BioC 3.2: CHECK report for rcellminer on zin1

Package: rcellminer

Version: 1.1.1

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings rcellminer_1.1.1.tar.gz

StartedAt: 2015-08-24 03:02:14 -0700 (Mon, 24 Aug 2015)

EndedAt: 2015-08-24 03:04:01 -0700 (Mon, 24 Aug 2015)

EllapsedTime: 107.1 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_1.1.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/rcellminer.Rcheck’
* using R version 3.2.2 (2015-08-14)
* 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 ‘1.1.1’
* 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 ... [6s/6s] OK
* checking installed package size ... OK
* 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 ... [10s/9s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [52s/51s]
 [53s/51s] 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	2.063	0.041	1.996
crossCors	0.009	0.000	0.009
crossCorsSpearman	0.000	0.000	0.001
getActivityRangeStats	0.050	0.000	0.054
getColumnQuantiles	0.003	0.000	0.005
getDrugActivityData	0.009	0.000	0.010
getDrugActivityRange	0.012	0.004	0.019
getDrugActivityRepeatData	0.008	0.000	0.012
getDrugMoaList	0.008	0.000	0.011
getDrugName	0.004	0.000	0.003
getFeatureDataFromMatList	2.354	0.099	2.609
getFingerprintList	0.243	0.004	0.134
getMedSenLineActivity	0.046	0.000	0.032
getMinDrugActivityRepeatCor	0.027	0.000	0.011
getMoaStr	0.018	0.000	0.006
getMoaToCompounds	0.011	0.000	0.005
getMolDataMatrices	0.280	0.028	0.248
getMolDataType	0.000	0.000	0.001
getNumDrugActivityRepeats	0.011	0.000	0.012
getNumMissingLines	0.003	0.000	0.003
getRsd	0.005	0.000	0.006
getSmiles	0.003	0.000	0.002
hasMoa	0.006	0.000	0.006
isPublic	0.002	0.000	0.002
loadNciColorSet	0.001	0.000	0.001
passRuleOf5	0.094	0.008	0.105
passRuleOf5FromNsc	0.048	0.000	0.049
patternComparison	0.358	0.016	0.374
plotCellMiner	0.272	0.016	0.294
plotDrugActivityRepeats	0.585	0.016	0.601
plotDrugSets	0.034	0.000	0.034
plotStructuresFromNscs	0.941	0.033	1.049
rcdkplot	0.075	0.004	0.072
removeMolDataType	0.001	0.000	0.001
restrictFeatureMat	0.001	0.000	0.001
runShinyComparePlots	0.001	0.000	0.000
runShinyCompareStructures	0.000	0.000	0.001
runShinyCompoundBrowser	0	0	0
selectCorrelatedRows	0.002	0.000	0.002
selectCorrelatedRows2	0.004	0.000	0.003