BioC 3.2: CHECK report for rcellminer on oaxaca

Package: rcellminer

Version: 1.2.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings rcellminer_1.2.1.tar.gz

StartedAt: 2015-10-27 07:03:16 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 07:06:38 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 201.6 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_1.2.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/rcellminer.Rcheck’
* using R version 3.2.2 (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 ‘rcellminer/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘rcellminer’ version ‘1.2.1’
* 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 ... [9s/9s] OK
* checking installed package size ... NOTE
  installed size is  7.9Mb
  sub-directories of 1Mb or more:
    data   2.9Mb
    doc    4.5Mb
* 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 loading without being on the library search path ... 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 ... OK
* 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 ... [14s/15s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [101s/98s]
 [101s/99s] 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	2.072	0.152	2.686
crossCors	0.013	0.002	0.015
crossCorsSpearman	0	0	0
getActivityRangeStats	0.064	0.006	0.070
getColumnQuantiles	0.004	0.000	0.004
getDrugActivityData	0.012	0.001	0.014
getDrugActivityRange	0.021	0.001	0.024
getDrugActivityRepeatData	0.012	0.001	0.013
getDrugMoaList	0.061	0.006	0.067
getDrugName	0.006	0.001	0.007
getFeatureDataFromMatList	2.606	0.301	3.032
getFingerprintList	0.210	0.009	0.094
getMedSenLineActivity	0.073	0.008	0.031
getMinDrugActivityRepeatCor	0.044	0.004	0.016
getMoaStr	0.459	0.056	0.273
getMoaToCompounds	0.051	0.001	0.053
getMolDataMatrices	0.441	0.122	0.564
getMolDataType	0.001	0.000	0.001
getNumDrugActivityRepeats	0.023	0.001	0.023
getNumMissingLines	0.007	0.001	0.008
getRsd	0.008	0.000	0.008
getSmiles	0.006	0.001	0.007
hasMoa	0.057	0.003	0.060
isPublic	0.003	0.000	0.004
loadCellminerPlotInfo	0.002	0.000	0.002
loadNciColorSet	0.002	0.000	0.002
passRuleOf5	0.070	0.004	0.130
passRuleOf5FromNsc	0.059	0.001	0.042
patternComparison	0.319	0.061	0.376
plotCellMiner	0.845	0.207	1.054
plotDrugActivityRepeats	0.600	0.143	0.742
plotDrugSets	0.060	0.025	0.086
plotStructures	1.361	0.200	2.162
plotStructuresFromNscs	0.831	0.050	0.373
rcdkplot	0.368	0.013	0.146
removeMolDataType	0.002	0.000	0.001
restrictFeatureMat	0.003	0.000	0.002
rowCors	0.001	0.001	0.001
runShinyApp	0.001	0.000	0.001
runShinyComparePlots	0.000	0.000	0.001
runShinyCompareStructures	0.000	0.000	0.001
runShinyCompoundBrowser	0.001	0.000	0.001
searchForNscs	0.019	0.000	0.010
selectCorrelatedRows	0.002	0.000	0.003
selectCorrelatedRowsFromMatrices	0.005	0.001	0.007