BioC 3.2: CHECK report for rcellminer on perceval

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 11:30:10 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 11:33:22 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 192.2 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 Patched (2015-10-08 r69496)
* 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 ‘1.2.1’
* 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 ... [10s/10s] OK
* checking installed package size ... NOTE
  installed size is  8.1Mb
  sub-directories of 1Mb or more:
    data   2.9Mb
    doc    4.6Mb
* 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 ... 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 ... [17s/20s] OK
Examples with CPU or elapsed time > 5s
                user system elapsed
plotStructures 1.428   0.27   5.073
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [100s/96s]
 [100s/96s] 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	2.551	0.228	3.613
crossCors	0.012	0.002	0.014
crossCorsSpearman	0.001	0.000	0.000
getActivityRangeStats	0.064	0.008	0.071
getColumnQuantiles	0.003	0.001	0.004
getDrugActivityData	0.012	0.002	0.013
getDrugActivityRange	0.021	0.002	0.023
getDrugActivityRepeatData	0.011	0.001	0.011
getDrugMoaList	0.062	0.008	0.070
getDrugName	0.004	0.001	0.005
getFeatureDataFromMatList	3.115	0.425	3.619
getFingerprintList	0.218	0.015	0.096
getMedSenLineActivity	0.043	0.011	0.019
getMinDrugActivityRepeatCor	0.061	0.007	0.022
getMoaStr	0.615	0.113	0.336
getMoaToCompounds	0.053	0.000	0.053
getMolDataMatrices	0.486	0.177	0.662
getMolDataType	0.001	0.000	0.001
getNumDrugActivityRepeats	0.020	0.002	0.022
getNumMissingLines	0.004	0.001	0.005
getRsd	0.011	0.001	0.012
getSmiles	0.004	0.001	0.005
hasMoa	0.058	0.002	0.060
isPublic	0.003	0.000	0.003
loadCellminerPlotInfo	0.002	0.000	0.002
loadNciColorSet	0.002	0.000	0.002
passRuleOf5	0.066	0.004	0.115
passRuleOf5FromNsc	0.066	0.001	0.044
patternComparison	0.334	0.081	0.411
plotCellMiner	0.911	0.282	1.189
plotDrugActivityRepeats	0.673	0.212	0.885
plotDrugSets	0.058	0.034	0.092
plotStructures	1.428	0.270	5.073
plotStructuresFromNscs	0.845	0.080	0.376
rcdkplot	0.258	0.017	0.097
removeMolDataType	0.001	0.000	0.001
restrictFeatureMat	0.003	0.000	0.002
rowCors	0.003	0.000	0.002
runShinyApp	0.010	0.000	0.001
runShinyComparePlots	0.001	0.000	0.001
runShinyCompareStructures	0.002	0.000	0.000
runShinyCompoundBrowser	0.002	0.000	0.001
searchForNscs	0.026	0.000	0.010
selectCorrelatedRows	0.007	0.001	0.002
selectCorrelatedRowsFromMatrices	0.021	0.003	0.007