metagenomeSeq 1.13.1
Joseph N. Paulson
| Snapshot Date: 2016-04-20 17:20:35 -0700 (Wed, 20 Apr 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/metagenomeSeq | | Last Changed Rev: 116425 / Revision: 116626 | | Last Changed Date: 2016-04-17 13:18:34 -0700 (Sun, 17 Apr 2016) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | OK | |  |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK | OK | |
| morelia | 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 metagenomeSeq_1.13.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/metagenomeSeq.Rcheck’
* using R version 3.3.0 beta (2016-04-06 r70435)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘metagenomeSeq/DESCRIPTION’ ... OK
* this is package ‘metagenomeSeq’ version ‘1.13.1’
* 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 ‘metagenomeSeq’ can be installed ... [8s/8s] 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
MRcoefs: no visible global function definition for ‘quantile’
MRcoefs: no visible global function definition for ‘p.adjust’
MRexperiment2biom: no visible global function definition for
‘packageVersion’
MRfulltable: no visible global function definition for ‘quantile’
MRfulltable: no visible global function definition for ‘p.adjust’
MRtable: no visible global function definition for ‘quantile’
MRtable: no visible global function definition for ‘p.adjust’
calcPosComponent: no visible global function definition for
‘coefficients’
calcPosComponent: no visible global function definition for ‘residuals’
calcShrinkParameters: no visible global function definition for ‘var’
calcZeroComponent : <anonymous>: no visible global function definition
for ‘glm.fit’
calcZeroComponent : <anonymous>: no visible global function definition
for ‘binomial’
calcZeroComponent : <anonymous>: no visible global function definition
for ‘coefficients’
correlationTest : <anonymous>: no visible global function definition
for ‘cor.test’
cumNormStat : <anonymous>: no visible global function definition for
‘quantile’
cumNormStat : <anonymous>: no visible global function definition for
‘approx’
cumNormStat: no visible global function definition for ‘plot’
cumNormStat: no visible global function definition for ‘abline’
cumNormStat: no visible global function definition for ‘axis’
cumNormStatFast : <anonymous>: no visible global function definition
for ‘quantile’
cumNormStatFast: no visible global function definition for ‘plot’
cumNormStatFast: no visible global function definition for ‘abline’
cumNormStatFast: no visible global function definition for ‘axis’
doZeroMStep: no visible global function definition for ‘lm.fit’
doZeroMStep: no visible global function definition for ‘qlogis’
doZeroMStep: no visible global function definition for ‘sd’
fitDO : <anonymous>: no visible global function definition for
‘fisher.test’
fitDO: no visible global function definition for ‘p.adjust’
fitFeatureModel: no visible global function definition for ‘median’
fitFeatureModel: no visible global function definition for ‘pnorm’
fitPA : <anonymous>: no visible global function definition for
‘fisher.test’
fitPA: no visible global function definition for ‘p.adjust’
fitZeroLogNormal: no visible global function definition for ‘median’
fitZeroLogNormal: no visible global function definition for ‘density’
fitZeroLogNormal : <anonymous>: no visible global function definition
for ‘coefficients’
fitZig: no visible global function definition for ‘model.matrix’
getCountDensity: no visible global function definition for ‘dnorm’
getPi: no visible global function definition for ‘plogis’
load_meta: no visible global function definition for ‘read.table’
load_metaQ: no visible global function definition for ‘read.delim’
load_phenoData: no visible global function definition for ‘read.table’
plotBubble: no visible global function definition for ‘quantile’
plotBubble : linMap: no visible global function definition for
‘approxfun’
plotBubble: no visible global function definition for ‘median’
plotBubble: no visible global function definition for ‘plot’
plotBubble: no visible global function definition for ‘rgb’
plotBubble: no visible global function definition for ‘points’
plotBubble: no visible global function definition for ‘axis’
plotClassTimeSeries: no visible global function definition for
‘predict’
plotClassTimeSeries: no visible global function definition for ‘plot’
plotClassTimeSeries: no visible global function definition for ‘lines’
plotCorr: no visible binding for global variable ‘cor’
plotCorr: no visible global function definition for ‘hclust’
plotCorr: no visible global function definition for ‘dist’
plotFeature: no visible global function definition for ‘plot’
plotGenus: no visible global function definition for ‘col2rgb’
plotGenus: no visible global function definition for ‘rgb’
plotGenus: no visible global function definition for ‘plot’
plotGenus: no visible global function definition for ‘axis’
plotMRheatmap: no visible binding for global variable ‘sd’
plotOTU: no visible global function definition for ‘col2rgb’
plotOTU: no visible global function definition for ‘rgb’
plotOTU: no visible global function definition for ‘plot’
plotOTU: no visible global function definition for ‘axis’
plotOrd: no visible global function definition for ‘cmdscale’
plotOrd: no visible global function definition for ‘prcomp’
plotOrd: no visible global function definition for ‘plot’
plotRare: no visible global function definition for ‘plot’
plotTimeSeries: no visible global function definition for ‘plot’
plotTimeSeries: no visible global function definition for ‘polygon’
plotTimeSeries: no visible global function definition for ‘lines’
plotTimeSeries: no visible global function definition for ‘abline’
ssFit: no visible global function definition for ‘predict’
ssIntervalCandidate: no visible global function definition for ‘tail’
ssPermAnalysis: no visible global function definition for ‘predict’
Undefined global functions or variables:
abline approx approxfun axis binomial cmdscale coefficients col2rgb
cor cor.test density dist dnorm fisher.test glm.fit hclust lines
lm.fit median model.matrix p.adjust packageVersion plogis plot pnorm
points polygon prcomp predict qlogis quantile read.delim read.table
residuals rgb sd tail var
Consider adding
importFrom("grDevices", "col2rgb", "rgb")
importFrom("graphics", "abline", "axis", "lines", "plot", "points",
"polygon")
importFrom("stats", "approx", "approxfun", "binomial", "cmdscale",
"coefficients", "cor", "cor.test", "density", "dist",
"dnorm", "fisher.test", "glm.fit", "hclust", "lm.fit",
"median", "model.matrix", "p.adjust", "plogis", "pnorm",
"prcomp", "predict", "qlogis", "quantile", "residuals",
"sd", "var")
importFrom("utils", "packageVersion", "read.delim", "read.table",
"tail")
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 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 ... [29s/37s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘runTests.R’ [11s/11s]
[12s/12s] 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/metagenomeSeq.Rcheck/00check.log’
for details.