BioC 3.2: CHECK report for IdMappingAnalysis on oaxaca

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: 2016-04-23 01:17:48 -0700 (Sat, 23 Apr 2016)

EndedAt: 2016-04-23 01:19:15 -0700 (Sat, 23 Apr 2016)

EllapsedTime: 86.9 seconds

RetCode: 0

Status:  OK

CheckDir: IdMappingAnalysis.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings IdMappingAnalysis_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/IdMappingAnalysis.Rcheck’
* using R version 3.2.4 (2016-03-10)
* 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 ‘1.14.0’
* 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 ... [6s/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 ... [29s/29s] OK
Examples with CPU or elapsed time > 5s
                               user system elapsed
getBootstrap.JointUniquePairs 7.305  0.059   7.390
Bootstrap                     7.163  0.079   7.255
* 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	0.193	0.012	0.204
Bootstrap	7.163	0.079	7.255
Corr	0.507	0.014	0.521
CorrData	0.046	0.001	0.048
CsvList.merge.Misc	0.002	0.000	0.002
IdMap	0.007	0.000	0.008
IdMapBase	0.002	0.000	0.002
IdMapCounts	0.430	0.008	0.438
IdMapDiff	0.461	0.004	0.465
IdMapDiffCounts	0.351	0.002	0.352
JointIdMap	0.07	0.00	0.07
JointUniquePairs	0.616	0.003	0.619
Mixture	0.198	0.001	0.273
UniquePairs	0.004	0.000	0.004
aligned.IdMapBase	0.007	0.000	0.008
as.IdMap.UniquePairs	0.038	0.000	0.039
as.MultiSet.CorrData	0.647	0.008	0.655
as.UniquePairs.IdMap	0.022	0.000	0.054
as.data.frame.IdMapBase	0.056	0.001	0.057
as.data.frame.JointIdMap	0.074	0.003	0.077
as.list.IdMap	0.01	0.00	0.01
boxplot.JointUniquePairs	0.067	0.001	0.069
byColNames.Subset	0.005	0.000	0.006
byColumn.Subset	0.006	0.001	0.006
byRow.Subset	0.005	0.000	0.005
byRowNames.Subset	0.007	0.000	0.007
clust.Mixture	0.002	0.001	0.002
copy.Display	0.000	0.000	0.001
corr.boxplot.JointUniquePairs	0.077	0.003	0.080
corr.plot.JointUniquePairs	0.052	0.001	0.053
create.Display	0	0	0
create.UniquePairs	0.138	0.001	0.143
diffCounts.plot.JointIdMap	0.503	0.006	0.509
dim.IdMapBase	0.002	0.000	0.002
dimnames.IdMapBase	0.002	0.001	0.002
do.glm.JointUniquePairs	0.017	0.000	0.016
ecdf.plot.JointIdMap	0.194	0.002	0.195
equals.UniquePairs	0.034	0.001	0.034
fisherTransform.DataFilter	0.001	0.000	0.001
fisherTransformInverse.DataFilter	0.000	0.000	0.001
fisherTransformJacobean.DataFilter	0	0	0
getBootstrap.JointUniquePairs	7.305	0.059	7.390
getCompoundEvents.IdMapDiffCounts	0.352	0.005	0.358
getCompoundGroups.IdMapDiffCounts	0.399	0.003	0.402
getCorr.JointUniquePairs	0.049	0.001	0.051
getCorrData.JointUniquePairs	0.051	0.000	0.051
getCorrDataFrame.JointUniquePairs	0.019	0.000	0.020
getCounts.IdMap	0.024	0.000	0.024
getCounts.JointIdMap	0.200	0.003	0.202
getData.Corr	0.001	0.000	0.001
getData.Mixture	0.002	0.001	0.001
getDiff.JointIdMap	0.278	0.002	0.281
getExperimentSet.CorrData	0.103	0.004	0.108
getIdMapList.JointIdMap	0.074	0.001	0.074
getMapNames.JointIdMap	0.066	0.001	0.066
getMapNames.JointUniquePairs	0.003	0.000	0.003
getMatch.UniquePairs	0.045	0.000	0.045
getMatchInfo.JointIdMap	0.077	0.001	0.078
getMatchInfo.JointUniquePairs	0.395	0.004	0.399
getMixture.JointUniquePairs	0.137	0.001	0.139
getSampleNames.CorrData	0.002	0.001	0.002
getStats.IdMapCounts	0.195	0.002	0.197
getStats.Mixture	0.003	0.000	0.004
getUnionIdMap.JointIdMap	0.449	0.003	0.452
getUniquePairs.Corr	0.005	0.000	0.005
getUniquePairs.CorrData	0.005	0.001	0.006
getUniquePairs.JointUniquePairs	0.006	0.000	0.006
interactive.corr.boxplot.JointUniquePairs	0.079	0.002	0.080
interactive.corr.plot.JointUniquePairs	0.053	0.006	0.059
interactive.mixture.boxplot.JointUniquePairs	0.210	0.007	0.241
interactive.mixture.plot.JointUniquePairs	0.161	0.006	0.191
interactive.plot.CorrData	0.040	0.000	0.042
interactive.plot.JointUniquePairs	0.001	0.000	0.001
interleave.Misc	0.000	0.000	0.001
line.loess.Display	0.000	0.000	0.001
line.unsorted.Display	0	0	0
logTen.DataFilter	0.102	0.009	0.110
merge.IdMap	0.703	0.006	0.710
minAvgCountConstraint.DataFilter	0.086	0.005	0.091
minCountConstraint.DataFilter	0.127	0.007	0.133
minCountGroupConstraint.DataFilter	0.165	0.004	0.169
mixture.boxplot.JointUniquePairs	0.206	0.007	0.212
mixture.plot.JointUniquePairs	0.146	0.001	0.149
plot.Bootstrap	0.082	0.002	0.150
plot.Corr	0.064	0.002	0.068
plot.CorrData	0.030	0.001	0.185
plot.IdMapCounts	0.208	0.001	0.209
plot.IdMapDiffCounts	0.648	0.003	0.660
plot.Mixture	0.016	0.001	0.016
primaryIDs.IdMapBase	0.002	0.000	0.003
primaryKey.CorrData	0.001	0.001	0.002
primaryKey.IdMapBase	0.003	0.000	0.002
primaryKey.Mixture	0.002	0.000	0.002
progressMsg.Display	0.001	0.001	0.000
removeNASeries.DataFilter	0.113	0.003	0.117
secondaryKey.CorrData	0.002	0.000	0.002
secondaryKey.IdMapBase	0.002	0.000	0.003
secondaryKey.Mixture	0.000	0.000	0.001
subsetCorr.JointUniquePairs	0.018	0.002	0.020
subsetData.JointUniquePairs	0.010	0.000	0.011
subsetGroups.JointUniquePairs	0.634	0.004	0.638
summary.IdMapDiffCounts	0.431	0.002	0.433
swapKeys.IdMap	0.063	0.000	0.163
swapKeys.UniquePairs	0.021	0.001	0.022
textBoundingBox.Display	0.001	0.000	0.000
to.base.Misc	0.002	0.000	0.001
to.binary.logical.Misc	0.002	0.000	0.002
to.index.expr.Misc	0.001	0.000	0.000
unique.UniquePairs	0.077	0.000	0.078
words.Misc	0.001	0.000	0.002
zoom.pars.Display	0	0	0