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This page was generated on 2024-03-28 11:32:16 -0400 (Thu, 28 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson1macOS 13.6.1 Venturaarm644.3.3 (2024-02-29) -- "Angel Food Cake" 4376
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Package 166/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
bioassayR 1.40.0  (landing page)
Daniela Cassol
Snapshot Date: 2024-03-26 09:00:03 -0400 (Tue, 26 Mar 2024)
git_url: https://git.bioconductor.org/packages/bioassayR
git_branch: RELEASE_3_18
git_last_commit: 817e51d
git_last_commit_date: 2023-10-24 09:56:08 -0400 (Tue, 24 Oct 2023)
kjohnson1macOS 13.6.1 Ventura / arm64  OK    OK    ERROR    OK  

CHECK results for bioassayR on kjohnson1


To the developers/maintainers of the bioassayR package:
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: bioassayR
Version: 1.40.0
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_1.40.0.tar.gz
StartedAt: 2024-03-27 06:37:44 -0400 (Wed, 27 Mar 2024)
EndedAt: 2024-03-27 06:39:25 -0400 (Wed, 27 Mar 2024)
EllapsedTime: 100.9 seconds
RetCode: 1
Status:   ERROR  
CheckDir: bioassayR.Rcheck
Warnings: NA

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_1.40.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/bioassayR.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘bioassayR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘bioassayR’ version ‘1.40.0’
* 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 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’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  > 
  > test_check("bioassayR")
  [ FAIL 2 | WARN 1 | SKIP 0 | PASS 20 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test_perTargetMatrix.R:80:5'): numeric Z-score activesFirst matrix is correct ──
  as.matrix(targetMatrix) not equal to as.matrix(expectedTargetMatrix).
  Attributes: < Component "dimnames": Component 2: 2 string mismatches >
  ── Failure ('test_perTargetMatrix.R:96:5'): numeric Z-score mean matrix is correct ──
  as.matrix(targetMatrix) not equal to as.matrix(expectedTargetMatrix).
  Attributes: < Component "dimnames": Component 2: 2 string mismatches >
  
  [ FAIL 2 | WARN 1 | SKIP 0 | PASS 20 ]
  Error: Test failures
  Execution halted
* 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: 1 ERROR
See
  ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/bioassayR.Rcheck/00check.log’
for details.


Installation output

bioassayR.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/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.fail


R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (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, aperm, 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 2 | WARN 1 | SKIP 0 | PASS 20 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test_perTargetMatrix.R:80:5'): numeric Z-score activesFirst matrix is correct ──
as.matrix(targetMatrix) not equal to as.matrix(expectedTargetMatrix).
Attributes: < Component "dimnames": Component 2: 2 string mismatches >
── Failure ('test_perTargetMatrix.R:96:5'): numeric Z-score mean matrix is correct ──
as.matrix(targetMatrix) not equal to as.matrix(expectedTargetMatrix).
Attributes: < Component "dimnames": Component 2: 2 string mismatches >

[ FAIL 2 | WARN 1 | SKIP 0 | PASS 20 ]
Error: Test failures
Execution halted

Example timings

bioassayR.Rcheck/bioassayR-Ex.timings

nameusersystemelapsed
BioAssayDB-class0.0010.0010.001
activeAgainst0.0250.0030.028
activeTargets0.0320.0010.033
addBioassayIndex0.0160.0090.027
addDataSource0.0200.0080.031
allCids0.0060.0010.007
allTargets0.0050.0010.006
assaySetTargets0.3510.0030.356
bioactivityFingerprint0.1880.0030.194
bioassay-class0.0220.0060.029
bioassaySet-class0.0010.0010.001
connectBioassayDB0.0100.0040.014
crossReactivityProbability0.1760.0030.184
disconnectBioassayDB0.0140.0060.020
dropBioassay0.0400.0110.052
dropBioassayIndex0.0170.0110.028
getAssay0.0080.0020.009
getAssays0.0150.0030.018
getBioassaySetByCids0.1700.0030.174
inactiveTargets0.0100.0010.012
loadBioassay0.0270.0080.036
loadIdMapping0.0100.0050.015
newBioassayDB0.0070.0040.011
parsePubChemBioassay0.0120.0010.013
perTargetMatrix0.1940.0060.202
queryBioassayDB0.0210.0180.041
samplebioassay0.0020.0030.004
scaleBioassaySet0.0260.0040.032
screenedAtLeast0.0110.0020.013
selectiveAgainst0.0740.0070.081
targetSelectivity0.0180.0020.020
translateTargetId0.0140.0070.021
trinarySimilarity0.1790.0040.184