BioC 3.2: CHECK report for rcellminer on zin1

Package: rcellminer

Version: 1.2.3

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings rcellminer_1.2.3.tar.gz

StartedAt: 2016-04-23 04:25:43 -0700 (Sat, 23 Apr 2016)

EndedAt: 2016-04-23 04:27:36 -0700 (Sat, 23 Apr 2016)

EllapsedTime: 112.3 seconds

RetCode: 0

Status:  OK

CheckDir: rcellminer.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings rcellminer_1.2.3.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/rcellminer.Rcheck’
* using R version 3.2.4 Revised (2016-03-16 r70336)
* using platform: x86_64-pc-linux-gnu (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 ... [6s/7s] OK
* checking installed package size ... NOTE
  installed size is  7.4Mb
  sub-directories of 1Mb or more:
    data   2.9Mb
    doc    3.8Mb
* 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 ... [11s/11s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [56s/54s]
 [56s/54s] 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
  ‘/home/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	2.028	0.053	2.643
crossCors	0.02	0.00	0.01
crossCorsSpearman	0.001	0.000	0.001
getActivityRangeStats	0.044	0.008	0.052
getColumnQuantiles	0.003	0.000	0.003
getDrugActivityData	0.011	0.000	0.011
getDrugActivityRange	0.016	0.000	0.016
getDrugActivityRepeatData	0.008	0.000	0.009
getDrugMoaList	0.051	0.008	0.059
getDrugName	0.001	0.004	0.004
getFeatureDataFromMatList	2.170	0.204	2.526
getFingerprintList	0.154	0.004	0.081
getMedSenLineActivity	0.018	0.004	0.011
getMinDrugActivityRepeatCor	0.021	0.000	0.011
getMoaStr	0.368	0.008	0.192
getMoaToCompounds	0.046	0.000	0.046
getMolDataMatrices	0.378	0.133	0.510
getMolDataType	0.000	0.000	0.001
getNumDrugActivityRepeats	0.012	0.000	0.012
getNumMissingLines	0.003	0.000	0.003
getRsd	0.006	0.000	0.006
getSmiles	0.003	0.000	0.003
hasMoa	0.051	0.000	0.051
isPublic	0.002	0.000	0.002
loadCellminerPlotInfo	0.002	0.000	0.002
loadNciColorSet	0.002	0.000	0.001
passRuleOf5	0.089	0.000	0.081
passRuleOf5FromNsc	0.054	0.000	0.040
patternComparison	0.231	0.024	0.255
plotCellMiner	0.632	0.020	0.650
plotDrugActivityRepeats	0.482	0.036	0.517
plotDrugSets	0.034	0.000	0.034
plotStructures	1.262	0.028	1.266
plotStructuresFromNscs	0.804	0.008	0.409
rcdkplot	0.131	0.004	0.074
removeMolDataType	0.001	0.000	0.001
restrictFeatureMat	0.003	0.000	0.001
rowCors	0.003	0.000	0.001
runShinyApp	0.001	0.000	0.001
runShinyComparePlots	0.001	0.000	0.000
runShinyCompareStructures	0.001	0.000	0.001
runShinyCompoundBrowser	0.001	0.000	0.000
searchForNscs	0.007	0.000	0.007
selectCorrelatedRows	0.002	0.000	0.002
selectCorrelatedRowsFromMatrices	0.005	0.000	0.004