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This page was generated on 2021-11-30 13:55:44 -0500 (Tue, 30 Nov 2021).

CHECK results for ToxicoGx on merida1

To the developers/maintainers of the ToxicoGx package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ToxicoGx.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
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raw results

Package 1960/2068HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ToxicoGx 1.5.0  (landing page)
Benjamin Haibe-Kains
Snapshot Date: 2021-11-29 14:50:17 -0500 (Mon, 29 Nov 2021)
git_url: https://git.bioconductor.org/packages/ToxicoGx
git_branch: master
git_last_commit: 1422492
git_last_commit_date: 2021-10-26 13:00:37 -0500 (Tue, 26 Oct 2021)
nebbiolo1Linux (Ubuntu 20.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  NO, package depends on 'CoreGx' which is not available

Summary

Package: ToxicoGx
Version: 1.5.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ToxicoGx.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ToxicoGx_1.5.0.tar.gz
StartedAt: 2021-11-30 08:55:43 -0500 (Tue, 30 Nov 2021)
EndedAt: 2021-11-30 09:02:17 -0500 (Tue, 30 Nov 2021)
EllapsedTime: 394.3 seconds
RetCode: 0
Status:   OK  
CheckDir: ToxicoGx.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ToxicoGx.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ToxicoGx_1.5.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/ToxicoGx.Rcheck’
* using R Under development (unstable) (2021-11-01 r81125)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ToxicoGx/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ToxicoGx’ version ‘1.5.0’
* package encoding: UTF-8
* 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 ‘ToxicoGx’ 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 ... NOTE
computeLimmaDiffExpr,ToxicoSet: no visible global function definition
  for ‘metadata<-’
computeLimmaDiffExpr,ToxicoSet: no visible binding for global variable
  ‘cell’
Undefined global functions or variables:
  cell metadata<-
* 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 ... NOTE
  Note: found 47 marked UTF-8 strings
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                      user system elapsed
ToxicoSet-class      4.093  0.383   5.706
geneDrugPerturbation 4.052  0.068   5.054
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.15-bioc/meat/ToxicoGx.Rcheck/00check.log’
for details.



Installation output

ToxicoGx.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library’
* installing *source* package ‘ToxicoGx’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** byte-compile and prepare package for lazy loading
** 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 (ToxicoGx)

Tests output

ToxicoGx.Rcheck/tests/testthat.Rout


R Under development (unstable) (2021-11-01 r81125) -- "Unsuffered Consequences"
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(ToxicoGx)
Loading required package: CoreGx
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

Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

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

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'Biobase'

The following object is masked from 'package:MatrixGenerics':

    rowMedians

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

    anyMissing, rowMedians


Attaching package: 'ToxicoGx'

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

    curation, curation<-, datasetType, datasetType<-, sensitivityRaw,
    sensitivityRaw<-, sensitivitySlot, sensitivitySlot<-, showSigAnnot,
    subsetTo, summarizeMolecularProfiles, summarizeSensitivityProfiles,
    updateCellId

> test_check("ToxicoGx")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 53 ]
> 
> proc.time()
   user  system elapsed 
 21.194   0.960  27.477 

Example timings

ToxicoGx.Rcheck/ToxicoGx-Ex.timings

nameusersystemelapsed
ToxicoSet-class4.0930.3835.706
annotation-set0.1070.0150.155
annotation0.0990.0120.144
availableTSets0.0010.0000.000
checkTSetStructure0.1540.0150.207
computeAUC1.3000.0781.715
computeICn2.5420.0163.171
computeLimmaDiffExpr-ToxicoSet-method000
curation-set0.0920.0030.124
curation0.1030.0100.141
datasetType-set0.1050.0130.151
dim-ToxicoSet-method0.0920.0030.125
downloadTSet000
drugGeneResponseCurve0.0000.0000.001
drugInfo-set0.1050.0090.148
drugInfo0.0940.0090.138
drugNames-set0.1490.0160.218
drugNames0.1070.0130.165
drugPerturbationSig000
drugTimeResponseCurve0.2870.0050.401
geneDrugPerturbation4.0520.0685.054
logLogisticRegression1.3290.0061.717
mDataNames-ToxicoSet-method0.0010.0000.001
name-ToxicoSet-method0.0000.0010.001
sensitivityRaw-set0.0040.0040.013
sensitivityRaw0.1950.0520.322
show-ToxicoSet-method0.0110.0010.015
show-ToxicoSig-method0.5630.0220.739
showSigAnnot0.5240.0370.705
sub-ToxicoSet-ANY-ANY-ANY-method0.0620.0010.078
subsetTo0.0720.0000.088
summarizeMolecularProfiles2.3570.0282.856
summarizeSensitivityProfiles0.1130.0090.148
updateCellId0.1690.0130.214
updateDrugId0.1470.0060.179