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This page was generated on 2022-06-24 12:05:30 -0400 (Fri, 24 Jun 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4380
palomino3Windows Server 2022 Datacenterx644.2.0 (2022-04-22 ucrt) -- "Vigorous Calisthenics" 4156
merida1macOS 10.14.6 Mojavex86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4221
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 ToxicoGx on nebbiolo1


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? 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 2028/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ToxicoGx 2.0.0  (landing page)
Benjamin Haibe-Kains
Snapshot Date: 2022-06-23 13:55:15 -0400 (Thu, 23 Jun 2022)
git_url: https://git.bioconductor.org/packages/ToxicoGx
git_branch: RELEASE_3_15
git_last_commit: 6150d7f
git_last_commit_date: 2022-04-26 12:06:13 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    NA  

Summary

Package: ToxicoGx
Version: 2.0.0
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:ToxicoGx.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings ToxicoGx_2.0.0.tar.gz
StartedAt: 2022-06-23 22:23:07 -0400 (Thu, 23 Jun 2022)
EndedAt: 2022-06-23 22:26:58 -0400 (Thu, 23 Jun 2022)
EllapsedTime: 231.1 seconds
RetCode: 0
Status:   OK  
CheckDir: ToxicoGx.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:ToxicoGx.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings ToxicoGx_2.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/ToxicoGx.Rcheck’
* using R version 4.2.0 (2022-04-22)
* using platform: x86_64-pc-linux-gnu (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 ‘2.0.0’
* 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 ... NOTE
':::' call which should be '::': ‘CoreGx:::updateSampleId’
  See the note in ?`:::` about the use of this operator.
Missing object imported by a ':::' call: ‘CoreGx:::updateTreamentId’
* 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
* 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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.15-bioc/meat/ToxicoGx.Rcheck/00check.log’
for details.



Installation output

ToxicoGx.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL ToxicoGx
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/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 version 4.2.0 (2022-04-22) -- "Vigorous Calisthenics"
Copyright (C) 2022 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(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':

    showSigAnnot, subsetTo, summarizeMolecularProfiles,
    summarizeSensitivityProfiles

> test_check("ToxicoGx")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 53 ]
> 
> proc.time()
   user  system elapsed 
 13.057   0.684  13.725 

Example timings

ToxicoGx.Rcheck/ToxicoGx-Ex.timings

nameusersystemelapsed
ToxicoSet-accessors1.4840.2881.772
availableTSets000
checkTSetStructure0.0890.0120.101
computeAUC0.7940.0720.866
computeICn1.5590.2521.811
computeLimmaDiffExpr-ToxicoSet-method0.0010.0000.000
dim-ToxicoSet-method0.0640.0160.079
downloadTSet0.0010.0000.000
drugGeneResponseCurve000
drugPerturbationSig000
drugTimeResponseCurve0.1740.0050.180
geneDrugPerturbation2.3860.1242.530
logLogisticRegression0.7790.1160.895
show-ToxicoSet-method0.0090.0000.009
show-ToxicoSig-method0.3060.0220.343
showSigAnnot0.2500.0320.280
sub-ToxicoSet-ANY-ANY-ANY-method0.0530.0000.053
subsetTo0.0420.0040.047
summarizeMolecularProfiles0.9150.0400.955
summarizeSensitivityProfiles0.0650.0000.065