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This page was generated on 2021-10-22 12:05:15 -0400 (Fri, 22 Oct 2021).

CHECK results for zinbwave on merida1

To the developers/maintainers of the zinbwave package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/zinbwave.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 2074/2075HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
zinbwave 1.15.3  (landing page)
Davide Risso
Snapshot Date: 2021-10-21 14:50:08 -0400 (Thu, 21 Oct 2021)
git_url: https://git.bioconductor.org/packages/zinbwave
git_branch: master
git_last_commit: 712b11d
git_last_commit_date: 2021-09-21 05:41:56 -0400 (Tue, 21 Sep 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    NA  

Summary

Package: zinbwave
Version: 1.15.3
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:zinbwave.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings zinbwave_1.15.3.tar.gz
StartedAt: 2021-10-22 11:07:14 -0400 (Fri, 22 Oct 2021)
EndedAt: 2021-10-22 11:13:03 -0400 (Fri, 22 Oct 2021)
EllapsedTime: 349.8 seconds
RetCode: 0
Status:   OK  
CheckDir: zinbwave.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:zinbwave.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings zinbwave_1.15.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/zinbwave.Rcheck’
* using R version 4.1.1 Patched (2021-08-22 r80813)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘zinbwave/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘zinbwave’ version ‘1.15.3’
* 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 ‘zinbwave’ 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 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: OK


Installation output

zinbwave.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘zinbwave’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** 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 (zinbwave)

Tests output

zinbwave.Rcheck/tests/testthat.Rout


R version 4.1.1 Patched (2021-08-22 r80813) -- "Kick Things"
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(zinbwave)
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

Loading required package: SingleCellExperiment
> 
> test_check("zinbwave")
   user  system elapsed 
  0.032   0.001   0.034 
   user  system elapsed 
  0.033   0.001   0.034 
   user  system elapsed 
  0.051   0.002   0.052 
   user  system elapsed 
  0.032   0.001   0.033 
══ Skipped tests ═══════════════════════════════════════════════════════════════
• empty test (1)

[ FAIL 0 | WARN 0 | SKIP 1 | PASS 219 ]
> 
> proc.time()
   user  system elapsed 
 98.224   2.605 100.798 

Example timings

zinbwave.Rcheck/zinbwave-Ex.timings

nameusersystemelapsed
computeDevianceResiduals0.5040.0090.513
computeObservationalWeights1.3220.0571.379
getAlpha_mu0.0030.0010.004
getAlpha_pi0.0030.0000.003
getBeta_mu0.0020.0000.003
getBeta_pi0.0030.0010.003
getEpsilon_W0.0030.0010.003
getEpsilon_alpha0.0020.0000.003
getEpsilon_beta_mu0.0030.0000.003
getEpsilon_beta_pi0.0030.0010.003
getEpsilon_gamma_mu0.0020.0010.003
getEpsilon_gamma_pi0.0030.0000.003
getEpsilon_zeta0.0030.0000.004
getGamma_mu0.0020.0010.003
getGamma_pi0.0030.0010.003
getLogMu0.0030.0000.003
getLogitPi0.0030.0000.004
getMu0.0030.0000.003
getPhi0.0030.0000.003
getPi0.0040.0010.004
getTheta0.0030.0010.003
getV_mu0.0020.0010.003
getV_pi0.0030.0000.004
getW0.0030.0000.003
getX_mu0.0020.0010.003
getX_pi0.0030.0010.003
getZeta0.0030.0000.003
imputeZeros0.2580.0310.290
loglik0.0030.0010.004
nFactors0.0030.0010.003
nFeatures0.0030.0000.003
nParams0.0030.0000.003
nSamples0.0030.0010.003
orthogonalizeTraceNorm0.0020.0010.003
penalty0.0030.0000.003
zinb.loglik0.0000.0000.001
zinb.loglik.dispersion000
zinbAIC0.2570.0310.288
zinbFit0.4530.0230.476
zinbInitialize0.0740.0010.074
zinbModel0.0030.0000.003
zinbOptimize0.0910.0000.092
zinbOptimizeDispersion0.0450.0000.046
zinbSim0.0310.0030.033
zinbsurf0.9630.0040.967
zinbwave0.9740.0130.987