Package: zinbwave

Version: 1.2.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:zinbwave.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings zinbwave_1.2.0.tar.gz

StartedAt: 2018-10-17 00:42:40 -0400 (Wed, 17 Oct 2018)

EndedAt: 2018-10-17 00:46:03 -0400 (Wed, 17 Oct 2018)

EllapsedTime: 203.0 seconds

RetCode: 0

Status:  OK

CheckDir: zinbwave.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:zinbwave.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings zinbwave_1.2.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/zinbwave.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.2.0’
* 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 ‘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 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

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL zinbwave
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘zinbwave’ ...
** 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
* DONE (zinbwave)

R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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: GenomicRanges
Loading required package: stats4
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, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    expand.grid

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")'.

Loading required package: DelayedArray
Loading required package: matrixStats

Attaching package: 'matrixStats'

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

    anyMissing, rowMedians

Loading required package: BiocParallel

Attaching package: 'DelayedArray'

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

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

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

    aperm, apply

Loading required package: SingleCellExperiment
> 
> test_check("zinbwave")
   user  system elapsed 
  0.037   0.000   0.036 
   user  system elapsed 
  0.028   0.000   0.028 
   user  system elapsed 
  0.042   0.000   0.043 
   user  system elapsed 
  0.012   0.000   0.012 
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 110 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 43.126   1.972  45.076 

name	user	system	elapsed
getAlpha_mu	0.003	0.000	0.003
getAlpha_pi	0.003	0.000	0.003
getBeta_mu	0.003	0.000	0.003
getBeta_pi	0.003	0.000	0.002
getEpsilon_W	0.002	0.000	0.002
getEpsilon_alpha	0.002	0.000	0.002
getEpsilon_beta_mu	0.003	0.000	0.002
getEpsilon_beta_pi	0.003	0.000	0.002
getEpsilon_gamma_mu	0.003	0.001	0.002
getEpsilon_gamma_pi	0.002	0.000	0.003
getEpsilon_zeta	0.002	0.000	0.003
getGamma_mu	0.002	0.000	0.003
getGamma_pi	0.002	0.000	0.002
getLogMu	0.003	0.000	0.002
getLogitPi	0.003	0.001	0.003
getMu	0.003	0.000	0.003
getPhi	0.003	0.000	0.002
getPi	0.003	0.001	0.003
getTheta	0.003	0.000	0.003
getV_mu	0.002	0.000	0.003
getV_pi	0.002	0.001	0.003
getW	0.002	0.000	0.002
getX_mu	0.003	0.000	0.003
getX_pi	0.003	0.001	0.003
getZeta	0.003	0.000	0.003
loglik	0.004	0.000	0.003
orthogonalizeTraceNorm	0.003	0.000	0.003
penalty	0.003	0.000	0.003
zinb.loglik	0.001	0.001	0.002
zinb.loglik.dispersion	0.001	0.000	0.001
zinbFit	2.246	2.458	2.349
zinbInitialize	0.664	0.903	0.766
zinbModel	0.004	0.001	0.004
zinbOptimize	0.742	0.944	0.880
zinbOptimizeDispersion	0.557	0.781	0.693
zinbSim	0.037	0.009	0.046
zinbwave	1.401	1.375	1.519