Package: EDASeq

Version: 2.16.3

Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:EDASeq.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings EDASeq_2.16.3.tar.gz

StartedAt: 2019-04-15 23:42:05 -0400 (Mon, 15 Apr 2019)

EndedAt: 2019-04-15 23:46:58 -0400 (Mon, 15 Apr 2019)

EllapsedTime: 292.7 seconds

RetCode: 0

Status:  OK

CheckDir: EDASeq.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:EDASeq.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings EDASeq_2.16.3.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/EDASeq.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘EDASeq/DESCRIPTION’ ... OK
* this is package ‘EDASeq’ version ‘2.16.3’
* 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 ‘EDASeq’ 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 ... NOTE
plot,BamFileList-FastqFileList: no visible global function definition
  for ‘elementMetadata’
plotQuality,BamFile: no visible global function definition for ‘narrow’
plotQuality,BamFileList : <anonymous>: no visible global function
  definition for ‘narrow’
plotQuality,FastqFileList : <anonymous>: no visible global function
  definition for ‘quality’
plotQuality,FastqFileList : <anonymous>: no visible global function
  definition for ‘narrow’
Undefined global functions or variables:
  elementMetadata narrow quality
* 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
getGeneLengthAndGCContent 1.788  0.048  15.769
* 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.8-bioc/meat/EDASeq.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL EDASeq
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘EDASeq’ ...
** R
** data
** 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 (EDASeq)

R version 3.5.3 (2019-03-11) -- "Great Truth"
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(EDASeq)
Loading required package: Biobase
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

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: ShortRead
Loading required package: BiocParallel
Loading required package: Biostrings
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

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

    expand.grid

Loading required package: IRanges
Loading required package: XVector

Attaching package: 'Biostrings'

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

    strsplit

Loading required package: Rsamtools
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: GenomicAlignments
Loading required package: SummarizedExperiment
Loading required package: DelayedArray
Loading required package: matrixStats

Attaching package: 'matrixStats'

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

    anyMissing, rowMedians


Attaching package: 'DelayedArray'

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

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

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

    type

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

    aperm, apply

> 
> test_check("EDASeq")
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 19 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 17.740   0.464  48.596 

name	user	system	elapsed
MDPlot-methods	0.328	0.008	0.361
SeqExpressionSet-class	0.192	0.000	0.194
betweenLaneNormalization-methods	0.868	0.008	0.877
biasBoxplot-methods	0.100	0.000	0.098
biasPlot-methods	0.236	0.008	0.242
getGeneLengthAndGCContent	1.788	0.048	15.769
newSeqExpressionSet	0.020	0.000	0.023
plotPCA-methods	0.688	0.032	0.721
plotRLE-methods	0.492	0.012	0.504
withinLaneNormalization-methods	0.120	0.008	0.127