Back to Multiple platform build/check report for BioC 3.19:   simplified   long
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This page was generated on 2024-05-17 11:38:13 -0400 (Fri, 17 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4751
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4485
lconwaymacOS 12.7.1 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4515
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

Package 1556/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
phenoTest 1.52.0  (landing page)
Evarist Planet
Snapshot Date: 2024-05-16 14:00:15 -0400 (Thu, 16 May 2024)
git_url: https://git.bioconductor.org/packages/phenoTest
git_branch: RELEASE_3_19
git_last_commit: e009c83
git_last_commit_date: 2024-04-30 10:23:22 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.6.5 Ventura / arm64see weekly results here

CHECK results for phenoTest on lconway


To the developers/maintainers of the phenoTest package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: phenoTest
Version: 1.52.0
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_1.52.0.tar.gz
StartedAt: 2024-05-16 23:00:03 -0400 (Thu, 16 May 2024)
EndedAt: 2024-05-16 23:04:17 -0400 (Thu, 16 May 2024)
EllapsedTime: 254.5 seconds
RetCode: 0
Status:   OK  
CheckDir: phenoTest.Rcheck
Warnings: 0

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_1.52.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/phenoTest.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘phenoTest/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘phenoTest’ version ‘1.52.0’
* 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 code 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 ... OK
* 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 ... NOTE
checkRd: (-1) ClusterPhenoTest.Rd:30: Escaped LaTeX specials: \$ \$
checkRd: (-1) ClusterPhenoTest.Rd:31: Escaped LaTeX specials: \$
checkRd: (-1) ClusterPhenoTest.Rd:33: Escaped LaTeX specials: \$
checkRd: (-1) heatmapPhenoTest.Rd:71: Escaped LaTeX specials: \$ \$
checkRd: (-1) heatmapPhenoTest.Rd:72: Escaped LaTeX specials: \$
checkRd: (-1) heatmapPhenoTest.Rd:73: Escaped LaTeX specials: \$
* 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 Rd file 'plot.gsea.Rd':
  ‘plot.gseaData’

S3 methods shown with full name in Rd file 'plot.gseaSignatures.Rd':
  ‘plot.gseaSignaturesSign’

S3 methods shown with full name in Rd file 'summary.gsea.Rd':
  ‘summary.gseaData’

S3 methods shown with full name in Rd file 'summary.gseaSignificance.Rd':
  ‘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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
ExpressionPhenoTest 6.826   0.16   7.058
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 7 NOTEs
See
  ‘/Users/biocbuild/bbs-3.19-bioc/meat/phenoTest.Rcheck/00check.log’
for details.


Installation output

phenoTest.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL phenoTest
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/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
ClusterPhenoTest0.1910.0130.207
ExpressionPhenoTest6.8260.1607.058
epheno-class0.0010.0010.001
epheno0.0180.0040.023
epheno2html0.0000.0000.001
eset0.1760.0110.189
eset.genelevel0.0710.0060.079
eset2genelevel0.0000.0000.001
findCopyNumber4.3920.3024.736
genesInArea0.2860.0100.297
getEsPositions0.2420.0110.255
getVars2test0.0210.0040.025
gsea0.1990.0170.218
gsea2html0.6110.0310.647
gseaData-class0.0010.0000.002
gseaSignatures-class0.0010.0000.001
gseaSignatures0.0190.0030.022
gseaSignaturesSign-class0.0010.0000.001
gseaSignaturesVar-class0.0010.0000.001
gseaSignificance0.0000.0000.001
gseaSignificanceSign-class0.0000.0010.001
gseaSignificanceVar-class0.0010.0000.001
heatmapPhenoTest0.3020.0110.316
pAdjust0.1150.0050.121
pca0.6340.0310.670
plot.gsea000
plot.gseaSignatures0.0010.0010.000
plots4epheno0.3830.0170.402
smoothCoxph0.1730.0080.182
summary.gsea000
summary.gseaSignificance000
write.html0.0000.0000.001