Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-01-19 13:08:33 -0500 (Wed, 19 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4328
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4077
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4138
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for phenoTest on machv2


To the developers/maintainers of the phenoTest package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/phenoTest.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1408/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
phenoTest 1.42.0  (landing page)
Evarist Planet
Snapshot Date: 2022-01-18 01:55:07 -0500 (Tue, 18 Jan 2022)
git_url: https://git.bioconductor.org/packages/phenoTest
git_branch: RELEASE_3_14
git_last_commit: 28925db
git_last_commit_date: 2021-10-26 11:57:57 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: phenoTest
Version: 1.42.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:phenoTest.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings phenoTest_1.42.0.tar.gz
StartedAt: 2022-01-18 16:21:04 -0500 (Tue, 18 Jan 2022)
EndedAt: 2022-01-18 16:26:41 -0500 (Tue, 18 Jan 2022)
EllapsedTime: 337.0 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: phenoTest.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:phenoTest.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings phenoTest_1.42.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/phenoTest.Rcheck’
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘phenoTest/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘phenoTest’ version ‘1.42.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'Biobase', 'annotate', 'Heatplus', 'BMA', 'ggplot2', 'Hmisc'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ‘phenoTest’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘annotate’ ‘GSEABase’
A package should be listed in only one of these fields.
* 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 ‘phenoTest’ for: ‘show’

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 ... NOTE
'library' or 'require' call to ‘ggplot2’ which was already attached by Depends.
  Please remove these calls from your code.
Namespace in Imports field not imported from: ‘annotate’
  All declared Imports should be used.
Packages in Depends field not imported from:
  ‘BMA’ ‘Heatplus’ ‘annotate’ ‘ggplot2’ ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘sortDragHtmlTable’
* checking S3 generic/method consistency ... NOTE
Found the following apparent S3 methods exported but not registered:
  plot.gseaData plot.gseaSignaturesSign plot.gseaSignaturesVar
  summary.gseaData summary.gseaSignificanceSign
  summary.gseaSignificanceVar
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
ClusterPhenoTest: no visible global function definition for ‘is’
ClusterPhenoTest: no visible global function definition for ‘pData’
ClusterPhenoTest : <anonymous>: no visible global function definition
  for ‘pData’
ClusterPhenoTest : <anonymous>: no visible global function definition
  for ‘kruskal.test’
ClusterPhenoTest : <anonymous>: no visible global function definition
  for ‘chisq.test’
ClusterPhenoTest: no visible global function definition for ‘p.adjust’
ExpressionPhenoTest : mycoxph: no visible global function definition
  for ‘coefficients’
ExpressionPhenoTest : mycoxph: no visible global function definition
  for ‘coef’
ExpressionPhenoTest : mycoxph: no visible global function definition
  for ‘anova’
ExpressionPhenoTest : mycoxph: no visible global function definition
  for ‘pData’
ExpressionPhenoTest : mycoxph: no visible global function definition
  for ‘bic.surv’
ExpressionPhenoTest : postprobBic: no visible global function
  definition for ‘BIC’
ExpressionPhenoTest : postprobBic: no visible global function
  definition for ‘lm’
ExpressionPhenoTest: no visible global function definition for ‘is’
ExpressionPhenoTest: no visible global function definition for ‘exprs’
ExpressionPhenoTest: no visible global function definition for ‘pData’
ExpressionPhenoTest: no visible global function definition for
  ‘model.matrix’
ExpressionPhenoTest : <anonymous>: no visible global function
  definition for ‘pData’
ExpressionPhenoTest: no visible global function definition for ‘coef’
ExpressionPhenoTest: no visible binding for global variable ‘y’
ExpressionPhenoTest: no visible global function definition for
  ‘featureNames’
ExpressionPhenoTest : <anonymous>: no visible global function
  definition for ‘p.adjust’
ExpressionPhenoTest: no visible global function definition for ‘new’
ExpressionPhenoTest: no visible global function definition for
  ‘annotation’
barplotCI: no visible global function definition for ‘lm’
barplotCI: no visible global function definition for ‘coef’
barplotCI: no visible global function definition for ‘confint’
checkGsetSimmetry: no visible global function definition for ‘pnorm’
checkGsetSimmetry: no visible global function definition for ‘sd’
epheno2html: no visible global function definition for ‘annotation’
epheno2html: no visible global function definition for ‘featureNames’
epheno2html : export2html: no visible global function definition for
  ‘featureNames’
epheno2html : export2html: no visible global function definition for
  ‘annotation’
epheno2html : export2html: no visible global function definition for
  ‘write.csv’
epheno2html : export2html: no visible global function definition for
  ‘pData’
epheno2html : export2html: no visible global function definition for
  ‘exprs’
epheno2html : export2html : myFun: no visible global function
  definition for ‘png’
epheno2html : export2html : myFun: no visible global function
  definition for ‘featureNames’
epheno2html : export2html : myFun: no visible global function
  definition for ‘legend’
epheno2html : export2html : myFun: no visible global function
  definition for ‘dev.off’
epheno2html : export2html : myFun: no visible global function
  definition for ‘pData’
epheno2html : export2html : myFun: no visible global function
  definition for ‘exprs’
epheno2html : export2html : myFun: no visible global function
  definition for ‘boxplot’
epheno2html : export2html : myFun: no visible global function
  definition for ‘dotchart’
eset2genelevel: no visible global function definition for ‘is’
eset2genelevel: no visible global function definition for ‘annotation’
eset2genelevel: no visible global function definition for
  ‘featureNames<-’
eset2genelevel: no visible global function definition for
  ‘annotation<-’
getChrWithMedVar: no visible global function definition for ‘quantile’
getEsPositions: no visible global function definition for ‘is’
getEsPositions: no visible global function definition for ‘annotation’
getEsPositions: no visible global function definition for
  ‘featureNames’
getIndivPvals: no visible global function definition for ‘pnorm’
getIndivPvals: no visible global function definition for ‘sd’
getIndivPvals: no visible global function definition for ‘density’
getIndivPvals: no visible global function definition for ‘approxfun’
getIndivPvals: no visible global function definition for ‘integrate’
getIndivPvals : getPval: no visible global function definition for
  ‘density’
getIndivPvals : getPval: no visible global function definition for
  ‘approxfun’
getIndivPvals : getPval: no visible global function definition for
  ‘integrate’
getIndivPvals : getPval: no visible global function definition for
  ‘pnorm’
getIndivPvals : getPval: no visible global function definition for ‘sd’
getIndivPvals: no visible global function definition for ‘p.adjust’
getPred: no visible global function definition for ‘predict’
getSummary : getNesPval: no visible global function definition for
  ‘density’
getSummary : getNesPval: no visible global function definition for
  ‘approxfun’
getSummary : getNesPval: no visible global function definition for
  ‘integrate’
getSummary : gseaSignificance : getEsPval: no visible global function
  definition for ‘density’
getSummary : gseaSignificance : getEsPval: no visible global function
  definition for ‘approxfun’
getSummary : gseaSignificance : getEsPval: no visible global function
  definition for ‘integrate’
getSummary : <anonymous>: no visible global function definition for
  ‘wilcox.test’
getSummary: no visible global function definition for ‘p.adjust’
getSummary: no visible global function definition for ‘is’
gsea: no visible global function definition for ‘new’
gsea.selGsets: no visible global function definition for ‘is’
gsea.selGsets: no visible global function definition for ‘new’
gsea.selVars: no visible global function definition for ‘new’
gsea2html: no visible global function definition for ‘is’
gsea2html: no visible global function definition for ‘annotation’
gsea2html: no visible global function definition for ‘exprs’
gsea2html: no visible global function definition for ‘pData’
gsea2html: no visible global function definition for ‘featureNames’
gsea2html: no visible global function definition for ‘Term’
gsea2html: no visible global function definition for ‘png’
gsea2html: no visible global function definition for ‘dev.off’
pca: no visible global function definition for ‘prcomp’
pca: no visible global function definition for ‘exprs’
pca.2d: no visible global function definition for ‘is’
pca.2d: no visible global function definition for ‘pData’
pca.2d: no visible global function definition for ‘dist’
pca.2d: no visible global function definition for ‘cov’
pca.2d: no visible global function definition for ‘qplot’
pca.2d: no visible binding for global variable ‘pc1’
pca.2d: no visible binding for global variable ‘pc2’
pca.2d: no visible global function definition for ‘geom_point’
pca.2d: no visible global function definition for ‘coord_cartesian’
pca.2d: no visible global function definition for ‘theme’
pca.2d: no visible global function definition for ‘ggtitle’
plot.gseaData: no visible global function definition for ‘is’
plot.gseaSignaturesSign: no visible global function definition for ‘is’
plot.gseaSignaturesVar: no visible global function definition for ‘is’
plotCopyNumber: no visible global function definition for ‘par’
plotCopyNumber: no visible global function definition for ‘layout’
plotCopyNumber: no visible global function definition for ‘densCols’
plotCopyNumber: no visible global function definition for ‘lines’
plotCopyNumber: no visible global function definition for ‘abline’
plotCopyNumber : <anonymous>: no visible global function definition for
  ‘rect’
plotCopyNumber : <anonymous>: no visible global function definition for
  ‘rgb’
plotGSEA : plot1.perm: no visible global function definition for
  ‘approx’
plotGSEA : plot1.perm: no visible global function definition for
  ‘abline’
plotGSEA : plot1.perm: no visible global function definition for ‘axis’
plotGSEA : plot1.wilcox: no visible global function definition for
  ‘density’
plotGSEA : plot1.wilcox: no visible global function definition for
  ‘abline’
plotGSEA : plot2: no visible global function definition for ‘par’
plotGSEA : plot2: no visible global function definition for ‘approx’
plotGSEA : plot2: no visible global function definition for ‘abline’
plotGSEA : plot2: no visible global function definition for ‘axis’
plotGSEA : plot2: no visible global function definition for ‘polygon’
plotGSEA : plot3: no visible global function definition for ‘par’
plotGSEA : plot3: no visible global function definition for ‘quantile’
plotGSEA : plot3: no visible global function definition for ‘image’
plotGSEA : plot3: no visible global function definition for ‘rgb’
plotGSEA : plot4: no visible global function definition for ‘par’
plotGSEA : plot4: no visible global function definition for ‘axTicks’
plotGSEA : plot4: no visible global function definition for ‘axis’
plotGSEA : plot4: no visible global function definition for ‘densCols’
plotGSEA : plot4: no visible global function definition for ‘abline’
plotGSEA: no visible global function definition for ‘par’
plotGSEA: no visible global function definition for ‘layout’
plotGseaPreprocess: no visible global function definition for ‘is’
preProcessX: no visible global function definition for ‘complete.cases’
preProcessX: no visible global function definition for ‘median’
qcPlot: no visible global function definition for ‘pdf’
qcPlot: no visible global function definition for ‘densCols’
qcPlot: no visible global function definition for ‘lm’
qcPlot: no visible global function definition for ‘abline’
qcPlot: no visible global function definition for ‘boxplot’
qcPlot: no visible global function definition for ‘density’
qcPlot: no visible global function definition for ‘lines’
qcPlot: no visible global function definition for ‘dev.off’
selSignatures: no visible global function definition for ‘is’
smoothCoxph: no visible global function definition for ‘predict’
smoothCoxph: no visible global function definition for ‘median’
smoothCoxph: no visible global function definition for ‘lines’
smoothCoxph: no visible global function definition for ‘abline’
tellNumPerm: no visible global function definition for ‘is’
write.html: no visible global function definition for ‘is’
[,epheno-ANY-ANY-ANY: no visible global function definition for ‘is’
[,epheno-ANY-ANY-ANY: no visible global function definition for
  ‘featureNames’
[,epheno-ANY-ANY-ANY: no visible global function definition for
  ‘exprs<-’
[,epheno-ANY-ANY-ANY: no visible global function definition for ‘exprs’
[,epheno-ANY-ANY-ANY: no visible global function definition for ‘pData’
[,epheno-ANY-ANY-ANY: no visible global function definition for ‘new’
[,epheno-ANY-ANY-ANY: no visible global function definition for
  ‘annotation’
barplotSignatures,epheno-list : <anonymous>: no visible global function
  definition for ‘featureNames’
barplotSignatures,epheno-list : <anonymous> : <anonymous>: no visible
  global function definition for ‘featureNames’
barplotSignatures,epheno-list: no visible global function definition
  for ‘abline’
barplotSignatures,epheno-list : <anonymous>: no visible global function
  definition for ‘wilcox.test’
barplotSignatures,epheno-list: no visible global function definition
  for ‘p.adjust’
barplotSignatures,epheno-list: no visible global function definition
  for ‘text’
barplotSignatures,epheno-list: no visible global function definition
  for ‘par’
barplotSignifSignatures,epheno-list : <anonymous>: no visible global
  function definition for ‘featureNames’
barplotSignifSignatures,epheno-list : myFun1 : <anonymous>: no visible
  global function definition for ‘featureNames’
barplotSignifSignatures,epheno-list : myFun2: no visible global
  function definition for ‘binom.test’
barplotSignifSignatures,epheno-list : myFun3 : <anonymous>: no visible
  global function definition for ‘chisq.test’
barplotSignifSignatures,epheno-list : myFun4 : <anonymous>: no visible
  global function definition for ‘chisq.test’
barplotSignifSignatures,epheno-list: no visible global function
  definition for ‘p.adjust’
barplotSignifSignatures,epheno-list : <anonymous>: no visible global
  function definition for ‘p.adjust’
barplotSignifSignatures,epheno-list: no visible global function
  definition for ‘barplot’
barplotSignifSignatures,epheno-list: no visible global function
  definition for ‘text’
boxplotSignatures,epheno-list : <anonymous>: no visible global function
  definition for ‘featureNames’
boxplotSignatures,epheno-list: no visible global function definition
  for ‘boxplot’
boxplotSignatures,epheno-list: no visible global function definition
  for ‘abline’
boxplotSignatures,epheno-list : <anonymous>: no visible global function
  definition for ‘wilcox.test’
boxplotSignatures,epheno-list: no visible global function definition
  for ‘text’
boxplotSignatures,epheno-list: no visible global function definition
  for ‘par’
dim,epheno: no visible global function definition for ‘exprs’
dim,epheno: no visible global function definition for ‘pData’
export2CSV,epheno: no visible global function definition for ‘fData’
export2CSV,epheno: no visible global function definition for
  ‘featureNames’
export2CSV,epheno: no visible global function definition for
  ‘write.csv’
getFc,epheno: no visible global function definition for ‘pData’
getFc,epheno: no visible global function definition for ‘exprs’
getHr,epheno: no visible global function definition for ‘pData’
getHr,epheno: no visible global function definition for ‘exprs’
getMeans,epheno: no visible global function definition for ‘pData’
getMeans,epheno: no visible global function definition for ‘exprs’
getPostProbs,epheno: no visible global function definition for ‘pData’
getPostProbs,epheno: no visible global function definition for ‘exprs’
getPvals,epheno: no visible global function definition for ‘pData’
getPvals,epheno: no visible global function definition for ‘exprs’
getSignif,epheno: no visible global function definition for ‘pData’
getSignif,epheno: no visible global function definition for ‘exprs’
getSummaryDif,epheno: no visible global function definition for ‘pData’
getSummaryDif,epheno: no visible global function definition for ‘exprs’
getVars2test,epheno: no visible global function definition for ‘pData’
gseaSignatures,epheno-list: no visible global function definition for
  ‘new’
gseaSignatures,matrix-list: no visible global function definition for
  ‘new’
gseaSignatures,numeric-list: no visible global function definition for
  ‘new’
gseaSignificance,gseaSignaturesSign: no visible global function
  definition for ‘is’
gseaSignificance,gseaSignaturesSign: no visible global function
  definition for ‘new’
gseaSignificance,gseaSignaturesVar: no visible global function
  definition for ‘new’
heatmapPhenoTest,ExpressionSet-character: no visible global function
  definition for ‘pData’
heatmapPhenoTest,ExpressionSet-character: no visible global function
  definition for ‘featureNames’
heatmapPhenoTest,ExpressionSet-character: no visible global function
  definition for ‘annotation’
heatmapPhenoTest,ExpressionSet-character: no visible global function
  definition for ‘exprs<-’
heatmapPhenoTest,ExpressionSet-character: no visible global function
  definition for ‘exprs’
heatmapPhenoTest,ExpressionSet-character: no visible global function
  definition for ‘hclust’
heatmapPhenoTest,ExpressionSet-character: no visible global function
  definition for ‘as.dist’
heatmapPhenoTest,ExpressionSet-character: no visible global function
  definition for ‘cor’
heatmapPhenoTest,ExpressionSet-character: no visible global function
  definition for ‘dist’
heatmapPhenoTest,ExpressionSet-character: no visible global function
  definition for ‘cutree’
heatmapPhenoTest,ExpressionSet-character: no visible global function
  definition for ‘model.matrix’
heatmapPhenoTest,ExpressionSet-character: no visible global function
  definition for ‘coef’
heatmapPhenoTest,ExpressionSet-character: no visible global function
  definition for ‘gray’
heatmapPhenoTest,ExpressionSet-character: no visible global function
  definition for ‘as.dendrogram’
heatmapPhenoTest,ExpressionSet-character: no visible global function
  definition for ‘par’
heatmapPhenoTest,ExpressionSet-character: no visible global function
  definition for ‘heatmap_plus’
heatmapPhenoTest,ExpressionSet-character: no visible global function
  definition for ‘pchisq’
heatmapPhenoTest,ExpressionSet-character: no visible global function
  definition for ‘text’
heatmapPhenoTest,ExpressionSet-missing: no visible global function
  definition for ‘featureNames’
pAdjust,epheno: no visible global function definition for ‘pData’
pAdjust,epheno: no visible global function definition for ‘new’
pAdjust,epheno: no visible global function definition for ‘exprs’
pAdjust,epheno : <anonymous>: no visible global function definition for
  ‘p.adjust’
pAdjust,epheno: no visible global function definition for ‘annotation’
phenoClass,epheno: no visible global function definition for ‘pData’
phenoNames,epheno: no visible global function definition for ‘pData’
show,epheno: no visible global function definition for ‘featureNames’
show,epheno: no visible global function definition for ‘annotation’
usedGam,gseaData: no visible global function definition for ‘is’
Undefined global functions or variables:
  BIC Term abline annotation annotation<- anova approx approxfun
  as.dendrogram as.dist axTicks axis barplot bic.surv binom.test
  boxplot chisq.test coef coefficients complete.cases confint
  coord_cartesian cor cov cutree densCols density dev.off dist dotchart
  exprs exprs<- fData featureNames featureNames<- geom_point ggtitle
  gray hclust heatmap_plus image integrate is kruskal.test layout
  legend lines lm median model.matrix new p.adjust pData par pc1 pc2
  pchisq pdf png pnorm polygon prcomp predict qplot quantile rect rgb
  sd text theme wilcox.test write.csv y
Consider adding
  importFrom("grDevices", "densCols", "dev.off", "gray", "pdf", "png",
             "rgb")
  importFrom("graphics", "abline", "axTicks", "axis", "barplot",
             "boxplot", "dotchart", "image", "layout", "legend", "lines",
             "par", "polygon", "rect", "text")
  importFrom("methods", "is", "new")
  importFrom("stats", "BIC", "anova", "approx", "approxfun",
             "as.dendrogram", "as.dist", "binom.test", "chisq.test",
             "coef", "coefficients", "complete.cases", "confint", "cor",
             "cov", "cutree", "density", "dist", "hclust", "integrate",
             "kruskal.test", "lm", "median", "model.matrix", "p.adjust",
             "pchisq", "pnorm", "prcomp", "predict", "quantile", "sd",
             "wilcox.test")
  importFrom("utils", "write.csv")
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 ... NOTE
S3 methods shown with full name in documentation object 'plot.gseaData':
  ‘plot.gseaData’

S3 methods shown with full name in documentation object 'plot.gseaSignatures':
  ‘plot.gseaSignaturesSign’

S3 methods shown with full name in documentation object 'summary.gseaData':
  ‘summary.gseaData’

S3 methods shown with full name in documentation object 'summary.gseaSignificance':
  ‘summary.gseaSignificanceSign’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 files in ‘vignettes’ ... OK
* checking examples ... WARNING
Found the following significant warnings:

  Warning: 'heatmap_plus' is deprecated.
  Warning: 'oldCutplot.dendrogram' is deprecated.
  Warning: 'oldPicketplot' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU (user + system) or elapsed time > 5s
                      user system elapsed
ExpressionPhenoTest 12.133  0.187  12.332
findCopyNumber       5.556  0.406   5.967
* 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 WARNING, 7 NOTEs
See
  ‘/Users/biocbuild/bbs-3.14-bioc/meat/phenoTest.Rcheck/00check.log’
for details.



Installation output

phenoTest.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL phenoTest
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘phenoTest’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (phenoTest)

Tests output


Example timings

phenoTest.Rcheck/phenoTest-Ex.timings

nameusersystemelapsed
ClusterPhenoTest0.2420.0150.257
ExpressionPhenoTest12.133 0.18712.332
epheno-class0.0020.0010.003
epheno0.0250.0050.030
epheno2html0.0010.0000.001
eset0.1850.0090.196
eset.genelevel0.1350.0090.145
eset2genelevel0.0000.0000.001
findCopyNumber5.5560.4065.967
genesInArea0.4040.0100.413
getEsPositions0.3250.0080.333
getVars2test0.0260.0040.030
gsea0.2590.0140.274
gsea2html0.7390.0310.770
gseaData-class0.0010.0010.001
gseaSignatures-class0.0000.0010.001
gseaSignatures0.0250.0050.030
gseaSignaturesSign-class0.0010.0010.002
gseaSignaturesVar-class0.0000.0010.001
gseaSignificance0.0000.0010.000
gseaSignificanceSign-class0.0020.0010.002
gseaSignificanceVar-class0.0010.0000.002
heatmapPhenoTest0.4280.0100.438
pAdjust0.1830.0070.190
pca0.5220.0140.537
plot.gsea0.0000.0000.001
plot.gseaSignatures000
plots4epheno0.5270.0470.574
smoothCoxph0.1620.0080.170
summary.gsea0.0000.0000.001
summary.gseaSignificance000
write.html000