MEAL 1.2.3
Carlos Ruiz
| Snapshot Date: 2016-10-12 17:20:15 -0700 (Wed, 12 Oct 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/MEAL | | Last Changed Rev: 117977 / Revision: 122332 | | Last Changed Date: 2016-05-30 08:31:30 -0700 (Mon, 30 May 2016) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | OK | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | 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 MEAL_1.2.3.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/MEAL.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MEAL/DESCRIPTION’ ... OK
* this is package ‘MEAL’ version ‘1.2.3’
* 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 ‘MEAL’ 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
DAPipeline: no visible global function definition for 'model.matrix'
DAProbe: no visible global function definition for 'contrasts'
DAProbe: no visible global function definition for 'qt'
DARegionAnalysis: no visible global function definition for
'model.matrix'
DARegionAnalysis: no visible global function definition for 'prcomp'
SNPsforCPG: no visible global function definition for 'formula'
correlationMethExprs: no visible global function definition for
'rowRanges'
correlationMethExprs : residualsCorr: no visible global function
definition for 'lm'
correlationMethExprs: no visible global function definition for
'p.adjust'
createModel: no visible global function definition for 'model.matrix'
createModel: no visible global function definition for 'formula'
explainedVariance: no visible global function definition for 'lm'
explainedVariance: no visible global function definition for 'formula'
explainedVariance : <anonymous>: no visible global function definition
for 'lm'
explainedVariance : <anonymous>: no visible global function definition
for 'formula'
plotFeature: no visible binding for global variable 'lm'
qqplotBand: no visible binding for global variable 'qbeta'
qqplotBand: no visible binding for global variable 'lm'
exportResults,AnalysisResults: no visible global function definition
for 'write.csv2'
plotRDA,AnalysisRegionResults: no visible global function definition
for 'plot'
plotRDA,AnalysisRegionResults: no visible global function definition
for 'text'
plotRDA,AnalysisRegionResults: no visible global function definition
for 'points'
plotRDA,AnalysisRegionResults: no visible global function definition
for 'legend'
topRDAhits,AnalysisRegionResults : <anonymous> : <anonymous>: no
visible global function definition for 'cor.test'
topRDAhits,AnalysisRegionResults : <anonymous>: no visible global
function definition for 'p.adjust'
Undefined global functions or variables:
contrasts cor.test formula legend lm model.matrix p.adjust plot
points prcomp qbeta qt rowRanges text write.csv2
Consider adding
importFrom("graphics", "legend", "plot", "points", "text")
importFrom("stats", "contrasts", "cor.test", "formula", "lm",
"model.matrix", "p.adjust", "prcomp", "qbeta", "qt")
importFrom("utils", "write.csv2")
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
plotRegion-methods 62.579 1.050 63.906
plotRDA-methods 58.677 0.830 59.597
topRDAhits-methods 55.417 0.859 56.330
DAPipeline 17.239 1.071 20.236
DARegionAnalysis 4.384 0.191 5.002
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.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: 1 NOTE
See
‘/Users/biocbuild/bbs-3.3-bioc/meat/MEAL.Rcheck/00check.log’
for details.