Package: bioassayR

Version: 1.20.1

Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:bioassayR.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings bioassayR_1.20.1.tar.gz

StartedAt: 2019-04-15 22:26:29 -0400 (Mon, 15 Apr 2019)

EndedAt: 2019-04-15 22:27:50 -0400 (Mon, 15 Apr 2019)

EllapsedTime: 80.4 seconds

RetCode: 0

Status:  OK

CheckDir: bioassayR.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:bioassayR.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings bioassayR_1.20.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/bioassayR.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.20.1’
* 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 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 include directives in Makefiles ... 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

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL bioassayR
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘bioassayR’ ...
** R
** data
** inst
** byte-compile and prepare 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)

R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(bioassayR)
Loading required package: DBI
Loading required package: RSQLite
Loading required package: Matrix
Loading required package: rjson
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:Matrix':

    colMeans, colSums, rowMeans, rowSums, which

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min


Attaching package: 'bioassayR'

The following objects are masked from 'package:BiocGenerics':

    organism, organism<-

> 
> test_check("bioassayR")
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 24 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  5.548   0.172   5.746 

name	user	system	elapsed
BioAssayDB-class	0.000	0.000	0.001
activeAgainst	0.024	0.004	0.041
activeTargets	0.056	0.000	0.054
addBioassayIndex	0.016	0.000	0.017
addDataSource	0.020	0.000	0.021
allCids	0.008	0.000	0.006
allTargets	0.004	0.000	0.006
assaySetTargets	0.052	0.000	0.054
bioactivityFingerprint	0.22	0.00	0.22
bioassay-class	0.004	0.008	0.016
bioassaySet-class	0	0	0
connectBioassayDB	0.012	0.000	0.012
crossReactivityProbability	0.212	0.000	0.211
disconnectBioassayDB	0.012	0.000	0.014
dropBioassay	0.072	0.000	0.117
dropBioassayIndex	0.028	0.000	0.028
getAssay	0.008	0.000	0.008
getAssays	0.024	0.000	0.024
getBioassaySetByCids	0.184	0.000	0.184
inactiveTargets	0.008	0.000	0.009
loadBioassay	0.040	0.000	0.041
loadIdMapping	0.012	0.004	0.014
newBioassayDB	0.004	0.008	0.011
parsePubChemBioassay	0.012	0.000	0.013
perTargetMatrix	0.232	0.000	0.230
queryBioassayDB	0.032	0.000	0.033
samplebioassay	0.004	0.000	0.002
scaleBioassaySet	0.032	0.004	0.034
screenedAtLeast	0.012	0.000	0.013
selectiveAgainst	0.1	0.0	0.1
targetSelectivity	0.024	0.004	0.025
translateTargetId	0.016	0.000	0.016
trinarySimilarity	0.216	0.004	0.226