BioC 3.0: CHECK report for IdMappingAnalysis on oaxaca

Package: IdMappingAnalysis

Version: 1.10.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch IdMappingAnalysis_1.10.0.tar.gz

StartedAt: 2015-04-10 00:37:02 -0700 (Fri, 10 Apr 2015)

EndedAt: 2015-04-10 00:38:40 -0700 (Fri, 10 Apr 2015)

EllapsedTime: 98.4 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 --no-multiarch IdMappingAnalysis_1.10.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/IdMappingAnalysis.Rcheck’
* using R version 3.1.3 (2015-03-09)
* 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 ‘1.10.0’
* 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 ... [7s/8s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 ... [32s/33s] OK
Examples with CPU or elapsed time > 5s
                               user system elapsed
getBootstrap.JointUniquePairs 7.604  0.057   7.959
Bootstrap                     7.274  0.074   7.414
* 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

NOTE: There were 3 notes.
See
  ‘/Users/biocbuild/bbs-3.0-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	0.256	0.014	0.270
Bootstrap	7.274	0.074	7.414
Corr	0.525	0.017	0.545
CorrData	0.055	0.005	0.058
CsvList.merge.Misc	0.003	0.000	0.003
IdMap	0.009	0.001	0.008
IdMapBase	0.002	0.000	0.002
IdMapCounts	0.448	0.007	0.455
IdMapDiff	0.553	0.003	0.557
IdMapDiffCounts	0.523	0.007	0.532
JointIdMap	0.083	0.002	0.085
JointUniquePairs	0.727	0.004	0.733
Mixture	0.204	0.003	0.236
UniquePairs	0.003	0.000	0.004
aligned.IdMapBase	0.033	0.003	0.036
as.IdMap.UniquePairs	0.048	0.000	0.048
as.MultiSet.CorrData	0.836	0.010	0.850
as.UniquePairs.IdMap	0.025	0.000	0.025
as.data.frame.IdMapBase	0.129	0.001	0.130
as.data.frame.JointIdMap	0.074	0.002	0.076
as.list.IdMap	0.014	0.000	0.015
boxplot.JointUniquePairs	0.073	0.002	0.076
byColNames.Subset	0.006	0.000	0.006
byColumn.Subset	0.006	0.001	0.006
byRow.Subset	0.005	0.000	0.005
byRowNames.Subset	0.012	0.000	0.011
clust.Mixture	0.002	0.000	0.002
copy.Display	0	0	0
corr.boxplot.JointUniquePairs	0.090	0.001	0.092
corr.plot.JointUniquePairs	0.067	0.001	0.072
create.Display	0.000	0.000	0.001
create.UniquePairs	0.156	0.001	0.161
diffCounts.plot.JointIdMap	0.566	0.002	0.579
dim.IdMapBase	0.002	0.000	0.002
dimnames.IdMapBase	0.003	0.000	0.003
do.glm.JointUniquePairs	0.019	0.001	0.019
ecdf.plot.JointIdMap	0.231	0.002	0.236
equals.UniquePairs	0.049	0.000	0.049
fisherTransform.DataFilter	0.000	0.000	0.001
fisherTransformInverse.DataFilter	0.000	0.001	0.001
fisherTransformJacobean.DataFilter	0.001	0.000	0.001
getBootstrap.JointUniquePairs	7.604	0.057	7.959
getCompoundEvents.IdMapDiffCounts	0.461	0.004	0.490
getCompoundGroups.IdMapDiffCounts	0.474	0.005	0.485
getCorr.JointUniquePairs	0.058	0.001	0.060
getCorrData.JointUniquePairs	0.072	0.002	0.075
getCorrDataFrame.JointUniquePairs	0.025	0.001	0.026
getCounts.IdMap	0.029	0.000	0.029
getCounts.JointIdMap	0.277	0.003	0.288
getData.Corr	0.001	0.000	0.001
getData.Mixture	0.002	0.000	0.003
getDiff.JointIdMap	0.252	0.002	0.258
getExperimentSet.CorrData	0.121	0.004	0.126
getIdMapList.JointIdMap	0.091	0.003	0.095
getMapNames.JointIdMap	0.077	0.003	0.079
getMapNames.JointUniquePairs	0.003	0.000	0.003
getMatch.UniquePairs	0.052	0.001	0.053
getMatchInfo.JointIdMap	0.081	0.002	0.082
getMatchInfo.JointUniquePairs	0.480	0.002	0.485
getMixture.JointUniquePairs	0.155	0.001	0.158
getSampleNames.CorrData	0.002	0.001	0.003
getStats.IdMapCounts	0.230	0.003	0.234
getStats.Mixture	0.004	0.000	0.005
getUnionIdMap.JointIdMap	0.570	0.008	0.598
getUniquePairs.Corr	0.006	0.001	0.006
getUniquePairs.CorrData	0.006	0.000	0.006
getUniquePairs.JointUniquePairs	0.006	0.001	0.007
interactive.corr.boxplot.JointUniquePairs	0.106	0.001	0.117
interactive.corr.plot.JointUniquePairs	0.060	0.006	0.075
interactive.mixture.boxplot.JointUniquePairs	0.233	0.008	0.241
interactive.mixture.plot.JointUniquePairs	0.159	0.007	0.166
interactive.plot.CorrData	0.061	0.001	0.082
interactive.plot.JointUniquePairs	0.001	0.000	0.001
interleave.Misc	0.001	0.000	0.000
line.loess.Display	0.001	0.000	0.001
line.unsorted.Display	0.001	0.000	0.001
logTen.DataFilter	0.208	0.010	0.217
merge.IdMap	0.792	0.002	0.798
minAvgCountConstraint.DataFilter	0.128	0.008	0.137
minCountConstraint.DataFilter	0.147	0.004	0.152
minCountGroupConstraint.DataFilter	0.189	0.005	0.194
mixture.boxplot.JointUniquePairs	0.222	0.002	0.224
mixture.plot.JointUniquePairs	0.156	0.002	0.160
plot.Bootstrap	0.084	0.002	0.093
plot.Corr	0.078	0.002	0.081
plot.CorrData	0.040	0.001	0.041
plot.IdMapCounts	0.228	0.001	0.231
plot.IdMapDiffCounts	0.772	0.003	0.784
plot.Mixture	0.020	0.001	0.022
primaryIDs.IdMapBase	0.004	0.001	0.004
primaryKey.CorrData	0.002	0.000	0.002
primaryKey.IdMapBase	0.003	0.000	0.003
primaryKey.Mixture	0.002	0.001	0.002
progressMsg.Display	0.000	0.000	0.001
removeNASeries.DataFilter	0.249	0.005	0.254
secondaryKey.CorrData	0.002	0.001	0.003
secondaryKey.IdMapBase	0.003	0.000	0.003
secondaryKey.Mixture	0	0	0
subsetCorr.JointUniquePairs	0.022	0.001	0.023
subsetData.JointUniquePairs	0.011	0.000	0.011
subsetGroups.JointUniquePairs	0.764	0.005	0.792
summary.IdMapDiffCounts	0.487	0.004	0.515
swapKeys.IdMap	0.07	0.00	0.07
swapKeys.UniquePairs	0.035	0.001	0.035
textBoundingBox.Display	0.001	0.000	0.001
to.base.Misc	0.002	0.000	0.001
to.binary.logical.Misc	0.003	0.000	0.002
to.index.expr.Misc	0.001	0.000	0.001
unique.UniquePairs	0.074	0.001	0.075
words.Misc	0.001	0.000	0.002
zoom.pars.Display	0.000	0.001	0.000