Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-01-26 13:05:43 -0500 (Wed, 26 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4329
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4080
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4141
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 NewWave on nebbiolo2


To the developers/maintainers of the NewWave package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/NewWave.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 1294/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
NewWave 1.4.0  (landing page)
Federico Agostinis
Snapshot Date: 2022-01-25 01:55:07 -0500 (Tue, 25 Jan 2022)
git_url: https://git.bioconductor.org/packages/NewWave
git_branch: RELEASE_3_14
git_last_commit: b524b24
git_last_commit_date: 2021-10-26 13:05:00 -0500 (Tue, 26 Oct 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    OK    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: NewWave
Version: 1.4.0
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:NewWave.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings NewWave_1.4.0.tar.gz
StartedAt: 2022-01-25 08:45:03 -0500 (Tue, 25 Jan 2022)
EndedAt: 2022-01-25 08:47:55 -0500 (Tue, 25 Jan 2022)
EllapsedTime: 172.4 seconds
RetCode: 0
Status:   OK  
CheckDir: NewWave.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:NewWave.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings NewWave_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/NewWave.Rcheck’
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘NewWave/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘NewWave’ version ‘1.4.0’
* 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 ‘NewWave’ 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 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

NewWave.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL NewWave
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’
* installing *source* package ‘NewWave’ ...
** using staged installation
** R
** 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 (NewWave)

Tests output

NewWave.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-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(NewWave)
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: 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: 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

> Sys.setenv("R_TESTS" = "")
> test_check("NewWave")
Time of setup
   user  system elapsed 
  0.013   0.000   0.280 
Time of initialization
   user  system elapsed 
  0.004   0.000   0.151 
Time of dispersion optimization
   user  system elapsed 
  0.002   0.000   0.003 
Time of right optimization
   user  system elapsed 
  0.002   0.000   0.088 
Time of left optimization
   user  system elapsed 
  0.001   0.000   0.013 
Time of dispersion optimization
   user  system elapsed 
  0.002   0.000   0.002 
Time of right optimization
   user  system elapsed 
  0.001   0.000   0.063 
Time of left optimization
   user  system elapsed 
  0.001   0.000   0.009 
[ FAIL 0 | WARN 0 | SKIP 1 | PASS 53 ]

══ Skipped tests ═══════════════════════════════════════════════════════════════
• empty test (1)

[ FAIL 0 | WARN 0 | SKIP 1 | PASS 53 ]
> 
> proc.time()
   user  system elapsed 
 10.101   0.818  37.983 

Example timings

NewWave.Rcheck/NewWave-Ex.timings

nameusersystemelapsed
newAIC0.0050.0000.004
newAlpha0.0010.0000.001
newBIC0.0190.0000.019
newBeta0.0020.0000.001
newEpsilon_W0.0010.0000.001
newEpsilon_alpha0.0010.0000.001
newEpsilon_beta0.0010.0000.001
newEpsilon_gamma0.0010.0000.001
newEpsilon_zeta0.0010.0000.001
newFit0.2190.0291.912
newGamma0.0030.0000.003
newLogMu0.0020.0000.002
newMu0.0000.0030.003
newPhi0.0020.0000.002
newSim0.0020.0030.005
newTheta0.0020.0000.002
newV0.0020.0000.001
newW0.0020.0000.002
newWave0.4310.1051.442
newX0.0010.0010.001
newZeta0.0000.0010.001
newloglik0.0000.0010.001
newmodel0.0000.0010.001
newpenalty0.0000.0010.001
numberFactors0.0010.0000.002
numberFeatures0.0020.0010.002
numberParams0.0010.0000.001
numberSamples0.0020.0000.002