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CHECK report for bioassayR on malbec1

This page was generated on 2019-04-16 11:50:14 -0400 (Tue, 16 Apr 2019).

Package 129/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
bioassayR 1.20.1
Tyler Backman
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/bioassayR
Branch: RELEASE_3_8
Last Commit: 022717e
Last Changed Date: 2019-01-04 13:20:39 -0400 (Fri, 04 Jan 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

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

Command output

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### Running 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
###
##############################################################################
##############################################################################


* 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


Installation output

bioassayR.Rcheck/00install.out

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###
### Running command:
###
###   /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)

Tests output

bioassayR.Rcheck/tests/testthat.Rout


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 

Example timings

bioassayR.Rcheck/bioassayR-Ex.timings

nameusersystemelapsed
BioAssayDB-class0.0000.0000.001
activeAgainst0.0240.0040.041
activeTargets0.0560.0000.054
addBioassayIndex0.0160.0000.017
addDataSource0.0200.0000.021
allCids0.0080.0000.006
allTargets0.0040.0000.006
assaySetTargets0.0520.0000.054
bioactivityFingerprint0.220.000.22
bioassay-class0.0040.0080.016
bioassaySet-class000
connectBioassayDB0.0120.0000.012
crossReactivityProbability0.2120.0000.211
disconnectBioassayDB0.0120.0000.014
dropBioassay0.0720.0000.117
dropBioassayIndex0.0280.0000.028
getAssay0.0080.0000.008
getAssays0.0240.0000.024
getBioassaySetByCids0.1840.0000.184
inactiveTargets0.0080.0000.009
loadBioassay0.0400.0000.041
loadIdMapping0.0120.0040.014
newBioassayDB0.0040.0080.011
parsePubChemBioassay0.0120.0000.013
perTargetMatrix0.2320.0000.230
queryBioassayDB0.0320.0000.033
samplebioassay0.0040.0000.002
scaleBioassaySet0.0320.0040.034
screenedAtLeast0.0120.0000.013
selectiveAgainst0.10.00.1
targetSelectivity0.0240.0040.025
translateTargetId0.0160.0000.016
trinarySimilarity0.2160.0040.226