BioC 3.2: CHECK report for rcellminer on oaxaca

Package: rcellminer

Version: 1.2.3

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings rcellminer_1.2.3.tar.gz

StartedAt: 2016-04-23 03:35:13 -0700 (Sat, 23 Apr 2016)

EndedAt: 2016-04-23 03:38:41 -0700 (Sat, 23 Apr 2016)

EllapsedTime: 208.3 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_1.2.3.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/rcellminer.Rcheck’
* using R version 3.2.4 (2016-03-10)
* 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 ‘1.2.3’
* 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/14s] OK
* checking installed package size ... NOTE
  installed size is  8.0Mb
  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 ... [15s/18s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [104s/102s]
 [105s/103s] 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	2.144	0.152	3.971
crossCors	0.013	0.001	0.015
crossCorsSpearman	0.001	0.000	0.000
getActivityRangeStats	0.077	0.006	0.083
getColumnQuantiles	0.004	0.001	0.004
getDrugActivityData	0.014	0.001	0.016
getDrugActivityRange	0.021	0.001	0.023
getDrugActivityRepeatData	0.010	0.000	0.012
getDrugMoaList	0.060	0.006	0.108
getDrugName	0.006	0.001	0.006
getFeatureDataFromMatList	2.654	0.313	3.237
getFingerprintList	0.277	0.016	0.132
getMedSenLineActivity	0.067	0.007	0.028
getMinDrugActivityRepeatCor	0.047	0.002	0.017
getMoaStr	0.417	0.061	0.286
getMoaToCompounds	0.052	0.002	0.053
getMolDataMatrices	0.468	0.130	0.598
getMolDataType	0.001	0.001	0.001
getNumDrugActivityRepeats	0.021	0.001	0.023
getNumMissingLines	0.009	0.001	0.009
getRsd	0.009	0.001	0.009
getSmiles	0.007	0.001	0.008
hasMoa	0.059	0.004	0.062
isPublic	0.005	0.001	0.006
loadCellminerPlotInfo	0.003	0.000	0.003
loadNciColorSet	0.003	0.000	0.003
passRuleOf5	0.075	0.005	0.148
passRuleOf5FromNsc	0.058	0.001	0.044
patternComparison	0.342	0.065	0.406
plotCellMiner	0.909	0.200	2.144
plotDrugActivityRepeats	0.633	0.157	0.800
plotDrugSets	0.065	0.024	0.091
plotStructures	1.431	0.202	2.877
plotStructuresFromNscs	0.762	0.044	0.353
rcdkplot	0.266	0.007	0.099
removeMolDataType	0.002	0.000	0.001
restrictFeatureMat	0.006	0.001	0.002
rowCors	0.002	0.001	0.001
runShinyApp	0.001	0.000	0.000
runShinyComparePlots	0.002	0.000	0.001
runShinyCompareStructures	0.001	0.000	0.001
runShinyCompoundBrowser	0.006	0.000	0.002
searchForNscs	0.026	0.000	0.013
selectCorrelatedRows	0.004	0.001	0.002
selectCorrelatedRowsFromMatrices	0.019	0.001	0.007