Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-01-17 13:07:20 -0500 (Mon, 17 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4328
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4077
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4138
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for bioassayR on machv2


To the developers/maintainers of the bioassayR package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/bioassayR.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 151/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
bioassayR 1.32.1  (landing page)
Daniela Cassol
Snapshot Date: 2022-01-16 01:55:05 -0500 (Sun, 16 Jan 2022)
git_url: https://git.bioconductor.org/packages/bioassayR
git_branch: RELEASE_3_14
git_last_commit: 05a9464
git_last_commit_date: 2021-12-04 14:55:17 -0500 (Sat, 04 Dec 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: bioassayR
Version: 1.32.1
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:bioassayR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings bioassayR_1.32.1.tar.gz
StartedAt: 2022-01-16 10:33:52 -0500 (Sun, 16 Jan 2022)
EndedAt: 2022-01-16 10:35:55 -0500 (Sun, 16 Jan 2022)
EllapsedTime: 123.3 seconds
RetCode: 0
Status:   OK  
CheckDir: bioassayR.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:bioassayR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings bioassayR_1.32.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/bioassayR.Rcheck’
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-apple-darwin17.0 (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 ‘1.32.1’
* 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

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL bioassayR
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/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 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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

Attaching package: 'BiocGenerics'

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 
  6.553   0.421   6.965 

Example timings

bioassayR.Rcheck/bioassayR-Ex.timings

nameusersystemelapsed
BioAssayDB-class0.0010.0010.002
activeAgainst0.0340.0030.038
activeTargets0.0700.0010.071
addBioassayIndex0.0200.0090.030
addDataSource0.0240.0070.030
allCids0.0070.0010.008
allTargets0.0080.0010.009
assaySetTargets0.1120.0040.116
bioactivityFingerprint0.2830.0030.287
bioassay-class0.0210.0060.027
bioassaySet-class0.0010.0010.001
connectBioassayDB0.0150.0060.021
crossReactivityProbability0.2420.0030.245
disconnectBioassayDB0.0170.0050.022
dropBioassay0.0640.0140.079
dropBioassayIndex0.0360.0190.055
getAssay0.0100.0020.011
getAssays0.0300.0020.031
getBioassaySetByCids0.2550.0020.258
inactiveTargets0.0100.0010.011
loadBioassay0.0430.0090.052
loadIdMapping0.0170.0060.022
newBioassayDB0.0100.0040.014
parsePubChemBioassay0.0100.0010.011
perTargetMatrix0.2240.0020.227
queryBioassayDB0.0250.0240.049
samplebioassay0.0020.0020.003
scaleBioassaySet0.0420.0030.046
screenedAtLeast0.0110.0010.012
selectiveAgainst0.2270.0040.230
targetSelectivity0.0240.0020.027
translateTargetId0.0190.0060.025
trinarySimilarity0.1850.0010.187