot.Bootstrap	0.110	0.001	0.112
plot.Corr	0.054	0.002	0.057
plot.CorrData	0.144	0.001	0.149
plot.IdMapCounts	0.358	0.003	0.368
plot.IdMapDiffCounts	0.802	0.008	0.824
plot.Mixture	0.017	0.001	0.018
primaryIDs.IdMapBase	0.003	0.000	0.003
primaryKey.CorrData	0.002	0.000	0.002
primaryKey.IdMapBase	0.003	0.000	0.003
primaryKey.Mixture	0.001	0.000	0.002
progressMsg.Display	0.001	0.001	0.001
removeNASeries.DataFilter	0.122	0.003	0.127
secondaryKey.CorrData	0.001	0.000	0.002
secondaryKey.IdMapBase	0.003	0.000	0.003
secondaryKey.Mixture	0.001	0.001	0.001
subsetCorr.JointUniquePairs	0.014	0.000	0.016
subsetData.JointUniquePairs	0.043	0.001	0.044
subsetGroups.JointUniquePairs	0.643	0.004	0.651
summary.IdMapDiffCounts	0.365	0.001	0.370
swapKeys.IdMap	0.082	0.001	0.083
swapKeys.UniquePairs	0.078	0.001	0.080
textBoundingBox.Display	0.000	0.000	0.001
to.base.Misc	0.001	0.000	0.001
to.binary.logical.Misc	0.001	0.000	0.002
to.index.expr.Misc	0.000	0.000	0.001
unique.UniquePairs	0.063	0.002	0.064
words.Misc	0.001	0.000	0.002
zoom.pars.Display	0.001	0.000	0.001