BioC 3.1: CHECK report for IdMappingAnalysis on morelia

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: 2015-10-09 03:05:27 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 03:06:44 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 76.6 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 (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 ‘1.12.0’
* 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 ... [7s/6s] 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 ... [28s/28s] OK
Examples with CPU or elapsed time > 5s
                               user system elapsed
getBootstrap.JointUniquePairs 6.643  0.361   7.004
Bootstrap                     6.562  0.293   6.847
* 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	0.182	0.028	0.211
Bootstrap	6.562	0.293	6.847
Corr	0.415	0.015	0.429
CorrData	0.045	0.003	0.048
CsvList.merge.Misc	0.003	0.000	0.003
IdMap	0.007	0.000	0.007
IdMapBase	0.002	0.000	0.002
IdMapCounts	0.390	0.051	0.441
IdMapDiff	0.428	0.006	0.433
IdMapDiffCounts	0.319	0.002	0.320
JointIdMap	0.061	0.001	0.062
JointUniquePairs	0.549	0.006	0.554
Mixture	0.179	0.001	0.213
UniquePairs	0.003	0.000	0.003
aligned.IdMapBase	0.007	0.000	0.007
as.IdMap.UniquePairs	0.045	0.001	0.046
as.MultiSet.CorrData	0.564	0.051	0.615
as.UniquePairs.IdMap	0.024	0.000	0.024
as.data.frame.IdMapBase	0.059	0.000	0.059
as.data.frame.JointIdMap	0.059	0.002	0.060
as.list.IdMap	0.014	0.000	0.014
boxplot.JointUniquePairs	0.066	0.002	0.067
byColNames.Subset	0.004	0.001	0.004
byColumn.Subset	0.005	0.000	0.005
byRow.Subset	0.003	0.000	0.003
byRowNames.Subset	0.012	0.001	0.013
clust.Mixture	0.002	0.000	0.002
copy.Display	0.001	0.000	0.000
corr.boxplot.JointUniquePairs	0.057	0.001	0.058
corr.plot.JointUniquePairs	0.037	0.002	0.039
create.Display	0	0	0
create.UniquePairs	0.124	0.028	0.152
diffCounts.plot.JointIdMap	0.469	0.032	0.501
dim.IdMapBase	0.002	0.000	0.003
dimnames.IdMapBase	0.002	0.000	0.002
do.glm.JointUniquePairs	0.010	0.000	0.011
ecdf.plot.JointIdMap	0.205	0.003	0.207
equals.UniquePairs	0.047	0.002	0.049
fisherTransform.DataFilter	0.001	0.001	0.001
fisherTransformInverse.DataFilter	0.001	0.000	0.001
fisherTransformJacobean.DataFilter	0.001	0.000	0.001
getBootstrap.JointUniquePairs	6.643	0.361	7.004
getCompoundEvents.IdMapDiffCounts	0.367	0.027	0.394
getCompoundGroups.IdMapDiffCounts	0.326	0.003	0.330
getCorr.JointUniquePairs	0.050	0.002	0.053
getCorrData.JointUniquePairs	0.040	0.003	0.043
getCorrDataFrame.JointUniquePairs	0.018	0.001	0.019
getCounts.IdMap	0.014	0.000	0.014
getCounts.JointIdMap	0.192	0.003	0.195
getData.Corr	0.001	0.000	0.001
getData.Mixture	0.002	0.001	0.003
getDiff.JointIdMap	0.257	0.055	0.312
getExperimentSet.CorrData	0.077	0.027	0.103
getIdMapList.JointIdMap	0.074	0.000	0.074
getMapNames.JointIdMap	0.051	0.002	0.051
getMapNames.JointUniquePairs	0.002	0.000	0.002
getMatch.UniquePairs	0.035	0.001	0.036
getMatchInfo.JointIdMap	0.047	0.001	0.048
getMatchInfo.JointUniquePairs	0.273	0.000	0.273
getMixture.JointUniquePairs	0.131	0.002	0.131
getSampleNames.CorrData	0.003	0.001	0.003
getStats.IdMapCounts	0.175	0.022	0.197
getStats.Mixture	0.002	0.001	0.003
getUnionIdMap.JointIdMap	0.437	0.051	0.488
getUniquePairs.Corr	0.005	0.001	0.005
getUniquePairs.CorrData	0.003	0.000	0.004
getUniquePairs.JointUniquePairs	0.004	0.000	0.003
interactive.corr.boxplot.JointUniquePairs	0.075	0.017	0.092
interactive.corr.plot.JointUniquePairs	0.042	0.006	0.048
interactive.mixture.boxplot.JointUniquePairs	0.140	0.007	0.146
interactive.mixture.plot.JointUniquePairs	0.125	0.040	0.165
interactive.plot.CorrData	0.045	0.013	0.059
interactive.plot.JointUniquePairs	0.001	0.000	0.001
interleave.Misc	0.001	0.000	0.001
line.loess.Display	0.001	0.000	0.001
line.unsorted.Display	0.001	0.000	0.000
logTen.DataFilter	0.096	0.011	0.107
merge.IdMap	0.713	0.097	0.810
minAvgCountConstraint.DataFilter	0.121	0.005	0.126
minCountConstraint.DataFilter	0.123	0.005	0.128
minCountGroupConstraint.DataFilter	0.157	0.052	0.209
mixture.boxplot.JointUniquePairs	0.193	0.002	0.195
mixture.plot.JointUniquePairs	0.157	0.006	0.164
plot.Bootstrap	0.076	0.009	0.086
plot.Corr	0.061	0.013	0.082
plot.CorrData	0.027	0.002	0.029
plot.IdMapCounts	0.179	0.032	0.212
plot.IdMapDiffCounts	0.559	0.101	0.660
plot.Mixture	0.012	0.001	0.014
primaryIDs.IdMapBase	0.007	0.000	0.007
primaryKey.CorrData	0.001	0.001	0.002
primaryKey.IdMapBase	0.003	0.000	0.003
primaryKey.Mixture	0.002	0.000	0.002
progressMsg.Display	0.001	0.001	0.001
removeNASeries.DataFilter	0.123	0.003	0.127
secondaryKey.CorrData	0.002	0.000	0.002
secondaryKey.IdMapBase	0.003	0.000	0.003
secondaryKey.Mixture	0.001	0.000	0.001
subsetCorr.JointUniquePairs	0.012	0.000	0.013
subsetData.JointUniquePairs	0.011	0.001	0.012
subsetGroups.JointUniquePairs	0.589	0.004	0.593
summary.IdMapDiffCounts	0.356	0.014	0.370
swapKeys.IdMap	0.07	0.00	0.07
swapKeys.UniquePairs	0.023	0.001	0.024
textBoundingBox.Display	0.001	0.000	0.001
to.base.Misc	0.001	0.000	0.000
to.binary.logical.Misc	0.001	0.000	0.001
to.index.expr.Misc	0.001	0.000	0.000
unique.UniquePairs	0.067	0.004	0.071
words.Misc	0.001	0.000	0.002
zoom.pars.Display	0.000	0.000	0.001