BioC 3.6: CHECK report for bioassayR on veracruz1

Package: bioassayR

Version: 1.15.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings bioassayR_1.15.0.tar.gz

StartedAt: 2017-08-16 00:21:42 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 00:23:12 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 89.9 seconds

RetCode: 0

Status:  OK

CheckDir: bioassayR.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings bioassayR_1.15.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/bioassayR.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.15.0’
* 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 ... OK
* 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 line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... 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: OK

* 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	0.169	0.001	0.172
activeTargets	0.053	0.001	0.057
addBioassayIndex	0.013	0.004	0.017
addDataSource	0.033	0.005	0.039
allCids	0.004	0.000	0.005
allTargets	0.006	0.001	0.006
assaySetTargets	0.141	0.007	0.150
bioactivityFingerprint	0.163	0.001	0.176
bioassay-class	0.015	0.002	0.018
bioassaySet-class	0.001	0.001	0.002
connectBioassayDB	0.010	0.002	0.013
crossReactivityProbability	0.289	0.002	0.305
disconnectBioassayDB	0.008	0.002	0.010
dropBioassay	0.163	0.004	0.172
dropBioassayIndex	0.021	0.005	0.027
getAssay	0.019	0.001	0.019
getAssays	0.054	0.001	0.059
getBioassaySetByCids	0.167	0.001	0.180
inactiveTargets	0.009	0.001	0.008
loadBioassay	0.229	0.004	0.242
loadIdMapping	0.008	0.001	0.009
newBioassayDB	0.006	0.001	0.007
parsePubChemBioassay	0.015	0.001	0.015
perTargetMatrix	0.177	0.001	0.183
queryBioassayDB	0.030	0.012	0.042
samplebioassay	0.002	0.001	0.004
scaleBioassaySet	0.031	0.002	0.033
screenedAtLeast	0.009	0.000	0.010
selectiveAgainst	0.080	0.001	0.083
targetSelectivity	0.118	0.001	0.123
translateTargetId	0.012	0.003	0.014
trinarySimilarity	0.186	0.001	0.189