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CHECK report for bioassayR on merida1

This page was generated on 2021-01-22 11:57:46 -0500 (Fri, 22 Jan 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 1.28.0
Tyler Backman
Snapshot Date: 2021-01-21 14:42:12 -0500 (Thu, 21 Jan 2021)
URL: https://git.bioconductor.org/packages/bioassayR
Branch: RELEASE_3_12
Last Commit: 490f2c7
Last Changed Date: 2020-10-27 10:53:10 -0500 (Tue, 27 Oct 2020)
malbec1 Linux (Ubuntu 18.04.5 LTS) / x86_64  OK  OK  ERROR 
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  ERROR 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  ERROR  OK 
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK [ ERROR ] OK 

Summary

Package: bioassayR
Version: 1.28.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:bioassayR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings bioassayR_1.28.0.tar.gz
StartedAt: 2021-01-21 23:26:08 -0500 (Thu, 21 Jan 2021)
EndedAt: 2021-01-21 23:28:17 -0500 (Thu, 21 Jan 2021)
EllapsedTime: 129.3 seconds
RetCode: 1
Status:  ERROR 
CheckDir: bioassayR.Rcheck
Warnings: NA

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:bioassayR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings bioassayR_1.28.0.tar.gz
###
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##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/bioassayR.Rcheck’
* using R version 4.0.3 (2020-10-10)
* 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 ‘1.28.0’
* 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:
  Error: no method or default for coercing "ldiMatrix" to "lgCMatrix"
  Backtrace:
      █
   1. ├─methods::new(...) test_scaleBioassaySet.R:18:0
   2. │ ├─methods::initialize(value, ...)
   3. │ └─methods::initialize(value, ...)
   4. └─methods::as(Matrix(sparse = T), "dgCMatrix")
   5.   └─Matrix:::asMethod(object)
   6.     ├─methods::as(as(from, "lgCMatrix"), "dgCMatrix")
   7.     │ └─methods:::.class1(object)
   8.     └─methods::as(from, "lgCMatrix")
  
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 21 ]
  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-3.12-bioc/meat/bioassayR.Rcheck/00check.log’
for details.


Installation output

bioassayR.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/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 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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
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")
══ Warnings ════════════════════════════════════════════════════════════════════
── Warning (test_bioactivityFingerprint.R:16:5): example matrix is correct ─────
RSQLite::dbGetPreparedQuery() is deprecated, please switch to DBI::dbGetQuery(params = bind.data).
Backtrace:
 1. bioassayR::getBioassaySetByCids(sampleDB, queryCids) test_bioactivityFingerprint.R:16:4
 2. bioassayR:::.activityByCids(database, cids)
 4. RSQLite::dbGetPreparedQuery(con, sql, bind.data = data.frame(CID = cids))
 5. RSQLite:::warning_once("RSQLite::dbGetPreparedQuery() is deprecated, please switch to DBI::dbGetQuery(params = bind.data).")
 7. RSQLite:::`_f`(... = ...)

══ Failed tests ════════════════════════════════════════════════════════════════
── Error (test_scaleBioassaySet.R:18:1): (code run outside of `test_that()`) ───
Error: no method or default for coercing "ldiMatrix" to "lgCMatrix"
Backtrace:
    █
 1. ├─methods::new(...) test_scaleBioassaySet.R:18:0
 2. │ ├─methods::initialize(value, ...)
 3. │ └─methods::initialize(value, ...)
 4. └─methods::as(Matrix(sparse = T), "dgCMatrix")
 5.   └─Matrix:::asMethod(object)
 6.     ├─methods::as(as(from, "lgCMatrix"), "dgCMatrix")
 7.     │ └─methods:::.class1(object)
 8.     └─methods::as(from, "lgCMatrix")

[ FAIL 1 | WARN 1 | SKIP 0 | PASS 21 ]
Error: Test failures
Execution halted

Example timings

bioassayR.Rcheck/bioassayR-Ex.timings

nameusersystemelapsed
BioAssayDB-class0.0020.0000.002
activeAgainst0.0380.0020.045
activeTargets0.2500.0010.253
addBioassayIndex0.0210.0090.032
addDataSource0.0220.0060.029
allCids0.0050.0010.006
allTargets0.0060.0010.007
assaySetTargets0.0650.0020.067
bioactivityFingerprint0.2330.0050.240
bioassay-class0.0240.0070.031
bioassaySet-class0.0010.0010.002
connectBioassayDB0.0150.0060.021
crossReactivityProbability0.1940.0050.200
disconnectBioassayDB0.0140.0060.027
dropBioassay0.0610.0180.175
dropBioassayIndex0.0380.0230.064
getAssay0.0100.0020.012
getAssays0.0290.0040.033
getBioassaySetByCids0.2090.0040.213
inactiveTargets0.0100.0010.010
loadBioassay0.0440.0130.064
loadIdMapping0.0170.0070.025
newBioassayDB0.0130.0050.019
parsePubChemBioassay0.0140.0020.017
perTargetMatrix0.2540.0080.263
queryBioassayDB0.0320.0310.064
samplebioassay0.0030.0030.005
scaleBioassaySet0.0400.0070.046
screenedAtLeast0.0130.0020.014
selectiveAgainst0.0920.0090.102
targetSelectivity0.0270.0030.033
translateTargetId0.0160.0080.024
trinarySimilarity0.2050.0060.211