BioC 3.1: CHECK report for IdMappingAnalysis on petty

Package: IdMappingAnalysis

Version: 1.12.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings IdMappingAnalysis_1.12.0.tar.gz

StartedAt: 2015-10-08 23:46:43 -0700 (Thu, 08 Oct 2015)

EndedAt: 2015-10-08 23:48:52 -0700 (Thu, 08 Oct 2015)

EllapsedTime: 128.8 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_1.12.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.1-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 ‘1.12.0’
* 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 ... [10s/11s] 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 ... [50s/51s] OK
Examples with CPU or elapsed time > 5s
                                user system elapsed
Bootstrap                     11.686  0.166  11.845
getBootstrap.JointUniquePairs 11.670  0.111  11.786
* 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-3.1-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	0.347	0.026	0.373
Bootstrap	11.686	0.166	11.845
Corr	0.819	0.027	0.847
CorrData	0.143	0.004	0.146
CsvList.merge.Misc	0.005	0.000	0.006
IdMap	0.010	0.001	0.010
IdMapBase	0.005	0.000	0.004
IdMapCounts	1.081	0.021	1.103
IdMapDiff	0.981	0.010	0.992
IdMapDiffCounts	0.884	0.009	0.893
JointIdMap	0.252	0.002	0.255
JointUniquePairs	1.109	0.003	1.111
Mixture	0.347	0.002	0.377
UniquePairs	0.004	0.000	0.004
aligned.IdMapBase	0.015	0.001	0.016
as.IdMap.UniquePairs	0.063	0.001	0.063
as.MultiSet.CorrData	0.933	0.016	0.949
as.UniquePairs.IdMap	0.024	0.000	0.025
as.data.frame.IdMapBase	0.059	0.001	0.060
as.data.frame.JointIdMap	0.195	0.008	0.202
as.list.IdMap	0.017	0.001	0.017
boxplot.JointUniquePairs	0.101	0.005	0.106
byColNames.Subset	0.009	0.001	0.010
byColumn.Subset	0.008	0.001	0.008
byRow.Subset	0.007	0.001	0.007
byRowNames.Subset	0.022	0.001	0.024
clust.Mixture	0.003	0.000	0.004
copy.Display	0.001	0.001	0.002
corr.boxplot.JointUniquePairs	0.145	0.002	0.148
corr.plot.JointUniquePairs	0.094	0.002	0.097
create.Display	0.001	0.000	0.001
create.UniquePairs	0.225	0.002	0.227
diffCounts.plot.JointIdMap	1.010	0.008	1.019
dim.IdMapBase	0.004	0.001	0.005
dimnames.IdMapBase	0.004	0.000	0.005
do.glm.JointUniquePairs	0.026	0.001	0.028
ecdf.plot.JointIdMap	0.468	0.012	0.479
equals.UniquePairs	0.071	0.001	0.071
fisherTransform.DataFilter	0.001	0.000	0.001
fisherTransformInverse.DataFilter	0.001	0.000	0.001
fisherTransformJacobean.DataFilter	0.001	0.000	0.002
getBootstrap.JointUniquePairs	11.670	0.111	11.786
getCompoundEvents.IdMapDiffCounts	0.750	0.006	0.755
getCompoundGroups.IdMapDiffCounts	0.799	0.005	0.804
getCorr.JointUniquePairs	0.067	0.002	0.070
getCorrData.JointUniquePairs	0.151	0.002	0.154
getCorrDataFrame.JointUniquePairs	0.034	0.001	0.035
getCounts.IdMap	0.037	0.000	0.037
getCounts.JointIdMap	0.452	0.002	0.455
getData.Corr	0.001	0.000	0.002
getData.Mixture	0.002	0.000	0.003
getDiff.JointIdMap	0.588	0.010	0.599
getExperimentSet.CorrData	0.137	0.005	0.143
getIdMapList.JointIdMap	0.233	0.001	0.234
getMapNames.JointIdMap	0.216	0.001	0.216
getMapNames.JointUniquePairs	0.004	0.000	0.004
getMatch.UniquePairs	0.063	0.001	0.064
getMatchInfo.JointIdMap	0.255	0.001	0.255
getMatchInfo.JointUniquePairs	0.555	0.002	0.557
getMixture.JointUniquePairs	0.254	0.003	0.256
getSampleNames.CorrData	0.005	0.001	0.006
getStats.IdMapCounts	0.403	0.010	0.413
getStats.Mixture	0.004	0.000	0.004
getUnionIdMap.JointIdMap	0.856	0.009	0.865
getUniquePairs.Corr	0.009	0.000	0.009
getUniquePairs.CorrData	0.007	0.001	0.007
getUniquePairs.JointUniquePairs	0.009	0.000	0.009
interactive.corr.boxplot.JointUniquePairs	0.147	0.002	0.150
interactive.corr.plot.JointUniquePairs	0.085	0.009	0.094
interactive.mixture.boxplot.JointUniquePairs	0.315	0.010	0.326
interactive.mixture.plot.JointUniquePairs	0.182	0.008	0.191
interactive.plot.CorrData	0.064	0.004	0.068
interactive.plot.JointUniquePairs	0.002	0.000	0.002
interleave.Misc	0.001	0.000	0.001
line.loess.Display	0.001	0.001	0.002
line.unsorted.Display	0.001	0.000	0.002
logTen.DataFilter	0.182	0.013	0.194
merge.IdMap	1.230	0.015	1.246
minAvgCountConstraint.DataFilter	0.171	0.007	0.179
minCountConstraint.DataFilter	0.183	0.008	0.191
minCountGroupConstraint.DataFilter	0.262	0.008	0.270
mixture.boxplot.JointUniquePairs	0.327	0.002	0.330
mixture.plot.JointUniquePairs	0.247	0.003	0.251
plot.Bootstrap	0.171	0.002	0.174
plot.Corr	0.104	0.004	0.228
plot.CorrData	0.046	0.001	0.048
plot.IdMapCounts	0.419	0.001	0.513
plot.IdMapDiffCounts	1.064	0.012	1.538
plot.Mixture	0.033	0.003	0.664
primaryIDs.IdMapBase	0.007	0.000	0.007
primaryKey.CorrData	0.004	0.000	0.003
primaryKey.IdMapBase	0.006	0.001	0.006
primaryKey.Mixture	0.003	0.000	0.004
progressMsg.Display	0.001	0.001	0.001
removeNASeries.DataFilter	0.238	0.006	0.244
secondaryKey.CorrData	0.004	0.000	0.004
secondaryKey.IdMapBase	0.006	0.000	0.006
secondaryKey.Mixture	0.001	0.000	0.001
subsetCorr.JointUniquePairs	0.029	0.001	0.030
subsetData.JointUniquePairs	0.026	0.002	0.027
subsetGroups.JointUniquePairs	1.036	0.005	1.041
summary.IdMapDiffCounts	0.781	0.004	0.785
swapKeys.IdMap	0.120	0.001	0.120
swapKeys.UniquePairs	0.026	0.000	0.026
textBoundingBox.Display	0	0	0
to.base.Misc	0.001	0.000	0.001
to.binary.logical.Misc	0.01	0.00	0.01
to.index.expr.Misc	0.001	0.000	0.001
unique.UniquePairs	0.078	0.000	0.078
words.Misc	0.003	0.000	0.003
zoom.pars.Display	0.001	0.000	0.001