EDASeq 2.10.0
Davide Risso
| Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/EDASeq | | Last Changed Rev: 129126 / Revision: 131943 | | Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |
| veracruz2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings EDASeq_2.10.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/EDASeq.Rcheck’
* using R version 3.4.1 (2017-06-30)
* 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 ‘2.10.0’
* 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 ‘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 ‘path’
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 ‘path’
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 ‘path’
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 path 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
getGeneLengthAndGCContent 2.596 0.059 8.441
* 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-3.5-bioc/meat/EDASeq.Rcheck/00check.log’
for details.