BioC 3.4: CHECK report for IdMappingAnalysis on morelia

Package: IdMappingAnalysis

Version: 1.18.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings IdMappingAnalysis_1.18.0.tar.gz

StartedAt: 2017-04-15 03:45:13 -0700 (Sat, 15 Apr 2017)

EndedAt: 2017-04-15 03:46:33 -0700 (Sat, 15 Apr 2017)

EllapsedTime: 80.1 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_1.18.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/IdMappingAnalysis.Rcheck’
* using R version 3.3.3 (2017-03-06)
* 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 ‘1.18.0’
* 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
Bootstrap                     6.166  0.073   6.853
getBootstrap.JointUniquePairs 5.787  0.069   5.873
* 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	0.168	0.012	0.179
Bootstrap	6.166	0.073	6.853
Corr	0.336	0.013	0.350
CorrData	0.051	0.002	0.054
CsvList.merge.Misc	0.002	0.000	0.003
IdMap	0.007	0.000	0.007
IdMapBase	0.002	0.000	0.002
IdMapCounts	0.417	0.010	0.428
IdMapDiff	0.472	0.009	0.481
IdMapDiffCounts	0.371	0.003	0.375
JointIdMap	0.059	0.001	0.060
JointUniquePairs	0.542	0.003	0.544
Mixture	0.188	0.002	0.215
UniquePairs	0.003	0.001	0.003
aligned.IdMapBase	0.008	0.000	0.007
as.IdMap.UniquePairs	0.059	0.001	0.059
as.MultiSet.CorrData	0.578	0.009	0.587
as.UniquePairs.IdMap	0.019	0.001	0.020
as.data.frame.IdMapBase	0.056	0.001	0.057
as.data.frame.JointIdMap	0.065	0.002	0.067
as.list.IdMap	0.013	0.001	0.013
boxplot.JointUniquePairs	0.064	0.002	0.085
byColNames.Subset	0.006	0.000	0.006
byColumn.Subset	0.005	0.001	0.005
byRow.Subset	0.005	0.000	0.005
byRowNames.Subset	0.006	0.001	0.006
clust.Mixture	0.002	0.000	0.002
copy.Display	0	0	0
corr.boxplot.JointUniquePairs	0.072	0.001	0.074
corr.plot.JointUniquePairs	0.039	0.001	0.040
create.Display	0.001	0.000	0.000
create.UniquePairs	0.116	0.001	0.116
diffCounts.plot.JointIdMap	0.487	0.002	0.490
dim.IdMapBase	0.001	0.001	0.002
dimnames.IdMapBase	0.002	0.000	0.002
do.glm.JointUniquePairs	0.016	0.001	0.017
ecdf.plot.JointIdMap	0.198	0.006	0.204
equals.UniquePairs	0.044	0.000	0.044
fisherTransform.DataFilter	0.001	0.001	0.000
fisherTransformInverse.DataFilter	0.000	0.000	0.001
fisherTransformJacobean.DataFilter	0	0	0
getBootstrap.JointUniquePairs	5.787	0.069	5.873
getCompoundEvents.IdMapDiffCounts	0.329	0.001	0.330
getCompoundGroups.IdMapDiffCounts	0.361	0.009	0.369
getCorr.JointUniquePairs	0.048	0.001	0.049
getCorrData.JointUniquePairs	0.048	0.003	0.050
getCorrDataFrame.JointUniquePairs	0.018	0.000	0.018
getCounts.IdMap	0.026	0.000	0.026
getCounts.JointIdMap	0.171	0.001	0.171
getData.Corr	0.001	0.000	0.001
getData.Mixture	0.002	0.000	0.003
getDiff.JointIdMap	0.222	0.002	0.225
getExperimentSet.CorrData	0.173	0.004	0.177
getIdMapList.JointIdMap	0.071	0.003	0.074
getMapNames.JointIdMap	0.060	0.001	0.061
getMapNames.JointUniquePairs	0.003	0.000	0.003
getMatch.UniquePairs	0.049	0.001	0.049
getMatchInfo.JointIdMap	0.069	0.000	0.070
getMatchInfo.JointUniquePairs	0.388	0.001	0.389
getMixture.JointUniquePairs	0.134	0.003	0.138
getSampleNames.CorrData	0.003	0.001	0.003
getStats.IdMapCounts	0.199	0.010	0.209
getStats.Mixture	0.004	0.000	0.004
getUnionIdMap.JointIdMap	0.428	0.001	0.430
getUniquePairs.Corr	0.003	0.000	0.003
getUniquePairs.CorrData	0.004	0.000	0.005
getUniquePairs.JointUniquePairs	0.003	0.000	0.004
interactive.corr.boxplot.JointUniquePairs	0.067	0.002	0.068
interactive.corr.plot.JointUniquePairs	0.047	0.006	0.053
interactive.mixture.boxplot.JointUniquePairs	0.195	0.009	0.204
interactive.mixture.plot.JointUniquePairs	0.132	0.005	0.136
interactive.plot.CorrData	0.048	0.001	0.050
interactive.plot.JointUniquePairs	0.001	0.000	0.001
interleave.Misc	0.000	0.000	0.001
line.loess.Display	0.001	0.000	0.001
line.unsorted.Display	0.001	0.000	0.001
logTen.DataFilter	0.093	0.009	0.101
merge.IdMap	0.647	0.007	0.654
minAvgCountConstraint.DataFilter	0.084	0.003	0.087
minCountConstraint.DataFilter	0.102	0.005	0.108
minCountGroupConstraint.DataFilter	0.161	0.010	0.171
mixture.boxplot.JointUniquePairs	0.184	0.002	0.186
mixture.plot.JointUniquePairs	0.149	0.003	0.153
plot.Bootstrap	0.082	0.002	0.084
plot.Corr	0.061	0.003	0.066
plot.CorrData	0.023	0.001	0.024
plot.IdMapCounts	0.199	0.001	0.200
plot.IdMapDiffCounts	0.637	0.002	0.640
plot.Mixture	0.018	0.001	0.019
primaryIDs.IdMapBase	0.003	0.000	0.003
primaryKey.CorrData	0.001	0.000	0.001
primaryKey.IdMapBase	0.003	0.001	0.003
primaryKey.Mixture	0.002	0.000	0.002
progressMsg.Display	0.000	0.000	0.001
removeNASeries.DataFilter	0.110	0.004	0.114
secondaryKey.CorrData	0.001	0.000	0.001
secondaryKey.IdMapBase	0.002	0.000	0.002
secondaryKey.Mixture	0.001	0.000	0.001
subsetCorr.JointUniquePairs	0.011	0.001	0.011
subsetData.JointUniquePairs	0.011	0.000	0.011
subsetGroups.JointUniquePairs	0.636	0.008	0.643
summary.IdMapDiffCounts	0.385	0.003	0.387
swapKeys.IdMap	0.075	0.001	0.075
swapKeys.UniquePairs	0.023	0.000	0.024
textBoundingBox.Display	0.001	0.000	0.001
to.base.Misc	0.002	0.000	0.002
to.binary.logical.Misc	0.002	0.000	0.003
to.index.expr.Misc	0.001	0.000	0.001
unique.UniquePairs	0.055	0.001	0.055
words.Misc	0.001	0.000	0.001
zoom.pars.Display	0.000	0.000	0.001