BioC 3.2: CHECK report for rcellminer on oaxaca

Package: rcellminer

Version: 1.1.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings rcellminer_1.1.1.tar.gz

StartedAt: 2015-08-24 03:07:53 -0700 (Mon, 24 Aug 2015)

EndedAt: 2015-08-24 03:11:13 -0700 (Mon, 24 Aug 2015)

EllapsedTime: 200.2 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_1.1.1.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 ‘1.1.1’
* 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 ... [9s/12s] 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 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 ... 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 ... [13s/14s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [99s/102s]
 [99s/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	2.137	0.157	2.851
crossCors	0.013	0.002	0.015
crossCorsSpearman	0.001	0.000	0.001
getActivityRangeStats	0.070	0.007	0.077
getColumnQuantiles	0.003	0.000	0.004
getDrugActivityData	0.013	0.001	0.014
getDrugActivityRange	0.021	0.001	0.022
getDrugActivityRepeatData	0.013	0.001	0.013
getDrugMoaList	0.013	0.001	0.014
getDrugName	0.005	0.001	0.006
getFeatureDataFromMatList	2.635	0.305	3.126
getFingerprintList	0.290	0.018	0.156
getMedSenLineActivity	0.057	0.006	0.026
getMinDrugActivityRepeatCor	0.055	0.001	0.021
getMoaStr	0.024	0.000	0.009
getMoaToCompounds	0.017	0.000	0.009
getMolDataMatrices	0.441	0.135	0.508
getMolDataType	0.001	0.000	0.001
getNumDrugActivityRepeats	0.021	0.001	0.024
getNumMissingLines	0.007	0.001	0.011
getRsd	0.008	0.000	0.009
getSmiles	0.006	0.001	0.009
hasMoa	0.009	0.001	0.011
isPublic	0.004	0.001	0.005
loadNciColorSet	0.002	0.000	0.002
passRuleOf5	0.080	0.005	0.277
passRuleOf5FromNsc	0.057	0.001	0.045
patternComparison	0.465	0.162	0.620
plotCellMiner	0.366	0.106	0.474
plotDrugActivityRepeats	0.739	0.172	0.912
plotDrugSets	0.065	0.028	0.095
plotStructuresFromNscs	1.223	0.115	2.238
rcdkplot	0.083	0.006	0.088
removeMolDataType	0.001	0.000	0.001
restrictFeatureMat	0.002	0.000	0.002
runShinyComparePlots	0.001	0.000	0.001
runShinyCompareStructures	0.001	0.000	0.001
runShinyCompoundBrowser	0.001	0.000	0.000
selectCorrelatedRows	0.002	0.001	0.002
selectCorrelatedRows2	0.005	0.001	0.006