BioC 3.3: CHECK report for IdMappingAnalysis on morelia

Package: IdMappingAnalysis

Version: 1.15.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings IdMappingAnalysis_1.15.0.tar.gz

StartedAt: 2015-10-22 07:18:44 -0400 (Thu, 22 Oct 2015)

EndedAt: 2015-10-22 07:19:45 -0400 (Thu, 22 Oct 2015)

EllapsedTime: 61.0 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_1.15.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/IdMappingAnalysis.Rcheck’
* using R Under development (unstable) (2015-10-08 r69496)
* 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 ‘1.15.0’
* 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 ... [5s/4s] 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’
Undefined global functions or variables:
  Object equals extend getName rselect.list throw
* 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 ... [19s/19s] OK
* 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-3.3-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	0.144	0.009	0.154
Bootstrap	4.799	0.067	4.866
Corr	0.365	0.012	0.371
CorrData	0.03	0.00	0.03
CsvList.merge.Misc	0.002	0.000	0.002
IdMap	0.004	0.000	0.004
IdMapBase	0.001	0.000	0.001
IdMapCounts	0.272	0.009	0.282
IdMapDiff	0.282	0.004	0.286
IdMapDiffCounts	0.238	0.001	0.239
JointIdMap	0.055	0.000	0.055
JointUniquePairs	0.399	0.001	0.401
Mixture	0.145	0.000	0.145
UniquePairs	0.002	0.000	0.002
aligned.IdMapBase	0.004	0.000	0.005
as.IdMap.UniquePairs	0.025	0.000	0.025
as.MultiSet.CorrData	0.395	0.005	0.401
as.UniquePairs.IdMap	0.014	0.000	0.014
as.data.frame.IdMapBase	0.045	0.000	0.046
as.data.frame.JointIdMap	0.045	0.005	0.050
as.list.IdMap	0.008	0.000	0.008
boxplot.JointUniquePairs	0.043	0.002	0.045
byColNames.Subset	0.003	0.000	0.003
byColumn.Subset	0.003	0.000	0.003
byRow.Subset	0.003	0.001	0.003
byRowNames.Subset	0.004	0.000	0.005
clust.Mixture	0.001	0.000	0.001
copy.Display	0.000	0.001	0.000
corr.boxplot.JointUniquePairs	0.051	0.001	0.053
corr.plot.JointUniquePairs	0.030	0.001	0.032
create.Display	0	0	0
create.UniquePairs	0.081	0.001	0.081
diffCounts.plot.JointIdMap	0.326	0.004	0.329
dim.IdMapBase	0.001	0.000	0.002
dimnames.IdMapBase	0.001	0.000	0.001
do.glm.JointUniquePairs	0.009	0.001	0.010
ecdf.plot.JointIdMap	0.141	0.004	0.145
equals.UniquePairs	0.025	0.000	0.025
fisherTransform.DataFilter	0	0	0
fisherTransformInverse.DataFilter	0.000	0.000	0.001
fisherTransformJacobean.DataFilter	0.000	0.001	0.001
getBootstrap.JointUniquePairs	4.848	0.060	4.948
getCompoundEvents.IdMapDiffCounts	0.315	0.006	0.323
getCompoundGroups.IdMapDiffCounts	0.245	0.005	0.249
getCorr.JointUniquePairs	0.032	0.001	0.033
getCorrData.JointUniquePairs	0.035	0.002	0.036
getCorrDataFrame.JointUniquePairs	0.012	0.000	0.012
getCounts.IdMap	0.014	0.000	0.014
getCounts.JointIdMap	0.125	0.002	0.127
getData.Corr	0.001	0.000	0.001
getData.Mixture	0.002	0.000	0.001
getDiff.JointIdMap	0.191	0.002	0.193
getExperimentSet.CorrData	0.059	0.003	0.062
getIdMapList.JointIdMap	0.049	0.002	0.051
getMapNames.JointIdMap	0.059	0.002	0.061
getMapNames.JointUniquePairs	0.002	0.000	0.002
getMatch.UniquePairs	0.035	0.002	0.036
getMatchInfo.JointIdMap	0.061	0.003	0.064
getMatchInfo.JointUniquePairs	0.222	0.002	0.223
getMixture.JointUniquePairs	0.099	0.001	0.100
getSampleNames.CorrData	0.002	0.000	0.002
getStats.IdMapCounts	0.129	0.004	0.133
getStats.Mixture	0.002	0.000	0.002
getUnionIdMap.JointIdMap	0.293	0.009	0.303
getUniquePairs.Corr	0.003	0.000	0.004
getUniquePairs.CorrData	0.003	0.000	0.004
getUniquePairs.JointUniquePairs	0.003	0.000	0.004
interactive.corr.boxplot.JointUniquePairs	0.047	0.001	0.049
interactive.corr.plot.JointUniquePairs	0.046	0.004	0.051
interactive.mixture.boxplot.JointUniquePairs	0.140	0.008	0.147
interactive.mixture.plot.JointUniquePairs	0.096	0.004	0.100
interactive.plot.CorrData	0.025	0.003	0.029
interactive.plot.JointUniquePairs	0.001	0.000	0.000
interleave.Misc	0.001	0.000	0.001
line.loess.Display	0.000	0.001	0.001
line.unsorted.Display	0	0	0
logTen.DataFilter	0.109	0.009	0.118
merge.IdMap	0.383	0.004	0.387
minAvgCountConstraint.DataFilter	0.075	0.004	0.079
minCountConstraint.DataFilter	0.079	0.004	0.082
minCountGroupConstraint.DataFilter	0.106	0.006	0.113
mixture.boxplot.JointUniquePairs	0.126	0.001	0.127
mixture.plot.JointUniquePairs	0.093	0.002	0.095
plot.Bootstrap	0.055	0.000	0.056
plot.Corr	0.039	0.001	0.040
plot.CorrData	0.015	0.000	0.017
plot.IdMapCounts	0.114	0.003	0.132
plot.IdMapDiffCounts	0.386	0.005	0.391
plot.Mixture	0.011	0.001	0.012
primaryIDs.IdMapBase	0.002	0.000	0.002
primaryKey.CorrData	0.002	0.000	0.002
primaryKey.IdMapBase	0.002	0.000	0.002
primaryKey.Mixture	0.001	0.000	0.001
progressMsg.Display	0.000	0.001	0.001
removeNASeries.DataFilter	0.078	0.002	0.082
secondaryKey.CorrData	0.002	0.000	0.001
secondaryKey.IdMapBase	0.001	0.000	0.002
secondaryKey.Mixture	0.001	0.000	0.001
subsetCorr.JointUniquePairs	0.009	0.000	0.010
subsetData.JointUniquePairs	0.006	0.000	0.006
subsetGroups.JointUniquePairs	0.386	0.002	0.388
summary.IdMapDiffCounts	0.258	0.005	0.262
swapKeys.IdMap	0.038	0.000	0.038
swapKeys.UniquePairs	0.014	0.001	0.014
textBoundingBox.Display	0.001	0.000	0.000
to.base.Misc	0.000	0.000	0.001
to.binary.logical.Misc	0.001	0.000	0.001
to.index.expr.Misc	0	0	0
unique.UniquePairs	0.043	0.001	0.043
words.Misc	0.001	0.000	0.001
zoom.pars.Display	0.001	0.000	0.000