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### Running command:
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### /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_1.48.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/phenoTest.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* 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 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘phenoTest/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘phenoTest’ version ‘1.48.0’
* 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 ... 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 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 6.683 0.196 10.492
findCopyNumber 4.250 0.154 6.657
* 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-3.17-bioc-mac-arm64/meat/phenoTest.Rcheck/00check.log’
for details.
