BioC 3.2: CHECK report for IdMappingAnalysis on oaxaca

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 00:57:06 -0700 (Mon, 24 Aug 2015)

EndedAt: 2015-08-24 00:58:36 -0700 (Mon, 24 Aug 2015)

EllapsedTime: 90.0 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 (2015-08-14)
* 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 ‘1.13.0’
* 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 ... [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
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 ... [30s/30s] OK
Examples with CPU or elapsed time > 5s
                               user system elapsed
Bootstrap                     7.470  0.085   7.672
getBootstrap.JointUniquePairs 7.451  0.070   7.568
* 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	0.200	0.013	0.213
Bootstrap	7.470	0.085	7.672
Corr	0.549	0.018	0.574
CorrData	0.053	0.003	0.055
CsvList.merge.Misc	0.003	0.001	0.003
IdMap	0.008	0.000	0.010
IdMapBase	0.002	0.000	0.002
IdMapCounts	0.453	0.008	0.464
IdMapDiff	0.506	0.003	0.510
IdMapDiffCounts	0.413	0.001	0.414
JointIdMap	0.076	0.004	0.079
JointUniquePairs	0.723	0.005	0.752
Mixture	0.206	0.001	0.232
UniquePairs	0.004	0.001	0.004
aligned.IdMapBase	0.007	0.000	0.008
as.IdMap.UniquePairs	0.046	0.001	0.046
as.MultiSet.CorrData	0.694	0.011	0.715
as.UniquePairs.IdMap	0.026	0.000	0.027
as.data.frame.IdMapBase	0.067	0.000	0.068
as.data.frame.JointIdMap	0.068	0.001	0.071
as.list.IdMap	0.018	0.001	0.018
boxplot.JointUniquePairs	0.068	0.001	0.069
byColNames.Subset	0.005	0.001	0.006
byColumn.Subset	0.005	0.000	0.006
byRow.Subset	0.005	0.000	0.006
byRowNames.Subset	0.012	0.001	0.014
clust.Mixture	0.002	0.000	0.003
copy.Display	0.001	0.000	0.001
corr.boxplot.JointUniquePairs	0.087	0.001	0.090
corr.plot.JointUniquePairs	0.062	0.002	0.064
create.Display	0	0	0
create.UniquePairs	0.162	0.000	0.163
diffCounts.plot.JointIdMap	0.544	0.002	0.547
dim.IdMapBase	0.002	0.001	0.002
dimnames.IdMapBase	0.003	0.000	0.002
do.glm.JointUniquePairs	0.017	0.001	0.017
ecdf.plot.JointIdMap	0.208	0.003	0.212
equals.UniquePairs	0.049	0.000	0.050
fisherTransform.DataFilter	0.000	0.000	0.001
fisherTransformInverse.DataFilter	0	0	0
fisherTransformJacobean.DataFilter	0.001	0.000	0.001
getBootstrap.JointUniquePairs	7.451	0.070	7.568
getCompoundEvents.IdMapDiffCounts	0.373	0.003	0.375
getCompoundGroups.IdMapDiffCounts	0.405	0.003	0.408
getCorr.JointUniquePairs	0.048	0.001	0.050
getCorrData.JointUniquePairs	0.053	0.001	0.055
getCorrDataFrame.JointUniquePairs	0.022	0.000	0.023
getCounts.IdMap	0.024	0.000	0.024
getCounts.JointIdMap	0.197	0.001	0.198
getData.Corr	0.001	0.000	0.001
getData.Mixture	0.002	0.001	0.002
getDiff.JointIdMap	0.288	0.008	0.296
getExperimentSet.CorrData	0.101	0.004	0.105
getIdMapList.JointIdMap	0.077	0.000	0.078
getMapNames.JointIdMap	0.069	0.002	0.072
getMapNames.JointUniquePairs	0.002	0.000	0.003
getMatch.UniquePairs	0.042	0.001	0.044
getMatchInfo.JointIdMap	0.070	0.002	0.072
getMatchInfo.JointUniquePairs	0.388	0.001	0.389
getMixture.JointUniquePairs	0.147	0.001	0.148
getSampleNames.CorrData	0.003	0.000	0.003
getStats.IdMapCounts	0.196	0.004	0.199
getStats.Mixture	0.002	0.000	0.003
getUnionIdMap.JointIdMap	0.470	0.003	0.474
getUniquePairs.Corr	0.005	0.001	0.005
getUniquePairs.CorrData	0.004	0.000	0.004
getUniquePairs.JointUniquePairs	0.005	0.000	0.005
interactive.corr.boxplot.JointUniquePairs	0.074	0.002	0.075
interactive.corr.plot.JointUniquePairs	0.042	0.006	0.048
interactive.mixture.boxplot.JointUniquePairs	0.188	0.008	0.196
interactive.mixture.plot.JointUniquePairs	0.163	0.007	0.169
interactive.plot.CorrData	0.040	0.001	0.041
interactive.plot.JointUniquePairs	0.001	0.000	0.001
interleave.Misc	0.001	0.000	0.001
line.loess.Display	0.001	0.000	0.000
line.unsorted.Display	0.001	0.000	0.001
logTen.DataFilter	0.107	0.007	0.114
merge.IdMap	0.672	0.003	0.677
minAvgCountConstraint.DataFilter	0.174	0.008	0.182
minCountConstraint.DataFilter	0.118	0.006	0.125
minCountGroupConstraint.DataFilter	0.169	0.005	0.175
mixture.boxplot.JointUniquePairs	0.192	0.001	0.193
mixture.plot.JointUniquePairs	0.146	0.003	0.149
plot.Bootstrap	0.081	0.001	0.083
plot.Corr	0.061	0.003	0.064
plot.CorrData	0.026	0.000	0.027
plot.IdMapCounts	0.179	0.002	0.181
plot.IdMapDiffCounts	0.585	0.003	0.608
plot.Mixture	0.024	0.001	0.027
primaryIDs.IdMapBase	0.003	0.000	0.003
primaryKey.CorrData	0.001	0.001	0.002
primaryKey.IdMapBase	0.003	0.000	0.003
primaryKey.Mixture	0.001	0.000	0.002
progressMsg.Display	0.000	0.001	0.000
removeNASeries.DataFilter	0.150	0.003	0.153
secondaryKey.CorrData	0.001	0.000	0.002
secondaryKey.IdMapBase	0.003	0.000	0.003
secondaryKey.Mixture	0.000	0.000	0.001
subsetCorr.JointUniquePairs	0.018	0.001	0.018
subsetData.JointUniquePairs	0.01	0.00	0.01
subsetGroups.JointUniquePairs	0.647	0.007	0.654
summary.IdMapDiffCounts	0.392	0.000	0.393
swapKeys.IdMap	0.066	0.000	0.066
swapKeys.UniquePairs	0.024	0.001	0.025
textBoundingBox.Display	0.000	0.000	0.001
to.base.Misc	0.002	0.000	0.001
to.binary.logical.Misc	0.002	0.000	0.003
to.index.expr.Misc	0.001	0.000	0.001
unique.UniquePairs	0.079	0.000	0.080
words.Misc	0.001	0.000	0.001
zoom.pars.Display	0.001	0.000	0.001