BioC 3.4: CHECK report for bioassayR on morelia

Package: bioassayR

Version: 1.12.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings bioassayR_1.12.1.tar.gz

StartedAt: 2017-04-14 23:08:23 -0700 (Fri, 14 Apr 2017)

EndedAt: 2017-04-14 23:09:50 -0700 (Fri, 14 Apr 2017)

EllapsedTime: 86.7 seconds

RetCode: 0

Status:  OK

CheckDir: bioassayR.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 bioassayR_1.12.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/bioassayR.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘bioassayR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘bioassayR’ version ‘1.12.1’
* 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 ‘bioassayR’ can be installed ... 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
crossReactivityPrior: no visible global function definition for ‘sd’
crossReactivityProbability : <anonymous>: no visible global function
  definition for ‘pbeta’
Undefined global functions or variables:
  pbeta sd
Consider adding
  importFrom("stats", "pbeta", "sd")
to your NAMESPACE file.
* 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 ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 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-3.4-bioc/meat/bioassayR.Rcheck/00check.log’
for details.

* installing *source* package ‘bioassayR’ ...
** R
** data
** inst
** preparing package for lazy loading
Creating a new generic function for ‘organism’ in package ‘bioassayR’
Creating a new generic function for ‘organism<-’ in package ‘bioassayR’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (bioassayR)

name	user	system	elapsed
BioAssayDB-class	0.001	0.000	0.001
activeAgainst	0.015	0.001	0.017
activeTargets	0.012	0.001	0.014
addBioassayIndex	0.017	0.005	0.025
addDataSource	0.027	0.004	0.033
allCids	0.005	0.001	0.005
allTargets	0.005	0.000	0.005
assaySetTargets	0.045	0.000	0.045
bioactivityFingerprint	0.248	0.002	0.250
bioassay-class	0.022	0.003	0.025
bioassaySet-class	0.001	0.001	0.001
connectBioassayDB	0.013	0.002	0.017
crossReactivityProbability	0.280	0.001	0.282
disconnectBioassayDB	0.012	0.003	0.014
dropBioassay	0.055	0.007	0.069
dropBioassayIndex	0.028	0.009	0.041
getAssay	0.010	0.001	0.012
getAssays	0.032	0.000	0.034
getBioassaySetByCids	0.242	0.001	0.244
inactiveTargets	0.010	0.001	0.011
loadBioassay	0.037	0.004	0.042
loadIdMapping	0.015	0.004	0.021
newBioassayDB	0.008	0.002	0.011
parsePubChemBioassay	0.020	0.000	0.021
perTargetMatrix	0.298	0.001	0.300
queryBioassayDB	0.024	0.011	0.035
samplebioassay	0.003	0.001	0.005
scaleBioassaySet	0.043	0.001	0.044
screenedAtLeast	0.017	0.001	0.018
selectiveAgainst	0.171	0.004	0.175
targetSelectivity	0.033	0.001	0.035
translateTargetId	0.014	0.002	0.019
trinarySimilarity	0.283	0.001	0.284