shinyMethyl 1.12.0
Jean-Philippe Fortin
| 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/shinyMethyl | | 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 | NotNeeded | OK | [ OK ] | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | OK | OK | |
| veracruz2 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | OK | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings shinyMethyl_1.12.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/shinyMethyl.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘shinyMethyl/DESCRIPTION’ ... OK
* this is package ‘shinyMethyl’ version ‘1.12.0’
* 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 ... NOTE
Found the following hidden files and directories:
.travis.yml
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘shinyMethyl’ 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 loading without being on the library search path ... 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
addHoverDensity: no visible global function definition for ‘lines’
addHoverPoints: no visible global function definition for ‘points’
addHoverQC: no visible global function definition for ‘points’
densitiesPlot: no visible global function definition for ‘plot’
densitiesPlot: no visible global function definition for ‘lines’
plotDesign450k: no visible global function definition for ‘par’
plotDesign450k: no visible global function definition for ‘plot’
plotDiscrepancyGenders: no visible global function definition for
‘legend’
plotInternalControls: no visible global function definition for ‘plot’
plotInternalControls: no visible global function definition for ‘grid’
plotInternalControls: no visible global function definition for
‘abline’
plotLegendDesign450k: no visible global function definition for ‘plot’
plotLegendDesign450k: no visible global function definition for
‘legend’
plotPCA: no visible global function definition for ‘plot’
plotPCA: no visible global function definition for ‘legend’
plotPCA: no visible global function definition for ‘grid’
plotPlate: no visible global function definition for ‘rect’
plotPredictedGender: no visible global function definition for ‘plot’
plotPredictedGender: no visible global function definition for ‘abline’
plotQC: no visible global function definition for ‘plot’
plotQC: no visible global function definition for ‘grid’
server.shinyMethyl : <anonymous>: no visible binding for '<<-'
assignment to ‘mouse.click.indices’
server.shinyMethyl : <anonymous>: no visible binding for '<<-'
assignment to ‘colorSet’
server.shinyMethyl : <anonymous>: no visible binding for '<<-'
assignment to ‘genderCutoff’
server.shinyMethyl : <anonymous>: no visible binding for '<<-'
assignment to ‘current.control.type’
server.shinyMethyl : <anonymous>: no visible binding for '<<-'
assignment to ‘current.probe.type’
server.shinyMethyl : <anonymous>: no visible binding for '<<-'
assignment to ‘current.density.type’
server.shinyMethyl : <anonymous> : set.palette: no visible global
function definition for ‘palette’
server.shinyMethyl : <anonymous>: no visible binding for global
variable ‘current.control.type’
server.shinyMethyl : <anonymous>: no visible binding for global
variable ‘mouse.click.indices’
server.shinyMethyl : <anonymous>: no visible binding for global
variable ‘current.probe.type’
server.shinyMethyl : <anonymous>: no visible binding for global
variable ‘current.density.type’
server.shinyMethyl : <anonymous> : content: no visible global function
definition for ‘write.csv’
server.shinyMethyl : <anonymous>: no visible global function definition
for ‘abline’
server.shinyMethyl : <anonymous>: no visible binding for global
variable ‘genderCutoff’
server.shinyMethyl : <anonymous>: no visible global function definition
for ‘complete.cases’
server.shinyMethyl : <anonymous>: no visible global function definition
for ‘lm’
server.shinyMethyl : <anonymous>: no visible global function definition
for ‘plot’
server.shinyMethyl : <anonymous>: no visible global function definition
for ‘lines’
server.shinyMethyl : <anonymous>: no visible global function definition
for ‘legend’
ui.shinyMethyl: no visible binding for '<<-' assignment to
‘sampleColors’
shinySummarize,GenomicRatioSet: no visible global function definition
for ‘prcomp’
shinySummarize,RGChannelSet: no visible global function definition for
‘prcomp’
Undefined global functions or variables:
abline complete.cases current.control.type current.density.type
current.probe.type genderCutoff grid legend lines lm
mouse.click.indices palette par plot points prcomp rect write.csv
Consider adding
importFrom("grDevices", "palette")
importFrom("graphics", "abline", "grid", "legend", "lines", "par",
"plot", "points", "rect")
importFrom("stats", "complete.cases", "lm", "prcomp")
importFrom("utils", "write.csv")
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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
shinySummarize-methods 36.28 0.512 37.283
* 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: 2 NOTEs
See
‘/home/biocbuild/bbs-3.5-bioc/meat/shinyMethyl.Rcheck/00check.log’
for details.