BioC 3.4: CHECK report for bioassayR on malbec1

Package: bioassayR

Version: 1.12.1

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings bioassayR_1.12.1.tar.gz

StartedAt: 2017-04-14 21:11:51 -0400 (Fri, 14 Apr 2017)

EndedAt: 2017-04-14 21:13:10 -0400 (Fri, 14 Apr 2017)

EllapsedTime: 78.6 seconds

RetCode: 0

Status:  OK

CheckDir: bioassayR.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings bioassayR_1.12.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/bioassayR.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-pc-linux-gnu (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
  ‘/home/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	0.000	0.000	0.001
activeAgainst	0.008	0.000	0.009
activeTargets	0.008	0.000	0.009
addBioassayIndex	0.012	0.000	0.011
addDataSource	0.016	0.000	0.014
allCids	0.008	0.004	0.011
allTargets	0.004	0.000	0.004
assaySetTargets	0.032	0.000	0.033
bioactivityFingerprint	0.176	0.000	0.174
bioassay-class	0.016	0.000	0.015
bioassaySet-class	0.000	0.000	0.001
connectBioassayDB	0.008	0.000	0.008
crossReactivityProbability	0.144	0.000	0.146
disconnectBioassayDB	0.008	0.000	0.008
dropBioassay	0.036	0.000	0.036
dropBioassayIndex	0.016	0.000	0.018
getAssay	0.004	0.000	0.006
getAssays	0.020	0.000	0.019
getBioassaySetByCids	0.128	0.000	0.130
inactiveTargets	0.008	0.000	0.006
loadBioassay	0.028	0.000	0.027
loadIdMapping	0.008	0.000	0.010
newBioassayDB	0.004	0.000	0.007
parsePubChemBioassay	0.008	0.000	0.011
perTargetMatrix	0.156	0.000	0.158
queryBioassayDB	0.020	0.000	0.017
samplebioassay	0.004	0.000	0.002
scaleBioassaySet	0.024	0.000	0.025
screenedAtLeast	0.008	0.004	0.010
selectiveAgainst	0.084	0.000	0.084
targetSelectivity	0.016	0.000	0.016
translateTargetId	0.012	0.000	0.010
trinarySimilarity	0.14	0.00	0.14