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CHECK report for zinbwave on malbec2

This page was generated on 2019-04-09 11:48:12 -0400 (Tue, 09 Apr 2019).

Package 1702/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
zinbwave 1.5.2
Davide Risso
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/zinbwave
Branch: master
Last Commit: 53dca9a
Last Changed Date: 2019-03-11 11:31:23 -0400 (Mon, 11 Mar 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK 

Summary

Package: zinbwave
Version: 1.5.2
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:zinbwave.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings zinbwave_1.5.2.tar.gz
StartedAt: 2019-04-09 04:23:00 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 04:26:46 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 226.2 seconds
RetCode: 0
Status:  OK 
CheckDir: zinbwave.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:zinbwave.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings zinbwave_1.5.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/zinbwave.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-pc-linux-gnu (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 ‘1.5.2’
* 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
Examples with CPU or elapsed time > 5s
         user system elapsed
zinbFit 3.438  3.984   3.376
* 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

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### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL zinbwave
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/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 Under development (unstable) (2019-03-18 r76245) -- "Unsuffered Consequences"
Copyright (C) 2019 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(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, 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, rowsum

Loading required package: SingleCellExperiment
> 
> test_check("zinbwave")
   user  system elapsed 
  0.047   0.000   0.047 
   user  system elapsed 
  0.036   0.000   0.036 
   user  system elapsed 
  0.035   0.000   0.034 
   user  system elapsed 
  0.010   0.000   0.009 
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 159 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 63.725   1.005  64.724 

Example timings

zinbwave.Rcheck/zinbwave-Ex.timings

nameusersystemelapsed
getAlpha_mu0.0020.0000.003
getAlpha_pi0.0020.0000.001
getBeta_mu0.0010.0000.001
getBeta_pi0.0010.0000.001
getEpsilon_W0.0010.0000.002
getEpsilon_alpha0.0010.0000.002
getEpsilon_beta_mu0.0020.0000.002
getEpsilon_beta_pi0.0020.0000.001
getEpsilon_gamma_mu0.0020.0000.001
getEpsilon_gamma_pi0.0010.0000.001
getEpsilon_zeta0.0010.0000.001
getGamma_mu0.0010.0000.002
getGamma_pi0.0020.0000.002
getLogMu0.0020.0000.002
getLogitPi0.0020.0000.002
getMu0.0020.0000.002
getPhi0.0020.0000.001
getPi0.0020.0000.001
getTheta0.0020.0000.001
getV_mu0.0010.0000.001
getV_pi0.0010.0000.001
getW0.0010.0000.002
getX_mu0.0010.0000.002
getX_pi0.0020.0000.002
getZeta0.0020.0000.001
loglik0.0020.0000.002
orthogonalizeTraceNorm0.0010.0000.001
penalty0.0010.0000.002
zinb.loglik0.0000.0000.001
zinb.loglik.dispersion0.0000.0000.001
zinbFit3.4383.9843.376
zinbInitialize0.9861.3230.959
zinbModel0.0060.0000.006
zinbOptimize1.3481.7261.289
zinbOptimizeDispersion0.6961.1850.823
zinbSim0.0900.1230.029
zinbsurf1.8481.9461.750
zinbwave1.9502.3561.779