BioC 3.2: CHECK report for rcellminer on perceval

Package: rcellminer

Version: 1.1.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings rcellminer_1.1.1.tar.gz

StartedAt: 2015-08-24 04:22:21 -0700 (Mon, 24 Aug 2015)

EndedAt: 2015-08-24 04:26:00 -0700 (Mon, 24 Aug 2015)

EllapsedTime: 219.0 seconds

RetCode: 0

Status:  OK

CheckDir: rcellminer.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 rcellminer_1.1.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/rcellminer.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘rcellminer/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘rcellminer’ version ‘1.1.1’
* 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 ‘rcellminer’ can be installed ... [10s/11s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
getSampleData,DrugData : .local: no visible global function definition
  for ‘samples’
getSampleData,MolData : .local: no visible global function definition
  for ‘samples’
* checking Rd files ... OK
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [19s/19s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [118s/117s]
 [119s/118s] 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/rcellminer.Rcheck/00check.log’
for details.

* installing *source* package ‘rcellminer’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (rcellminer)

name	user	system	elapsed
compareFingerprints	2.977	0.334	3.370
crossCors	0.014	0.004	0.018
crossCorsSpearman	0.001	0.000	0.000
getActivityRangeStats	0.072	0.013	0.085
getColumnQuantiles	0.004	0.001	0.004
getDrugActivityData	0.013	0.002	0.016
getDrugActivityRange	0.024	0.004	0.028
getDrugActivityRepeatData	0.014	0.002	0.017
getDrugMoaList	0.014	0.005	0.019
getDrugName	0.005	0.002	0.006
getFeatureDataFromMatList	4.250	0.639	4.946
getFingerprintList	0.182	0.016	0.084
getMedSenLineActivity	0.073	0.015	0.037
getMinDrugActivityRepeatCor	0.031	0.003	0.016
getMoaStr	0.030	0.004	0.011
getMoaToCompounds	0.033	0.005	0.014
getMolDataMatrices	0.723	0.268	0.759
getMolDataType	0.001	0.000	0.001
getNumDrugActivityRepeats	0.018	0.002	0.019
getNumMissingLines	0.005	0.001	0.006
getRsd	0.008	0.001	0.009
getSmiles	0.005	0.001	0.007
hasMoa	0.008	0.002	0.009
isPublic	0.003	0.001	0.004
loadNciColorSet	0.002	0.001	0.003
passRuleOf5	0.068	0.006	0.073
passRuleOf5FromNsc	0.069	0.002	0.050
patternComparison	0.836	0.324	1.157
plotCellMiner	0.751	0.251	1.002
plotDrugActivityRepeats	1.401	0.336	1.736
plotDrugSets	0.070	0.054	0.125
plotStructuresFromNscs	1.167	0.183	2.069
rcdkplot	0.099	0.013	0.107
removeMolDataType	0.001	0.000	0.001
restrictFeatureMat	0.002	0.000	0.001
runShinyComparePlots	0	0	0
runShinyCompareStructures	0.001	0.000	0.000
runShinyCompoundBrowser	0.001	0.000	0.001
selectCorrelatedRows	0.002	0.001	0.003
selectCorrelatedRows2	0.005	0.001	0.006