BioC 3.2: CHECK report for IdMappingAnalysis on perceval

Package: IdMappingAnalysis

Version: 1.13.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings IdMappingAnalysis_1.13.0.tar.gz

StartedAt: 2015-08-24 01:52:28 -0700 (Mon, 24 Aug 2015)

EndedAt: 2015-08-24 01:54:04 -0700 (Mon, 24 Aug 2015)

EllapsedTime: 95.8 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_1.13.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/IdMappingAnalysis.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (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 ‘1.13.0’
* 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 ... [8s/9s] 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
as.data.frame.IdMapBase: no visible global function definition for
  ‘getName’
as.data.frame.IdMapBase: no visible global function definition for
  ‘throw’
as.IdMap.UniquePairs: no visible global function definition for
  ‘getName’
as.list.IdMap: no visible global function definition for ‘throw’
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’
diffCounts.plot.JointIdMap: no visible global function definition for
  ‘rselect.list’
Display: no visible global function definition for ‘extend’
Display: no visible global function definition for ‘Object’
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’
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’
interactive.plot.CorrData: no visible global function definition for
  ‘rselect.list’
interactive.plot.JointUniquePairs: no visible global function
  definition for ‘rselect.list’
JointIdMap: no visible global function definition for ‘extend’
JointUniquePairs: no visible global function definition for ‘extend’
merge.IdMap: no visible global function definition for ‘getName’
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’
unique.UniquePairs: no visible global function definition for ‘getName’
UniquePairs: no visible global function definition for ‘throw’
UniquePairs: no visible global function definition for ‘extend’
* 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 ... [35s/35s] OK
Examples with CPU or elapsed time > 5s
                               user system elapsed
getBootstrap.JointUniquePairs 7.853  0.128   7.978
Bootstrap                     7.808  0.155   7.951
* 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	0.285	0.026	0.310
Bootstrap	7.808	0.155	7.951
Corr	0.576	0.032	0.607
CorrData	0.111	0.006	0.116
CsvList.merge.Misc	0.004	0.000	0.004
IdMap	0.013	0.000	0.014
IdMapBase	0.003	0.000	0.003
IdMapCounts	0.752	0.023	0.774
IdMapDiff	0.679	0.004	0.682
IdMapDiffCounts	0.581	0.002	0.582
JointIdMap	0.194	0.001	0.196
JointUniquePairs	0.790	0.002	0.791
Mixture	0.241	0.000	0.242
UniquePairs	0.005	0.000	0.005
aligned.IdMapBase	0.008	0.001	0.009
as.IdMap.UniquePairs	0.053	0.001	0.054
as.MultiSet.CorrData	0.731	0.018	0.750
as.UniquePairs.IdMap	0.022	0.000	0.022
as.data.frame.IdMapBase	0.059	0.001	0.060
as.data.frame.JointIdMap	0.171	0.005	0.176
as.list.IdMap	0.021	0.000	0.022
boxplot.JointUniquePairs	0.066	0.004	0.070
byColNames.Subset	0.005	0.000	0.006
byColumn.Subset	0.006	0.000	0.007
byRow.Subset	0.005	0.000	0.006
byRowNames.Subset	0.019	0.001	0.020
clust.Mixture	0.002	0.000	0.003
copy.Display	0	0	0
corr.boxplot.JointUniquePairs	0.086	0.003	0.089
corr.plot.JointUniquePairs	0.062	0.005	0.066
create.Display	0.001	0.000	0.001
create.UniquePairs	0.158	0.002	0.159
diffCounts.plot.JointIdMap	0.692	0.011	0.703
dim.IdMapBase	0.003	0.000	0.002
dimnames.IdMapBase	0.002	0.001	0.003
do.glm.JointUniquePairs	0.016	0.001	0.016
ecdf.plot.JointIdMap	0.375	0.014	0.389
equals.UniquePairs	0.042	0.000	0.042
fisherTransform.DataFilter	0.001	0.000	0.000
fisherTransformInverse.DataFilter	0	0	0
fisherTransformJacobean.DataFilter	0.001	0.000	0.000
getBootstrap.JointUniquePairs	7.853	0.128	7.978
getCompoundEvents.IdMapDiffCounts	0.593	0.008	0.605
getCompoundGroups.IdMapDiffCounts	0.592	0.008	0.603
getCorr.JointUniquePairs	0.053	0.002	0.055
getCorrData.JointUniquePairs	0.110	0.004	0.114
getCorrDataFrame.JointUniquePairs	0.022	0.001	0.023
getCounts.IdMap	0.023	0.001	0.023
getCounts.JointIdMap	0.342	0.007	0.354
getData.Corr	0.001	0.000	0.001
getData.Mixture	0.003	0.000	0.003
getDiff.JointIdMap	0.471	0.013	0.488
getExperimentSet.CorrData	0.106	0.007	0.113
getIdMapList.JointIdMap	0.187	0.002	0.189
getMapNames.JointIdMap	0.172	0.001	0.173
getMapNames.JointUniquePairs	0.003	0.000	0.003
getMatch.UniquePairs	0.051	0.001	0.050
getMatchInfo.JointIdMap	0.183	0.001	0.184
getMatchInfo.JointUniquePairs	0.360	0.004	0.364
getMixture.JointUniquePairs	0.181	0.002	0.186
getSampleNames.CorrData	0.003	0.000	0.004
getStats.IdMapCounts	0.323	0.007	0.330
getStats.Mixture	0.004	0.000	0.005
getUnionIdMap.JointIdMap	0.614	0.003	0.619
getUniquePairs.Corr	0.007	0.000	0.007
getUniquePairs.CorrData	0.008	0.001	0.008
getUniquePairs.JointUniquePairs	0.010	0.001	0.011
interactive.corr.boxplot.JointUniquePairs	0.105	0.003	0.107
interactive.corr.plot.JointUniquePairs	0.064	0.010	0.074
interactive.mixture.boxplot.JointUniquePairs	0.243	0.016	0.259
interactive.mixture.plot.JointUniquePairs	0.188	0.010	0.202
interactive.plot.CorrData	0.043	0.002	0.047
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	0.169	0.018	0.191
merge.IdMap	0.892	0.021	0.925
minAvgCountConstraint.DataFilter	0.128	0.006	0.134
minCountConstraint.DataFilter	0.139	0.011	0.150
minCountGroupConstraint.DataFilter	0.188	0.014	0.202
mixture.boxplot.JointUniquePairs	0.220	0.003	0.222
mixture.plot.JointUniquePairs	0.187	0.010	0.196
plot.Bootstrap	0.097	0.002	0.102
plot.Corr	0.080	0.004	0.093
plot.CorrData	0.030	0.001	0.031
plot.IdMapCounts	0.333	0.004	0.338
plot.IdMapDiffCounts	0.878	0.012	0.903
plot.Mixture	0.021	0.002	0.022
primaryIDs.IdMapBase	0.004	0.000	0.004
primaryKey.CorrData	0.002	0.000	0.002
primaryKey.IdMapBase	0.011	0.000	0.011
primaryKey.Mixture	0.002	0.001	0.002
progressMsg.Display	0.000	0.000	0.001
removeNASeries.DataFilter	0.155	0.006	0.162
secondaryKey.CorrData	0.002	0.001	0.003
secondaryKey.IdMapBase	0.004	0.000	0.004
secondaryKey.Mixture	0.001	0.001	0.001
subsetCorr.JointUniquePairs	0.021	0.000	0.021
subsetData.JointUniquePairs	0.011	0.000	0.011
subsetGroups.JointUniquePairs	0.814	0.011	0.826
summary.IdMapDiffCounts	0.640	0.006	0.646
swapKeys.IdMap	0.108	0.001	0.108
swapKeys.UniquePairs	0.022	0.000	0.022
textBoundingBox.Display	0.000	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	0.060	0.001	0.060
words.Misc	0.002	0.000	0.002
zoom.pars.Display	0.001	0.000	0.001