BioC 3.2: CHECK report for IdMappingAnalysis on perceval

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: 2015-11-10 06:03:18 -0800 (Tue, 10 Nov 2015)

EndedAt: 2015-11-10 06:04:46 -0800 (Tue, 10 Nov 2015)

EllapsedTime: 88.5 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_1.14.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/IdMappingAnalysis.Rcheck’
* using R version 3.2.2 Patched (2015-10-08 r69496)
* 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 ‘1.14.0’
* 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 ... [7s/7s] 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 ... [34s/34s] OK
Examples with CPU or elapsed time > 5s
                               user system elapsed
getBootstrap.JointUniquePairs 8.010  0.109   8.114
Bootstrap                     7.587  0.101   7.677
* 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	0.231	0.016	0.246
Bootstrap	7.587	0.101	7.677
Corr	0.551	0.022	0.572
CorrData	0.098	0.003	0.100
CsvList.merge.Misc	0.003	0.000	0.003
IdMap	0.010	0.000	0.009
IdMapBase	0.002	0.001	0.002
IdMapCounts	0.669	0.008	0.677
IdMapDiff	0.625	0.006	0.630
IdMapDiffCounts	0.557	0.003	0.560
JointIdMap	0.181	0.001	0.182
JointUniquePairs	0.749	0.005	0.753
Mixture	0.258	0.000	0.258
UniquePairs	0.003	0.000	0.004
aligned.IdMapBase	0.007	0.000	0.009
as.IdMap.UniquePairs	0.053	0.001	0.054
as.MultiSet.CorrData	0.728	0.009	0.737
as.UniquePairs.IdMap	0.022	0.001	0.023
as.data.frame.IdMapBase	0.054	0.001	0.055
as.data.frame.JointIdMap	0.185	0.004	0.188
as.list.IdMap	0.020	0.002	0.022
boxplot.JointUniquePairs	0.071	0.002	0.073
byColNames.Subset	0.006	0.001	0.006
byColumn.Subset	0.006	0.000	0.006
byRow.Subset	0.004	0.001	0.004
byRowNames.Subset	0.009	0.000	0.010
clust.Mixture	0.002	0.000	0.003
copy.Display	0.001	0.000	0.001
corr.boxplot.JointUniquePairs	0.091	0.003	0.095
corr.plot.JointUniquePairs	0.057	0.004	0.061
create.Display	0.001	0.001	0.001
create.UniquePairs	0.132	0.000	0.133
diffCounts.plot.JointIdMap	0.649	0.008	0.658
dim.IdMapBase	0.002	0.000	0.003
dimnames.IdMapBase	0.003	0.000	0.003
do.glm.JointUniquePairs	0.017	0.000	0.017
ecdf.plot.JointIdMap	0.335	0.008	0.344
equals.UniquePairs	0.044	0.000	0.044
fisherTransform.DataFilter	0.001	0.001	0.001
fisherTransformInverse.DataFilter	0.000	0.000	0.001
fisherTransformJacobean.DataFilter	0	0	0
getBootstrap.JointUniquePairs	8.010	0.109	8.114
getCompoundEvents.IdMapDiffCounts	0.561	0.008	0.568
getCompoundGroups.IdMapDiffCounts	0.562	0.003	0.565
getCorr.JointUniquePairs	0.059	0.001	0.061
getCorrData.JointUniquePairs	0.108	0.001	0.109
getCorrDataFrame.JointUniquePairs	0.024	0.001	0.025
getCounts.IdMap	0.023	0.000	0.024
getCounts.JointIdMap	0.309	0.003	0.311
getData.Corr	0.001	0.000	0.001
getData.Mixture	0.003	0.000	0.003
getDiff.JointIdMap	0.427	0.007	0.434
getExperimentSet.CorrData	0.095	0.005	0.099
getIdMapList.JointIdMap	0.183	0.002	0.185
getMapNames.JointIdMap	0.174	0.000	0.174
getMapNames.JointUniquePairs	0.003	0.000	0.004
getMatch.UniquePairs	0.046	0.001	0.047
getMatchInfo.JointIdMap	0.184	0.001	0.185
getMatchInfo.JointUniquePairs	0.384	0.003	0.388
getMixture.JointUniquePairs	0.183	0.002	0.186
getSampleNames.CorrData	0.003	0.000	0.004
getStats.IdMapCounts	0.313	0.009	0.322
getStats.Mixture	0.003	0.000	0.004
getUnionIdMap.JointIdMap	0.560	0.004	0.564
getUniquePairs.Corr	0.006	0.000	0.006
getUniquePairs.CorrData	0.006	0.001	0.007
getUniquePairs.JointUniquePairs	0.007	0.000	0.007
interactive.corr.boxplot.JointUniquePairs	0.092	0.001	0.094
interactive.corr.plot.JointUniquePairs	0.055	0.007	0.062
interactive.mixture.boxplot.JointUniquePairs	0.235	0.008	0.241
interactive.mixture.plot.JointUniquePairs	0.186	0.007	0.193
interactive.plot.CorrData	0.042	0.001	0.044
interactive.plot.JointUniquePairs	0.001	0.000	0.000
interleave.Misc	0.000	0.000	0.001
line.loess.Display	0.000	0.000	0.001
line.unsorted.Display	0.001	0.000	0.001
logTen.DataFilter	0.129	0.017	0.146
merge.IdMap	0.750	0.012	0.763
minAvgCountConstraint.DataFilter	0.121	0.003	0.124
minCountConstraint.DataFilter	0.137	0.008	0.146
minCountGroupConstraint.DataFilter	0.180	0.008	0.187
mixture.boxplot.JointUniquePairs	0.229	0.001	0.230
mixture.plot.JointUniquePairs	0.187	0.007	0.194
plot.Bootstrap	0.108	0.002	0.110
plot.Corr	0.067	0.003	0.071
plot.CorrData	0.029	0.001	0.030
plot.IdMapCounts	0.316	0.006	0.322
plot.IdMapDiffCounts	0.810	0.007	0.817
plot.Mixture	0.021	0.001	0.023
primaryIDs.IdMapBase	0.003	0.000	0.004
primaryKey.CorrData	0.002	0.000	0.002
primaryKey.IdMapBase	0.008	0.001	0.009
primaryKey.Mixture	0.002	0.000	0.003
progressMsg.Display	0.001	0.000	0.001
removeNASeries.DataFilter	0.169	0.005	0.174
secondaryKey.CorrData	0.002	0.000	0.002
secondaryKey.IdMapBase	0.004	0.000	0.003
secondaryKey.Mixture	0.001	0.000	0.001
subsetCorr.JointUniquePairs	0.018	0.000	0.019
subsetData.JointUniquePairs	0.011	0.000	0.012
subsetGroups.JointUniquePairs	0.742	0.008	0.750
summary.IdMapDiffCounts	0.590	0.009	0.599
swapKeys.IdMap	0.118	0.001	0.119
swapKeys.UniquePairs	0.024	0.003	0.027
textBoundingBox.Display	0.001	0.000	0.001
to.base.Misc	0.001	0.000	0.002
to.binary.logical.Misc	0.003	0.000	0.003
to.index.expr.Misc	0.001	0.000	0.000
unique.UniquePairs	0.064	0.003	0.067
words.Misc	0.002	0.000	0.002
zoom.pars.Display	0.000	0.000	0.001