CHECK report for SpeCond on malbec1
This page was generated on 2019-04-16 11:48:49 -0400 (Tue, 16 Apr 2019).
SpeCond 1.36.0
Florence Cavalli
| Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019) |
| URL: https://git.bioconductor.org/packages/SpeCond |
| Branch: RELEASE_3_8 |
| Last Commit: a425ae7 |
| Last Changed Date: 2018-10-30 11:41:45 -0400 (Tue, 30 Oct 2018) |
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | [ OK ] | |  |
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
Summary
Command output
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### Running command:
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### /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:SpeCond.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings SpeCond_1.36.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/SpeCond.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SpeCond/DESCRIPTION’ ... OK
* this is package ‘SpeCond’ version ‘1.36.0’
* 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 ‘SpeCond’ 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
Packages in Depends field not imported from:
‘Biobase’ ‘fields’ ‘hwriter’ ‘mclust’ ‘methods’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
SpeCond: warning in getSpecificOutliersStep1(expressionMatrix, fit =
fit1, param.detection = param.detection, multitest.correction.method
= "BY", prefix.file = prefix.file, print.hist.pv = FALSE): partial
argument match of 'fit' to 'fit1'
SpeCond: warning in getSpecificResult(expressionMatrix, fit = fit2,
specificOutlierStep1 = specificOutlierStep1, param.detection =
param.detection, multitest.correction.method =
multitest.correction.method, prefix.file = prefix.file, print.hist.pv
= print.hist.pv): partial argument match of 'fit' to 'fit2'
createSingleGeneHtmlPage: warning in matrix(c("color:#000DFE", NA), nr
= 1, nc = 2): partial argument match of 'nr' to 'nrow'
createSingleGeneHtmlPage: warning in matrix(c("color:#000DFE", NA), nr
= 1, nc = 2): partial argument match of 'nc' to 'ncol'
getExpressionpatternLegend: warning in matrix(" ", nr = 2, nc =
1): partial argument match of 'nr' to 'nrow'
getExpressionpatternLegend: warning in matrix(" ", nr = 2, nc =
1): partial argument match of 'nc' to 'ncol'
SpeCond: no visible global function definition for ‘is’
SpeCond: no visible global function definition for ‘new’
callMclustInStep2: no visible global function definition for ‘Mclust’
callMclustInStep2: no visible global function definition for
‘priorControl’
createSingleGeneHtmlPage: no visible global function definition for
‘openPage’
createSingleGeneHtmlPage: no visible global function definition for
‘hwrite’
createSingleGeneHtmlPage: no visible global function definition for
‘sessionInfo’
createSingleGeneHtmlPage: no visible global function definition for
‘closePage’
fitNoPriorWithExclusion : <anonymous>: no visible global function
definition for ‘Mclust’
fitPrior : <anonymous>: no visible global function definition for
‘Mclust’
fitPrior : <anonymous>: no visible global function definition for
‘priorControl’
getDifferenceMedian: no visible global function definition for ‘median’
getExpressionpatternLegend: no visible global function definition for
‘hwrite’
getFullHtmlSpeCondResult: no visible global function definition for
‘openPage’
getFullHtmlSpeCondResult: no visible global function definition for
‘is’
getFullHtmlSpeCondResult: no visible global function definition for
‘hwrite’
getFullHtmlSpeCondResult: no visible global function definition for
‘png’
getFullHtmlSpeCondResult: no visible global function definition for
‘barplot’
getFullHtmlSpeCondResult: no visible global function definition for
‘dev.off’
getFullHtmlSpeCondResult: no visible global function definition for
‘par’
getFullHtmlSpeCondResult: no visible global function definition for
‘plot’
getFullHtmlSpeCondResult: no visible global function definition for
‘axis’
getFullHtmlSpeCondResult: no visible global function definition for
‘points’
getFullHtmlSpeCondResult: no visible global function definition for
‘legend’
getFullHtmlSpeCondResult: no visible global function definition for
‘mtext’
getFullHtmlSpeCondResult: no visible global function definition for
‘hwriteImage’
getFullHtmlSpeCondResult: no visible global function definition for
‘colorRampPalette’
getFullHtmlSpeCondResult: no visible global function definition for
‘sessionInfo’
getFullHtmlSpeCondResult: no visible global function definition for
‘closePage’
getFullHtmlSpeCondResult: no visible global function definition for
‘write.table’
getGeneHtmlPage: no visible global function definition for ‘is’
getGeneHtmlPage: no visible global function definition for ‘openPage’
getGeneHtmlPage: no visible global function definition for ‘hwrite’
getGeneHtmlPage: no visible global function definition for
‘sessionInfo’
getGeneHtmlPage: no visible global function definition for ‘closePage’
getHeatmap: no visible global function definition for ‘png’
getHeatmap: no visible global function definition for ‘heatmap’
getHeatmap: no visible global function definition for ‘colorbar.plot’
getHeatmap: no visible global function definition for ‘dev.off’
getHeatmap: no visible global function definition for ‘pdf’
getMatrixFromExpressionSet: no visible global function definition for
‘is’
getMatrixFromExpressionSet: no visible global function definition for
‘exprs’
getMinLoglikelihoodNull: no visible global function definition for
‘dnorm’
getPValueMean : <anonymous>: no visible global function definition for
‘pnorm’
getProfileHeatmap: no visible global function definition for ‘png’
getProfileHeatmap: no visible global function definition for ‘heatmap’
getProfileHeatmap: no visible global function definition for ‘dev.off’
getProfileHeatmap: no visible global function definition for ‘pdf’
getScaleMAD: no visible global function definition for ‘mad’
getSpecific: no visible global function definition for ‘pdf’
getSpecific: no visible global function definition for ‘hist’
getSpecific: no visible global function definition for ‘dev.off’
getSpecific: no visible global function definition for ‘p.adjust’
getSpecific: no visible global function definition for ‘new’
plotNormalMixture: no visible global function definition for ‘png’
plotNormalMixture: no visible global function definition for ‘plot’
plotNormalMixture: no visible global function definition for ‘points’
plotNormalMixture: no visible global function definition for
‘hwriteImage’
plotNormalMixture: no visible global function definition for ‘dev.off’
plotNormalMixture: no visible global function definition for ‘hist’
plotNormalMixture : f1: no visible global function definition for
‘dnorm’
plotNormalMixture : f2: no visible global function definition for
‘dnorm’
plotNormalMixture : f3: no visible global function definition for
‘dnorm’
plotNormalMixture : f4: no visible global function definition for
‘dnorm’
plotNormalMixture : f5: no visible global function definition for
‘dnorm’
plotNormalMixture: no visible global function definition for ‘lines’
plotNormalMixture: no visible global function definition for ‘legend’
plotNormalMixture : f_null : <anonymous>: no visible global function
definition for ‘dnorm’
show.sp_list: no visible global function definition for ‘is’
writeGeneResult: no visible global function definition for
‘write.table’
writeSpeCondResult: no visible global function definition for
‘write.table’
writeUniqueProfileSpecificResult: no visible global function definition
for ‘write.table’
Undefined global functions or variables:
Mclust axis barplot closePage colorRampPalette colorbar.plot dev.off
dnorm exprs heatmap hist hwrite hwriteImage is legend lines mad
median mtext new openPage p.adjust par pdf plot png pnorm points
priorControl sessionInfo write.table
Consider adding
importFrom("grDevices", "colorRampPalette", "dev.off", "pdf", "png")
importFrom("graphics", "axis", "barplot", "hist", "legend", "lines",
"mtext", "par", "plot", "points")
importFrom("methods", "is", "new")
importFrom("stats", "dnorm", "heatmap", "mad", "median", "p.adjust",
"pnorm")
importFrom("utils", "sessionInfo", "write.table")
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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
getFullHtmlSpeCondResult 6.808 1.072 8.276
getGeneHtmlPage 6.316 0.992 7.650
SpeCond 5.672 0.004 5.679
getProfile 5.372 0.000 5.382
* 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-3.8-bioc/meat/SpeCond.Rcheck/00check.log’
for details.
Installation output
SpeCond.Rcheck/00install.out
Tests output
Example timings
SpeCond.Rcheck/SpeCond-Ex.timings