BioC 3.1: CHECK report for rcellminer on petty

Package: rcellminer

Version: 1.0.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings rcellminer_1.0.1.tar.gz

StartedAt: 2015-10-09 01:27:48 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 01:32:00 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 251.8 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_1.0.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.1-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 ‘1.0.1’
* 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 ... [12s/14s] OK
* checking installed package size ... NOTE
  installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   2.9Mb
    doc    2.0Mb
* 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/20s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [132s/131s]
 [132s/132s] 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.1-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	3.183	0.290	4.137
crossCors	0.020	0.003	0.022
crossCorsSpearman	0.001	0.000	0.001
getActivityRangeStats	0.094	0.010	0.104
getColumnQuantiles	0.005	0.001	0.005
getDrugActivityData	0.014	0.001	0.015
getDrugActivityRange	0.029	0.002	0.031
getDrugActivityRepeatData	0.015	0.001	0.016
getDrugMoaList	0.018	0.003	0.022
getDrugName	0.005	0.002	0.006
getFeatureDataFromMatList	3.896	0.527	4.553
getFingerprintList	0.290	0.016	0.130
getMedSenLineActivity	0.069	0.014	0.029
getMinDrugActivityRepeatCor	0.062	0.006	0.022
getMoaStr	0.039	0.003	0.015
getMoaToCompounds	0.037	0.004	0.013
getMolDataMatrices	0.782	0.234	0.650
getMolDataType	0.001	0.000	0.001
getNumDrugActivityRepeats	0.021	0.002	0.022
getNumMissingLines	0.005	0.001	0.006
getRsd	0.008	0.001	0.008
getSmiles	0.005	0.001	0.007
hasMoa	0.007	0.001	0.007
isPublic	0.005	0.001	0.006
loadNciColorSet	0.003	0.001	0.003
passRuleOf5	0.100	0.007	0.224
passRuleOf5FromNsc	0.086	0.002	0.071
patternComparison	0.609	0.240	0.849
plotCellMiner	0.516	0.209	0.725
plotDrugActivityRepeats	1.057	0.276	1.332
plotDrugSets	0.094	0.043	0.138
plotStructuresFromNscs	1.586	0.191	3.267
rcdkplot	0.122	0.010	0.127
removeMolDataType	0.001	0.000	0.001
restrictFeatureMat	0.002	0.000	0.002
runShinyComparePlots	0.001	0.001	0.001
runShinyCompareStructures	0.001	0.000	0.001
runShinyCompoundBrowser	0.001	0.000	0.001
selectCorrelatedRows	0.003	0.000	0.004
selectCorrelatedRows2	0.007	0.001	0.008