BioC 3.2: CHECK report for IdMappingAnalysis on oaxaca

Package: IdMappingAnalysis

Version: 1.14.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings IdMappingAnalysis_1.14.0.tar.gz

StartedAt: 2015-10-27 04:45:00 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 04:46:22 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 82.3 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_1.14.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/IdMappingAnalysis.Rcheck’
* using R version 3.2.2 (2015-08-14)
* 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 ‘1.14.0’
* 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 ... [6s/6s] 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
Bootstrap: no visible global function definition for ‘extend’
Corr: no visible global function definition for ‘extend’
Corr: no visible global function definition for ‘throw’
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’
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.data.frame.IdMapBase: no visible global function definition for
  ‘getName’
as.data.frame.IdMapBase: no visible global function definition for
  ‘throw’
as.list.IdMap: no visible global function definition for ‘throw’
diffCounts.plot.JointIdMap: no visible global function definition for
  ‘rselect.list’
ecdf.plot.JointIdMap: no visible global function definition for
  ‘rselect.list’
getCorr.JointUniquePairs: no visible global function definition for
  ‘equals’
getExperimentSet.CorrData: no visible global function definition for
  ‘throw’
getIdMapList.JointIdMap: no visible global function definition for
  ‘throw’
interactive.plot.CorrData: no visible global function definition for
  ‘rselect.list’
interactive.plot.JointUniquePairs: no visible global function
  definition for ‘rselect.list’
merge.IdMap: no visible global function definition for ‘getName’
unique.UniquePairs: no visible global function definition for ‘getName’
* 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 ... [29s/28s] OK
Examples with CPU or elapsed time > 5s
                               user system elapsed
getBootstrap.JointUniquePairs 7.387  0.063   7.460
Bootstrap                     7.034  0.073   7.103
* 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-3.2-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	0.183	0.011	0.195
Bootstrap	7.034	0.073	7.103
Corr	0.519	0.014	0.533
CorrData	0.051	0.004	0.055
CsvList.merge.Misc	0.002	0.000	0.003
IdMap	0.007	0.000	0.008
IdMapBase	0.001	0.000	0.002
IdMapCounts	0.402	0.009	0.413
IdMapDiff	0.488	0.002	0.490
IdMapDiffCounts	0.350	0.004	0.354
JointIdMap	0.065	0.001	0.066
JointUniquePairs	0.661	0.002	0.663
Mixture	0.183	0.000	0.183
UniquePairs	0.004	0.001	0.004
aligned.IdMapBase	0.008	0.000	0.008
as.IdMap.UniquePairs	0.045	0.001	0.046
as.MultiSet.CorrData	0.628	0.011	0.640
as.UniquePairs.IdMap	0.023	0.000	0.023
as.data.frame.IdMapBase	0.058	0.001	0.058
as.data.frame.JointIdMap	0.074	0.002	0.076
as.list.IdMap	0.018	0.001	0.020
boxplot.JointUniquePairs	0.067	0.002	0.068
byColNames.Subset	0.004	0.000	0.004
byColumn.Subset	0.003	0.000	0.003
byRow.Subset	0.004	0.000	0.005
byRowNames.Subset	0.008	0.000	0.007
clust.Mixture	0.002	0.000	0.002
copy.Display	0.001	0.000	0.000
corr.boxplot.JointUniquePairs	0.090	0.001	0.091
corr.plot.JointUniquePairs	0.056	0.002	0.057
create.Display	0.000	0.000	0.001
create.UniquePairs	0.133	0.001	0.134
diffCounts.plot.JointIdMap	0.505	0.002	0.507
dim.IdMapBase	0.002	0.000	0.002
dimnames.IdMapBase	0.003	0.000	0.002
do.glm.JointUniquePairs	0.015	0.001	0.016
ecdf.plot.JointIdMap	0.207	0.001	0.215
equals.UniquePairs	0.040	0.000	0.041
fisherTransform.DataFilter	0.001	0.000	0.000
fisherTransformInverse.DataFilter	0.001	0.000	0.000
fisherTransformJacobean.DataFilter	0.001	0.000	0.001
getBootstrap.JointUniquePairs	7.387	0.063	7.460
getCompoundEvents.IdMapDiffCounts	0.355	0.009	0.365
getCompoundGroups.IdMapDiffCounts	0.365	0.003	0.368
getCorr.JointUniquePairs	0.059	0.002	0.061
getCorrData.JointUniquePairs	0.051	0.001	0.051
getCorrDataFrame.JointUniquePairs	0.019	0.000	0.020
getCounts.IdMap	0.019	0.000	0.019
getCounts.JointIdMap	0.181	0.004	0.184
getData.Corr	0.001	0.000	0.001
getData.Mixture	0.001	0.001	0.001
getDiff.JointIdMap	0.271	0.003	0.275
getExperimentSet.CorrData	0.101	0.004	0.106
getIdMapList.JointIdMap	0.072	0.002	0.075
getMapNames.JointIdMap	0.061	0.001	0.062
getMapNames.JointUniquePairs	0.002	0.000	0.002
getMatch.UniquePairs	0.043	0.000	0.044
getMatchInfo.JointIdMap	0.066	0.001	0.067
getMatchInfo.JointUniquePairs	0.404	0.001	0.405
getMixture.JointUniquePairs	0.155	0.001	0.157
getSampleNames.CorrData	0.002	0.001	0.002
getStats.IdMapCounts	0.190	0.003	0.193
getStats.Mixture	0.003	0.001	0.002
getUnionIdMap.JointIdMap	0.478	0.001	0.485
getUniquePairs.Corr	0.005	0.000	0.005
getUniquePairs.CorrData	0.004	0.000	0.004
getUniquePairs.JointUniquePairs	0.005	0.001	0.005
interactive.corr.boxplot.JointUniquePairs	0.091	0.001	0.092
interactive.corr.plot.JointUniquePairs	0.055	0.008	0.062
interactive.mixture.boxplot.JointUniquePairs	0.214	0.007	0.220
interactive.mixture.plot.JointUniquePairs	0.148	0.007	0.154
interactive.plot.CorrData	0.041	0.001	0.043
interactive.plot.JointUniquePairs	0.001	0.000	0.001
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	0.165	0.008	0.173
merge.IdMap	0.636	0.002	0.638
minAvgCountConstraint.DataFilter	0.126	0.005	0.132
minCountConstraint.DataFilter	0.118	0.004	0.122
minCountGroupConstraint.DataFilter	0.159	0.012	0.170
mixture.boxplot.JointUniquePairs	0.174	0.002	0.175
mixture.plot.JointUniquePairs	0.148	0.001	0.150
plot.Bootstrap	0.069	0.001	0.072
plot.Corr	0.058	0.003	0.060
plot.CorrData	0.030	0.001	0.047
plot.IdMapCounts	0.200	0.001	0.202
plot.IdMapDiffCounts	0.593	0.003	0.596
plot.Mixture	0.023	0.001	0.025
primaryIDs.IdMapBase	0.003	0.000	0.003
primaryKey.CorrData	0.001	0.000	0.001
primaryKey.IdMapBase	0.002	0.000	0.002
primaryKey.Mixture	0.002	0.000	0.002
progressMsg.Display	0.001	0.000	0.001
removeNASeries.DataFilter	0.141	0.004	0.144
secondaryKey.CorrData	0.001	0.001	0.002
secondaryKey.IdMapBase	0.003	0.000	0.003
secondaryKey.Mixture	0	0	0
subsetCorr.JointUniquePairs	0.015	0.001	0.015
subsetData.JointUniquePairs	0.009	0.000	0.009
subsetGroups.JointUniquePairs	0.636	0.002	0.638
summary.IdMapDiffCounts	0.416	0.004	0.421
swapKeys.IdMap	0.066	0.001	0.066
swapKeys.UniquePairs	0.024	0.000	0.025
textBoundingBox.Display	0.000	0.000	0.001
to.base.Misc	0.001	0.000	0.002
to.binary.logical.Misc	0.002	0.000	0.002
to.index.expr.Misc	0.000	0.000	0.001
unique.UniquePairs	0.062	0.001	0.063
words.Misc	0.001	0.000	0.002
zoom.pars.Display	0	0	0