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) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:49:57 -0400 (Wed, 17 Oct 2018).
| Package 431/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| EDASeq 2.14.1 Davide Risso
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| 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 |
##############################################################################
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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.
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)
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
EDASeq.Rcheck/EDASeq-Ex.timings
| name | user | system | elapsed | |
| MDPlot-methods | 0.337 | 0.014 | 0.357 | |
| SeqExpressionSet-class | 0.144 | 0.003 | 0.149 | |
| betweenLaneNormalization-methods | 0.687 | 0.011 | 0.704 | |
| biasBoxplot-methods | 0.092 | 0.008 | 0.104 | |
| biasPlot-methods | 0.183 | 0.007 | 0.194 | |
| getGeneLengthAndGCContent | 2.420 | 0.056 | 8.398 | |
| newSeqExpressionSet | 0.039 | 0.005 | 0.044 | |
| plotPCA-methods | 1.077 | 0.115 | 1.203 | |
| plotRLE-methods | 0.716 | 0.011 | 0.736 | |
| withinLaneNormalization-methods | 0.173 | 0.012 | 0.189 | |