BioC 3.4: CHECK report for IdMappingAnalysis on morelia

Package: IdMappingAnalysis

Version: 1.17.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings IdMappingAnalysis_1.17.0.tar.gz

StartedAt: 2016-09-20 08:03:43 -0700 (Tue, 20 Sep 2016)

EndedAt: 2016-09-20 08:04:45 -0700 (Tue, 20 Sep 2016)

EllapsedTime: 61.5 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_1.17.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/IdMappingAnalysis.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘1.17.0’
* 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
  ‘/Users/biocbuild/bbs-3.4-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	0.134	0.009	0.144
Bootstrap	3.860	0.070	3.927
Corr	0.235	0.012	0.247
CorrData	0.033	0.002	0.035
CsvList.merge.Misc	0.002	0.000	0.002
IdMap	0.005	0.000	0.005
IdMapBase	0.002	0.000	0.001
IdMapCounts	0.311	0.009	0.318
IdMapDiff	0.281	0.004	0.285
IdMapDiffCounts	0.235	0.003	0.239
JointIdMap	0.047	0.001	0.047
JointUniquePairs	0.406	0.006	0.407
Mixture	0.147	0.002	0.190
UniquePairs	0.002	0.000	0.002
aligned.IdMapBase	0.005	0.000	0.005
as.IdMap.UniquePairs	0.028	0.000	0.028
as.MultiSet.CorrData	0.402	0.006	0.407
as.UniquePairs.IdMap	0.014	0.000	0.014
as.data.frame.IdMapBase	0.037	0.001	0.037
as.data.frame.JointIdMap	0.045	0.002	0.048
as.list.IdMap	0.008	0.000	0.008
boxplot.JointUniquePairs	0.040	0.002	0.041
byColNames.Subset	0.004	0.000	0.003
byColumn.Subset	0.004	0.000	0.004
byRow.Subset	0.003	0.000	0.003
byRowNames.Subset	0.005	0.001	0.005
clust.Mixture	0.002	0.000	0.001
copy.Display	0.001	0.000	0.001
corr.boxplot.JointUniquePairs	0.054	0.002	0.056
corr.plot.JointUniquePairs	0.031	0.001	0.033
create.Display	0.000	0.000	0.001
create.UniquePairs	0.081	0.000	0.082
diffCounts.plot.JointIdMap	0.335	0.003	0.338
dim.IdMapBase	0.001	0.000	0.002
dimnames.IdMapBase	0.001	0.001	0.001
do.glm.JointUniquePairs	0.011	0.000	0.011
ecdf.plot.JointIdMap	0.137	0.004	0.142
equals.UniquePairs	0.026	0.001	0.025
fisherTransform.DataFilter	0.001	0.000	0.001
fisherTransformInverse.DataFilter	0.001	0.000	0.000
fisherTransformJacobean.DataFilter	0	0	0
getBootstrap.JointUniquePairs	4.196	0.061	4.256
getCompoundEvents.IdMapDiffCounts	0.233	0.004	0.237
getCompoundGroups.IdMapDiffCounts	0.248	0.007	0.254
getCorr.JointUniquePairs	0.031	0.001	0.033
getCorrData.JointUniquePairs	0.035	0.002	0.037
getCorrDataFrame.JointUniquePairs	0.012	0.000	0.012
getCounts.IdMap	0.014	0.001	0.015
getCounts.JointIdMap	0.116	0.000	0.116
getData.Corr	0.001	0.000	0.000
getData.Mixture	0.001	0.001	0.001
getDiff.JointIdMap	0.190	0.004	0.195
getExperimentSet.CorrData	0.057	0.003	0.060
getIdMapList.JointIdMap	0.049	0.001	0.049
getMapNames.JointIdMap	0.045	0.000	0.045
getMapNames.JointUniquePairs	0.001	0.000	0.002
getMatch.UniquePairs	0.031	0.001	0.031
getMatchInfo.JointIdMap	0.052	0.001	0.054
getMatchInfo.JointUniquePairs	0.232	0.000	0.233
getMixture.JointUniquePairs	0.101	0.001	0.101
getSampleNames.CorrData	0.002	0.001	0.002
getStats.IdMapCounts	0.124	0.004	0.128
getStats.Mixture	0.003	0.000	0.003
getUnionIdMap.JointIdMap	0.280	0.004	0.285
getUniquePairs.Corr	0.003	0.000	0.004
getUniquePairs.CorrData	0.003	0.000	0.003
getUniquePairs.JointUniquePairs	0.003	0.000	0.003
interactive.corr.boxplot.JointUniquePairs	0.049	0.002	0.050
interactive.corr.plot.JointUniquePairs	0.028	0.004	0.032
interactive.mixture.boxplot.JointUniquePairs	0.124	0.006	0.130
interactive.mixture.plot.JointUniquePairs	0.102	0.006	0.107
interactive.plot.CorrData	0.026	0.001	0.027
interactive.plot.JointUniquePairs	0.000	0.000	0.001
interleave.Misc	0	0	0
line.loess.Display	0	0	0
line.unsorted.Display	0.001	0.000	0.001
logTen.DataFilter	0.119	0.009	0.127
merge.IdMap	0.427	0.002	0.430
minAvgCountConstraint.DataFilter	0.076	0.006	0.081
minCountConstraint.DataFilter	0.089	0.006	0.095
minCountGroupConstraint.DataFilter	0.107	0.005	0.112
mixture.boxplot.JointUniquePairs	0.127	0.003	0.138
mixture.plot.JointUniquePairs	0.099	0.001	0.101
plot.Bootstrap	0.056	0.001	0.057
plot.Corr	0.036	0.001	0.039
plot.CorrData	0.017	0.001	0.017
plot.IdMapCounts	0.125	0.002	0.128
plot.IdMapDiffCounts	0.405	0.003	0.408
plot.Mixture	0.012	0.001	0.012
primaryIDs.IdMapBase	0.001	0.000	0.002
primaryKey.CorrData	0.001	0.000	0.001
primaryKey.IdMapBase	0.001	0.000	0.002
primaryKey.Mixture	0.001	0.000	0.001
progressMsg.Display	0	0	0
removeNASeries.DataFilter	0.089	0.003	0.093
secondaryKey.CorrData	0.001	0.001	0.001
secondaryKey.IdMapBase	0.001	0.000	0.001
secondaryKey.Mixture	0.001	0.000	0.001
subsetCorr.JointUniquePairs	0.01	0.00	0.01
subsetData.JointUniquePairs	0.006	0.001	0.007
subsetGroups.JointUniquePairs	0.397	0.004	0.401
summary.IdMapDiffCounts	0.240	0.003	0.243
swapKeys.IdMap	0.038	0.000	0.039
swapKeys.UniquePairs	0.013	0.001	0.014
textBoundingBox.Display	0.001	0.000	0.000
to.base.Misc	0.001	0.000	0.001
to.binary.logical.Misc	0.001	0.000	0.001
to.index.expr.Misc	0	0	0
unique.UniquePairs	0.042	0.001	0.042
words.Misc	0.001	0.000	0.001
zoom.pars.Display	0.000	0.000	0.001