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CHECK report for bioassayR on malbec1

This page was generated on 2021-05-06 12:26:58 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the bioassayR package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 151/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
bioassayR 1.28.3  (landing page)
Daniela Cassol
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/bioassayR
Branch: RELEASE_3_12
Last Commit: bc3e252
Last Changed Date: 2021-04-18 15:15:48 -0400 (Sun, 18 Apr 2021)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: bioassayR
Version: 1.28.3
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:bioassayR.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings bioassayR_1.28.3.tar.gz
StartedAt: 2021-05-05 23:24:03 -0400 (Wed, 05 May 2021)
EndedAt: 2021-05-05 23:25:37 -0400 (Wed, 05 May 2021)
EllapsedTime: 94.2 seconds
RetCode: 0
Status:   OK  
CheckDir: bioassayR.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:bioassayR.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings bioassayR_1.28.3.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/bioassayR.Rcheck’
* using R version 4.0.5 (2021-03-31)
* 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 ‘1.28.3’
* 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:
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###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL bioassayR
###
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* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* installing *source* package ‘bioassayR’ ...
** using staged installation
** 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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (bioassayR)

Tests output

bioassayR.Rcheck/tests/testthat.Rout


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 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: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, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min


Attaching package: 'bioassayR'

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

    organism, organism<-

> 
> test_check("bioassayR")
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 22 ]
> 
> proc.time()
   user  system elapsed 
  4.888   0.148   5.044 

Example timings

bioassayR.Rcheck/bioassayR-Ex.timings

nameusersystemelapsed
BioAssayDB-class0.0000.0000.001
activeAgainst0.0360.0000.160
activeTargets0.0520.0080.061
addBioassayIndex0.0120.0080.021
addDataSource0.0240.0000.023
allCids0.0080.0000.008
allTargets0.0040.0000.007
assaySetTargets0.0600.0040.065
bioactivityFingerprint0.2080.0120.219
bioassay-class0.0080.0080.016
bioassaySet-class0.0000.0000.001
connectBioassayDB0.0080.0000.010
crossReactivityProbability0.1320.0040.136
disconnectBioassayDB0.0120.0000.010
dropBioassay0.0520.0040.260
dropBioassayIndex0.0320.0040.033
getAssay0.0080.0000.010
getAssays0.0280.0000.026
getBioassaySetByCids0.2120.0000.212
inactiveTargets0.0080.0000.008
loadBioassay0.0280.0040.030
loadIdMapping0.0120.0000.011
newBioassayDB0.0040.0040.009
parsePubChemBioassay0.0120.0000.009
perTargetMatrix0.1960.0080.204
queryBioassayDB0.0200.0080.029
samplebioassay0.0040.0000.002
scaleBioassaySet0.0360.0040.039
screenedAtLeast0.0120.0000.013
selectiveAgainst0.1440.0040.149
targetSelectivity0.0280.0000.026
translateTargetId0.0160.0040.022
trinarySimilarity0.1440.0040.150