motifStack 1.19.2
Jianhong Ou
| Snapshot Date: 2017-03-03 17:15:47 -0500 (Fri, 03 Mar 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/motifStack | | Last Changed Rev: 126666 / Revision: 127142 | | Last Changed Date: 2017-02-10 08:04:17 -0500 (Fri, 10 Feb 2017) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |
| toluca2 | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | OK | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / 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 motifStack_1.19.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/motifStack.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘motifStack/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘motifStack’ version ‘1.19.2’
* 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 ‘motifStack’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 6.0Mb
sub-directories of 1Mb or more:
doc 5.2Mb
* 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 ... NOTE
Warning: no function found corresponding to methods exports from ‘motifStack’ for: ‘plot’
A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.
Probably some imports need to be declared in the NAMESPACE file.
* 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
browseMotifs : <anonymous>: no visible binding for global variable
‘pfm’
browseMotifs : <anonymous>: no visible binding for global variable
‘nodeName’
getoffsetPosByIC_old: no visible global function definition for ‘sd’
getoffsetPosByIC_old: no visible global function definition for ‘cor’
hex2psrgb: no visible global function definition for ‘col2rgb’
highlightCol: no visible global function definition for ‘col2rgb’
highlightCol : <anonymous>: no visible global function definition for
‘rgb’
isHomoDimer: no visible global function definition for ‘loess’
isHomoDimer: no visible global function definition for ‘predict’
mergeMotifs : rdirichlet: no visible global function definition for
‘rgamma’
motifCircos: no visible global function definition for ‘par’
motifCircos: no visible global function definition for ‘dev.size’
motifCircos: no visible global function definition for ‘plot.default’
motifCircos: no visible binding for global variable ‘strwidth’
motifCircos : plotBgArc: no visible global function definition for
‘polygon’
motifCircos: no visible global function definition for ‘text’
motifCircos: no visible global function definition for ‘segments’
motifCircos: no visible global function definition for ‘grey’
motifCircos : drawPFMcir: no visible global function definition for
‘median’
motifCircos: no visible global function definition for ‘points’
motifCircos: no visible global function definition for ‘lines’
motifCircos: no visible global function definition for ‘symbols’
motifCircos: no visible global function definition for ‘strwidth’
motifCircos: no visible global function definition for ‘box’
motifCloud: no visible global function definition for ‘par’
motifCloud: no visible global function definition for ‘plot.new’
motifCloud: no visible global function definition for ‘strheight’
motifCloud: no visible global function definition for ‘plot.window’
motifCloud: no visible global function definition for ‘runif’
motifCloud: no visible global function definition for ‘plot.default’
motifCloud : plotUnrootedTree: no visible global function definition
for ‘segments’
motifCloud : plotUnrootedTree: no visible global function definition
for ‘strheight’
motifCloud: no visible global function definition for ‘segments’
motifCloud: no visible global function definition for ‘legend’
motifPiles: no visible global function definition for ‘par’
motifPiles: no visible global function definition for ‘dev.size’
motifPiles: no visible global function definition for ‘plot.default’
motifPiles: no visible binding for global variable ‘strwidth’
motifPiles: no visible global function definition for ‘strwidth’
motifPiles: no visible global function definition for ‘points’
motifPiles: no visible global function definition for ‘col2rgb’
motifPiles: no visible global function definition for ‘rgb’
motifPiles: no visible global function definition for ‘segments’
motifPiles: no visible global function definition for ‘abline’
motifPiles: no visible global function definition for ‘rect’
motifPiles: no visible global function definition for ‘text’
motifPiles: no visible global function definition for ‘grey’
motifStack: no visible global function definition for ‘plot’
plotMotifLogo: no visible global function definition for ‘plot.new’
plotMotifLogo: no visible global function definition for ‘text’
plotMotifLogo: no visible global function definition for ‘mtext’
plotMotifLogoStack: no visible global function definition for ‘par’
plotMotifLogoStack: no visible global function definition for ‘plot’
plotMotifLogoStackWithTree: no visible global function definition for
‘par’
plotMotifLogoStackWithTree: no visible global function definition for
‘layout’
plotMotifLogoStackWithTree: no visible global function definition for
‘plot.new’
plotMotifLogoStackWithTree: no visible global function definition for
‘plot’
plotMotifOverMotif : rdirichlet: no visible global function definition
for ‘rgamma’
plotMotifOverMotif: no visible global function definition for
‘plot.new’
plotMotifOverMotif: no visible global function definition for
‘dev.size’
plotMotifStackWithPhylog: no visible global function definition for
‘par’
plotMotifStackWithPhylog: no visible global function definition for
‘plot.default’
plotMotifStackWithPhylog: no visible binding for global variable
‘strwidth’
plotMotifStackWithPhylog: no visible global function definition for
‘strwidth’
plotMotifStackWithPhylog: no visible global function definition for
‘text’
plotMotifStackWithPhylog: no visible global function definition for
‘segments’
plotMotifStackWithPhylog: no visible global function definition for
‘grey’
plotMotifStackWithPhylog: no visible global function definition for
‘points’
plotMotifStackWithRadialPhylog: no visible global function definition
for ‘par’
plotMotifStackWithRadialPhylog: no visible global function definition
for ‘plot.default’
plotMotifStackWithRadialPhylog: no visible global function definition
for ‘dev.size’
plotMotifStackWithRadialPhylog: no visible binding for global variable
‘strwidth’
plotMotifStackWithRadialPhylog : plotBgArc: no visible global function
definition for ‘polygon’
plotMotifStackWithRadialPhylog: no visible global function definition
for ‘text’
plotMotifStackWithRadialPhylog: no visible global function definition
for ‘segments’
plotMotifStackWithRadialPhylog: no visible global function definition
for ‘grey’
plotMotifStackWithRadialPhylog: no visible global function definition
for ‘median’
plotMotifStackWithRadialPhylog: no visible global function definition
for ‘points’
plotMotifStackWithRadialPhylog: no visible global function definition
for ‘lines’
plotMotifStackWithRadialPhylog: no visible global function definition
for ‘symbols’
plotMotifStackWithRadialPhylog: no visible global function definition
for ‘strwidth’
plotMotifStackWithRadialPhylog: no visible global function definition
for ‘box’
plotXaxis: no visible global function definition for ‘axis’
plotYaxis: no visible global function definition for ‘axis’
plotYaxis: no visible global function definition for ‘par’
readPCM : <anonymous>: no visible global function definition for
‘read.table’
Undefined global functions or variables:
abline axis box col2rgb cor dev.size grey layout legend lines loess
median mtext nodeName par pfm plot plot.default plot.new plot.window
points polygon predict read.table rect rgamma rgb runif sd segments
strheight strwidth symbols text
Consider adding
importFrom("grDevices", "col2rgb", "dev.size", "grey", "rgb")
importFrom("graphics", "abline", "axis", "box", "layout", "legend",
"lines", "mtext", "par", "plot", "plot.default", "plot.new",
"plot.window", "points", "polygon", "rect", "segments",
"strheight", "strwidth", "symbols", "text")
importFrom("stats", "cor", "loess", "median", "predict", "rgamma",
"runif", "sd")
importFrom("utils", "read.table")
to your NAMESPACE file.
* 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 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
browseMotifs 2.652 0.04 9.806
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘runTests.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: 3 NOTEs
See
‘/Users/biocbuild/bbs-3.5-bioc/meat/motifStack.Rcheck/00check.log’
for details.