BioC 3.5: CHECK report for bioassayR on oaxaca

Package: bioassayR

Version: 1.13.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings bioassayR_1.13.1.tar.gz

StartedAt: 2017-02-14 22:50:08 -0800 (Tue, 14 Feb 2017)

EndedAt: 2017-02-14 22:51:34 -0800 (Tue, 14 Feb 2017)

EllapsedTime: 86.1 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_1.13.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/bioassayR.Rcheck’
* using R Under development (unstable) (2016-10-26 r71594)
* 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 ‘1.13.1’
* 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-3.5-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	0.012	0.001	0.014
activeTargets	0.007	0.001	0.007
addBioassayIndex	0.011	0.004	0.016
addDataSource	0.014	0.003	0.018
allCids	0.026	0.000	0.027
allTargets	0.007	0.001	0.009
assaySetTargets	0.051	0.001	0.053
bioactivityFingerprint	0.434	0.002	0.437
bioassay-class	0.006	0.002	0.008
bioassaySet-class	0.002	0.000	0.002
connectBioassayDB	0.011	0.002	0.013
crossReactivityProbability	0.157	0.001	0.158
disconnectBioassayDB	0.009	0.002	0.011
dropBioassay	0.048	0.008	0.058
dropBioassayIndex	0.022	0.013	0.038
getAssay	0.010	0.002	0.011
getAssays	0.028	0.003	0.031
getBioassaySetByCids	0.195	0.004	0.199
inactiveTargets	0.011	0.001	0.012
loadBioassay	0.039	0.004	0.045
loadIdMapping	0.010	0.003	0.013
newBioassayDB	0.010	0.002	0.013
parsePubChemBioassay	0.017	0.001	0.017
perTargetMatrix	0.325	0.001	0.326
queryBioassayDB	0.033	0.010	0.044
samplebioassay	0.003	0.001	0.004
scaleBioassaySet	0.040	0.001	0.041
screenedAtLeast	0.015	0.001	0.015
selectiveAgainst	0.098	0.002	0.100
targetSelectivity	0.025	0.001	0.026
translateTargetId	0.011	0.002	0.014
trinarySimilarity	0.282	0.002	0.284