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CHECK report for EDASeq on merida2

This page was generated on 2018-10-17 08:49:57 -0400 (Wed, 17 Oct 2018).

Package 431/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
EDASeq 2.14.1
Davide Risso
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/EDASeq
Branch: RELEASE_3_7
Last Commit: e2c7e38
Last Changed Date: 2018-06-21 16:26:58 -0400 (Thu, 21 Jun 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  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 UNNEEDED, same version exists in internal repository

Summary

Package: EDASeq
Version: 2.14.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:EDASeq.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings EDASeq_2.14.1.tar.gz
StartedAt: 2018-10-16 21:08:22 -0400 (Tue, 16 Oct 2018)
EndedAt: 2018-10-16 21:13:08 -0400 (Tue, 16 Oct 2018)
EllapsedTime: 285.4 seconds
RetCode: 0
Status:  OK 
CheckDir: EDASeq.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:EDASeq.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings EDASeq_2.14.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/EDASeq.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 ‘EDASeq/DESCRIPTION’ ... OK
* this is package ‘EDASeq’ version ‘2.14.1’
* 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 ... NOTE
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.availableOrgPkgs: no visible global function definition for
  ‘available.packages’
.gcLoess : ff: no visible global function definition for ‘quantile’
.gcLoess : ff: no visible global function definition for ‘loess’
.gcLoess : ff: no visible global function definition for ‘predict’
.gcLoess : ff: no visible global function definition for ‘median’
.gcQuant: no visible global function definition for ‘quantile’
.gcQuant : f : <anonymous>: no visible global function definition for
  ‘median’
.gcQuant : f : <anonymous>: no visible global function definition for
  ‘quantile’
.isAvailable: no visible global function definition for ‘biocLite’
newSeqExpressionSet: no visible global function definition for ‘new’
MDPlot,SeqExpressionSet-numeric: no visible global function definition
  for ‘smoothScatter’
MDPlot,SeqExpressionSet-numeric: no visible global function definition
  for ‘lines’
MDPlot,SeqExpressionSet-numeric: no visible global function definition
  for ‘lowess’
MDPlot,SeqExpressionSet-numeric: no visible global function definition
  for ‘abline’
MDPlot,SeqExpressionSet-numeric: no visible global function definition
  for ‘points’
MDPlot,matrix-numeric: no visible global function definition for
  ‘smoothScatter’
MDPlot,matrix-numeric: no visible global function definition for
  ‘lines’
MDPlot,matrix-numeric: no visible global function definition for
  ‘lowess’
MDPlot,matrix-numeric: no visible global function definition for
  ‘abline’
MDPlot,matrix-numeric: no visible global function definition for
  ‘points’
barplot,BamFileList: no visible global function definition for
  ‘countBam’
betweenLaneNormalization,matrix: no visible binding for global variable
  ‘quantile’
betweenLaneNormalization,matrix: no visible binding for global variable
  ‘median’
biasBoxplot,numeric-numeric: no visible global function definition for
  ‘quantile’
biasBoxplot,numeric-numeric: no visible global function definition for
  ‘abline’
biasPlot,matrix-numeric: no visible global function definition for
  ‘lowess’
biasPlot,matrix-numeric: no visible global function definition for
  ‘lines’
boxplot,FastqQuality: no visible global function definition for ‘as’
counts<-,SeqExpressionSet-ANY: no visible global function definition
  for ‘validObject’
exprs<-,SeqExpressionSet-ANY: no visible global function definition for
  ‘validObject’
initialize,SeqExpressionSet: no visible global function definition for
  ‘callNextMethod’
meanVarPlot,SeqExpressionSet: no visible global function definition for
  ‘quantile’
meanVarPlot,SeqExpressionSet: no visible global function definition for
  ‘smoothScatter’
meanVarPlot,SeqExpressionSet: no visible global function definition for
  ‘lines’
meanVarPlot,SeqExpressionSet: no visible global function definition for
  ‘abline’
meanVarPlot,SeqExpressionSet: no visible global function definition for
  ‘lowess’
normCounts<-,SeqExpressionSet: no visible global function definition
  for ‘validObject’
offst<-,SeqExpressionSet: no visible global function definition for
  ‘validObject’
plot,BamFileList-FastqFileList: no visible global function definition
  for ‘elementMetadata’
plot,BamFileList-FastqFileList: no visible global function definition
  for ‘countBam’
plotNtFrequency,BamFile: no visible global function definition for
  ‘matplot’
plotNtFrequency,BamFile: no visible global function definition for
  ‘abline’
plotNtFrequency,BamFile: no visible global function definition for
  ‘legend’
plotNtFrequency,ShortRead: no visible global function definition for
  ‘matplot’
plotNtFrequency,ShortRead: no visible global function definition for
  ‘abline’
plotNtFrequency,ShortRead: no visible global function definition for
  ‘legend’
plotPCA,matrix: no visible global function definition for ‘text’
plotPCA,matrix: no visible global function definition for ‘pairs’
plotQuality,BamFile: no visible global function definition for
  ‘rainbow’
plotQuality,BamFile: no visible global function definition for ‘narrow’
plotQuality,BamFile: no visible global function definition for ‘as’
plotQuality,BamFileList: no visible global function definition for
  ‘rainbow’
plotQuality,BamFileList : <anonymous>: no visible global function
  definition for ‘narrow’
plotQuality,BamFileList : <anonymous>: no visible global function
  definition for ‘as’
plotQuality,BamFileList: no visible global function definition for
  ‘lines’
plotQuality,FastqFileList: no visible global function definition for
  ‘rainbow’
plotQuality,FastqFileList : <anonymous>: no visible global function
  definition for ‘quality’
plotQuality,FastqFileList : <anonymous>: no visible global function
  definition for ‘narrow’
plotQuality,FastqFileList : <anonymous>: no visible global function
  definition for ‘as’
plotQuality,FastqFileList: no visible global function definition for
  ‘lines’
plotRLE,matrix: no visible global function definition for ‘abline’
updateObject,SeqExpressionSet: no visible global function definition
  for ‘callNextMethod’
Undefined global functions or variables:
  abline as available.packages biocLite callNextMethod countBam
  elementMetadata legend lines loess lowess matplot median narrow new
  pairs points predict quality quantile rainbow smoothScatter text
  validObject
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "abline", "legend", "lines", "matplot", "pairs",
             "points", "smoothScatter", "text")
  importFrom("methods", "as", "callNextMethod", "new", "validObject")
  importFrom("stats", "loess", "lowess", "median", "predict", "quantile")
  importFrom("utils", "available.packages")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
getGeneLengthAndGCContent 2.42  0.056   8.398
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘getLengthAndGC.R’
  Running ‘plots.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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.7-bioc/meat/EDASeq.Rcheck/00check.log’
for details.



Installation output

EDASeq.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL EDASeq
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/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)

Tests output

EDASeq.Rcheck/tests/getLengthAndGC.Rout


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(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

> library(yeastRNASeq)
> 
> getGeneLengthAndGCContent(id=c("ENSG00000012048", "ENSG00000139618"), org="hsa", mode = "biomart")
Connecting to BioMart ...
Downloading sequences ...
                length        gc
ENSG00000012048   9187 0.4607598
ENSG00000139618  12273 0.3644586
> 
> proc.time()
   user  system elapsed 
 15.665   0.657  21.818 

EDASeq.Rcheck/tests/plots.Rout


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(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

> 
> mat <- matrix(data=rpois(1000, lambda=10), ncol=10)
> rownames(mat) <- paste("gene", 1:nrow(mat), sep="")
> colnames(mat) <- paste("sample", 1:ncol(mat), sep="")
> 
> es <- newSeqExpressionSet(mat)
> 
> ## PCA
> ks <- 2:5
> 
> ## matrix
> lapply(ks, function(k) plotPCA(mat, k=k))
[[1]]
NULL

[[2]]
NULL

[[3]]
NULL

[[4]]
NULL

> lapply(ks, function(k) plotPCA(mat, k=k, labels=FALSE))
[[1]]
NULL

[[2]]
NULL

[[3]]
NULL

[[4]]
NULL

> lapply(ks, function(k) plotPCA(mat, k=k))
[[1]]
NULL

[[2]]
NULL

[[3]]
NULL

[[4]]
NULL

> lapply(ks, function(k) plotPCA(mat, k=k, labels=FALSE, pch=20, col=1:2))
[[1]]
NULL

[[2]]
NULL

[[3]]
NULL

[[4]]
NULL

> 
> ## expressionset
> lapply(ks, function(k) plotPCA(es, k=k))
[[1]]
NULL

[[2]]
NULL

[[3]]
NULL

[[4]]
NULL

> lapply(ks, function(k) plotPCA(es, k=k, labels=FALSE))
[[1]]
NULL

[[2]]
NULL

[[3]]
NULL

[[4]]
NULL

> lapply(ks, function(k) plotPCA(es, k=k, labels=FALSE, pch=20, col=1:2))
[[1]]
NULL

[[2]]
NULL

[[3]]
NULL

[[4]]
NULL

> 
> ## RLE
> 
> ## matrix
> rle <- plotRLE(mat)
> stopifnot(all(dim(mat)==dim(rle)))
> 
> ## expressionset
> rle <- plotRLE(es)
> stopifnot(all(dim(mat)==dim(rle)))
> stopifnot(all(mat==counts(es)))
> 
> proc.time()
   user  system elapsed 
 13.076   0.698  13.932 

Example timings

EDASeq.Rcheck/EDASeq-Ex.timings

nameusersystemelapsed
MDPlot-methods0.3370.0140.357
SeqExpressionSet-class0.1440.0030.149
betweenLaneNormalization-methods0.6870.0110.704
biasBoxplot-methods0.0920.0080.104
biasPlot-methods0.1830.0070.194
getGeneLengthAndGCContent2.4200.0568.398
newSeqExpressionSet0.0390.0050.044
plotPCA-methods1.0770.1151.203
plotRLE-methods0.7160.0110.736
withinLaneNormalization-methods0.1730.0120.189