BioC 3.5: CHECK report for bioassayR on veracruz2

Package: bioassayR

Version: 1.14.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings bioassayR_1.14.0.tar.gz

StartedAt: 2017-10-18 00:56:12 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 00:57:41 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 88.2 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_1.14.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/bioassayR.Rcheck’
* using R version 3.4.2 (2017-09-28)
* 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 ‘1.14.0’
* 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	0.002	0.000	0.002
activeAgainst	0.028	0.002	0.031
activeTargets	0.205	0.002	0.211
addBioassayIndex	0.015	0.004	0.021
addDataSource	0.038	0.005	0.046
allCids	0.007	0.001	0.008
allTargets	0.006	0.001	0.006
assaySetTargets	0.167	0.014	0.187
bioactivityFingerprint	0.188	0.002	0.195
bioassay-class	0.019	0.003	0.023
bioassaySet-class	0.001	0.000	0.001
connectBioassayDB	0.014	0.004	0.019
crossReactivityProbability	0.306	0.003	0.324
disconnectBioassayDB	0.008	0.002	0.010
dropBioassay	0.146	0.006	0.158
dropBioassayIndex	0.024	0.006	0.031
getAssay	0.019	0.001	0.020
getAssays	0.062	0.001	0.064
getBioassaySetByCids	0.175	0.002	0.182
inactiveTargets	0.008	0.001	0.009
loadBioassay	0.247	0.006	0.264
loadIdMapping	0.009	0.002	0.011
newBioassayDB	0.008	0.002	0.011
parsePubChemBioassay	0.015	0.001	0.016
perTargetMatrix	0.197	0.002	0.204
queryBioassayDB	0.029	0.011	0.041
samplebioassay	0.002	0.001	0.004
scaleBioassaySet	0.038	0.001	0.040
screenedAtLeast	0.016	0.000	0.017
selectiveAgainst	0.089	0.001	0.093
targetSelectivity	0.131	0.001	0.132
translateTargetId	0.012	0.002	0.015
trinarySimilarity	0.202	0.001	0.218