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: 2015-10-27 09:00:25 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 09:01:56 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 90.9 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 ... [35s/35s] OK
Examples with CPU or elapsed time > 5s
                               user system elapsed
getBootstrap.JointUniquePairs 8.289  0.089   8.379
Bootstrap                     7.735  0.101   7.822
* 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	0.251	0.018	0.268
Bootstrap	7.735	0.101	7.822
Corr	0.554	0.022	0.577
CorrData	0.098	0.003	0.102
CsvList.merge.Misc	0.004	0.000	0.003
IdMap	0.009	0.001	0.010
IdMapBase	0.002	0.000	0.002
IdMapCounts	0.683	0.009	0.690
IdMapDiff	0.625	0.006	0.630
IdMapDiffCounts	0.566	0.003	0.569
JointIdMap	0.183	0.001	0.183
JointUniquePairs	0.770	0.005	0.775
Mixture	0.267	0.000	0.267
UniquePairs	0.004	0.000	0.004
aligned.IdMapBase	0.009	0.000	0.008
as.IdMap.UniquePairs	0.056	0.000	0.056
as.MultiSet.CorrData	0.738	0.010	0.747
as.UniquePairs.IdMap	0.024	0.000	0.025
as.data.frame.IdMapBase	0.060	0.001	0.060
as.data.frame.JointIdMap	0.195	0.004	0.199
as.list.IdMap	0.020	0.002	0.023
boxplot.JointUniquePairs	0.071	0.001	0.074
byColNames.Subset	0.005	0.000	0.006
byColumn.Subset	0.005	0.001	0.006
byRow.Subset	0.005	0.000	0.005
byRowNames.Subset	0.010	0.001	0.009
clust.Mixture	0.002	0.000	0.002
copy.Display	0.001	0.000	0.000
corr.boxplot.JointUniquePairs	0.093	0.004	0.096
corr.plot.JointUniquePairs	0.057	0.004	0.062
create.Display	0	0	0
create.UniquePairs	0.133	0.000	0.134
diffCounts.plot.JointIdMap	0.656	0.008	0.664
dim.IdMapBase	0.002	0.000	0.002
dimnames.IdMapBase	0.003	0.000	0.002
do.glm.JointUniquePairs	0.021	0.002	0.023
ecdf.plot.JointIdMap	0.350	0.005	0.354
equals.UniquePairs	0.044	0.001	0.045
fisherTransform.DataFilter	0.001	0.000	0.001
fisherTransformInverse.DataFilter	0.001	0.000	0.001
fisherTransformJacobean.DataFilter	0.001	0.000	0.001
getBootstrap.JointUniquePairs	8.289	0.089	8.379
getCompoundEvents.IdMapDiffCounts	0.569	0.014	0.582
getCompoundGroups.IdMapDiffCounts	0.569	0.005	0.573
getCorr.JointUniquePairs	0.058	0.002	0.060
getCorrData.JointUniquePairs	0.106	0.001	0.107
getCorrDataFrame.JointUniquePairs	0.024	0.001	0.024
getCounts.IdMap	0.027	0.000	0.028
getCounts.JointIdMap	0.324	0.002	0.327
getData.Corr	0.001	0.000	0.001
getData.Mixture	0.002	0.000	0.003
getDiff.JointIdMap	0.435	0.006	0.440
getExperimentSet.CorrData	0.105	0.006	0.111
getIdMapList.JointIdMap	0.196	0.005	0.200
getMapNames.JointIdMap	0.185	0.004	0.189
getMapNames.JointUniquePairs	0.003	0.000	0.003
getMatch.UniquePairs	0.048	0.001	0.048
getMatchInfo.JointIdMap	0.187	0.000	0.188
getMatchInfo.JointUniquePairs	0.383	0.003	0.387
getMixture.JointUniquePairs	0.185	0.002	0.187
getSampleNames.CorrData	0.003	0.000	0.003
getStats.IdMapCounts	0.327	0.008	0.335
getStats.Mixture	0.004	0.000	0.004
getUnionIdMap.JointIdMap	0.577	0.009	0.585
getUniquePairs.Corr	0.006	0.000	0.007
getUniquePairs.CorrData	0.007	0.001	0.007
getUniquePairs.JointUniquePairs	0.006	0.000	0.006
interactive.corr.boxplot.JointUniquePairs	0.097	0.001	0.099
interactive.corr.plot.JointUniquePairs	0.057	0.008	0.066
interactive.mixture.boxplot.JointUniquePairs	0.247	0.017	0.264
interactive.mixture.plot.JointUniquePairs	0.192	0.013	0.205
interactive.plot.CorrData	0.044	0.001	0.046
interactive.plot.JointUniquePairs	0.001	0.000	0.001
interleave.Misc	0.000	0.000	0.001
line.loess.Display	0.000	0.001	0.001
line.unsorted.Display	0.000	0.000	0.001
logTen.DataFilter	0.133	0.014	0.146
merge.IdMap	0.769	0.011	0.781
minAvgCountConstraint.DataFilter	0.122	0.004	0.127
minCountConstraint.DataFilter	0.150	0.012	0.163
minCountGroupConstraint.DataFilter	0.187	0.015	0.203
mixture.boxplot.JointUniquePairs	0.232	0.005	0.238
mixture.plot.JointUniquePairs	0.191	0.007	0.199
plot.Bootstrap	0.108	0.001	0.111
plot.Corr	0.067	0.003	0.072
plot.CorrData	0.029	0.002	0.044
plot.IdMapCounts	0.312	0.005	0.317
plot.IdMapDiffCounts	0.818	0.010	0.827
plot.Mixture	0.022	0.002	0.024
primaryIDs.IdMapBase	0.004	0.000	0.004
primaryKey.CorrData	0.002	0.001	0.002
primaryKey.IdMapBase	0.008	0.000	0.008
primaryKey.Mixture	0.003	0.001	0.004
progressMsg.Display	0.001	0.000	0.001
removeNASeries.DataFilter	0.170	0.007	0.176
secondaryKey.CorrData	0.002	0.001	0.002
secondaryKey.IdMapBase	0.004	0.000	0.003
secondaryKey.Mixture	0.001	0.000	0.001
subsetCorr.JointUniquePairs	0.019	0.000	0.019
subsetData.JointUniquePairs	0.012	0.002	0.013
subsetGroups.JointUniquePairs	0.759	0.008	0.766
summary.IdMapDiffCounts	0.600	0.012	0.612
swapKeys.IdMap	0.126	0.002	0.129
swapKeys.UniquePairs	0.026	0.001	0.027
textBoundingBox.Display	0.001	0.001	0.001
to.base.Misc	0.002	0.000	0.002
to.binary.logical.Misc	0.003	0.000	0.003
to.index.expr.Misc	0.001	0.000	0.001
unique.UniquePairs	0.069	0.002	0.071
words.Misc	0.002	0.000	0.002
zoom.pars.Display	0.001	0.000	0.000